https://launchpad.net/ubuntu/+archive/test-rebuild-20210805-impish/+build/21852219 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux bos02-s390x-014 4.15.0-154-generic #161-Ubuntu SMP Fri Jul 30 12:59:37 UTC 2021 s390x Buildd toolchain package versions: launchpad-buildd_200~495~ubuntu18.04.1 python3-lpbuildd_200~495~ubuntu18.04.1 sbuild_0.75.0-1ubuntu1 bzr-builder_0.7.3+bzr174~ppa13~ubuntu16.04.1 bzr_2.7.0+bzr6622-10 git-build-recipe_0.3.6~git201906051340.ff11471~ubuntu18.04.1 git_1:2.17.1-1ubuntu0.8 dpkg-dev_1.19.0.5ubuntu2.3 python-debian_0.1.32 python3-debian_0.1.32. Syncing the system clock with the buildd NTP service... 3 Sep 00:30:33 ntpdate[1721]: adjust time server 10.211.37.1 offset 0.434384 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=impish --arch=s390x PACKAGEBUILD-21852219 --image-type chroot /home/buildd/filecache-default/b6a0d461e155d890cb32ede1aba203da854405ed Creating target for build PACKAGEBUILD-21852219 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=impish --arch=s390x PACKAGEBUILD-21852219 Starting target for build PACKAGEBUILD-21852219 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=impish --arch=s390x PACKAGEBUILD-21852219 'deb http://ppa.launchpad.net/ubuntu-toolchain-r/volatile/ubuntu impish main' 'deb http://ftpmaster.internal/ubuntu impish main restricted universe multiverse' Overriding sources.list in build-PACKAGEBUILD-21852219 RUN: /usr/share/launchpad-buildd/bin/in-target add-trusted-keys --backend=chroot --series=impish --arch=s390x PACKAGEBUILD-21852219 Adding trusted keys to build-PACKAGEBUILD-21852219 Warning: apt-key is deprecated. Manage keyring files in trusted.gpg.d instead (see apt-key(8)). OK Warning: apt-key is deprecated. Manage keyring files in trusted.gpg.d instead (see apt-key(8)). /etc/apt/trusted.gpg -------------------- pub rsa1024 2009-10-22 [SC] 60C3 1780 3A41 BA51 845E 371A 1E93 77A2 BA9E F27F uid [ unknown] Launchpad Toolchain builds /etc/apt/trusted.gpg.d/ubuntu-keyring-2012-cdimage.gpg ------------------------------------------------------ pub rsa4096 2012-05-11 [SC] 8439 38DF 228D 22F7 B374 2BC0 D94A A3F0 EFE2 1092 uid [ unknown] Ubuntu CD Image Automatic Signing Key (2012) /etc/apt/trusted.gpg.d/ubuntu-keyring-2018-archive.gpg ------------------------------------------------------ pub rsa4096 2018-09-17 [SC] F6EC B376 2474 EDA9 D21B 7022 8719 20D1 991B C93C uid [ unknown] Ubuntu Archive Automatic Signing Key (2018) RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=impish --arch=s390x PACKAGEBUILD-21852219 Updating target for build PACKAGEBUILD-21852219 Get:1 http://ppa.launchpad.net/ubuntu-toolchain-r/volatile/ubuntu impish InRelease [17.5 kB] Get:2 http://ftpmaster.internal/ubuntu impish InRelease [269 kB] Get:3 http://ppa.launchpad.net/ubuntu-toolchain-r/volatile/ubuntu impish/main s390x Packages [22.4 kB] Get:4 http://ftpmaster.internal/ubuntu impish/main s390x Packages [1340 kB] Get:5 http://ppa.launchpad.net/ubuntu-toolchain-r/volatile/ubuntu impish/main Translation-en [11.9 kB] Get:6 http://ftpmaster.internal/ubuntu impish/main Translation-en [513 kB] Get:7 http://ftpmaster.internal/ubuntu impish/restricted s390x Packages [4096 B] Get:8 http://ftpmaster.internal/ubuntu impish/restricted Translation-en [12.5 kB] Get:9 http://ftpmaster.internal/ubuntu impish/universe s390x Packages [12.5 MB] Get:10 http://ftpmaster.internal/ubuntu impish/universe Translation-en [5464 kB] Get:11 http://ftpmaster.internal/ubuntu impish/multiverse s390x Packages [157 kB] Get:12 http://ftpmaster.internal/ubuntu impish/multiverse Translation-en [108 kB] Fetched 20.4 MB in 4s (5301 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages were automatically installed and are no longer required: g++-10 libstdc++-10-dev Use 'sudo apt autoremove' to remove them. The following NEW packages will be installed: cpp-11 g++-11 gcc-11 libexpat1 libgcc-11-dev libmpdec3 libpython3-stdlib libpython3.9-minimal libpython3.9-stdlib libstdc++-11-dev media-types python3 python3-minimal python3-psutil python3.9 python3.9-minimal The following packages will be upgraded: advancecomp apt base-files base-passwd bash binutils binutils-common binutils-s390x-linux-gnu bsdutils build-essential cpp cpp-10 dash debconf diffutils dpkg dpkg-dev e2fsprogs findutils g++ g++-10 gcc gcc-10 gcc-10-base gcc-11-base gpg gpg-agent gpgconf gpgv gzip libapparmor1 libapt-pkg6.0 libasan6 libassuan0 libatomic1 libaudit-common libaudit1 libbinutils libblkid1 libc-bin libc-dev-bin libc6 libc6-dev libcc1-0 libcom-err2 libcrypt-dev libcrypt1 libctf-nobfd0 libctf0 libdb5.3 libdevmapper1.02.1 libdpkg-perl libext2fs2 libgcc-10-dev libgcc-s1 libgcrypt20 libgnutls30 libgomp1 libgssapi-krb5-2 libhogweed6 libidn2-0 libisl23 libitm1 libk5crypto3 libkmod2 libkrb5-3 libkrb5support0 liblz4-1 liblzma5 libmount1 libnettle8 libnsl-dev libnsl2 libpam-modules libpam-modules-bin libpam-runtime libpam0g libperl5.32 libprocps8 libreadline8 libsmartcols1 libsqlite3-0 libss2 libssl1.1 libstdc++-10-dev libstdc++6 libsystemd0 libubsan1 libudev1 libuuid1 libzstd1 linux-libc-dev login logsave lto-disabled-list mount openssl passwd perl perl-base perl-modules-5.32 pinentry-curses pkgbinarymangler procps readline-common systemd systemd-sysv systemd-timesyncd sysvinit-utils usrmerge util-linux xz-utils zlib1g 113 upgraded, 16 newly installed, 0 to remove and 0 not upgraded. Need to get 234 MB of archives. After this operation, 440 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu impish/main s390x libcrypt-dev s390x 1:4.4.18-4ubuntu1 [111 kB] Get:2 http://ppa.launchpad.net/ubuntu-toolchain-r/volatile/ubuntu impish/main s390x libc6-dev s390x 2.34-0ubuntu1~ppa5 [1546 kB] Get:3 http://ftpmaster.internal/ubuntu impish/main s390x libnsl-dev s390x 1.3.0-2 [67.5 kB] Get:4 http://ftpmaster.internal/ubuntu impish/main s390x libcrypt1 s390x 1:4.4.18-4ubuntu1 [84.8 kB] Get:5 http://ftpmaster.internal/ubuntu impish/main s390x libnsl2 s390x 1.3.0-2 [40.4 kB] Get:6 http://ftpmaster.internal/ubuntu impish/main s390x libasan6 s390x 11.2.0-1ubuntu2 [2229 kB] Get:7 http://ppa.launchpad.net/ubuntu-toolchain-r/volatile/ubuntu impish/main s390x libc-dev-bin s390x 2.34-0ubuntu1~ppa5 [19.9 kB] Get:8 http://ppa.launchpad.net/ubuntu-toolchain-r/volatile/ubuntu impish/main s390x linux-libc-dev s390x 5.13.0-14.14 [1214 kB] Get:9 http://ppa.launchpad.net/ubuntu-toolchain-r/volatile/ubuntu impish/main s390x libc6 s390x 2.34-0ubuntu1~ppa5 [2784 kB] Get:10 http://ftpmaster.internal/ubuntu impish/main s390x libubsan1 s390x 11.2.0-1ubuntu2 [909 kB] Get:11 http://ppa.launchpad.net/ubuntu-toolchain-r/volatile/ubuntu impish/main s390x libc-bin s390x 2.34-0ubuntu1~ppa5 [948 kB] Get:12 http://ftpmaster.internal/ubuntu impish/main s390x libitm1 s390x 11.2.0-1ubuntu2 [29.7 kB] Get:13 http://ftpmaster.internal/ubuntu impish/main s390x libgomp1 s390x 11.2.0-1ubuntu2 [113 kB] Get:14 http://ppa.launchpad.net/ubuntu-toolchain-r/volatile/ubuntu impish/main s390x dpkg s390x 1.20.9ubuntu13 [1290 kB] Get:15 http://ftpmaster.internal/ubuntu impish/main s390x gcc-11-base s390x 11.2.0-1ubuntu2 [21.5 kB] Get:16 http://ftpmaster.internal/ubuntu impish/main s390x libgcc-s1 s390x 11.2.0-1ubuntu2 [28.4 kB] Get:17 http://ftpmaster.internal/ubuntu impish/main s390x libcc1-0 s390x 11.2.0-1ubuntu2 [52.8 kB] Get:18 http://ftpmaster.internal/ubuntu impish/main s390x libatomic1 s390x 11.2.0-1ubuntu2 [9036 B] Get:19 http://ftpmaster.internal/ubuntu impish/main s390x libstdc++6 s390x 11.2.0-1ubuntu2 [689 kB] Get:20 http://ppa.launchpad.net/ubuntu-toolchain-r/volatile/ubuntu impish/main s390x g++ s390x 4:11.2.0-1ubuntu1 [1408 B] Get:21 http://ppa.launchpad.net/ubuntu-toolchain-r/volatile/ubuntu impish/main s390x gcc s390x 4:11.2.0-1ubuntu1 [5118 B] Get:22 http://ppa.launchpad.net/ubuntu-toolchain-r/volatile/ubuntu impish/main s390x cpp s390x 4:11.2.0-1ubuntu1 [27.7 kB] Get:23 http://ppa.launchpad.net/ubuntu-toolchain-r/volatile/ubuntu impish/main s390x dpkg-dev all 1.20.9ubuntu13 [938 kB] Get:24 http://ftpmaster.internal/ubuntu impish/main s390x base-files s390x 11.1ubuntu3 [60.8 kB] Get:25 http://ftpmaster.internal/ubuntu impish/main s390x bash s390x 5.1-3ubuntu1 [746 kB] Get:26 http://ppa.launchpad.net/ubuntu-toolchain-r/volatile/ubuntu impish/main s390x libdpkg-perl all 1.20.9ubuntu13 [235 kB] Get:27 http://ftpmaster.internal/ubuntu impish/main s390x bsdutils s390x 1:2.36.1-8ubuntu1 [82.2 kB] Get:28 http://ftpmaster.internal/ubuntu impish/main s390x libperl5.32 s390x 5.32.1-3ubuntu3 [4713 kB] Get:29 http://ftpmaster.internal/ubuntu impish/main s390x perl s390x 5.32.1-3ubuntu3 [227 kB] Get:30 http://ftpmaster.internal/ubuntu impish/main s390x perl-base s390x 5.32.1-3ubuntu3 [1701 kB] Get:31 http://ftpmaster.internal/ubuntu impish/main s390x perl-modules-5.32 all 5.32.1-3ubuntu3 [2945 kB] Get:32 http://ftpmaster.internal/ubuntu impish/main s390x libdb5.3 s390x 5.3.28+dfsg1-0.8ubuntu1 [638 kB] Get:33 http://ftpmaster.internal/ubuntu impish/main s390x zlib1g s390x 1:1.2.11.dfsg-2ubuntu7 [64.9 kB] Get:34 http://ftpmaster.internal/ubuntu impish/main s390x debconf all 1.5.77 [121 kB] Get:35 http://ftpmaster.internal/ubuntu impish/main s390x dash s390x 0.5.11+git20210120+802ebd4-1 [94.5 kB] Get:36 http://ftpmaster.internal/ubuntu impish/main s390x diffutils s390x 1:3.7-5ubuntu1 [206 kB] Get:37 http://ftpmaster.internal/ubuntu impish/main s390x findutils s390x 4.8.0-1ubuntu2 [353 kB] Get:38 http://ftpmaster.internal/ubuntu impish/main s390x gzip s390x 1.10-4ubuntu1 [102 kB] Get:39 http://ftpmaster.internal/ubuntu impish/main s390x login s390x 1:4.8.1-1ubuntu9 [223 kB] Get:40 http://ftpmaster.internal/ubuntu impish/main s390x util-linux s390x 2.36.1-8ubuntu1 [1010 kB] Get:41 http://ftpmaster.internal/ubuntu impish/main s390x base-passwd s390x 3.5.51 [49.3 kB] Get:42 http://ftpmaster.internal/ubuntu impish/main s390x sysvinit-utils s390x 2.96-7ubuntu1 [20.1 kB] Get:43 http://ftpmaster.internal/ubuntu impish/main s390x libgcrypt20 s390x 1.8.7-5ubuntu1 [401 kB] Get:44 http://ftpmaster.internal/ubuntu impish/main s390x liblz4-1 s390x 1.9.3-2 [55.8 kB] Get:45 http://ftpmaster.internal/ubuntu impish/main s390x liblzma5 s390x 5.2.5-2 [102 kB] Get:46 http://ftpmaster.internal/ubuntu impish/main s390x systemd-sysv s390x 248.3-1ubuntu3 [10.5 kB] Get:47 http://ftpmaster.internal/ubuntu impish/main s390x systemd-timesyncd s390x 248.3-1ubuntu3 [30.3 kB] Get:48 http://ftpmaster.internal/ubuntu impish/main s390x libapparmor1 s390x 3.0.3-0ubuntu1 [37.7 kB] Get:49 http://ftpmaster.internal/ubuntu impish/main s390x libaudit-common all 1:3.0-2ubuntu2 [4788 B] Get:50 http://ftpmaster.internal/ubuntu impish/main s390x libaudit1 s390x 1:3.0-2ubuntu2 [39.0 kB] Get:51 http://ftpmaster.internal/ubuntu impish/main s390x libnettle8 s390x 3.7.3-1 [157 kB] Get:52 http://ftpmaster.internal/ubuntu impish/main s390x libhogweed6 s390x 3.7.3-1 [194 kB] Get:53 http://ftpmaster.internal/ubuntu impish/main s390x libidn2-0 s390x 2.3.1-1 [49.5 kB] Get:54 http://ftpmaster.internal/ubuntu impish/main s390x libgnutls30 s390x 3.7.1-4ubuntu1 [903 kB] Get:55 http://ftpmaster.internal/ubuntu impish/main s390x libssl1.1 s390x 1.1.1j-1ubuntu5 [1247 kB] Get:56 http://ftpmaster.internal/ubuntu impish/main s390x libzstd1 s390x 1.4.8+dfsg-2.1 [287 kB] Get:57 http://ftpmaster.internal/ubuntu impish/main s390x libkmod2 s390x 28-1ubuntu4 [45.9 kB] Get:58 http://ftpmaster.internal/ubuntu impish/main s390x libblkid1 s390x 2.36.1-8ubuntu1 [95.8 kB] Get:59 http://ftpmaster.internal/ubuntu impish/main s390x libmount1 s390x 2.36.1-8ubuntu1 [114 kB] Get:60 http://ftpmaster.internal/ubuntu impish/main s390x libpam0g s390x 1.3.1-5ubuntu8 [60.7 kB] Get:61 http://ftpmaster.internal/ubuntu impish/main s390x mount s390x 2.36.1-8ubuntu1 [110 kB] Get:62 http://ftpmaster.internal/ubuntu impish/main s390x systemd s390x 248.3-1ubuntu3 [4604 kB] Get:63 http://ftpmaster.internal/ubuntu impish/main s390x libsystemd0 s390x 248.3-1ubuntu3 [344 kB] Get:64 http://ftpmaster.internal/ubuntu impish/main s390x libudev1 s390x 248.3-1ubuntu3 [84.7 kB] Get:65 http://ftpmaster.internal/ubuntu impish/main s390x libapt-pkg6.0 s390x 2.3.7 [876 kB] Get:66 http://ftpmaster.internal/ubuntu impish/main s390x gpgv s390x 2.2.20-1ubuntu4 [144 kB] Get:67 http://ftpmaster.internal/ubuntu impish/main s390x apt s390x 2.3.7 [1379 kB] Get:68 http://ftpmaster.internal/ubuntu impish/main s390x libpam-modules-bin s390x 1.3.1-5ubuntu8 [53.3 kB] Get:69 http://ftpmaster.internal/ubuntu impish/main s390x libpam-modules s390x 1.3.1-5ubuntu8 [291 kB] Get:70 http://ftpmaster.internal/ubuntu impish/main s390x logsave s390x 1.46.2-1ubuntu2 [11.6 kB] Get:71 http://ftpmaster.internal/ubuntu impish/main s390x libext2fs2 s390x 1.46.2-1ubuntu2 [203 kB] Get:72 http://ftpmaster.internal/ubuntu impish/main s390x e2fsprogs s390x 1.46.2-1ubuntu2 [565 kB] Get:73 http://ftpmaster.internal/ubuntu impish/main s390x libpython3.9-minimal s390x 3.9.6-1 [751 kB] Get:74 http://ftpmaster.internal/ubuntu impish/main s390x libexpat1 s390x 2.3.0-1 [95.5 kB] Get:75 http://ftpmaster.internal/ubuntu impish/main s390x python3.9-minimal s390x 3.9.6-1 [1898 kB] Get:76 http://ftpmaster.internal/ubuntu impish/main s390x python3-minimal s390x 3.9.4-1 [23.8 kB] Get:77 http://ftpmaster.internal/ubuntu impish/main s390x media-types all 4.0.0 [22.2 kB] Get:78 http://ftpmaster.internal/ubuntu impish/main s390x libmpdec3 s390x 2.5.1-2 [84.5 kB] Get:79 http://ftpmaster.internal/ubuntu impish/main s390x readline-common all 8.1-2 [54.1 kB] Get:80 http://ftpmaster.internal/ubuntu impish/main s390x libreadline8 s390x 8.1-2 [142 kB] Get:81 http://ftpmaster.internal/ubuntu impish/main s390x