https://launchpad.net/ubuntu/+archive/test-rebuild-20210805-impish/+build/21852218 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux riscv64-qemu-lcy01-019 5.11.0-1017-generic #18~20.04.1-Ubuntu SMP Thu Aug 12 00:38:00 UTC 2021 riscv64 Buildd toolchain package versions: launchpad-buildd_200~495~ubuntu18.04.1 python3-lpbuildd_200~495~ubuntu18.04.1 sbuild_0.79.0-1ubuntu1 git_1:2.25.1-1ubuntu3.1 dpkg-dev_1.19.7ubuntu3 python3-debian_0.1.36ubuntu1. Syncing the system clock with the buildd NTP service... 2 Sep 11:45:32 ntpdate[670712]: adjust time server 10.211.37.1 offset -0.001102 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=impish --arch=riscv64 PACKAGEBUILD-21852218 --image-type chroot /home/buildd/filecache-default/613cd932d11b682280b371d3f989e54c6e87a7f9 Creating target for build PACKAGEBUILD-21852218 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=impish --arch=riscv64 PACKAGEBUILD-21852218 Starting target for build PACKAGEBUILD-21852218 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=impish --arch=riscv64 PACKAGEBUILD-21852218 '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-21852218 RUN: /usr/share/launchpad-buildd/bin/in-target add-trusted-keys --backend=chroot --series=impish --arch=riscv64 PACKAGEBUILD-21852218 Adding trusted keys to build-PACKAGEBUILD-21852218 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=riscv64 PACKAGEBUILD-21852218 Updating target for build PACKAGEBUILD-21852218 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 riscv64 Packages [20.0 kB] Get:4 http://ppa.launchpad.net/ubuntu-toolchain-r/volatile/ubuntu impish/main Translation-en [11.9 kB] Get:5 http://ftpmaster.internal/ubuntu impish/main riscv64 Packages [1294 kB] Get:6 http://ftpmaster.internal/ubuntu impish/main Translation-en [513 kB] Get:7 http://ftpmaster.internal/ubuntu impish/restricted riscv64 Packages [4096 B] Get:8 http://ftpmaster.internal/ubuntu impish/restricted Translation-en [12.5 kB] Get:9 http://ftpmaster.internal/ubuntu impish/universe riscv64 Packages [12.3 MB] Get:10 http://ftpmaster.internal/ubuntu impish/universe Translation-en [5464 kB] Get:11 http://ftpmaster.internal/ubuntu impish/multiverse riscv64 Packages [157 kB] Get:12 http://ftpmaster.internal/ubuntu impish/multiverse Translation-en [108 kB] Fetched 20.2 MB in 37s (552 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 libasan6 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-riscv64-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 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 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 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 110 upgraded, 17 newly installed, 0 to remove and 0 not upgraded. Need to get 124 MB of archives. After this operation, 159 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu impish/main riscv64 libcrypt-dev riscv64 1:4.4.18-4ubuntu1 [199 kB] Get:2 http://ppa.launchpad.net/ubuntu-toolchain-r/volatile/ubuntu impish/main riscv64 libc6-dev riscv64 2.34-0ubuntu1~ppa5 [3146 kB] Get:3 http://ftpmaster.internal/ubuntu impish/main riscv64 libcrypt1 riscv64 1:4.4.18-4ubuntu1 [90.1 kB] Get:4 http://ftpmaster.internal/ubuntu impish/main riscv64 libnsl-dev riscv64 1.3.0-2 [107 kB] Get:5 http://ftpmaster.internal/ubuntu impish/main riscv64 libnsl2 riscv64 1.3.0-2 [34.5 kB] Get:6 http://ftpmaster.internal/ubuntu impish/main riscv64 libatomic1 riscv64 11.2.0-1ubuntu2 [7808 B] Get:7 http://ftpmaster.internal/ubuntu impish/main riscv64 libgomp1 riscv64 11.2.0-1ubuntu2 [103 kB] Get:8 http://ftpmaster.internal/ubuntu impish/main riscv64 gcc-11-base riscv64 11.2.0-1ubuntu2 [21.5 kB] Get:9 http://ftpmaster.internal/ubuntu impish/main riscv64 libgcc-s1 riscv64 11.2.0-1ubuntu2 [43.4 kB] Get:10 http://ftpmaster.internal/ubuntu impish/main riscv64 libcc1-0 riscv64 11.2.0-1ubuntu2 [41.9 kB] Get:11 http://ftpmaster.internal/ubuntu impish/main riscv64 libstdc++6 riscv64 11.2.0-1ubuntu2 [667 kB] Get:12 http://ftpmaster.internal/ubuntu impish/main riscv64 base-files riscv64 11.1ubuntu3 [60.5 kB] Get:13 http://ftpmaster.internal/ubuntu impish/main riscv64 bash riscv64 5.1-3ubuntu1 [610 kB] Get:14 http://ftpmaster.internal/ubuntu impish/main riscv64 bsdutils riscv64 1:2.36.1-8ubuntu1 [85.9 kB] Get:15 http://ppa.launchpad.net/ubuntu-toolchain-r/volatile/ubuntu impish/main riscv64 libc-dev-bin riscv64 2.34-0ubuntu1~ppa5 [18.8 kB] Get:16 http://ftpmaster.internal/ubuntu impish/main riscv64 libperl5.32 riscv64 5.32.1-3ubuntu3 [4131 kB] Get:17 http://ppa.launchpad.net/ubuntu-toolchain-r/volatile/ubuntu impish/main riscv64 linux-libc-dev riscv64 5.13.0-14.14 [1176 kB] Get:18 http://ppa.launchpad.net/ubuntu-toolchain-r/volatile/ubuntu impish/main riscv64 libc6 riscv64 2.34-0ubuntu1~ppa5 [2626 kB] Get:19 http://ppa.launchpad.net/ubuntu-toolchain-r/volatile/ubuntu impish/main riscv64 libc-bin riscv64 2.34-0ubuntu1~ppa5 [940 kB] Get:20 http://ftpmaster.internal/ubuntu impish/main riscv64 perl riscv64 5.32.1-3ubuntu3 [227 kB] Get:21 http://ppa.launchpad.net/ubuntu-toolchain-r/volatile/ubuntu impish/main riscv64 dpkg riscv64 1.20.9ubuntu13 [1223 kB] Get:22 http://ftpmaster.internal/ubuntu impish/main riscv64 perl-base riscv64 5.32.1-3ubuntu3 [1627 kB] Get:23 http://ppa.launchpad.net/ubuntu-toolchain-r/volatile/ubuntu impish/main riscv64 g++ riscv64 4:11.2.0-1ubuntu1 [1398 B] Get:24 http://ppa.launchpad.net/ubuntu-toolchain-r/volatile/ubuntu impish/main riscv64 gcc riscv64 4:11.2.0-1ubuntu1 [5136 B] Get:25 http://ppa.launchpad.net/ubuntu-toolchain-r/volatile/ubuntu impish/main riscv64 cpp riscv64 4:11.2.0-1ubuntu1 [27.7 kB] Get:26 http://ppa.launchpad.net/ubuntu-toolchain-r/volatile/ubuntu impish/main riscv64 dpkg-dev all 1.20.9ubuntu13 [938 kB] Get:27 http://ftpmaster.internal/ubuntu impish/main riscv64 perl-modules-5.32 all 5.32.1-3ubuntu3 [2945 kB] Get:28 http://ppa.launchpad.net/ubuntu-toolchain-r/volatile/ubuntu impish/main riscv64 libdpkg-perl all 1.20.9ubuntu13 [235 kB] Get:29 http://ftpmaster.internal/ubuntu impish/main riscv64 libdb5.3 riscv64 5.3.28+dfsg1-0.8ubuntu1 [613 kB] Get:30 http://ftpmaster.internal/ubuntu impish/main riscv64 zlib1g riscv64 1:1.2.11.dfsg-2ubuntu7 [55.7 kB] Get:31 http://ftpmaster.internal/ubuntu impish/main riscv64 debconf all 1.5.77 [121 kB] Get:32 http://ftpmaster.internal/ubuntu impish/main riscv64 dash riscv64 0.5.11+git20210120+802ebd4-1 [81.7 kB] Get:33 http://ftpmaster.internal/ubuntu impish/main riscv64 diffutils riscv64 1:3.7-5ubuntu1 [183 kB] Get:34 http://ftpmaster.internal/ubuntu impish/main riscv64 findutils riscv64 4.8.0-1ubuntu2 [328 kB] Get:35 http://ftpmaster.internal/ubuntu impish/main riscv64 gzip riscv64 1.10-4ubuntu1 [91.6 kB] Get:36 http://ftpmaster.internal/ubuntu impish/main riscv64 login riscv64 1:4.8.1-1ubuntu9 [218 kB] Get:37 http://ftpmaster.internal/ubuntu impish/main riscv64 util-linux riscv64 2.36.1-8ubuntu1 [1057 kB] Get:38 http://ftpmaster.internal/ubuntu impish/main riscv64 base-passwd riscv64 3.5.51 [48.4 kB] Get:39 http://ftpmaster.internal/ubuntu impish/main riscv64 sysvinit-utils riscv64 2.96-7ubuntu1 [19.5 kB] Get:40 http://ftpmaster.internal/ubuntu impish/main riscv64 libgcrypt20 riscv64 1.8.7-5ubuntu1 [390 kB] Get:41 