make[3]: Leaving directory '/var/tmp/portage/sci-biology/ucsc-genome-browser-260-r1/work/kent/src/hg/makeDb/schema/dbSnoop' make[2]: Leaving directory '/var/tmp/portage/sci-biology/ucsc-genome-browser-260-r1/work/kent/src/hg/makeDb/schema' ( cd tfbsConsLoc && echo tfbsConsLoc && make ) tfbsConsLoc make[2]: Entering directory '/var/tmp/portage/sci-biology/ucsc-genome-browser-260-r1/work/kent/src/hg/makeDb/tfbsConsLoc' clang -O2 -pipe -march=native -fno-diagnostics-color -fcommon ./tfbsConsLoc.c ./matt-maf.c ./util.c ./tfbsConsLocUtil.c ./seq.c -I -g -O -w -W -lm -o /var/tmp/portage/sci-biology/ucsc-genome-browser-260-r1/work/destdir/opt/ucsc-genome-browser/bin/tfbsConsLoc ./tfbsConsLoc.c:44:13: error: call to undeclared function 'do_revcomp'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration] ------------------------------------------------------------------- This is an unstable amd64 chroot image at a tinderbox (==build bot) name: 17.1_desktop_systemd_merged_usr-20231128-203237 ------------------------------------------------------------------- CC=clang CXX=clang++ gcc-config -l: [1] x86_64-pc-linux-gnu-10 [2] x86_64-pc-linux-gnu-13 * clang/llvm (if any): clang version 17.0.6 Target: x86_64-pc-linux-gnu Thread model: posix InstalledDir: /usr/lib/llvm/17/bin Configuration file: /etc/clang/x86_64-pc-linux-gnu-clang.cfg /usr/lib/llvm/17 17.0.6 Python 3.11.6 Available Ruby profiles: [1] ruby31 (with Rubygems) * Available Rust versions: [1] rust-1.73.0 * The following VMs are available for generation-2: 1) Eclipse Temurin JDK 11.0.20.1_p1 [openjdk-bin-11] 2) Eclipse Temurin JDK 17.0.8.1_p1 [openjdk-bin-17] *) Eclipse Temurin JDK 21.0.1_p12 [openjdk-bin-21] 4) Eclipse Temurin JDK 8.382_p05 [openjdk-bin-8] Available Java Virtual Machines: [1] openjdk-bin-8 [2] openjdk-bin-11 [3] openjdk-bin-17 [4] openjdk-bin-21 system-vm The Glorious Glasgow Haskell Compilation System, version 9.0.2 php cli (if any): [1] php8.1 * [2] php8.2 go version go1.21.4 linux/amd64 HEAD of ::gentoo commit 9fbac9a87a3f54ee750529d7650d1bab53f12910 Author: Repository mirror & CI <repomirrorci@gentoo.org> Date: Mon Dec 4 14:16:57 2023 +0000 2023-12-04 14:16:56 UTC emerge -qpvO sci-biology/ucsc-genome-browser [ebuild N ] sci-biology/ucsc-genome-browser-260-r1 USE="mysql server -static-libs -vhosts"
Created attachment 876930 [details] emerge-info.txt
Created attachment 876931 [details] emerge-history.txt
Created attachment 876932 [details] environment
Created attachment 876933 [details] etc.clang.tar.xz
Created attachment 876934 [details] etc.portage.tar.xz
Created attachment 876935 [details] logs.tar.xz
Created attachment 876936 [details] qlist-info.txt.xz
Created attachment 876937 [details] sci-biology:ucsc-genome-browser-260-r1:20231204-154850.log.xz
Created attachment 876938 [details] temp.tar.xz
The bug has been closed via the following commit(s): https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=b7cf0f3d7cbe8fa13b188d50b16f47fd726c4e2a commit b7cf0f3d7cbe8fa13b188d50b16f47fd726c4e2a Author: Sam James <sam@gentoo.org> AuthorDate: 2024-06-01 23:15:05 +0000 Commit: Sam James <sam@gentoo.org> CommitDate: 2024-06-01 23:15:05 +0000 sci-biology/ucsc-genome-browser: workaround modern C issues Build with -std=gnu89 as it has many issues. Closes: https://bugs.gentoo.org/831491 Closes: https://bugs.gentoo.org/919200 Closes: https://bugs.gentoo.org/921261 Signed-off-by: Sam James <sam@gentoo.org> sci-biology/ucsc-genome-browser/ucsc-genome-browser-260-r1.ebuild | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-)
