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Gentoo's Bugzilla – Attachment 659228 Details for
Bug 741376
sci-chemistry/propka-3.2.0 fails tests
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build.log
build.log (text/plain), 13.58 KB, created by
Agostino Sarubbo
on 2020-09-09 07:38:52 UTC
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Description:
build.log
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Creator:
Agostino Sarubbo
Created:
2020-09-09 07:38:52 UTC
Size:
13.58 KB
patch
obsolete
> * Package: sci-chemistry/propka-3.2.0 > * Repository: gentoo > * Maintainer: sci-chemistry@gentoo.org > * USE: abi_x86_64 amd64 elibc_glibc kernel_linux python_targets_python3_7 python_targets_python3_8 test userland_GNU > * FEATURES: network-sandbox preserve-libs sandbox test userpriv usersandbox > > >@@@@@ PLEASE PAY ATTENTION HERE!!! @@@@@ >This information may help you to understand if this is a duplicate or if this bug exists after you pushed a fix; >This ebuild was merged at the following commit: >https://github.com/gentoo-mirror/gentoo/commit/8eed8db679caaf42c25efbeb348e1e07a2175091 (Tue Sep 8 17:35:30 UTC 2020) >@@@@@ END @@@@@ > > > >emerge --info: >Portage 3.0.6 (python 3.8.5-final-0, default/linux/amd64/17.1, gcc-10.2.0, glibc-2.32-r1, 5.4.0-1021-aws x86_64) >================================================================= >System uname: Linux-5.4.0-1021-aws-x86_64-Intel-R-_Xeon-R-_Platinum_8175M_CPU_@_2.50GHz-with-glibc2.2.5 >KiB Mem: 64359960 total, 25921156 free >KiB Swap: 0 total, 0 free >Timestamp of repository gentoo: Tue, 08 Sep 2020 17:35:29 +0000 >sh bash 5.0_p18 >ld GNU ld (Gentoo 2.34 p6) 2.34.0 >app-shells/bash: 5.0_p18::gentoo >dev-lang/perl: 5.30.3-r1::gentoo >dev-lang/python: 2.7.18-r1::gentoo, 3.6.12::gentoo, 3.7.9::gentoo, 3.8.5::gentoo, 3.9.0_rc1::gentoo >dev-util/cmake: 3.18.2::gentoo >sys-apps/baselayout: 2.7::gentoo >sys-apps/openrc: 0.42.1::gentoo >sys-apps/sandbox: 2.20::gentoo >sys-devel/autoconf: 2.13-r1::gentoo, 2.69-r5::gentoo >sys-devel/automake: 1.16.2::gentoo >sys-devel/binutils: 2.34-r2::gentoo >sys-devel/gcc: 10.2.0-r1::gentoo >sys-devel/gcc-config: 2.3.2::gentoo >sys-devel/libtool: 2.4.6-r6::gentoo >sys-devel/make: 4.3::gentoo >sys-kernel/linux-headers: 5.8::gentoo (virtual/os-headers) >sys-libs/glibc: 2.32-r1::gentoo >Repositories: > >gentoo > location: /usr/portage > sync-type: rsync > sync-uri: rsync://rsync.gentoo.org/gentoo-portage > priority: -1000 > sync-rsync-extra-opts: > sync-rsync-verify-max-age: 24 > sync-rsync-verify-metamanifest: yes > sync-rsync-verify-jobs: 1 > >ACCEPT_KEYWORDS="amd64 ~amd64" >ACCEPT_LICENSE="* LGPL-2.1" >CBUILD="x86_64-pc-linux-gnu" >CC="x86_64-pc-linux-gnu-clang" >CFLAGS="-O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color" >CHOST="x86_64-pc-linux-gnu" >CONFIG_PROTECT="/etc /usr/share/gnupg/qualified.txt" >CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/gconf /etc/gentoo-release /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo" >CXX="x86_64-pc-linux-gnu-clang++" >CXXFLAGS="-O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color" >DISTDIR="/var/tmp/portage/sci-chemistry/propka-3.2.0/distdir" >EMERGE_DEFAULT_OPTS="--with-bdeps=y -1 -b -k" >ENV_UNSET="CARGO_HOME DBUS_SESSION_BUS_ADDRESS DISPLAY GOBIN GOPATH PERL5LIB PERL5OPT PERLPREFIX PERL_CORE PERL_MB_OPT PERL_MM_OPT XAUTHORITY XDG_CACHE_HOME XDG_CONFIG_HOME XDG_DATA_HOME XDG_RUNTIME_DIR" >FCFLAGS="-O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color" >FEATURES="assume-digests binpkg-docompress binpkg-dostrip binpkg-logs buildpkg