libsqlite3-0 s390x 3.35.5-1 [659 kB] Get:82 http://ftpmaster.internal/ubuntu impish/main s390x libuuid1 s390x 2.36.1-8ubuntu1 [23.3 kB] Get:83 http://ftpmaster.internal/ubuntu impish/main s390x libpython3.9-stdlib s390x 3.9.6-1 [1653 kB] Get:84 http://ftpmaster.internal/ubuntu impish/main s390x python3.9 s390x 3.9.6-1 [426 kB] Get:85 http://ftpmaster.internal/ubuntu impish/main s390x libpython3-stdlib s390x 3.9.4-1 [6984 B] Get:86 http://ftpmaster.internal/ubuntu impish/main s390x python3 s390x 3.9.4-1 [22.2 kB] Get:87 http://ftpmaster.internal/ubuntu impish/main s390x libcom-err2 s390x 1.46.2-1ubuntu2 [10.7 kB] Get:88 http://ftpmaster.internal/ubuntu impish/main s390x libpam-runtime all 1.3.1-5ubuntu8 [38.7 kB] Get:89 http://ftpmaster.internal/ubuntu impish/main s390x libsmartcols1 s390x 2.36.1-8ubuntu1 [48.8 kB] Get:90 http://ftpmaster.internal/ubuntu impish/main s390x passwd s390x 1:4.8.1-1ubuntu9 [841 kB] Get:91 http://ftpmaster.internal/ubuntu impish/main s390x libk5crypto3 s390x 1.18.3-6 [93.0 kB] Get:92 http://ftpmaster.internal/ubuntu impish/main s390x libkrb5support0 s390x 1.18.3-6 [33.5 kB] Get:93 http://ftpmaster.internal/ubuntu impish/main s390x libkrb5-3 s390x 1.18.3-6 [420 kB] Get:94 http://ftpmaster.internal/ubuntu impish/main s390x libgssapi-krb5-2 s390x 1.18.3-6 [162 kB] Get:95 http://ftpmaster.internal/ubuntu impish/main s390x libprocps8 s390x 2:3.3.17-5ubuntu3 [37.3 kB] Get:96 http://ftpmaster.internal/ubuntu impish/main s390x libss2 s390x 1.46.2-1ubuntu2 [11.2 kB] Get:97 http://ftpmaster.internal/ubuntu impish/main s390x procps s390x 2:3.3.17-5ubuntu3 [390 kB] Get:98 http://ftpmaster.internal/ubuntu impish/main s390x usrmerge all 25ubuntu1 [53.5 kB] Get:99 http://ftpmaster.internal/ubuntu impish/main s390x libdevmapper1.02.1 s390x 2:1.02.175-2.1ubuntu1 [122 kB] Get:100 http://ftpmaster.internal/ubuntu impish/main s390x openssl s390x 1.1.1j-1ubuntu5 [680 kB] Get:101 http://ftpmaster.internal/ubuntu impish/main s390x xz-utils s390x 5.2.5-2 [91.0 kB] Get:102 http://ftpmaster.internal/ubuntu impish/main s390x advancecomp s390x 2.1-2.1ubuntu1 [163 kB] Get:103 http://ftpmaster.internal/ubuntu impish/main s390x libctf0 s390x 2.37-1ubuntu1 [121 kB] Get:104 http://ftpmaster.internal/ubuntu impish/main s390x libctf-nobfd0 s390x 2.37-1ubuntu1 [122 kB] Get:105 http://ftpmaster.internal/ubuntu impish/main s390x binutils-s390x-linux-gnu s390x 2.37-1ubuntu1 [2070 kB] Get:106 http://ftpmaster.internal/ubuntu impish/main s390x libbinutils s390x 2.37-1ubuntu1 [510 kB] Get:107 http://ftpmaster.internal/ubuntu impish/main s390x binutils s390x 2.37-1ubuntu1 [3150 B] Get:108 http://ftpmaster.internal/ubuntu impish/main s390x binutils-common s390x 2.37-1ubuntu1 [52.6 kB] Get:109 http://ftpmaster.internal/ubuntu impish/main s390x libisl23 s390x 0.24-1 [693 kB] Get:110 http://ftpmaster.internal/ubuntu impish/main s390x cpp-11 s390x 11.2.0-1ubuntu2 [43.1 MB] Get:111 http://ftpmaster.internal/ubuntu impish/main s390x libgcc-11-dev s390x 11.2.0-1ubuntu2 [825 kB] Get:112 http://ftpmaster.internal/ubuntu impish/main s390x gcc-11 s390x 11.2.0-1ubuntu2 [49.6 MB] Get:113 http://ftpmaster.internal/ubuntu impish/main s390x libstdc++-11-dev s390x 11.2.0-1ubuntu2 [2109 kB] Get:114 http://ftpmaster.internal/ubuntu impish/main s390x g++-11 s390x 11.2.0-1ubuntu2 [47.6 MB] Get:115 http://ftpmaster.internal/ubuntu impish/main s390x lto-disabled-list all 16 [12.5 kB] Get:116 http://ftpmaster.internal/ubuntu impish/main s390x python3-psutil s390x 5.8.0-1 [152 kB] Get:117 http://ftpmaster.internal/ubuntu impish/main s390x build-essential s390x 12.9ubuntu1 [4740 B] Get:118 http://ftpmaster.internal/ubuntu impish/universe s390x g++-10 s390x 10.3.0-6ubuntu1 [9875 kB] Get:119 http://ftpmaster.internal/ubuntu impish/universe s390x gcc-10 s390x 10.3.0-6ubuntu1 [16.9 MB] Get:120 http://ftpmaster.internal/ubuntu impish/main s390x libstdc++-10-dev s390x 10.3.0-6ubuntu1 [1896 kB] Get:121 http://ftpmaster.internal/ubuntu impish/main s390x libgcc-10-dev s390x 10.3.0-6ubuntu1 [905 kB] Get:122 http://ftpmaster.internal/ubuntu impish/universe s390x cpp-10 s390x 10.3.0-6ubuntu1 [8385 kB] Get:123 http://ftpmaster.internal/ubuntu impish/main s390x gcc-10-base s390x 10.3.0-6ubuntu1 [21.5 kB] Get:124 http://ftpmaster.internal/ubuntu impish/main s390x libassuan0 s390x 2.5.5-1 [35.9 kB] Get:125 http://ftpmaster.internal/ubuntu impish/main s390x pinentry-curses s390x 1.1.1-1 [34.8 kB] Get:126 http://ftpmaster.internal/ubuntu impish/main s390x gpg s390x 2.2.20-1ubuntu4 [520 kB] Get:127 http://ftpmaster.internal/ubuntu impish/main s390x gpgconf s390x 2.2.20-1ubuntu4 [96.1 kB] Get:128 http://ftpmaster.internal/ubuntu impish/main s390x gpg-agent s390x 2.2.20-1ubuntu4 [199 kB] Get:129 http://ftpmaster.internal/ubuntu impish/main s390x pkgbinarymangler all 148 [32.3 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 234 MB in 4s (57.8 MB/s) (Reading database ... 12912 files and directories currently installed.) Preparing to unpack .../libcrypt-dev_1%3a4.4.18-4ubuntu1_s390x.deb ... Unpacking libcrypt-dev:s390x (1:4.4.18-4ubuntu1) over (1:4.4.17-1ubuntu3) ... Preparing to unpack .../libnsl-dev_1.3.0-2_s390x.deb ... Unpacking libnsl-dev:s390x (1.3.0-2) over (1.3.0-0ubuntu3) ... Preparing to unpack .../libc6-dev_2.34-0ubuntu1~ppa5_s390x.deb ... Unpacking libc6-dev:s390x (2.34-0ubuntu1~ppa5) over (2.33-0ubuntu5) ... Preparing to unpack .../libc-dev-bin_2.34-0ubuntu1~ppa5_s390x.deb ... Unpacking libc-dev-bin (2.34-0ubuntu1~ppa5) over (2.33-0ubuntu5) ... Preparing to unpack .../libcrypt1_1%3a4.4.18-4ubuntu1_s390x.deb ... Unpacking libcrypt1:s390x (1:4.4.18-4ubuntu1) over (1:4.4.17-1ubuntu3) ... Setting up libcrypt1:s390x (1:4.4.18-4ubuntu1) ... (Reading database ... 12918 files and directories currently installed.) Preparing to unpack .../libnsl2_1.3.0-2_s390x.deb ... Unpacking libnsl2:s390x (1.3.0-2) over (1.3.0-0ubuntu3) ... Setting up libnsl2:s390x (1.3.0-2) ... 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Setting up libubsan1:s390x (11.2.0-1ubuntu2) ... Setting up advancecomp (2.1-2.1ubuntu1) ... Setting up libdevmapper1.02.1:s390x (2:1.02.175-2.1ubuntu1) ... Setting up mount (2.36.1-8ubuntu1) ... Setting up libnsl-dev:s390x (1.3.0-2) ... Setting up libcrypt-dev:s390x (1:4.4.18-4ubuntu1) ... Setting up libmpdec3:s390x (2.5.1-2) ... Setting up libbinutils:s390x (2.37-1ubuntu1) ... Setting up libisl23:s390x (0.24-1) ... Setting up libc-dev-bin (2.34-0ubuntu1~ppa5) ... Setting up openssl (1.1.1j-1ubuntu5) ... Setting up readline-common (8.1-2) ... Setting up libcc1-0:s390x (11.2.0-1ubuntu2) ... Setting up libprocps8:s390x (2:3.3.17-5ubuntu3) ... Setting up cpp-10 (10.3.0-6ubuntu1) ... Setting up libitm1:s390x (11.2.0-1ubuntu2) ... Setting up libkmod2:s390x (28-1ubuntu4) ... Setting up libctf0:s390x (2.37-1ubuntu1) ... Setting up pinentry-curses (1.1.1-1) ... Setting up cpp-11 (11.2.0-1ubuntu2) ... Setting up binutils-s390x-linux-gnu (2.37-1ubuntu1) ... Setting up pkgbinarymangler (148) ... Setting up libgcc-10-dev:s390x (10.3.0-6ubuntu1) ... Setting up libreadline8:s390x (8.1-2) ... Setting up e2fsprogs (1.46.2-1ubuntu2) ... Setting up binutils (2.37-1ubuntu1) ... Setting up perl (5.32.1-3ubuntu3) ... Setting up gcc-10 (10.3.0-6ubuntu1) ... Setting up libdpkg-perl (1.20.9ubuntu13) ... Setting up libgcc-11-dev:s390x (11.2.0-1ubuntu2) ... Setting up gcc-11 (11.2.0-1ubuntu2) ... Setting up cpp (4:11.2.0-1ubuntu1) ... Setting up procps (2:3.3.17-5ubuntu3) ... update-alternatives: warning: alternative /usr/bin/w.procps (part of link group w) doesn't exist; removing from list of alternatives update-alternatives: warning: /etc/alternatives/w is dangling; it will be updated with best choice Setting up gpgconf (2.2.20-1ubuntu4) ... Setting up libc6-dev:s390x (2.34-0ubuntu1~ppa5) ... Setting up gpg (2.2.20-1ubuntu4) ... Setting up libpython3.9-stdlib:s390x (3.9.6-1) ... Setting up libpython3-stdlib:s390x (3.9.4-1) ... Setting up libstdc++-10-dev:s390x (10.3.0-6ubuntu1) ... Setting up gpg-agent (2.2.20-1ubuntu4) ... Setting up g++-10 (10.3.0-6ubuntu1) ... Setting up gcc (4:11.2.0-1ubuntu1) ... Setting up libstdc++-11-dev:s390x (11.2.0-1ubuntu2) ... Setting up python3.9 (3.9.6-1) ... Setting up g++-11 (11.2.0-1ubuntu2) ... Setting up python3 (3.9.4-1) ... Setting up python3-psutil (5.8.0-1) ... Setting up dpkg-dev (1.20.9ubuntu13) ... Setting up g++ (4:11.2.0-1ubuntu1) ... Setting up build-essential (12.9ubuntu1) ... Setting up systemd-timesyncd (248.3-1ubuntu3) ... Installing new version of config file /etc/systemd/timesyncd.conf ... Setting up systemd (248.3-1ubuntu3) ... Installing new version of config file /etc/systemd/journald.conf ... Installing new version of config file /etc/systemd/logind.conf ... Installing new version of config file /etc/systemd/networkd.conf ... Installing new version of config file /etc/systemd/pstore.conf ... Installing new version of config file /etc/systemd/resolved.conf ... Installing new version of config file /etc/systemd/sleep.conf ... Installing new version of config file /etc/systemd/system.conf ... Installing new version of config file /etc/systemd/user.conf ... Initializing machine ID from random generator. Setting up systemd-sysv (248.3-1ubuntu3) ... Processing triggers for libc-bin (2.34-0ubuntu1~ppa5) ... RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-21852219 s390x impish -c chroot:build-PACKAGEBUILD-21852219 --arch=s390x --dist=impish --nolog cufflinks_2.2.1+dfsg.1-8build1.dsc Initiating build PACKAGEBUILD-21852219 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.15.0-154-generic #161-Ubuntu SMP Fri Jul 30 12:59:37 UTC 2021 s390x sbuild (Debian sbuild) 0.75.0 (21 Mar 2018) on bos02-s390x-014.buildd +==============================================================================+ | cufflinks 2.2.1+dfsg.1-8build1 (s390x) Fri, 03 Sep 2021 00:31:05 +0000 | +==============================================================================+ Package: cufflinks Version: 2.2.1+dfsg.1-8build1 Source Version: 2.2.1+dfsg.1-8build1 Distribution: impish Machine Architecture: s390x Host Architecture: s390x Build Architecture: s390x Build Type: any I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-21852219/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- cufflinks_2.2.1+dfsg.1-8build1.dsc exists in .; copying to chroot I: NOTICE: Log filtering will replace 'build/cufflinks-KmZWNv/cufflinks-2.2.1+dfsg.1' with '<>' I: NOTICE: Log filtering will replace 'build/cufflinks-KmZWNv' with '<>' +------------------------------------------------------------------------------+ | Install build-essential | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<>/resolver-B0Ii6W/apt_archive/sbuild-build-depends-core-dummy.deb'. dpkg-scanpackages: warning: Packages in archive but missing from override file: dpkg-scanpackages: warning: sbuild-build-depends-core-dummy dpkg-scanpackages: info: Wrote 1 entries to output Packages file. Ign:1 copy:/<>/resolver-B0Ii6W/apt_archive ./ InRelease Get:2 copy:/<>/resolver-B0Ii6W/apt_archive ./ Release [957 B] Ign:3 copy:/<>/resolver-B0Ii6W/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-B0Ii6W/apt_archive ./ Sources [349 B] Get:5 copy:/<>/resolver-B0Ii6W/apt_archive ./ Packages [433 B] Fetched 1739 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 packages were automatically installed and are no longer required: cpp-10 g++-10 gcc-10 gcc-10-base libgcc-10-dev libstdc++-10-dev Use 'apt autoremove' to remove them. 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 652 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-B0Ii6W/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [652 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 652 B in 0s (0 B/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 14740 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) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (s390x included in any) +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), 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 (= 13), 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-B0Ii6W/apt_archive/sbuild-build-depends-cufflinks-dummy.deb'. dpkg-scanpackages: warning: Packages in archive but missing from override file: dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-cufflinks-dummy dpkg-scanpackages: info: Wrote 2 entries to output Packages file. Ign:1 copy:/<>/resolver-B0Ii6W/apt_archive ./ InRelease Get:2 copy:/<>/resolver-B0Ii6W/apt_archive ./ Release [963 B] Ign:3 copy:/<>/resolver-B0Ii6W/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-B0Ii6W/apt_archive ./ Sources [556 B] Get:5 copy:/<>/resolver-B0Ii6W/apt_archive ./ Packages [643 B] Fetched 2162 B in 0s (149 kB/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 package was automatically installed and is no longer required: g++-10 Use 'apt autoremove' to remove it. The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils debhelper debugedit dh-autoreconf dh-python dh-strip-nondeterminism dwz file gettext gettext-base groff-base help2man intltool-debian libarchive-zip-perl libbam-dev libboost-atomic1.74-dev libboost-atomic1.74.0 libboost-chrono1.74-dev libboost-chrono1.74.0 libboost-date-time1.74-dev libboost-date-time1.74.0 libboost-dev libboost-serialization-dev libboost-serialization1.74-dev libboost-serialization1.74.0 libboost-system-dev libboost-system1.74-dev libboost-system1.74.0 libboost-thread-dev libboost-thread1.74-dev libboost-thread1.74.0 libboost1.74-dev libdebhelper-perl libdw1 libeigen3-dev libelf1 libfile-stripnondeterminism-perl libglib2.0-0 libicu67 liblocale-gettext-perl libmagic-mgc libmagic1 libpipeline1 libsigsegv2 libsub-override-perl