https://launchpad.net/ubuntu/+archive/test-rebuild-20200728-groovy/+build/19659198 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux bos02-s390x-019 4.4.0-177-generic #207-Ubuntu SMP Mon Mar 16 01:15:38 UTC 2020 s390x Buildd toolchain package versions: launchpad-buildd_188 python-lpbuildd_188 sbuild_0.67.0-2ubuntu7.1 bzr-builder_0.7.3+bzr174~ppa13~ubuntu14.10.1 bzr_2.7.0-2ubuntu3.1 git-build-recipe_0.3.6~git201906051340.ff11471~ubuntu16.04.1 git_1:2.7.4-0ubuntu1.7 dpkg-dev_1.18.4ubuntu1.6 python-debian_0.1.27ubuntu2. Syncing the system clock with the buildd NTP service... 3 Aug 16:24:20 ntpdate[1854]: adjust time server 10.211.37.1 offset 0.005867 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=groovy --arch=s390x PACKAGEBUILD-19659198 --image-type chroot /home/buildd/filecache-default/c742ba36b312cb05af21d0da5b96b5d4203afb06 Creating target for build PACKAGEBUILD-19659198 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=groovy --arch=s390x PACKAGEBUILD-19659198 Starting target for build PACKAGEBUILD-19659198 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=groovy --arch=s390x PACKAGEBUILD-19659198 'deb http://ftpmaster.internal/ubuntu groovy main restricted universe multiverse' Overriding sources.list in build-PACKAGEBUILD-19659198 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=groovy --arch=s390x PACKAGEBUILD-19659198 Updating target for build PACKAGEBUILD-19659198 Get:1 http://ftpmaster.internal/ubuntu groovy InRelease [267 kB] Get:2 http://ftpmaster.internal/ubuntu groovy/main s390x Packages [926 kB] Get:3 http://ftpmaster.internal/ubuntu groovy/main Translation-en [510 kB] Get:4 http://ftpmaster.internal/ubuntu groovy/restricted Translation-en [7884 B] Get:5 http://ftpmaster.internal/ubuntu groovy/universe s390x Packages [8429 kB] Get:6 http://ftpmaster.internal/ubuntu groovy/universe Translation-en [5251 kB] Get:7 http://ftpmaster.internal/ubuntu groovy/multiverse s390x Packages [115 kB] Fetched 15.5 MB in 3s (5339 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: base-files bsdutils build-essential ca-certificates libblkid1 liblzma5 libmount1 libselinux1 libsemanage-common libsemanage1 libsmartcols1 libuuid1 mount util-linux xz-utils 15 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 2115 kB of archives. After this operation, 10.2 kB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu groovy/main s390x base-files s390x 11ubuntu10 [60.2 kB] Get:2 http://ftpmaster.internal/ubuntu groovy/main s390x bsdutils s390x 1:2.35.2-9ubuntu1 [82.5 kB] Get:3 http://ftpmaster.internal/ubuntu groovy/main s390x libselinux1 s390x 3.1-2 [65.7 kB] Get:4 http://ftpmaster.internal/ubuntu groovy/main s390x util-linux s390x 2.35.2-9ubuntu1 [1010 kB] Get:5 http://ftpmaster.internal/ubuntu groovy/main s390x mount s390x 2.35.2-9ubuntu1 [113 kB] Get:6 http://ftpmaster.internal/ubuntu groovy/main s390x libblkid1 s390x 2.35.2-9ubuntu1 [124 kB] Get:7 http://ftpmaster.internal/ubuntu groovy/main s390x liblzma5 s390x 5.2.4-1ubuntu1 [90.5 kB] Get:8 http://ftpmaster.internal/ubuntu groovy/main s390x libmount1 s390x 2.35.2-9ubuntu1 [135 kB] Get:9 http://ftpmaster.internal/ubuntu groovy/main s390x libsemanage-common all 3.1-1 [10.2 kB] Get:10 http://ftpmaster.internal/ubuntu groovy/main s390x libsemanage1 s390x 3.1-1 [80.7 kB] Get:11 http://ftpmaster.internal/ubuntu groovy/main s390x libsmartcols1 s390x 2.35.2-9ubuntu1 [89.3 kB] Get:12 http://ftpmaster.internal/ubuntu groovy/main s390x libuuid1 s390x 2.35.2-9ubuntu1 [22.0 kB] Get:13 http://ftpmaster.internal/ubuntu groovy/main s390x ca-certificates all 20200601 [147 kB] Get:14 http://ftpmaster.internal/ubuntu groovy/main s390x xz-utils s390x 5.2.4-1ubuntu1 [80.5 kB] Get:15 http://ftpmaster.internal/ubuntu groovy/main s390x build-essential s390x 12.8ubuntu3 [4636 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 2115 kB in 0s (30.0 MB/s) (Reading database ... 12573 files and directories currently installed.) Preparing to unpack .../base-files_11ubuntu10_s390x.deb ... Unpacking base-files (11ubuntu10) over (11ubuntu9) ... Setting up base-files (11ubuntu10) ... Installing new version of config file /etc/update-motd.d/50-motd-news ... (Reading database ... 12573 files and directories currently installed.) Preparing to unpack .../bsdutils_1%3a2.35.2-9ubuntu1_s390x.deb ... Unpacking bsdutils (1:2.35.2-9ubuntu1) over (1:2.35.2-7ubuntu3) ... Setting up bsdutils (1:2.35.2-9ubuntu1) ... (Reading database ... 12573 files and directories currently installed.) Preparing to unpack .../libselinux1_3.1-2_s390x.deb ... Unpacking libselinux1:s390x (3.1-2) over (3.0-1build2) ... Setting up libselinux1:s390x (3.1-2) ... (Reading database ... 12573 files and directories currently installed.) Preparing to unpack .../util-linux_2.35.2-9ubuntu1_s390x.deb ... Unpacking util-linux (2.35.2-9ubuntu1) over (2.35.2-7ubuntu3) ... Setting up util-linux (2.35.2-9ubuntu1) ... (Reading database ... 12573 files and directories currently installed.) Preparing to unpack .../mount_2.35.2-9ubuntu1_s390x.deb ... Unpacking mount (2.35.2-9ubuntu1) over (2.35.2-7ubuntu3) ... Preparing to unpack .../libblkid1_2.35.2-9ubuntu1_s390x.deb ... Unpacking libblkid1:s390x (2.35.2-9ubuntu1) over (2.35.2-7ubuntu3) ... Setting up libblkid1:s390x (2.35.2-9ubuntu1) ... (Reading database ... 12573 files and directories currently installed.) Preparing to unpack .../liblzma5_5.2.4-1ubuntu1_s390x.deb ... Unpacking liblzma5:s390x (5.2.4-1ubuntu1) over (5.2.4-1) ... Setting up liblzma5:s390x (5.2.4-1ubuntu1) ... (Reading database ... 12573 files and directories currently installed.) Preparing to unpack .../libmount1_2.35.2-9ubuntu1_s390x.deb ... Unpacking libmount1:s390x (2.35.2-9ubuntu1) over (2.35.2-7ubuntu3) ... Setting up libmount1:s390x (2.35.2-9ubuntu1) ... (Reading database ... 12573 files and directories currently installed.) Preparing to unpack .../libsemanage-common_3.1-1_all.deb ... Unpacking libsemanage-common (3.1-1) over (3.0-1build2) ... Setting up libsemanage-common (3.1-1) ... (Reading database ... 12573 files and directories currently installed.) Preparing to unpack .../libsemanage1_3.1-1_s390x.deb ... Unpacking libsemanage1:s390x (3.1-1) over (3.0-1build2) ... Setting up libsemanage1:s390x (3.1-1) ... (Reading database ... 12573 files and directories currently installed.) Preparing to unpack .../libsmartcols1_2.35.2-9ubuntu1_s390x.deb ... Unpacking libsmartcols1:s390x (2.35.2-9ubuntu1) over (2.35.2-7ubuntu3) ... Setting up libsmartcols1:s390x (2.35.2-9ubuntu1) ... (Reading database ... 12573 files and directories currently installed.) Preparing to unpack .../libuuid1_2.35.2-9ubuntu1_s390x.deb ... Unpacking libuuid1:s390x (2.35.2-9ubuntu1) over (2.35.2-7ubuntu3) ... Setting up libuuid1:s390x (2.35.2-9ubuntu1) ... (Reading database ... 12573 files and directories currently installed.) Preparing to unpack .../ca-certificates_20200601_all.deb ... Unpacking ca-certificates (20200601) over (20190110ubuntu2) ... Preparing to unpack .../xz-utils_5.2.4-1ubuntu1_s390x.deb ... Unpacking xz-utils (5.2.4-1ubuntu1) over (5.2.4-1) ... Preparing to unpack .../build-essential_12.8ubuntu3_s390x.deb ... Unpacking build-essential (12.8ubuntu3) over (12.8ubuntu1) ... Setting up ca-certificates (20200601) ... Updating certificates in /etc/ssl/certs... 13 added, 14 removed; done. Setting up xz-utils (5.2.4-1ubuntu1) ... Setting up mount (2.35.2-9ubuntu1) ... Setting up build-essential (12.8ubuntu3) ... Processing triggers for libc-bin (2.31-0ubuntu10) ... Processing triggers for ca-certificates (20200601) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-19659198 s390x groovy -c chroot:build-PACKAGEBUILD-19659198 --arch=s390x --dist=groovy --nolog cufflinks_2.2.1+dfsg.1-7.dsc Initiating build PACKAGEBUILD-19659198 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.4.0-177-generic #207-Ubuntu SMP Mon Mar 16 01:15:38 UTC 2020 s390x sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on bos02-s390x-019.buildd +==============================================================================+ | cufflinks 2.2.1+dfsg.1-7 (s390x) 03 Aug 2020 16:24 | +==============================================================================+ Package: cufflinks Version: 2.2.1+dfsg.1-7 Source Version: 2.2.1+dfsg.1-7 Distribution: groovy Machine Architecture: s390x Host Architecture: s390x Build Architecture: s390x I: NOTICE: Log filtering will replace 'build/cufflinks-kSbI0G/cufflinks-2.2.1+dfsg.1' with '<>' I: NOTICE: Log filtering will replace 'build/cufflinks-kSbI0G' with '<>' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-19659198/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- cufflinks_2.2.1+dfsg.1-7.dsc exists in .; copying to chroot Check architectures ------------------- Check dependencies ------------------ Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<>/resolver-VDqImA/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign:1 copy:/<>/resolver-VDqImA/apt_archive ./ InRelease Get:2 copy:/<>/resolver-VDqImA/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-VDqImA/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-VDqImA/apt_archive ./ Sources [214 B] Get:5 copy:/<>/resolver-VDqImA/apt_archive ./ Packages [527 B] Fetched 2860 B in 0s (0 B/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install core build dependencies (apt-based resolver) | +------------------------------------------------------------------------------+ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following NEW packages will be installed: sbuild-build-depends-core-dummy 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 856 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-VDqImA/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [856 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 856 B in 0s (0 B/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 12572 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_s390x.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... Merged Build-Depends: debhelper-compat (= 12), dh-python, help2man, libboost-dev, libboost-serialization-dev, libboost-system-dev, libboost-thread-dev, libbam-dev, zlib1g-dev, python3, libeigen3-dev Filtered Build-Depends: debhelper-compat (= 12), dh-python, help2man, libboost-dev, libboost-serialization-dev, libboost-system-dev, libboost-thread-dev, libbam-dev, zlib1g-dev, python3, libeigen3-dev dpkg-deb: building package 'sbuild-build-depends-cufflinks-dummy' in '/<>/resolver-3GUFhF/apt_archive/sbuild-build-depends-cufflinks-dummy.deb'. Ign:1 copy:/<>/resolver-3GUFhF/apt_archive ./ InRelease Get:2 copy:/<>/resolver-3GUFhF/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-3GUFhF/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-3GUFhF/apt_archive ./ Sources [281 B] Get:5 copy:/<>/resolver-3GUFhF/apt_archive ./ Packages [598 B] Fetched 2998 B in 0s (0 B/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install cufflinks build dependencies (apt-based resolver) | +------------------------------------------------------------------------------+ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils debhelper dh-autoreconf dh-python dh-strip-nondeterminism dwz file gettext gettext-base groff-base help2man intltool-debian libarchive-zip-perl libbam-dev libboost-atomic1.71-dev libboost-atomic1.71.0 libboost-chrono1.71-dev libboost-chrono1.71.0 libboost-date-time1.71-dev libboost-date-time1.71.0 libboost-dev libboost-serialization-dev libboost-serialization1.71-dev libboost-serialization1.71.0 libboost-system-dev libboost-system1.71-dev libboost-system1.71.0 libboost-thread-dev libboost-thread1.71-dev libboost-thread1.71.0 libboost1.71-dev libcroco3 libdebhelper-perl libeigen3-dev libelf1 libexpat1 libfile-stripnondeterminism-perl libglib2.0-0 libicu66 liblocale-gettext-perl libmagic-mgc libmagic1 libmpdec2 libpipeline1 libpython3-stdlib libpython3.8-minimal libpython3.8-stdlib libsigsegv2 libsub-override-perl libtool libuchardet0 libxml2 m4 man-db mime-support pkg-config po-debconf python3 python3-distutils python3-lib2to3 python3-minimal python3.8 python3.8-minimal zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc dh-make gettext-doc libasprintf-dev libgettextpo-dev groff libboost-doc libboost1.71-doc libboost-container1.71-dev libboost-context1.71-dev libboost-contract1.71-dev libboost-coroutine1.71-dev libboost-exception1.71-dev libboost-fiber1.71-dev libboost-filesystem1.71-dev libboost-graph1.71-dev libboost-graph-parallel1.71-dev libboost-iostreams1.71-dev libboost-locale1.71-dev libboost-log1.71-dev libboost-math1.71-dev libboost-mpi1.71-dev libboost-mpi-python1.71-dev libboost-numpy1.71-dev libboost-program-options1.71-dev libboost-python1.71-dev libboost-random1.71-dev libboost-regex1.71-dev libboost-stacktrace1.71-dev libboost-test1.71-dev libboost-timer1.71-dev libboost-type-erasure1.71-dev libboost-wave1.71-dev libboost1.71-tools-dev libmpfrc++-dev libntl-dev libeigen3-doc libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl python3-doc python3-tk python3-venv python3.8-venv python3.8-doc binfmt-support Recommended packages: curl | wget | lynx libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs libltdl-dev libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils debhelper dh-autoreconf dh-python dh-strip-nondeterminism dwz file gettext gettext-base groff-base help2man intltool-debian libarchive-zip-perl libbam-dev libboost-atomic1.71-dev libboost-atomic1.71.0 libboost-chrono1.71-dev libboost-chrono1.71.0 libboost-date-time1.71-dev libboost-date-time1.71.0 libboost-dev libboost-serialization-dev libboost-serialization1.71-dev libboost-serialization1.71.0 libboost-system-dev libboost-system1.71-dev libboost-system1.71.0 libboost-thread-dev libboost-thread1.71-dev libboost-thread1.71.0 libboost1.71-dev libcroco3 libdebhelper-perl libeigen3-dev libelf1 libexpat1 libfile-stripnondeterminism-perl libglib2.0-0 libicu66 liblocale-gettext-perl libmagic-mgc libmagic1 libmpdec2 libpipeline1 libpython3-stdlib libpython3.8-minimal libpython3.8-stdlib libsigsegv2 libsub-override-perl libtool libuchardet0 libxml2 m4 man-db mime-support pkg-config po-debconf python3 python3-distutils python3-lib2to3 python3-minimal python3.8 python3.8-minimal sbuild-build-depends-cufflinks-dummy zlib1g-dev 0 upgraded, 69 newly installed, 0 to remove and 0 not upgraded. Need to get 35.0 MB of archives. After this operation, 266 MB of additional disk space will be used. Get:1 copy:/<>/resolver-3GUFhF/apt_archive ./ sbuild-build-depends-cufflinks-dummy 0.invalid.0 [928 B] Get:2 http://ftpmaster.internal/ubuntu groovy/main s390x liblocale-gettext-perl s390x 1.07-4 [16.5 kB] Get:3 http://ftpmaster.internal/ubuntu groovy/main s390x libpython3.8-minimal s390x 3.8.5-1 [711 kB] Get:4 http://ftpmaster.internal/ubuntu groovy/main s390x libexpat1 s390x 2.2.9-1build1 [69.8 kB] Get:5 http://ftpmaster.internal/ubuntu groovy/main s390x python3.8-minimal s390x 3.8.5-1 [1747 kB] Get:6 http://ftpmaster.internal/ubuntu groovy/main s390x python3-minimal s390x 3.8.2-0ubuntu2 [23.6 kB] Get:7 http://ftpmaster.internal/ubuntu groovy/main s390x mime-support all 3.64ubuntu1 [30.6 kB] Get:8 http://ftpmaster.internal/ubuntu groovy/main s390x libmpdec2 s390x 2.4.2-3 [82.4 kB] Get:9 http://ftpmaster.internal/ubuntu groovy/main s390x libpython3.8-stdlib s390x 3.8.5-1 [1630 kB] Get:10 http://ftpmaster.internal/ubuntu groovy/main s390x python3.8 s390x 3.8.5-1 [373 kB] Get:11 http://ftpmaster.internal/ubuntu groovy/main s390x libpython3-stdlib s390x 3.8.2-0ubuntu2 [7068 B] Get:12 http://ftpmaster.internal/ubuntu groovy/main s390x python3 s390x 3.8.2-0ubuntu2 [47.6 kB] Get:13 http://ftpmaster.internal/ubuntu groovy/main s390x bsdextrautils s390x 2.35.2-9ubuntu1 [75.1 kB] Get:14 http://ftpmaster.internal/ubuntu groovy/main s390x libuchardet0 s390x 0.0.7-1 [67.5 kB] Get:15 http://ftpmaster.internal/ubuntu groovy/main s390x groff-base s390x 1.22.4-5 [812 kB] Get:16 http://ftpmaster.internal/ubuntu groovy/main s390x libpipeline1 s390x 1.5.2-2build1 [26.5 kB] Get:17 http://ftpmaster.internal/ubuntu groovy/main s390x man-db s390x 2.9.3-2 [1106 kB] Get:18 http://ftpmaster.internal/ubuntu groovy/main s390x libmagic-mgc s390x 1:5.38-5 [219 kB] Get:19 http://ftpmaster.internal/ubuntu groovy/main s390x libmagic1 s390x 1:5.38-5 [72.9 kB] Get:20 http://ftpmaster.internal/ubuntu groovy/main s390x file s390x 1:5.38-5 [23.1 kB] Get:21 http://ftpmaster.internal/ubuntu groovy/main s390x libelf1 s390x 0.180-0ubuntu1 [47.3 kB] Get:22 http://ftpmaster.internal/ubuntu groovy/main s390x libglib2.0-0 s390x 2.64.4-1 [1181 kB] Get:23 http://ftpmaster.internal/ubuntu groovy/main s390x libicu66 s390x 66.1-2ubuntu3 [8260 kB] Get:24 http://ftpmaster.internal/ubuntu groovy/main s390x libxml2 s390x 2.9.10+dfsg-5 [659 kB] Get:25 http://ftpmaster.internal/ubuntu groovy/main s390x gettext-base s390x 0.19.8.1-10build1 [49.0 kB] Get:26 http://ftpmaster.internal/ubuntu groovy/main s390x libsigsegv2 s390x 2.12-2build1 [13.7 kB] Get:27 http://ftpmaster.internal/ubuntu groovy/main s390x m4 s390x 1.4.18-4 [196 kB] Get:28 http://ftpmaster.internal/ubuntu groovy/main s390x autoconf all 2.69-11.1 [321 kB] Get:29 http://ftpmaster.internal/ubuntu groovy/main s390x autotools-dev all 20180224.1 [39.6 kB] Get:30 http://ftpmaster.internal/ubuntu groovy/main s390x automake all 1:1.16.2-3ubuntu1 [548 kB] Get:31 http://ftpmaster.internal/ubuntu groovy/main s390x autopoint all 0.19.8.1-10build1 [412 kB] Get:32 http://ftpmaster.internal/ubuntu groovy/main s390x libtool all 2.4.6-14 [161 kB] Get:33 http://ftpmaster.internal/ubuntu groovy/main s390x dh-autoreconf all 19 [16.1 kB] Get:34 http://ftpmaster.internal/ubuntu groovy/main s390x libdebhelper-perl all 13.2ubuntu1 [64.2 kB] Get:35 http://ftpmaster.internal/ubuntu groovy/main s390x libarchive-zip-perl all 1.68-1 [90.2 kB] Get:36 http://ftpmaster.internal/ubuntu groovy/main s390x libsub-override-perl all 0.09-2 [9532 B] Get:37 http://ftpmaster.internal/ubuntu groovy/main s390x libfile-stripnondeterminism-perl all 1.9.0-1 [17.2 kB] Get:38 http://ftpmaster.internal/ubuntu groovy/main s390x dh-strip-nondeterminism all 1.9.0-1 [5192 B] Get:39 http://ftpmaster.internal/ubuntu groovy/main s390x dwz s390x 0.13-5 [146 kB] Get:40 http://ftpmaster.internal/ubuntu groovy/main s390x libcroco3 s390x 0.6.13-1 [73.7 kB] Get:41 http://ftpmaster.internal/ubuntu groovy/main s390x gettext s390x 0.19.8.1-10build1 [867 kB] Get:42 http://ftpmaster.internal/ubuntu groovy/main s390x intltool-debian all 0.35.0+20060710.5 [24.9 kB] Get:43 http://ftpmaster.internal/ubuntu groovy/main s390x po-debconf all 1.0.21 [233 kB] Get:44 http://ftpmaster.internal/ubuntu groovy/main s390x debhelper all 13.2ubuntu1 [878 kB] Get:45 http://ftpmaster.internal/ubuntu groovy/main s390x python3-lib2to3 all 3.8.5-1 [75.6 kB] Get:46 http://ftpmaster.internal/ubuntu groovy/main s390x python3-distutils all 3.8.5-1 [141 kB] Get:47 http://ftpmaster.internal/ubuntu groovy/universe s390x dh-python all 4.20200315ubuntu1 [85.8 kB] Get:48 http://ftpmaster.internal/ubuntu groovy/universe s390x help2man s390x 1.47.16 [173 kB] Get:49 http://ftpmaster.internal/ubuntu groovy/universe s390x libbam-dev s390x 0.1.19-4 [107 kB] Get:50 http://ftpmaster.internal/ubuntu groovy/main s390x libboost1.71-dev s390x 1.71.0-6ubuntu8 [9070 kB] Get:51 http://ftpmaster.internal/ubuntu groovy/main s390x libboost-atomic1.71.0 s390x 1.71.0-6ubuntu8 [205 kB] Get:52 http://ftpmaster.internal/ubuntu groovy/main s390x libboost-atomic1.71-dev s390x 1.71.0-6ubuntu8 [205 kB] Get:53 http://ftpmaster.internal/ubuntu groovy/main s390x libboost-chrono1.71.0 s390x 1.71.0-6ubuntu8 [216 kB] Get:54 http://ftpmaster.internal/ubuntu groovy/main s390x libboost-chrono1.71-dev s390x 1.71.0-6ubuntu8 [223 kB] Get:55 http://ftpmaster.internal/ubuntu groovy/main s390x libboost-date-time1.71.0 s390x 1.71.0-6ubuntu8 [218 kB] Get:56 http://ftpmaster.internal/ubuntu groovy/main s390x libboost-serialization1.71.0 s390x 1.71.0-6ubuntu8 [295 kB] Get:57 http://ftpmaster.internal/ubuntu groovy/main s390x libboost-serialization1.71-dev s390x 1.71.0-6ubuntu8 [334 kB] Get:58 http://ftpmaster.internal/ubuntu groovy/main s390x libboost-date-time1.71-dev s390x 1.71.0-6ubuntu8 [227 kB] Get:59 http://ftpmaster.internal/ubuntu groovy/main s390x libboost-dev s390x 1.71.0.0ubuntu4 [3504 B] Get:60 http://ftpmaster.internal/ubuntu groovy/universe s390x libboost-serialization-dev s390x 1.71.0.0ubuntu4 [3520 B] Get:61 http://ftpmaster.internal/ubuntu groovy/main s390x libboost-system1.71.0 s390x 1.71.0-6ubuntu8 [205 kB] Get:62 http://ftpmaster.internal/ubuntu groovy/main s390x libboost-system1.71-dev s390x 1.71.0-6ubuntu8 [205 kB] Get:63 http://ftpmaster.internal/ubuntu groovy/main s390x libboost-system-dev s390x 1.71.0.0ubuntu4 [3440 B] Get:64 http://ftpmaster.internal/ubuntu groovy/main s390x libboost-thread1.71.0 s390x 1.71.0-6ubuntu8 [245 kB] Get:65 http://ftpmaster.internal/ubuntu groovy/main s390x libboost-thread1.71-dev s390x 1.71.0-6ubuntu8 [253 kB] Get:66 http://ftpmaster.internal/ubuntu groovy/main s390x libboost-thread-dev s390x 1.71.0.0ubuntu4 [3324 B] Get:67 http://ftpmaster.internal/ubuntu groovy/main s390x pkg-config s390x 0.29.2-1ubuntu1 [45.0 kB] Get:68 http://ftpmaster.internal/ubuntu groovy/main s390x zlib1g-dev s390x 1:1.2.11.dfsg-2ubuntu1 [166 kB] Get:69 http://ftpmaster.internal/ubuntu groovy/universe s390x libeigen3-dev all 3.3.7-2 [815 kB] 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Setting up man-db (2.9.3-2) ... Not building database; man-db/auto-update is not 'true'. Created symlink /etc/systemd/system/timers.target.wants/man-db.timer → /lib/systemd/system/man-db.timer. Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libboost-thread-dev:s390x (1.71.0.0ubuntu4) ... Setting up po-debconf (1.0.21) ... Setting up debhelper (13.2ubuntu1) ... Setting up dh-autoreconf (19) ... Setting up sbuild-build-depends-cufflinks-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.31-0ubuntu10) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.4.0-177-generic s390x (s390x) Toolchain package versions: binutils_2.35-1ubuntu1 dpkg-dev_1.19.7ubuntu4 g++-10_10.2.0-3ubuntu1 gcc-10_10.2.0-3ubuntu1 libc6-dev_2.31-0ubuntu10 libstdc++-10-dev_10.2.0-3ubuntu1 libstdc++6_10.2.0-3ubuntu1 linux-libc-dev_5.4.0-42.46 Package versions: adduser_3.118ubuntu2 advancecomp_2.1-2.1build1 apt_2.1.7 autoconf_2.69-11.1 automake_1:1.16.2-3ubuntu1 autopoint_0.19.8.1-10build1 autotools-dev_20180224.1 base-files_11ubuntu10 base-passwd_3.5.47 bash_5.0-6ubuntu2 binutils_2.35-1ubuntu1 binutils-common_2.35-1ubuntu1 binutils-s390x-linux-gnu_2.35-1ubuntu1 bsdextrautils_2.35.2-9ubuntu1 bsdutils_1:2.35.2-9ubuntu1 build-essential_12.8ubuntu3 bzip2_1.0.8-4ubuntu2 ca-certificates_20200601 coreutils_8.30-3ubuntu3 cpp_4:10.1.0-1ubuntu1 cpp-10_10.2.0-3ubuntu1 dash_0.5.10.2-7 debconf_1.5.74 debhelper_13.2ubuntu1 debianutils_4.11 dh-autoreconf_19 dh-python_4.20200315ubuntu1 dh-strip-nondeterminism_1.9.0-1 diffutils_1:3.7-3build1 dpkg_1.19.7ubuntu4 dpkg-dev_1.19.7ubuntu4 dwz_0.13-5 e2fsprogs_1.45.6-1ubuntu1 fakeroot_1.24-1 file_1:5.38-5 findutils_4.7.0-1ubuntu1 g++_4:10.1.0-1ubuntu1 g++-10_10.2.0-3ubuntu1 gcc_4:10.1.0-1ubuntu1 gcc-10_10.2.0-3ubuntu1 gcc-10-base_10.2.0-3ubuntu1 gettext_0.19.8.1-10build1 gettext-base_0.19.8.1-10build1 gpg_2.2.20-1ubuntu1 gpg-agent_2.2.20-1ubuntu1 gpgconf_2.2.20-1ubuntu1 gpgv_2.2.20-1ubuntu1 grep_3.4-1 groff-base_1.22.4-5 gzip_1.10-2ubuntu1 help2man_1.47.16 hostname_3.23 init_1.58 init-system-helpers_1.58 intltool-debian_0.35.0+20060710.5 libacl1_2.2.53-8 libapparmor1_2.13.3-7ubuntu6 libapt-pkg6.0_2.1.7 libarchive-zip-perl_1.68-1 libargon2-1_0~20171227-0.2build20.10.0 libasan6_10.2.0-3ubuntu1 libassuan0_2.5.3-7.1 libatomic1_10.2.0-3ubuntu1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-2ubuntu6 libaudit1_1:2.8.5-2ubuntu6 libbam-dev_0.1.19-4 libbinutils_2.35-1ubuntu1 libblkid1_2.35.2-9ubuntu1 libboost-atomic1.71-dev_1.71.0-6ubuntu8 libboost-atomic1.71.0_1.71.0-6ubuntu8 libboost-chrono1.71-dev_1.71.0-6ubuntu8 libboost-chrono1.71.0_1.71.0-6ubuntu8 libboost-date-time1.71-dev_1.71.0-6ubuntu8 libboost-date-time1.71.0_1.71.0-6ubuntu8 libboost-dev_1.71.0.0ubuntu4 libboost-serialization-dev_1.71.0.0ubuntu4 libboost-serialization1.71-dev_1.71.0-6ubuntu8 libboost-serialization1.71.0_1.71.0-6ubuntu8 libboost-system-dev_1.71.0.0ubuntu4 libboost-system1.71-dev_1.71.0-6ubuntu8 libboost-system1.71.0_1.71.0-6ubuntu8 libboost-thread-dev_1.71.0.0ubuntu4 libboost-thread1.71-dev_1.71.0-6ubuntu8 libboost-thread1.71.0_1.71.0-6ubuntu8 libboost1.71-dev_1.71.0-6ubuntu8 libbz2-1.0_1.0.8-4ubuntu2 libc-bin_2.31-0ubuntu10 libc-dev-bin_2.31-0ubuntu10 libc6_2.31-0ubuntu10 libc6-dev_2.31-0ubuntu10 libcap-ng0_0.7.9-2.2 libcap2_1:2.36-1 libcc1-0_10.2.0-3ubuntu1 libcom-err2_1.45.6-1ubuntu1 libcroco3_0.6.13-1 libcrypt-dev_1:4.4.16-1ubuntu1 libcrypt1_1:4.4.16-1ubuntu1 libcryptsetup12_2:2.3.3-1ubuntu3 libctf-nobfd0_2.35-1ubuntu1 libctf0_2.35-1ubuntu1 libdb5.3_5.3.28+dfsg1-0.6ubuntu2 libdebconfclient0_0.252ubuntu1 libdebhelper-perl_13.2ubuntu1 libdevmapper1.02.1_2:1.02.167-1ubuntu3 libdpkg-perl_1.19.7ubuntu4 libeigen3-dev_3.3.7-2 libelf1_0.180-0ubuntu1 libexpat1_2.2.9-1build1 libext2fs2_1.45.6-1ubuntu1 libfakeroot_1.24-1 libffi7_3.3-4 libfile-stripnondeterminism-perl_1.9.0-1 libgcc-10-dev_10.2.0-3ubuntu1 libgcc-s1_10.2.0-3ubuntu1 libgcrypt20_1.8.5-5ubuntu2 libgdbm-compat4_1.18.1-5 libgdbm6_1.18.1-5 libglib2.0-0_2.64.4-1 libgmp10_2:6.2.0+dfsg-6 libgnutls30_3.6.13-4ubuntu4 libgomp1_10.2.0-3ubuntu1 libgpg-error0_1.38-2 libhogweed6_3.6-2 libicu66_66.1-2ubuntu3 libidn2-0_2.3.0-1 libip4tc2_1.8.4-3ubuntu2 libisl22_0.22.1-1 libitm1_10.2.0-3ubuntu1 libjson-c4_0.13.1+dfsg-9 libkmod2_27+20200310-2ubuntu1 liblocale-gettext-perl_1.07-4 liblockfile-bin_1.16-1.1 liblockfile1_1.16-1.1 liblz4-1_1.9.2-2 liblzma5_5.2.4-1ubuntu1 libmagic-mgc_1:5.38-5 libmagic1_1:5.38-5 libmount1_2.35.2-9ubuntu1 libmpc3_1.1.0-1 libmpdec2_2.4.2-3 libmpfr6_4.0.2-1build1 libncurses6_6.2-1 libncursesw6_6.2-1 libnettle8_3.6-2 libnpth0_1.6-2 libp11-kit0_0.23.20-1build1 libpam-modules_1.3.1-5ubuntu5 libpam-modules-bin_1.3.1-5ubuntu5 libpam-runtime_1.3.1-5ubuntu5 libpam0g_1.3.1-5ubuntu5 libpcre2-8-0_10.34-7 libpcre3_2:8.39-13 libperl5.30_5.30.3-4 libpipeline1_1.5.2-2build1 libpng16-16_1.6.37-2 libprocps8_2:3.3.16-5ubuntu1 libpython3-stdlib_3.8.2-0ubuntu2 libpython3.8-minimal_3.8.5-1 libpython3.8-stdlib_3.8.5-1 libreadline8_8.0-4 libseccomp2_2.4.3-1ubuntu4 libselinux1_3.1-2 libsemanage-common_3.1-1 libsemanage1_3.1-1 libsepol1_3.1-1 libsigsegv2_2.12-2build1 libsmartcols1_2.35.2-9ubuntu1 libsqlite3-0_3.32.3-1 libss2_1.45.6-1ubuntu1 libssl1.1_1.1.1f-1ubuntu3 libstdc++-10-dev_10.2.0-3ubuntu1 libstdc++6_10.2.0-3ubuntu1 libsub-override-perl_0.09-2 libsystemd0_245.6-3ubuntu3 libtasn1-6_4.16.0-2 libtinfo6_6.2-1 libtool_2.4.6-14 libubsan1_10.2.0-3ubuntu1 libuchardet0_0.0.7-1 libudev1_245.6-3ubuntu3 libunistring2_0.9.10-4 libuuid1_2.35.2-9ubuntu1 libxml2_2.9.10+dfsg-5 libzstd1_1.4.5+dfsg-3 linux-libc-dev_5.4.0-42.46 lockfile-progs_0.1.18 login_1:4.8.1-1ubuntu6 logsave_1.45.6-1ubuntu1 lsb-base_11.1.0ubuntu2 m4_1.4.18-4 make_4.3-4ubuntu1 man-db_2.9.3-2 mawk_1.3.4.20200120-2 mime-support_3.64ubuntu1 mount_2.35.2-9ubuntu1 ncurses-base_6.2-1 ncurses-bin_6.2-1 openssl_1.1.1f-1ubuntu3 optipng_0.7.7-1 passwd_1:4.8.1-1ubuntu6 patch_2.7.6-6 perl_5.30.3-4 perl-base_5.30.3-4 perl-modules-5.30_5.30.3-4 pinentry-curses_1.1.0-4build1 pkg-config_0.29.2-1ubuntu1 pkgbinarymangler_146 po-debconf_1.0.21 policyrcd-script-zg2_0.1-3 procps_2:3.3.16-5ubuntu1 python3_3.8.2-0ubuntu2 python3-distutils_3.8.5-1 python3-lib2to3_3.8.5-1 python3-minimal_3.8.2-0ubuntu2 python3.8_3.8.5-1 python3.8-minimal_3.8.5-1 readline-common_8.0-4 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-cufflinks-dummy_0.invalid.0 sed_4.7-1build1 sensible-utils_0.0.12+nmu1 systemd_245.6-3ubuntu3 systemd-sysv_245.6-3ubuntu3 systemd-timesyncd_245.6-3ubuntu3 sysvinit-utils_2.96-3ubuntu1 tar_1.30+dfsg-7 tzdata_2020a-0ubuntu1 ubuntu-keyring_2020.06.17.1 util-linux_2.35.2-9ubuntu1 xz-utils_5.2.4-1ubuntu1 zlib1g_1:1.2.11.dfsg-2ubuntu1 zlib1g-dev_1:1.2.11.dfsg-2ubuntu1 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Fri Feb 21 15:39:57 2020 UTC gpgv: using RSA key 92978A6E195E4921825F7FF0F34F09744E9F5DD9 gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./cufflinks_2.2.1+dfsg.1-7.dsc dpkg-source: info: extracting cufflinks in cufflinks-2.2.1+dfsg.1 dpkg-source: info: unpacking cufflinks_2.2.1+dfsg.1.orig.tar.gz dpkg-source: info: unpacking cufflinks_2.2.1+dfsg.1-7.