/usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: CMakeFiles/diamond.dir/src/align/greedy_pipeline.cpp.o: in function `ExtensionPipeline::Greedy::Target::align_target(QueryMapper&, Statistics&)': greedy_pipeline.cpp:(.text._ZN17ExtensionPipeline6Greedy6Target12align_targetER11QueryMapperR10Statistics[_ZN17ExtensionPipeline6Greedy6Target12align_targetER11QueryMapperR10Statistics]+0x4c5): undefined reference to `Fixed_score_buffer<int> const& needleman_wunsch<int, Local>(sequence, sequence, int&, Local const&, int const&)' collect2: error: ld returned 1 exit status make[2]: *** [CMakeFiles/diamond.dir/build.make:1274: diamond] Error 1 make[2]: Leaving directory '/var/tmp/portage/sci-biology/diamond-0.9.19/work/diamond-0.9.19_build' ------------------------------------------------------------------- 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 Wed Nov 18 11:37:21 AM UTC 2020 /var/db/repos/libressl Sat Nov 7 03:06:11 PM UTC 2020 emerge -qpvO sci-biology/diamond [ebuild N ] sci-biology/diamond-0.9.19
Created attachment 672211 [details] emerge-info.txt
Created attachment 672214 [details] emerge-history.txt
Created attachment 672217 [details] environment
Created attachment 672220 [details] etc.portage.tbz2
Created attachment 672223 [details] logs.tbz2
Created attachment 672226 [details] sci-biology:diamond-0.9.19:20201118-121002.log
Created attachment 672229 [details] temp.tbz2
Created attachment 714429 [details] emerge.log
Created attachment 714432 [details] emerge-history.txt
Created attachment 714435 [details] emerge --info
Created attachment 714438 [details] etc/portage
Created attachment 714441 [details] ebuildtester emerge log
This bug has been fixed due to updates. This bug was reported for version 0.9.19; however, the current version is 2.0.6, so it has received two major releases since this bug report. The current version compiles and runs correctly on a clean and current gentoo stage3 image created using ebuildtester.
Maybe this bug is actually obsolete? Also, the files I uploaded are from a successful ebuildtester emerge.
Created attachment 728919 [details] emerge.log
Created attachment 728922 [details] emerge-history.txt
Created attachment 728925 [details] emerge-info.txt
Created attachment 728928 [details] etc/portage
Created attachment 728931 [details] ebuildtester emerge log
I retested this package within an isolated ebuildtester and the package still builds correctly. This is probably due to a version update, so this bug can confidently be closed.