libtool libuchardet0 libxml2 m4 man-db pkg-config po-debconf python3-distutils python3-lib2to3 zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc dh-make gettext-doc libasprintf-dev libgettextpo-dev groff libboost-doc libboost1.74-doc libboost-container1.74-dev libboost-context1.74-dev libboost-contract1.74-dev libboost-coroutine1.74-dev libboost-exception1.74-dev libboost-fiber1.74-dev libboost-filesystem1.74-dev libboost-graph1.74-dev libboost-graph-parallel1.74-dev libboost-iostreams1.74-dev libboost-locale1.74-dev libboost-log1.74-dev libboost-math1.74-dev libboost-mpi1.74-dev libboost-mpi-python1.74-dev libboost-numpy1.74-dev libboost-program-options1.74-dev libboost-python1.74-dev libboost-random1.74-dev libboost-regex1.74-dev libboost-stacktrace1.74-dev libboost-test1.74-dev libboost-timer1.74-dev libboost-type-erasure1.74-dev libboost-wave1.74-dev libboost1.74-tools-dev libmpfrc++-dev libntl-dev libboost-nowide1.74-dev libeigen3-doc libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl 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 debugedit dh-autoreconf dh-python dh-strip-nondeterminism dwz file gettext gettext-base groff-base help2man intltool-debian libarchive-zip-perl libbam-dev libboost-atomic1.74-dev libboost-atomic1.74.0 libboost-chrono1.74-dev libboost-chrono1.74.0 libboost-date-time1.74-dev libboost-date-time1.74.0 libboost-dev libboost-serialization-dev libboost-serialization1.74-dev libboost-serialization1.74.0 libboost-system-dev libboost-system1.74-dev libboost-system1.74.0 libboost-thread-dev libboost-thread1.74-dev libboost-thread1.74.0 libboost1.74-dev libdebhelper-perl libdw1 libeigen3-dev libelf1 libfile-stripnondeterminism-perl libglib2.0-0 libicu67 liblocale-gettext-perl libmagic-mgc libmagic1 libpipeline1 libsigsegv2 libsub-override-perl libtool libuchardet0 libxml2 m4 man-db pkg-config po-debconf python3-distutils python3-lib2to3 sbuild-build-depends-cufflinks-dummy zlib1g-dev 0 upgraded, 60 newly installed, 0 to remove and 0 not upgraded. Need to get 31.5 MB of archives. After this operation, 250 MB of additional disk space will be used. Get:1 copy:/<>/resolver-B0Ii6W/apt_archive ./ sbuild-build-depends-cufflinks-dummy 0.invalid.0 [724 B] Get:2 http://ftpmaster.internal/ubuntu impish/main s390x liblocale-gettext-perl s390x 1.07-4build1 [16.4 kB] Get:3 http://ftpmaster.internal/ubuntu impish/main s390x bsdextrautils s390x 2.36.1-8ubuntu1 [75.8 kB] Get:4 http://ftpmaster.internal/ubuntu impish/main s390x libuchardet0 s390x 0.0.7-1 [67.5 kB] Get:5 http://ftpmaster.internal/ubuntu impish/main s390x groff-base s390x 1.22.4-6 [912 kB] Get:6 http://ftpmaster.internal/ubuntu impish/main s390x libpipeline1 s390x 1.5.3-1 [28.7 kB] Get:7 http://ftpmaster.internal/ubuntu impish/main s390x man-db s390x 2.9.4-2 [1168 kB] Get:8 http://ftpmaster.internal/ubuntu impish/main s390x libelf1 s390x 0.185-1 [54.6 kB] Get:9 http://ftpmaster.internal/ubuntu impish/main s390x libglib2.0-0 s390x 2.68.3-1ubuntu1 [1368 kB] Get:10 http://ftpmaster.internal/ubuntu impish/main s390x libicu67 s390x 67.1-6ubuntu2 [8483 kB] Get:11 http://ftpmaster.internal/ubuntu impish/main s390x libxml2 s390x 2.9.10+dfsg-6.7 [615 kB] Get:12 http://ftpmaster.internal/ubuntu impish/main s390x libmagic-mgc s390x 1:5.39-3 [229 kB] Get:13 http://ftpmaster.internal/ubuntu impish/main s390x libmagic1 s390x 1:5.39-3 [83.6 kB] Get:14 http://ftpmaster.internal/ubuntu impish/main s390x file s390x 1:5.39-3 [24.0 kB] Get:15 http://ftpmaster.internal/ubuntu impish/main s390x gettext-base s390x 0.21-4ubuntu3 [38.4 kB] Get:16 http://ftpmaster.internal/ubuntu impish/main s390x libsigsegv2 s390x 2.13-1ubuntu1 [14.2 kB] Get:17 http://ftpmaster.internal/ubuntu impish/main s390x m4 s390x 1.4.18-5 [209 kB] Get:18 http://ftpmaster.internal/ubuntu impish/main s390x autoconf all 2.69-14 [293 kB] Get:19 http://ftpmaster.internal/ubuntu impish/main s390x autotools-dev all 20180224.1+nmu1 [39.4 kB] Get:20 http://ftpmaster.internal/ubuntu impish/main s390x automake all 1:1.16.4-1ubuntu1 [557 kB] Get:21 http://ftpmaster.internal/ubuntu impish/main s390x autopoint all 0.21-4ubuntu3 [422 kB] Get:22 http://ftpmaster.internal/ubuntu impish/main s390x libdebhelper-perl all 13.3.4ubuntu2 [62.5 kB] Get:23 http://ftpmaster.internal/ubuntu impish/main s390x libtool all 2.4.6-15 [161 kB] Get:24 http://ftpmaster.internal/ubuntu impish/main s390x dh-autoreconf all 20 [16.1 kB] Get:25 http://ftpmaster.internal/ubuntu impish/main s390x libarchive-zip-perl all 1.68-1 [90.2 kB] Get:26 http://ftpmaster.internal/ubuntu impish/main s390x libsub-override-perl all 0.09-2 [9532 B] Get:27 http://ftpmaster.internal/ubuntu impish/main s390x libfile-stripnondeterminism-perl all 1.12.0-1 [17.5 kB] Get:28 http://ftpmaster.internal/ubuntu impish/main s390x dh-strip-nondeterminism all 1.12.0-1 [5228 B] Get:29 http://ftpmaster.internal/ubuntu impish/main s390x libdw1 s390x 0.185-1 [218 kB] Get:30 http://ftpmaster.internal/ubuntu impish/main s390x debugedit s390x 1:5.0-0ubuntu1 [51.4 kB] Get:31 http://ftpmaster.internal/ubuntu impish/main s390x dwz s390x 0.14-1 [110 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[116 kB] Get:42 http://ftpmaster.internal/ubuntu impish/main s390x libboost1.74-dev s390x 1.74.0-8ubuntu2 [9509 kB] Get:43 http://ftpmaster.internal/ubuntu impish/main s390x libboost-atomic1.74.0 s390x 1.74.0-8ubuntu2 [217 kB] Get:44 http://ftpmaster.internal/ubuntu impish/main s390x libboost-atomic1.74-dev s390x 1.74.0-8ubuntu2 [215 kB] Get:45 http://ftpmaster.internal/ubuntu impish/main s390x libboost-chrono1.74.0 s390x 1.74.0-8ubuntu2 [225 kB] Get:46 http://ftpmaster.internal/ubuntu impish/main s390x libboost-chrono1.74-dev s390x 1.74.0-8ubuntu2 [229 kB] Get:47 http://ftpmaster.internal/ubuntu impish/main s390x libboost-date-time1.74.0 s390x 1.74.0-8ubuntu2 [215 kB] Get:48 http://ftpmaster.internal/ubuntu impish/main s390x libboost-serialization1.74.0 s390x 1.74.0-8ubuntu2 [308 kB] Get:49 http://ftpmaster.internal/ubuntu impish/main s390x libboost-serialization1.74-dev s390x 1.74.0-8ubuntu2 [344 kB] Get:50 http://ftpmaster.internal/ubuntu impish/main s390x libboost-date-time1.74-dev 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0.29.2-1ubuntu1 [45.0 kB] Get:60 http://ftpmaster.internal/ubuntu impish/universe s390x libeigen3-dev all 3.3.9-2 [817 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 31.5 MB in 1s (32.7 MB/s) Selecting previously unselected package liblocale-gettext-perl. 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Setting up libboost-serialization-dev:s390x (1.74.0.3ubuntu5) ... Setting up libboost-thread1.74-dev:s390x (1.74.0-8ubuntu2) ... Setting up libboost-thread-dev:s390x (1.74.0.3ubuntu5) ... Setting up debhelper (13.3.4ubuntu2) ... Setting up sbuild-build-depends-cufflinks-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.34-0ubuntu1~ppa5) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.15.0-154-generic s390x (s390x) Toolchain package versions: binutils_2.37-1ubuntu1 dpkg-dev_1.20.9ubuntu13 g++-10_10.3.0-6ubuntu1 g++-11_11.2.0-1ubuntu2 gcc-10_10.3.0-6ubuntu1 gcc-11_11.2.0-1ubuntu2 libc6-dev_2.34-0ubuntu1~ppa5 libstdc++-10-dev_10.3.0-6ubuntu1 libstdc++-11-dev_11.2.0-1ubuntu2 libstdc++6_11.2.0-1ubuntu2 linux-libc-dev_5.13.0-14.14 Package versions: adduser_3.118ubuntu5 advancecomp_2.1-2.1ubuntu1 apt_2.3.7 autoconf_2.69-14 automake_1:1.16.4-1ubuntu1 autopoint_0.21-4ubuntu3 autotools-dev_20180224.1+nmu1 base-files_11.1ubuntu3 base-passwd_3.5.51 bash_5.1-3ubuntu1 binutils_2.37-1ubuntu1 binutils-common_2.37-1ubuntu1 binutils-s390x-linux-gnu_2.37-1ubuntu1 bsdextrautils_2.36.1-8ubuntu1 bsdutils_1:2.36.1-8ubuntu1 build-essential_12.9ubuntu1 bzip2_1.0.8-4ubuntu3 ca-certificates_20210119build1 coreutils_8.32-4ubuntu2 cpp_4:11.2.0-1ubuntu1 cpp-10_10.3.0-6ubuntu1 cpp-11_11.2.0-1ubuntu2 dash_0.5.11+git20210120+802ebd4-1 debconf_1.5.77 debhelper_13.3.4ubuntu2 debianutils_4.11.2 debugedit_1:5.0-0ubuntu1 dh-autoreconf_20 dh-python_4.20201102ubuntu4 dh-strip-nondeterminism_1.12.0-1 diffutils_1:3.7-5ubuntu1 dpkg_1.20.9ubuntu13 dpkg-dev_1.20.9ubuntu13 dwz_0.14-1 e2fsprogs_1.46.2-1ubuntu2 fakeroot_1.25.3-1.1ubuntu2 file_1:5.39-3 findutils_4.8.0-1ubuntu2 g++_4:11.2.0-1ubuntu1 g++-10_10.3.0-6ubuntu1 g++-11_11.2.0-1ubuntu2 gcc_4:11.2.0-1ubuntu1 gcc-10_10.3.0-6ubuntu1 gcc-10-base_10.3.0-6ubuntu1 gcc-11_11.2.0-1ubuntu2 gcc-11-base_11.2.0-1ubuntu2 gettext_0.21-4ubuntu3 gettext-base_0.21-4ubuntu3 gpg_2.2.20-1ubuntu4 gpg-agent_2.2.20-1ubuntu4 gpgconf_2.2.20-1ubuntu4 gpgv_2.2.20-1ubuntu4 grep_3.6-1 groff-base_1.22.4-6 gzip_1.10-4ubuntu1 help2man_1.48.4 hostname_3.23 init_1.60 init-system-helpers_1.60 intltool-debian_0.35.0+20060710.5 libacl1_2.2.53-10ubuntu1 libapparmor1_3.0.3-0ubuntu1 libapt-pkg6.0_2.3.7 libarchive-zip-perl_1.68-1 libargon2-1_0~20171227-0.2build21.04.0 libasan6_11.2.0-1ubuntu2 libassuan0_2.5.5-1 libatomic1_11.2.0-1ubuntu2 libattr1_1:2.4.48-6build1 libaudit-common_1:3.0-2ubuntu2 libaudit1_1:3.0-2ubuntu2 libbam-dev_0.1.19+dfsg-2 libbinutils_2.37-1ubuntu1 libblkid1_2.36.1-8ubuntu1 libboost-atomic1.74-dev_1.74.0-8ubuntu2 libboost-atomic1.74.0_1.74.0-8ubuntu2 libboost-chrono1.74-dev_1.74.0-8ubuntu2 libboost-chrono1.74.0_1.74.0-8ubuntu2 libboost-date-time1.74-dev_1.74.0-8ubuntu2 libboost-date-time1.74.0_1.74.0-8ubuntu2 libboost-dev_1.74.0.3ubuntu5 libboost-serialization-dev_1.74.0.3ubuntu5 libboost-serialization1.74-dev_1.74.0-8ubuntu2 libboost-serialization1.74.0_1.74.0-8ubuntu2 libboost-system-dev_1.74.0.3ubuntu5 libboost-system1.74-dev_1.74.0-8ubuntu2 libboost-system1.74.0_1.74.0-8ubuntu2 libboost-thread-dev_1.74.0.3ubuntu5 libboost-thread1.74-dev_1.74.0-8ubuntu2 libboost-thread1.74.0_1.74.0-8ubuntu2 libboost1.74-dev_1.74.0-8ubuntu2 libbz2-1.0_1.0.8-4ubuntu3 libc-bin_2.34-0ubuntu1~ppa5 libc-dev-bin_2.34-0ubuntu1~ppa5 libc6_2.34-0ubuntu1~ppa5 libc6-dev_2.34-0ubuntu1~ppa5 libcap-ng0_0.7.9-2.2build1 libcap2_1:2.44-1build1 libcc1-0_11.2.0-1ubuntu2 libcom-err2_1.46.2-1ubuntu2 libcrypt-dev_1:4.4.18-4ubuntu1 libcrypt1_1:4.4.18-4ubuntu1 libcryptsetup12_2:2.3.4-1ubuntu3 libctf-nobfd0_2.37-1ubuntu1 libctf0_2.37-1ubuntu1 libdb5.3_5.3.28+dfsg1-0.8ubuntu1 libdebconfclient0_0.256ubuntu3 libdebhelper-perl_13.3.4ubuntu2 libdevmapper1.02.1_2:1.02.175-2.1ubuntu1 libdpkg-perl_1.20.9ubuntu13 libdw1_0.185-1 libeigen3-dev_3.3.9-2 libelf1_0.185-1 libexpat1_2.3.0-1 libext2fs2_1.46.2-1ubuntu2 libfakeroot_1.25.3-1.1ubuntu2 libffi8ubuntu1_3.4~20200819gead65ca871-0ubuntu5 libfile-stripnondeterminism-perl_1.12.0-1 libgcc-10-dev_10.3.0-6ubuntu1 libgcc-11-dev_11.2.0-1ubuntu2 libgcc-s1_11.2.0-1ubuntu2 libgcrypt20_1.8.7-5ubuntu1 libgdbm-compat4_1.19-2 libgdbm6_1.19-2 libglib2.0-0_2.68.3-1ubuntu1 libgmp10_2:6.2.1+dfsg-1ubuntu2 libgnutls30_3.7.1-4ubuntu1 libgomp1_11.2.0-1ubuntu2 libgpg-error0_1.38-2build1 libgssapi-krb5-2_1.18.3-6 libhogweed6_3.7.3-1 libicu67_67.1-6ubuntu2 libidn2-0_2.3.1-1 libip4tc2_1.8.7-1ubuntu2 libisl23_0.24-1 libitm1_11.2.0-1ubuntu2 libjson-c5_0.15-2build2 libk5crypto3_1.18.3-6 libkeyutils1_1.6.1-2ubuntu1 libkmod2_28-1ubuntu4 libkrb5-3_1.18.3-6 libkrb5support0_1.18.3-6 liblocale-gettext-perl_1.07-4build1 liblockfile-bin_1.17-1 liblockfile1_1.17-1 liblz4-1_1.9.3-2 liblzma5_5.2.5-2 libmagic-mgc_1:5.39-3 libmagic1_1:5.39-3 libmount1_2.36.1-8ubuntu1 libmpc3_1.2.0-1build1 libmpdec3_2.5.1-2 libmpfr6_4.1.0-3build1 libncurses6_6.2+20201114-2build1 libncursesw6_6.2+20201114-2build1 libnettle8_3.7.3-1 libnpth0_1.6-3 libnsl-dev_1.3.0-2 libnsl2_1.3.0-2 libp11-kit0_0.23.22-1 libpam-modules_1.3.1-5ubuntu8 libpam-modules-bin_1.3.1-5ubuntu8 libpam-runtime_1.3.1-5ubuntu8 libpam0g_1.3.1-5ubuntu8 libpcre2-8-0_10.36-2ubuntu5 libpcre3_2:8.39-13build3 libperl5.32_5.32.1-3ubuntu3 libpipeline1_1.5.3-1 libpng16-16_1.6.37-3build3 libprocps8_2:3.3.17-5ubuntu3 libpython3-stdlib_3.9.4-1 libpython3.9-minimal_3.9.6-1 libpython3.9-stdlib_3.9.6-1 libreadline8_8.1-2 libseccomp2_2.5.1-1ubuntu1 libselinux1_3.1-3build1 libsemanage-common_3.1-1ubuntu1 libsemanage1_3.1-1ubuntu1 libsepol1_3.1-1ubuntu1 libsigsegv2_2.13-1ubuntu1 libsmartcols1_2.36.1-8ubuntu1 libsqlite3-0_3.35.5-1 libss2_1.46.2-1ubuntu2 libssl1.1_1.1.1j-1ubuntu5 libstdc++-10-dev_10.3.0-6ubuntu1 libstdc++-11-dev_11.2.0-1ubuntu2 libstdc++6_11.2.0-1ubuntu2 libsub-override-perl_0.09-2 libsystemd0_248.3-1ubuntu3 libtasn1-6_4.16.0-2 libtinfo6_6.2+20201114-2build1 libtirpc-common_1.3.1-1build1 libtirpc-dev_1.3.1-1build1 libtirpc3_1.3.1-1build1 libtool_2.4.6-15 libubsan1_11.2.0-1ubuntu2 libuchardet0_0.0.7-1 libudev1_248.3-1ubuntu3 libunistring2_0.9.10-4 libuuid1_2.36.1-8ubuntu1 libxml2_2.9.10+dfsg-6.7 libxxhash0_0.8.0-2 libzstd1_1.4.8+dfsg-2.1 linux-libc-dev_5.13.0-14.14 lockfile-progs_0.1.18 login_1:4.8.1-1ubuntu9 logsave_1.46.2-1ubuntu2 lsb-base_11.1.0ubuntu2 lto-disabled-list_16 m4_1.4.18-5 make_4.3-4ubuntu1 man-db_2.9.4-2 mawk_1.3.4.20200120-2 media-types_4.0.0 mount_2.36.1-8ubuntu1 ncurses-base_6.2+20201114-2build1 ncurses-bin_6.2+20201114-2build1 openssl_1.1.1j-1ubuntu5 optipng_0.7.7-1 passwd_1:4.8.1-1ubuntu9 patch_2.7.6-7 perl_5.32.1-3ubuntu3 perl-base_5.32.1-3ubuntu3 perl-modules-5.32_5.32.1-3ubuntu3 pinentry-curses_1.1.1-1 pkg-config_0.29.2-1ubuntu1 pkgbinarymangler_148 po-debconf_1.0.21+nmu1 policyrcd-script-zg2_0.1-3 procps_2:3.3.17-5ubuntu3 python3_3.9.4-1 python3-distutils_3.9.5-0ubuntu3 python3-lib2to3_3.9.5-0ubuntu3 python3-minimal_3.9.4-1 python3-psutil_5.8.0-1 python3.9_3.9.6-1 python3.9-minimal_3.9.6-1 readline-common_8.1-2 rpcsvc-proto_1.4.2-0ubuntu4 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-cufflinks-dummy_0.invalid.0 sed_4.7-1ubuntu1 sensible-utils_0.0.14 systemd_248.3-1ubuntu3 systemd-sysv_248.3-1ubuntu3 systemd-timesyncd_248.3-1ubuntu3 sysvinit-utils_2.96-7ubuntu1 tar_1.34+dfsg-1build1 tzdata_2021a-1ubuntu1 ubuntu-keyring_2021.03.26 usrmerge_25ubuntu1 util-linux_2.36.1-8ubuntu1 xz-utils_5.2.5-2 zlib1g_1:1.2.11.dfsg-2ubuntu7 zlib1g-dev_1:1.2.11.dfsg-2ubuntu7 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Sat Dec 12 12:17:46 2020 UTC gpgv: using RSA key D56571B88A8BBAF140BF63D6BD7EAA60778FA6F5 gpgv: issuer "doko@ubuntu.com" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./cufflinks_2.2.1+dfsg.1-8build1.