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying py2to3.patch dpkg-source: warning: unexpected end of diff 'cufflinks-2.2.1+dfsg.1/debian/patches/boost1.65.patch' dpkg-source: info: applying boost1.65.patch dpkg-source: info: applying fix_gcc-7_ftbfs.patch dpkg-source: info: applying 0004-fix-m64-usage-and-lfs.patch dpkg-source: info: applying 0001-fix_spelling.patch dpkg-source: info: applying 0002-bam2samtools.patch dpkg-source: info: applying 0003-fix_includes_path.patch dpkg-source: info: applying format-security.patch dpkg-source: info: applying lib_eigen.patch dpkg-source: info: applying fix_gcc-6.1_issue_in_liblemon_code_copy.patch Check disc space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=noautodbgsym parallel=4 HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=build-PACKAGEBUILD-19659198 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-19659198 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-19659198 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package cufflinks dpkg-buildpackage: info: source version 2.2.1+dfsg.1-7 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build . dpkg-buildpackage: info: host architecture s390x debian/rules clean dh clean --with python3 debian/rules override_dh_auto_clean make[1]: Entering directory '/<>/cufflinks-2.2.1+dfsg.1' dh_auto_clean rm -rf autom4te.cache make[1]: Leaving directory '/<>/cufflinks-2.2.1+dfsg.1' dh_clean debian/rules binary-arch dh binary-arch --with python3 dh_update_autotools_config -a dh_autoreconf -a sh: 1: svnversion: not found configure.ac:39: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body ../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from... ../../lib/autoconf/general.m4:2601: _AC_COMPILE_IFELSE is expanded from... ../../lib/autoconf/general.m4:2617: AC_COMPILE_IFELSE is expanded from... ../../lib/m4sugar/m4sh.m4:639: AS_IF is expanded from... ../../lib/autoconf/general.m4:2042: AC_CACHE_VAL is expanded from... ../../lib/autoconf/general.m4:2063: AC_CACHE_CHECK is expanded from... ax_boost_system.m4:33: AX_BOOST_SYSTEM is expanded from... configure.ac:39: the top level configure.ac:40: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body ../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from... ../../lib/autoconf/general.m4:2601: _AC_COMPILE_IFELSE is expanded from... ../../lib/autoconf/general.m4:2617: AC_COMPILE_IFELSE is expanded from... ../../lib/m4sugar/m4sh.m4:639: AS_IF is expanded from... ../../lib/autoconf/general.m4:2042: AC_CACHE_VAL is expanded from... ../../lib/autoconf/general.m4:2063: AC_CACHE_CHECK is expanded from... ax_boost_serialization.m4:33: AX_BOOST_SERIALIZATION is expanded from... configure.ac:40: the top level configure.ac:41: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body ../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from... ../../lib/autoconf/general.m4:2601: _AC_COMPILE_IFELSE is expanded from... ../../lib/autoconf/general.m4:2617: AC_COMPILE_IFELSE is expanded from... ../../lib/m4sugar/m4sh.m4:639: AS_IF is expanded from... ../../lib/autoconf/general.m4:2042: AC_CACHE_VAL is expanded from... ../../lib/autoconf/general.m4:2063: AC_CACHE_CHECK is expanded from... ax_boost_thread.m4:33: AX_BOOST_THREAD is expanded from... configure.ac:41: the top level sh: 1: svnversion: not found configure.ac:39: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body ../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from... ../../lib/autoconf/general.m4:2601: _AC_COMPILE_IFELSE is expanded from... ../../lib/autoconf/general.m4:2617: AC_COMPILE_IFELSE is expanded from... ../../lib/m4sugar/m4sh.m4:639: AS_IF is expanded from... ../../lib/autoconf/general.m4:2042: AC_CACHE_VAL is expanded from... ../../lib/autoconf/general.m4:2063: AC_CACHE_CHECK is expanded from... ax_boost_system.m4:33: AX_BOOST_SYSTEM is expanded from... configure.ac:39: the top level configure.ac:40: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body ../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from... ../../lib/autoconf/general.m4:2601: _AC_COMPILE_IFELSE is expanded from... ../../lib/autoconf/general.m4:2617: AC_COMPILE_IFELSE is expanded from... ../../lib/m4sugar/m4sh.m4:639: AS_IF is expanded from... ../../lib/autoconf/general.m4:2042: AC_CACHE_VAL is expanded from... ../../lib/autoconf/general.m4:2063: AC_CACHE_CHECK is expanded from... ax_boost_serialization.m4:33: AX_BOOST_SERIALIZATION is expanded from... configure.ac:40: the top level configure.ac:41: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body ../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from... ../../lib/autoconf/general.m4:2601: _AC_COMPILE_IFELSE is expanded from... ../../lib/autoconf/general.m4:2617: AC_COMPILE_IFELSE is expanded from... ../../lib/m4sugar/m4sh.m4:639: AS_IF is expanded from... ../../lib/autoconf/general.m4:2042: AC_CACHE_VAL is expanded from... ../../lib/autoconf/general.m4:2063: AC_CACHE_CHECK is expanded from... ax_boost_thread.m4:33: AX_BOOST_THREAD is expanded from... configure.ac:41: the top level sh: 1: svnversion: not found configure.ac:39: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body ../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from... ../../lib/autoconf/general.m4:2601: _AC_COMPILE_IFELSE is expanded from... ../../lib/autoconf/general.m4:2617: AC_COMPILE_IFELSE is expanded from... ../../lib/m4sugar/m4sh.m4:639: AS_IF is expanded from... ../../lib/autoconf/general.m4:2042: AC_CACHE_VAL is expanded from... ../../lib/autoconf/general.m4:2063: AC_CACHE_CHECK is expanded from... ax_boost_system.m4:33: AX_BOOST_SYSTEM is expanded from... configure.ac:39: the top level configure.ac:40: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body ../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from... ../../lib/autoconf/general.m4:2601: _AC_COMPILE_IFELSE is expanded from... ../../lib/autoconf/general.m4:2617: AC_COMPILE_IFELSE is expanded from... ../../lib/m4sugar/m4sh.m4:639: AS_IF is expanded from... ../../lib/autoconf/general.m4:2042: AC_CACHE_VAL is expanded from... ../../lib/autoconf/general.m4:2063: AC_CACHE_CHECK is expanded from... ax_boost_serialization.m4:33: AX_BOOST_SERIALIZATION is expanded from... configure.ac:40: the top level configure.ac:41: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body ../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from... ../../lib/autoconf/general.m4:2601: _AC_COMPILE_IFELSE is expanded from... ../../lib/autoconf/general.m4:2617: AC_COMPILE_IFELSE is expanded from... ../../lib/m4sugar/m4sh.m4:639: AS_IF is expanded from... ../../lib/autoconf/general.m4:2042: AC_CACHE_VAL is expanded from... ../../lib/autoconf/general.m4:2063: AC_CACHE_CHECK is expanded from... ax_boost_thread.m4:33: AX_BOOST_THREAD is expanded from... configure.ac:41: the top level sh: 1: svnversion: not found configure.ac:39: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body ../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from... ../../lib/autoconf/general.m4:2601: _AC_COMPILE_IFELSE is expanded from... ../../lib/autoconf/general.m4:2617: AC_COMPILE_IFELSE is expanded from... ../../lib/m4sugar/m4sh.m4:639: AS_IF is expanded from... ../../lib/autoconf/general.m4:2042: AC_CACHE_VAL is expanded from... ../../lib/autoconf/general.m4:2063: AC_CACHE_CHECK is expanded from... ax_boost_system.m4:33: AX_BOOST_SYSTEM is expanded from... configure.ac:39: the top level configure.ac:40: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body ../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from... ../../lib/autoconf/general.m4:2601: _AC_COMPILE_IFELSE is expanded from... ../../lib/autoconf/general.m4:2617: AC_COMPILE_IFELSE is expanded from... ../../lib/m4sugar/m4sh.m4:639: AS_IF is expanded from... ../../lib/autoconf/general.m4:2042: AC_CACHE_VAL is expanded from... ../../lib/autoconf/general.m4:2063: AC_CACHE_CHECK is expanded from... ax_boost_serialization.m4:33: AX_BOOST_SERIALIZATION is expanded from... configure.ac:40: the top level configure.ac:41: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body ../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from... ../../lib/autoconf/general.m4:2601: _AC_COMPILE_IFELSE is expanded from... ../../lib/autoconf/general.m4:2617: AC_COMPILE_IFELSE is expanded from... ../../lib/m4sugar/m4sh.m4:639: AS_IF is expanded from... ../../lib/autoconf/general.m4:2042: AC_CACHE_VAL is expanded from... ../../lib/autoconf/general.m4:2063: AC_CACHE_CHECK is expanded from... ax_boost_thread.m4:33: AX_BOOST_THREAD is expanded from... configure.ac:41: the top level sh: 1: svnversion: not found configure.ac:39: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body ../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from... ../../lib/autoconf/general.m4:2601: _AC_COMPILE_IFELSE is expanded from... ../../lib/autoconf/general.m4:2617: AC_COMPILE_IFELSE is expanded from... ../../lib/m4sugar/m4sh.m4:639: AS_IF is expanded from... ../../lib/autoconf/general.m4:2042: AC_CACHE_VAL is expanded from... ../../lib/autoconf/general.m4:2063: AC_CACHE_CHECK is expanded from... ax_boost_system.m4:33: AX_BOOST_SYSTEM is expanded from... configure.ac:39: the top level configure.ac:40: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body ../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from... ../../lib/autoconf/general.m4:2601: _AC_COMPILE_IFELSE is expanded from... ../../lib/autoconf/general.m4:2617: AC_COMPILE_IFELSE is expanded from... ../../lib/m4sugar/m4sh.m4:639: AS_IF is expanded from... ../../lib/autoconf/general.m4:2042: AC_CACHE_VAL is expanded from... ../../lib/autoconf/general.m4:2063: AC_CACHE_CHECK is expanded from... ax_boost_serialization.m4:33: AX_BOOST_SERIALIZATION is expanded from... configure.ac:40: the top level configure.ac:41: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body ../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from... ../../lib/autoconf/general.m4:2601: _AC_COMPILE_IFELSE is expanded from... ../../lib/autoconf/general.m4:2617: AC_COMPILE_IFELSE is expanded from... ../../lib/m4sugar/m4sh.m4:639: AS_IF is expanded from... ../../lib/autoconf/general.m4:2042: AC_CACHE_VAL is expanded from... ../../lib/autoconf/general.m4:2063: AC_CACHE_CHECK is expanded from... ax_boost_thread.m4:33: AX_BOOST_THREAD is expanded from... configure.ac:41: the top level configure.ac:35: installing 'build-aux/ar-lib' configure.ac:31: installing 'build-aux/compile' configure.ac:39: installing 'build-aux/config.guess' configure.ac:39: installing 'build-aux/config.sub' configure.ac:16: installing 'build-aux/install-sh' configure.ac:16: installing 'build-aux/missing' src/Makefile.am:113: warning: source file 'locfit/adap.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled automake: warning: possible forward-incompatibility. automake: At least a source file is in a subdirectory, but the 'subdir-objects' automake: automake option hasn't been enabled. For now, the corresponding output automake: object file(s) will be placed in the top-level directory. However, automake: this behaviour will change in future Automake versions: they will automake: unconditionally cause object files to be placed in the same subdirectory automake: of the corresponding sources. automake: You are advised to start using 'subdir-objects' option throughout your automake: project, to avoid future incompatibilities. src/Makefile.am:113: warning: source file 'locfit/ar_funs.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/arith.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/band.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/c_args.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/c_plot.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/cmd.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/dens_haz.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/dens_int.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/dens_odi.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/density.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/dist.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/ev_atree.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/ev_interp.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/ev_kdtre.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/ev_main.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/ev_trian.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/family.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/fitted.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/frend.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/help.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/lf_dercor.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/lf_fitfun.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/lf_robust.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/lf_vari.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/lfd.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/lfstr.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/linalg.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/locfit.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/m_chol.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/m_eigen.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/m_jacob.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/m_max.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/makecmd.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/math.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/minmax.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/nbhd.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/pcomp.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/pout.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/preplot.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/random.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/readfile.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/scb.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/scb_cons.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/simul.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/solve.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/startlf.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/strings.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/vari.cpp' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/wdiag.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/weight.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am: installing 'build-aux/depcomp' debian/rules override_dh_auto_configure make[1]: Entering directory '/<>/cufflinks-2.2.1+dfsg.1' dh_auto_configure -- LIBS="-lboost_system -lboost_thread -lboost_serialization" ./configure --build=s390x-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/s390x-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking "LIBS=-lboost_system -lboost_thread -lboost_serialization" checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking for gawk... (cached) mawk checking for g++... g++ checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking whether make supports the include directive... yes (GNU style) checking dependency style of g++... none checking for gcc... gcc checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... none checking whether make sets $(MAKE)... (cached) yes checking for ranlib... ranlib checking for ar... ar checking the archiver (ar) interface... ar checking for a Python interpreter with version >= 2.4... python3 checking for python3... /usr/bin/python3 checking for python3 version... 3.8 checking for python3 platform... linux checking for python3 script directory... ${prefix}/lib/python3.8/site-packages checking for python3 extension module directory... ${exec_prefix}/lib/python3.8/site-packages checking for boostlib >= 1.47.0... yes checking for bamlib... yes checking build system type... s390x-ibm-linux-gnu checking whether the Boost::System library is available... yes checking whether the Boost::Serialization library is available... yes checking whether the Boost::Thread library is available... yes checking how to run the C preprocessor... gcc -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking if zlib is wanted... yes checking for inflateEnd in -lz... yes checking zlib.h usability... yes checking zlib.h presence... yes checking for zlib.h... yes checking for inflateEnd in -lz... (cached) yes checking zlib in /usr... ok checking for eigenlib... yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for unistd.h... (cached) yes checking for stdbool.h that conforms to C99... yes checking for _Bool... yes checking for inline... inline checking for pid_t... yes checking for size_t... yes checking for ptrdiff_t... yes checking host system type... s390x-ibm-linux-gnu checking for struct sysinfo.totalram... yes checking whether sysctl is declared... yes checking whether CTL_HW is declared... no checking whether HW_PHYSMEM is declared... no checking how to create a pax tar archive... gnutar checking dependency style of gcc... (cached) none checking dependency style of g++... (cached) none checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating config.h config.status: executing depfiles commands -- cufflinks 2.2.1 Configuration Results -- C++ compiler: g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -g -O2 -fdebug-prefix-map=/<>/cufflinks-2.2.1+dfsg.1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now GCC version: gcc (Ubuntu 10.2.0-3ubuntu1) 10.2.0 Host System type: s390x-ibm-linux-gnu Install prefix: /usr Install eprefix: ${prefix} See config.h for further configuration information. Email with questions and bug reports. make[1]: Leaving directory '/<>/cufflinks-2.2.1+dfsg.1' dh_auto_build -a make -j4 make[1]: Entering directory '/<>/cufflinks-2.2.1+dfsg.1' make all-recursive make[2]: Entering directory '/<>/cufflinks-2.2.1+dfsg.1' Making all in src make[3]: Entering directory '/<>/cufflinks-2.2.1+dfsg.1/src' g++ -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -g -O2 -fdebug-prefix-map=/<>/cufflinks-2.2.1+dfsg.1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o cufflinks.o cufflinks.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -g -O2 -fdebug-prefix-map=/<>/cufflinks-2.2.1+dfsg.1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o clustering.o clustering.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -g -O2 -fdebug-prefix-map=/<>/cufflinks-2.2.1+dfsg.1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o differential.o differential.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -g -O2 -fdebug-prefix-map=/<>/cufflinks-2.2.1+dfsg.1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o common.o common.cpp In file included from bundles.h:20, from replicates.h:10, from common.cpp:28: hits.h: In constructor ‘PrecomputedExpressionHitFactory::PrecomputedExpressionHitFactory(const string&, ReadTable&, RefSequenceTable&)’: hits.h:928:12: warning: ‘PrecomputedExpressionHitFactory::_expression_file_name’ will be initialized after [-Wreorder] 928 | string _expression_file_name; | ^~~~~~~~~~~~~~~~~~~~~ hits.h:927:19: warning: ‘std::ifstream PrecomputedExpressionHitFactory::_ifs’ [-Wreorder] 927 | std::ifstream _ifs; | ^~~~ In file included from bundles.h:20, from replicates.h:10, from common.cpp:28: hits.h:814:5: warning: when initialized here [-Wreorder] 814 | PrecomputedExpressionHitFactory(const string& expression_file_name, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from common.cpp:28: replicates.h: In member function ‘bool ReplicatedBundleFactory::next_bundle(HitBundle&, bool)’: replicates.h:224:57: warning: unused variable ‘s2’ [-Wunused-variable] 224 | const vector >& s2 = bundles[i-1]->ref_scaffolds(); | ^~ In file included from cufflinks.cpp:15: hits.h: In constructor ‘PrecomputedExpressionHitFactory::PrecomputedExpressionHitFactory(const string&, ReadTable&, RefSequenceTable&)’: hits.h:928:12: warning: ‘PrecomputedExpressionHitFactory::_expression_file_name’ will be initialized after [-Wreorder] 928 | string _expression_file_name; | ^~~~~~~~~~~~~~~~~~~~~ hits.h:927:19: warning: ‘std::ifstream PrecomputedExpressionHitFactory::_ifs’ [-Wreorder] 927 | std::ifstream _ifs; | ^~~~ In file included from cufflinks.cpp:15: hits.h:814:5: warning: when initialized here [-Wreorder] 814 | PrecomputedExpressionHitFactory(const string& expression_file_name, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from cufflinks.cpp:19: update_check.h: In function ‘bool get_current_version(char*)’: update_check.h:81:22: warning: argument to ‘sizeof’ in ‘void bzero(void*, size_t)’ call is the same expression as the destination; did you mean to provide an explicit length? [-Wsizeof-pointer-memaccess] 81 | bzero(curr_version, sizeof(curr_version)); | ^~~~~~~~~~~~~~~~~~~~ In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:10, from gtf_tracking.h:12, from bundles.h:22, from replicates.h:10, from common.cpp:28: GVec.hh: In instantiation of ‘void GVec::Grow(int, OBJ&) [with OBJ = GISeg]’: GVec.hh:422:9: required from ‘void GVec::Insert(int, OBJ*) [with OBJ = GISeg]’ GVec.hh:81:48: required from ‘void GVec::idxInsert(int, OBJ&) [with OBJ = GISeg]’ gtf_tracking.h:210:29: required from here GVec.hh:350:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class GISeg’; use assignment or value-initialization instead [-Wclass-memaccess] 350 | memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from bundles.h:22, from replicates.h:10, from common.cpp:28: gtf_tracking.h:188:7: note: ‘class GISeg’ declared here 188 | class GISeg: public GSeg { | ^~~~~ In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:10, from gtf_tracking.h:12, from bundles.h:22, from replicates.h:10, from common.cpp:28: GVec.hh: In instantiation of ‘void GVec::Grow(int, OBJ&) [with OBJ = GXSeg]’: GVec.hh:422:9: required from ‘void GVec::Insert(int, OBJ*) [with OBJ = GXSeg]’ GVec.hh:79:44: required from ‘void GVec::Insert(int, OBJ) [with OBJ = GXSeg]’ GList.hh:230:21: required from ‘int GArray::Add(OBJ*) [with OBJ = GXSeg]’ GList.hh:51:36: required from ‘int GArray::Add(OBJ&) [with OBJ = GXSeg]’ gtf_tracking.h:419:20: required from here GVec.hh:350:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class GXSeg’; use assignment or value-initialization instead [-Wclass-memaccess] 350 | memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from bundles.h:22, from replicates.h:10, from common.cpp:28: gtf_tracking.h:359:7: note: ‘class GXSeg’ declared here 359 | class GXSeg : public GSeg { | ^~~~~ In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:10, from gtf_tracking.h:12, from bundles.h:22, from replicates.h:10, from common.cpp:28: GVec.hh: In instantiation of ‘void GVec::Grow(int, OBJ&) [with OBJ = GSeg]’: GVec.hh:422:9: required from ‘void GVec::Insert(int, OBJ*) [with OBJ = GSeg]’ GVec.hh:79:44: required from ‘void GVec::Insert(int, OBJ) [with OBJ = GSeg]’ GList.hh:230:21: required from ‘int GArray::Add(OBJ*) [with OBJ = GSeg]’ GList.hh:51:36: required from ‘int GArray::Add(OBJ&) [with OBJ = GSeg]’ gtf_tracking.h:420:19: required from here GVec.hh:350:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class GSeg’; use assignment or value-initialization instead [-Wclass-memaccess] 350 | memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from gff.h:7, from gtf_tracking.h:12, from bundles.h:22, from replicates.h:10, from common.cpp:28: GBase.h:279:7: note: ‘class GSeg’ declared here 279 | class GSeg { | ^~~~ In file included from abundances.h:23, from differential.cpp:20: hits.h: In constructor ‘PrecomputedExpressionHitFactory::PrecomputedExpressionHitFactory(const string&, ReadTable&, RefSequenceTable&)’: hits.h:928:12: warning: ‘PrecomputedExpressionHitFactory::_expression_file_name’ will be initialized after [-Wreorder] 928 | string _expression_file_name; | ^~~~~~~~~~~~~~~~~~~~~ hits.h:927:19: warning: ‘std::ifstream PrecomputedExpressionHitFactory::_ifs’ [-Wreorder] 927 | std::ifstream _ifs; | ^~~~ In file included from abundances.h:23, from differential.cpp:20: hits.h:814:5: warning: when initialized here [-Wreorder] 814 | PrecomputedExpressionHitFactory(const string& expression_file_name, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from differential.h:29, from differential.cpp:21: replicates.h: In member function ‘bool ReplicatedBundleFactory::next_bundle(HitBundle&, bool)’: replicates.h:224:57: warning: unused variable ‘s2’ [-Wunused-variable] 224 | const vector >& s2 = bundles[i-1]->ref_scaffolds(); | ^~ In file included from differential.cpp:21: differential.h: In constructor ‘TrackingDataWriter::TrackingDataWriter(int, Outfiles*, Tracking*, const std::vector >&, std::vector >, ProgressBar*)’: differential.h:225:20: warning: ‘TrackingDataWriter::sample_labels’ will be initialized after [-Wreorder] 225 | vector sample_labels; | ^~~~~~~~~~~~~ differential.h:224:10: warning: ‘bool TrackingDataWriter::headers_written’ [-Wreorder] 224 | bool headers_written; // this flag records whether we've written out the file headers yet. | ^~~~~~~~~~~~~~~ differential.h:202:5: warning: when initialized here [-Wreorder] 202 | TrackingDataWriter(int num_samples, | ^~~~~~~~~~~~~~~~~~ In file included from differential.cpp:21: differential.h: In member function ‘void TrackingDataWriter::print_FPKM_tracking(const string&, FILE*, const FPKMTrackingTable&)’: differential.h:316:29: warning: variable ‘status’ set but not used [-Wunused-but-set-variable] 316 | AbundanceStatus status = NUMERIC_OK; | ^~~~~~ differential.h: In member function ‘void TrackingDataWriter::print_count_tracking(const string&, FILE*, const FPKMTrackingTable&)’: differential.h:397:29: warning: variable ‘status’ set but not used [-Wunused-but-set-variable] 397 | AbundanceStatus status = NUMERIC_OK; | ^~~~~~ In file included from abundances.h:23, from clustering.h:38, from clustering.cpp:10: hits.h: In constructor ‘PrecomputedExpressionHitFactory::PrecomputedExpressionHitFactory(const string&, ReadTable&, RefSequenceTable&)’: hits.h:928:12: warning: ‘PrecomputedExpressionHitFactory::_expression_file_name’ will be initialized after [-Wreorder] 928 | string _expression_file_name; | ^~~~~~~~~~~~~~~~~~~~~ hits.h:927:19: warning: ‘std::ifstream PrecomputedExpressionHitFactory::_ifs’ [-Wreorder] 927 | std::ifstream _ifs; | ^~~~ In file included from abundances.h:23, from clustering.h:38, from clustering.cpp:10: hits.h:814:5: warning: when initialized here [-Wreorder] 814 | PrecomputedExpressionHitFactory(const string& expression_file_name, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from cufflinks.cpp:28: replicates.h: In member function ‘bool ReplicatedBundleFactory::next_bundle(HitBundle&, bool)’: replicates.h:224:57: warning: unused variable ‘s2’ [-Wunused-variable] 224 | const vector >& s2 = bundles[i-1]->ref_scaffolds(); | ^~ cufflinks.cpp: In function ‘bool scaffolds_for_bundle(const HitBundle&, std::vector >&, std::vector >*, BundleStats*)’: cufflinks.cpp:690:30: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 690 | if (bundle.hits().size() >= max_frags_per_bundle) | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ cufflinks.cpp:690:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 690 | if (bundle.hits().size() >= max_frags_per_bundle) | ^~ cufflinks.cpp:693:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 693 | bool ref_guided = (ref_scaffs != NULL); | ^~~~ cufflinks.cpp: In function ‘void quantitate_transcript_cluster(AbundanceGroup&, double, std::vector&, bool)’: cufflinks.cpp:980:30: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 