>>> Emerging (2 of 3) dev-python/numpy-9999::gentoo * Using following Fortran compiler: * F77: x86_64-pc-linux-gnu-gfortran * FC: x86_64-pc-linux-gnu-gfortran >>> Unpacking source... Initialized empty Git repository in /apps/gentoo/usr/portage/distfiles/git3-src/numpy_numpy.git/ * Fetching https://github.com/numpy/numpy.git ... git fetch https://github.com/numpy/numpy.git +HEAD:refs/git-r3/HEAD remote: Counting objects: 119082, done. remote: Compressing objects: 100% (21/21), done. remote: Total 119082 (delta 8), reused 7 (delta 6), pack-reused 119055 Receiving objects: 100% (119082/119082), 48.98 MiB | 104.00 KiB/s, done. Resolving deltas: 100% (94795/94795), done. From https://github.com/numpy/numpy * [new ref] -> refs/git-r3/HEAD * [new tag] pre-removal-numpybook -> pre-removal-numpybook * [new tag] v0.2.2 -> v0.2.2 * [new tag] v0.3.0 -> v0.3.0 * [new tag] with_maskna -> with_maskna git symbolic-ref refs/git-r3/dev-python/numpy/0/__main__ refs/git-r3/HEAD Initialized empty Git repository in /apps/gentoo/usr/portage/distfiles/git3-src/scipy_scipy-sphinx-theme.git/ * Fetching https://github.com/scipy/scipy-sphinx-theme.git ... git fetch https://github.com/scipy/scipy-sphinx-theme.git --prune +refs/heads/*:refs/heads/* +refs/tags/*:refs/tags/* +refs/notes/*:refs/notes/* +HEAD:refs/git-r3/HEAD remote: Counting objects: 610, done. remote: Total 610 (delta 0), reused 0 (delta 0), pack-reused 610 Receiving objects: 100% (610/610), 717.13 KiB | 841.00 KiB/s, done. Resolving deltas: 100% (229/229), done. From https://github.com/scipy/scipy-sphinx-theme * [new branch] master -> master * [new ref] -> refs/git-r3/HEAD git update-ref --no-deref refs/git-r3/dev-python/numpy/0/doc_scipy-sphinx-theme/__main__ c466764e2231ba132c09826b5b138fffa1cfcec3 Initialized empty Git repository in /apps/gentoo/usr/portage/distfiles/git3-src/numpy_numpydoc.git/ * Fetching https://github.com/numpy/numpydoc.git ... git fetch https://github.com/numpy/numpydoc.git --prune +refs/heads/*:refs/heads/* +refs/tags/*:refs/tags/* +refs/notes/*:refs/notes/* +HEAD:refs/git-r3/HEAD remote: Counting objects: 1100, done. remote: Total 1100 (delta 0), reused 0 (delta 0), pack-reused 1100 Receiving objects: 100% (1100/1100), 233.90 KiB | 527.00 KiB/s, done. Resolving deltas: 100% (727/727), done. From https://github.com/numpy/numpydoc * [new branch] master -> master * [new tag] v0.4 -> v0.4 * [new tag] v0.5 -> v0.5 * [new tag] v0.6 -> v0.6 * [new tag] v0.7.0 -> v0.7.0 * [new ref] -> refs/git-r3/HEAD git update-ref --no-deref refs/git-r3/dev-python/numpy/0/doc_sphinxext/__main__ ef988a4a4658c991f4445f6241ab02d74710c6e3 * Checking out https://github.com/numpy/numpy.git to /apps/gentoo/var/tmp/portage/dev-python/numpy-9999/work/numpy-9999 ... git checkout --quiet refs/git-r3/HEAD GIT NEW branch --> repository: https://github.com/numpy/numpy.git at the commit: 12668b65791ef5a5104007e26c53e598b4416235 * Checking out https://github.com/scipy/scipy-sphinx-theme.git to /apps/gentoo/var/tmp/portage/dev-python/numpy-9999/work/numpy-9999/doc/scipy-sphinx-theme ... git checkout --quiet c466764e2231ba132c09826b5b138fffa1cfcec3 GIT NEW branch --> repository: https://github.com/scipy/scipy-sphinx-theme.git at the commit: c466764e2231ba132c09826b5b138fffa1cfcec3 * Checking out https://github.com/numpy/numpydoc.git to /apps/gentoo/var/tmp/portage/dev-python/numpy-9999/work/numpy-9999/doc/sphinxext ... git checkout --quiet ef988a4a4658c991f4445f6241ab02d74710c6e3 GIT NEW branch --> repository: https://github.com/numpy/numpydoc.git at the commit: ef988a4a4658c991f4445f6241ab02d74710c6e3 >>> Source unpacked in /apps/gentoo/var/tmp/portage/dev-python/numpy-9999/work >>> Preparing source in /apps/gentoo/var/tmp/portage/dev-python/numpy-9999/work/numpy-9999 ... * Applying numpy-1.9.2-no-hardcode-blas.patch ... * Failed Patch: numpy-1.9.2-no-hardcode-blas.patch ! * ( /apps/gentoo/var/tmp/portage/dev-python/numpy-9999/files/numpy-1.9.2-no-hardcode-blas.patch ) * * Include in your bugreport the contents of: * * /apps/gentoo/var/tmp/portage/dev-python/numpy-9999/temp/numpy-1.9.2-no-hardcode-blas.patch.out * ERROR: dev-python/numpy-9999::gentoo failed (prepare phase): * Failed Patch: numpy-1.9.2-no-hardcode-blas.patch! * * Call stack: * ebuild.sh, line 124: Called src_prepare * environment, line 4792: Called distutils-r1_src_prepare * environment, line 1455: Called python_prepare_all * environment, line 4504: Called distutils-r1_python_prepare_all * environment, line 1362: Called epatch '/apps/gentoo/var/tmp/portage/dev-python/numpy-9999/files/numpy-1.9.2-no-hardcode-blas.patch' * environment, line 1835: Called die * The specific snippet of code: * die "Failed Patch: ${patchname}!"; * * If you need support, post the output of `emerge --info '=dev-python/numpy-9999::gentoo'`, * the complete build log and the output of `emerge -pqv '=dev-python/numpy-9999::gentoo'`. * The complete build log is located at '/apps/gentoo/var/tmp/portage/dev-python/numpy-9999/temp/build.log'. * The ebuild environment file is located at '/apps/gentoo/var/tmp/portage/dev-python/numpy-9999/temp/environment'. * Working directory: '/apps/gentoo/var/tmp/portage/dev-python/numpy-9999/work/numpy-9999' * S: '/apps/gentoo/var/tmp/portage/dev-python/numpy-9999/work/numpy-9999' $ emerge --info Portage 2.3.24 (python 2.7.14-final-0, default/linux/amd64/17.0/no-multilib/prefix/kernel-3.2+, gcc-6.3.0, glibc-2.25-r10, 2.6.32-696.10.3.el6.x86_64 x86_64) ================================================================= System uname: Linux-2.6.32-696.10.3.el6.x86_64-x86_64-Intel-R-_Xeon-R-_CPU_E5-2695_v3_@_2.30GHz-with-centos-6.9-Final KiB Mem: 132049160 total, 50429048 free KiB Swap: 2097148 total, 1883496 free Timestamp of repository gentoo: Thu, 08 Feb 2018 17:30:01 +0000 Head commit of repository gentoo: ac9f1eb326a0cac717b48c577b08e86f87b97686 sh bash 4.4_p18 ld GNU ld (Gentoo 2.29.1 p3) 2.29.1 app-shells/bash: 4.4_p18::gentoo dev-java/java-config: 2.2.0-r3::gentoo dev-lang/perl: 5.26.1-r1::gentoo dev-lang/python: 2.7.14-r1::gentoo, 3.4.6::gentoo, 3.5.4-r1::gentoo, 3.6.4::gentoo dev-util/cmake: 3.10.2::gentoo dev-util/pkgconfig: 0.29.2::gentoo sys-apps/baselayout: 2.4.1-r2::gentoo sys-apps/sandbox: 2.12::gentoo sys-devel/autoconf: 2.13::gentoo, 2.69-r4::gentoo sys-devel/automake: 1.14.1-r1::gentoo, 1.15.1-r1::gentoo sys-devel/binutils: 2.29.1-r1::gentoo, 2.30::gentoo sys-devel/gcc: 3.4.6-r2::gentoo, 4.1.2::gentoo, 4.2.4-r1::gentoo, 4.4.7::gentoo, 4.5.4::gentoo, 4.7.4::gentoo, 4.8.5::gentoo, 4.9.3::gentoo, 4.9.4::gentoo, 5.4.0-r4::gentoo, 6.3.0::gentoo, 7.1.0-r1::gentoo, 7.2.0-r1::gentoo, 7.3.0::gentoo sys-devel/gcc-config: 