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.1-8build1.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 dpkg-source: info: applying gcc10.patch Check disk 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-21852219 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-21852219 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-21852219 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- dpkg-buildpackage.pl: info: source package cufflinks dpkg-buildpackage.pl: info: source version 2.2.1+dfsg.1-8build1 dpkg-buildpackage.pl: info: source distribution hirsute dpkg-source --before-build . dpkg-buildpackage.pl: 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 one 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, this automake: behavior may change in a future Automake major version, with object automake: files being placed in the same subdirectory as 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... /usr/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... 3.9 checking for python3 prefix... /usr checking for python3 exec_prefix... /usr checking for python3 platform... linux checking for python3 script directory... ${PYTHON_PREFIX}/lib/python3.9/site-packages checking for python3 extension module directory... ${PYTHON_EXEC_PREFIX}/lib/python3.9/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... /usr/bin/grep checking for egrep... /usr/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... no 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 -ffile-prefix-map=/<>/cufflinks-2.2.1+dfsg.1=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -Wl,-Bsymbolic-functions -flto=auto -Wl,-z,relro -Wl,-z,now GCC version: gcc (Ubuntu 11.2.0-1ubuntu2) 11.2.0 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 -ffile-prefix-map=/<>/cufflinks-2.2.1+dfsg.1=. -flto=auto -ffat-lto-objects -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 -ffile-prefix-map=/<>/cufflinks-2.2.1+dfsg.1=. -flto=auto -ffat-lto-objects -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 -ffile-prefix-map=/<>/cufflinks-2.2.1+dfsg.1=. -flto=auto -ffat-lto-objects -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 -ffile-prefix-map=/<>/cufflinks-2.2.1+dfsg.1=. -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o common.o common.cpp In file included from /usr/include/boost/math/tools/cxx03_warn.hpp:9, from /usr/include/boost/math/constants/constants.hpp:11, from /usr/include/boost/math/special_functions/gamma.hpp:24, from /usr/include/boost/math/special_functions/erf.hpp:15, from /usr/include/boost/math/distributions/normal.hpp:19, from common.h:27, from common.cpp:27: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ 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 gff.h:8, from gtf_tracking.h:12, from bundles.h:22, from replicates.h:10, from common.cpp:28: gdna.h: At global scope: gdna.h:12:1: error: reference to ‘byte’ is ambiguous 12 | byte gdna2bit(char* &nt, int n=4); //pack n bases into a byte (n can be 1..4) | ^~~~ In file included from /usr/include/boost/config/compiler/gcc.hpp:165, from /usr/include/boost/config.hpp:39, from /usr/include/boost/math/special_functions/detail/round_fwd.hpp:11, from /usr/include/boost/math/special_functions/math_fwd.hpp:27, from /usr/include/boost/math/special_functions/erf.hpp:13, from /usr/include/boost/math/distributions/normal.hpp:19, from common.h:27, from common.cpp:27: /usr/include/c++/11/cstddef:69:14: note: candidates are: ‘enum class std::byte’ 69 | enum class byte : unsigned char {}; | ^~~~ 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:75:23: note: ‘typedef unsigned char byte’ 75 | typedef unsigned char byte; | ^~~~ In file included from gff.h:8, from gtf_tracking.h:12, from bundles.h:22, from replicates.h:10, from common.cpp:28: gdna.h:13:17: error: reference to ‘byte’ is ambiguous 13 | char g2bit2base(byte v2bit); //convert the 2-bit value into 'A', 'C', 'G' or 'T' | ^~~~ In file included from /usr/include/boost/config/compiler/gcc.hpp:165, from /usr/include/boost/config.hpp:39, from /usr/include/boost/math/special_functions/detail/round_fwd.hpp:11, from /usr/include/boost/math/special_functions/math_fwd.hpp:27, from /usr/include/boost/math/special_functions/erf.hpp:13, from /usr/include/boost/math/distributions/normal.hpp:19, from common.h:27, from common.cpp:27: /usr/include/c++/11/cstddef:69:14: note: candidates are: ‘enum class std::byte’ 69 | enum class byte : unsigned char {}; | ^~~~ 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:75:23: note: ‘typedef unsigned char byte’ 75 | typedef unsigned char byte; | ^~~~ In file included from gff.h:12, from gtf_tracking.h:12, from bundles.h:22, from replicates.h:10, from common.cpp:28: GHash.hh: In member function ‘GHash::GHashEntry* GHash::NextEntry()’: GHash.hh:90:23: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 90 | register int pos=fCurrentEntry; | ^~~ GHash.hh: In member function ‘void GHash::Resize(int)’: GHash.hh:168:16: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 168 | register int i,n,p,x,h; | ^ GHash.hh:168:18: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 168 | register int i,n,p,x,h; | ^ GHash.hh:168:20: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 168 | register int i,n,p,x,h; | ^ GHash.hh:168:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 168 | register int i,n,p,x,h; | ^ GHash.hh:168:24: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 168 | register int i,n,p,x,h; | ^ GHash.hh: In member function ‘const OBJ* GHash::Add(const char*, const OBJ*, bool)’: GHash.hh:202:16: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 202 | register int p,i,x,h,n; | ^ GHash.hh:202:18: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 202 | register int p,i,x,h,n; | ^ GHash.hh:202:20: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 202 | register int p,i,x,h,n; | ^ GHash.hh:202:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 202 | register int p,i,x,h,n; | ^ GHash.hh:202:24: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 202 | register int p,i,x,h,n; | ^ GHash.hh: In member function ‘const OBJ* GHash::shkAdd(const char*, const OBJ*, bool)’: GHash.hh:243:16: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 243 | register int p,i,x,h,n; | ^ GHash.hh:243:18: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 243 | register int p,i,x,h,n; | ^ GHash.hh:243:20: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 243 | register int p,i,x,h,n; | ^ GHash.hh:243:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 243 | register int p,i,x,h,n; | ^ GHash.hh:243:24: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 243 | register int p,i,x,h,n; | ^ GHash.hh: In member function ‘OBJ* GHash::Replace(const char*, const OBJ*, bool)’: GHash.hh:285:16: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 285 | register int p,i,x,h,n; | ^ GHash.hh:285:18: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 285 | register int p,i,x,h,n; | ^ GHash.hh:285:20: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 285 | register int p,i,x,h,n; | ^ GHash.hh:285:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 285 | register int p,i,x,h,n; | ^ GHash.hh:285:24: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 285 | register int p,i,x,h,n; | ^ GHash.hh: In member function ‘OBJ* GHash::Remove(const char*)’: GHash.hh:327:16: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 327 | register int p,x,h,n; | ^ GHash.hh:327:18: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 327 | register int p,x,h,n; | ^ GHash.hh:327:20: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 327 | register int p,x,h,n; | ^ GHash.hh:327:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 327 | register int p,x,h,n; | ^ GHash.hh: In member function ‘bool GHash::hasKey(const char*)’: GHash.hh:362:16: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 362 | register int p,x,h,n; | ^ GHash.hh:362:18: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 362 | register int p,x,h,n; | ^ GHash.hh:362:20: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 362 | register int p,x,h,n; | ^ GHash.hh:362:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 362 | register int p,x,h,n; | ^ GHash.hh: In member function ‘OBJ* GHash::Find(const char*, char**)’: GHash.hh:385:16: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 385 | register int p,x,h,n; | ^ GHash.hh:385:18: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 385 | register int p,x,h,n; | ^ GHash.hh:385:20: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 385 | register int p,x,h,n; | ^ GHash.hh:385:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 385 | register int p,x,h,n; | ^ GHash.hh: In member function ‘char* GHash::NextKey()’: GHash.hh:414:15: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 414 | register int pos=fCurrentEntry; | ^~~ GHash.hh: In member function ‘OBJ* GHash::NextData()’: GHash.hh:427:15: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 427 | register int pos=fCurrentEntry; | ^~~ GHash.hh: In member function ‘OBJ* GHash::NextData(char*&)’: GHash.hh:441:15: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 441 | register int pos=fCurrentEntry; | ^~~ GHash.hh: In member function ‘int GHash::First() const’: GHash.hh:459:16: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 459 | register int pos=0; | ^~~ GHash.hh: In member function ‘int GHash::Last() const’: GHash.hh:467:16: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 467 | register int pos=fCapacity-1; | ^~~ GHash.hh: In member function ‘void GHash::Clear()’: GHash.hh:494:16: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 494 | register int i; | ^ GHash.hh: In destructor ‘virtual GHash::~GHash()’: GHash.hh:551:16: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 551 | register int i; | ^ In file included from gtf_tracking.h:12, from bundles.h:22, from replicates.h:10, from common.cpp:28: gff.h: At global scope: gff.h:46:14: error: reference to ‘byte’ is ambiguous 46 | extern const byte gfo_flagShift_LEVEL; | ^~~~ In file included from /usr/include/boost/config/compiler/gcc.hpp:165, from /usr/include/boost/config.hpp:39, from /usr/include/boost/math/special_functions/detail/round_fwd.hpp:11, from /usr/include/boost/math/special_functions/math_fwd.hpp:27, from /usr/include/boost/math/special_functions/erf.hpp:13, from /usr/include/boost/math/distributions/normal.hpp:19, from common.h:27, from common.cpp:27: /usr/include/c++/11/cstddef:69:14: note: candidates are: ‘enum class std::byte’ 69 | enum class byte : unsigned char {}; | ^~~~ 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:75:23: note: ‘typedef unsigned char byte’ 75 | typedef unsigned char byte; | ^~~~ In file included from gtf_tracking.h:12, from bundles.h:22, from replicates.h:10, from common.cpp:28: gff.h:505:17: error: reference to ‘byte’ is ambiguous 505 | void setLevel(byte v) { | ^~~~ In file included from /usr/include/boost/config/compiler/gcc.hpp:165, from /usr/include/boost/config.hpp:39, from /usr/include/boost/math/special_functions/detail/round_fwd.hpp:11, from /usr/include/boost/math/special_functions/math_fwd.hpp:27, from /usr/include/boost/math/special_functions/erf.hpp:13, from /usr/include/boost/math/distributions/normal.hpp:19, from common.h:27, from common.cpp:27: /usr/include/c++/11/cstddef:69:14: note: candidates are: ‘enum class std::byte’ 69 | enum class byte : unsigned char {}; | ^~~~ 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:75:23: note: ‘typedef unsigned char byte’ 75 | typedef unsigned char byte; | ^~~~ In file included from gtf_tracking.h:12, from bundles.h:22, from replicates.h:10, from common.cpp:28: gff.h:505:17: error: ‘byte’ has not been declared 505 | void setLevel(byte v) { | ^~~~ gff.h:509:3: error: reference to ‘byte’ is ambiguous 509 | byte incLevel() { | ^~~~ In file included from /usr/include/boost/config/compiler/gcc.hpp:165, from /usr/include/boost/config.hpp:39, from /usr/include/boost/math/special_functions/detail/round_fwd.hpp:11, from /usr/include/boost/math/special_functions/math_fwd.hpp:27, from /usr/include/boost/math/special_functions/erf.hpp:13, from /usr/include/boost/math/distributions/normal.hpp:19, from common.h:27, from common.cpp:27: /usr/include/c++/11/cstddef:69:14: note: candidates are: ‘enum class std::byte’ 69 | enum class byte : unsigned char {}; | ^~~~ 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:75:23: note: ‘typedef unsigned char byte’ 75 | typedef unsigned char byte; | ^~~~ In file included from gtf_tracking.h:12, from bundles.h:22, from replicates.h:10, from common.cpp:28: gff.h:515:3: error: reference to ‘byte’ is ambiguous 515 | byte getLevel() { | ^~~~ In file included from /usr/include/boost/config/compiler/gcc.hpp:165, from /usr/include/boost/config.hpp:39, from /usr/include/boost/math/special_functions/detail/round_fwd.hpp:11, from /usr/include/boost/math/special_functions/math_fwd.hpp:27, from /usr/include/boost/math/special_functions/erf.hpp:13, from /usr/include/boost/math/distributions/normal.hpp:19, from common.h:27, from common.cpp:27: /usr/include/c++/11/cstddef:69:14: note: candidates are: ‘enum class std::byte’ 69 | enum class byte : unsigned char {}; | ^~~~ 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:75:23: note: ‘typedef unsigned char byte’ 75 | typedef unsigned char byte; | ^~~~ In file included from gtf_tracking.h:12, from bundles.h:22, from replicates.h:10, from common.cpp:28: gff.h: In member function ‘void GffObj::setLevel(int)’: gff.h:507:39: error: ‘gfo_flagShift_LEVEL’ was not declared in this scope 507 | else flags &= ~(((uint)v) << gfo_flagShift_LEVEL); | ^~~~~~~~~~~~~~~~~~~ gff.h: In member function ‘bool GffObj::operator>(GffObj&)’: gff.h:822:14: error: ‘getLevel’ was not declared in this scope; did you mean ‘setLevel’? 