980 | for (size_t j = 0; j < N; ++j) | ~~^~~ cufflinks.cpp:988:30: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 988 | for (size_t j = 0; j < N; ++j) | ~~^~~ cufflinks.cpp: In function ‘void assemble_bundle(const RefSequenceTable&, HitBundle*, boost::shared_ptr, boost::shared_ptr, FILE*, FILE*, FILE*, FILE*)’: cufflinks.cpp:1264:55: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 1264 | bool bundle_too_large = bundle_ptr->hits().size() >= max_frags_per_bundle; | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ cufflinks.cpp:1275:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1275 | if (allow_junk_filtering) | ^~ cufflinks.cpp:1279:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1279 | if (!final_est_run && bundle_mode==REF_DRIVEN) // Bias needs to be learned | ^~ cufflinks.cpp:1176:17: warning: unused variable ‘map_mass’ [-Wunused-variable] 1176 | long double map_mass = rg_props->normalized_map_mass(); | ^~~~~~~~ cufflinks.cpp: In function ‘bool assemble_hits(BundleFactory&, boost::shared_ptr)’: cufflinks.cpp:1489:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 1489 | if (bundle.right() - bundle.left() > max_gene_length) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ In file included from differential.cpp:24: sampling.h: In function ‘double boost::numeric::ublas::cholesky_factorize(M&)’: sampling.h:50:13: warning: typedef ‘matrix_type’ locally defined but not used [-Wunused-local-typedefs] 50 | typedef M matrix_type; | ^~~~~~~~~~~ In file included from differential.cpp:24: sampling.h: In function ‘void boost::numeric::ublas::cholesky_substitute(const M&, boost::numeric::ublas::vector_expression&)’: sampling.h:113:19: warning: typedef ‘const_matrix_type’ locally defined but not used [-Wunused-local-typedefs] 113 | typedef const M const_matrix_type; | ^~~~~~~~~~~~~~~~~ sampling.h:114:42: warning: typedef ‘vector_type’ locally defined but not used [-Wunused-local-typedefs] 114 | typedef vector vector_type; | ^~~~~~~~~~~ sampling.h: In function ‘void boost::numeric::ublas::cholesky_substitute(const M&, boost::numeric::ublas::matrix_expression&)’: sampling.h:120:19: warning: typedef ‘const_matrix_type’ locally defined but not used [-Wunused-local-typedefs] 120 | typedef const M const_matrix_type; | ^~~~~~~~~~~~~~~~~ sampling.h:121:42: warning: typedef ‘matrix_type’ locally defined but not used [-Wunused-local-typedefs] 121 | typedef matrix matrix_type; | ^~~~~~~~~~~ sampling.h: In function ‘void boost::numeric::ublas::cholesky_substitute_left(boost::numeric::ublas::vector_expression&, const M&)’: sampling.h:127:19: warning: typedef ‘const_matrix_type’ locally defined but not used [-Wunused-local-typedefs] 127 | typedef const M const_matrix_type; | ^~~~~~~~~~~~~~~~~ sampling.h:128:42: warning: typedef ‘vector_type’ locally defined but not used [-Wunused-local-typedefs] 128 | typedef vector vector_type; | ^~~~~~~~~~~ sampling.h: In function ‘void boost::numeric::ublas::cholesky_substitute_left(boost::numeric::ublas::matrix_expression&, const M&)’: sampling.h:134:19: warning: typedef ‘const_matrix_type’ locally defined but not used [-Wunused-local-typedefs] 134 | typedef const M const_matrix_type; | ^~~~~~~~~~~~~~~~~ sampling.h:135:42: warning: typedef ‘matrix_type’ locally defined but not used [-Wunused-local-typedefs] 135 | typedef matrix matrix_type; | ^~~~~~~~~~~ differential.cpp: In member function ‘virtual void TestLauncher::perform_testing(std::vector >)’: differential.cpp:131:31: warning: unused variable ‘s2’ [-Wunused-variable] 131 | const AbundanceGroup& s2 = prev.transcripts; | ^~ differential.cpp: In member function ‘void TestLauncher::record_tracking_data(std::vector >&)’: differential.cpp:157:31: warning: unused variable ‘s2’ [-Wunused-variable] 157 | const AbundanceGroup& s2 = prev.transcripts; | ^~ differential.cpp: In function ‘SampleDifference test_diffexp(const FPKMContext&, const FPKMContext&)’: differential.cpp:344:61: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 344 | if (next_sample_idx >= 0 && next_sample_idx < prev.fpkm_samples.size()) | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ differential.cpp:352:61: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 352 | if (next_sample_idx >= 0 && next_sample_idx < prev.fpkm_samples.size()) | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ differential.cpp:374:61: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 374 | if (next_sample_idx >= 0 && next_sample_idx < curr.fpkm_samples.size()) | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ differential.cpp:382:61: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 382 | if (next_sample_idx >= 0 && next_sample_idx < curr.fpkm_samples.size()) | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ differential.cpp: In function ‘bool test_js(const AbundanceGroup&, const AbundanceGroup&, double&, double&)’: differential.cpp:626:57: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 626 | if (next_sample_idx >= 0 && next_sample_idx < prev_abundance.member_fpkm_samples().size()) | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ differential.cpp:638:57: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 638 | if (next_sample_idx >= 0 && next_sample_idx < prev_abundance.member_fpkm_samples().size()) | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ differential.cpp:664:57: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 664 | if (next_sample_idx >= 0 && next_sample_idx < curr_abundance.member_fpkm_samples().size()) | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ differential.cpp:676:57: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 676 | if (next_sample_idx >= 0 && next_sample_idx < curr_abundance.member_fpkm_samples().size()) | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ differential.cpp: In function ‘void test_differential(const string&, const std::vector >&, const std::vector >&, Tests&, Tracking&)’: differential.cpp:1394:76: warning: comparison of integer expressions of different signedness: ‘std::map, double>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 1394 | bool enough_reads = (curr_abundance.FPKM_by_replicate().size() >= min_reps_for_js_test && | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ differential.cpp:1395:76: warning: comparison of integer expressions of different signedness: ‘std::map, double>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 1395 | prev_abundance.FPKM_by_replicate().size() >= min_reps_for_js_test); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ differential.cpp:1433:77: warning: comparison of integer expressions of different signedness: ‘std::map, double>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 1433 | bool enough_reads = (curr_abundance.FPKM_by_replicate().size() >= min_reps_for_js_test && | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ differential.cpp:1434:77: warning: comparison of integer expressions of different signedness: ‘std::map, double>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 1434 | prev_abundance.FPKM_by_replicate().size() >= min_reps_for_js_test); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ differential.cpp:1471:76: warning: comparison of integer expressions of different signedness: ‘std::map, double>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 1471 | bool enough_reads = (curr_abundance.FPKM_by_replicate().size() >= min_reps_for_js_test && | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ differential.cpp:1472:76: warning: comparison of integer expressions of different signedness: ‘std::map, double>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 1472 | prev_abundance.FPKM_by_replicate().size() >= min_reps_for_js_test); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:10, from gtf_tracking.h:12, from bundles.h:22, from abundances.h:25, from clustering.h:38, from clustering.cpp:10: GVec.hh: In instantiation of ‘void GVec::Grow(int, OBJ&) [with OBJ = GISeg]’: GVec.hh:422:9: required from ‘void GVec::Insert(int, OBJ*) [with OBJ = GISeg]’ GVec.hh:81:48: required from ‘void GVec::idxInsert(int, OBJ&) [with OBJ = GISeg]’ gtf_tracking.h:210:29: required from here GVec.hh:350:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class GISeg’; use assignment or value-initialization instead [-Wclass-memaccess] 350 | memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from bundles.h:22, from abundances.h:25, from clustering.h:38, from clustering.cpp:10: gtf_tracking.h:188:7: note: ‘class GISeg’ declared here 188 | class GISeg: public GSeg { | ^~~~~ In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:10, from gtf_tracking.h:12, from bundles.h:22, from abundances.h:25, from clustering.h:38, from cufflinks.cpp:20: GVec.hh: In instantiation of ‘void GVec::Grow(int, OBJ&) [with OBJ = GISeg]’: GVec.hh:422:9: required from ‘void GVec::Insert(int, OBJ*) [with OBJ = GISeg]’ GVec.hh:81:48: required from ‘void GVec::idxInsert(int, OBJ&) [with OBJ = GISeg]’ gtf_tracking.h:210:29: required from here GVec.hh:350:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class GISeg’; use assignment or value-initialization instead [-Wclass-memaccess] 350 | memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from bundles.h:22, from abundances.h:25, from clustering.h:38, from cufflinks.cpp:20: gtf_tracking.h:188:7: note: ‘class GISeg’ declared here 188 | class GISeg: public GSeg { | ^~~~~ In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:10, from gtf_tracking.h:12, from bundles.h:22, from abundances.h:25, from clustering.h:38, from clustering.cpp:10: GVec.hh: In instantiation of ‘void GVec::Grow(int, OBJ&) [with OBJ = GXSeg]’: GVec.hh:422:9: required from ‘void GVec::Insert(int, OBJ*) [with OBJ = GXSeg]’ GVec.hh:79:44: required from ‘void GVec::Insert(int, OBJ) [with OBJ = GXSeg]’ GList.hh:230:21: required from ‘int GArray::Add(OBJ*) [with OBJ = GXSeg]’ GList.hh:51:36: required from ‘int GArray::Add(OBJ&) [with OBJ = GXSeg]’ gtf_tracking.h:419:20: required from here GVec.hh:350:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class GXSeg’; use assignment or value-initialization instead [-Wclass-memaccess] 350 | memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from bundles.h:22, from abundances.h:25, from clustering.h:38, from clustering.cpp:10: gtf_tracking.h:359:7: note: ‘class GXSeg’ declared here 359 | class GXSeg : public GSeg { | ^~~~~ In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:10, from gtf_tracking.h:12, from bundles.h:22, from abundances.h:25, from clustering.h:38, from clustering.cpp:10: GVec.hh: In instantiation of ‘void GVec::Grow(int, OBJ&) [with OBJ = GSeg]’: GVec.hh:422:9: required from ‘void GVec::Insert(int, OBJ*) [with OBJ = GSeg]’ GVec.hh:79:44: required from ‘void GVec::Insert(int, OBJ) [with OBJ = GSeg]’ GList.hh:230:21: required from ‘int GArray::Add(OBJ*) [with OBJ = GSeg]’ GList.hh:51:36: required from ‘int GArray::Add(OBJ&) [with OBJ = GSeg]’ gtf_tracking.h:420:19: required from here GVec.hh:350:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class GSeg’; use assignment or value-initialization instead [-Wclass-memaccess] 350 | memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from gff.h:7, from gtf_tracking.h:12, from bundles.h:22, from abundances.h:25, from clustering.h:38, from clustering.cpp:10: GBase.h:279:7: note: ‘class GSeg’ declared here 279 | class GSeg { | ^~~~ In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:10, from gtf_tracking.h:12, from bundles.h:22, from abundances.h:25, from clustering.h:38, from cufflinks.cpp:20: GVec.hh: In instantiation of ‘void GVec::Grow(int, OBJ&) [with OBJ = GXSeg]’: GVec.hh:422:9: required from ‘void GVec::Insert(int, OBJ*) [with OBJ = GXSeg]’ GVec.hh:79:44: required from ‘void GVec::Insert(int, OBJ) [with OBJ = GXSeg]’ GList.hh:230:21: required from ‘int GArray::Add(OBJ*) [with OBJ = GXSeg]’ GList.hh:51:36: required from ‘int GArray::Add(OBJ&) [with OBJ = GXSeg]’ gtf_tracking.h:419:20: required from here GVec.hh:350:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class GXSeg’; use assignment or value-initialization instead [-Wclass-memaccess] 350 | memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from bundles.h:22, from abundances.h:25, from clustering.h:38, from cufflinks.cpp:20: gtf_tracking.h:359:7: note: ‘class GXSeg’ declared here 359 | class GXSeg : public GSeg { | ^~~~~ In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:10, from gtf_tracking.h:12, from bundles.h:22, from abundances.h:25, from clustering.h:38, from cufflinks.cpp:20: GVec.hh: In instantiation of ‘void GVec::Grow(int, OBJ&) [with OBJ = GSeg]’: GVec.hh:422:9: required from ‘void GVec::Insert(int, OBJ*) [with OBJ = GSeg]’ GVec.hh:79:44: required from ‘void GVec::Insert(int, OBJ) [with OBJ = GSeg]’ GList.hh:230:21: required from ‘int GArray::Add(OBJ*) [with OBJ = GSeg]’ GList.hh:51:36: required from ‘int GArray::Add(OBJ&) [with OBJ = GSeg]’ gtf_tracking.h:420:19: required from here GVec.hh:350:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class GSeg’; use assignment or value-initialization instead [-Wclass-memaccess] 350 | memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from gff.h:7, from gtf_tracking.h:12, from bundles.h:22, from abundances.h:25, from clustering.h:38, from cufflinks.cpp:20: GBase.h:279:7: note: ‘class GSeg’ declared here 279 | class GSeg { | ^~~~ In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:10, from gtf_tracking.h:12, from bundles.h:22, from abundances.h:25, from differential.cpp:20: GVec.hh: In instantiation of ‘void GVec::Grow(int, OBJ&) [with OBJ = GISeg]’: GVec.hh:422:9: required from ‘void GVec::Insert(int, OBJ*) [with OBJ = GISeg]’ GVec.hh:81:48: required from ‘void GVec::idxInsert(int, OBJ&) [with OBJ = GISeg]’ gtf_tracking.h:210:29: required from here GVec.hh:350:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class GISeg’; use assignment or value-initialization instead [-Wclass-memaccess] 350 | memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from bundles.h:22, from abundances.h:25, from differential.cpp:20: gtf_tracking.h:188:7: note: ‘class GISeg’ declared here 188 | class GISeg: public GSeg { | ^~~~~ In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:10, from gtf_tracking.h:12, from bundles.h:22, from abundances.h:25, from differential.cpp:20: GVec.hh: In instantiation of ‘void GVec::Grow(int, OBJ&) [with OBJ = GXSeg]’: GVec.hh:422:9: required from ‘void GVec::Insert(int, OBJ*) [with OBJ = GXSeg]’ GVec.hh:79:44: required from ‘void GVec::Insert(int, OBJ) [with OBJ = GXSeg]’ GList.hh:230:21: required from ‘int GArray::Add(OBJ*) [with OBJ = GXSeg]’ GList.hh:51:36: required from ‘int GArray::Add(OBJ&) [with OBJ = GXSeg]’ gtf_tracking.h:419:20: required from here GVec.hh:350:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class GXSeg’; use assignment or value-initialization instead [-Wclass-memaccess] 350 | memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from bundles.h:22, from abundances.h:25, from differential.cpp:20: gtf_tracking.h:359:7: note: ‘class GXSeg’ declared here 359 | class GXSeg : public GSeg { | ^~~~~ In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:10, from gtf_tracking.h:12, from bundles.h:22, from abundances.h:25, from differential.cpp:20: GVec.hh: In instantiation of ‘void GVec::Grow(int, OBJ&) [with OBJ = GSeg]’: GVec.hh:422:9: required from ‘void GVec::Insert(int, OBJ*) [with OBJ = GSeg]’ GVec.hh:79:44: required from ‘void GVec::Insert(int, OBJ) [with OBJ = GSeg]’ GList.hh:230:21: required from ‘int GArray::Add(OBJ*) [with OBJ = GSeg]’ GList.hh:51:36: required from ‘int GArray::Add(OBJ&) [with OBJ = GSeg]’ gtf_tracking.h:420:19: required from here GVec.hh:350:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class GSeg’; use assignment or value-initialization instead [-Wclass-memaccess] 350 | memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from gff.h:7, from gtf_tracking.h:12, from bundles.h:22, from abundances.h:25, from differential.cpp:20: GBase.h:279:7: note: ‘class GSeg’ declared here 279 | class GSeg { | ^~~~ g++ -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -g -O2 -fdebug-prefix-map=/<>/cufflinks-2.2.1+dfsg.1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o assemble.o assemble.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -g -O2 -fdebug-prefix-map=/<>/cufflinks-2.2.1+dfsg.1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o tokenize.o tokenize.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -g -O2 -fdebug-prefix-map=/<>/cufflinks-2.2.1+dfsg.1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o abundances.o abundances.cpp In file included from bundles.h:23, from abundances.h:25, from differential.cpp:20: progressbar.h: In member function ‘virtual std::vector > > TestLauncher::test_finished_loci()’: progressbar.h:70:57: warning: ‘%3d’ directive output may be truncated writing between 3 and 11 bytes into a region of size between 6 and 33 [-Wformat-truncation=] 70 | snprintf(line_buf, 82, "\r> Processing Locus %-27s %s %3d%%", bundle_buf, _bar_buf, percent); | ^~~ progressbar.h:70:26: note: directive argument in the range [-2147483648, 99] 70 | snprintf(line_buf, 82, "\r> Processing Locus %-27s %s %3d%%", bundle_buf, _bar_buf, percent); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:867, from /usr/include/c++/10/cstdio:42, from /usr/include/c++/10/ext/string_conversions.h:43, from /usr/include/c++/10/bits/basic_string.h:6535, from /usr/include/c++/10/string:55, from /usr/include/c++/10/bits/locale_classes.h:40, from /usr/include/c++/10/bits/ios_base.h:41, from /usr/include/c++/10/streambuf:41, from /usr/include/c++/10/bits/streambuf_iterator.h:35, from /usr/include/c++/10/iterator:66, from /usr/include/boost/operators.hpp:98, from /usr/include/boost/serialization/strong_typedef.hpp:27, from /usr/include/boost/serialization/collection_size_type.hpp:10, from /usr/include/boost/serialization/array_wrapper.hpp:22, from /usr/include/boost/serialization/array.hpp:26, from /usr/include/boost/numeric/ublas/storage.hpp:21, from /usr/include/boost/numeric/ublas/vector.hpp:21, from differential.cpp:13: /usr/include/s390x-linux-gnu/bits/stdio2.h:67:35: note: ‘__builtin___snprintf_chk’ output between 54 and 89 bytes into a destination of size 82 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ./lemon/bits/base_extender.h:23, from ./lemon/list_graph.h:26, from ./lemon/dfs.h:26, from ./lemon/topology.h:22, from assemble.cpp:19: ./lemon/error.h:93:10: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 93 | std::auto_ptr<_Type> ptr; | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from ./lemon/error.h:31, from ./lemon/bits/base_extender.h:23, from ./lemon/list_graph.h:26, from ./lemon/dfs.h:26, from ./lemon/topology.h:22, from assemble.cpp:19: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from ./lemon/bits/base_extender.h:23, from ./lemon/list_graph.h:26, from ./lemon/dfs.h:26, from ./lemon/topology.h:22, from assemble.cpp:19: ./lemon/error.h:108:10: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 108 | std::auto_ptr buf; | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from ./lemon/error.h:31, from ./lemon/bits/base_extender.h:23, from ./lemon/list_graph.h:26, from ./lemon/dfs.h:26, from ./lemon/topology.h:22, from assemble.cpp:19: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from /usr/include/boost/math/policies/error_handling.hpp:14, from /usr/include/boost/math/special_functions/gamma.hpp:23, from /usr/include/boost/math/special_functions/erf.hpp:15, from /usr/include/boost/math/distributions/normal.hpp:19, from common.h:27, from cufflinks.cpp:14: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘void ProgressBar::update(const char*, double)’ at progressbar.h:59:10, inlined from ‘bool assemble_hits(BundleFactory&, boost::shared_ptr)’ at cufflinks.cpp:1513:15: /usr/include/s390x-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ output may be truncated copying 27 bytes from a string of length 2047 [-Wstringop-truncation] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from assemble.cpp:19: ./lemon/topology.h: In function ‘bool lemon::stronglyConnected(const Graph&)’: ./lemon/topology.h:249:34: warning: typedef ‘Node’ locally defined but not used [-Wunused-local-typedefs] 249 | typedef typename Graph::Node Node; | ^~~~ ./lemon/topology.h: In function ‘int lemon::countStronglyConnectedComponents(const Graph&)’: ./lemon/topology.h:311:34: warning: typedef ‘Edge’ locally defined but not used [-Wunused-local-typedefs] 311 | typedef typename Graph::Edge Edge; | ^~~~ ./lemon/topology.h:313:36: warning: typedef ‘EdgeIt’ locally defined but not used [-Wunused-local-typedefs] 313 | typedef typename Graph::EdgeIt EdgeIt; | ^~~~~~ ./lemon/topology.h: In function ‘void lemon::topologicalSort(const Graph&, NodeMap&)’: ./lemon/topology.h:1213:34: warning: typedef ‘Node’ locally defined but not used [-Wunused-local-typedefs] 1213 | typedef typename Graph::Node Node; | ^~~~ ./lemon/topology.h:1215:34: warning: typedef ‘Edge’ locally defined but not used [-Wunused-local-typedefs] 1215 | typedef typename Graph::Edge Edge; | ^~~~ ./lemon/topology.h: In function ‘bool lemon::bipartite(const UGraph&)’: ./lemon/topology.h:1470:37: warning: typedef ‘EdgeIt’ locally defined but not used [-Wunused-local-typedefs] 1470 | typedef typename UGraph::EdgeIt EdgeIt; | ^~~~~~ ./lemon/topology.h: In function ‘bool lemon::bipartitePartitions(const UGraph&, NodeMap&)’: ./lemon/topology.h:1514:35: warning: typedef ‘Node’ locally defined but not used [-Wunused-local-typedefs] 1514 | typedef typename UGraph::Node Node; | ^~~~ ./lemon/topology.h:1516:37: warning: typedef ‘EdgeIt’ locally defined but not used [-Wunused-local-typedefs] 1516 | typedef typename UGraph::EdgeIt EdgeIt; | ^~~~~~ In file included from assemble.cpp:44: transitive_closure.h: In function ‘void transitive_closure(const Graph&, GraphTC&, G_to_TC_VertexMap, VertexIndexMap)’: transitive_closure.h:85:62: warning: typedef ‘edge’ locally defined but not used [-Wunused-local-typedefs] 85 | typedef typename graph_traits < Graph >::edge_descriptor edge; | ^~~~ transitive_closure.h:226:66: warning: typedef ‘tc_vertex’ locally defined but not used [-Wunused-local-typedefs] 226 | typedef typename graph_traits < GraphTC >::vertex_descriptor tc_vertex; | ^~~~~~~~~ transitive_closure.h: In function ‘void warshall_transitive_closure(G&)’: transitive_closure.h:323:60: warning: typedef ‘vertex’ locally defined but not used [-Wunused-local-typedefs] 323 | typedef typename graph_traits < G >::vertex_descriptor vertex; | ^~~~~~ transitive_closure.h: In function ‘void warren_transitive_closure(G&)’: transitive_closure.h:349:60: warning: typedef ‘vertex’ locally defined but not used [-Wunused-local-typedefs] 349 | typedef typename graph_traits < G >::vertex_descriptor vertex; | ^~~~~~ In file included from assemble.cpp:45: transitive_reduction.h: In function ‘boost::ccheck_aux::unaryfunptr_arg_type::type boost::transitive_reduction(const Graph&, GraphTR&, G_to_TR_VertexMap, VertexIndexMap)’: transitive_reduction.h:53:63: warning: typedef ‘VertexIterator’ locally defined but not used [-Wunused-local-typedefs] 53 | typedef typename graph_traits::vertex_iterator VertexIterator; | ^~~~~~~~~~~~~~ In file included from abundances.h:23, from abundances.cpp:16: hits.h: In constructor ‘PrecomputedExpressionHitFactory::PrecomputedExpressionHitFactory(const string&, ReadTable&, RefSequenceTable&)’: hits.h:928:12: warning: ‘PrecomputedExpressionHitFactory::_expression_file_name’ will be initialized after [-Wreorder] 928 | string _expression_file_name; | ^~~~~~~~~~~~~~~~~~~~~ hits.h:927:19: warning: ‘std::ifstream PrecomputedExpressionHitFactory::_ifs’ [-Wreorder] 927 | std::ifstream _ifs; | ^~~~ In file included from abundances.h:23, from abundances.cpp:16: hits.h:814:5: warning: when initialized here [-Wreorder] 814 | PrecomputedExpressionHitFactory(const string& expression_file_name, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -g -O2 -fdebug-prefix-map=/<>/cufflinks-2.2.1+dfsg.1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o scaffolds.o scaffolds.cpp In file included from bundles.h:20, from assemble.h:21, from assemble.cpp:48: hits.h: In constructor ‘PrecomputedExpressionHitFactory::PrecomputedExpressionHitFactory(const string&, ReadTable&, RefSequenceTable&)’: hits.h:928:12: warning: ‘PrecomputedExpressionHitFactory::_expression_file_name’ will be initialized after [-Wreorder] 928 | string _expression_file_name; | ^~~~~~~~~~~~~~~~~~~~~ hits.h:927:19: warning: ‘std::ifstream PrecomputedExpressionHitFactory::_ifs’ [-Wreorder] 927 | std::ifstream _ifs; | ^~~~ In file included from bundles.h:20, from assemble.h:21, from assemble.cpp:48: hits.h:814:5: warning: when initialized here [-Wreorder] 814 | PrecomputedExpressionHitFactory(const string& expression_file_name, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from abundances.cpp:43: replicates.h: In member function ‘bool ReplicatedBundleFactory::next_bundle(HitBundle&, bool)’: replicates.h:224:57: warning: unused variable ‘s2’ [-Wunused-variable] 224 | const vector >& s2 = bundles[i-1]->ref_scaffolds(); | ^~ In file included from abundances.cpp:44: sampling.h: In function ‘double boost::numeric::ublas::cholesky_factorize(M&)’: sampling.h:50:13: warning: typedef ‘matrix_type’ locally defined but not used [-Wunused-local-typedefs] 50 | typedef M matrix_type; | ^~~~~~~~~~~ In file included from abundances.cpp:44: sampling.h: In function ‘void boost::numeric::ublas::cholesky_substitute(const M&, boost::numeric::ublas::vector_expression&)’: sampling.h:113:19: warning: typedef ‘const_matrix_type’ locally defined but not used [-Wunused-local-typedefs] 113 | typedef const M const_matrix_type; | ^~~~~~~~~~~~~~~~~ sampling.h:114:42: warning: typedef ‘vector_type’ locally defined but not used [-Wunused-local-typedefs] 114 | typedef vector vector_type; | ^~~~~~~~~~~ sampling.h: In function ‘void boost::numeric::ublas::cholesky_substitute(const M&, boost::numeric::ublas::matrix_expression&)’: sampling.h:120:19: warning: typedef ‘const_matrix_type’ locally defined but not used [-Wunused-local-typedefs] 120 | typedef const M const_matrix_type; | ^~~~~~~~~~~~~~~~~ sampling.h:121:42: warning: typedef ‘matrix_type’ locally defined but not used [-Wunused-local-typedefs] 121 | typedef matrix matrix_type; | ^~~~~~~~~~~ sampling.h: In function ‘void boost::numeric::ublas::cholesky_substitute_left(boost::numeric::ublas::vector_expression&, const M&)’: sampling.h:127:19: warning: typedef ‘const_matrix_type’ locally defined but not used [-Wunused-local-typedefs] 127 | typedef const M const_matrix_type; | ^~~~~~~~~~~~~~~~~ sampling.h:128:42: warning: typedef ‘vector_type’ locally defined but not used [-Wunused-local-typedefs] 128 | typedef vector vector_type; | ^~~~~~~~~~~ sampling.h: In function ‘void boost::numeric::ublas::cholesky_substitute_left(boost::numeric::ublas::matrix_expression&, const M&)’: sampling.h:134:19: warning: typedef ‘const_matrix_type’ locally defined but not used [-Wunused-local-typedefs] 134 | typedef const M const_matrix_type; | ^~~~~~~~~~~~~~~~~ sampling.h:135:42: warning: typedef ‘matrix_type’ locally defined but not used [-Wunused-local-typedefs] 135 | typedef matrix matrix_type; | ^~~~~~~~~~~ abundances.cpp: In constructor ‘AbundanceGroup::AbundanceGroup(const std::vector >&, const boost::numeric::ublas::matrix&, const boost::numeric::ublas::matrix&, const boost::numeric::ublas::matrix&, const boost::numeric::ublas::matrix&, const std::set >&)’: abundances.cpp:518:58: warning: comparison of integer expressions of different signedness: ‘std::set >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 518 | if (no_js_tests == false && _read_group_props.size() >= min_reps_for_js_test) | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ abundances.cpp: In member function ‘virtual AbundanceStatus AbundanceGroup::status() const’: abundances.cpp:549:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 