Sorry, my git repo is unusable and this either disappears soon from my /tmp or you take it. sci-biology/abyss: ebuild tweaks Improve description line. Add github-hosted homepage. Introduce IUSE=sqlite optional dependency. Currently the binaries are silently linked against -lsqlite3 and -lmpi, which is bad. This change should at least make them recorded through portage. Add runtime dependency on sci-biology/bwa. Document current default k-mer size value. Try to respect USE=mpi although it seems configure ignores that and sniffs out openmpi headers and libs. Somebody could improve further the other MPI implementations and come up with proper USE dependencies.
Created attachment 517640 [details] abyss-2.0.2-r1.ebuild I know, a patch would be preferred ...
If you want to tackle also the MPI depencies, see https://github.com/bcgsc/abyss/pull/184#issuecomment-362745505 . Furthermore, let me say that if I have openmpi installed but run abysss's configure it sniffs out my mpi headers and libs and practically creates a MPI-dependent binaries, like /usr/bin/ABYSS-P. That is maybe why there was IUSE=+mpi in the ebuild so far? Also the existing haskell tweak (not by me) does not work for me, you can see: Making all in Misc make[2]: Entering directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/Misc' make -O2 -hidir ./ -odir ./ -o abyss-samtobreak samtobreak.hs Usage: make [options] [target] ... Options: -b, -m Ignored for compatibility. -B, --always-make Unconditionally make all targets. -C DIRECTORY, --directory=DIRECTORY Change to DIRECTORY before doing anything. -d Print lots of debugging information. --debug[=FLAGS] Print various types of debugging information. -e, --environment-overrides Environment variables override makefiles. --eval=STRING Evaluate STRING as a makefile statement. -f FILE, --file=FILE, --makefile=FILE Read FILE as a makefile. -h, --help Print this message and exit. -i, --ignore-errors Ignore errors from recipes. -I DIRECTORY, --include-dir=DIRECTORY Search DIRECTORY for included makefiles. -j [N], --jobs[=N] Allow N jobs at once; infinite jobs with no arg. -k, --keep-going Keep going when some targets can't be made. -l [N], --load-average[=N], --max-load[=N] Don't start multiple jobs unless load is below N. -L, --check-symlink-times Use the latest mtime between symlinks and target. -n, --just-print, --dry-run, --recon Don't actually run any recipe; just print them. -o FILE, --old-file=FILE, --assume-old=FILE Consider FILE to be very old and don't remake it. -O[TYPE], --output-sync[=TYPE] Synchronize output of parallel jobs by TYPE. -p, --print-data-base Print make's internal database. -q, --question Run no recipe; exit status says if up to date. -r, --no-builtin-rules Disable the built-in implicit rules. -R, --no-builtin-variables Disable the built-in variable settings. -s, --silent, --quiet Don't echo recipes. -S, --no-keep-going, --stop Turns off -k. -t, --touch Touch targets instead of remaking them. --trace Print tracing information. -v, --version Print the version number of make and exit. -w, --print-directory Print the current directory. --no-print-directory Turn off -w, even if it was turned on implicitly. -W FILE, --what-if=FILE, --new-file=FILE, --assume-new=FILE Consider FILE to be infinitely new. --warn-undefined-variables Warn when an undefined variable is referenced. This program built for x86_64-pc-linux-gnu Report bugs to <bug-make@gnu.org> make[2]: Leaving directory '/scratch/var/tmp/portage/sci-biology/abyss-2.0.2-r1/work/abyss-2.0.2/Misc'