822 | if (getLevel()==d.getLevel()) { | ^~~~~~~~ | setLevel gff.h:822:28: error: ‘class GffObj’ has no member named ‘getLevel’; did you mean ‘setLevel’? 822 | if (getLevel()==d.getLevel()) { | ^~~~~~~~ | setLevel gff.h:825:42: error: ‘class GffObj’ has no member named ‘getLevel’; did you mean ‘setLevel’? 825 | } else return (getLevel()>d.getLevel()); | ^~~~~~~~ | setLevel gff.h: In member function ‘bool GffObj::operator<(GffObj&)’: gff.h:831:14: error: ‘getLevel’ was not declared in this scope; did you mean ‘setLevel’? 831 | if (getLevel()==d.getLevel()) { | ^~~~~~~~ | setLevel gff.h:831:28: error: ‘class GffObj’ has no member named ‘getLevel’; did you mean ‘setLevel’? 831 | if (getLevel()==d.getLevel()) { | ^~~~~~~~ | setLevel gff.h:834:41: error: ‘class GffObj’ has no member named ‘getLevel’; did you mean ‘setLevel’? 834 | } else return (getLevel() >& s2 = bundles[i-1]->ref_scaffolds(); | ^~ In file included from gff.h:12, from gtf_tracking.h:12, from bundles.h:22, from replicates.h:10, from common.cpp:28: GHash.hh: In instantiation of ‘const OBJ* GHash::shkAdd(const char*, const OBJ*, bool) [with OBJ = GffNameInfo]’: gff.h:249:19: required from here GHash.hh:243:16: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 243 | register int p,i,x,h,n; | ^ GHash.hh:243:18: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 243 | register int p,i,x,h,n; | ^ GHash.hh:243:20: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 243 | register int p,i,x,h,n; | ^ GHash.hh:243:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 243 | register int p,i,x,h,n; | ^ GHash.hh:243:24: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 243 | register int p,i,x,h,n; | ^ GHash.hh: In instantiation of ‘GHash::~GHash() [with OBJ = GffNameInfo]’: gff.h:252:87: required from here GHash.hh:551:16: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 551 | register int i; | ^ GHash.hh: In instantiation of ‘OBJ* GHash::Find(const char*, char**) [with OBJ = GffNameInfo]’: gff.h:268:30: required from here GHash.hh:385:16: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 385 | register int p,x,h,n; | ^ GHash.hh:385:18: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 385 | register int p,x,h,n; | ^ GHash.hh:385:20: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 385 | register int p,x,h,n; | ^ GHash.hh:385:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 385 | register int p,x,h,n; | ^ GHash.hh: In instantiation of ‘GHash::~GHash() [with OBJ = int]’: gff.h:1034:68: required from here GHash.hh:551:16: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 551 | register int i; | ^ GHash.hh: In instantiation of ‘GHash::~GHash() [with OBJ = GPVec]’: gff.h:1035:24: required from here GHash.hh:551:16: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] GHash.hh: In instantiation of ‘void GHash::Clear() [with OBJ = int]’: gff.h:1073:26: required from here GHash.hh:494:16: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 494 | register int i; | ^ GHash.hh: In instantiation of ‘void GHash::Clear() [with OBJ = GPVec]’: gff.h:1074:18: required from here GHash.hh:494:16: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] GHash.hh: In instantiation of ‘OBJ* GHash::Find(const char*, char**) [with OBJ = GFastaRec]’: GFastaIndex.h:50:24: required from here GHash.hh:385:16: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 385 | register int p,x,h,n; | ^ GHash.hh:385:18: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 385 | register int p,x,h,n; | ^ GHash.hh:385:20: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 385 | register int p,x,h,n; | ^ GHash.hh:385:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 385 | register int p,x,h,n; | ^ GHash.hh: In instantiation of ‘GHash::~GHash() [with OBJ = GFastaRec]’: GFastaIndex.h:58:59: required from here GHash.hh:551:16: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 551 | register int i; | ^ 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, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ GHash.hh: In instantiation of ‘void GHash::Resize(int) [with OBJ = GffNameInfo]’: GHash.hh:277:42: required from ‘const OBJ* GHash::shkAdd(const char*, const OBJ*, bool) [with OBJ = GffNameInfo]’ gff.h:249:19: required from here GHash.hh:168:16: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 168 | register int i,n,p,x,h; | ^ In file included from cufflinks.cpp:19: update_check.h: In function ‘bool get_current_version(char*)’: update_check.h:81:29: 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)); | ^~~~~~~~~~~~~~~~~~~~ GHash.hh:168:18: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 168 | register int i,n,p,x,h; | ^ GHash.hh:168:20: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 168 | register int i,n,p,x,h; | ^ GHash.hh:168:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 168 | register int i,n,p,x,h; | ^ GHash.hh:168:24: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 168 | register int i,n,p,x,h; | ^ 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:210:15: 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:419:15: 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:420:15: 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 { | ^~~~ make[3]: *** [Makefile:1677: common.o] Error 1 make[3]: *** Waiting for unfinished jobs.... 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 /usr/include/boost/math/tools/cxx03_warn.hpp:9, from /usr/include/boost/math/constants/constants.hpp:11, from /usr/include/boost/math/special_functions/gamma.hpp:24, from differential.cpp:16: /usr/include/boost/bind.hpp: At global scope: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ In file included from gff.h:8, from gtf_tracking.h:12, from bundles.h:22, from abundances.h:25, from differential.cpp:20: gdna.h:12:1: error: reference to ‘byte’ is ambiguous 12 | byte gdna2bit(char* &nt, int n=4); //pack n bases into a byte (n can be 1..4) | ^~~~ In file included from /usr/include/boost/config/compiler/gcc.hpp:165, from /usr/include/boost/config.hpp:39, from /usr/include/boost/numeric/ublas/vector.hpp:20, from differential.cpp:13: /usr/include/c++/11/cstddef:69:14: note: candidates are: ‘enum class std::byte’ 69 | enum class byte : unsigned char {}; | ^~~~ 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:75:23: note: ‘typedef unsigned char byte’ 75 | typedef unsigned char byte; | ^~~~ In file included from gff.h:8, from gtf_tracking.h:12, from bundles.h:22, from abundances.h:25, from differential.cpp:20: gdna.h:13:17: error: reference to ‘byte’ is ambiguous 13 | char g2bit2base(byte v2bit); //convert the 2-bit value into 'A', 'C', 'G' or 'T' | ^~~~ In file included from /usr/include/boost/config/compiler/gcc.hpp:165, from /usr/include/boost/config.hpp:39, from /usr/include/boost/numeric/ublas/vector.hpp:20, from differential.cpp:13: /usr/include/c++/11/cstddef:69:14: note: candidates are: ‘enum class std::byte’ 69 | enum class byte : unsigned char {}; | ^~~~ 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:75:23: note: ‘typedef unsigned char byte’ 75 | typedef unsigned char byte; | ^~~~ In file included from gff.h:12, from gtf_tracking.h:12, from bundles.h:22, from abundances.h:25, from differential.cpp:20: GHash.hh: In member function ‘GHash::GHashEntry* GHash::NextEntry()’: GHash.hh:90:23: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 90 | register int pos=fCurrentEntry; | ^~~ GHash.hh: In member function ‘void GHash::Resize(int)’: GHash.hh:168:16: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 168 | register int i,n,p,x,h; | ^ GHash.hh:168:18: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 168 | register int i,n,p,x,h; | ^ GHash.hh:168:20: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 168 | register int i,n,p,x,h; | ^ GHash.hh:168:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 168 | register int i,n,p,x,h; | ^ GHash.hh:168:24: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 168 | register int i,n,p,x,h; | ^ GHash.hh: In member function ‘const OBJ* GHash::Add(const char*, const OBJ*, bool)’: GHash.hh:202:16: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 202 | register int p,i,x,h,n; | ^ GHash.hh:202:18: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 202 | register int p,i,x,h,n; | ^ GHash.hh:202:20: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 202 | register int p,i,x,h,n; | ^ GHash.hh:202:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 202 | register int p,i,x,h,n; | ^ GHash.hh:202:24: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 202 | register int p,i,x,h,n; | ^ GHash.hh: In member function ‘const OBJ* GHash::shkAdd(const char*, const OBJ*, bool)’: GHash.hh:243:16: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 243 | register int p,i,x,h,n; | ^ GHash.hh:243:18: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 243 | register int p,i,x,h,n; | ^ GHash.hh:243:20: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 243 | register int p,i,x,h,n; | ^ GHash.hh:243:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 243 | register int p,i,x,h,n; | ^ GHash.hh:243:24: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 243 | register int p,i,x,h,n; | ^ GHash.hh: In member function ‘OBJ* GHash::Replace(const char*, const OBJ*, bool)’: GHash.hh:285:16: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 285 | register int p,i,x,h,n; | ^ GHash.hh:285:18: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 285 | register int p,i,x,h,n; | ^ GHash.hh:285:20: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 285 | register int p,i,x,h,n; | ^ GHash.hh:285:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 285 | register int p,i,x,h,n; | ^ GHash.hh:285:24: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 285 | register int p,i,x,h,n; | ^ GHash.hh: In member function ‘OBJ* GHash::Remove(const char*)’: GHash.hh:327:16: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 327 | register int p,x,h,n; | ^ GHash.hh:327:18: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 327 | register int p,x,h,n; | ^ GHash.hh:327:20: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 327 | register int p,x,h,n; | ^ GHash.hh:327:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 327 | register int p,x,h,n; | ^ GHash.hh: In member function ‘bool GHash::hasKey(const char*)’: GHash.hh:362:16: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 362 | register int p,x,h,n; | ^ GHash.hh:362:18: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 362 | register int p,x,h,n; | ^ GHash.hh:362:20: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 362 | register int p,x,h,n; | ^ GHash.hh:362:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 362 | register int p,x,h,n; | ^ GHash.hh: In member function ‘OBJ* GHash::Find(const char*, char**)’: GHash.hh:385:16: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 385 | register int p,x,h,n; | ^ GHash.hh:385:18: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 385 | register int p,x,h,n; | ^ GHash.hh:385:20: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 385 | register int p,x,h,n; | ^ GHash.hh:385:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 385 | register int p,x,h,n; | ^ GHash.hh: In member function ‘char* GHash::NextKey()’: GHash.hh:414:15: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 414 | register int pos=fCurrentEntry; | ^~~ GHash.hh: In member function ‘OBJ* GHash::NextData()’: GHash.hh:427:15: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 427 | register int pos=fCurrentEntry; | ^~~ GHash.hh: In member function ‘OBJ* GHash::NextData(char*&)’: GHash.hh:441:15: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 441 | register int pos=fCurrentEntry; | ^~~ GHash.hh: In member function ‘int GHash::First() const’: GHash.hh:459:16: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 459 | register int pos=0; | ^~~ GHash.hh: In member function ‘int GHash::Last() const’: GHash.hh:467:16: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 467 | register int pos=fCapacity-1; | ^~~ GHash.hh: In member function ‘void GHash::Clear()’: GHash.hh:494:16: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 494 | register int i; | ^ GHash.hh: In destructor ‘virtual GHash::~GHash()’: GHash.hh:551:16: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 551 | register int i; | ^ In file included from gtf_tracking.h:12, from bundles.h:22, from abundances.h:25, from differential.cpp:20: gff.h: At global scope: gff.h:46:14: error: reference to ‘byte’ is ambiguous 46 | extern const byte gfo_flagShift_LEVEL; | ^~~~ In file included from /usr/include/boost/config/compiler/gcc.hpp:165, from /usr/include/boost/config.hpp:39, from /usr/include/boost/numeric/ublas/vector.hpp:20, from differential.cpp:13: /usr/include/c++/11/cstddef:69:14: note: candidates are: ‘enum class std::byte’ 69 | enum class byte : unsigned char {}; | ^~~~ 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:75:23: note: ‘typedef unsigned char byte’ 75 | typedef unsigned char byte; | ^~~~ In file included from gtf_tracking.h:12, from bundles.h:22, from abundances.h:25, from differential.cpp:20: gff.h:505:17: error: reference to ‘byte’ is ambiguous 505 | void setLevel(byte v) { | ^~~~ In file included from /usr/include/boost/config/compiler/gcc.hpp:165, from /usr/include/boost/config.hpp:39, from /usr/include/boost/numeric/ublas/vector.hpp:20, from differential.cpp:13: /usr/include/c++/11/cstddef:69:14: note: candidates are: ‘enum class std::byte’ 69 | enum class byte : unsigned char {}; | ^~~~ 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:75:23: note: ‘typedef unsigned char byte’ 75 | typedef unsigned char byte; | ^~~~ In file included from gtf_tracking.h:12, from bundles.h:22, from abundances.h:25, from differential.cpp:20: gff.h:505:17: error: ‘byte’ has not been declared 505 | void setLevel(byte v) { | ^~~~ gff.h:509:3: error: reference to ‘byte’ is ambiguous 509 | byte incLevel() { | ^~~~ In file included from /usr/include/boost/config/compiler/gcc.hpp:165, from /usr/include/boost/config.hpp:39, from /usr/include/boost/numeric/ublas/vector.hpp:20, from differential.cpp:13: /usr/include/c++/11/cstddef:69:14: note: candidates are: ‘enum class std::byte’ 69 | enum class byte : unsigned char {}; | ^~~~ 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:75:23: note: ‘typedef unsigned char byte’ 75 | typedef unsigned char byte; | ^~~~ In file included from gtf_tracking.h:12, from bundles.h:22, from abundances.h:25, from differential.cpp:20: gff.h:515:3: error: reference to ‘byte’ is ambiguous 515 | byte getLevel() { | ^~~~ In file included from /usr/include/boost/config/compiler/gcc.hpp:165, from /usr/include/boost/config.hpp:39, from /usr/include/boost/numeric/ublas/vector.hpp:20, from differential.cpp:13: /usr/include/c++/11/cstddef:69:14: note: candidates are: ‘enum class std::byte’ 69 | enum class byte : unsigned char {}; | ^~~~ 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:75:23: note: ‘typedef unsigned char byte’ 75 | typedef unsigned char byte; | ^~~~ In file included from gtf_tracking.h:12, from bundles.h:22, from abundances.h:25, from differential.cpp:20: gff.h: In member function ‘void GffObj::setLevel(int)’: gff.h:507:39: error: ‘gfo_flagShift_LEVEL’ was not declared in this scope 507 | else flags &= ~(((uint)v) << gfo_flagShift_LEVEL); | ^~~~~~~~~~~~~~~~~~~ gff.h: In member function ‘bool GffObj::operator>(GffObj&)’: gff.h:822:14: error: ‘getLevel’ was not declared in this scope; did you mean ‘setLevel’? 822 | if (getLevel()==d.getLevel()) { | ^~~~~~~~ | setLevel gff.h:822:28: error: ‘class GffObj’ has no member named ‘getLevel’; did you mean ‘setLevel’? 822 | if (getLevel()==d.getLevel()) { | ^~~~~~~~ | setLevel gff.h:825:42: error: ‘class GffObj’ has no member named ‘getLevel’; did you mean ‘setLevel’? 825 | } else return (getLevel()>d.getLevel()); | ^~~~~~~~ | setLevel gff.h: In member function ‘bool GffObj::operator<(GffObj&)’: gff.h:831:14: error: ‘getLevel’ was not declared in this scope; did you mean ‘setLevel’? 831 | if (getLevel()==d.getLevel()) { | ^~~~~~~~ | setLevel gff.h:831:28: error: ‘class GffObj’ has no member named ‘getLevel’; did you mean ‘setLevel’? 831 | if (getLevel()==d.getLevel()) { | ^~~~~~~~ | setLevel gff.h:834:41: error: ‘class GffObj’ has no member named ‘getLevel’; did you mean ‘setLevel’? 834 | } else return (getLevel() + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/math/tools/cxx03_warn.hpp:9, from /usr/include/boost/math/constants/constants.hpp:11, from /usr/include/boost/math/special_functions/gamma.hpp:24, 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: /usr/include/boost/bind.hpp: At global scope: /usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’ 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ In file included from gff.h:8, from gtf_tracking.h:12, from bundles.h:22, from abundances.h:25, from clustering.h:38, from clustering.cpp:10: gdna.h:12:1: error: reference to ‘byte’ is ambiguous 12 | byte gdna2bit(char* &nt, int n=4); //pack n bases into a byte (n can be 1..4) | ^~~~ In file included from /usr/include/boost/graph/vector_as_graph.hpp:20, from clustering.h:17, from clustering.cpp:10: /usr/include/c++/11/cstddef:69:14: note: candidates are: ‘enum class std::byte’ 69 | enum class byte : unsigned char {}; | ^~~~ 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:75:23: note: ‘typedef unsigned char byte’ 75 | typedef unsigned char byte; | ^~~~ In file included from gff.h:8, from gtf_tracking.h:12, from bundles.h:22, from abundances.h:25, from clustering.h:38, from clustering.cpp:10: gdna.h:13:17: error: reference to ‘byte’ is ambiguous 13 | char g2bit2base(byte v2bit); //convert the 2-bit value into 'A', 'C', 'G' or 'T' | ^~~~ In file included from /usr/include/boost/graph/vector_as_graph.hpp:20, from clustering.h:17, from clustering.cpp:10: /usr/include/c++/11/cstddef:69:14: note: candidates are: ‘enum class std::byte’ 69 | enum class byte : unsigned char {}; | ^~~~ 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:75:23: note: ‘typedef unsigned char byte’ 75 | typedef unsigned char byte; | ^~~~ In file included from gff.h:12, from gtf_tracking.h:12, from bundles.h:22, from abundances.h:25, from clustering.h:38, from clustering.cpp:10: GHash.hh: In member function ‘GHash::GHashEntry* GHash::NextEntry()’: GHash.hh:90:23: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 90 | register int pos=fCurrentEntry; | ^~~ GHash.hh: In member function ‘void GHash::Resize(int)’: GHash.hh:168:16: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 168 | register int i,n,p,x,h; | ^ GHash.hh:168:18: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 168 | register int i,n,p,x,h; | ^ GHash.hh:168:20: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 168 | register int i,n,p,x,h; | ^ GHash.hh:168:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 168 | register int i,n,p,x,h; | ^ GHash.hh:168:24: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 168 | register int i,n,p,x,h; | ^ GHash.hh: In member function ‘const OBJ* GHash::Add(const char*, const OBJ*, bool)’: GHash.hh:202:16: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 202 | register int p,i,x,h,n; | ^ GHash.hh:202:18: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 202 | register int p,i,x,h,n; | ^ GHash.hh:202:20: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 202 | register int p,i,x,h,n; | ^ GHash.hh:202:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 202 | register int p,i,x,h,n; | ^ GHash.hh:202:24: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 202 | register int p,i,x,h,n; | ^ GHash.hh: In member function ‘const OBJ* GHash::shkAdd(const char*, const OBJ*, bool)’: GHash.hh:243:16: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 243 | register int p,i,x,h,n; | ^ GHash.hh:243:18: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 243 | register int p,i,x,h,n; | ^ GHash.hh:243:20: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 243 | register int p,i,x,h,n; | ^ GHash.hh:243:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 243 | register int p,i,x,h,n; | ^ GHash.hh:243:24: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 243 | register int p,i,x,h,n; | ^ GHash.hh: In member function ‘OBJ* GHash::Replace(const char*, const OBJ*, bool)’: GHash.hh:285:16: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 285 | register int p,i,x,h,n; | ^ GHash.hh:285:18: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 285 | register int p,i,x,h,n; | ^ GHash.hh:285:20: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 285 | register int p,i,x,h,n; | ^ GHash.hh:285:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 285 | register int p,i,x,h,n; | ^ GHash.hh:285:24: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 285 | register int p,i,x,h,n; | ^ GHash.hh: In member function ‘OBJ* GHash::Remove(const char*)’: GHash.hh:327:16: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 327 | register int p,x,h,n; | ^ GHash.hh:327:18: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 327 | register int p,x,h,n; | ^ GHash.hh:327:20: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 327 | register int p,x,h,n; | ^ GHash.hh:327:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 327 | register int p,x,h,n; | ^ GHash.hh: In member function ‘bool GHash::hasKey(const char*)’: GHash.hh:362:16: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 362 | register int p,x,h,n; | ^ GHash.hh:362:18: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 362 | register int p,x,h,n; | ^ GHash.hh:362:20: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 362 | register int p,x,h,n; | ^ GHash.hh:362:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 362 | register int p,x,h,n; | ^ GHash.hh: In member function ‘OBJ* GHash::Find(const char*, char**)’: GHash.hh:385:16: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 385 | register int p,x,h,n; | ^ GHash.hh:385:18: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 385 | register int p,x,h,n; | ^ GHash.hh:385:20: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 385 | register int p,x,h,n; | ^ GHash.hh:385:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 385 | register int p,x,h,n; | ^ GHash.hh: In member function ‘char* GHash::NextKey()’: GHash.hh:414:15: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 414 | register int pos=fCurrentEntry; | ^~~ GHash.hh: In member function ‘OBJ* GHash::NextData()’: GHash.hh:427:15: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 427 | register int pos=fCurrentEntry; | ^~~ GHash.hh: In member function ‘OBJ* GHash::NextData(char*&)’: GHash.hh:441:15: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 441 | register int pos=fCurrentEntry; | ^~~ GHash.hh: In member function ‘int GHash::First() const’: GHash.hh:459:16: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 459 | register int pos=0; | ^~~ GHash.hh: In member function ‘int GHash::Last() const’: GHash.hh:467:16: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 467 | register int pos=fCapacity-1; | ^~~ GHash.hh: In member function ‘void GHash::Clear()’: GHash.hh:494:16: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 494 | register int i; | ^ GHash.hh: In destructor ‘virtual GHash::~GHash()’: GHash.hh:551:16: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 551 | register int i; | ^ In file included from gtf_tracking.h:12, from bundles.h:22, from abundances.h:25, from clustering.h:38, from clustering.cpp:10: gff.h: At global scope: gff.h:46:14: error: reference to ‘byte’ is ambiguous 46 | extern const byte gfo_flagShift_LEVEL; | ^~~~ In file included from /usr/include/boost/graph/vector_as_graph.hpp:20, from clustering.h:17, from clustering.cpp:10: /usr/include/c++/11/cstddef:69:14: note: candidates are: ‘enum class std::byte’ 69 | enum class byte : unsigned char {}; | ^~~~ 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:75:23: note: ‘typedef unsigned char byte’ 75 | typedef unsigned char byte; | ^~~~ In file included from gtf_tracking.h:12, from bundles.h:22, from abundances.h:25, from clustering.h:38, from clustering.cpp:10: gff.h:505:17: error: reference to ‘byte’ is ambiguous 505 | void setLevel(byte v) { | ^~~~ In file included from /usr/include/boost/graph/vector_as_graph.hpp:20, from clustering.h:17, from clustering.cpp:10: /usr/include/c++/11/cstddef:69:14: note: candidates are: ‘enum class std::byte’ 69 | enum class byte : unsigned char {}; | ^~~~ 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:75:23: note: ‘typedef unsigned char byte’ 75 | typedef unsigned char byte; | ^~~~ In file included from gtf_tracking.h:12, from bundles.h:22, from abundances.h:25, from clustering.h:38, from clustering.cpp:10: gff.h:505:17: error: ‘byte’ has not been declared 505 | void setLevel(byte v) { | ^~~~ gff.h:509:3: error: reference to ‘byte’ is ambiguous 509 | byte incLevel() { | ^~~~ In file included from /usr/include/boost/graph/vector_as_graph.hpp:20, from clustering.h:17, from clustering.cpp:10: /usr/include/c++/11/cstddef:69:14: note: candidates are: ‘enum class std::byte’ 69 | enum class byte : unsigned char {}; | ^~~~ 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:75:23: note: ‘typedef unsigned char byte’ 75 | typedef unsigned char byte; | ^~~~ In file included from gtf_tracking.h:12, from bundles.h:22, from abundances.h:25, from clustering.h:38, from clustering.cpp:10: gff.h:515:3: error: reference to ‘byte’ is ambiguous 515 | byte getLevel() { | ^~~~ In file included from /usr/include/boost/graph/vector_as_graph.hpp:20, from clustering.h:17, from clustering.cpp:10: /usr/include/c++/11/cstddef:69:14: note: candidates are: ‘enum class std::byte’ 69 | enum class byte : unsigned char {}; | ^~~~ 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:75:23: note: ‘typedef unsigned char byte’ 75 | typedef unsigned char byte; | ^~~~ In file included from gtf_tracking.h:12, from bundles.h:22, from abundances.h:25, from clustering.h:38, from clustering.cpp:10: gff.h: In member function ‘void GffObj::setLevel(int)’: gff.h:507:39: error: ‘gfo_flagShift_LEVEL’ was not declared in this scope 507 | else flags &= ~(((uint)v) << gfo_flagShift_LEVEL); | ^~~~~~~~~~~~~~~~~~~ In file included from gff.h:8, from gtf_tracking.h:12, from bundles.h:22, from abundances.h:25, from clustering.h:38, from cufflinks.cpp:20: gdna.h:12:1: error: reference to ‘byte’ is ambiguous 12 | byte gdna2bit(char* &nt, int n=4); //pack n bases into a byte (n can be 1..4) | ^~~~ In file included from /usr/include/boost/config/compiler/gcc.hpp:165, from /usr/include/boost/config.hpp:39, from /usr/include/boost/math/special_functions/detail/round_fwd.hpp:11, from /usr/include/boost/math/special_functions/math_fwd.hpp:27, from /usr/include/boost/math/special_functions/erf.hpp:13, from /usr/include/boost/math/distributions/normal.hpp:19, from common.h:27, from cufflinks.cpp:14: /usr/include/c++/11/cstddef:69:14: note: candidates are: ‘enum class std::byte’ 69 | enum class byte : unsigned char {}; | ^~~~ 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:75:23: note: ‘typedef unsigned char byte’ 75 | typedef unsigned char byte; | ^~~~ In file included from gff.h:8, from gtf_tracking.h:12, from bundles.h:22, from abundances.h:25, from clustering.h:38, from cufflinks.cpp:20: gdna.h:13:17: error: reference to ‘byte’ is ambiguous 13 | char g2bit2base(byte v2bit); //convert the 2-bit value into 'A', 'C', 'G' or 'T' | ^~~~ In file included from /usr/include/boost/config/compiler/gcc.hpp:165, from /usr/include/boost/config.hpp:39, from /usr/include/boost/math/special_functions/detail/round_fwd.hpp:11, from /usr/include/boost/math/special_functions/math_fwd.hpp:27, from /usr/include/boost/math/special_functions/erf.hpp:13, from /usr/include/boost/math/distributions/normal.hpp:19, from common.h:27, from cufflinks.cpp:14: /usr/include/c++/11/cstddef:69:14: note: candidates are: ‘enum class std::byte’ 69 | enum class byte : unsigned char {}; | ^~~~ 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:75:23: note: ‘typedef unsigned char byte’ 75 | typedef unsigned char byte; | ^~~~ gff.h: In member function ‘bool GffObj::operator>(GffObj&)’: gff.h:822:14: error: ‘getLevel’ was not declared in this scope; did you mean ‘setLevel’? 