/usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: src/seecer_main.o: relocation R_X86_64_32 against `.bss' can not be used when making a PIE object; recompile with -fPIE /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: src/common.o: relocation R_X86_64_32 against `.bss' can not be used when making a PIE object; recompile with -fPIE /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: src/hashmap_read_finder.o: relocation R_X86_64_32 against `.bss' can not be used when making a PIE object; recompile with -fPIE /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: src/hmm_cluster.o: relocation R_X86_64_32 against `.bss' can not be used when making a PIE object; recompile with -fPIE ------------------------------------------------------------------- This is an unstable amd64 chroot image at a tinderbox (==build bot) name: 17.1_no-multilib-libressl_science-20201116-220441 ------------------------------------------------------------------- gcc-config -l: [1] x86_64-pc-linux-gnu-10.2.0 * /usr/lib/llvm/11 11.0.0 Available Python interpreters, in order of preference: [1] python3.7 [2] python3.9 (fallback) [3] python3.8 (fallback) [4] python2.7 (fallback) The following VMs are available for generation-2: *) AdoptOpenJDK 8.272_p10 [openjdk-bin-8] Available Java Virtual Machines: [1] openjdk-bin-8 system-vm The Glorious Glasgow Haskell Compilation System, version 8.8.4 timestamp(s) of HEAD at this tinderbox image: /var/db/repos/gentoo Fri Nov 20 05:46:41 AM UTC 2020 /var/db/repos/libressl Sat Nov 7 03:06:11 PM UTC 2020 emerge -qpvO sci-biology/SEECER [ebuild N ] sci-biology/SEECER-0.1.3-r2
Created attachment 673654 [details] emerge-info.txt
Created attachment 673657 [details] emerge-history.txt
Created attachment 673660 [details] environment
Created attachment 673663 [details] etc.portage.tbz2
Created attachment 673666 [details] logs.tbz2
Created attachment 673669 [details] sci-biology:SEECER-0.1.3-r2:20201120-061354.log
The bug has been closed via the following commit(s): https://gitweb.gentoo.org/proj/sci.git/commit/?id=ecafe6de617cdf6c61a300eafffca973aeac428b commit ecafe6de617cdf6c61a300eafffca973aeac428b Author: Lucas Mitrak <lucas@lucasmitrak.com> AuthorDate: 2021-08-05 00:54:17 +0000 Commit: Andrew Ammerlaan <andrewammerlaan@gentoo.org> CommitDate: 2021-08-05 11:15:46 +0000 sci-biology/SEECER: EAPI bump, patch, remove files, fix build system * EAPI bump * Remove "rename_jellyfish_binary.patch" from ebuild which does nothing * Add a patch that increases the max sequence length * Add a patch that removes CXXFLAGS, CFLAGS, LDFLAGS * Add tc-check-openmp so the ebuild fails without OpenMP support * Remove copying a new replace_ids.cc file which is now a patch * Delete all object files * Delete packaged seqan * Add eautoreconf to recreate the build system * Add system seqan include path and CXXFLAGS to econf Currently, sci-biology/SEECER will not compile due to object files remaining in the package. This was fixed by deleting all object files and so forcing them to be rebuilt. The packaged seqan was deleted as well so the system's seqan is used. In order to achieve this, the system's seqan include path was passed into econf as "/usr/include/seqan". The user's CXXFLAGS were passed into econf also. The patch SEECER-remove-flags.patch removes any other CXXFLAGS, CFLAGS, and LDFLAGS present in configure.ac and Makefile.am. Since configure.ac and Makefile.am were updated, the build system was recreated using eautoreconf -i to account for this. The -i was needed because the "compile" file is missing, so it had to be added. The patch SEECER-increase-max-sequence-length.patch increases the max sequence length from 256 to 10000. This patch was made from an updated replace_ids.cc downloaded from an archived upstream mail list that is no longer available online [1]. The previous revision ebuild included this same replace_ids.cc file; however, despite it appearing as a text file, it was actually a gzipped file with an incorrect extension. In addition, this gzipped file was copied into the src/ directory when the replace_ids.cc file is in the pipeline/ directory. The patch file "rename_jellyfish_binary.patch" also did nothing but modify a comment so it was removed as well. In addition, a tc-check-openmp was added so the ebuild fails without OpenMP support. OpenMP cannot be added as a use flag or a configure enable flag because gomp is always enabled and the source code assumes the system has OpenMP installed. Finally, the EAPI was bumped. [1] URL Split into three parts for the sake of the commit message: https://web.archive.org/web/20150911132231/ http://seecer-rna-read-error-correction-mailing-list.21961.x6.nabble.com /Segmentation-fault-in-step-4-td41.html Closes: https://bugs.gentoo.org/755776 Package-Manager: Portage-3.0.20, Repoman-3.0.2 Signed-off-by: Lucas Mitrak <lucas@lucasmitrak.com> Closes: https://github.com/gentoo/sci/pull/1105 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org> sci-biology/SEECER/SEECER-0.1.3-r3.ebuild | 66 ++++++++++++++++++++++ .../SEECER-increase-max-sequence-length.patch | 44 +++++++++++++++ sci-biology/SEECER/files/SEECER-remove-flags.patch | 30 ++++++++++ 3 files changed, 140 insertions(+)