Created attachment 517650 [details] build.log # emerge -pv abyss These are the packages that would be merged, in order: Calculating dependencies... done! [ebuild R ] sci-biology/abyss-2.0.2-r1::gentoo USE="openmp sqlite -misc-haskell -mpi" 0 KiB Note libmpi.so.20 below: # ldd /usr/bin/ABYSS-P linux-vdso.so.1 (0x00007ffd48366000) libsqlite3.so.0 => /usr/lib64/libsqlite3.so.0 (0x00007fb056a62000) libdl.so.2 => /lib64/libdl.so.2 (0x00007fb05685e000) libmpi.so.20 => /usr/lib64/libmpi.so.20 (0x00007fb056574000) libm.so.6 => /lib64/libm.so.6 (0x00007fb05622a000) libstdc++.so.6 => /usr/lib/gcc/x86_64-pc-linux-gnu/7.3.0/libstdc++.so.6 (0x00007fb055e25000) libgcc_s.so.1 => /usr/lib/gcc/x86_64-pc-linux-gnu/7.3.0/libgcc_s.so.1 (0x00007fb055c0e000) libc.so.6 => /lib64/libc.so.6 (0x00007fb055846000) libpthread.so.0 => /lib64/libpthread.so.0 (0x00007fb055626000) /lib64/ld-linux-x86-64.so.2 (0x00007fb056e31000) libopen-rte.so.20 => /usr/lib64/libopen-rte.so.20 (0x00007fb0553a1000) libopen-pal.so.20 => /usr/lib64/libopen-pal.so.20 (0x00007fb055107000) librt.so.1 => /lib64/librt.so.1 (0x00007fb054eff000) libutil.so.1 => /lib64/libutil.so.1 (0x00007fb054cfc000) libhwloc.so.5 => /usr/lib64/libhwloc.so.5 (0x00007fb054abd000) libnuma.so.1 => /usr/lib64/libnuma.so.1 (0x00007fb0548b1000) libudev.so.1 => /lib64/libudev.so.1 (0x00007fb05468e000) libpciaccess.so.0 => /usr/lib64/libpciaccess.so.0 (0x00007fb054484000) libxml2.so.2 => /usr/lib64/libxml2.so.2 (0x00007fb054121000) libevent-2.1.so.6 => /usr/lib64/libevent-2.1.so.6 (0x00007fb053ecd000) libevent_pthreads-2.1.so.6 => /usr/lib64/libevent_pthreads-2.1.so.6 (0x00007fb053cca000) libz.so.1 => /lib64/libz.so.1 (0x00007fb053ab2000) libicuuc.so.60 => /usr/lib64/libicuuc.so.60 (0x00007fb0536f7000) libicudata.so.60 => /usr/lib64/libicudata.so.60 (0x00007fb051b4e000)
And why there is /usr/lib/gcc/x86_64-pc-linux-gnu/7.3.0/libstdc++.so.6 and /usr/lib/gcc/x86_64-pc-linux-gnu/7.3.0/libgcc_s.so.1 in the ldd output I have no clue. I used gcc-6.3.0 to build. # gcc-config -l [1] x86_64-pc-linux-gnu-4.3.6 [2] x86_64-pc-linux-gnu-4.4.7 [3] x86_64-pc-linux-gnu-4.6.4 [4] x86_64-pc-linux-gnu-4.7.4 [5] x86_64-pc-linux-gnu-4.8.5 [6] x86_64-pc-linux-gnu-4.9.4 [7] x86_64-pc-linux-gnu-5.3.0 [8] x86_64-pc-linux-gnu-5.4.0 [9] x86_64-pc-linux-gnu-6.2.0 [10] x86_64-pc-linux-gnu-6.3.0 * [11] x86_64-pc-linux-gnu-7.1.0 [12] x86_64-pc-linux-gnu-7.2.0 [13] x86_64-pc-linux-gnu-7.3.0 #
https://github.com/gentoo/gentoo/pull/7136
Ping sci-biology. This has been sitting there for a long time.
The bug has been closed via the following commit(s): https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=03ada3844855dd1c9ff2627e7f9239d0248e7cc6 commit 03ada3844855dd1c9ff2627e7f9239d0248e7cc6 Author: Andrew Ammerlaan <andrewammerlaan@gentoo.org> AuthorDate: 2022-01-13 11:19:37 +0000 Commit: Andrew Ammerlaan <andrewammerlaan@gentoo.org> CommitDate: 2022-01-13 11:21:36 +0000 sci-biology/abyss: add version 2.3.4 Closes: https://bugs.gentoo.org/646478 Package-Manager: Portage-3.0.30, Repoman-3.0.3 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org> sci-biology/abyss/Manifest | 1 + sci-biology/abyss/abyss-2.3.4.ebuild | 57 ++++++++++++++++++++++++++++++++++++ 2 files changed, 58 insertions(+)