822 | if (getLevel()==d.getLevel()) { | ^~~~~~~~ | setLevel gff.h:822:28: error: ‘class GffObj’ has no member named ‘getLevel’; did you mean ‘setLevel’? 822 | if (getLevel()==d.getLevel()) { | ^~~~~~~~ | setLevel gff.h:825:42: error: ‘class GffObj’ has no member named ‘getLevel’; did you mean ‘setLevel’? 825 | } else return (getLevel()>d.getLevel()); | ^~~~~~~~ | setLevel gff.h: In member function ‘bool GffObj::operator<(GffObj&)’: gff.h:831:14: error: ‘getLevel’ was not declared in this scope; did you mean ‘setLevel’? 831 | if (getLevel()==d.getLevel()) { | ^~~~~~~~ | setLevel gff.h:831:28: error: ‘class GffObj’ has no member named ‘getLevel’; did you mean ‘setLevel’? 831 | if (getLevel()==d.getLevel()) { | ^~~~~~~~ | setLevel gff.h:834:41: error: ‘class GffObj’ has no member named ‘getLevel’; did you mean ‘setLevel’? 834 | } else return (getLevel()::GHashEntry* GHash::NextEntry()’: GHash.hh:90:23: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 90 | register int pos=fCurrentEntry; | ^~~ GHash.hh: In member function ‘void GHash::Resize(int)’: GHash.hh:168:16: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 168 | register int i,n,p,x,h; | ^ GHash.hh:168:18: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 168 | register int i,n,p,x,h; | ^ GHash.hh:168:20: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 168 | register int i,n,p,x,h; | ^ GHash.hh:168:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 168 | register int i,n,p,x,h; | ^ GHash.hh:168:24: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 168 | register int i,n,p,x,h; | ^ GHash.hh: In member function ‘const OBJ* GHash::Add(const char*, const OBJ*, bool)’: GHash.hh:202:16: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 202 | register int p,i,x,h,n; | ^ GHash.hh:202:18: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 202 | register int p,i,x,h,n; | ^ GHash.hh:202:20: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 202 | register int p,i,x,h,n; | ^ GHash.hh:202:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 202 | register int p,i,x,h,n; | ^ GHash.hh:202:24: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 202 | register int p,i,x,h,n; | ^ GHash.hh: In member function ‘const OBJ* GHash::shkAdd(const char*, const OBJ*, bool)’: GHash.hh:243:16: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 243 | register int p,i,x,h,n; | ^ GHash.hh:243:18: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 243 | register int p,i,x,h,n; | ^ GHash.hh:243:20: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 243 | register int p,i,x,h,n; | ^ GHash.hh:243:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 243 | register int p,i,x,h,n; | ^ GHash.hh:243:24: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 243 | register int p,i,x,h,n; | ^ GHash.hh: In member function ‘OBJ* GHash::Replace(const char*, const OBJ*, bool)’: GHash.hh:285:16: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 285 | register int p,i,x,h,n; | ^ GHash.hh:285:18: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 285 | register int p,i,x,h,n; | ^ GHash.hh:285:20: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 285 | register int p,i,x,h,n; | ^ GHash.hh:285:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 285 | register int p,i,x,h,n; | ^ GHash.hh:285:24: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 285 | register int p,i,x,h,n; | ^ GHash.hh: In member function ‘OBJ* GHash::Remove(const char*)’: GHash.hh:327:16: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 327 | register int p,x,h,n; | ^ GHash.hh:327:18: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 327 | register int p,x,h,n; | ^ GHash.hh:327:20: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 327 | register int p,x,h,n; | ^ GHash.hh:327:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 327 | register int p,x,h,n; | ^ GHash.hh: In member function ‘bool GHash::hasKey(const char*)’: GHash.hh:362:16: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 362 | register int p,x,h,n; | ^ GHash.hh:362:18: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 362 | register int p,x,h,n; | ^ GHash.hh:362:20: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 362 | register int p,x,h,n; | ^ GHash.hh:362:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 362 | register int p,x,h,n; | ^ GHash.hh: In member function ‘OBJ* GHash::Find(const char*, char**)’: GHash.hh:385:16: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 385 | register int p,x,h,n; | ^ GHash.hh:385:18: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 385 | register int p,x,h,n; | ^ GHash.hh:385:20: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 385 | register int p,x,h,n; | ^ GHash.hh:385:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 385 | register int p,x,h,n; | ^ GHash.hh: In member function ‘char* GHash::NextKey()’: GHash.hh:414:15: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 414 | register int pos=fCurrentEntry; | ^~~ GHash.hh: In member function ‘OBJ* GHash::NextData()’: GHash.hh:427:15: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 427 | register int pos=fCurrentEntry; | ^~~ GHash.hh: In member function ‘OBJ* GHash::NextData(char*&)’: GHash.hh:441:15: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 441 | register int pos=fCurrentEntry; | ^~~ GHash.hh: In member function ‘int GHash::First() const’: GHash.hh:459:16: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 459 | register int pos=0; | ^~~ GHash.hh: In member function ‘int GHash::Last() const’: GHash.hh:467:16: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 467 | register int pos=fCapacity-1; | ^~~ GHash.hh: In member function ‘void GHash::Clear()’: GHash.hh:494:16: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 494 | register int i; | ^ GHash.hh: In destructor ‘virtual GHash::~GHash()’: GHash.hh:551:16: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 551 | register int i; | ^ In file included from gtf_tracking.h:12, from bundles.h:22, from abundances.h:25, from clustering.h:38, from cufflinks.cpp:20: gff.h: At global scope: gff.h:46:14: error: reference to ‘byte’ is ambiguous 46 | extern const byte gfo_flagShift_LEVEL; | ^~~~ In file included from /usr/include/boost/config/compiler/gcc.hpp:165, from /usr/include/boost/config.hpp:39, from /usr/include/boost/math/special_functions/detail/round_fwd.hpp:11, from /usr/include/boost/math/special_functions/math_fwd.hpp:27, from /usr/include/boost/math/special_functions/erf.hpp:13, from /usr/include/boost/math/distributions/normal.hpp:19, from common.h:27, from cufflinks.cpp:14: /usr/include/c++/11/cstddef:69:14: note: candidates are: ‘enum class std::byte’ 69 | enum class byte : unsigned char {}; | ^~~~ 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:75:23: note: ‘typedef unsigned char byte’ 75 | typedef unsigned char byte; | ^~~~ In file included from gtf_tracking.h:12, from bundles.h:22, from abundances.h:25, from clustering.h:38, from cufflinks.cpp:20: gff.h:505:17: error: reference to ‘byte’ is ambiguous 505 | void setLevel(byte v) { | ^~~~ In file included from /usr/include/boost/config/compiler/gcc.hpp:165, from /usr/include/boost/config.hpp:39, from /usr/include/boost/math/special_functions/detail/round_fwd.hpp:11, from /usr/include/boost/math/special_functions/math_fwd.hpp:27, from /usr/include/boost/math/special_functions/erf.hpp:13, from /usr/include/boost/math/distributions/normal.hpp:19, from common.h:27, from cufflinks.cpp:14: /usr/include/c++/11/cstddef:69:14: note: candidates are: ‘enum class std::byte’ 69 | enum class byte : unsigned char {}; | ^~~~ 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:75:23: note: ‘typedef unsigned char byte’ 75 | typedef unsigned char byte; | ^~~~ In file included from gtf_tracking.h:12, from bundles.h:22, from abundances.h:25, from clustering.h:38, from cufflinks.cpp:20: gff.h:505:17: error: ‘byte’ has not been declared 505 | void setLevel(byte v) { | ^~~~ gff.h:509:3: error: reference to ‘byte’ is ambiguous 509 | byte incLevel() { | ^~~~ In file included from /usr/include/boost/config/compiler/gcc.hpp:165, from /usr/include/boost/config.hpp:39, from /usr/include/boost/math/special_functions/detail/round_fwd.hpp:11, from /usr/include/boost/math/special_functions/math_fwd.hpp:27, from /usr/include/boost/math/special_functions/erf.hpp:13, from /usr/include/boost/math/distributions/normal.hpp:19, from common.h:27, from cufflinks.cpp:14: /usr/include/c++/11/cstddef:69:14: note: candidates are: ‘enum class std::byte’ 69 | enum class byte : unsigned char {}; | ^~~~ 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:75:23: note: ‘typedef unsigned char byte’ 75 | typedef unsigned char byte; | ^~~~ In file included from gtf_tracking.h:12, from bundles.h:22, from abundances.h:25, from clustering.h:38, from cufflinks.cpp:20: gff.h:515:3: error: reference to ‘byte’ is ambiguous 515 | byte getLevel() { | ^~~~ In file included from /usr/include/boost/config/compiler/gcc.hpp:165, from /usr/include/boost/config.hpp:39, from /usr/include/boost/math/special_functions/detail/round_fwd.hpp:11, from /usr/include/boost/math/special_functions/math_fwd.hpp:27, from /usr/include/boost/math/special_functions/erf.hpp:13, from /usr/include/boost/math/distributions/normal.hpp:19, from common.h:27, from cufflinks.cpp:14: /usr/include/c++/11/cstddef:69:14: note: candidates are: ‘enum class std::byte’ 69 | enum class byte : unsigned char {}; | ^~~~ 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:75:23: note: ‘typedef unsigned char byte’ 75 | typedef unsigned char byte; | ^~~~ In file included from gtf_tracking.h:12, from bundles.h:22, from abundances.h:25, from clustering.h:38, from cufflinks.cpp:20: gff.h: In member function ‘void GffObj::setLevel(int)’: gff.h:507:39: error: ‘gfo_flagShift_LEVEL’ was not declared in this scope 507 | else flags &= ~(((uint)v) << gfo_flagShift_LEVEL); | ^~~~~~~~~~~~~~~~~~~ gff.h: In member function ‘bool GffObj::operator>(GffObj&)’: gff.h:822:14: error: ‘getLevel’ was not declared in this scope; did you mean ‘setLevel’? 822 | if (getLevel()==d.getLevel()) { | ^~~~~~~~ | setLevel gff.h:822:28: error: ‘class GffObj’ has no member named ‘getLevel’; did you mean ‘setLevel’? 822 | if (getLevel()==d.getLevel()) { | ^~~~~~~~ | setLevel gff.h:825:42: error: ‘class GffObj’ has no member named ‘getLevel’; did you mean ‘setLevel’? 825 | } else return (getLevel()>d.getLevel()); | ^~~~~~~~ | setLevel gff.h: In member function ‘bool GffObj::operator<(GffObj&)’: gff.h:831:14: error: ‘getLevel’ was not declared in this scope; did you mean ‘setLevel’? 831 | if (getLevel()==d.getLevel()) { | ^~~~~~~~ | setLevel gff.h:831:28: error: ‘class GffObj’ has no member named ‘getLevel’; did you mean ‘setLevel’? 831 | if (getLevel()==d.getLevel()) { | ^~~~~~~~ | setLevel gff.h:834:41: error: ‘class GffObj’ has no member named ‘getLevel’; did you mean ‘setLevel’? 