/usr/bin/x86_64-pc-linux-gnu-g++ -O2 -pipe -march=native -fno-common -Wl,-O1 -Wl,--as-needed -rdynamic CMakeFiles/kallisto.dir/main.cpp.o -o kallisto libkallisto_core.a -lpthread -lhdf5 -ldl -lm -lrt /usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: libkallisto_core.a(KmerIndex.cpp.o): in function `ks_getuntil2(__kstream_t*, int, __kstring_t*, int*, int) [clone .constprop.0]': KmerIndex.cpp:(.text+0x332): undefined reference to `gzread' /usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: libkallisto_core.a(KmerIndex.cpp.o): in function `KmerIndex::BuildTranscripts(ProgramOptions const&)': KmerIndex.cpp:(.text+0x9fd5): undefined reference to `gzopen' /usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: KmerIndex.cpp:(.text+0xa08e): undefined reference to `gzread' ------------------------------------------------------------------- This is an unstable amd64 chroot image at a tinderbox (==build bot) name: 17.1-libressl-20200203-131554 ------------------------------------------------------------------- gcc-config -l: [1] x86_64-pc-linux-gnu-9.2.0 * clang: clang version 9.0.1 Target: x86_64-pc-linux-gnu Thread model: posix InstalledDir: /usr/lib/llvm/9/bin llvm: 9.0.1 Available Python interpreters, in order of preference: [1] python3.8 [2] python3.7 [3] python3.6 [4] python2.7 (fallback) Available Ruby profiles: [1] ruby24 (with Rubygems) [2] ruby25 (with Rubygems) * Available Rust versions: [1] rust-1.41.0 * ghc: The Glorious Glasgow Haskell Compilation System, version 8.0.2 repository: ==> /var/db/repos/gentoo/metadata/timestamp.chk <== Fri, 07 Feb 2020 18:47:08 +0000 emerge -qpvO sci-biology/kallisto [ebuild N ] sci-biology/kallisto-0.43.1
Created attachment 612596 [details] emerge-info.txt
Created attachment 612598 [details] emerge-history.txt
Created attachment 612600 [details] environment
Created attachment 612602 [details] etc.portage.tbz2
Created attachment 612604 [details] logs.tbz2
Created attachment 612606 [details] sci-biology:kallisto-0.43.1:20200207-200750.log
Created attachment 612608 [details] temp.tbz2
The bug has been closed via the following commit(s): https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=06fc538689feab7fb91e62f619cfdc213074e8e3 commit 06fc538689feab7fb91e62f619cfdc213074e8e3 Author: David Seifert <soap@gentoo.org> AuthorDate: 2021-05-08 14:14:57 +0000 Commit: David Seifert <soap@gentoo.org> CommitDate: 2021-05-08 14:14:57 +0000 sci-biology/kallisto: Remove old 0.43.1 Closes: https://bugs.gentoo.org/696504 Closes: https://bugs.gentoo.org/708658 Closes: https://bugs.gentoo.org/788427 Package-Manager: Portage-3.0.18, Repoman-3.0.3 Signed-off-by: David Seifert <soap@gentoo.org> sci-biology/kallisto/Manifest | 1 - sci-biology/kallisto/kallisto-0.43.1.ebuild | 25 ------------------------- 2 files changed, 26 deletions(-) Additionally, it has been referenced in the following commit(s): https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=5c94901047b60e7e21d38dea38be43e2d5f7a816 commit 5c94901047b60e7e21d38dea38be43e2d5f7a816 Author: David Seifert <soap@gentoo.org> AuthorDate: 2021-05-08 14:14:54 +0000 Commit: David Seifert <soap@gentoo.org> CommitDate: 2021-05-08 14:14:54 +0000 sci-biology/kallisto: Bump to 0.46.2 Bug: https://bugs.gentoo.org/696504 Bug: https://bugs.gentoo.org/708658 Bug: https://bugs.gentoo.org/788427 Package-Manager: Portage-3.0.18, Repoman-3.0.3 Signed-off-by: David Seifert <soap@gentoo.org> sci-biology/kallisto/Manifest | 1 + .../kallisto/files/kallisto-0.46.2-catch2.patch | 38 ++++++ .../kallisto/files/kallisto-0.46.2-cmake.patch | 149 +++++++++++++++++++++ .../kallisto/files/kallisto-0.46.2-gcc11.patch | 21 +++ .../kallisto/files/kallisto-0.46.2-htslib.patch | 52 +++++++ sci-biology/kallisto/kallisto-0.46.2.ebuild | 64 +++++++++ 6 files changed, 325 insertions(+)