http://ftpmaster.internal/ubuntu impish/main riscv64 liblz4-1 riscv64 1.9.3-2 [65.9 kB] Get:42 http://ftpmaster.internal/ubuntu impish/main riscv64 liblzma5 riscv64 5.2.5-2 [91.2 kB] Get:43 http://ftpmaster.internal/ubuntu impish/main riscv64 systemd-sysv riscv64 248.3-1ubuntu3 [10.5 kB] Get:44 http://ftpmaster.internal/ubuntu impish/main riscv64 systemd-timesyncd riscv64 248.3-1ubuntu3 [28.5 kB] Get:45 http://ftpmaster.internal/ubuntu impish/main riscv64 libapparmor1 riscv64 3.0.3-0ubuntu1 [33.8 kB] Get:46 http://ftpmaster.internal/ubuntu impish/main riscv64 libaudit-common all 1:3.0-2ubuntu2 [4788 B] Get:47 http://ftpmaster.internal/ubuntu impish/main riscv64 libaudit1 riscv64 1:3.0-2ubuntu2 [38.6 kB] Get:48 http://ftpmaster.internal/ubuntu impish/main riscv64 libnettle8 riscv64 3.7.3-1 [176 kB] Get:49 http://ftpmaster.internal/ubuntu impish/main riscv64 libhogweed6 riscv64 3.7.3-1 [188 kB] Get:50 http://ftpmaster.internal/ubuntu impish/main riscv64 libidn2-0 riscv64 2.3.1-1 [50.5 kB] Get:51 http://ftpmaster.internal/ubuntu impish/main riscv64 libgnutls30 riscv64 3.7.1-4ubuntu1 [795 kB] Get:52 http://ftpmaster.internal/ubuntu impish/main riscv64 libssl1.1 riscv64 1.1.1j-1ubuntu5 [1080 kB] Get:53 http://ftpmaster.internal/ubuntu impish/main riscv64 libzstd1 riscv64 1.4.8+dfsg-2.1 [344 kB] Get:54 http://ftpmaster.internal/ubuntu impish/main riscv64 libkmod2 riscv64 28-1ubuntu4 [39.3 kB] Get:55 http://ftpmaster.internal/ubuntu impish/main riscv64 libblkid1 riscv64 2.36.1-8ubuntu1 [138 kB] Get:56 http://ftpmaster.internal/ubuntu impish/main riscv64 libmount1 riscv64 2.36.1-8ubuntu1 [146 kB] Get:57 http://ftpmaster.internal/ubuntu impish/main riscv64 libpam0g riscv64 1.3.1-5ubuntu8 [54.7 kB] Get:58 http://ftpmaster.internal/ubuntu impish/main riscv64 mount riscv64 2.36.1-8ubuntu1 [120 kB] Get:59 http://ftpmaster.internal/ubuntu impish/main riscv64 systemd riscv64 248.3-1ubuntu3 [4006 kB] Get:60 http://ftpmaster.internal/ubuntu impish/main riscv64 libsystemd0 riscv64 248.3-1ubuntu3 [282 kB] Get:61 http://ftpmaster.internal/ubuntu impish/main riscv64 libudev1 riscv64 248.3-1ubuntu3 [70.7 kB] Get:62 http://ftpmaster.internal/ubuntu impish/main riscv64 libapt-pkg6.0 riscv64 2.3.7 [915 kB] Get:63 http://ftpmaster.internal/ubuntu impish/main riscv64 gpgv riscv64 2.2.20-1ubuntu4 [183 kB] Get:64 http://ftpmaster.internal/ubuntu impish/main riscv64 apt riscv64 2.3.7 [1344 kB] Get:65 http://ftpmaster.internal/ubuntu impish/main riscv64 libpam-modules-bin riscv64 1.3.1-5ubuntu8 [41.1 kB] Get:66 http://ftpmaster.internal/ubuntu impish/main riscv64 libpam-modules riscv64 1.3.1-5ubuntu8 [258 kB] Get:67 http://ftpmaster.internal/ubuntu impish/main riscv64 logsave riscv64 1.46.2-1ubuntu2 [10.9 kB] Get:68 http://ftpmaster.internal/ubuntu impish/main riscv64 libext2fs2 riscv64 1.46.2-1ubuntu2 [182 kB] Get:69 http://ftpmaster.internal/ubuntu impish/main riscv64 e2fsprogs riscv64 1.46.2-1ubuntu2 [513 kB] Get:70 http://ftpmaster.internal/ubuntu impish/main riscv64 libpython3.9-minimal riscv64 3.9.6-1 [745 kB] Get:71 http://ftpmaster.internal/ubuntu impish/main riscv64 libexpat1 riscv64 2.3.0-1 [69.9 kB] Get:72 http://ftpmaster.internal/ubuntu impish/main riscv64 python3.9-minimal riscv64 3.9.6-1 [1495 kB] Get:73 http://ftpmaster.internal/ubuntu impish/main riscv64 python3-minimal riscv64 3.9.4-1 [23.8 kB] Get:74 http://ftpmaster.internal/ubuntu impish/main riscv64 media-types all 4.0.0 [22.2 kB] Get:75 http://ftpmaster.internal/ubuntu impish/main riscv64 libmpdec3 riscv64 2.5.1-2 [77.8 kB] Get:76 http://ftpmaster.internal/ubuntu impish/main riscv64 readline-common all 8.1-2 [54.1 kB] Get:77 http://ftpmaster.internal/ubuntu impish/main riscv64 libreadline8 riscv64 8.1-2 [118 kB] Get:78 http://ftpmaster.internal/ubuntu impish/main riscv64 libsqlite3-0 riscv64 3.35.5-1 [534 kB] Get:79 http://ftpmaster.internal/ubuntu impish/main riscv64 libuuid1 riscv64 2.36.1-8ubuntu1 [26.4 kB] Get:80 http://ftpmaster.internal/ubuntu impish/main riscv64 libpython3.9-stdlib riscv64 3.9.6-1 [1579 kB] Get:81 http://ftpmaster.internal/ubuntu impish/main riscv64 python3.9 riscv64 3.9.6-1 [426 kB] Get:82 http://ftpmaster.internal/ubuntu impish/main riscv64 libpython3-stdlib riscv64 3.9.4-1 [6988 B] Get:83 http://ftpmaster.internal/ubuntu impish/main riscv64 python3 riscv64 3.9.4-1 [22.2 kB] Get:84 http://ftpmaster.internal/ubuntu impish/main riscv64 libcom-err2 riscv64 1.46.2-1ubuntu2 [9724 B] Get:85 http://ftpmaster.internal/ubuntu impish/main riscv64 libpam-runtime all 1.3.1-5ubuntu8 [38.7 kB] Get:86 http://ftpmaster.internal/ubuntu impish/main riscv64 libsmartcols1 riscv64 2.36.1-8ubuntu1 [94.8 kB] Get:87 http://ftpmaster.internal/ubuntu impish/main riscv64 passwd riscv64 1:4.8.1-1ubuntu9 [782 kB] Get:88 http://ftpmaster.internal/ubuntu impish/main riscv64 libk5crypto3 riscv64 1.18.3-6 [103 kB] Get:89 http://ftpmaster.internal/ubuntu impish/main riscv64 libkrb5support0 riscv64 1.18.3-6 [30.5 kB] Get:90 http://ftpmaster.internal/ubuntu impish/main riscv64 libkrb5-3 riscv64 1.18.3-6 [336 kB] Get:91 http://ftpmaster.internal/ubuntu impish/main riscv64 libgssapi-krb5-2 riscv64 1.18.3-6 [126 kB] Get:92 http://ftpmaster.internal/ubuntu impish/main riscv64 libprocps8 riscv64 2:3.3.17-5ubuntu3 [32.4 kB] Get:93 http://ftpmaster.internal/ubuntu impish/main riscv64 libss2 riscv64 1.46.2-1ubuntu2 [9932 B] Get:94 http://ftpmaster.internal/ubuntu impish/main riscv64 procps riscv64 2:3.3.17-5ubuntu3 [372 kB] Get:95 http://ftpmaster.internal/ubuntu impish/main riscv64 usrmerge all 25ubuntu1 [53.5 kB] Get:96 http://ftpmaster.internal/ubuntu impish/main riscv64 libdevmapper1.02.1 riscv64 2:1.02.175-2.1ubuntu1 [119 kB] Get:97 http://ftpmaster.internal/ubuntu impish/main riscv64 openssl riscv64 1.1.1j-1ubuntu5 [620 kB] Get:98 http://ftpmaster.internal/ubuntu impish/main riscv64 xz-utils riscv64 5.2.5-2 [78.2 kB] Get:99 http://ftpmaster.internal/ubuntu impish/main riscv64 advancecomp riscv64 2.1-2.1ubuntu1 [209 kB] Get:100 http://ftpmaster.internal/ubuntu impish/main riscv64 libctf0 riscv64 2.37-1ubuntu1 [98.3 kB] Get:101 http://ftpmaster.internal/ubuntu impish/main riscv64 libctf-nobfd0 riscv64 2.37-1ubuntu1 [99.3 kB] Get:102 http://ftpmaster.internal/ubuntu impish/main riscv64 binutils-riscv64-linux-gnu riscv64 2.37-1ubuntu1 [932 kB] Get:103 http://ftpmaster.internal/ubuntu impish/main riscv64 libbinutils riscv64 2.37-1ubuntu1 [477 kB] Get:104 http://ftpmaster.internal/ubuntu impish/main riscv64 binutils riscv64 2.37-1ubuntu1 [3082 B] Get:105 http://ftpmaster.internal/ubuntu impish/main riscv64 binutils-common riscv64 2.37-1ubuntu1 [45.1 kB] Get:106 http://ftpmaster.internal/ubuntu impish/main riscv64 libisl23 riscv64 0.24-1 [542 kB] Get:107 http://ftpmaster.internal/ubuntu impish/main riscv64 cpp-11 riscv64 11.2.0-1ubuntu2 [7984 kB] Get:108 http://ftpmaster.internal/ubuntu impish/main riscv64 libasan6 riscv64 11.2.0-1ubuntu2 [2105 kB] Get:109 http://ftpmaster.internal/ubuntu impish/main riscv64 libgcc-11-dev riscv64 11.2.0-1ubuntu2 [2391 kB] Get:110 http://ftpmaster.internal/ubuntu impish/main riscv64 gcc-11 riscv64 11.2.0-1ubuntu2 [15.8 MB] Get:111 http://ftpmaster.internal/ubuntu impish/main riscv64 libstdc++-11-dev