549 | if (has_ok_member == false) | ^~ abundances.cpp:552:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 552 | return NUMERIC_OK; | ^~~~~~ abundances.cpp:526:10: warning: variable ‘has_lowdata_member’ set but not used [-Wunused-but-set-variable] 526 | bool has_lowdata_member = false; | ^~~~~~~~~~~~~~~~~~ assemble.cpp: In function ‘void create_reachability_bp_graph(DAG&, ReachGraph&, std::vector::BNode, std::allocator::BNode> >, DagToBp&, const boost::adjacency_list<>&, const std::vector&)’: assemble.cpp:188:21: warning: variable ‘a_for_b’ set but not used [-Wunused-but-set-variable] 188 | ReachGraph::ANode a_for_b = b_to_a[b_id]; | ^~~~~~~ assemble.cpp:123:17: warning: variable ‘hits_for_node’ set but not used [-Wunused-but-set-variable] 123 | HitsForNodeMap hits_for_node = get(vertex_name, dag); | ^~~~~~~~~~~~~ assemble.cpp: In function ‘void add_weights_to_reachability_bp_graph(ReachGraph&, const HitsForNodeMap&, const std::vector&, const std::vector&, lemon::BpUGraphExtender >::UEdgeMap&)’: assemble.cpp:262:21: warning: variable ‘a_for_b’ set but not used [-Wunused-but-set-variable] 262 | ReachGraph::ANode a_for_b = bp.nodeFromANodeId(a_id_for_b); | ^~~~~~~ abundances.cpp: In member function ‘void AbundanceGroup::collect_per_replicate_mass(const std::vector&, std::vector >&)’: abundances.cpp:1043:20: warning: unused variable ‘curr_mass’ [-Wunused-variable] 1043 | double curr_mass = inserted.first->second; | ^~~~~~~~~ abundances.cpp: In function ‘void collapse_equivalent_hits(const std::vector&, std::vector >&, std::vector&, std::vector&, bool)’: abundances.cpp:1160:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 1160 | for (size_t j = 0; j < N; ++j) | ~~^~~ abundances.cpp:1347:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1347 | for(int i = 0 ; i < nr_alignments.size(); ++i) | ~~^~~~~~~~~~~~~~~~~~~~~~ abundances.cpp: In function ‘AbundanceStatus bootstrap_gamma_mle(const std::vector >&, const std::vector&, const std::vector&, boost::numeric::ublas::vector > >&, boost::numeric::ublas::matrix&, double&)’: abundances.cpp:1488:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 1488 | for (size_t i = 0; i < num_bootstrap_samples; ++i) | ~~^~~~~~~~~~~~~~~~~~~~~~~ abundances.cpp:1491:30: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 1491 | for (size_t j = 0; j < num_sample_frags; ++j) | ~~^~~~~~~~~~~~~~~~~~ abundances.cpp:1505:45: warning: comparison of integer expressions of different signedness: ‘__gnu_cxx::__alloc_traits, int>::value_type’ {aka ‘int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 1505 | sample_idxs[curr_sample] >= processed_hits && abundances.cpp: In function ‘bool generate_count_assignment_samples(int, const std::vector&, const boost::numeric::ublas::matrix&, std::vector > > >&)’: abundances.cpp:1693:44: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 1693 | for (size_t assign_idx = 0; assign_idx < num_draws; ++assign_idx) | ~~~~~~~~~~~^~~~~~~~~~~ abundances.cpp: In function ‘void calculate_gamma_mle_covariance(const std::map, boost::shared_ptr >&, boost::numeric::ublas::vector > >&, boost::numeric::ublas::matrix&)’: abundances.cpp:1760:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘boost::numeric::ublas::vector > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1760 | for (int j = 0; j < all_assigned_count_samples[i].size(); ++j) | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ abundances.cpp:1775:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 1775 | for (size_t i = 0; i < num_transcripts; ++i) | ~~^~~~~~~~~~~~~~~~~ abundances.cpp:1777:30: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 1777 | for (size_t j = 0; j < num_transcripts; ++j) | ~~^~~~~~~~~~~~~~~~~ abundances.cpp: In function ‘void calculate_fragment_assignment_distribution(const std::map, boost::shared_ptr >&, boost::numeric::ublas::vector > >&, boost::numeric::ublas::matrix&, std::vector > > >&)’: abundances.cpp:1870:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘boost::numeric::ublas::vector > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1870 | for (int j = 0; j < all_assigned_count_samples[i].size(); ++j) | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ abundances.cpp:1885:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 1885 | for (size_t i = 0; i < num_transcripts; ++i) | ~~^~~~~~~~~~~~~~~~~ abundances.cpp:1887:30: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 1887 | for (size_t j = 0; j < num_transcripts; ++j) | ~~^~~~~~~~~~~~~~~~~ abundances.cpp: In member function ‘void AbundanceGroup::calculate_abundance_group_variance(const std::vector >&, const std::map, boost::shared_ptr >&)’: abundances.cpp:1968:62: warning: comparison of integer expressions of different signedness: ‘std::set >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 1968 | if (no_js_tests == false && _read_group_props.size() >= min_reps_for_js_test) | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ abundances.cpp: In member function ‘void AbundanceGroup::aggregate_replicate_abundances(const std::map, boost::shared_ptr >&)’: abundances.cpp:2070:58: warning: unused variable ‘sc_ab’ [-Wunused-variable] 2070 | const vector >& sc_ab = itr->second->abundances(); | ^~~~~ abundances.cpp: In function ‘bool estimate_count_variance(long double&, double, double, double, double, double)’: abundances.cpp:2277:17: warning: variable ‘bnb_mean’ set but not used [-Wunused-but-set-variable] 2277 | long double bnb_mean = 0.0; | ^~~~~~~~ abundances.cpp: In member function ‘void AbundanceGroup::generate_fpkm_samples()’: abundances.cpp:2668:30: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase >::Index’ {aka ‘long int’} [-Wsign-compare] 2668 | for (size_t j = 0; j < sample.size(); ++j) | ~~^~~~~~~~~~~~~~~ abundances.cpp: In member function ‘void AbundanceGroup::calculate_FPKM_covariance()’: abundances.cpp:2783:42: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses] 2783 | if (length_i > 0 && length_j > 0 & M > 0) | ~~~~~~~~~^~~ abundances.cpp:2796:24: warning: unused variable ‘fpkm’ [-Wunused-variable] 2796 | double fpkm = _abundances[i]->FPKM(); | ^~~~ abundances.cpp: In member function ‘void AbundanceGroup::calculate_conf_intervals()’: abundances.cpp:2920:34: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 2920 | for (size_t j = 0; j < N; ++j) | ~~^~~ abundances.cpp:2939:34: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 2939 | for (size_t j = 0; j < N; ++j) | ~~^~~ abundances.cpp: In function ‘void calculate_assignment_probs(const VectorXd&, const MatrixXd&, const VectorXd&, Eigen::MatrixXd&)’: abundances.cpp:3352:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase >::Index’ {aka ‘long int’} [-Wsign-compare] 3352 | for (size_t i = 0; i < alignment_multiplicities.size(); ++i) | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ abundances.cpp: In function ‘void calculate_average_assignment_probs(const VectorXd&, const MatrixXd&, const VectorXd&, Eigen::MatrixXd&)’: abundances.cpp:3378:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase >::Index’ {aka ‘long int’} [-Wsign-compare] 3378 | for (size_t i = 0; i < alignment_multiplicities.size(); ++i) | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ abundances.cpp:3393:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase >::Index’ {aka ‘long int’} [-Wsign-compare] 3393 | for (size_t i = 0; i < alignment_multiplicities.size(); ++i) | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ abundances.cpp:3395:30: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase >::Index’ {aka ‘long int’} [-Wsign-compare] 3395 | for (size_t j = 0; j < proposed_gammas.size(); ++j) | ~~^~~~~~~~~~~~~~~~~~~~~~~~ abundances.cpp:3408:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase >::Index’ {aka ‘long int’} [-Wsign-compare] 3408 | for (size_t j = 0; j < proposed_gammas.size(); ++j) | ~~^~~~~~~~~~~~~~~~~~~~~~~~ abundances.cpp: In member function ‘AbundanceStatus AbundanceGroup::calculate_per_replicate_abundances(std::vector >&, const std::map, std::vector >&, std::map, boost::shared_ptr >&, bool)’: abundances.cpp:4066:94: warning: variable ‘al_itr’ set but not used [-Wunused-but-set-variable] 4066 | map, vector >::const_iterator al_itr = | ^~~~~~ abundances.cpp: In function ‘bool is_identifiable(M&, PM&)’: abundances.cpp:4254:15: warning: typedef ‘matrix_type’ locally defined but not used [-Wunused-local-typedefs] 4254 | typedef M matrix_type; | ^~~~~~~~~~~ abundances.cpp: In function ‘AbundanceStatus gamma_mle(const std::vector >&, const std::vector&, const std::vector&, std::vector&, bool)’: abundances.cpp:4322:30: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::Index’ {aka ‘long int’} [-Wsign-compare] 4322 | for (size_t j = 0; j < cond_probs.rows(); ++j) | ~~^~~~~~~~~~~~~~~~~~~ abundances.cpp:4324:34: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::Index’ {aka ‘long int’} [-Wsign-compare] 4324 | for (size_t i = 0; i < cond_probs.cols(); ++i) | ~~^~~~~~~~~~~~~~~~~~~ abundances.cpp:4318:10: warning: variable ‘logL’ set but not used [-Wunused-but-set-variable] 4318 | double logL; | ^~~~ In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:10, from gtf_tracking.h:12, from bundles.h:22, from assemble.h:21, from assemble.cpp:48: GVec.hh: In instantiation of ‘void GVec::Grow(int, OBJ&) [with OBJ = GISeg]’: GVec.hh:422:9: required from ‘void GVec::Insert(int, OBJ*) [with OBJ = GISeg]’ GVec.hh:81:48: required from ‘void GVec::idxInsert(int, OBJ&) [with OBJ = GISeg]’ gtf_tracking.h:210:29: required from here GVec.hh:350:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class GISeg’; use assignment or value-initialization instead [-Wclass-memaccess] 350 | memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from bundles.h:22, from assemble.h:21, from assemble.cpp:48: gtf_tracking.h:188:7: note: ‘class GISeg’ declared here 188 | class GISeg: public GSeg { | ^~~~~ In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:10, from gtf_tracking.h:12, from bundles.h:22, from abundances.h:25, from abundances.cpp:16: GVec.hh: In instantiation of ‘void GVec::Grow(int, OBJ&) [with OBJ = GISeg]’: GVec.hh:422:9: required from ‘void GVec::Insert(int, OBJ*) [with OBJ = GISeg]’ GVec.hh:81:48: required from ‘void GVec::idxInsert(int, OBJ&) [with OBJ = GISeg]’ gtf_tracking.h:210:29: required from here GVec.hh:350:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class GISeg’; use assignment or value-initialization instead [-Wclass-memaccess] 350 | memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from bundles.h:22, from abundances.h:25, from abundances.cpp:16: gtf_tracking.h:188:7: note: ‘class GISeg’ declared here 188 | class GISeg: public GSeg { | ^~~~~ In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:10, from gtf_tracking.h:12, from bundles.h:22, from assemble.h:21, from assemble.cpp:48: GVec.hh: In instantiation of ‘void GVec::Grow(int, OBJ&) [with OBJ = GXSeg]’: GVec.hh:422:9: required from ‘void GVec::Insert(int, OBJ*) [with OBJ = GXSeg]’ GVec.hh:79:44: required from ‘void GVec::Insert(int, OBJ) [with OBJ = GXSeg]’ GList.hh:230:21: required from ‘int GArray::Add(OBJ*) [with OBJ = GXSeg]’ GList.hh:51:36: required from ‘int GArray::Add(OBJ&) [with OBJ = GXSeg]’ gtf_tracking.h:419:20: required from here GVec.hh:350:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class GXSeg’; use assignment or value-initialization instead [-Wclass-memaccess] 350 | memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from bundles.h:22, from assemble.h:21, from assemble.cpp:48: gtf_tracking.h:359:7: note: ‘class GXSeg’ declared here 359 | class GXSeg : public GSeg { | ^~~~~ In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:10, from gtf_tracking.h:12, from bundles.h:22, from assemble.h:21, from assemble.cpp:48: GVec.hh: In instantiation of ‘void GVec::Grow(int, OBJ&) [with OBJ = GSeg]’: GVec.hh:422:9: required from ‘void GVec::Insert(int, OBJ*) [with OBJ = GSeg]’ GVec.hh:79:44: required from ‘void GVec::Insert(int, OBJ) [with OBJ = GSeg]’ GList.hh:230:21: required from ‘int GArray::Add(OBJ*) [with OBJ = GSeg]’ GList.hh:51:36: required from ‘int GArray::Add(OBJ&) [with OBJ = GSeg]’ gtf_tracking.h:420:19: required from here GVec.hh:350:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class GSeg’; use assignment or value-initialization instead [-Wclass-memaccess] 350 | memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from gff.h:7, from gtf_tracking.h:12, from bundles.h:22, from assemble.h:21, from assemble.cpp:48: GBase.h:279:7: note: ‘class GSeg’ declared here 279 | class GSeg { | ^~~~ In file included from scaffolds.h:20, from scaffolds.cpp:14: hits.h: In constructor ‘PrecomputedExpressionHitFactory::PrecomputedExpressionHitFactory(const string&, ReadTable&, RefSequenceTable&)’: hits.h:928:12: warning: ‘PrecomputedExpressionHitFactory::_expression_file_name’ will be initialized after [-Wreorder] 928 | string _expression_file_name; | ^~~~~~~~~~~~~~~~~~~~~ hits.h:927:19: warning: ‘std::ifstream PrecomputedExpressionHitFactory::_ifs’ [-Wreorder] 927 | std::ifstream _ifs; | ^~~~ In file included from scaffolds.h:20, from scaffolds.cpp:14: hits.h:814:5: warning: when initialized here [-Wreorder] 814 | PrecomputedExpressionHitFactory(const string& expression_file_name, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ scaffolds.cpp: In member function ‘void Scaffold::fill_gaps(int)’: scaffolds.cpp:835:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 835 | if (filled_gap_size <= 0) | ^~ scaffolds.cpp:838:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 838 | const vector& orig_ops = augmented_ops(); | ^~~~~ scaffolds.cpp: In member function ‘void Scaffold::fill_gaps(const std::vector&)’: scaffolds.cpp:933:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 933 | if (overlapping.empty()) | ^~ scaffolds.cpp:936:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 936 | AugmentedCuffOp::merge_ops(overlapping, _augmented_ops, true); | ^~~~~~~~~~~~~~~ In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:10, from gtf_tracking.h:12, from bundles.h:22, from abundances.h:25, from abundances.cpp:16: GVec.hh: In instantiation of ‘void GVec::Grow(int, OBJ&) [with OBJ = GXSeg]’: GVec.hh:422:9: required from ‘void GVec::Insert(int, OBJ*) [with OBJ = GXSeg]’ GVec.hh:79:44: required from ‘void GVec::Insert(int, OBJ) [with OBJ = GXSeg]’ GList.hh:230:21: required from ‘int GArray::Add(OBJ*) [with OBJ = GXSeg]’ GList.hh:51:36: required from ‘int GArray::Add(OBJ&) [with OBJ = GXSeg]’ gtf_tracking.h:419:20: required from here GVec.hh:350:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class GXSeg’; use assignment or value-initialization instead [-Wclass-memaccess] 350 | memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from bundles.h:22, from abundances.h:25, from abundances.cpp:16: gtf_tracking.h:359:7: note: ‘class GXSeg’ declared here 359 | class GXSeg : public GSeg { | ^~~~~ In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:10, from gtf_tracking.h:12, from bundles.h:22, from abundances.h:25, from abundances.cpp:16: GVec.hh: In instantiation of ‘void GVec::Grow(int, OBJ&) [with OBJ = GSeg]’: GVec.hh:422:9: required from ‘void GVec::Insert(int, OBJ*) [with OBJ = GSeg]’ GVec.hh:79:44: required from ‘void GVec::Insert(int, OBJ) [with OBJ = GSeg]’ GList.hh:230:21: required from ‘int GArray::Add(OBJ*) [with OBJ = GSeg]’ GList.hh:51:36: required from ‘int GArray::Add(OBJ&) [with OBJ = GSeg]’ gtf_tracking.h:420:19: required from here GVec.hh:350:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class GSeg’; use assignment or value-initialization instead [-Wclass-memaccess] 350 | memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from gff.h:7, from gtf_tracking.h:12, from bundles.h:22, from abundances.h:25, from abundances.cpp:16: GBase.h:279:7: note: ‘class GSeg’ declared here 279 | class GSeg { | ^~~~ g++ -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -g -O2 -fdebug-prefix-map=/<>/cufflinks-2.2.1+dfsg.1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o hits.o hits.cpp In file included from hits.cpp:22: hits.h: In constructor ‘PrecomputedExpressionHitFactory::PrecomputedExpressionHitFactory(const string&, ReadTable&, RefSequenceTable&)’: hits.h:928:12: warning: ‘PrecomputedExpressionHitFactory::_expression_file_name’ will be initialized after [-Wreorder] 928 | string _expression_file_name; | ^~~~~~~~~~~~~~~~~~~~~ hits.h:927:19: warning: ‘std::ifstream PrecomputedExpressionHitFactory::_ifs’ [-Wreorder] 927 | std::ifstream _ifs; | ^~~~ In file included from hits.cpp:22: hits.h:814:5: warning: when initialized here [-Wreorder] 814 | PrecomputedExpressionHitFactory(const string& expression_file_name, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ hits.cpp: In member function ‘void ReadHit::trim(int)’: hits.cpp:40:9: warning: variable ‘new_left’ set but not used [-Wunused-but-set-variable] 40 | int new_left = 0; | ^~~~~~~~ hits.cpp: In member function ‘virtual bool BAMHitFactory::next_record(const char*&, size_t&)’: hits.cpp:394:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 394 | if (records_remain() == false) | ^~ hits.cpp:397:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 397 | mark_curr_pos(); | ^~~~~~~~~~~~~ In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:10, from gtf_tracking.h:12, from bundles.h:22, from abundances.h:25, from hits.cpp:25: GVec.hh: In instantiation of ‘void GVec::Grow(int, OBJ&) [with OBJ = GISeg]’: GVec.hh:422:9: required from ‘void GVec::Insert(int, OBJ*) [with OBJ = GISeg]’ GVec.hh:81:48: required from ‘void GVec::idxInsert(int, OBJ&) [with OBJ = GISeg]’ gtf_tracking.h:210:29: required from here GVec.hh:350:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class GISeg’; use assignment or value-initialization instead [-Wclass-memaccess] 350 | memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from bundles.h:22, from abundances.h:25, from hits.cpp:25: gtf_tracking.h:188:7: note: ‘class GISeg’ declared here 188 | class GISeg: public GSeg { | ^~~~~ In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:10, from gtf_tracking.h:12, from bundles.h:22, from abundances.h:25, from hits.cpp:25: GVec.hh: In instantiation of ‘void GVec::Grow(int, OBJ&) [with OBJ = GXSeg]’: GVec.hh:422:9: required from ‘void GVec::Insert(int, OBJ*) [with OBJ = GXSeg]’ GVec.hh:79:44: required from ‘void GVec::Insert(int, OBJ) [with OBJ = GXSeg]’ GList.hh:230:21: required from ‘int GArray::Add(OBJ*) [with OBJ = GXSeg]’ GList.hh:51:36: required from ‘int GArray::Add(OBJ&) [with OBJ = GXSeg]’ gtf_tracking.h:419:20: required from here GVec.hh:350:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class GXSeg’; use assignment or value-initialization instead [-Wclass-memaccess] 350 | memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from bundles.h:22, from abundances.h:25, from hits.cpp:25: gtf_tracking.h:359:7: note: ‘class GXSeg’ declared here 359 | class GXSeg : public GSeg { | ^~~~~ In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:10, from gtf_tracking.h:12, from bundles.h:22, from abundances.h:25, from hits.cpp:25: GVec.hh: In instantiation of ‘void GVec::Grow(int, OBJ&) [with OBJ = GSeg]’: GVec.hh:422:9: required from ‘void GVec::Insert(int, OBJ*) [with OBJ = GSeg]’ GVec.hh:79:44: required from ‘void GVec::Insert(int, OBJ) [with OBJ = GSeg]’ GList.hh:230:21: required from ‘int GArray::Add(OBJ*) [with OBJ = GSeg]’ GList.hh:51:36: required from ‘int GArray::Add(OBJ&) [with OBJ = GSeg]’ gtf_tracking.h:420:19: required from here GVec.hh:350:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class GSeg’; use assignment or value-initialization instead [-Wclass-memaccess] 350 | memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from gff.h:7, from gtf_tracking.h:12, from bundles.h:22, from abundances.h:25, from hits.cpp:25: GBase.h:279:7: note: ‘class GSeg’ declared here 279 | class GSeg { | ^~~~ g++ -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -g -O2 -fdebug-prefix-map=/<>/cufflinks-2.2.1+dfsg.1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o genes.o genes.cpp assemble.cpp: In function ‘void create_reachability_bp_graph(DAG&, ReachGraph&, std::vector::BNode, std::allocator::BNode> >, DagToBp&, const boost::adjacency_list<>&, const std::vector&)’: assemble.cpp:150:51: warning: ‘*((void*)& i +48)’ may be used uninitialized in this function [-Wmaybe-uninitialized] 150 | graph_traits < adjacency_list<> >::edge_iterator i, end; | ^ In file included from scaffolds.h:20, from genes.h:17, from genes.cpp:10: hits.h: In constructor ‘PrecomputedExpressionHitFactory::PrecomputedExpressionHitFactory(const string&, ReadTable&, RefSequenceTable&)’: hits.h:928:12: warning: ‘PrecomputedExpressionHitFactory::_expression_file_name’ will be initialized after [-Wreorder] 928 | string _expression_file_name; | ^~~~~~~~~~~~~~~~~~~~~ hits.h:927:19: warning: ‘std::ifstream PrecomputedExpressionHitFactory::_ifs’ [-Wreorder] 927 | std::ifstream _ifs; | ^~~~ In file included from scaffolds.h:20, from genes.h:17, from genes.cpp:10: hits.h:814:5: warning: when initialized here [-Wreorder] 814 | PrecomputedExpressionHitFactory(const string& expression_file_name, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -g -O2 -fdebug-prefix-map=/<>/cufflinks-2.2.1+dfsg.1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o bundles.o bundles.cpp In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:10, from gtf_tracking.h:12, from bundles.h:22, from abundances.h:25, from genes.h:18, from genes.cpp:10: GVec.hh: In instantiation of ‘void GVec::Grow(int, OBJ&) [with OBJ = GISeg]’: GVec.hh:422:9: required from ‘void GVec::Insert(int, OBJ*) [with OBJ = GISeg]’ GVec.hh:81:48: required from ‘void GVec::idxInsert(int, OBJ&) [with OBJ = GISeg]’ gtf_tracking.h:210:29: required from here GVec.hh:350:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class GISeg’; use assignment or value-initialization instead [-Wclass-memaccess] 350 | memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from bundles.h:22, from abundances.h:25, from genes.h:18, from genes.cpp:10: gtf_tracking.h:188:7: note: ‘class GISeg’ declared here 188 | class GISeg: public GSeg { | ^~~~~ In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:10, from gtf_tracking.h:12, from bundles.h:22, from abundances.h:25, from genes.h:18, from genes.cpp:10: GVec.hh: In instantiation of ‘void GVec::Grow(int, OBJ&) [with OBJ = GXSeg]’: GVec.hh:422:9: required from ‘void GVec::Insert(int, OBJ*) [with OBJ = GXSeg]’ GVec.hh:79:44: required from ‘void GVec::Insert(int, OBJ) [with OBJ = GXSeg]’ GList.hh:230:21: required from ‘int GArray::Add(OBJ*) [with OBJ = GXSeg]’ GList.hh:51:36: required from ‘int GArray::Add(OBJ&) [with OBJ = GXSeg]’ gtf_tracking.h:419:20: required from here GVec.hh:350:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class GXSeg’; use assignment or value-initialization instead [-Wclass-memaccess] 350 | memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from bundles.h:22, from abundances.h:25, from genes.h:18, from genes.cpp:10: gtf_tracking.h:359:7: note: ‘class GXSeg’ declared here 359 | class GXSeg : public GSeg { | ^~~~~ In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:10, from gtf_tracking.h:12, from bundles.h:22, from abundances.h:25, from genes.h:18, from genes.cpp:10: GVec.hh: In instantiation of ‘void GVec::Grow(int, OBJ&) [with OBJ = GSeg]’: GVec.hh:422:9: required from ‘void GVec::Insert(int, OBJ*) [with OBJ = GSeg]’ GVec.hh:79:44: required from ‘void GVec::Insert(int, OBJ) [with OBJ = GSeg]’ GList.hh:230:21: required from ‘int GArray::Add(OBJ*) [with OBJ = GSeg]’ GList.hh:51:36: required from ‘int GArray::Add(OBJ&) [with OBJ = GSeg]’ gtf_tracking.h:420:19: required from here GVec.hh:350:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class GSeg’; use assignment or value-initialization instead [-Wclass-memaccess] 350 | memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from gff.h:7, from gtf_tracking.h:12, from bundles.h:22, from abundances.h:25, from genes.h:18, from genes.cpp:10: GBase.h:279:7: note: ‘class GSeg’ declared here 279 | class GSeg { | ^~~~ bundles.cpp:701:23: warning: integer constant is so large that it is unsigned 701 | if (tmp.ref_id() == 12638153115695167477) // corresponds to SAM "*" under FNV hash. unaligned read record | ^~~~~~~~~~~~~~~~~~~~ In file included from bundles.h:20, from bundles.cpp:17: hits.h: In constructor ‘PrecomputedExpressionHitFactory::PrecomputedExpressionHitFactory(const string&, ReadTable&, RefSequenceTable&)’: hits.h:928:12: warning: ‘PrecomputedExpressionHitFactory::_expression_file_name’ will be initialized after [-Wreorder] 928 | string _expression_file_name; | ^~~~~~~~~~~~~~~~~~~~~ hits.h:927:19: warning: ‘std::ifstream PrecomputedExpressionHitFactory::_ifs’ [-Wreorder] 927 | std::ifstream _ifs; | ^~~~ In file included from bundles.h:20, from bundles.cpp:17: hits.h:814:5: warning: when initialized here [-Wreorder] 814 | PrecomputedExpressionHitFactory(const string& expression_file_name, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bundles.cpp: In function ‘void load_ref_rnas(FILE*, RefSequenceTable&, std::vector >&, boost::crc_32_type&, bool, bool)’: bundles.cpp:87:5: warning: this ‘else’ clause does not guard... [-Wmisleading-indentation] 87 | else | ^~~~ bundles.cpp:90:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘else’ 90 | GList ref_rnas; | ^~~~~ bundles.cpp: In member function ‘bool HitBundle::add_open_hit(boost::shared_ptr, const ReadHit*, bool)’: bundles.cpp:300:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘uint32_t’ {aka ‘unsigned int’} [-Wsign-compare] 300 | if (m.right() - m.left() > max_gene_length) | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ bundles.cpp: In member function ‘double BundleFactory::next_valid_alignment(const ReadHit*&)’: bundles.cpp:741:18: warning: variable ‘found_scaff’ set but not used [-Wunused-but-set-variable] 741 | bool found_scaff = false; | ^~~~~~~~~~~ bundles.cpp: In member function ‘bool BundleFactory::next_bundle_hit_driven(HitBundle&)’: bundles.cpp:817:34: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 817 | if (bundle.hits().size() >= max_frags_per_bundle) | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ bundles.cpp: In member function ‘bool BundleFactory::next_bundle_ref_driven(HitBundle&)’: bundles.cpp:859:38: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 859 | if (bundle.hits().size() < max_frags_per_bundle) | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ bundles.cpp:900:34: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 900 | if (bundle.hits().size() >= max_frags_per_bundle) | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ bundles.cpp:889:8: warning: variable ‘last_hit_ref_id_seen’ set but not used [-Wunused-but-set-variable] 889 | RefID last_hit_ref_id_seen = 0; | ^~~~~~~~~~~~~~~~~~~~ bundles.cpp:890:6: warning: variable ‘last_hit_pos_seen’ set but not used [-Wunused-but-set-variable] 890 | int last_hit_pos_seen = 0; | ^~~~~~~~~~~~~~~~~ bundles.cpp: In member function ‘virtual bool PrecomputedExpressionBundleFactory::next_bundle(HitBundle&, bool)’: bundles.cpp:2090:128: warning: format ‘%d’ expects argument of type ‘int’, but argument 6 has type ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wformat=] 2090 | fprintf (stderr, "Error in file %s: reconstituted expression bundle %s (%lu transcripts) does not match GTF (%d transcripts):\n", read_group_properties()->file_path().c_str(), bundle_label_buf, ab->abundances().size(), bundle.ref_scaffolds().size()); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | int std::vector >::size_type {aka long unsigned int} | %ld g++ -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -g -O2 -fdebug-prefix-map=/<>/cufflinks-2.2.1+dfsg.1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o filters.o filters.