834 | } else return (getLevel() >& s2 = bundles[i-1]->ref_scaffolds(); | ^~ 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(); | ^~ In file included from gff.h:12, from gtf_tracking.h:12, from bundles.h:22, from abundances.h:25, from clustering.h:38, from clustering.cpp:10: GHash.hh: In instantiation of ‘const OBJ* GHash::shkAdd(const char*, const OBJ*, bool) [with OBJ = GffNameInfo]’: gff.h:249:19: required from here GHash.hh:243:16: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 243 | register int p,i,x,h,n; | ^ GHash.hh:243:18: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 243 | register int p,i,x,h,n; | ^ GHash.hh:243:20: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 243 | register int p,i,x,h,n; | ^ GHash.hh:243:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 243 | register int p,i,x,h,n; | ^ GHash.hh:243:24: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 243 | register int p,i,x,h,n; | ^ GHash.hh: In instantiation of ‘GHash::~GHash() [with OBJ = GffNameInfo]’: gff.h:252:87: required from here GHash.hh:551:16: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 551 | register int i; | ^ GHash.hh: In instantiation of ‘OBJ* GHash::Find(const char*, char**) [with OBJ = GffNameInfo]’: gff.h:268:30: required from here GHash.hh:385:16: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 385 | register int p,x,h,n; | ^ GHash.hh:385:18: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 385 | register int p,x,h,n; | ^ GHash.hh:385:20: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 385 | register int p,x,h,n; | ^ GHash.hh:385:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 385 | register int p,x,h,n; | ^ GHash.hh: In instantiation of ‘GHash::~GHash() [with OBJ = int]’: gff.h:1034:68: required from here GHash.hh:551:16: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 551 | register int i; | ^ GHash.hh: In instantiation of ‘GHash::~GHash() [with OBJ = GPVec]’: gff.h:1035:24: required from here GHash.hh:551:16: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] GHash.hh: In instantiation of ‘void GHash::Clear() [with OBJ = int]’: gff.h:1073:26: required from here GHash.hh:494:16: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 494 | register int i; | ^ GHash.hh: In instantiation of ‘void GHash::Clear() [with OBJ = GPVec]’: gff.h:1074:18: required from here GHash.hh:494:16: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] GHash.hh: In instantiation of ‘OBJ* GHash::Find(const char*, char**) [with OBJ = GFastaRec]’: GFastaIndex.h:50:24: required from here GHash.hh:385:16: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 385 | register int p,x,h,n; | ^ GHash.hh:385:18: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 385 | register int p,x,h,n; | ^ GHash.hh:385:20: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 385 | register int p,x,h,n; | ^ GHash.hh:385:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 385 | register int p,x,h,n; | ^ GHash.hh: In instantiation of ‘GHash::~GHash() [with OBJ = GFastaRec]’: GFastaIndex.h:58:59: required from here GHash.hh:551:16: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 551 | register int i; | ^ 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, | ^~~~~~~~~~~~~~~~~~ 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:693:9: 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:1279:9: 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:1489:52: 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) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ GHash.hh: In instantiation of ‘void GHash::Resize(int) [with OBJ = GffNameInfo]’: GHash.hh:277:42: required from ‘const OBJ* GHash::shkAdd(const char*, const OBJ*, bool) [with OBJ = GffNameInfo]’ gff.h:249:19: required from here GHash.hh:168:16: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 168 | register int i,n,p,x,h; | ^ GHash.hh:168:18: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 168 | register int i,n,p,x,h; | ^ GHash.hh:168:20: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 168 | register int i,n,p,x,h; | ^ GHash.hh:168:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 168 | register int i,n,p,x,h; | ^ GHash.hh:168:24: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 168 | register int i,n,p,x,h; | ^ In file included from gff.h:12, from gtf_tracking.h:12, from bundles.h:22, from abundances.h:25, from clustering.h:38, from cufflinks.cpp:20: GHash.hh: In instantiation of ‘const OBJ* GHash::shkAdd(const char*, const OBJ*, bool) [with OBJ = GffNameInfo]’: gff.h:249:19: required from here GHash.hh:243:16: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 243 | register int p,i,x,h,n; | ^ GHash.hh:243:18: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 243 | register int p,i,x,h,n; | ^ GHash.hh:243:20: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 243 | register int p,i,x,h,n; | ^ GHash.hh:243:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 243 | register int p,i,x,h,n; | ^ GHash.hh:243:24: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 243 | register int p,i,x,h,n; | ^ GHash.hh: In instantiation of ‘GHash::~GHash() [with OBJ = GffNameInfo]’: gff.h:252:87: required from here GHash.hh:551:16: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 551 | register int i; | ^ GHash.hh: In instantiation of ‘OBJ* GHash::Find(const char*, char**) [with OBJ = GffNameInfo]’: gff.h:268:30: required from here GHash.hh:385:16: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 385 | register int p,x,h,n; | ^ GHash.hh:385:18: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 385 | register int p,x,h,n; | ^ GHash.hh:385:20: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 385 | register int p,x,h,n; | ^ GHash.hh:385:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 385 | register int p,x,h,n; | ^ GHash.hh: In instantiation of ‘GHash::~GHash() [with OBJ = int]’: gff.h:1034:68: required from here GHash.hh:551:16: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 551 | register int i; | ^ GHash.hh: In instantiation of ‘GHash::~GHash() [with OBJ = GPVec]’: gff.h:1035:24: required from here GHash.hh:551:16: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] GHash.hh: In instantiation of ‘void GHash::Clear() [with OBJ = int]’: gff.h:1073:26: required from here GHash.hh:494:16: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 494 | register int i; | ^ GHash.hh: In instantiation of ‘void GHash::Clear() [with OBJ = GPVec]’: gff.h:1074:18: required from here GHash.hh:494:16: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] GHash.hh: In instantiation of ‘OBJ* GHash::Find(const char*, char**) [with OBJ = GFastaRec]’: GFastaIndex.h:50:24: required from here GHash.hh:385:16: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 385 | register int p,x,h,n; | ^ GHash.hh:385:18: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 385 | register int p,x,h,n; | ^ GHash.hh:385:20: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 385 | register int p,x,h,n; | ^ GHash.hh:385:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 385 | register int p,x,h,n; | ^ GHash.hh: In instantiation of ‘GHash::~GHash() [with OBJ = GFastaRec]’: GFastaIndex.h:58:59: required from here GHash.hh:551:16: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 551 | register int i; | ^ 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:210:15: 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 { | ^~~~~ 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()) | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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:419:15: 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:420:15: 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 { | ^~~~ 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); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ GHash.hh: In instantiation of ‘void GHash::Resize(int) [with OBJ = GffNameInfo]’: GHash.hh:277:42: required from ‘const OBJ* GHash::shkAdd(const char*, const OBJ*, bool) [with OBJ = GffNameInfo]’ gff.h:249:19: required from here GHash.hh:168:16: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 168 | register int i,n,p,x,h; | ^ GHash.hh:168:18: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 168 | register int i,n,p,x,h; | ^ GHash.hh:168:20: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 168 | register int i,n,p,x,h; | ^ GHash.hh:168:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 168 | register int i,n,p,x,h; | ^ GHash.hh:168:24: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 168 | register int i,n,p,x,h; | ^ In file included from gff.h:12, from gtf_tracking.h:12, from bundles.h:22, from abundances.h:25, from differential.cpp:20: GHash.hh: In instantiation of ‘const OBJ* GHash::shkAdd(const char*, const OBJ*, bool) [with OBJ = GffNameInfo]’: gff.h:249:19: required from here GHash.hh:243:16: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 243 | register int p,i,x,h,n; | ^ GHash.hh:243:18: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 243 | register int p,i,x,h,n; | ^ GHash.hh:243:20: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 243 | register int p,i,x,h,n; | ^ GHash.hh:243:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 243 | register int p,i,x,h,n; | ^ GHash.hh:243:24: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 243 | register int p,i,x,h,n; | ^ GHash.hh: In instantiation of ‘GHash::~GHash() [with OBJ = GffNameInfo]’: gff.h:252:87: required from here GHash.hh:551:16: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 551 | register int i; | ^ GHash.hh: In instantiation of ‘OBJ* GHash::Find(const char*, char**) [with OBJ = GffNameInfo]’: gff.h:268:30: required from here GHash.hh:385:16: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 385 | register int p,x,h,n; | ^ GHash.hh:385:18: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 385 | register int p,x,h,n; | ^ GHash.hh:385:20: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 385 | register int p,x,h,n; | ^ GHash.hh:385:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 385 | register int p,x,h,n; | ^ GHash.hh: In instantiation of ‘GHash::~GHash() [with OBJ = int]’: gff.h:1034:68: required from here GHash.hh:551:16: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 551 | register int i; | ^ GHash.hh: In instantiation of ‘GHash::~GHash() [with OBJ = GPVec]’: gff.h:1035:24: required from here GHash.hh:551:16: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] GHash.hh: In instantiation of ‘void GHash::Clear() [with OBJ = int]’: gff.h:1073:26: required from here GHash.hh:494:16: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 494 | register int i; | ^ GHash.hh: In instantiation of ‘void GHash::Clear() [with OBJ = GPVec]’: gff.h:1074:18: required from here GHash.hh:494:16: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] GHash.hh: In instantiation of ‘OBJ* GHash::Find(const char*, char**) [with OBJ = GFastaRec]’: GFastaIndex.h:50:24: required from here GHash.hh:385:16: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 385 | register int p,x,h,n; | ^ GHash.hh:385:18: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 385 | register int p,x,h,n; | ^ GHash.hh:385:20: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 385 | register int p,x,h,n; | ^ GHash.hh:385:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 385 | register int p,x,h,n; | ^ GHash.hh: In instantiation of ‘GHash::~GHash() [with OBJ = GFastaRec]’: GFastaIndex.h:58:59: required from here GHash.hh:551:16: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 551 | register int i; | ^ 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:210:15: 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 { | ^~~~~ make[3]: *** [Makefile:1677: clustering.o] Error 1 GHash.hh: In instantiation of ‘void GHash::Resize(int) [with OBJ = GffNameInfo]’: GHash.hh:277:42: required from ‘const OBJ* GHash::shkAdd(const char*, const OBJ*, bool) [with OBJ = GffNameInfo]’ gff.h:249:19: required from here GHash.hh:168:16: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 168 | register int i,n,p,x,h; | ^ GHash.hh:168:18: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 168 | register int i,n,p,x,h; | ^ GHash.hh:168:20: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 168 | register int i,n,p,x,h; | ^ GHash.hh:168:22: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 168 | register int i,n,p,x,h; | ^ GHash.hh:168:24: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister] 168 | register int i,n,p,x,h; | ^ 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:419:15: 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:420:15: 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:210:15: 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:419:15: 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:420:15: 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 { | ^~~~ make[3]: *** [Makefile:1677: cufflinks.o] Error 1 make[3]: *** [Makefile:1677: differential.o] Error 1 make[3]: Leaving directory '/<>/cufflinks-2.2.1+dfsg.1/src' make[2]: *** [Makefile:402: all-recursive] Error 1 make[2]: Leaving directory '/<>/cufflinks-2.2.1+dfsg.1' make[1]: *** [Makefile:343: 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.pl: error: debian/rules binary-arch subprocess returned exit status 2 === USAGE-SUMMARY BEGIN === SUMMARY: host: bos02-s390x-014; CPUs: 4/4; CPU avg: 49%; CPU max: 100%; base memory: 0.2 GB; peak memory: 2.3 GB; total memory: 7.9 GB SUMMARY: swap peak/total: 0.0/0.0 GB; disk start/end/total: 3.0/3.0/58.1 GB; disk delta: 0.0 GB === USAGE-SUMMARY END === -------------------------------------------------------------------------------- Build finished at 2021-09-03T00:31:34Z Finished -------- +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested E: Build failure (dpkg-buildpackage died) +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: s390x Build Type: any Build-Space: n/a Build-Time: 18 Distribution: impish Fail-Stage: build Host Architecture: s390x Install-Time: 11 Job: cufflinks_2.2.1+dfsg.1-8build1.dsc Machine Architecture: s390x Package: cufflinks Package-Time: 29 Source-Version: 2.2.1+dfsg.1-8build1 Space: n/a Status: attempted Version: 2.2.1+dfsg.1-8build1 -------------------------------------------------------------------------------- Finished at 2021-09-03T00:31:34Z Build needed 00:00:29, no disk space E: Build failure (dpkg-buildpackage died) Adding user buildd to group lxd RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=impish --arch=s390x PACKAGEBUILD-21852219 Scanning for processes to kill in build PACKAGEBUILD-21852219