riscv64 11.2.0-1ubuntu2 [4738 kB] Get:112 http://ftpmaster.internal/ubuntu impish/main riscv64 g++-11 riscv64 11.2.0-1ubuntu2 [9286 kB] Get:113 http://ftpmaster.internal/ubuntu impish/main riscv64 lto-disabled-list all 16 [12.5 kB] Get:114 http://ftpmaster.internal/ubuntu impish/main riscv64 python3-psutil riscv64 5.8.0-1 [151 kB] Get:115 http://ftpmaster.internal/ubuntu impish/main riscv64 build-essential riscv64 12.9ubuntu1 [4744 B] Get:116 http://ftpmaster.internal/ubuntu impish/universe riscv64 g++-10 riscv64 10.3.0-6ubuntu1 [8193 kB] Get:117 http://ftpmaster.internal/ubuntu impish/universe riscv64 gcc-10 riscv64 10.3.0-6ubuntu1 [14.3 MB] Get:118 http://ftpmaster.internal/ubuntu impish/main riscv64 libstdc++-10-dev riscv64 10.3.0-6ubuntu1 [4455 kB] Get:119 http://ftpmaster.internal/ubuntu impish/main riscv64 libgcc-10-dev riscv64 10.3.0-6ubuntu1 [590 kB] Get:120 http://ftpmaster.internal/ubuntu impish/universe riscv64 cpp-10 riscv64 10.3.0-6ubuntu1 [7167 kB] Get:121 http://ftpmaster.internal/ubuntu impish/main riscv64 gcc-10-base riscv64 10.3.0-6ubuntu1 [21.5 kB] Get:122 http://ftpmaster.internal/ubuntu impish/main riscv64 libassuan0 riscv64 2.5.5-1 [33.0 kB] Get:123 http://ftpmaster.internal/ubuntu impish/main riscv64 pinentry-curses riscv64 1.1.1-1 [33.4 kB] Get:124 http://ftpmaster.internal/ubuntu impish/main riscv64 gpg riscv64 2.2.20-1ubuntu4 [441 kB] Get:125 http://ftpmaster.internal/ubuntu impish/main riscv64 gpgconf riscv64 2.2.20-1ubuntu4 [110 kB] Get:126 http://ftpmaster.internal/ubuntu impish/main riscv64 gpg-agent riscv64 2.2.20-1ubuntu4 [203 kB] Get:127 http://ftpmaster.internal/ubuntu impish/main riscv64 pkgbinarymangler all 148 [32.3 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 124 MB in 37s (3383 kB/s) (Reading database ... 13038 files and directories currently installed.) Preparing to unpack .../libcrypt-dev_1%3a4.4.18-4ubuntu1_riscv64.deb ... Unpacking libcrypt-dev:riscv64 (1:4.4.18-4ubuntu1) over (1:4.4.17-1ubuntu3) ... Preparing to unpack .../libcrypt1_1%3a4.4.18-4ubuntu1_riscv64.deb ... Unpacking libcrypt1:riscv64 (1:4.4.18-4ubuntu1) over (1:4.4.17-1ubuntu3) ... Setting up libcrypt1:riscv64 (1:4.4.18-4ubuntu1) ... (Reading database ... 13038 files and directories currently installed.) Preparing to unpack .../libnsl-dev_1.3.0-2_riscv64.deb ... Unpacking libnsl-dev:riscv64 (1.3.0-2) over (1.3.0-0ubuntu3) ... Preparing to unpack .../libc6-dev_2.34-0ubuntu1~ppa5_riscv64.deb ... Unpacking libc6-dev:riscv64 (2.34-0ubuntu1~ppa5) over (2.33-0ubuntu5) ... Preparing to unpack .../libc-dev-bin_2.34-0ubuntu1~ppa5_riscv64.deb ... Unpacking libc-dev-bin (2.34-0ubuntu1~ppa5) over (2.33-0ubuntu5) ... Preparing to unpack .../libnsl2_1.3.0-2_riscv64.deb ... Unpacking libnsl2:riscv64 (1.3.0-2) over (1.3.0-0ubuntu3) ... Setting up libnsl2:riscv64 (1.3.0-2) ... 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RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-21852218 riscv64 impish -c chroot:build-PACKAGEBUILD-21852218 --arch=riscv64 --dist=impish --nolog cufflinks_2.2.1+dfsg.1-8build1.dsc Initiating build PACKAGEBUILD-21852218 with 8 jobs across 8 processor cores. Kernel reported to sbuild: 5.11.0-1017-generic #18~20.04.1-Ubuntu SMP Thu Aug 12 00:38:00 UTC 2021 riscv64 sbuild (Debian sbuild) 0.79.0 (05 February 2020) on riscv64-qemu-lcy01-019.buildd +==============================================================================+ | cufflinks 2.2.1+dfsg.1-8build1 (riscv64) Thu, 02 Sep 2021 12:03:41 +0000 | +==============================================================================+ Package: cufflinks Version: 2.2.1+dfsg.1-8build1 Source Version: 2.2.1+dfsg.1-8build1 Distribution: impish Machine Architecture: riscv64 Host Architecture: riscv64 Build Architecture: riscv64 Build Type: any I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-21852218/chroot-autobuild' with '<>' I: NOTICE: Log filtering will replace 'build/cufflinks-3Tiz4q/resolver-u2LyQT' 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-3Tiz4q/cufflinks-2.2.1+dfsg.1' with '<>' I: NOTICE: Log filtering will replace 'build/cufflinks-3Tiz4q' with '<>' +------------------------------------------------------------------------------+ | 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, build-essential, fakeroot 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, build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<>/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [957 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [433 B] Get:5 copy:/<>/apt_archive ./ Packages [517 B] Fetched 1907 B in 1s (2508 B/s) Reading package lists... Reading package lists... Install main 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-main-dummy zlib1g-dev 0 upgraded, 60 newly installed, 0 to remove and 0 not upgraded. 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1.74.0-8ubuntu2 [368 kB] Get:58 http://ftpmaster.internal/ubuntu impish/main riscv64 libboost-thread-dev riscv64 1.74.0.3ubuntu5 [3368 B] Get:59 http://ftpmaster.internal/ubuntu impish/main riscv64 pkg-config riscv64 0.29.2-1ubuntu1 [43.7 kB] Get:60 http://ftpmaster.internal/ubuntu impish/universe riscv64 libeigen3-dev all 3.3.9-2 [817 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 31.8 MB in 10s (3115 kB/s) Selecting previously unselected package liblocale-gettext-perl. 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Processing triggers for libc-bin (2.34-0ubuntu1~ppa5) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (riscv64 included in any) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 5.11.0-1017-generic #18~20.04.1-Ubuntu SMP Thu Aug 12 00:38:00 UTC 2021 riscv64 (riscv64) 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-riscv64-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 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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 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readline-common_8.1-2 rpcsvc-proto_1.4.2-0ubuntu4 sbuild-build-depends-main-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 ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: cufflinks Binary: cufflinks Architecture: any Version: 2.2.1+dfsg.1-8build1 Maintainer: Debian Med Packaging Team Uploaders: Alexandre Mestiashvili , Andreas Tille , Charles Plessy Homepage: https://cufflinks.cbcb.umd.edu Standards-Version: 4.5.0 Vcs-Browser: https://salsa.debian.org/med-team/cufflinks Vcs-Git: https://salsa.debian.org/med-team/cufflinks.git 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 Package-List: cufflinks deb non-free/science optional arch=any Checksums-Sha1: 9fdcb7443683c21c93a16213dd86e18e59722cbf 637715 cufflinks_2.2.1+dfsg.1.orig.tar.gz d6982bc87042dd9ff3820aa37ddb4489d349f17d 15340 cufflinks_2.2.1+dfsg.1-8build1.debian.tar.xz Checksums-Sha256: 3759d56fe85365ebca156bc302b5248a95bd386d34eb7c5e4900f267414e8ea3 637715 cufflinks_2.2.1+dfsg.1.orig.tar.gz add1f1d6a93960bc7700f4e377192ebea00859c15a186215d34776d232c71f73 15340 cufflinks_2.2.1+dfsg.1-8build1.debian.tar.xz Files: f78d52ba36268987dc7a44c74c4c5d06 637715 cufflinks_2.2.1+dfsg.1.orig.tar.gz 8a79ceee628d07dc2a9d825ced434edb 15340 cufflinks_2.2.1+dfsg.1-8build1.debian.tar.xz