x86_64-pc-linux-gnu-ranlib libgc.a x86_64-pc-linux-gnu-g++ -Wall -Wno-strict-aliasing -Wunused -Wuninitialized -O2 -pipe -march=native -std=c++14 -Wl,-O1 -Wl,--as-needed -L/usr/lib64/ -L/usr//lib -Wl,-O1 -Wl,--as-needed -o cufflinks cufflinks.o libcufflinks.a libgc.a -lboost_thread-mt -lboost_system-mt -lboost_serialization-mt -lbam-0.1-legacy -lz /usr/lib/gcc/x86_64-pc-linux-gnu/8.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: cufflinks.o: undefined reference to symbol 'pthread_condattr_setclock@@GLIBC_2.3.3' /lib64/libpthread.so.0: error adding symbols: DSO missing from command line collect2: error: ld returned 1 exit status make[2]: *** [Makefile:801: cufflinks] Error 1 ------------------------------------------------------------------- This is an unstable amd64 chroot image at a tinderbox (==build bot) name: 17.0-no-multilib-hardened_libressl_20181112-131207 ------------------------------------------------------------------- gcc-config -l: [1] x86_64-pc-linux-gnu-7.3.1 [2] x86_64-pc-linux-gnu-8.2.0 * Available Python interpreters, in order of preference: [1] python3.7 [2] python3.6 [3] python2.7 (fallback) [4] pypy3 (fallback) [5] pypy (fallback) Available Ruby profiles: [1] ruby23 (with Rubygems) [2] ruby24 (with Rubygems) [3] ruby25 (with Rubygems) * emerge -qpvO sci-biology/cufflinks [ebuild R ] sci-biology/cufflinks-2.2.1-r2 USE="-debug" PYTHON_TARGETS="python2_7"
Created attachment 555602 [details] emerge-info.txt
Created attachment 555604 [details] emerge-history.txt
Created attachment 555606 [details] environment
Created attachment 555608 [details] etc.portage.tbz2
Created attachment 555610 [details] logs.tbz2
Created attachment 555612 [details] sci-biology:cufflinks-2.2.1-r2:20181118-134952.log
Created attachment 555614 [details] temp.tbz2
The bug has been referenced in the following commit(s): https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=ed1988a3d90251013691277fb7111cabfd57ca85 commit ed1988a3d90251013691277fb7111cabfd57ca85 Author: David Seifert <soap@gentoo.org> AuthorDate: 2019-04-20 13:00:54 +0000 Commit: David Seifert <soap@gentoo.org> CommitDate: 2019-04-20 13:00:54 +0000 package.mask: Last rite sci-biology/cufflinks Bug: https://bugs.gentoo.org/671432 Signed-off-by: David Seifert <soap@gentoo.org> profiles/package.mask | 6 ++++++ 1 file changed, 6 insertions(+)
The bug has been closed via the following commit(s): https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=824a86b1faf1f0fa081621f7608d617db1799ed1 commit 824a86b1faf1f0fa081621f7608d617db1799ed1 Author: David Seifert <soap@gentoo.org> AuthorDate: 2019-05-19 21:49:59 +0000 Commit: David Seifert <soap@gentoo.org> CommitDate: 2019-05-19 21:49:59 +0000 sci-biology/cufflinks: Remove last-rited pkg Closes: https://bugs.gentoo.org/671432 Signed-off-by: David Seifert <soap@gentoo.org> profiles/package.mask | 6 - sci-biology/cufflinks/Manifest | 1 - sci-biology/cufflinks/cufflinks-2.2.1-r2.ebuild | 57 ---------- .../cufflinks-2.2.1-boost-1.65-tr1-removal.patch | 14 --- .../cufflinks/files/cufflinks-2.2.1-flags.patch | 28 ----- .../files/cufflinks-2.2.1-format-security.patch | 16 --- .../files/cufflinks-2.2.1-gcc5-make_shared.patch | 11 -- .../cufflinks/files/cufflinks-2.2.1-gcc6.patch | 14 --- .../cufflinks/files/cufflinks-2.2.1-gcc7.patch | 121 --------------------- .../files/cufflinks-2.2.1-samtools-legacy.patch | 44 -------- sci-biology/cufflinks/metadata.xml | 8 -- 11 files changed, 320 deletions(-)