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -g -O2 -fdebug-prefix-map=/<>/cufflinks-2.2.1+dfsg.1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o scaffold_graph.o scaffold_graph.cpp In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:10, from gtf_tracking.h:12, from bundles.h:22, from bundles.cpp:17: GVec.hh: In instantiation of ‘void GVec::Grow(int, OBJ&) [with OBJ = GISeg]’: GVec.hh:422:9: required from ‘void GVec::Insert(int, OBJ*) [with OBJ = GISeg]’ GVec.hh:81:48: required from ‘void GVec::idxInsert(int, OBJ&) [with OBJ = GISeg]’ gtf_tracking.h:210:29: required from here GVec.hh:350:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class GISeg’; use assignment or value-initialization instead [-Wclass-memaccess] 350 | memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from bundles.h:22, from bundles.cpp:17: gtf_tracking.h:188:7: note: ‘class GISeg’ declared here 188 | class GISeg: public GSeg { | ^~~~~ In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:10, from gtf_tracking.h:12, from bundles.h:22, from bundles.cpp:17: GVec.hh: In instantiation of ‘void GVec::Grow(int, OBJ&) [with OBJ = GXSeg]’: GVec.hh:422:9: required from ‘void GVec::Insert(int, OBJ*) [with OBJ = GXSeg]’ GVec.hh:79:44: required from ‘void GVec::Insert(int, OBJ) [with OBJ = GXSeg]’ GList.hh:230:21: required from ‘int GArray::Add(OBJ*) [with OBJ = GXSeg]’ GList.hh:51:36: required from ‘int GArray::Add(OBJ&) [with OBJ = GXSeg]’ gtf_tracking.h:419:20: required from here GVec.hh:350:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class GXSeg’; use assignment or value-initialization instead [-Wclass-memaccess] 350 | memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from bundles.h:22, from bundles.cpp:17: gtf_tracking.h:359:7: note: ‘class GXSeg’ declared here 359 | class GXSeg : public GSeg { | ^~~~~ In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:10, from gtf_tracking.h:12, from bundles.h:22, from bundles.cpp:17: GVec.hh: In instantiation of ‘void GVec::Grow(int, OBJ&) [with OBJ = GSeg]’: GVec.hh:422:9: required from ‘void GVec::Insert(int, OBJ*) [with OBJ = GSeg]’ GVec.hh:79:44: required from ‘void GVec::Insert(int, OBJ) [with OBJ = GSeg]’ GList.hh:230:21: required from ‘int GArray::Add(OBJ*) [with OBJ = GSeg]’ GList.hh:51:36: required from ‘int GArray::Add(OBJ&) [with OBJ = GSeg]’ gtf_tracking.h:420:19: required from here GVec.hh:350:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class GSeg’; use assignment or value-initialization instead [-Wclass-memaccess] 350 | memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from gff.h:7, from gtf_tracking.h:12, from bundles.h:22, from bundles.cpp:17: GBase.h:279:7: note: ‘class GSeg’ declared here 279 | class GSeg { | ^~~~ In file included from scaffolds.h:20, from filters.h:17, from filters.cpp:10: hits.h: In constructor ‘PrecomputedExpressionHitFactory::PrecomputedExpressionHitFactory(const string&, ReadTable&, RefSequenceTable&)’: hits.h:928:12: warning: ‘PrecomputedExpressionHitFactory::_expression_file_name’ will be initialized after [-Wreorder] 928 | string _expression_file_name; | ^~~~~~~~~~~~~~~~~~~~~ hits.h:927:19: warning: ‘std::ifstream PrecomputedExpressionHitFactory::_ifs’ [-Wreorder] 927 | std::ifstream _ifs; | ^~~~ In file included from scaffolds.h:20, from filters.h:17, from filters.cpp:10: hits.h:814:5: warning: when initialized here [-Wreorder] 814 | PrecomputedExpressionHitFactory(const string& expression_file_name, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from scaffolds.h:20, from scaffold_graph.cpp:12: hits.h: In constructor ‘PrecomputedExpressionHitFactory::PrecomputedExpressionHitFactory(const string&, ReadTable&, RefSequenceTable&)’: hits.h:928:12: warning: ‘PrecomputedExpressionHitFactory::_expression_file_name’ will be initialized after [-Wreorder] 928 | string _expression_file_name; | ^~~~~~~~~~~~~~~~~~~~~ hits.h:927:19: warning: ‘std::ifstream PrecomputedExpressionHitFactory::_ifs’ [-Wreorder] 927 | std::ifstream _ifs; | ^~~~ In file included from scaffolds.h:20, from scaffold_graph.cpp:12: hits.h:814:5: warning: when initialized here [-Wreorder] 814 | PrecomputedExpressionHitFactory(const string& expression_file_name, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ filters.cpp: In function ‘void clip_by_3_prime_dropoff(std::vector&)’: filters.cpp:876:63: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘const int’ [-Wsign-compare] 876 | if (avg_cov >= trim_3_avgcov_thresh && min_cost_x < exon_3->genomic_length) | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ filters.cpp:802:20: warning: variable ‘mean_to_keep’ set but not used [-Wunused-but-set-variable] 802 | double mean_to_keep = 0.0; | ^~~~~~~~~~~~ filters.cpp:803:20: warning: variable ‘mean_to_trim’ set but not used [-Wunused-but-set-variable] 803 | double mean_to_trim = 0.0; | ^~~~~~~~~~~~ filters.cpp:930:36: warning: variable ‘exon_3’ set but not used [-Wunused-but-set-variable] 930 | const AugmentedCuffOp* exon_3 = NULL; | ^~~~~~ filters.cpp:931:17: warning: variable ‘mult’ set but not used [-Wunused-but-set-variable] 931 | int mult; | ^~~~ filters.cpp:932:17: warning: variable ‘offset’ set but not used [-Wunused-but-set-variable] 932 | int offset; | ^~~~~~ In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:10, from gtf_tracking.h:12, from bundles.h:22, from abundances.h:25, from genes.h:18, from filters.h:18, from filters.cpp:10: GVec.hh: In instantiation of ‘void GVec::Grow(int, OBJ&) [with OBJ = GISeg]’: GVec.hh:422:9: required from ‘void GVec::Insert(int, OBJ*) [with OBJ = GISeg]’ GVec.hh:81:48: required from ‘void GVec::idxInsert(int, OBJ&) [with OBJ = GISeg]’ gtf_tracking.h:210:29: required from here GVec.hh:350:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class GISeg’; use assignment or value-initialization instead [-Wclass-memaccess] 350 | memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from bundles.h:22, from abundances.h:25, from genes.h:18, from filters.h:18, from filters.cpp:10: gtf_tracking.h:188:7: note: ‘class GISeg’ declared here 188 | class GISeg: public GSeg { | ^~~~~ In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:10, from gtf_tracking.h:12, from bundles.h:22, from abundances.h:25, from genes.h:18, from filters.h:18, from filters.cpp:10: GVec.hh: In instantiation of ‘void GVec::Grow(int, OBJ&) [with OBJ = GXSeg]’: GVec.hh:422:9: required from ‘void GVec::Insert(int, OBJ*) [with OBJ = GXSeg]’ GVec.hh:79:44: required from ‘void GVec::Insert(int, OBJ) [with OBJ = GXSeg]’ GList.hh:230:21: required from ‘int GArray::Add(OBJ*) [with OBJ = GXSeg]’ GList.hh:51:36: required from ‘int GArray::Add(OBJ&) [with OBJ = GXSeg]’ gtf_tracking.h:419:20: required from here GVec.hh:350:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class GXSeg’; use assignment or value-initialization instead [-Wclass-memaccess] 350 | memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from bundles.h:22, from abundances.h:25, from genes.h:18, from filters.h:18, from filters.cpp:10: gtf_tracking.h:359:7: note: ‘class GXSeg’ declared here 359 | class GXSeg : public GSeg { | ^~~~~ In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:10, from gtf_tracking.h:12, from bundles.h:22, from abundances.h:25, from genes.h:18, from filters.h:18, from filters.cpp:10: GVec.hh: In instantiation of ‘void GVec::Grow(int, OBJ&) [with OBJ = GSeg]’: GVec.hh:422:9: required from ‘void GVec::Insert(int, OBJ*) [with OBJ = GSeg]’ GVec.hh:79:44: required from ‘void GVec::Insert(int, OBJ) [with OBJ = GSeg]’ GList.hh:230:21: required from ‘int GArray::Add(OBJ*) [with OBJ = GSeg]’ GList.hh:51:36: required from ‘int GArray::Add(OBJ&) [with OBJ = GSeg]’ gtf_tracking.h:420:19: required from here GVec.hh:350:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class GSeg’; use assignment or value-initialization instead [-Wclass-memaccess] 350 | memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from gff.h:7, from gtf_tracking.h:12, from bundles.h:22, from abundances.h:25, from genes.h:18, from filters.h:18, from filters.cpp:10: GBase.h:279:7: note: ‘class GSeg’ declared here 279 | class GSeg { | ^~~~ g++ -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -g -O2 -fdebug-prefix-map=/<>/cufflinks-2.2.1+dfsg.1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o matching_merge.o matching_merge.cpp In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from /usr/include/boost/math/policies/error_handling.hpp:14, from /usr/include/boost/math/special_functions/gamma.hpp:23, from /usr/include/boost/math/special_functions/beta.hpp:15, from /usr/include/boost/math/distributions/binomial.hpp:83, from bundles.cpp:13: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘void ProgressBar::update(const char*, double)’ at progressbar.h:59:10, inlined from ‘void inspect_map(boost::shared_ptr, BadIntronTable*, std::vector&, std::vector&, bool, bool)’ at bundles.cpp:1726:16: /usr/include/s390x-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ output may be truncated copying 27 bytes from a string of length 2047 [-Wstringop-truncation] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ./lemon/bits/base_extender.h:23, from ./lemon/smart_graph.h:30, from matching_merge.h:16, from matching_merge.cpp:10: ./lemon/error.h:93:10: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 93 | std::auto_ptr<_Type> ptr; | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from ./lemon/error.h:31, from ./lemon/bits/base_extender.h:23, from ./lemon/smart_graph.h:30, from matching_merge.h:16, from matching_merge.cpp:10: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from ./lemon/bits/base_extender.h:23, from ./lemon/smart_graph.h:30, from matching_merge.h:16, from matching_merge.cpp:10: ./lemon/error.h:108:10: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 108 | std::auto_ptr buf; | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from ./lemon/error.h:31, from ./lemon/bits/base_extender.h:23, from ./lemon/smart_graph.h:30, from matching_merge.h:16, from matching_merge.cpp:10: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -g -O2 -fdebug-prefix-map=/<>/cufflinks-2.2.1+dfsg.1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o graph_optimize.o graph_optimize.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -g -O2 -fdebug-prefix-map=/<>/cufflinks-2.2.1+dfsg.1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o biascorrection.o biascorrection.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -g -O2 -fdebug-prefix-map=/<>/cufflinks-2.2.1+dfsg.1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o sampling.o sampling.cpp In file included from scaffolds.h:20, from matching_merge.h:20, from matching_merge.cpp:10: hits.h: In constructor ‘PrecomputedExpressionHitFactory::PrecomputedExpressionHitFactory(const string&, ReadTable&, RefSequenceTable&)’: hits.h:928:12: warning: ‘PrecomputedExpressionHitFactory::_expression_file_name’ will be initialized after [-Wreorder] 928 | string _expression_file_name; | ^~~~~~~~~~~~~~~~~~~~~ hits.h:927:19: warning: ‘std::ifstream PrecomputedExpressionHitFactory::_ifs’ [-Wreorder] 927 | std::ifstream _ifs; | ^~~~ In file included from scaffolds.h:20, from matching_merge.h:20, from matching_merge.cpp:10: hits.h:814:5: warning: when initialized here [-Wreorder] 814 | PrecomputedExpressionHitFactory(const string& expression_file_name, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from scaffolds.h:20, from biascorrection.cpp:11: hits.h: In constructor ‘PrecomputedExpressionHitFactory::PrecomputedExpressionHitFactory(const string&, ReadTable&, RefSequenceTable&)’: hits.h:928:12: warning: ‘PrecomputedExpressionHitFactory::_expression_file_name’ will be initialized after [-Wreorder] 928 | string _expression_file_name; | ^~~~~~~~~~~~~~~~~~~~~ hits.h:927:19: warning: ‘std::ifstream PrecomputedExpressionHitFactory::_ifs’ [-Wreorder] 927 | std::ifstream _ifs; | ^~~~ In file included from scaffolds.h:20, from biascorrection.cpp:11: hits.h:814:5: warning: when initialized here [-Wreorder] 814 | PrecomputedExpressionHitFactory(const string& expression_file_name, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from sampling.cpp:9: sampling.h: In function ‘double boost::numeric::ublas::cholesky_factorize(M&)’: sampling.h:50:13: warning: typedef ‘matrix_type’ locally defined but not used [-Wunused-local-typedefs] 50 | typedef M matrix_type; | ^~~~~~~~~~~ In file included from sampling.cpp:9: sampling.h: In function ‘void boost::numeric::ublas::cholesky_substitute(const M&, boost::numeric::ublas::vector_expression&)’: sampling.h:113:19: warning: typedef ‘const_matrix_type’ locally defined but not used [-Wunused-local-typedefs] 113 | typedef const M const_matrix_type; | ^~~~~~~~~~~~~~~~~ sampling.h:114:42: warning: typedef ‘vector_type’ locally defined but not used [-Wunused-local-typedefs] 114 | typedef vector vector_type; | ^~~~~~~~~~~ sampling.h: In function ‘void boost::numeric::ublas::cholesky_substitute(const M&, boost::numeric::ublas::matrix_expression&)’: sampling.h:120:19: warning: typedef ‘const_matrix_type’ locally defined but not used [-Wunused-local-typedefs] 120 | typedef const M const_matrix_type; | ^~~~~~~~~~~~~~~~~ sampling.h:121:42: warning: typedef ‘matrix_type’ locally defined but not used [-Wunused-local-typedefs] 121 | typedef matrix matrix_type; | ^~~~~~~~~~~ sampling.h: In function ‘void boost::numeric::ublas::cholesky_substitute_left(boost::numeric::ublas::vector_expression&, const M&)’: sampling.h:127:19: warning: typedef ‘const_matrix_type’ locally defined but not used [-Wunused-local-typedefs] 127 | typedef const M const_matrix_type; | ^~~~~~~~~~~~~~~~~ sampling.h:128:42: warning: typedef ‘vector_type’ locally defined but not used [-Wunused-local-typedefs] 128 | typedef vector vector_type; | ^~~~~~~~~~~ sampling.h: In function ‘void boost::numeric::ublas::cholesky_substitute_left(boost::numeric::ublas::matrix_expression&, const M&)’: sampling.h:134:19: warning: typedef ‘const_matrix_type’ locally defined but not used [-Wunused-local-typedefs] 134 | typedef const M const_matrix_type; | ^~~~~~~~~~~~~~~~~ sampling.h:135:42: warning: typedef ‘matrix_type’ locally defined but not used [-Wunused-local-typedefs] 135 | typedef matrix matrix_type; | ^~~~~~~~~~~ biascorrection.cpp: In member function ‘double BiasCorrectionHelper::get_cond_prob(const MateHit&)’: biascorrection.cpp:794:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 794 | if (isinf(cond_prob) || isnan(cond_prob)) | ^~ biascorrection.cpp:797:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 797 | return cond_prob; | ^~~~~~ biascorrection.cpp: In member function ‘double BiasCorrectionHelper::get_effective_length()’: biascorrection.cpp:809:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 809 | if (no_length_correction) | ^~ biascorrection.cpp:812:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 812 | double tot_mass = accumulate( _rg_masses.begin(), _rg_masses.end(), 0.0 ); | ^~~~~~ In file included from bundles.h:20, from graph_optimize.h:17, from graph_optimize.cpp:13: hits.h: In constructor ‘PrecomputedExpressionHitFactory::PrecomputedExpressionHitFactory(const string&, ReadTable&, RefSequenceTable&)’: hits.h:928:12: warning: ‘PrecomputedExpressionHitFactory::_expression_file_name’ will be initialized after [-Wreorder] 928 | string _expression_file_name; | ^~~~~~~~~~~~~~~~~~~~~ hits.h:927:19: warning: ‘std::ifstream PrecomputedExpressionHitFactory::_ifs’ [-Wreorder] 927 | std::ifstream _ifs; | ^~~~ In file included from bundles.h:20, from graph_optimize.h:17, from graph_optimize.cpp:13: hits.h:814:5: warning: when initialized here [-Wreorder] 814 | PrecomputedExpressionHitFactory(const string& expression_file_name, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:10, from gtf_tracking.h:12, from bundles.h:22, from abundances.h:25, from biascorrection.cpp:12: GVec.hh: In instantiation of ‘void GVec::Grow(int, OBJ&) [with OBJ = GISeg]’: GVec.hh:422:9: required from ‘void GVec::Insert(int, OBJ*) [with OBJ = GISeg]’ GVec.hh:81:48: required from ‘void GVec::idxInsert(int, OBJ&) [with OBJ = GISeg]’ gtf_tracking.h:210:29: required from here GVec.hh:350:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class GISeg’; use assignment or value-initialization instead [-Wclass-memaccess] 350 | memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from bundles.h:22, from abundances.h:25, from biascorrection.cpp:12: gtf_tracking.h:188:7: note: ‘class GISeg’ declared here 188 | class GISeg: public GSeg { | ^~~~~ In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:10, from gtf_tracking.h:12, from bundles.h:22, from abundances.h:25, from biascorrection.cpp:12: GVec.hh: In instantiation of ‘void GVec::Grow(int, OBJ&) [with OBJ = GXSeg]’: GVec.hh:422:9: required from ‘void GVec::Insert(int, OBJ*) [with OBJ = GXSeg]’ GVec.hh:79:44: required from ‘void GVec::Insert(int, OBJ) [with OBJ = GXSeg]’ GList.hh:230:21: required from ‘int GArray::Add(OBJ*) [with OBJ = GXSeg]’ GList.hh:51:36: required from ‘int GArray::Add(OBJ&) [with OBJ = GXSeg]’ gtf_tracking.h:419:20: required from here GVec.hh:350:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class GXSeg’; use assignment or value-initialization instead [-Wclass-memaccess] 350 | memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from bundles.h:22, from abundances.h:25, from biascorrection.cpp:12: gtf_tracking.h:359:7: note: ‘class GXSeg’ declared here 359 | class GXSeg : public GSeg { | ^~~~~ In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:10, from gtf_tracking.h:12, from bundles.h:22, from abundances.h:25, from biascorrection.cpp:12: GVec.hh: In instantiation of ‘void GVec::Grow(int, OBJ&) [with OBJ = GSeg]’: GVec.hh:422:9: required from ‘void GVec::Insert(int, OBJ*) [with OBJ = GSeg]’ GVec.hh:79:44: required from ‘void GVec::Insert(int, OBJ) [with OBJ = GSeg]’ GList.hh:230:21: required from ‘int GArray::Add(OBJ*) [with OBJ = GSeg]’ GList.hh:51:36: required from ‘int GArray::Add(OBJ&) [with OBJ = GSeg]’ gtf_tracking.h:420:19: required from here GVec.hh:350:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class GSeg’; use assignment or value-initialization instead [-Wclass-memaccess] 350 | memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from gff.h:7, from gtf_tracking.h:12, from bundles.h:22, from abundances.h:25, from biascorrection.cpp:12: GBase.h:279:7: note: ‘class GSeg’ declared here 279 | class GSeg { | ^~~~ In file included from ./lemon/bits/base_extender.h:23, from ./lemon/list_graph.h:26, from ./lemon/dfs.h:26, from ./lemon/topology.h:22, from graph_optimize.cpp:16: ./lemon/error.h: At global scope: ./lemon/error.h:93:10: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 93 | std::auto_ptr<_Type> ptr; | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/boost/config/no_tr1/memory.hpp:21, from /usr/include/boost/smart_ptr/shared_ptr.hpp:23, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/property_map/vector_property_map.hpp:14, from /usr/include/boost/property_map/property_map.hpp:602, from /usr/include/boost/graph/graph_concepts.hpp:17, from /usr/include/boost/graph/depth_first_search.hpp:18, from graph_optimize.h:14, from graph_optimize.cpp:13: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from ./lemon/bits/base_extender.h:23, from ./lemon/list_graph.h:26, from ./lemon/dfs.h:26, from ./lemon/topology.h:22, from graph_optimize.cpp:16: ./lemon/error.h:108:10: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 108 | std::auto_ptr buf; | ^~~~~~~~ In file included from /usr/include/c++/10/memory:83, from /usr/include/boost/config/no_tr1/memory.hpp:21, from /usr/include/boost/smart_ptr/shared_ptr.hpp:23, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/property_map/vector_property_map.hpp:14, from /usr/include/boost/property_map/property_map.hpp:602, from /usr/include/boost/graph/graph_concepts.hpp:17, from /usr/include/boost/graph/depth_first_search.hpp:18, from graph_optimize.h:14, from graph_optimize.cpp:13: /usr/include/c++/10/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from graph_optimize.cpp:16: ./lemon/topology.h: In function ‘bool lemon::stronglyConnected(const Graph&)’: ./lemon/topology.h:249:34: warning: typedef ‘Node’ locally defined but not used [-Wunused-local-typedefs] 249 | typedef typename Graph::Node Node; | ^~~~ ./lemon/topology.h: In function ‘int lemon::countStronglyConnectedComponents(const Graph&)’: ./lemon/topology.h:311:34: warning: typedef ‘Edge’ locally defined but not used [-Wunused-local-typedefs] 311 | typedef typename Graph::Edge Edge; | ^~~~ ./lemon/topology.h:313:36: warning: typedef ‘EdgeIt’ locally defined but not used [-Wunused-local-typedefs] 313 | typedef typename Graph::EdgeIt EdgeIt; | ^~~~~~ ./lemon/topology.h: In function ‘void lemon::topologicalSort(const Graph&, NodeMap&)’: ./lemon/topology.h:1213:34: warning: typedef ‘Node’ locally defined but not used [-Wunused-local-typedefs] 1213 | typedef typename Graph::Node Node; | ^~~~ ./lemon/topology.h:1215:34: warning: typedef ‘Edge’ locally defined but not used [-Wunused-local-typedefs] 1215 | typedef typename Graph::Edge Edge; | ^~~~ ./lemon/topology.h: In function ‘bool lemon::bipartite(const UGraph&)’: ./lemon/topology.h:1470:37: warning: typedef ‘EdgeIt’ locally defined but not used [-Wunused-local-typedefs] 1470 | typedef typename UGraph::EdgeIt EdgeIt; | ^~~~~~ ./lemon/topology.h: In function ‘bool lemon::bipartitePartitions(const UGraph&, NodeMap&)’: ./lemon/topology.h:1514:35: warning: typedef ‘Node’ locally defined but not used [-Wunused-local-typedefs] 1514 | typedef typename UGraph::Node Node; | ^~~~ ./lemon/topology.h:1516:37: warning: typedef ‘EdgeIt’ locally defined but not used [-Wunused-local-typedefs] 1516 | typedef typename UGraph::EdgeIt EdgeIt; | ^~~~~~ graph_optimize.cpp: In function ‘bool collapse_contained_transfrags(std::vector&, uint32_t)’: graph_optimize.cpp:264:30: warning: variable ‘e’ set but not used [-Wunused-but-set-variable] 264 | ContainmentGraph::UEdge e = containment.addEdge(nj.first, | ^ graph_optimize.cpp: In function ‘bool collapse_equivalent_transfrags(std::vector&, uint32_t)’: graph_optimize.cpp:342:31: warning: typedef ‘ContainmentGraph’ locally defined but not used [-Wunused-local-typedefs] 342 | typedef lemon::SmartBpUGraph ContainmentGraph; | ^~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -g -O2 -fdebug-prefix-map=/<>/cufflinks-2.2.1+dfsg.1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o adap.o `test -f 'locfit/adap.c' || echo './'`locfit/adap.c cc1: warning: command-line option ‘-ftemplate-depth=1024’ is valid for C++/ObjC++ but not for C locfit/adap.c: In function ‘mmse’: locfit/adap.c:29:17: warning: variable ‘p’ set but not used [-Wunused-but-set-variable] 29 | { int i, ii, j, p, p1; | ^ locfit/adap.c: In function ‘aband3’: locfit/adap.c:157:17: warning: variable ‘n’ set but not used [-Wunused-but-set-variable] 157 | INT i, i0, d, n; | ^ locfit/adap.c:157:14: warning: variable ‘d’ set but not used [-Wunused-but-set-variable] 157 | INT i, i0, d, n; | ^ gcc -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -g -O2 -fdebug-prefix-map=/<>/cufflinks-2.2.1+dfsg.1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o ar_funs.o `test -f 'locfit/ar_funs.c' || echo './'`locfit/ar_funs.c cc1: warning: command-line option ‘-ftemplate-depth=1024’ is valid for C++/ObjC++ but not for C gcc -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -g -O2 -fdebug-prefix-map=/<>/cufflinks-2.2.1+dfsg.1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o arith.o `test -f 'locfit/arith.c' || echo './'`locfit/arith.c cc1: warning: command-line option ‘-ftemplate-depth=1024’ is valid for C++/ObjC++ but not for C In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:10, from gtf_tracking.h:12, from bundles.h:22, from graph_optimize.h:17, from graph_optimize.cpp:13: GVec.hh: In instantiation of ‘void GVec::Grow(int, OBJ&) [with OBJ = GISeg]’: GVec.hh:422:9: required from ‘void GVec::Insert(int, OBJ*) [with OBJ = GISeg]’ GVec.hh:81:48: required from ‘void GVec::idxInsert(int, OBJ&) [with OBJ = GISeg]’ gtf_tracking.h:210:29: required from here GVec.hh:350:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class GISeg’; use assignment or value-initialization instead [-Wclass-memaccess] 350 | memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from bundles.h:22, from graph_optimize.h:17, from graph_optimize.cpp:13: gtf_tracking.h:188:7: note: ‘class GISeg’ declared here 188 | class GISeg: public GSeg { | ^~~~~ gcc -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -g -O2 -fdebug-prefix-map=/<>/cufflinks-2.2.1+dfsg.1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o band.o `test -f 'locfit/band.c' || echo './'`locfit/band.c cc1: warning: command-line option ‘-ftemplate-depth=1024’ is valid for C++/ObjC++ but not for C gcc -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -g -O2 -fdebug-prefix-map=/<>/cufflinks-2.2.1+dfsg.1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o c_args.o `test -f 'locfit/c_args.c' || echo './'`locfit/c_args.c cc1: warning: command-line option ‘-ftemplate-depth=1024’ is valid for C++/ObjC++ but not for C locfit/c_args.c: In function ‘readilist’: locfit/c_args.c:58:13: warning: variable ‘nd’ set but not used [-Wunused-but-set-variable] 58 | { int i, n, nd; | ^~ gcc -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -g -O2 -fdebug-prefix-map=/<>/cufflinks-2.2.1+dfsg.1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o c_plot.o `test -f 'locfit/c_plot.c' || echo './'`locfit/c_plot.c cc1: warning: command-line option ‘-ftemplate-depth=1024’ is valid for C++/ObjC++ but not for C In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:10, from gtf_tracking.h:12, from bundles.h:22, from graph_optimize.h:17, from graph_optimize.cpp:13: GVec.hh: In instantiation of ‘void GVec::Grow(int, OBJ&) [with OBJ = GXSeg]’: GVec.hh:422:9: required from ‘void GVec::Insert(int, OBJ*) [with OBJ = GXSeg]’ GVec.hh:79:44: required from ‘void GVec::Insert(int, OBJ) [with OBJ = GXSeg]’ GList.hh:230:21: required from ‘int GArray::Add(OBJ*) [with OBJ = GXSeg]’ GList.hh:51:36: required from ‘int GArray::Add(OBJ&) [with OBJ = GXSeg]’ gtf_tracking.h:419:20: required from here GVec.hh:350:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class GXSeg’; use assignment or value-initialization instead [-Wclass-memaccess] 350 | memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from bundles.h:22, from graph_optimize.h:17, from graph_optimize.cpp:13: gtf_tracking.h:359:7: note: ‘class GXSeg’ declared here 359 | class GXSeg : public GSeg { | ^~~~~ In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:10, from gtf_tracking.h:12, from bundles.h:22, from graph_optimize.h:17, from graph_optimize.cpp:13: GVec.hh: In instantiation of ‘void GVec::Grow(int, OBJ&) [with OBJ = GSeg]’: GVec.hh:422:9: required from ‘void GVec::Insert(int, OBJ*) [with OBJ = GSeg]’ GVec.hh:79:44: required from ‘void GVec::Insert(int, OBJ) [with OBJ = GSeg]’ GList.hh:230:21: required from ‘int GArray::Add(OBJ*) [with OBJ = GSeg]’ GList.hh:51:36: required from ‘int GArray::Add(OBJ&) [with OBJ = GSeg]’ gtf_tracking.h:420:19: required from here GVec.hh:350:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class GSeg’; use assignment or value-initialization instead [-Wclass-memaccess] 350 | memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from gff.h:7, from gtf_tracking.h:12, from bundles.h:22, from graph_optimize.h:17, from graph_optimize.cpp:13: GBase.h:279:7: note: ‘class GSeg’ declared here 279 | class GSeg { | ^~~~ locfit/c_plot.c: In function ‘plotfit’: locfit/c_plot.c:228:13: warning: variable ‘sd’ set but not used [-Wunused-but-set-variable] 228 | double c, sd, xl[2*MXDIM], xll[2]; | ^~ locfit/c_plot.c:226:36: warning: variable ‘sef’ set but not used [-Wunused-but-set-variable] 226 | { INT add, d, dp, i = 0, j = 0, n, sef; | ^~~ locfit/c_plot.c: In function ‘setplot’: locfit/c_plot.c:470:14: warning: passing argument 1 of ‘setvarname’ from incompatible pointer type [-Wincompatible-pointer-types] 470 | setvarname(curstr,tname); | ^~~~~~ | | | char * In file included from locfit/lffuns.h:214, from locfit/local.h:106, from locfit/c_plot.c:6: locfit/vari.hpp:16:27: note: expected ‘vari *’ but argument is of type ‘char *’ 16 | void setvarname(vari* v, varname name); | ~~~~~~^ gcc -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -g -O2 -fdebug-prefix-map=/<>/cufflinks-2.2.1+dfsg.1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o cmd.o `test -f 'locfit/cmd.c' || echo './'`locfit/cmd.c cc1: warning: command-line option ‘-ftemplate-depth=1024’ is valid for C++/ObjC++ but not for C locfit/cmd.c: In function ‘ckap’: locfit/cmd.c:101:10: warning: variable ‘nd’ set but not used [-Wunused-but-set-variable] 101 | { INT i, nd; | ^~ locfit/cmd.c: In function ‘predict’: locfit/cmd.c:197:13: warning: variable ‘data’ set but not used [-Wunused-but-set-variable] 197 | double *data[MXDIM]; | ^~~~ locfit/cmd.c: In function ‘table’: locfit/cmd.c:539:7: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 539 | { if (my>0) | ^~ locfit/cmd.c:542:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 542 | for (i=0; i<=mx; i++) | ^~~ locfit/cmd.c: In function ‘cmdint’: locfit/cmd.c:675:19: warning: variable ‘nr’ set but not used [-Wunused-but-set-variable] 675 | INT i, j, mn, nr; | ^~ In file included from locfit/local.h:104, from locfit/c_plot.c:6: locfit/c_plot.c: In function ‘plotfit’: locfit/lfstruc.h:67:30: warning: ‘iy’ may be used uninitialized in this function [-Wmaybe-uninitialized] 67 | #define datum(lf,i,j) (lf)->x[i][j] | ^ locfit/c_plot.c:227:26: note: ‘iy’ was declared here 227 | INT dt, mg[MXDIM], ix, iy; | ^~ In file included from locfit/local.h:104, from locfit/c_plot.c:6: locfit/lfstruc.h:67:30: warning: ‘ix’ may be used uninitialized in this function [-Wmaybe-uninitialized] 67 | #define datum(lf,i,j) (lf)->x[i][j] | ^ locfit/c_plot.c:227:22: note: ‘ix’ was declared here 227 | INT dt, mg[MXDIM], ix, iy; | ^~ gcc -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -g -O2 -fdebug-prefix-map=/<>/cufflinks-2.2.1+dfsg.1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o dens_haz.o `test -f 'locfit/dens_haz.c' || echo './'`locfit/dens_haz.c cc1: warning: command-line option ‘-ftemplate-depth=1024’ is valid for C++/ObjC++ but not for C locfit/cmd.c: In function ‘table’: locfit/cmd.c:528:24: warning: ‘iy’ may be used uninitialized in this function [-Wmaybe-uninitialized] 528 | count[ix*(my+1)+iy]++; | ~~~~~~~~~^~~ locfit/cmd.c:528:17: warning: ‘ix’ may be used uninitialized in this function [-Wmaybe-uninitialized] 528 | count[ix*(my+1)+iy]++; | ~~^~~~~~~ gcc -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -g -O2 -fdebug-prefix-map=/<>/cufflinks-2.2.1+dfsg.1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o dens_int.o `test -f 'locfit/dens_int.c' || echo './'`locfit/dens_int.c cc1: warning: command-line option ‘-ftemplate-depth=1024’ is valid for C++/ObjC++ but not for C locfit/cmd.c: In function ‘setuplf’: locfit/cmd.c:796:28: warning: ‘%s’ directive writing up to 99 bytes into a region of size 96 [-Wformat-overflow=] 796 | { sprintf(command,"run %s",filename); | ^~ ~~~~~~~~ In file included from /usr/include/stdio.h:867, from locfit/local.h:86, from locfit/cmd.c:11: /usr/include/s390x-linux-gnu/bits/stdio2.h:36:10: note: ‘__builtin___sprintf_chk’ output between 5 and 104 bytes into a destination of size 100 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -g -O2 -fdebug-prefix-map=/<>/cufflinks-2.2.1+dfsg.1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o dens_odi.o `test -f 'locfit/dens_odi.c' || echo './'`locfit/dens_odi.c cc1: warning: command-line option ‘-ftemplate-depth=1024’ is valid for C++/ObjC++ but not for C gcc -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -g -O2 -fdebug-prefix-map=/<>/cufflinks-2.2.1+dfsg.1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o density.o `test -f 'locfit/density.c' || echo './'`locfit/density.c cc1: warning: command-line option ‘-ftemplate-depth=1024’ is valid for C++/ObjC++ but not for C In file included from /usr/include/string.h:495, from /usr/include/c++/10/cstring:42, from /usr/include/boost/container_hash/detail/hash_float.hpp:21, from /usr/include/boost/container_hash/hash.hpp:21, from /usr/include/boost/functional/hash.hpp:6, from /usr/include/boost/unordered/unordered_map.hpp:18, from /usr/include/boost/unordered_map.hpp:17, from biascorrection.h:18, from biascorrection.cpp:10: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘void ProgressBar::update(const char*, double)’ at progressbar.h:59:10, inlined from ‘void learn_bias(BundleFactory&, BiasLearner&, bool)’ at biascorrection.cpp:121:16: /usr/include/s390x-linux-gnu/bits/string_fortified.h:106:34: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ output may be truncated copying 27 bytes from a string of length 2047 [-Wstringop-truncation] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from bundles.h:23, from abundances.h:25, from biascorrection.cpp:12: progressbar.h: In function ‘void learn_bias(BundleFactory&, BiasLearner&, bool)’: progressbar.h:70:57: warning: ‘%3d’ directive output may be truncated writing between 3 and 11 bytes into a region of size between 6 and 33 [-Wformat-truncation=] 70 | snprintf(line_buf, 82, "\r> Processing Locus %-27s %s %3d%%", bundle_buf, _bar_buf, percent); | ^~~ progressbar.h:70:26: note: directive argument in the range [-2147483648, 99] 70 | snprintf(line_buf, 82, "\r> Processing Locus %-27s %s %3d%%", bundle_buf, _bar_buf, percent); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:867, from /usr/include/c++/10/cstdio:42, from /usr/include/c++/10/ext/string_conversions.h:43, from /usr/include/c++/10/bits/basic_string.h:6535, from /usr/include/c++/10/string:55, from /usr/include/c++/10/bits/locale_classes.h:40, from /usr/include/c++/10/bits/ios_base.h:41, from /usr/include/c++/10/streambuf:41, from /usr/include/c++/10/bits/streambuf_iterator.h:35, from /usr/include/c++/10/iterator:66, from /usr/include/boost/operators.hpp:98, from /usr/include/boost/serialization/strong_typedef.hpp:27, from /usr/include/boost/serialization/collection_size_type.hpp:10, from /usr/include/boost/serialization/array_wrapper.hpp:22, from /usr/include/boost/serialization/array.hpp:26, from /usr/include/boost/numeric/ublas/storage.hpp:21, from /usr/include/boost/numeric/ublas/vector.hpp:21, from /usr/include/boost/numeric/ublas/matrix.hpp:18, from biascorrection.h:14, from biascorrection.cpp:10: /usr/include/s390x-linux-gnu/bits/stdio2.h:67:35: note: ‘__builtin___snprintf_chk’ output between 54 and 89 bytes into a destination of size 82 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -g -O2 -fdebug-prefix-map=/<>/cufflinks-2.2.1+dfsg.1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o dist.o `test -f 'locfit/dist.c' || echo './'`locfit/dist.c cc1: warning: command-line option ‘-ftemplate-depth=1024’ is valid for C++/ObjC++ but not for C gcc -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -g -O2 -fdebug-prefix-map=/<>/cufflinks-2.2.1+dfsg.1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o ev_atree.o `test -f 'locfit/ev_atree.c' || echo './'`locfit/ev_atree.c cc1: warning: command-line option ‘-ftemplate-depth=1024’ is valid for C++/ObjC++ but not for C gcc -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -g -O2 -fdebug-prefix-map=/<>/cufflinks-2.2.1+dfsg.1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o ev_interp.o `test -f 'locfit/ev_interp.c' || echo './'`locfit/ev_interp.c cc1: warning: command-line option ‘-ftemplate-depth=1024’ is valid for C++/ObjC++ but not for C locfit/ev_atree.c: In function ‘atree_int’: locfit/ev_atree.c:203:10: warning: ‘nc’ may be used uninitialized in this function [-Wmaybe-uninitialized] 203 | return(rectcell_interp(x,vdptr(tr->xxev),vv,ll,ur,d,nc)); | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -g -O2 -fdebug-prefix-map=/<>/cufflinks-2.2.1+dfsg.1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o ev_kdtre.o `test -f 'locfit/ev_kdtre.c' || echo './'`locfit/ev_kdtre.c cc1: warning: command-line option ‘-ftemplate-depth=1024’ is valid for C++/ObjC++ but not for C locfit/ev_interp.c: In function ‘fitpint’: locfit/ev_interp.c:218:12: warning: ‘vv[0]’ may be used uninitialized in this function [-Wmaybe-uninitialized] 218 | return(vv[0]); | ~~~^~~~ locfit/ev_interp.c: In function ‘xbarint’: locfit/ev_interp.c:240:5: warning: ‘vv[0]’ may be used uninitialized in this function [-Wmaybe-uninitialized] 240 | f = vv[0]; | ~~^~~~~~~ locfit/ev_interp.c: In function ‘dointpoint’: locfit/ev_interp.c:218:12: warning: ‘vv[0]’ may be used uninitialized in this function [-Wmaybe-uninitialized] 218 | return(vv[0]); | ~~~^~~~ locfit/ev_interp.c:240:5: warning: ‘vv[0]’ may be used uninitialized in this function [-Wmaybe-uninitialized] 240 | f = vv[0]; | ~~^~~~~~~ gcc -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -g -O2 -fdebug-prefix-map=/<>/cufflinks-2.2.1+dfsg.1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o ev_main.o `test -f 'locfit/ev_main.c' || echo './'`locfit/ev_main.c cc1: warning: command-line option ‘-ftemplate-depth=1024’ is valid for C++/ObjC++ but not for C locfit/ev_main.c: In function ‘dataf’: locfit/ev_main.c:156:3: warning: ‘nv’ may be used uninitialized in this function [-Wmaybe-uninitialized] 156 | trchck(lf,nv,0,d,des->p,0); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -g -O2 -fdebug-prefix-map=/<>/cufflinks-2.2.1+dfsg.1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o ev_trian.o `test -f 'locfit/ev_trian.c' || echo './'`locfit/ev_trian.c cc1: warning: command-line option ‘-ftemplate-depth=1024’ is valid for C++/ObjC++ but not for C gcc -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -g -O2 -fdebug-prefix-map=/<>/cufflinks-2.2.1+dfsg.1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o family.o `test -f 'locfit/family.c' || echo './'`locfit/family.c cc1: warning: command-line option ‘-ftemplate-depth=1024’ is valid for C++/ObjC++ but not for C locfit/ev_trian.c: In function ‘triang_grow’: locfit/ev_trian.c:77:13: warning: ‘jm’ may be used uninitialized in this function [-Wmaybe-uninitialized] 77 | nce[jm] = pv[0]; triang_grow(des,tr,nce,ct,term); | ~~~~~~~~^~~~~~~ locfit/ev_trian.c:76:63: warning: ‘im’ may be used uninitialized in this function [-Wmaybe-uninitialized] 76 | nce[im] = pv[0]; triang_grow(des,tr,nce,ct,term); nce[im] = ce[im]; | ~~~~~~~~^~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -g -O2 -fdebug-prefix-map=/<>/cufflinks-2.2.1+dfsg.1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o fitted.o `test -f 'locfit/fitted.c' || echo './'`locfit/fitted.c cc1: warning: command-line option ‘-ftemplate-depth=1024’ is valid for C++/ObjC++ but not for C gcc -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -g -O2 -fdebug-prefix-map=/<>/cufflinks-2.2.1+dfsg.1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o frend.o `test -f 'locfit/frend.c' || echo './'`locfit/frend.c cc1: warning: command-line option ‘-ftemplate-depth=1024’ is valid for C++/ObjC++ but not for C gcc -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -g -O2 -fdebug-prefix-map=/<>/cufflinks-2.2.1+dfsg.1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o help.o `test -f 'locfit/help.c' || echo './'`locfit/help.c cc1: warning: command-line option ‘-ftemplate-depth=1024’ is valid for C++/ObjC++ but not for C locfit/frend.c: In function ‘procvvord’: locfit/frend.c:205:39: warning: variable ‘ip’ set but not used [-Wunused-but-set-variable] 205 | INT i, j, k = 0, d1, *mi, i0, p1, ip; | ^~ locfit/frend.c:204:48: warning: variable ‘t2’ set but not used [-Wunused-but-set-variable] 204 | double tr[6], gcv, g0, ap, coef[x_1][y_1], t2[4], th, md = 0.0; | ^~ locfit/frend.c: In function ‘ressumm’: locfit/frend.c:380:15: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 380 | { for (j=0; jmi[MN]; i++) | ^~~ locfit/frend.c:403:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 403 | *df = lf->mi[MN]-lf->mi[MP]; | ^ gcc -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -g -O2 -fdebug-prefix-map=/<>/cufflinks-2.2.1+dfsg.1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o lf_dercor.o `test -f 'locfit/lf_dercor.c' || echo './'`locfit/lf_dercor.c cc1: warning: command-line option ‘-ftemplate-depth=1024’ is valid for C++/ObjC++ but not for C gcc -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -g -O2 -fdebug-prefix-map=/<>/cufflinks-2.2.1+dfsg.1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o lf_fitfun.o `test -f 'locfit/lf_fitfun.c' || echo './'`locfit/lf_fitfun.c cc1: warning: command-line option ‘-ftemplate-depth=1024’ is valid for C++/ObjC++ but not for C locfit/lf_fitfun.c: In function ‘fitfun’: locfit/lf_fitfun.c:182:7: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 182 | { for (j=1; j<=deg; j++) | ^~~ locfit/lf_fitfun.c:185:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 185 | return; | ^~~~~~ gcc -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -g -O2 -fdebug-prefix-map=/<>/cufflinks-2.2.1+dfsg.1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o lf_robust.o `test -f 'locfit/lf_robust.c' || echo './'`locfit/lf_robust.c cc1: warning: command-line option ‘-ftemplate-depth=1024’ is valid for C++/ObjC++ but not for C gcc -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -g -O2 -fdebug-prefix-map=/<>/cufflinks-2.2.1+dfsg.1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o lf_vari.o `test -f 'locfit/lf_vari.c' || echo './'`locfit/lf_vari.c cc1: warning: command-line option ‘-ftemplate-depth=1024’ is valid for C++/ObjC++ but not for C gcc -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -g -O2 -fdebug-prefix-map=/<>/cufflinks-2.2.1+dfsg.1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o lfd.o `test -f 'locfit/lfd.c' || echo './'`locfit/lfd.c cc1: warning: command-line option ‘-ftemplate-depth=1024’ is valid for C++/ObjC++ but not for C locfit/lfd.c: In function ‘setfilename’: locfit/lfd.c:60:20: warning: zero-length gnu_printf format string [-Wformat-zero-length] 60 | sprintf(subp,""); | ^~ locfit/lfd.c:77:11: warning: ignoring return value of ‘system’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 77 | system("mkdir LFData"); | ^~~~~~~~~~~~~~~~~~~~~~ locfit/lfd.c: In function ‘readchar’: locfit/lfd.c:111:3: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 111 | { fread(c,1,n,lfd); | ^~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -g -O2 -fdebug-prefix-map=/<>/cufflinks-2.2.1+dfsg.1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o lfstr.o `test -f 'locfit/lfstr.c' || echo './'`locfit/lfstr.c cc1: warning: command-line option ‘-ftemplate-depth=1024’ is valid for C++/ObjC++ but not for C gcc -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -g -O2 -fdebug-prefix-map=/<>/cufflinks-2.2.1+dfsg.1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o linalg.o `test -f 'locfit/linalg.c' || echo './'`locfit/linalg.c cc1: warning: command-line option ‘-ftemplate-depth=1024’ is valid for C++/ObjC++ but not for C gcc -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -g -O2 -fdebug-prefix-map=/<>/cufflinks-2.2.1+dfsg.1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o locfit.o `test -f 'locfit/locfit.c' || echo './'`locfit/locfit.c cc1: warning: command-line option ‘-ftemplate-depth=1024’ is valid for C++/ObjC++ but not for C gcc -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -g -O2 -fdebug-prefix-map=/<>/cufflinks-2.2.1+dfsg.1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o m_chol.o `test -f 'locfit/m_chol.c' || echo './'`locfit/m_chol.c cc1: warning: command-line option ‘-ftemplate-depth=1024’ is valid for C++/ObjC++ but not for C gcc -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -g -O2 -fdebug-prefix-map=/<>/cufflinks-2.2.1+dfsg.1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o m_eigen.o `test -f 'locfit/m_eigen.c' || echo './'`locfit/m_eigen.c cc1: warning: command-line option ‘-ftemplate-depth=1024’ is valid for C++/ObjC++ but not for C gcc -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -g -O2 -fdebug-prefix-map=/<>/cufflinks-2.2.1+dfsg.1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o m_jacob.o `test -f 'locfit/m_jacob.c' || echo './'`locfit/m_jacob.c cc1: warning: command-line option ‘-ftemplate-depth=1024’ is valid for C++/ObjC++ but not for C gcc -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -g -O2 -fdebug-prefix-map=/<>/cufflinks-2.2.1+dfsg.1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o m_max.o `test -f 'locfit/m_max.c' || echo './'`locfit/m_max.c cc1: warning: command-line option ‘-ftemplate-depth=1024’ is valid for C++/ObjC++ but not for C gcc -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -g -O2 -fdebug-prefix-map=/<>/cufflinks-2.2.1+dfsg.1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o makecmd.o `test -f 'locfit/makecmd.c' || echo './'`locfit/makecmd.c cc1: warning: command-line option ‘-ftemplate-depth=1024’ is valid for C++/ObjC++ but not for C gcc -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -g -O2 -fdebug-prefix-map=/<>/cufflinks-2.2.1+dfsg.1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o math.o `test -f 'locfit/math.c' || echo './'`locfit/math.c locfit/makecmd.c: In function ‘makefields’: locfit/makecmd.c:88:36: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] 88 | } while ((instr) || (*z !=' ') && (!isterminator(*z))); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ cc1: warning: command-line option ‘-ftemplate-depth=1024’ is valid for C++/ObjC++ but not for C gcc -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -g -O2 -fdebug-prefix-map=/<>/cufflinks-2.2.1+dfsg.1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o minmax.o `test -f 'locfit/minmax.c' || echo './'`locfit/minmax.c cc1: warning: command-line option ‘-ftemplate-depth=1024’ is valid for C++/ObjC++ but not for C gcc -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -g -O2 -fdebug-prefix-map=/<>/cufflinks-2.2.1+dfsg.1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o nbhd.o `test -f 'locfit/nbhd.c' || echo './'`locfit/nbhd.c cc1: warning: command-line option ‘-ftemplate-depth=1024’ is valid for C++/ObjC++ but not for C gcc -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -g -O2 -fdebug-prefix-map=/<>/cufflinks-2.2.1+dfsg.1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o pcomp.o `test -f 'locfit/pcomp.c' || echo './'`locfit/pcomp.c locfit/minmax.c: In function ‘updatesd’: locfit/minmax.c:94:21: warning: ‘sd’ may be used uninitialized in this function [-Wmaybe-uninitialized] 94 | if (des->xtwx.dg[sd]>0) | ^ cc1: warning: command-line option ‘-ftemplate-depth=1024’ is valid for C++/ObjC++ but not for C locfit/minmax.c: In function ‘mmax’: locfit/minmax.c:217:8: warning: ‘sing’ may be used uninitialized in this function [-Wmaybe-uninitialized] 217 | if (sing) printf("final singular\n"); | ^ gcc -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -g -O2 -fdebug-prefix-map=/<>/cufflinks-2.2.1+dfsg.1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o pout.o `test -f 'locfit/pout.c' || echo './'`locfit/pout.c cc1: warning: command-line option ‘-ftemplate-depth=1024’ is valid for C++/ObjC++ but not for C locfit/pout.c: In function ‘plotxwin’: locfit/pout.c:447:38: warning: variable ‘vz’ set but not used [-Wunused-but-set-variable] 447 | double z[3], z2[3], xx[2], vx, vy, vz; | ^~ locfit/pout.c:447:34: warning: variable ‘vy’ set but not used [-Wunused-but-set-variable] 447 | double z[3], z2[3], xx[2], vx, vy, vz; | ^~ locfit/pout.c:447:30: warning: variable ‘vx’ set but not used [-Wunused-but-set-variable] 447 | double z[3], z2[3], xx[2], vx, vy, vz; | ^~ gcc -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -g -O2 -fdebug-prefix-map=/<>/cufflinks-2.2.1+dfsg.1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o preplot.o `test -f 'locfit/preplot.c' || echo './'`locfit/preplot.c cc1: warning: command-line option ‘-ftemplate-depth=1024’ is valid for C++/ObjC++ but not for C gcc -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -g -O2 -fdebug-prefix-map=/<>/cufflinks-2.2.1+dfsg.1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o random.o `test -f 'locfit/random.c' || echo './'`locfit/random.c cc1: warning: command-line option ‘-ftemplate-depth=1024’ is valid for C++/ObjC++ but not for C locfit/pout.c: In function ‘contour3d.part.0’: locfit/pout.c:111:13: warning: ‘x3[1]’ may be used uninitialized in this function [-Wmaybe-uninitialized] 111 | z1 = (z[1]-yl[0])/(yl[1]-yl[0]); | ~~~~~^~~~~~~ locfit/pout.c:221:48: note: ‘x3[1]’ was declared here 221 | double xyz[4][3], u[4], x0[3], x1[3], x2[3], x3[3], r; | ^~ locfit/pout.c:110:13: warning: ‘x3[0]’ may be used uninitialized in this function [-Wmaybe-uninitialized] 110 | z0 = (z[0]-xl[0])/(xl[1]-xl[0]); | ~~~~~^~~~~~~ locfit/pout.c:221:48: note: ‘x3[0]’ was declared here 221 | double xyz[4][3], u[4], x0[3], x1[3], x2[3], x3[3], r; | ^~ locfit/pout.c:111:13: warning: ‘x2[1]’ may be used uninitialized in this function [-Wmaybe-uninitialized] 111 | z1 = (z[1]-yl[0])/(yl[1]-yl[0]); | ~~~~~^~~~~~~ locfit/pout.c:221:41: note: ‘x2[1]’ was declared here 221 | double xyz[4][3], u[4], x0[3], x1[3], x2[3], x3[3], r; | ^~ locfit/pout.c:110:13: warning: ‘x2[0]’ may be used uninitialized in this function [-Wmaybe-uninitialized] 110 | z0 = (z[0]-xl[0])/(xl[1]-xl[0]); | ~~~~~^~~~~~~ locfit/pout.c:221:41: note: ‘x2[0]’ was declared here 221 | double xyz[4][3], u[4], x0[3], x1[3], x2[3], x3[3], r; | ^~ locfit/pout.c:111:13: warning: ‘*((void *)&x1+8)’ may be used uninitialized in this function [-Wmaybe-uninitialized] 111 | z1 = (z[1]-yl[0])/(yl[1]-yl[0]); | ~~~~~^~~~~~~ locfit/pout.c:221:34: note: ‘*((void *)&x1+8)’ was declared here 221 | double xyz[4][3], u[4], x0[3], x1[3], x2[3], x3[3], r; | ^~ locfit/pout.c:110:13: warning: ‘x1[0]’ may be used uninitialized in this function [-Wmaybe-uninitialized] 110 | z0 = (z[0]-xl[0])/(xl[1]-xl[0]); | ~~~~~^~~~~~~ locfit/pout.c:221:34: note: ‘x1[0]’ was declared here 221 | double xyz[4][3], u[4], x0[3], x1[3], x2[3], x3[3], r; | ^~ locfit/pout.c:111:13: warning: ‘*((void *)&x0+8)’ may be used uninitialized in this function [-Wmaybe-uninitialized] 111 | z1 = (z[1]-yl[0])/(yl[1]-yl[0]); | ~~~~~^~~~~~~ locfit/pout.c:221:27: note: ‘*((void *)&x0+8)’ was declared here 221 | double xyz[4][3], u[4], x0[3], x1[3], x2[3], x3[3], r; | ^~ locfit/pout.c:110:13: warning: ‘x0[0]’ may be used uninitialized in this function [-Wmaybe-uninitialized] 110 | z0 = (z[0]-xl[0])/(xl[1]-xl[0]); | ~~~~~^~~~~~~ locfit/pout.c:221:27: note: ‘x0[0]’ was declared here 221 | double xyz[4][3], u[4], x0[3], x1[3], x2[3], x3[3], r; | ^~ gcc -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -g -O2 -fdebug-prefix-map=/<>/cufflinks-2.2.1+dfsg.1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o readfile.o `test -f 'locfit/readfile.c' || echo './'`locfit/readfile.c cc1: warning: command-line option ‘-ftemplate-depth=1024’ is valid for C++/ObjC++ but not for C gcc -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -g -O2 -fdebug-prefix-map=/<>/cufflinks-2.2.1+dfsg.1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o scb.o `test -f 'locfit/scb.c' || echo './'`locfit/scb.c cc1: warning: command-line option ‘-ftemplate-depth=1024’ is valid for C++/ObjC++ but not for C locfit/scb.c: In function ‘cumulant’: locfit/scb.c:61:10: warning: variable ‘b2i’ set but not used [-Wunused-but-set-variable] 61 | { double b2i, b3i, b3j, b4i; | ^~~ gcc -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -g -O2 -fdebug-prefix-map=/<>/cufflinks-2.2.1+dfsg.1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o scb_cons.o `test -f 'locfit/scb_cons.c' || echo './'`locfit/scb_cons.c cc1: warning: command-line option ‘-ftemplate-depth=1024’ is valid for C++/ObjC++ but not for C locfit/pout.c: In function ‘lines3d’: locfit/pout.c:112:13: warning: ‘*((void *)&x1+16)’ may be used uninitialized in this function [-Wmaybe-uninitialized] 112 | z2 = (z[2]-zl[0])/(zl[1]-zl[0]); | ~~~~~^~~~~~~ locfit/pout.c:180:17: note: ‘*((void *)&x1+16)’ was declared here 180 | double x0[3], x1[3]; | ^~ locfit/pout.c:111:13: warning: ‘*((void *)&x1+8)’ may be used uninitialized in this function [-Wmaybe-uninitialized] 111 | z1 = (z[1]-yl[0])/(yl[1]-yl[0]); | ~~~~~^~~~~~~ locfit/pout.c:180:17: note: ‘*((void *)&x1+8)’ was declared here 180 | double x0[3], x1[3]; | ^~ locfit/pout.c:110:13: warning: ‘x1’ may be used uninitialized in this function [-Wmaybe-uninitialized] 110 | z0 = (z[0]-xl[0])/(xl[1]-xl[0]); | ~~~~~^~~~~~~ locfit/pout.c:180:17: note: ‘x1’ was declared here 180 | double x0[3], x1[3]; | ^~ gcc -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -g -O2 -fdebug-prefix-map=/<>/cufflinks-2.2.1+dfsg.1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o simul.o `test -f 'locfit/simul.c' || echo './'`locfit/simul.c cc1: warning: command-line option ‘-ftemplate-depth=1024’ is valid for C++/ObjC++ but not for C locfit/simul.c: In function ‘cp’: locfit/simul.c:108:9: warning: ‘hm’ may be used uninitialized in this function [-Wmaybe-uninitialized] 108 | return(hm); | ^ locfit/simul.c: In function ‘rband’: locfit/simul.c:208:23: warning: ‘hm’ may be used uninitialized in this function [-Wmaybe-uninitialized] 208 | case 2: hhat[i] = cp(des,tr,2); | ~~~~~~~~^~~~~~~~~~~~~~ locfit/simul.c:206:23: warning: ‘hm’ may be used uninitialized in this function [-Wmaybe-uninitialized] 206 | { case 1: hhat[i] = cp(des,tr,1); | ~~~~~~~~^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -g -O2 -fdebug-prefix-map=/<>/cufflinks-2.2.1+dfsg.1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o solve.o `test -f 'locfit/solve.c' || echo './'`locfit/solve.c cc1: warning: command-line option ‘-ftemplate-depth=1024’ is valid for C++/ObjC++ but not for C gcc -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -g -O2 -fdebug-prefix-map=/<>/cufflinks-2.2.1+dfsg.1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o startlf.o `test -f 'locfit/startlf.c' || echo './'`locfit/startlf.c cc1: warning: command-line option ‘-ftemplate-depth=1024’ is valid for C++/ObjC++ but not for C gcc -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -g -O2 -fdebug-prefix-map=/<>/cufflinks-2.2.1+dfsg.1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o strings.o `test -f 'locfit/strings.c' || echo './'`locfit/strings.c cc1: warning: command-line option ‘-ftemplate-depth=1024’ is valid for C++/ObjC++ but not for C g++ -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -g -O2 -fdebug-prefix-map=/<>/cufflinks-2.2.1+dfsg.1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o vari.o `test -f 'locfit/vari.cpp' || echo './'`locfit/vari.cpp gcc -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -g -O2 -fdebug-prefix-map=/<>/cufflinks-2.2.1+dfsg.1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o wdiag.o `test -f 'locfit/wdiag.c' || echo './'`locfit/wdiag.c cc1: warning: command-line option ‘-ftemplate-depth=1024’ is valid for C++/ObjC++ but not for C gcc -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -g -O2 -fdebug-prefix-map=/<>/cufflinks-2.2.1+dfsg.1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -c -o weight.o `test -f 'locfit/weight.c' || echo './'`locfit/weight.c cc1: warning: command-line option ‘-ftemplate-depth=1024’ is valid for C++/ObjC++ but not for C locfit/weight.c: In function ‘weightdd’: locfit/weight.c:162:10: warning: variable ‘w’ set but not used [-Wunused-but-set-variable] 162 | { double w; | ^ g++ -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -g -O2 -fdebug-prefix-map=/<>/cufflinks-2.2.1+dfsg.1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o replicates.o replicates.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -g -O2 -fdebug-prefix-map=/<>/cufflinks-2.2.1+dfsg.1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o multireads.o multireads.