Autobuild: yes -----BEGIN PGP SIGNATURE----- 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public key dpkg-source: warning: failed to verify signature on ./cufflinks_2.2.1+dfsg.1-8build1.dsc dpkg-source: info: extracting cufflinks in /<> 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 '/<>/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=8 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-21852218 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-21852218 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-21852218 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- Command: dpkg-buildpackage -us -uc -mLaunchpad Build Daemon -B -rfakeroot 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 riscv64 debian/rules clean dh clean --with python3 debian/rules override_dh_auto_clean make[1]: Entering directory '/<>' dh_auto_clean rm -rf autom4te.cache make[1]: Leaving directory '/<>' 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 '/<>' dh_auto_configure -- LIBS="-lboost_system -lboost_thread -lboost_serialization" ./configure --build=riscv64-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/riscv64-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... riscv64-unknown-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... riscv64-unknown-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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now GCC version: gcc (Ubuntu 11.2.0-1ubuntu2) 11.2.0 Host System type: riscv64-unknown-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 '/<>' dh_auto_build -a make -j8 make[1]: Entering directory '/<>' make all-recursive make[2]: Entering directory '/<>' Making all in src make[3]: Entering directory '/<>/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=/<>=. -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=/<>=. -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=/<>=. -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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o common.o common.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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o assemble.o assemble.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o tokenize.o tokenize.cpp g++ -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o abundances.o abundances.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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o scaffolds.o scaffolds.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=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -pthread -I/usr/include -c -o hits.o hits.cpp In file included from ./lemon/bits/base_extender.h:23, from ./lemon/list_graph.h:26, from ./lemon/dfs.h:26, from ./lemon/topology.h:22, from assemble.cpp:19: ./lemon/error.h:93:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 93 | std::auto_ptr<_Type> ptr; | ^~~~~~~~ In file included from /usr/include/c++/11/memory:76, from ./lemon/error.h:31, from ./lemon/bits/base_extender.h:23, from ./lemon/list_graph.h:26, from ./lemon/dfs.h:26, from ./lemon/topology.h:22, from assemble.cpp:19: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from ./lemon/bits/base_extender.h:23, from ./lemon/list_graph.h:26, from ./lemon/dfs.h:26, from ./lemon/topology.h:22, from assemble.cpp:19: ./lemon/error.h:108:10: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 108 | std::auto_ptr buf; | ^~~~~~~~ In file included from /usr/include/c++/11/memory:76, from ./lemon/error.h:31, from ./lemon/bits/base_extender.h:23, from ./lemon/list_graph.h:26, from ./lemon/dfs.h:26, from ./lemon/topology.h:22, from assemble.cpp:19: /usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here 57 | template class auto_ptr; | ^~~~~~~~ In file included from assemble.cpp:19: ./lemon/topology.h: In function ‘bool lemon::stronglyConnected(const Graph&)’: ./lemon/topology.h:249:34: warning: typedef ‘Node’ locally defined but not used [-Wunused-local-typedefs] 249 | typedef typename Graph::Node Node; | ^~~~ ./lemon/topology.h: In function ‘int lemon::countStronglyConnectedComponents(const Graph&)’: ./lemon/topology.h:311:34: warning: typedef ‘Edge’ locally defined but not used [-Wunused-local-typedefs] 311 | typedef typename Graph::Edge Edge; | ^~~~ ./lemon/topology.h:313:36: warning: typedef ‘EdgeIt’ locally defined but not used [-Wunused-local-typedefs] 313 | typedef typename Graph::EdgeIt EdgeIt; | ^~~~~~ ./lemon/topology.h: In function ‘void lemon::topologicalSort(const Graph&, NodeMap&)’: ./lemon/topology.h:1213:34: warning: typedef ‘Node’ locally defined but not used [-Wunused-local-typedefs] 1213 | typedef typename Graph::Node Node; | ^~~~ ./lemon/topology.h:1215:34: warning: typedef ‘Edge’ locally defined but not used [-Wunused-local-typedefs] 1215 | typedef typename Graph::Edge Edge; | ^~~~ ./lemon/topology.h: In function ‘bool lemon::bipartite(const UGraph&)’: ./lemon/topology.h:1470:37: warning: typedef ‘EdgeIt’ locally defined but not used [-Wunused-local-typedefs] 1470 | typedef typename UGraph::EdgeIt EdgeIt; | ^~~~~~ ./lemon/topology.h: In function ‘bool lemon::bipartitePartitions(const UGraph&, NodeMap&)’: ./lemon/topology.h:1514:35: warning: typedef ‘Node’ locally defined but not used [-Wunused-local-typedefs] 1514 | typedef typename UGraph::Node Node; | ^~~~ ./lemon/topology.h:1516:37: warning: typedef ‘EdgeIt’ locally defined but not used [-Wunused-local-typedefs] 1516 | typedef typename UGraph::EdgeIt EdgeIt; | ^~~~~~ In file included from scaffolds.h:20, from scaffolds.cpp:14: hits.h: In constructor ‘PrecomputedExpressionHitFactory::PrecomputedExpressionHitFactory(const string&, ReadTable&, RefSequenceTable&)’: hits.h:928:12: warning: ‘PrecomputedExpressionHitFactory::_expression_file_name’ will be initialized after [-Wreorder] 928 | string _expression_file_name; | ^~~~~~~~~~~~~~~~~~~~~ hits.h:927:19: warning: ‘std::ifstream PrecomputedExpressionHitFactory::_ifs’ [-Wreorder] 927 | std::ifstream _ifs; | ^~~~ In file included from scaffolds.h:20, from scaffolds.cpp:14: hits.h:814:5: warning: when initialized here [-Wreorder] 814 | PrecomputedExpressionHitFactory(const string& expression_file_name, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ scaffolds.cpp: In member function ‘void Scaffold::fill_gaps(int)’: scaffolds.cpp:835:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 835 | if (filled_gap_size <= 0) | ^~ scaffolds.cpp:838:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 838 | const vector& orig_ops = augmented_ops(); | ^~~~~ scaffolds.cpp: In member function ‘void Scaffold::fill_gaps(const std::vector&)’: scaffolds.cpp:933:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 933 | if (overlapping.empty()) | ^~ scaffolds.cpp:936:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 936 | AugmentedCuffOp::merge_ops(overlapping, _augmented_ops, true); | ^~~~~~~~~~~~~~~ In file included from /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 /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/property_map/vector_property_map.hpp:14, from /usr/include/boost/property_map/property_map.hpp:602, from /usr/include/boost/graph/vector_as_graph.hpp:25, from assemble.cpp:26: /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: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 hits.cpp:22: hits.h: In constructor ‘PrecomputedExpressionHitFactory::PrecomputedExpressionHitFactory(const string&, ReadTable&, RefSequenceTable&)’: hits.h:928:12: warning: ‘PrecomputedExpressionHitFactory::_expression_file_name’ will be initialized after [-Wreorder] 928 | string _expression_file_name; | ^~~~~~~~~~~~~~~~~~~~~ hits.h:927:19: warning: ‘std::ifstream PrecomputedExpressionHitFactory::_ifs’ [-Wreorder] 927 | std::ifstream _ifs; | ^~~~ In file included from hits.cpp:22: hits.h:814:5: warning: when initialized here [-Wreorder] 814 | PrecomputedExpressionHitFactory(const string& expression_file_name, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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; | ^ 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 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)); | ^~~~~~~~~~~~~~~~~~~~ In file included from assemble.cpp:44: transitive_closure.h: In function ‘void transitive_closure(const Graph&, GraphTC&, G_to_TC_VertexMap, VertexIndexMap)’: transitive_closure.h:85:62: warning: typedef ‘edge’ locally defined but not used [-Wunused-local-typedefs] 85 | typedef typename graph_traits < Graph >::edge_descriptor edge; | ^~~~ transitive_closure.h:226:66: warning: typedef ‘tc_vertex’ locally defined but not used [-Wunused-local-typedefs] 226 | typedef typename graph_traits < GraphTC >::vertex_descriptor tc_vertex; | ^~~~~~~~~ transitive_closure.h: In function ‘void warshall_transitive_closure(G&)’: transitive_closure.h:323:60: warning: typedef ‘vertex’ locally defined but not used [-Wunused-local-typedefs] 323 | typedef typename graph_traits < G >::vertex_descriptor vertex; | ^~~~~~ transitive_closure.h: In function ‘void warren_transitive_closure(G&)’: transitive_closure.h:349:60: warning: typedef ‘vertex’ locally defined but not used [-Wunused-local-typedefs] 349 | typedef typename graph_traits < G >::vertex_descriptor vertex; | ^~~~~~ In file included from assemble.cpp:45: transitive_reduction.h: In function ‘boost::ccheck_aux::unaryfunptr_arg_type::type boost::transitive_reduction(const Graph&, GraphTR&, G_to_TR_VertexMap, VertexIndexMap)’: transitive_reduction.h:53:63: warning: typedef ‘VertexIterator’ locally defined but not used [-Wunused-local-typedefs] 53 | typedef typename graph_traits::vertex_iterator VertexIterator; | ^~~~~~~~~~~~~~ In file included from 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 /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 hits.cpp:21: /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 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 gff.h:8, from gtf_tracking.h:12, from bundles.h:22, from abundances.h:25, from hits.cpp:25: 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 hits.cpp:21: /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 hits.cpp:25: 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 hits.cpp:25: 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 hits.cpp:21: /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 hits.cpp:25: 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 hits.cpp:25: 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 hits.cpp:25: 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 hits.cpp:21: /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 hits.cpp:25: GBase.h:75:23: note: ‘typedef unsigned char byte’ 75 | typedef unsigned char byte; | ^~~~ 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 gtf_tracking.h:12, from bundles.h:22, from abundances.h:25, from hits.cpp:25: 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 hits.cpp:21: /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 hits.cpp:25: 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 hits.cpp:25: 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 hits.cpp:21: /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 hits.cpp:25: 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 hits.cpp:25: 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 hits.cpp:21: /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 hits.cpp:25: GBase.h:75:23: note: ‘typedef unsigned char byte’ 75 | typedef unsigned char byte; | ^~~~ In file included from abundances.h:23, from abundances.cpp:16: hits.h: In constructor ‘PrecomputedExpressionHitFactory::PrecomputedExpressionHitFactory(const string&, ReadTable&, RefSequenceTable&)’: hits.h:928:12: warning: ‘PrecomputedExpressionHitFactory::_expression_file_name’ will be initialized after [-Wreorder] 928 | string _expression_file_name; | ^~~~~~~~~~~~~~~~~~~~~ hits.h:927:19: warning: ‘std::ifstream PrecomputedExpressionHitFactory::_ifs’ [-Wreorder] 927 | std::ifstream _ifs; | ^~~~ In file included from abundances.h:23, from abundances.cpp:16: hits.h:814:5: warning: when initialized here [-Wreorder] 814 | PrecomputedExpressionHitFactory(const string& expression_file_name, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from gtf_tracking.h:12, from bundles.h:22, from abundances.h:25, from hits.cpp:25: 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 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 gff.h:8, from gtf_tracking.h:12, from bundles.h:22, from abundances.h:25, from abundances.cpp:16: 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/matrix.hpp:17, from abundances.h:18, from abundances.cpp:16: /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 abundances.cpp:16: 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 abundances.cpp:16: 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/matrix.hpp:17, from abundances.h:18, from abundances.cpp:16: /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 abundances.cpp:16: 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 gff.h:12, from gtf_tracking.h:12, from bundles.h:22, from abundances.h:25, from abundances.cpp:16: 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; | ^~~ 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); | ^~~~~~~~~~~~~~~~~~~ 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 abundances.cpp:16: 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/matrix.hpp:17, from abundances.h:18, from abundances.cpp:16: /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 abundances.cpp:16: 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()(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()::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 gff.h:8, from gtf_tracking.h:12, from bundles.h:22, from assemble.h:21, from assemble.cpp:48: 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/core/ref.hpp:10, from /usr/include/boost/ref.hpp:15, from assemble.cpp:24: /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 assemble.h:21, from assemble.cpp:48: 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 assemble.h:21, from assemble.cpp:48: 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/core/ref.hpp:10, from /usr/include/boost/ref.hpp:15, from assemble.cpp:24: /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 assemble.h:21, from assemble.cpp:48: 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 assemble.h:21, from assemble.cpp:48: 