collision-protect config-protect-if-modified distlocks ebuild-locks fixlafiles ipc-sandbox merge-sync multilib-strict network-sandbox news parallel-fetch pid-sandbox preserve-libs protect-owned qa-unresolved-soname-deps sandbox sfperms sign split-log strict test unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr" >FFLAGS="-O2 -pipe -march=native -frecord-gcc-switches -fno-diagnostics-color" >GENTOO_MIRRORS="http://distfiles.gentoo.org" >LANG="C.UTF-8" >LDFLAGS="-Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -fuse-ld=lld" >MAKEOPTS="-j16 V=1" >PKGDIR="/root/.packages" >PORTAGE_CONFIGROOT="/" >PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --omit-dir-times --compress --force --whole-file --delete --stats --human-readable --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages --exclude=/.git" >PORTAGE_TMPDIR="/var/tmp" >USE="acl amd64 berkdb bzip2 cli crypt dri elogind fortran gdbm iconv ipv6 jumbo-build libglvnd libtirpc multilib native-symlinks ncurses nls nptl openmp pam pcre readline seccomp split-usr ssl tcpd test unicode xattr zlib" ABI_X86="64" ELIBC="glibc" KERNEL="linux" PYTHON_TARGETS="python3_7 python3_8" USERLAND="GNU" >Unset: CPPFLAGS, CTARGET, INSTALL_MASK, LC_ALL, LINGUAS, PORTAGE_BINHOST, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS > > > >>>> Unpacking source... >>>> Unpacking propka-3.2.0.tar.gz to /var/tmp/portage/sci-chemistry/propka-3.2.0/work >>>> Source unpacked in /var/tmp/portage/sci-chemistry/propka-3.2.0/work >>>> Preparing source in /var/tmp/portage/sci-chemistry/propka-3.2.0/work/propka-3.2.0 ... >>>> Source prepared. >>>> Configuring source in /var/tmp/portage/sci-chemistry/propka-3.2.0/work/propka-3.2.0 ... >>>> Source configured. >>>> Compiling source in /var/tmp/portage/sci-chemistry/propka-3.2.0/work/propka-3.2.0 ... > * python3_7: running distutils-r1_run_phase distutils-r1_python_compile > * DISTUTILS_USE_SETUPTOOLS value is probably incorrect > * value: DISTUTILS_USE_SETUPTOOLS=bdepend (default?) > * expected: DISTUTILS_USE_SETUPTOOLS=rdepend >python3.7 setup.py build -j 16 >running build >running build_py >creating /var/tmp/portage/sci-chemistry/propka-3.2.0/work/propka-3.2.0-python3_7/lib/propka >copying propka/__main__.py -> /var/tmp/portage/sci-chemistry/propka-3.2.0/work/propka-3.2.0-python3_7/lib/propka >copying propka/__init__.py -> /var/tmp/portage/sci-chemistry/propka-3.2.0/work/propka-3.2.0-python3_7/lib/propka >copying propka/ligand_pka_values.py -> /var/tmp/portage/sci-chemistry/propka-3.2.0/work/propka-3.2.0-python3_7/lib/propka >copying propka/hydrogens.py -> /var/tmp/portage/sci-chemistry/propka-3.2.0/work/propka-3.2.0-python3_7/lib/propka >copying propka/calculations.py -> /var/tmp/portage/sci-chemistry/propka-3.2.0/work/propka-3.2.0-python3_7/lib/propka >copying propka/lib.py -> /var/tmp/portage/sci-chemistry/propka-3.2.0/work/propka-3.2.0-python3_7/lib/propka >copying propka/ligand.py -> /var/tmp/portage/sci-chemistry/propka-3.2.0/work/propka-3.2.0-python3_7/lib/propka >copying propka/molecular_container.py -> /var/tmp/portage/sci-chemistry/propka-3.2.0/work/propka-3.2.0-python3_7/lib/propka >copying propka/iterative.py -> /var/tmp/portage/sci-chemistry/propka-3.2.0/work/propka-3.2.0-python3_7/lib/propka >copying propka/bonds.py -> /var/tmp/portage/sci-chemistry/propka-3.2.0/work/propka-3.2.0-python3_7/lib/propka >copying propka/parameters.py -> /var/tmp/portage/sci-chemistry/propka-3.2.0/work/propka-3.2.0-python3_7/lib/propka >copying propka/determinant.py -> /var/tmp/portage/sci-chemistry/propka-3.2.0/work/propka-3.2.0-python3_7/lib/propka >copying propka/coupled_groups.py -> /var/tmp/portage/sci-chemistry/propka-3.2.0/work/propka-3.2.0-python3_7/lib/propka >copying propka/group.py -> /var/tmp/portage/sci-chemistry/propka-3.2.0/work/propka-3.2.0-python3_7/lib/propka >copying propka/hybrid36.py -> /var/tmp/portage/sci-chemistry/propka-3.2.0/work/propka-3.2.0-python3_7/lib/propka >copying propka/conformation_container.py -> /var/tmp/portage/sci-chemistry/propka-3.2.0/work/propka-3.2.0-python3_7/lib/propka >copying propka/run.py -> /var/tmp/portage/sci-chemistry/propka-3.2.0/work/propka-3.2.0-python3_7/lib/propka >copying propka/output.py -> /var/tmp/portage/sci-chemistry/propka-3.2.0/work/propka-3.2.0-python3_7/lib/propka >copying propka/input.py -> /var/tmp/portage/sci-chemistry/propka-3.2.0/work/propka-3.2.0-python3_7/lib/propka >copying propka/vector_algebra.py -> /var/tmp/portage/sci-chemistry/propka-3.2.0/work/propka-3.2.0-python3_7/lib/propka >copying propka/protonate.py -> /var/tmp/portage/sci-chemistry/propka-3.2.0/work/propka-3.2.0-python3_7/lib/propka >copying propka/version.py -> /var/tmp/portage/sci-chemistry/propka-3.2.0/work/propka-3.2.0-python3_7/lib/propka >copying propka/determinants.py -> /var/tmp/portage/sci-chemistry/propka-3.2.0/work/propka-3.2.0-python3_7/lib/propka >copying propka/energy.py -> /var/tmp/portage/sci-chemistry/propka-3.2.0/work/propka-3.2.0-python3_7/lib/propka >copying propka/atom.py -> /var/tmp/portage/sci-chemistry/propka-3.2.0/work/propka-3.2.0-python3_7/lib/propka >copying propka/propka.cfg -> /var/tmp/portage/sci-chemistry/propka-3.2.0/work/propka-3.2.0-python3_7/lib/propka >copying propka/protein_bonds.json -> /var/tmp/portage/sci-chemistry/propka-3.2.0/work/propka-3.2.0-python3_7/lib/propka >warning: build_py: byte-compiling is disabled, skipping. > > * python3_8: running distutils-r1_run_phase distutils-r1_python_compile >python3.8 setup.py build -j 16 >running build >running build_py >creating /var/tmp/portage/sci-chemistry/propka-3.2.0/work/propka-3.2.0-python3_8/lib/propka >copying propka/__main__.py -> /var/tmp/portage/sci-chemistry/propka-3.2.0/work/propka-3.2.0-python3_8/lib/propka >copying propka/__init__.py -> /var/tmp/portage/sci-chemistry/propka-3.2.0/work/propka-3.2.0-python3_8/lib/propka >copying propka/ligand_pka_values.py -> /var/tmp/portage/sci-chemistry/propka-3.2.0/work/propka-3.2.0-python3_8/lib/propka >copying propka/hydrogens.py -> /var/tmp/portage/sci-chemistry/propka-3.2.0/work/propka-3.2.0-python3_8/lib/propka >copying propka/calculations.py -> /var/tmp/portage/sci-chemistry/propka-3.2.0/work/propka-3.2.0-python3_8/lib/propka >copying propka/lib.py -> /var/tmp/portage/sci-chemistry/propka-3.2.0/work/propka-3.2.0-python3_8/lib/propka >copying propka/ligand.py -> /var/tmp/portage/sci-chemistry/propka-3.2.0/work/propka-3.2.0-python3_8/lib/propka >copying propka/molecular_container.py -> /var/tmp/portage/sci-chemistry/propka-3.2.0/work/propka-3.2.0-python3_8/lib/propka >copying propka/iterative.py -> /var/tmp/portage/sci-chemistry/propka-3.2.0/work/propka-3.2.0-python3_8/lib/propka >copying propka/bonds.py -> /var/tmp/portage/sci-chemistry/propka-3.2.0/work/propka-3.2.0-python3_8/lib/propka >copying propka/parameters.py -> /var/tmp/portage/sci-chemistry/propka-3.2.0/work/propka-3.2.0-python3_8/lib/propka >copying propka/determinant.py -> /var/tmp/portage/sci-chemistry/propka-3.2.0/work/propka-3.2.0-python3_8/lib/propka >copying propka/coupled_groups.py -> /var/tmp/portage/sci-chemistry/propka-3.2.0/work/propka-3.2.0-python3_8/lib/propka >copying propka/group.py -> /var/tmp/portage/sci-chemistry/propka-3.2.0/work/propka-3.2.0-python3_8/lib/propka >copying propka/hybrid36.py -> /var/tmp/portage/sci-chemistry/propka-3.2.0/work/propka-3.2.0-python3_8/lib/propka >copying propka/conformation_container.py -> /var/tmp/portage/sci-chemistry/propka-3.2.0/work/propka-3.2.0-python3_8/lib/propka >copying propka/run.py -> /var/tmp/portage/sci-chemistry/propka-3.2.0/work/propka-3.2.0-python3_8/lib/propka >copying propka/output.py -> /var/tmp/portage/sci-chemistry/propka-3.2.0/work/propka-3.2.0-python3_8/lib/propka >copying propka/input.py -> /var/tmp/portage/sci-chemistry/propka-3.2.0/work/propka-3.2.0-python3_8/lib/propka >copying propka/vector_algebra.py -> /var/tmp/portage/sci-chemistry/propka-3.2.0/work/propka-3.2.0-python3_8/lib/propka >copying propka/protonate.py -> /var/tmp/portage/sci-chemistry/propka-3.2.0/work/propka-3.2.0-python3_8/lib/propka >copying propka/version.py -> /var/tmp/portage/sci-chemistry/propka-3.2.0/work/propka-3.2.0-python3_8/lib/propka >copying propka/determinants.py -> /var/tmp/portage/sci-chemistry/propka-3.2.0/work/propka-3.2.0-python3_8/lib/propka >copying propka/energy.py -> /var/tmp/portage/sci-chemistry/propka-3.2.0/work/propka-3.2.0-python3_8/lib/propka >copying propka/atom.py -> /var/tmp/portage/sci-chemistry/propka-3.2.0/work/propka-3.2.0-python3_8/lib/propka >copying propka/propka.cfg -> /var/tmp/portage/sci-chemistry/propka-3.2.0/work/propka-3.2.0-python3_8/lib/propka >copying propka/protein_bonds.json -> /var/tmp/portage/sci-chemistry/propka-3.2.0/work/propka-3.2.0-python3_8/lib/propka >warning: build_py: byte-compiling is disabled, skipping. > >>>> Source compiled. >>>> Test phase: sci-chemistry/propka-3.2.0 > * python3_7: running distutils-r1_run_phase python_test >/var/tmp/portage/sci-chemistry/propka-3.2.0/temp/environment: line 2984: cd: Tests: No such file or directory > * ERROR: sci-chemistry/propka-3.2.0::gentoo failed (test phase): > * (no error message) > * > * Call stack: > * ebuild.sh, line 125: Called src_test > * environment, line 3025: Called distutils-r1_src_test > * environment, line 1306: Called _distutils-r1_run_foreach_impl 'python_test' > * environment, line 486: Called python_foreach_impl 'distutils-r1_run_phase' 'python_test' > * environment, line 2625: Called multibuild_foreach_variant '_python_multibuild_wrapper' 'distutils-r1_run_phase' 'python_test' > * environment, line 2089: Called _multibuild_run '_python_multibuild_wrapper' 'distutils-r1_run_phase' 'python_test' > * environment, line 2087: Called _python_multibuild_wrapper 'distutils-r1_run_phase' 'python_test' > * environment, line 879: Called distutils-r1_run_phase 'python_test' > * environment, line 1243: Called python_test > * environment, line 2984: Called die > * The specific snippet of code: > * cd Tests || die; > * > * If you need support, post the output of `emerge --info '=sci-chemistry/propka-3.2.0::gentoo'`, > * the complete build log and the output of `emerge -pqv '=sci-chemistry/propka-3.2.0::gentoo'`. > * The complete build log is located at '/var/log/emerge-log/build/sci-chemistry/propka-3.2.0:20200908-185519.log'. > * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-chemistry/propka-3.2.0/temp/build.log'. > * The ebuild environment file is located at '/var/tmp/portage/sci-chemistry/propka-3.2.0/temp/environment'. > * Working directory: '/var/tmp/portage/sci-chemistry/propka-3.2.0/work/propka-3.2.0' > * S: '/var/tmp/portage/sci-chemistry/propka-3.2.0/work/propka-3.2.0'
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bug 741376
: 659228