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -g -O2 -fdebug-prefix-map=/<>/cufflinks-2.2.1+dfsg.1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o jensen_shannon.o jensen_shannon.cpp jensen_shannon.cpp: In function ‘double entropy(const VectorXd&)’: jensen_shannon.cpp:21:23: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase >::Index’ {aka ‘long int’} [-Wsign-compare] 21 | for (size_t i = 0; i < p.size(); ++i) | ~~^~~~~~~~~~ jensen_shannon.cpp:29:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 29 | if (e < 0) | ^~ jensen_shannon.cpp:31:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 31 | return e; | ^~~~~~ jensen_shannon.cpp: In function ‘double jensen_shannon_distance(std::vector >&)’: jensen_shannon.cpp:65:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 65 | if (js < 0) // can happen due to underflow or rounding errors. | ^~ jensen_shannon.cpp:67:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 67 | return sqrt(js); | ^~~~~~ jensen_shannon.cpp: In function ‘void jensen_shannon_gradient(std::vector >&, double, boost::numeric::ublas::vector&)’: jensen_shannon.cpp:100:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase >::Index’ {aka ‘long int’} [-Wsign-compare] 100 | for (size_t j = 0; j < sample_kappas[i].size(); ++j) | ~~^~~~~~~~~~~~~~~~~~~~~~~~~ jensen_shannon.cpp:132:24: warning: unused variable ‘curr_grad’ [-Wunused-variable] 132 | double curr_grad = gradient(i*kappa_length + k); | ^~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -g -O2 -fdebug-prefix-map=/<>/cufflinks-2.2.1+dfsg.1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o tracking.o tracking.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -g -O2 -fdebug-prefix-map=/<>/cufflinks-2.2.1+dfsg.1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o codons.o codons.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -g -O2 -fdebug-prefix-map=/<>/cufflinks-2.2.1+dfsg.1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o GArgs.o GArgs.cpp In file included from bundles.h:20, from replicates.h:10, from replicates.cpp:18: hits.h: In constructor ‘PrecomputedExpressionHitFactory::PrecomputedExpressionHitFactory(const string&, ReadTable&, RefSequenceTable&)’: hits.h:928:12: warning: ‘PrecomputedExpressionHitFactory::_expression_file_name’ will be initialized after [-Wreorder] 928 | string _expression_file_name; | ^~~~~~~~~~~~~~~~~~~~~ hits.h:927:19: warning: ‘std::ifstream PrecomputedExpressionHitFactory::_ifs’ [-Wreorder] 927 | std::ifstream _ifs; | ^~~~ In file included from bundles.h:20, from replicates.h:10, from replicates.cpp:18: hits.h:814:5: warning: when initialized here [-Wreorder] 814 | PrecomputedExpressionHitFactory(const string& expression_file_name, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -g -O2 -fdebug-prefix-map=/<>/cufflinks-2.2.1+dfsg.1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o GBase.o GBase.cpp In file included from multireads.cpp:11: hits.h: In constructor ‘PrecomputedExpressionHitFactory::PrecomputedExpressionHitFactory(const string&, ReadTable&, RefSequenceTable&)’: hits.h:928:12: warning: ‘PrecomputedExpressionHitFactory::_expression_file_name’ will be initialized after [-Wreorder] 928 | string _expression_file_name; | ^~~~~~~~~~~~~~~~~~~~~ hits.h:927:19: warning: ‘std::ifstream PrecomputedExpressionHitFactory::_ifs’ [-Wreorder] 927 | std::ifstream _ifs; | ^~~~ In file included from multireads.cpp:11: hits.h:814:5: warning: when initialized here [-Wreorder] 814 | PrecomputedExpressionHitFactory(const string& expression_file_name, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from replicates.cpp:18: replicates.h: In member function ‘bool ReplicatedBundleFactory::next_bundle(HitBundle&, bool)’: replicates.h:224:57: warning: unused variable ‘s2’ [-Wunused-variable] 224 | const vector >& s2 = bundles[i-1]->ref_scaffolds(); | ^~ replicates.cpp: In member function ‘virtual double MassDispersionModel::scale_mass_variance(double) const’: replicates.cpp:146:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 146 | if (d >= _scaled_compatible_mass_means.size()) | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ replicates.cpp:150:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 150 | if (d >= _scaled_mass_variances.size()) | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ replicates.cpp: In member function ‘virtual double MleErrorModel::scale_mle_variance(double) const’: replicates.cpp:260:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 260 | if (d >= _scaled_compatible_mass_means.size()) | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ replicates.cpp:264:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 264 | if (d >= _scaled_mle_variances.size()) | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ replicates.cpp: In member function ‘double SCVInterpolator::interpolate_scv(double)’: replicates.cpp:593:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 593 | if (d >= est_scvs.size()) | ~~^~~~~~~~~~~~~~~~~~ replicates.cpp:597:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 597 | if (d >= true_scvs.size()) | ~~^~~~~~~~~~~~~~~~~~~ replicates.cpp: In function ‘void build_scv_correction_fit(int, int, int, SCVInterpolator&)’: replicates.cpp:671:30: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 671 | for (size_t i = 0; i < ngenes; ++i) | ~~^~~~~~~~ replicates.cpp:674:46: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 674 | for (size_t rep_idx = 0; rep_idx < nreps; ++rep_idx) | ~~~~~~~~^~~~~~~ replicates.cpp:772:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘INT’ {aka ‘int’} [-Wsign-compare] 772 | for (size_t i = 0; i < cp->n; ++i) | ~~^~~~~~~ replicates.cpp: In function ‘boost::shared_ptr fit_dispersion_model_helper(const string&, const std::vector&, const std::vector&)’: replicates.cpp:896:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘INT’ {aka ‘int’} [-Wsign-compare] 896 | for (size_t i = 0; i < cp->n; ++i) | ~~^~~~~~~ GBase.cpp: In function ‘char* commaprint(uint64)’: GBase.cpp:779:10: warning: function may return address of local variable [-Wreturn-local-addr] 779 | return p; | ^ GBase.cpp:758:8: note: declared here 758 | char retbuf[48]; | ^~~~~~ g++ -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -g -O2 -fdebug-prefix-map=/<>/cufflinks-2.2.1+dfsg.1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o gdna.o gdna.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -g -O2 -fdebug-prefix-map=/<>/cufflinks-2.2.1+dfsg.1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o GStr.o GStr.cpp In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:10, from gtf_tracking.h:12, from bundles.h:22, from replicates.h:10, from replicates.cpp:18: GVec.hh: In instantiation of ‘void GVec::Grow(int, OBJ&) [with OBJ = GISeg]’: GVec.hh:422:9: required from ‘void GVec::Insert(int, OBJ*) [with OBJ = GISeg]’ GVec.hh:81:48: required from ‘void GVec::idxInsert(int, OBJ&) [with OBJ = GISeg]’ gtf_tracking.h:210:29: required from here GVec.hh:350:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class GISeg’; use assignment or value-initialization instead [-Wclass-memaccess] 350 | memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from bundles.h:22, from replicates.h:10, from replicates.cpp:18: gtf_tracking.h:188:7: note: ‘class GISeg’ declared here 188 | class GISeg: public GSeg { | ^~~~~ In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:10, from gtf_tracking.h:12, from bundles.h:22, from replicates.h:10, from replicates.cpp:18: GVec.hh: In instantiation of ‘void GVec::Grow(int, OBJ&) [with OBJ = GXSeg]’: GVec.hh:422:9: required from ‘void GVec::Insert(int, OBJ*) [with OBJ = GXSeg]’ GVec.hh:79:44: required from ‘void GVec::Insert(int, OBJ) [with OBJ = GXSeg]’ GList.hh:230:21: required from ‘int GArray::Add(OBJ*) [with OBJ = GXSeg]’ GList.hh:51:36: required from ‘int GArray::Add(OBJ&) [with OBJ = GXSeg]’ gtf_tracking.h:419:20: required from here GVec.hh:350:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class GXSeg’; use assignment or value-initialization instead [-Wclass-memaccess] 350 | memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from bundles.h:22, from replicates.h:10, from replicates.cpp:18: gtf_tracking.h:359:7: note: ‘class GXSeg’ declared here 359 | class GXSeg : public GSeg { | ^~~~~ In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:10, from gtf_tracking.h:12, from bundles.h:22, from replicates.h:10, from replicates.cpp:18: GVec.hh: In instantiation of ‘void GVec::Grow(int, OBJ&) [with OBJ = GSeg]’: GVec.hh:422:9: required from ‘void GVec::Insert(int, OBJ*) [with OBJ = GSeg]’ GVec.hh:79:44: required from ‘void GVec::Insert(int, OBJ) [with OBJ = GSeg]’ GList.hh:230:21: required from ‘int GArray::Add(OBJ*) [with OBJ = GSeg]’ GList.hh:51:36: required from ‘int GArray::Add(OBJ&) [with OBJ = GSeg]’ gtf_tracking.h:420:19: required from here GVec.hh:350:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class GSeg’; use assignment or value-initialization instead [-Wclass-memaccess] 350 | memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from gff.h:7, from gtf_tracking.h:12, from bundles.h:22, from replicates.h:10, from replicates.cpp:18: GBase.h:279:7: note: ‘class GSeg’ declared here 279 | class GSeg { | ^~~~ g++ -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -g -O2 -fdebug-prefix-map=/<>/cufflinks-2.2.1+dfsg.1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o GFaSeqGet.o GFaSeqGet.cpp In file included from abundances.h:23, from tracking.h:1, from tracking.cpp:1: hits.h: In constructor ‘PrecomputedExpressionHitFactory::PrecomputedExpressionHitFactory(const string&, ReadTable&, RefSequenceTable&)’: hits.h:928:12: warning: ‘PrecomputedExpressionHitFactory::_expression_file_name’ will be initialized after [-Wreorder] 928 | string _expression_file_name; | ^~~~~~~~~~~~~~~~~~~~~ hits.h:927:19: warning: ‘std::ifstream PrecomputedExpressionHitFactory::_ifs’ [-Wreorder] 927 | std::ifstream _ifs; | ^~~~ In file included from abundances.h:23, from tracking.h:1, from tracking.cpp:1: hits.h:814:5: warning: when initialized here [-Wreorder] 814 | PrecomputedExpressionHitFactory(const string& expression_file_name, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -g -O2 -fdebug-prefix-map=/<>/cufflinks-2.2.1+dfsg.1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o GFastaIndex.o GFastaIndex.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -g -O2 -fdebug-prefix-map=/<>/cufflinks-2.2.1+dfsg.1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o gff.o gff.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -g -O2 -fdebug-prefix-map=/<>/cufflinks-2.2.1+dfsg.1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o gff_utils.o gff_utils.cpp In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:10, from gtf_tracking.h:12, from bundles.h:22, from abundances.h:25, from tracking.h:1, from tracking.cpp:1: GVec.hh: In instantiation of ‘void GVec::Grow(int, OBJ&) [with OBJ = GISeg]’: GVec.hh:422:9: required from ‘void GVec::Insert(int, OBJ*) [with OBJ = GISeg]’ GVec.hh:81:48: required from ‘void GVec::idxInsert(int, OBJ&) [with OBJ = GISeg]’ gtf_tracking.h:210:29: required from here GVec.hh:350:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class GISeg’; use assignment or value-initialization instead [-Wclass-memaccess] 350 | memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from bundles.h:22, from abundances.h:25, from tracking.h:1, from tracking.cpp:1: gtf_tracking.h:188:7: note: ‘class GISeg’ declared here 188 | class GISeg: public GSeg { | ^~~~~ In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:10, from gff.cpp:1: GVec.hh: In instantiation of ‘void GVec::Grow(int, OBJ&) [with OBJ = GffCDSeg]’: GVec.hh:422:9: required from ‘void GVec::Insert(int, OBJ*) [with OBJ = GffCDSeg]’ GVec.hh:79:44: required from ‘void GVec::Insert(int, OBJ) [with OBJ = GffCDSeg]’ GList.hh:230:21: required from ‘int GArray::Add(OBJ*) [with OBJ = GffCDSeg]’ GList.hh:51:36: required from ‘int GArray::Add(OBJ&) [with OBJ = GffCDSeg]’ gff.cpp:2103:22: required from here GVec.hh:350:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class GffCDSeg’; use assignment or value-initialization instead [-Wclass-memaccess] 350 | memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from gff.cpp:1: gff.h:419:7: note: ‘class GffCDSeg’ declared here 419 | class GffCDSeg:public GSeg { | ^~~~~~~~ In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:10, from gff_utils.h:3, from gff_utils.cpp:1: GVec.hh: In instantiation of ‘void GVec::Grow(int, OBJ&) [with OBJ = GSeg]’: GVec.hh:422:9: required from ‘void GVec::Insert(int, OBJ*) [with OBJ = GSeg]’ GVec.hh:79:44: required from ‘void GVec::Insert(int, OBJ) [with OBJ = GSeg]’ GList.hh:230:21: required from ‘int GArray::Add(OBJ*) [with OBJ = GSeg]’ GList.hh:51:36: required from ‘int GArray::Add(OBJ&) [with OBJ = GSeg]’ gff_utils.h:321:31: required from here GVec.hh:350:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class GSeg’; use assignment or value-initialization instead [-Wclass-memaccess] 350 | memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from gff.h:7, from gff_utils.h:3, from gff_utils.cpp:1: GBase.h:279:7: note: ‘class GSeg’ declared here 279 | class GSeg { | ^~~~ In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:10, from gtf_tracking.h:12, from bundles.h:22, from abundances.h:25, from tracking.h:1, from tracking.cpp:1: GVec.hh: In instantiation of ‘void GVec::Grow(int, OBJ&) [with OBJ = GXSeg]’: GVec.hh:422:9: required from ‘void GVec::Insert(int, OBJ*) [with OBJ = GXSeg]’ GVec.hh:79:44: required from ‘void GVec::Insert(int, OBJ) [with OBJ = GXSeg]’ GList.hh:230:21: required from ‘int GArray::Add(OBJ*) [with OBJ = GXSeg]’ GList.hh:51:36: required from ‘int GArray::Add(OBJ&) [with OBJ = GXSeg]’ gtf_tracking.h:419:20: required from here GVec.hh:350:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class GXSeg’; use assignment or value-initialization instead [-Wclass-memaccess] 350 | memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from bundles.h:22, from abundances.h:25, from tracking.h:1, from tracking.cpp:1: gtf_tracking.h:359:7: note: ‘class GXSeg’ declared here 359 | class GXSeg : public GSeg { | ^~~~~ In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:10, from gtf_tracking.h:12, from bundles.h:22, from abundances.h:25, from tracking.h:1, from tracking.cpp:1: GVec.hh: In instantiation of ‘void GVec::Grow(int, OBJ&) [with OBJ = GSeg]’: GVec.hh:422:9: required from ‘void GVec::Insert(int, OBJ*) [with OBJ = GSeg]’ GVec.hh:79:44: required from ‘void GVec::Insert(int, OBJ) [with OBJ = GSeg]’ GList.hh:230:21: required from ‘int GArray::Add(OBJ*) [with OBJ = GSeg]’ GList.hh:51:36: required from ‘int GArray::Add(OBJ&) [with OBJ = GSeg]’ gtf_tracking.h:420:19: required from here GVec.hh:350:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class GSeg’; use assignment or value-initialization instead [-Wclass-memaccess] 350 | memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from gff.h:7, from gtf_tracking.h:12, from bundles.h:22, from abundances.h:25, from tracking.h:1, from tracking.cpp:1: GBase.h:279:7: note: ‘class GSeg’ declared here 279 | class GSeg { | ^~~~ g++ -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -g -O2 -fdebug-prefix-map=/<>/cufflinks-2.2.1+dfsg.1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o gtf_tracking.o gtf_tracking.cpp In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:10, from gtf_tracking.h:12, from gtf_tracking.cpp:10: GVec.hh: In instantiation of ‘void GVec::Grow(int, OBJ&) [with OBJ = GISeg]’: GVec.hh:422:9: required from ‘void GVec::Insert(int, OBJ*) [with OBJ = GISeg]’ GVec.hh:81:48: required from ‘void GVec::idxInsert(int, OBJ&) [with OBJ = GISeg]’ gtf_tracking.h:210:29: required from here GVec.hh:350:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class GISeg’; use assignment or value-initialization instead [-Wclass-memaccess] 350 | memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from gtf_tracking.cpp:10: gtf_tracking.h:188:7: note: ‘class GISeg’ declared here 188 | class GISeg: public GSeg { | ^~~~~ In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:10, from gtf_tracking.h:12, from gtf_tracking.cpp:10: GVec.hh: In instantiation of ‘void GVec::Grow(int, OBJ&) [with OBJ = GXSeg]’: GVec.hh:422:9: required from ‘void GVec::Insert(int, OBJ*) [with OBJ = GXSeg]’ GVec.hh:79:44: required from ‘void GVec::Insert(int, OBJ) [with OBJ = GXSeg]’ GList.hh:230:21: required from ‘int GArray::Add(OBJ*) [with OBJ = GXSeg]’ GList.hh:51:36: required from ‘int GArray::Add(OBJ&) [with OBJ = GXSeg]’ gtf_tracking.h:419:20: required from here GVec.hh:350:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class GXSeg’; use assignment or value-initialization instead [-Wclass-memaccess] 350 | memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from gtf_tracking.cpp:10: gtf_tracking.h:359:7: note: ‘class GXSeg’ declared here 359 | class GXSeg : public GSeg { | ^~~~~ In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:10, from gtf_tracking.h:12, from gtf_tracking.cpp:10: GVec.hh: In instantiation of ‘void GVec::Grow(int, OBJ&) [with OBJ = GSeg]’: GVec.hh:422:9: required from ‘void GVec::Insert(int, OBJ*) [with OBJ = GSeg]’ GVec.hh:79:44: required from ‘void GVec::Insert(int, OBJ) [with OBJ = GSeg]’ GList.hh:230:21: required from ‘int GArray::Add(OBJ*) [with OBJ = GSeg]’ GList.hh:51:36: required from ‘int GArray::Add(OBJ&) [with OBJ = GSeg]’ gtf_tracking.h:420:19: required from here GVec.hh:350:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class GSeg’; use assignment or value-initialization instead [-Wclass-memaccess] 350 | memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from gff.h:7, from gtf_tracking.h:12, from gtf_tracking.cpp:10: GBase.h:279:7: note: ‘class GSeg’ declared here 279 | class GSeg { | ^~~~ In file included from tracking.cpp:1: tracking.h: In constructor ‘FPKMContext::FPKMContext(double, double, double, double, const CountPerReplicateTable&, double, const FPKMPerReplicateTable&, double, double, double, AbundanceStatus, const StatusPerReplicateTable&, const std::vector&, double)’: tracking.h:3:8: warning: ‘*((void*)& info +32)’ may be used uninitialized in this function [-Wmaybe-uninitialized] 3 | struct TrackingInfoPerRep | ^~~~~~~~~~~~~~~~~~ tracking.h:48:32: note: ‘*((void*)& info +32)’ was declared here 48 | TrackingInfoPerRep info; | ^~~~ tracking.h:3:8: warning: ‘info.TrackingInfoPerRep::fpkm’ may be used uninitialized in this function [-Wmaybe-uninitialized] 3 | struct TrackingInfoPerRep | ^~~~~~~~~~~~~~~~~~ tracking.h:48:32: note: ‘info.TrackingInfoPerRep::fpkm’ was declared here 48 | TrackingInfoPerRep info; | ^~~~ g++ -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -g -O2 -fdebug-prefix-map=/<>/cufflinks-2.2.1+dfsg.1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o cuffcompare.o cuffcompare.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -g -O2 -fdebug-prefix-map=/<>/cufflinks-2.2.1+dfsg.1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o cuffdiff.o cuffdiff.cpp In file included from cuffcompare.cpp:7: update_check.h: In function ‘bool get_current_version(char*)’: update_check.h:81:22: warning: argument to ‘sizeof’ in ‘void bzero(void*, size_t)’ call is the same expression as the destination; did you mean to provide an explicit length? [-Wsizeof-pointer-memaccess] 81 | bzero(curr_version, sizeof(curr_version)); | ^~~~~~~~~~~~~~~~~~~~ In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:10, from gtf_tracking.h:12, from cuffcompare.cpp:4: GVec.hh: In instantiation of ‘void GVec::Grow(int, OBJ&) [with OBJ = GISeg]’: GVec.hh:422:9: required from ‘void GVec::Insert(int, OBJ*) [with OBJ = GISeg]’ GVec.hh:81:48: required from ‘void GVec::idxInsert(int, OBJ&) [with OBJ = GISeg]’ gtf_tracking.h:210:29: required from here GVec.hh:350:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class GISeg’; use assignment or value-initialization instead [-Wclass-memaccess] 350 | memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from cuffcompare.cpp:4: gtf_tracking.h:188:7: note: ‘class GISeg’ declared here 188 | class GISeg: public GSeg { | ^~~~~ In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:10, from gtf_tracking.h:12, from cuffcompare.cpp:4: GVec.hh: In instantiation of ‘void GVec::Grow(int, OBJ&) [with OBJ = GXSeg]’: GVec.hh:422:9: required from ‘void GVec::Insert(int, OBJ*) [with OBJ = GXSeg]’ GVec.hh:79:44: required from ‘void GVec::Insert(int, OBJ) [with OBJ = GXSeg]’ GList.hh:230:21: required from ‘int GArray::Add(OBJ*) [with OBJ = GXSeg]’ GList.hh:51:36: required from ‘int GArray::Add(OBJ&) [with OBJ = GXSeg]’ gtf_tracking.h:419:20: required from here GVec.hh:350:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class GXSeg’; use assignment or value-initialization instead [-Wclass-memaccess] 350 | memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from cuffcompare.cpp:4: gtf_tracking.h:359:7: note: ‘class GXSeg’ declared here 359 | class GXSeg : public GSeg { | ^~~~~ In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:10, from gtf_tracking.h:12, from cuffcompare.cpp:4: GVec.hh: In instantiation of ‘void GVec::Grow(int, OBJ&) [with OBJ = GSeg]’: GVec.hh:422:9: required from ‘void GVec::Insert(int, OBJ*) [with OBJ = GSeg]’ GVec.hh:79:44: required from ‘void GVec::Insert(int, OBJ) [with OBJ = GSeg]’ GList.hh:230:21: required from ‘int GArray::Add(OBJ*) [with OBJ = GSeg]’ GList.hh:51:36: required from ‘int GArray::Add(OBJ&) [with OBJ = GSeg]’ gtf_tracking.h:420:19: required from here GVec.hh:350:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class GSeg’; use assignment or value-initialization instead [-Wclass-memaccess] 350 | memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from gff.h:7, from gtf_tracking.h:12, from cuffcompare.cpp:4: GBase.h:279:7: note: ‘class GSeg’ declared here 279 | class GSeg { | ^~~~ g++ -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -g -O2 -fdebug-prefix-map=/<>/cufflinks-2.2.1+dfsg.1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o gtf_to_sam.o gtf_to_sam.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -g -O2 -fdebug-prefix-map=/<>/cufflinks-2.2.1+dfsg.1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o compress_gtf.o compress_gtf.cpp In file included from cuffdiff.cpp:18: hits.h: In constructor ‘PrecomputedExpressionHitFactory::PrecomputedExpressionHitFactory(const string&, ReadTable&, RefSequenceTable&)’: hits.h:928:12: warning: ‘PrecomputedExpressionHitFactory::_expression_file_name’ will be initialized after [-Wreorder] 928 | string _expression_file_name; | ^~~~~~~~~~~~~~~~~~~~~ hits.h:927:19: warning: ‘std::ifstream PrecomputedExpressionHitFactory::_ifs’ [-Wreorder] 927 | std::ifstream _ifs; | ^~~~ In file included from cuffdiff.cpp:18: hits.h:814:5: warning: when initialized here [-Wreorder] 814 | PrecomputedExpressionHitFactory(const string& expression_file_name, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from cuffdiff.cpp:23: update_check.h: In function ‘bool get_current_version(char*)’: update_check.h:81:22: warning: argument to ‘sizeof’ in ‘void bzero(void*, size_t)’ call is the same expression as the destination; did you mean to provide an explicit length? [-Wsizeof-pointer-memaccess] 81 | bzero(curr_version, sizeof(curr_version)); | ^~~~~~~~~~~~~~~~~~~~ In file included from gtf_to_sam.cpp:22: hits.h: In constructor ‘PrecomputedExpressionHitFactory::PrecomputedExpressionHitFactory(const string&, ReadTable&, RefSequenceTable&)’: hits.h:928:12: warning: ‘PrecomputedExpressionHitFactory::_expression_file_name’ will be initialized after [-Wreorder] 928 | string _expression_file_name; | ^~~~~~~~~~~~~~~~~~~~~ hits.h:927:19: warning: ‘std::ifstream PrecomputedExpressionHitFactory::_ifs’ [-Wreorder] 927 | std::ifstream _ifs; | ^~~~ In file included from gtf_to_sam.cpp:22: hits.h:814:5: warning: when initialized here [-Wreorder] 814 | PrecomputedExpressionHitFactory(const string& expression_file_name, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from differential.h:29, from cuffdiff.cpp:36: replicates.h: In member function ‘bool ReplicatedBundleFactory::next_bundle(HitBundle&, bool)’: replicates.h:224:57: warning: unused variable ‘s2’ [-Wunused-variable] 224 | const vector >& s2 = bundles[i-1]->ref_scaffolds(); | ^~ In file included from cuffdiff.cpp:36: differential.h: In constructor ‘TrackingDataWriter::TrackingDataWriter(int, Outfiles*, Tracking*, const std::vector >&, std::vector >, ProgressBar*)’: differential.h:225:20: warning: ‘TrackingDataWriter::sample_labels’ will be initialized after [-Wreorder] 225 | vector sample_labels; | ^~~~~~~~~~~~~ differential.h:224:10: warning: ‘bool TrackingDataWriter::headers_written’ [-Wreorder] 224 | bool headers_written; // this flag records whether we've written out the file headers yet. | ^~~~~~~~~~~~~~~ differential.h:202:5: warning: when initialized here [-Wreorder] 202 | TrackingDataWriter(int num_samples, | ^~~~~~~~~~~~~~~~~~ In file included from cuffdiff.cpp:36: differential.h: In member function ‘void TrackingDataWriter::print_FPKM_tracking(const string&, FILE*, const FPKMTrackingTable&)’: differential.h:316:29: warning: variable ‘status’ set but not used [-Wunused-but-set-variable] 316 | AbundanceStatus status = NUMERIC_OK; | ^~~~~~ differential.h: In member function ‘void TrackingDataWriter::print_count_tracking(const string&, FILE*, const FPKMTrackingTable&)’: differential.h:397:29: warning: variable ‘status’ set but not used [-Wunused-but-set-variable] 397 | AbundanceStatus status = NUMERIC_OK; | ^~~~~~ cuffdiff.cpp: In function ‘void print_FPKM_tracking(FILE*, const FPKMTrackingTable&)’: cuffdiff.cpp:651:25: warning: variable ‘status’ set but not used [-Wunused-but-set-variable] 651 | AbundanceStatus status = NUMERIC_OK; | ^~~~~~ cuffdiff.cpp: In function ‘void print_count_tracking(FILE*, const FPKMTrackingTable&)’: cuffdiff.cpp:742:25: warning: variable ‘status’ set but not used [-Wunused-but-set-variable] 742 | AbundanceStatus status = NUMERIC_OK; | ^~~~~~ gtf_to_sam.cpp: In function ‘void print_scaff_as_sam(FILE*, const RefSequenceTable&, const Scaffold&)’: gtf_to_sam.cpp:142:70: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘RefID’ {aka ‘long unsigned int’} [-Wformat=] 142 | fprintf(stderr, "Warning: Could not find contig name for ID %d, skipping\n", scaff.ref_id()); | ~^ ~~~~~~~~~~~~~~ | | | | int RefID {aka long unsigned int} | %ld cuffdiff.cpp: In function ‘void driver(FILE*, FILE*, FILE*, FILE*, std::vector >&, Outfiles&)’: cuffdiff.cpp:1700:9: warning: variable ‘most_reps_idx’ set but not used [-Wunused-but-set-variable] 1700 | int most_reps_idx = 0; | ^~~~~~~~~~~~~ cuffdiff.cpp:1702:10: warning: variable ‘single_replicate_fac’ set but not used [-Wunused-but-set-variable] 1702 | bool single_replicate_fac = false; | ^~~~~~~~~~~~~~~~~~~~ cuffdiff.cpp: In function ‘int main(int, char**)’: cuffdiff.cpp:2363:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2363 | if (random_seed == -1) | ^~ cuffdiff.cpp:2368:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2368 | srand48(random_seed); | ^~~~~~~ In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:10, from gtf_tracking.h:12, from bundles.h:22, from gtf_to_sam.cpp:23: GVec.hh: In instantiation of ‘void GVec::Grow(int, OBJ&) [with OBJ = GISeg]’: GVec.hh:422:9: required from ‘void GVec::Insert(int, OBJ*) [with OBJ = GISeg]’ GVec.hh:81:48: required from ‘void GVec::idxInsert(int, OBJ&) [with OBJ = GISeg]’ gtf_tracking.h:210:29: required from here GVec.hh:350:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class GISeg’; use assignment or value-initialization instead [-Wclass-memaccess] 350 | memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from bundles.h:22, from gtf_to_sam.cpp:23: gtf_tracking.h:188:7: note: ‘class GISeg’ declared here 188 | class GISeg: public GSeg { | ^~~~~ In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:10, from gtf_tracking.h:12, from bundles.h:22, from gtf_to_sam.cpp:23: GVec.hh: In instantiation of ‘void GVec::Grow(int, OBJ&) [with OBJ = GXSeg]’: GVec.hh:422:9: required from ‘void GVec::Insert(int, OBJ*) [with OBJ = GXSeg]’ GVec.hh:79:44: required from ‘void GVec::Insert(int, OBJ) [with OBJ = GXSeg]’ GList.hh:230:21: required from ‘int GArray::Add(OBJ*) [with OBJ = GXSeg]’ GList.hh:51:36: required from ‘int GArray::Add(OBJ&) [with