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 assemble.h:21, from assemble.cpp:48: 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/core/ref.hpp:10, from /usr/include/boost/ref.hpp:15, from assemble.cpp:24: /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 assemble.h:21, from assemble.cpp:48: 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 assemble.h:21, from assemble.cpp:48: 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/core/ref.hpp:10, from /usr/include/boost/ref.hpp:15, from assemble.cpp:24: /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 assemble.h:21, from assemble.cpp:48: 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 assemble.h:21, from assemble.cpp:48: 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/core/ref.hpp:10, from /usr/include/boost/ref.hpp:15, from assemble.cpp:24: /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 assemble.h:21, from assemble.cpp:48: 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 assemble.h:21, from assemble.cpp:48: 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/core/ref.hpp:10, from /usr/include/boost/ref.hpp:15, from assemble.cpp:24: /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 assemble.h:21, from assemble.cpp:48: 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 assemble.h:21, from assemble.cpp:48: 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 abundances.cpp:43: replicates.h: In member function ‘bool ReplicatedBundleFactory::next_bundle(HitBundle&, bool)’: replicates.h:224:57: warning: unused variable ‘s2’ [-Wunused-variable] 224 | const vector >& s2 = bundles[i-1]->ref_scaffolds(); | ^~ 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: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; | ^~~~ 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 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; | ^~~ In file included from differential.h:29, from differential.cpp:21: replicates.h: In member function ‘bool ReplicatedBundleFactory::next_bundle(HitBundle&, bool)’: replicates.h:224:57: warning: unused variable ‘s2’ [-Wunused-variable] 224 | const vector >& s2 = bundles[i-1]->ref_scaffolds(); | ^~ 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); | ^~~~~~~~~~~~~~~~~~~ In file included from abundances.h:23, from clustering.h:38, from clustering.cpp:10: hits.h: In constructor ‘PrecomputedExpressionHitFactory::PrecomputedExpressionHitFactory(const string&, ReadTable&, RefSequenceTable&)’: hits.h:928:12: warning: ‘PrecomputedExpressionHitFactory::_expression_file_name’ will be initialized after [-Wreorder] 928 | string _expression_file_name; | ^~~~~~~~~~~~~~~~~~~~~ hits.h:927:19: warning: ‘std::ifstream PrecomputedExpressionHitFactory::_ifs’ [-Wreorder] 927 | std::ifstream _ifs; | ^~~~ In file included from abundances.h:23, from clustering.h:38, from clustering.cpp:10: hits.h:814:5: warning: when initialized here [-Wreorder] 814 | PrecomputedExpressionHitFactory(const string& expression_file_name, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 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, | ^~~~~~~~~~~~~~~~~~ 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 GList.hh:8, from GFaSeqGet.h:3, from gff.h:10, from gtf_tracking.h:12, from bundles.h:22, from abundances.h:25, from hits.cpp:25: GVec.hh: In instantiation of ‘void GVec::Grow(int, OBJ&) [with OBJ = GISeg]’: GVec.hh:422:9: required from ‘void GVec::Insert(int, OBJ*) [with OBJ = GISeg]’ GVec.hh:81:48: required from ‘void GVec::idxInsert(int, OBJ&) [with OBJ = GISeg]’ gtf_tracking.h:210:15: 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 hits.cpp:25: gtf_tracking.h:188:7: note: ‘class GISeg’ declared here 188 | class GISeg: public GSeg { | ^~~~~ 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); | ^~~~~~~~~~~~~~~~~~~ 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()::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 hits.cpp:25: gtf_tracking.h:359:7: note: ‘class GXSeg’ declared here 359 | class GXSeg : public GSeg { | ^~~~~ In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:10, from gtf_tracking.h:12, from bundles.h:22, from abundances.h:25, from hits.cpp:25: GVec.hh: In instantiation of ‘void GVec::Grow(int, OBJ&) [with OBJ = GSeg]’: GVec.hh:422:9: required from ‘void GVec::Insert(int, OBJ*) [with OBJ = GSeg]’ GVec.hh:79:44: required from ‘void GVec::Insert(int, OBJ) [with OBJ = GSeg]’ GList.hh:230:21: required from ‘int GArray::Add(OBJ*) [with OBJ = GSeg]’ GList.hh:51:36: required from ‘int GArray::Add(OBJ&) [with OBJ = GSeg]’ gtf_tracking.h:420:15: 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 hits.cpp:25: GBase.h:279:7: note: ‘class GSeg’ declared here 279 | class GSeg { | ^~~~ In file included from cufflinks.cpp:28: replicates.h: In member function ‘bool ReplicatedBundleFactory::next_bundle(HitBundle&, bool)’: replicates.h:224:57: warning: unused variable ‘s2’ [-Wunused-variable] 224 | const vector >& s2 = bundles[i-1]->ref_scaffolds(); | ^~ cufflinks.cpp: In function ‘bool scaffolds_for_bundle(const HitBundle&, std::vector >&, std::vector >*, BundleStats*)’: cufflinks.cpp:690:30: warning: comparison of integer expressions of different signedness: ‘std::vector::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 690 | if (bundle.hits().size() >= max_frags_per_bundle) | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ cufflinks.cpp:690:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 690 | if (bundle.hits().size() >= max_frags_per_bundle) | ^~ cufflinks.cpp:693:9: 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 | ^~ 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; | ^~ 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) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 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()) | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ abundances.cpp: In constructor ‘AbundanceGroup::AbundanceGroup(const std::vector >&, const boost::numeric::ublas::matrix&, const boost::numeric::ublas::matrix&, const boost::numeric::ublas::matrix&, const boost::numeric::ublas::matrix&, const std::set >&)’: abundances.cpp:518:58: warning: comparison of integer expressions of different signedness: ‘std::set >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 518 | if (no_js_tests == false && _read_group_props.size() >= min_reps_for_js_test) | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ abundances.cpp: In member function ‘virtual AbundanceStatus AbundanceGroup::status() const’: abundances.cpp:549:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 549 | if (has_ok_member == false) | ^~ abundances.cpp:552:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 552 | return NUMERIC_OK; | ^~~~~~ 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()) | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ abundances.cpp: In member function ‘void AbundanceGroup::collect_per_replicate_mass(const std::vector&, std::vector >&)’: abundances.cpp:1043:20: warning: unused variable ‘curr_mass’ [-Wunused-variable] 1043 | double curr_mass = inserted.first->second; | ^~~~~~~~~ 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()) | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ abundances.cpp: In function ‘void collapse_equivalent_hits(const std::vector&, std::vector >&, std::vector&, std::vector&, bool)’: abundances.cpp:1160:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 1160 | for (size_t j = 0; j < N; ++j) | ~~^~~ 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()) | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ abundances.cpp:1347:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1347 | for(int i = 0 ; i < nr_alignments.size(); ++i) | ~~^~~~~~~~~~~~~~~~~~~~~~ abundances.cpp: In function ‘AbundanceStatus bootstrap_gamma_mle(const std::vector >&, const std::vector&, const std::vector&, boost::numeric::ublas::vector > >&, boost::numeric::ublas::matrix&, double&)’: abundances.cpp:1488:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 1488 | for (size_t i = 0; i < num_bootstrap_samples; ++i) | ~~^~~~~~~~~~~~~~~~~~~~~~~ abundances.cpp:1491:30: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 1491 | for (size_t j = 0; j < num_sample_frags; ++j) | ~~^~~~~~~~~~~~~~~~~~ abundances.cpp:1505:45: warning: comparison of integer expressions of different signedness: ‘__gnu_cxx::__alloc_traits, int>::value_type’ {aka ‘int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 1505 | sample_idxs[curr_sample] >= processed_hits && abundances.cpp: In function ‘bool generate_count_assignment_samples(int, const std::vector&, const boost::numeric::ublas::matrix&, std::vector > > >&)’: abundances.cpp:1693:44: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 1693 | for (size_t assign_idx = 0; assign_idx < num_draws; ++assign_idx) | ~~~~~~~~~~~^~~~~~~~~~~ abundances.cpp: In function ‘void calculate_gamma_mle_covariance(const std::map, boost::shared_ptr >&, boost::numeric::ublas::vector > >&, boost::numeric::ublas::matrix&)’: abundances.cpp:1760:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘boost::numeric::ublas::vector > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1760 | for (int j = 0; j < all_assigned_count_samples[i].size(); ++j) | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ abundances.cpp:1775:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 1775 | for (size_t i = 0; i < num_transcripts; ++i) | ~~^~~~~~~~~~~~~~~~~ abundances.cpp:1777:30: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 1777 | for (size_t j = 0; j < num_transcripts; ++j) | ~~^~~~~~~~~~~~~~~~~ abundances.cpp: In function ‘void calculate_fragment_assignment_distribution(const std::map, boost::shared_ptr >&, boost::numeric::ublas::vector > >&, boost::numeric::ublas::matrix&, std::vector > > >&)’: abundances.cpp:1870:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘boost::numeric::ublas::vector > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1870 | for (int j = 0; j < all_assigned_count_samples[i].size(); ++j) | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ abundances.cpp:1885:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 1885 | for (size_t i = 0; i < num_transcripts; ++i) | ~~^~~~~~~~~~~~~~~~~ abundances.cpp:1887:30: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 1887 | for (size_t j = 0; j < num_transcripts; ++j) | ~~^~~~~~~~~~~~~~~~~ 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; | ^ abundances.cpp: In member function ‘void AbundanceGroup::calculate_abundance_group_variance(const std::vector >&, const std::map, boost::shared_ptr >&)’: abundances.cpp:1968:62: warning: comparison of integer expressions of different signedness: ‘std::set >::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 1968 | if (no_js_tests == false && _read_group_props.size() >= min_reps_for_js_test) | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ 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] 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); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ 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; | ^ 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); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ 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; | ^ 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); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ abundances.cpp: In member function ‘void AbundanceGroup::aggregate_replicate_abundances(const std::map, boost::shared_ptr >&)’: abundances.cpp:2070:58: warning: unused variable ‘sc_ab’ [-Wunused-variable] 2070 | const vector >& sc_ab = itr->second->abundances(); | ^~~~~ 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; | ^ abundances.cpp: In member function ‘void AbundanceGroup::generate_fpkm_samples()’: abundances.cpp:2668:30: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase >::Index’ {aka ‘long int’} [-Wsign-compare] 2668 | for (size_t j = 0; j < sample.size(); ++j) | ~~^~~~~~~~~~~~~~~ abundances.cpp: In member function ‘void AbundanceGroup::calculate_FPKM_covariance()’: abundances.cpp:2783:42: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses] 2783 | if (length_i > 0 && length_j > 0 & M > 0) | ~~~~~~~~~^~~ abundances.cpp:2796:24: warning: unused variable ‘fpkm’ [-Wunused-variable] 2796 | double fpkm = _abundances[i]->FPKM(); | ^~~~ abundances.cpp: In member function ‘void AbundanceGroup::calculate_conf_intervals()’: abundances.cpp:2920:34: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 2920 | for (size_t j = 0; j < N; ++j) | ~~^~~ abundances.cpp:2939:34: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 2939 | for (size_t j = 0; j < N; ++j) | ~~^~~ abundances.cpp: In function ‘void calculate_assignment_probs(const VectorXd&, const MatrixXd&, const VectorXd&, Eigen::MatrixXd&)’: abundances.cpp:3352:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase >::Index’ {aka ‘long int’} [-Wsign-compare] 3352 | for (size_t i = 0; i < alignment_multiplicities.size(); ++i) | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ abundances.cpp: In function ‘void calculate_average_assignment_probs(const VectorXd&, const MatrixXd&, const VectorXd&, Eigen::MatrixXd&)’: abundances.cpp:3378:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase >::Index’ {aka ‘long int’} [-Wsign-compare] 3378 | for (size_t i = 0; i < alignment_multiplicities.size(); ++i) | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ abundances.cpp:3393:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase >::Index’ {aka ‘long int’} [-Wsign-compare] 3393 | for (size_t i = 0; i < alignment_multiplicities.size(); ++i) | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ abundances.cpp:3395:30: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase >::Index’ {aka ‘long int’} [-Wsign-compare] 3395 | for (size_t j = 0; j < proposed_gammas.size(); ++j) | ~~^~~~~~~~~~~~~~~~~~~~~~~~ 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; | ^ 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; | ^ abundances.cpp:3408:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::EigenBase >::Index’ {aka ‘long int’} [-Wsign-compare] 3408 | for (size_t j = 0; j < proposed_gammas.size(); ++j) | ~~^~~~~~~~~~~~~~~~~~~~~~~~ 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 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 { | ^~~~~ abundances.cpp: In function ‘AbundanceStatus