| ^~~~~ /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: bam_cat.o: in function `bam_cat(int, char* const*, bam_hdr_t const*, char const*)': bam_cat.c:(.text+0x310): undefined reference to `bam_hdr_destroy' collect2: error: ld returned 1 exit status make: *** [Makefile:90: STAR] Error 1 make: Leaving directory '/var/tmp/portage/sci-biology/STAR-2.5.3a/work/STAR-2.5.3a/source' ------------------------------------------------------------------- This is an unstable amd64 chroot image at a tinderbox (==build bot) name: 17.1_hardened-libressl_abi32+64-20200802-103910 ------------------------------------------------------------------- gcc-config -l: [1] x86_64-pc-linux-gnu-10.2.0 * clang version 10.0.1 Target: x86_64-pc-linux-gnu Thread model: posix InstalledDir: /usr/lib/llvm/10/bin /usr/lib/llvm/10 10.0.1 Available Python interpreters, in order of preference: [1] python3.7 [2] python3.9 (fallback) [3] python3.8 (fallback) [4] python3.6 (fallback) [5] python2.7 (fallback) [6] pypy3 (fallback) Available Ruby profiles: [1] ruby25 (with Rubygems) * Available Rust versions: [1] rust-bin-1.45.2 * The following VMs are available for generation-2: *) AdoptOpenJDK 8.265_p01 [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 Aug 5 06:05:36 AM UTC 2020 /var/db/repos/libressl Fri Jul 24 09:42:51 PM UTC 2020 emerge -qpvO sci-biology/STAR [ebuild N ] sci-biology/STAR-2.5.3a
Created attachment 653258 [details] emerge-info.txt
Created attachment 653262 [details] emerge-history.txt
Created attachment 653264 [details] environment
Created attachment 653266 [details] etc.portage.tbz2
Created attachment 653268 [details] sci-biology:STAR-2.5.3a:20200805-064032.log
Created attachment 653270 [details] temp.tbz2
I assume this explains what needs to be done: http://dev.thep.lu.se/yat/ticket/934 if >=htslib-1.10 is to be used. Or bump to STAR-2.7.6a.
Dear treecleaner@: I'm still able to reproduce this issue right now. Since it has not been fixed for a long time, I'd suggest to evaluate if it is the case to remove this package from the tree. Thanks
The bug has been referenced in the following commit(s): https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=3596083589625a3c954deccfdfb899b49a53a131 commit 3596083589625a3c954deccfdfb899b49a53a131 Author: Andrew Ammerlaan <andrewammerlaan@gentoo.org> AuthorDate: 2022-02-19 11:43:23 +0000 Commit: Andrew Ammerlaan <andrewammerlaan@gentoo.org> CommitDate: 2022-02-19 11:43:23 +0000 sci-biology/STAR: add version 2.7.10a Closes: https://bugs.gentoo.org/696714 Bug: https://bugs.gentoo.org/741152 Bug: https://bugs.gentoo.org/736056 Bug: https://bugs.gentoo.org/716300 Package-Manager: Portage-3.0.30, Repoman-3.0.3 Signed-off-by: Andrew Ammerlaan <andrewammerlaan@gentoo.org> sci-biology/STAR/Manifest | 1 + sci-biology/STAR/STAR-2.7.10a.ebuild | 41 ++++++++++++++++++++++++++++++++++++ 2 files changed, 42 insertions(+)
The bug has been closed via the following commit(s): https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=bcd5ba73fe296ee35a11a3ee96a62a35afa4ac0a commit bcd5ba73fe296ee35a11a3ee96a62a35afa4ac0a Author: David Seifert <soap@gentoo.org> AuthorDate: 2022-05-07 11:01:01 +0000 Commit: David Seifert <soap@gentoo.org> CommitDate: 2022-05-07 11:01:01 +0000 sci-biology/STAR: drop 2.5.3a Closes: https://bugs.gentoo.org/716300 Closes: https://bugs.gentoo.org/736056 Closes: https://bugs.gentoo.org/741152 Signed-off-by: David Seifert <soap@gentoo.org> sci-biology/STAR/Manifest | 1 - sci-biology/STAR/STAR-2.5.3a.ebuild | 42 ------- .../STAR/files/STAR-2.5.3a-fix-build-system.patch | 123 --------------------- 3 files changed, 166 deletions(-)