OBJ = GXSeg]’ gtf_tracking.h:419:20: required from here GVec.hh:350:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class GXSeg’; use assignment or value-initialization instead [-Wclass-memaccess] 350 | memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from bundles.h:22, from gtf_to_sam.cpp:23: gtf_tracking.h:359:7: note: ‘class GXSeg’ declared here 359 | class GXSeg : public GSeg { | ^~~~~ In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:10, from gtf_tracking.h:12, from bundles.h:22, from gtf_to_sam.cpp:23: GVec.hh: In instantiation of ‘void GVec::Grow(int, OBJ&) [with OBJ = GSeg]’: GVec.hh:422:9: required from ‘void GVec::Insert(int, OBJ*) [with OBJ = GSeg]’ GVec.hh:79:44: required from ‘void GVec::Insert(int, OBJ) [with OBJ = GSeg]’ GList.hh:230:21: required from ‘int GArray::Add(OBJ*) [with OBJ = GSeg]’ GList.hh:51:36: required from ‘int GArray::Add(OBJ&) [with OBJ = GSeg]’ gtf_tracking.h:420:19: required from here GVec.hh:350:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class GSeg’; use assignment or value-initialization instead [-Wclass-memaccess] 350 | memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from gff.h:7, from gtf_tracking.h:12, from bundles.h:22, from gtf_to_sam.cpp:23: GBase.h:279:7: note: ‘class GSeg’ declared here 279 | class GSeg { | ^~~~ In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:10, from gtf_tracking.h:12, from bundles.h:22, from cuffdiff.cpp:19: GVec.hh: In instantiation of ‘void GVec::Grow(int, OBJ&) [with OBJ = GISeg]’: GVec.hh:422:9: required from ‘void GVec::Insert(int, OBJ*) [with OBJ = GISeg]’ GVec.hh:81:48: required from ‘void GVec::idxInsert(int, OBJ&) [with OBJ = GISeg]’ gtf_tracking.h:210:29: required from here GVec.hh:350:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class GISeg’; use assignment or value-initialization instead [-Wclass-memaccess] 350 | memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from bundles.h:22, from cuffdiff.cpp:19: gtf_tracking.h:188:7: note: ‘class GISeg’ declared here 188 | class GISeg: public GSeg { | ^~~~~ In file included from compress_gtf.cpp:23: hits.h: In constructor ‘PrecomputedExpressionHitFactory::PrecomputedExpressionHitFactory(const string&, ReadTable&, RefSequenceTable&)’: hits.h:928:12: warning: ‘PrecomputedExpressionHitFactory::_expression_file_name’ will be initialized after [-Wreorder] 928 | string _expression_file_name; | ^~~~~~~~~~~~~~~~~~~~~ hits.h:927:19: warning: ‘std::ifstream PrecomputedExpressionHitFactory::_ifs’ [-Wreorder] 927 | std::ifstream _ifs; | ^~~~ In file included from compress_gtf.cpp:23: hits.h:814:5: warning: when initialized here [-Wreorder] 814 | PrecomputedExpressionHitFactory(const string& expression_file_name, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -g -O2 -fdebug-prefix-map=/<>/cufflinks-2.2.1+dfsg.1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o gffread.o gffread.cpp In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:10, from gtf_tracking.h:12, from bundles.h:22, from cuffdiff.cpp:19: GVec.hh: In instantiation of ‘void GVec::Grow(int, OBJ&) [with OBJ = GXSeg]’: GVec.hh:422:9: required from ‘void GVec::Insert(int, OBJ*) [with OBJ = GXSeg]’ GVec.hh:79:44: required from ‘void GVec::Insert(int, OBJ) [with OBJ = GXSeg]’ GList.hh:230:21: required from ‘int GArray::Add(OBJ*) [with OBJ = GXSeg]’ GList.hh:51:36: required from ‘int GArray::Add(OBJ&) [with OBJ = GXSeg]’ gtf_tracking.h:419:20: required from here GVec.hh:350:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class GXSeg’; use assignment or value-initialization instead [-Wclass-memaccess] 350 | memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from bundles.h:22, from cuffdiff.cpp:19: gtf_tracking.h:359:7: note: ‘class GXSeg’ declared here 359 | class GXSeg : public GSeg { | ^~~~~ In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:10, from gtf_tracking.h:12, from bundles.h:22, from cuffdiff.cpp:19: GVec.hh: In instantiation of ‘void GVec::Grow(int, OBJ&) [with OBJ = GSeg]’: GVec.hh:422:9: required from ‘void GVec::Insert(int, OBJ*) [with OBJ = GSeg]’ GVec.hh:79:44: required from ‘void GVec::Insert(int, OBJ) [with OBJ = GSeg]’ GList.hh:230:21: required from ‘int GArray::Add(OBJ*) [with OBJ = GSeg]’ GList.hh:51:36: required from ‘int GArray::Add(OBJ&) [with OBJ = GSeg]’ gtf_tracking.h:420:19: required from here GVec.hh:350:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class GSeg’; use assignment or value-initialization instead [-Wclass-memaccess] 350 | memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from gff.h:7, from gtf_tracking.h:12, from bundles.h:22, from cuffdiff.cpp:19: GBase.h:279:7: note: ‘class GSeg’ declared here 279 | class GSeg { | ^~~~ In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:10, from gff_utils.h:3, from gffread.cpp:2: GVec.hh: In instantiation of ‘void GVec::Grow(int, OBJ&) [with OBJ = GSeg]’: GVec.hh:422:9: required from ‘void GVec::Insert(int, OBJ*) [with OBJ = GSeg]’ GVec.hh:79:44: required from ‘void GVec::Insert(int, OBJ) [with OBJ = GSeg]’ GList.hh:230:21: required from ‘int GArray::Add(OBJ*) [with OBJ = GSeg]’ GList.hh:51:36: required from ‘int GArray::Add(OBJ&) [with OBJ = GSeg]’ gff_utils.h:321:31: required from here GVec.hh:350:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class GSeg’; use assignment or value-initialization instead [-Wclass-memaccess] 350 | memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from gff.h:7, from gff_utils.h:3, from gffread.cpp:2: GBase.h:279:7: note: ‘class GSeg’ declared here 279 | class GSeg { | ^~~~ In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:10, from gtf_tracking.h:12, from bundles.h:22, from compress_gtf.cpp:24: GVec.hh: In instantiation of ‘void GVec::Grow(int, OBJ&) [with OBJ = GISeg]’: GVec.hh:422:9: required from ‘void GVec::Insert(int, OBJ*) [with OBJ = GISeg]’ GVec.hh:81:48: required from ‘void GVec::idxInsert(int, OBJ&) [with OBJ = GISeg]’ gtf_tracking.h:210:29: required from here GVec.hh:350:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class GISeg’; use assignment or value-initialization instead [-Wclass-memaccess] 350 | memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from bundles.h:22, from compress_gtf.cpp:24: gtf_tracking.h:188:7: note: ‘class GISeg’ declared here 188 | class GISeg: public GSeg { | ^~~~~ In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:10, from gtf_tracking.h:12, from bundles.h:22, from compress_gtf.cpp:24: GVec.hh: In instantiation of ‘void GVec::Grow(int, OBJ&) [with OBJ = GXSeg]’: GVec.hh:422:9: required from ‘void GVec::Insert(int, OBJ*) [with OBJ = GXSeg]’ GVec.hh:79:44: required from ‘void GVec::Insert(int, OBJ) [with OBJ = GXSeg]’ GList.hh:230:21: required from ‘int GArray::Add(OBJ*) [with OBJ = GXSeg]’ GList.hh:51:36: required from ‘int GArray::Add(OBJ&) [with OBJ = GXSeg]’ gtf_tracking.h:419:20: required from here GVec.hh:350:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class GXSeg’; use assignment or value-initialization instead [-Wclass-memaccess] 350 | memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from bundles.h:22, from compress_gtf.cpp:24: gtf_tracking.h:359:7: note: ‘class GXSeg’ declared here 359 | class GXSeg : public GSeg { | ^~~~~ In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:10, from gtf_tracking.h:12, from bundles.h:22, from compress_gtf.cpp:24: GVec.hh: In instantiation of ‘void GVec::Grow(int, OBJ&) [with OBJ = GSeg]’: GVec.hh:422:9: required from ‘void GVec::Insert(int, OBJ*) [with OBJ = GSeg]’ GVec.hh:79:44: required from ‘void GVec::Insert(int, OBJ) [with OBJ = GSeg]’ GList.hh:230:21: required from ‘int GArray::Add(OBJ*) [with OBJ = GSeg]’ GList.hh:51:36: required from ‘int GArray::Add(OBJ&) [with OBJ = GSeg]’ gtf_tracking.h:420:19: required from here GVec.hh:350:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class GSeg’; use assignment or value-initialization instead [-Wclass-memaccess] 350 | memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from gff.h:7, from gtf_tracking.h:12, from bundles.h:22, from compress_gtf.cpp:24: GBase.h:279:7: note: ‘class GSeg’ declared here 279 | class GSeg { | ^~~~ g++ -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -g -O2 -fdebug-prefix-map=/<>/cufflinks-2.2.1+dfsg.1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o cuffquant.o cuffquant.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -g -O2 -fdebug-prefix-map=/<>/cufflinks-2.2.1+dfsg.1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o cuffnorm.o cuffnorm.cpp In file included from cuffquant.cpp:19: hits.h: In constructor ‘PrecomputedExpressionHitFactory::PrecomputedExpressionHitFactory(const string&, ReadTable&, RefSequenceTable&)’: hits.h:928:12: warning: ‘PrecomputedExpressionHitFactory::_expression_file_name’ will be initialized after [-Wreorder] 928 | string _expression_file_name; | ^~~~~~~~~~~~~~~~~~~~~ hits.h:927:19: warning: ‘std::ifstream PrecomputedExpressionHitFactory::_ifs’ [-Wreorder] 927 | std::ifstream _ifs; | ^~~~ In file included from cuffquant.cpp:19: hits.h:814:5: warning: when initialized here [-Wreorder] 814 | PrecomputedExpressionHitFactory(const string& expression_file_name, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from cuffquant.cpp:24: update_check.h: In function ‘bool get_current_version(char*)’: update_check.h:81:22: warning: argument to ‘sizeof’ in ‘void bzero(void*, size_t)’ call is the same expression as the destination; did you mean to provide an explicit length? [-Wsizeof-pointer-memaccess] 81 | bzero(curr_version, sizeof(curr_version)); | ^~~~~~~~~~~~~~~~~~~~ rm -f libcufflinks.a ar cru libcufflinks.a clustering.o differential.o common.o assemble.o tokenize.o abundances.o scaffolds.o hits.o genes.o bundles.o filters.o scaffold_graph.o matching_merge.o graph_optimize.o biascorrection.o sampling.o adap.o ar_funs.o arith.o band.o c_args.o c_plot.o cmd.o dens_haz.o dens_int.o dens_odi.o density.o dist.o ev_atree.o ev_interp.o ev_kdtre.o ev_main.o ev_trian.o family.o fitted.o frend.o help.o lf_dercor.o lf_fitfun.o lf_robust.o lf_vari.o lfd.o lfstr.o linalg.o locfit.o m_chol.o m_eigen.o m_jacob.o m_max.o makecmd.o math.o minmax.o nbhd.o pcomp.o pout.o preplot.o random.o readfile.o scb.o scb_cons.o simul.o solve.o startlf.o strings.o vari.o wdiag.o weight.o replicates.o multireads.o jensen_shannon.o tracking.o ar: `u' modifier ignored since `D' is the default (see `U') In file included from cuffquant.cpp:37: replicates.h: In member function ‘bool ReplicatedBundleFactory::next_bundle(HitBundle&, bool)’: replicates.h:224:57: warning: unused variable ‘s2’ [-Wunused-variable] 224 | const vector >& s2 = bundles[i-1]->ref_scaffolds(); | ^~ cuffquant.cpp: In function ‘void print_FPKM_tracking(FILE*, const FPKMTrackingTable&)’: cuffquant.cpp:423:25: warning: variable ‘status’ set but not used [-Wunused-but-set-variable] 423 | AbundanceStatus status = NUMERIC_OK; | ^~~~~~ cuffquant.cpp: In function ‘void print_count_tracking(FILE*, const FPKMTrackingTable&)’: cuffquant.cpp:514:25: warning: variable ‘status’ set but not used [-Wunused-but-set-variable] 514 | AbundanceStatus status = NUMERIC_OK; | ^~~~~~ cuffquant.cpp: In member function ‘void AbundanceRecorder::record_tracking_data(int, std::vector >&)’: cuffquant.cpp:746:31: warning: unused variable ‘s2’ [-Wunused-variable] 746 | const AbundanceGroup& s2 = prev.transcripts; | ^~ cuffquant.cpp:764:25: warning: unused variable ‘ab_group’ [-Wunused-variable] 764 | const AbundanceGroup& ab_group = abundances[i]->transcripts; | ^~~~~~~~ cuffquant.cpp: In function ‘void driver(const string&, const string&, FILE*, std::vector >&, Outfiles&)’: cuffquant.cpp:1423:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1423 | for (int i = 0; i < single_sample_tracking.size(); ++i) | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cuffquant.cpp: In function ‘int main(int, char**)’: cuffquant.cpp:1539:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1539 | if (random_seed == -1) | ^~ cuffquant.cpp:1544:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1544 | srand48(random_seed); | ^~~~~~~ ranlib libcufflinks.a rm -f libgc.a ar cru libgc.a codons.o GArgs.o GBase.o gdna.o GStr.o GFaSeqGet.o GFastaIndex.o gff.o gff_utils.o gtf_tracking.o ar: `u' modifier ignored since `D' is the default (see `U') ranlib libgc.a g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -g -O2 -fdebug-prefix-map=/<>/cufflinks-2.2.1+dfsg.1=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -L/usr/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o cufflinks cufflinks.o libcufflinks.a libgc.a -lbam -lz -lboost_system -lboost_thread -lboost_serialization /usr/bin/ld: libcufflinks.a(c_plot.o):./src/locfit/c_plot.c:12: multiple definition of `curwin'; libcufflinks.a(startlf.o):./src/locfit/startlf.c:236: first defined here In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:10, from gtf_tracking.h:12, from bundles.h:22, from cuffquant.cpp:20: GVec.hh: In instantiation of ‘void GVec::Grow(int, OBJ&) [with OBJ = GISeg]’: GVec.hh:422:9: required from ‘void GVec::Insert(int, OBJ*) [with OBJ = GISeg]’ GVec.hh:81:48: required from ‘void GVec::idxInsert(int, OBJ&) [with OBJ = GISeg]’ gtf_tracking.h:210:29: required from here GVec.hh:350:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class GISeg’; use assignment or value-initialization instead [-Wclass-memaccess] 350 | memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from bundles.h:22, from cuffquant.cpp:20: gtf_tracking.h:188:7: note: ‘class GISeg’ declared here 188 | class GISeg: public GSeg { | ^~~~~ In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:10, from gtf_tracking.h:12, from bundles.h:22, from cuffquant.cpp:20: GVec.hh: In instantiation of ‘void GVec::Grow(int, OBJ&) [with OBJ = GXSeg]’: GVec.hh:422:9: required from ‘void GVec::Insert(int, OBJ*) [with OBJ = GXSeg]’ GVec.hh:79:44: required from ‘void GVec::Insert(int, OBJ) [with OBJ = GXSeg]’ GList.hh:230:21: required from ‘int GArray::Add(OBJ*) [with OBJ = GXSeg]’ GList.hh:51:36: required from ‘int GArray::Add(OBJ&) [with OBJ = GXSeg]’ gtf_tracking.h:419:20: required from here GVec.hh:350:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class GXSeg’; use assignment or value-initialization instead [-Wclass-memaccess] 350 | memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from bundles.h:22, from cuffquant.cpp:20: gtf_tracking.h:359:7: note: ‘class GXSeg’ declared here 359 | class GXSeg : public GSeg { | ^~~~~ In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:10, from gtf_tracking.h:12, from bundles.h:22, from cuffquant.cpp:20: GVec.hh: In instantiation of ‘void GVec::Grow(int, OBJ&) [with OBJ = GSeg]’: GVec.hh:422:9: required from ‘void GVec::Insert(int, OBJ*) [with OBJ = GSeg]’ GVec.hh:79:44: required from ‘void GVec::Insert(int, OBJ) [with OBJ = GSeg]’ GList.hh:230:21: required from ‘int GArray::Add(OBJ*) [with OBJ = GSeg]’ GList.hh:51:36: required from ‘int GArray::Add(OBJ&) [with OBJ = GSeg]’ gtf_tracking.h:420:19: required from here GVec.hh:350:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class GSeg’; use assignment or value-initialization instead [-Wclass-memaccess] 350 | memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from gff.h:7, from gtf_tracking.h:12, from bundles.h:22, from cuffquant.cpp:20: GBase.h:279:7: note: ‘class GSeg’ declared here 279 | class GSeg { | ^~~~ In file included from cuffnorm.cpp:18: hits.h: In constructor ‘PrecomputedExpressionHitFactory::PrecomputedExpressionHitFactory(const string&, ReadTable&, RefSequenceTable&)’: hits.h:928:12: warning: ‘PrecomputedExpressionHitFactory::_expression_file_name’ will be initialized after [-Wreorder] 928 | string _expression_file_name; | ^~~~~~~~~~~~~~~~~~~~~ hits.h:927:19: warning: ‘std::ifstream PrecomputedExpressionHitFactory::_ifs’ [-Wreorder] 927 | std::ifstream _ifs; | ^~~~ In file included from cuffnorm.cpp:18: hits.h:814:5: warning: when initialized here [-Wreorder] 814 | PrecomputedExpressionHitFactory(const string& expression_file_name, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ collect2: error: ld returned 1 exit status make[3]: *** [Makefile:802: cufflinks] Error 1 make[3]: *** Waiting for unfinished jobs.... cuffdiff.cpp:2448:35: warning: ‘isoform_exp.diff’ directive writing 16 bytes into a region of size between 1 and 2048 [-Wformat-overflow=] 2448 | sprintf(iso_out_file_name, "%sisoform_exp.diff", out_file_prefix); | ^~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:867, from /usr/include/c++/10/cstdio:42, from /usr/include/c++/10/ext/string_conversions.h:43, from /usr/include/c++/10/bits/basic_string.h:6535, from /usr/include/c++/10/string:55, from cuffdiff.cpp:12: /usr/include/s390x-linux-gnu/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 17 and 2064 bytes into a destination of size 2048 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cuffdiff.cpp:2458:37: warning: ‘tss_group_exp.diff’ directive writing 18 bytes into a region of size between 1 and 2048 [-Wformat-overflow=] 2458 | sprintf(group_out_file_name, "%stss_group_exp.diff", out_file_prefix); | ^~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:867, from /usr/include/c++/10/cstdio:42, from /usr/include/c++/10/ext/string_conversions.h:43, from /usr/include/c++/10/bits/basic_string.h:6535, from /usr/include/c++/10/string:55, from cuffdiff.cpp:12: /usr/include/s390x-linux-gnu/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 19 and 2066 bytes into a destination of size 2048 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cuffdiff.cpp:2468:36: warning: ‘gene_exp.diff’ directive writing 13 bytes into a region of size between 1 and 2048 [-Wformat-overflow=] 2468 | sprintf(gene_out_file_name, "%sgene_exp.diff", out_file_prefix); | ^~~~~~~~~~~~~ In file included from /usr/include/stdio.h:867, from /usr/include/c++/10/cstdio:42, from /usr/include/c++/10/ext/string_conversions.h:43, from /usr/include/c++/10/bits/basic_string.h:6535, from /usr/include/c++/10/string:55, from cuffdiff.cpp:12: /usr/include/s390x-linux-gnu/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 14 and 2061 bytes into a destination of size 2048 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cuffdiff.cpp:2478:35: warning: ‘cds_exp.diff’ directive writing 12 bytes into a region of size between 1 and 2048 [-Wformat-overflow=] 2478 | sprintf(cds_out_file_name, "%scds_exp.diff", out_file_prefix); | ^~~~~~~~~~~~ In file included from /usr/include/stdio.h:867, from /usr/include/c++/10/cstdio:42, from /usr/include/c++/10/ext/string_conversions.h:43, from /usr/include/c++/10/bits/basic_string.h:6535, from /usr/include/c++/10/string:55, from cuffdiff.cpp:12: /usr/include/s390x-linux-gnu/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 13 and 2060 bytes into a destination of size 2048 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cuffdiff.cpp:2488:45: warning: ‘splicing.diff’ directive writing 13 bytes into a region of size between 1 and 2048 [-Wformat-overflow=] 2488 | sprintf(diff_splicing_out_file_name, "%ssplicing.diff", out_file_prefix); | ^~~~~~~~~~~~~ In file included from /usr/include/stdio.h:867, from /usr/include/c++/10/cstdio:42, from /usr/include/c++/10/ext/string_conversions.h:43, from /usr/include/c++/10/bits/basic_string.h:6535, from /usr/include/c++/10/string:55, from cuffdiff.cpp:12: /usr/include/s390x-linux-gnu/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 14 and 2061 bytes into a destination of size 2048 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cuffdiff.cpp:2498:45: warning: ‘promoters.diff’ directive writing 14 bytes into a region of size between 1 and 2048 [-Wformat-overflow=] 2498 | sprintf(diff_promoter_out_file_name, "%spromoters.diff", out_file_prefix); | ^~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:867, from /usr/include/c++/10/cstdio:42, from /usr/include/c++/10/ext/string_conversions.h:43, from /usr/include/c++/10/bits/basic_string.h:6535, from /usr/include/c++/10/string:55, from cuffdiff.cpp:12: /usr/include/s390x-linux-gnu/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 15 and 2062 bytes into a destination of size 2048 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cuffdiff.cpp:2508:40: warning: ‘cds.diff’ directive writing 8 bytes into a region of size between 1 and 2048 [-Wformat-overflow=] 2508 | sprintf(diff_cds_out_file_name, "%scds.diff", out_file_prefix); | ^~~~~~~~ In file included from /usr/include/stdio.h:867, from /usr/include/c++/10/cstdio:42, from /usr/include/c++/10/ext/string_conversions.h:43, from /usr/include/c++/10/bits/basic_string.h:6535, from /usr/include/c++/10/string:55, from cuffdiff.cpp:12: /usr/include/s390x-linux-gnu/bits/stdio2.h:36:34: note: ‘__builtin___sprintf_chk’ output between 9 and 2056 bytes into a destination of size 2048 36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 37 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from cuffnorm.cpp:23: update_check.h: In function ‘bool get_current_version(char*)’: update_check.h:81:22: warning: argument to ‘sizeof’ in ‘void bzero(void*, size_t)’ call is the same expression as the destination; did you mean to provide an explicit length? [-Wsizeof-pointer-memaccess] 81 | bzero(curr_version, sizeof(curr_version)); | ^~~~~~~~~~~~~~~~~~~~ In file included from differential.h:29, from cuffnorm.cpp:36: replicates.h: In member function ‘bool ReplicatedBundleFactory::next_bundle(HitBundle&, bool)’: replicates.h:224:57: warning: unused variable ‘s2’ [-Wunused-variable] 224 | const vector >& s2 = bundles[i-1]->ref_scaffolds(); | ^~ In file included from cuffnorm.cpp:36: differential.h: In constructor ‘TrackingDataWriter::TrackingDataWriter(int, Outfiles*, Tracking*, const std::vector >&, std::vector >, ProgressBar*)’: differential.h:225:20: warning: ‘TrackingDataWriter::sample_labels’ will be initialized after [-Wreorder] 225 | vector sample_labels; | ^~~~~~~~~~~~~ differential.h:224:10: warning: ‘bool TrackingDataWriter::headers_written’ [-Wreorder] 224 | bool headers_written; // this flag records whether we've written out the file headers yet. | ^~~~~~~~~~~~~~~ differential.h:202:5: warning: when initialized here [-Wreorder] 202 | TrackingDataWriter(int num_samples, | ^~~~~~~~~~~~~~~~~~ In file included from cuffnorm.cpp:36: differential.h: In member function ‘void TrackingDataWriter::print_FPKM_tracking(const string&, FILE*, const FPKMTrackingTable&)’: differential.h:316:29: warning: variable ‘status’ set but not used [-Wunused-but-set-variable] 316 | AbundanceStatus status = NUMERIC_OK; | ^~~~~~ differential.h: In member function ‘void TrackingDataWriter::print_count_tracking(const string&, FILE*, const FPKMTrackingTable&)’: differential.h:397:29: warning: variable ‘status’ set but not used [-Wunused-but-set-variable] 397 | AbundanceStatus status = NUMERIC_OK; | ^~~~~~ cuffnorm.cpp: In function ‘int main(int, char**)’: cuffnorm.cpp:1211:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 1211 | if (random_seed == -1) | ^~ cuffnorm.cpp:1216:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 1216 | srand48(random_seed); | ^~~~~~~ In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:10, from gtf_tracking.h:12, from bundles.h:22, from cuffnorm.cpp:19: GVec.hh: In instantiation of ‘void GVec::Grow(int, OBJ&) [with OBJ = GISeg]’: GVec.hh:422:9: required from ‘void GVec::Insert(int, OBJ*) [with OBJ = GISeg]’ GVec.hh:81:48: required from ‘void GVec::idxInsert(int, OBJ&) [with OBJ = GISeg]’ gtf_tracking.h:210:29: required from here GVec.hh:350:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class GISeg’; use assignment or value-initialization instead [-Wclass-memaccess] 350 | memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from bundles.h:22, from cuffnorm.cpp:19: gtf_tracking.h:188:7: note: ‘class GISeg’ declared here 188 | class GISeg: public GSeg { | ^~~~~ In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:10, from gtf_tracking.h:12, from bundles.h:22, from cuffnorm.cpp:19: GVec.hh: In instantiation of ‘void GVec::Grow(int, OBJ&) [with OBJ = GXSeg]’: GVec.hh:422:9: required from ‘void GVec::Insert(int, OBJ*) [with OBJ = GXSeg]’ GVec.hh:79:44: required from ‘void GVec::Insert(int, OBJ) [with OBJ = GXSeg]’ GList.hh:230:21: required from ‘int GArray::Add(OBJ*) [with OBJ = GXSeg]’ GList.hh:51:36: required from ‘int GArray::Add(OBJ&) [with OBJ = GXSeg]’ gtf_tracking.h:419:20: required from here GVec.hh:350:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class GXSeg’; use assignment or value-initialization instead [-Wclass-memaccess] 350 | memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from bundles.h:22, from cuffnorm.cpp:19: gtf_tracking.h:359:7: note: ‘class GXSeg’ declared here 359 | class GXSeg : public GSeg { | ^~~~~ In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:10, from gtf_tracking.h:12, from bundles.h:22, from cuffnorm.cpp:19: GVec.hh: In instantiation of ‘void GVec::Grow(int, OBJ&) [with OBJ = GSeg]’: GVec.hh:422:9: required from ‘void GVec::Insert(int, OBJ*) [with OBJ = GSeg]’ GVec.hh:79:44: required from ‘void GVec::Insert(int, OBJ) [with OBJ = GSeg]’ GList.hh:230:21: required from ‘int GArray::Add(OBJ*) [with OBJ = GSeg]’ GList.hh:51:36: required from ‘int GArray::Add(OBJ&) [with OBJ = GSeg]’ gtf_tracking.h:420:19: required from here GVec.hh:350:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class GSeg’; use assignment or value-initialization instead [-Wclass-memaccess] 350 | memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from gff.h:7, from gtf_tracking.h:12, from bundles.h:22, from cuffnorm.cpp:19: GBase.h:279:7: note: ‘class GSeg’ declared here 279 | class GSeg { | ^~~~ In file included from bundles.h:23, from cuffquant.cpp:20: progressbar.h: In member function ‘void AbundanceRecorder::record_finished_loci()’: progressbar.h:70:57: warning: ‘%3d’ directive output may be truncated writing between 3 and 11 bytes into a region of size between 6 and 33 [-Wformat-truncation=] 70 | snprintf(line_buf, 82, "\r> Processing Locus %-27s %s %3d%%", bundle_buf, _bar_buf, percent); | ^~~ progressbar.h:70:26: note: directive argument in the range [-2147483648, 99] 70 | snprintf(line_buf, 82, "\r> Processing Locus %-27s %s %3d%%", bundle_buf, _bar_buf, percent); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:867, from /usr/include/c++/10/cstdio:42, from /usr/include/c++/10/ext/string_conversions.h:43, from /usr/include/c++/10/bits/basic_string.h:6535, from /usr/include/c++/10/string:55, from cuffquant.cpp:12: /usr/include/s390x-linux-gnu/bits/stdio2.h:67:35: note: ‘__builtin___snprintf_chk’ output between 54 and 89 bytes into a destination of size 82 67 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 68 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ make[3]: Leaving directory '/<>/cufflinks-2.2.1+dfsg.1/src' make[2]: *** [Makefile:400: all-recursive] Error 1 make[2]: Leaving directory '/<>/cufflinks-2.2.1+dfsg.1' make[1]: *** [Makefile:341: all] Error 2 make[1]: Leaving directory '/<>/cufflinks-2.2.1+dfsg.1' dh_auto_build: error: make -j4 returned exit code 2 make: *** [debian/rules:10: binary-arch] Error 25 dpkg-buildpackage: error: debian/rules binary-arch subprocess returned exit status 2 -------------------------------------------------------------------------------- Build finished at 20200803-1626 Finished -------- E: Build failure (dpkg-buildpackage died) +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: s390x Build-Space: 386688 Build-Time: 89 Distribution: groovy Fail-Stage: build Host Architecture: s390x Install-Time: 11 Job: cufflinks_2.2.1+dfsg.1-7.dsc Machine Architecture: s390x Package: cufflinks Package-Time: 100 Source-Version: 2.2.1+dfsg.1-7 Space: 386688 Status: attempted Version: 2.2.1+dfsg.1-7 -------------------------------------------------------------------------------- Finished at 20200803-1626 Build needed 00:01:40, 386688k disc space RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=groovy --arch=s390x PACKAGEBUILD-19659198 Scanning for processes to kill in build PACKAGEBUILD-19659198