gamma_mle(const std::vector >&, const std::vector&, const std::vector&, std::vector&, bool)’: abundances.cpp:4322:30: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::Index’ {aka ‘long int’} [-Wsign-compare] 4322 | for (size_t j = 0; j < cond_probs.rows(); ++j) | ~~^~~~~~~~~~~~~~~~~~~ abundances.cpp:4324:34: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::Index’ {aka ‘long int’} [-Wsign-compare] 4324 | for (size_t i = 0; i < cond_probs.cols(); ++i) | ~~^~~~~~~~~~~~~~~~~~~ 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 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 { | ^~~~ In file included from gff.h:12, from gtf_tracking.h:12, from bundles.h:22, from assemble.h:21, from assemble.cpp:48: 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: hits.o] Error 1 In file included from gff.h:12, from gtf_tracking.h:12, from bundles.h:22, from abundances.h:25, from abundances.cpp:16: 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; | ^ 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 { | ^~~~~ 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; | ^ make[3]: *** [Makefile:1677: clustering.o] Error 1 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 { | ^~~~ 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 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 { | ^~~~ 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 assemble.h:21, from assemble.cpp:48: GVec.hh: In instantiation of ‘void GVec::Grow(int, OBJ&) [with OBJ = GISeg]’: GVec.hh:422:9: required from ‘void GVec::Insert(int, OBJ*) [with OBJ = GISeg]’ GVec.hh:81:48: required from ‘void GVec::idxInsert(int, OBJ&) [with OBJ = GISeg]’ gtf_tracking.h:210:15: 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 assemble.h:21, from assemble.cpp:48: gtf_tracking.h:188:7: note: ‘class GISeg’ declared here 188 | class GISeg: public GSeg { | ^~~~~ make[3]: *** [Makefile:1677: differential.o] Error 1 In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:10, from gtf_tracking.h:12, from bundles.h:22, from abundances.h:25, from abundances.cpp:16: GVec.hh: In instantiation of ‘void GVec::Grow(int, OBJ&) [with OBJ = GISeg]’: GVec.hh:422:9: required from ‘void GVec::Insert(int, OBJ*) [with OBJ = GISeg]’ GVec.hh:81:48: required from ‘void GVec::idxInsert(int, OBJ&) [with OBJ = GISeg]’ gtf_tracking.h:210:15: 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 abundances.cpp:16: gtf_tracking.h:188:7: note: ‘class GISeg’ declared here 188 | class GISeg: public GSeg { | ^~~~~ make[3]: *** [Makefile:1677: cufflinks.o] Error 1 In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:10, from gtf_tracking.h:12, from bundles.h:22, from assemble.h:21, from assemble.cpp:48: GVec.hh: In instantiation of ‘void GVec::Grow(int, OBJ&) [with OBJ = GXSeg]’: GVec.hh:422:9: required from ‘void GVec::Insert(int, OBJ*) [with OBJ = GXSeg]’ GVec.hh:79:44: required from ‘void GVec::Insert(int, OBJ) [with OBJ = GXSeg]’ GList.hh:230:21: required from ‘int GArray::Add(OBJ*) [with OBJ = GXSeg]’ GList.hh:51:36: required from ‘int GArray::Add(OBJ&) [with OBJ = GXSeg]’ gtf_tracking.h:419:15: 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 assemble.h:21, from assemble.cpp:48: gtf_tracking.h:359:7: note: ‘class GXSeg’ declared here 359 | class GXSeg : public GSeg { | ^~~~~ In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:10, from gtf_tracking.h:12, from bundles.h:22, from assemble.h:21, from assemble.cpp:48: GVec.hh: In instantiation of ‘void GVec::Grow(int, OBJ&) [with OBJ = GSeg]’: GVec.hh:422:9: required from ‘void GVec::Insert(int, OBJ*) [with OBJ = GSeg]’ GVec.hh:79:44: required from ‘void GVec::Insert(int, OBJ) [with OBJ = GSeg]’ GList.hh:230:21: required from ‘int GArray::Add(OBJ*) [with OBJ = GSeg]’ GList.hh:51:36: required from ‘int GArray::Add(OBJ&) [with OBJ = GSeg]’ gtf_tracking.h:420:15: 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 assemble.h:21, from assemble.cpp:48: 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 abundances.cpp:16: GVec.hh: In instantiation of ‘void GVec::Grow(int, OBJ&) [with OBJ = GXSeg]’: GVec.hh:422:9: required from ‘void GVec::Insert(int, OBJ*) [with OBJ = GXSeg]’ GVec.hh:79:44: required from ‘void GVec::Insert(int, OBJ) [with OBJ = GXSeg]’ GList.hh:230:21: required from ‘int GArray::Add(OBJ*) [with OBJ = GXSeg]’ GList.hh:51:36: required from ‘int GArray::Add(OBJ&) [with OBJ = GXSeg]’ gtf_tracking.h:419:15: 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 abundances.cpp:16: gtf_tracking.h:359:7: note: ‘class GXSeg’ declared here 359 | class GXSeg : public GSeg { | ^~~~~ In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:10, from gtf_tracking.h:12, from bundles.h:22, from abundances.h:25, from abundances.cpp:16: GVec.hh: In instantiation of ‘void GVec::Grow(int, OBJ&) [with OBJ = GSeg]’: GVec.hh:422:9: required from ‘void GVec::Insert(int, OBJ*) [with OBJ = GSeg]’ GVec.hh:79:44: required from ‘void GVec::Insert(int, OBJ) [with OBJ = GSeg]’ GList.hh:230:21: required from ‘int GArray::Add(OBJ*) [with OBJ = GSeg]’ GList.hh:51:36: required from ‘int GArray::Add(OBJ&) [with OBJ = GSeg]’ gtf_tracking.h:420:15: 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 abundances.cpp:16: GBase.h:279:7: note: ‘class GSeg’ declared here 279 | class GSeg { | ^~~~ make[3]: *** [Makefile:1677: assemble.o] Error 1 make[3]: *** [Makefile:1677: abundances.o] Error 1 make[3]: Leaving directory '/<>/src' make[2]: *** [Makefile:402: all-recursive] Error 1 make[2]: Leaving directory '/<>' make[1]: *** [Makefile:343: all] Error 2 make[1]: Leaving directory '/<>' dh_auto_build: error: make -j8 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: riscv64-qemu-lcy01-019; CPUs: 8/8; CPU avg: 36%; CPU max: 100%; base memory: 0.3 GB; peak memory: 4.6 GB; total memory: 15.6 GB SUMMARY: swap peak/total: 0.0/0.0 GB; disk start/end/total: 6.6/6.6/68.4 GB; disk delta: 0.0 GB === USAGE-SUMMARY END === -------------------------------------------------------------------------------- Build finished at 2021-09-02T12:21:42Z Finished -------- +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested E: Build failure (dpkg-buildpackage died) +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: riscv64 Build Type: any Build-Space: 12748 Build-Time: 617 Distribution: impish Fail-Stage: build Host Architecture: riscv64 Install-Time: 428 Job: cufflinks_2.2.1+dfsg.1-8build1.dsc Machine Architecture: riscv64 Package: cufflinks Package-Time: 1081 Source-Version: 2.2.1+dfsg.1-8build1 Space: 12748 Status: attempted Version: 2.2.1+dfsg.1-8build1 -------------------------------------------------------------------------------- Finished at 2021-09-02T12:21:42Z Build needed 00:18:01, 12748k 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=riscv64 PACKAGEBUILD-21852218 Scanning for processes to kill in build PACKAGEBUILD-21852218 RUN: /usr/share/launchpad-buildd/bin/in-target umount-chroot --backend=chroot --series=impish --arch=riscv64 PACKAGEBUILD-21852218 Stopping target for build PACKAGEBUILD-21852218 RUN: /usr/share/launchpad-buildd/bin/in-target remove-build --backend=chroot --series=impish --arch=riscv64 PACKAGEBUILD-21852218 Removing build PACKAGEBUILD-21852218