1.9.1::gentoo sys-devel/libtool: 2.4.6-r4::gentoo sys-devel/make: 4.2.1-r1::gentoo sys-kernel/linux-headers: 4.15::gentoo (virtual/os-headers) sys-libs/glibc: 2.25-r10::gentoo Repositories: gentoo location: /apps/gentoo/usr/portage sync-type: rsync sync-uri: rsync://rsync.gentoo.org/gentoo-portage priority: -1000 sync-rsync-verify-metamanifest: yes sync-rsync-extra-opts: haskell location: /apps/gentoo/var/lib/layman/haskell masters: gentoo priority: 50 science location: /apps/gentoo/var/lib/layman/science masters: gentoo priority: 50 ACCEPT_KEYWORDS="amd64 ~amd64" ACCEPT_LICENSE="* -@EULA dlj-1.1 sun-bcla-java-vm Oracle-BCLA-JavaSE IBM-J1.6 skype-eula Nero-EULA-US AdobeFlash-10.3 skype-4.0.0.7-copyright AdobeFlash-11.x Intel-SDP OPERA-2014" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-O2 -pipe -O2 -pipe -march=native -ftree-vectorize" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/share/gnupg/qualified.txt /usr/share/maven-bin-3.3/conf" CONFIG_PROTECT_MASK="/apps/gentoo/etc/gentoo-release /etc/ca-certificates.conf /etc/dconf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo /etc/texmf/language.dat.d /etc/texmf/language.def.d /etc/texmf/updmap.d /etc/texmf/web2c" CXXFLAGS="-O2 -pipe -O2 -pipe -march=native -ftree-vectorize" DISTDIR="/apps/gentoo/usr/portage/distfiles" FCFLAGS="-O2 -pipe" FEATURES="assume-digests binpkg-logs config-protect-if-modified distlocks ebuild-locks fixlafiles force-prefix merge-sync multilib-strict news nostrip parallel-fetch preserve-libs protect-owned sfperms splitdebug strict unknown-features-warn unmerge-logs unmerge-orphans unprivileged" FFLAGS="-O2 -pipe" GENTOO_MIRRORS="http://ftp.fi.muni.cz/pub/linux/gentoo/ http://gentoo.mirror.web4u.cz/ rsync://gentoo.mirror.dkm.cz/gentoo/ ftp://gentoo.mirror.web4u.cz/" LDFLAGS="-Wl,-O1 -Wl,--as-needed" LINGUAS="en_US en_GB en cs" MAKEOPTS="-j4" PKGDIR="/apps/gentoo/usr/portage/packages" PORTAGE_CONFIGROOT="/apps/gentoo/" 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="/apps/gentoo/var/tmp" USE="X alsa amd64 apache apache2 avx avx2 berkdb boost bzip2 cairo cgi cli coin cracklib crypt cryptlib cxx dbus device-mapper dhcp dri emboss encode fax fbcon ffmpeg fontconfig fortran gbm gd gdbm gimp glpk gnutls gtk hal hwdb iconv imaging innodb ithreads java javafx javascript jce jpeg jpg js jscript keymap ladspa lapack lcms libnotify lm_sensors mad mmx modules mpi mpich2 mysql ncurses nfs nls nptl nptlonly nscd objc openmp openssl pcre pdf perl php png policykit polkit postscript ppds pppd prefix python qt3support readline resolvconf seccomp server session slideshow sndfile sqlite sse sse2 sse3 sse4_1 sse4_2 ssl ssse3 suexec svg syslog tcl tcpd threads tiff tk truetype unicode usb v4l v4l2 vim-syntax vnc wavpack wifi x11 xcb xml xorg xrandr xv xvid xvmc zlib" ABI_X86="64" ALSA_CARDS="ali5451 als4000 atiixp atiixp-modem bt87x ca0106 cmipci emu10k1x ens1370 ens1371 es1938 es1968 fm801 hda-intel intel8x0 intel8x0m maestro3 trident usb-audio via82xx via82xx-modem ymfpci" APACHE2_MODULES="authn_core authz_core socache_shmcb unixd actions alias auth_basic authn_alias authn_anon authn_dbm authn_default authn_file authz_dbm authz_default authz_groupfile authz_host authz_owner authz_user autoindex cache cgi cgid dav dav_fs dav_lock deflate dir disk_cache env expires ext_filter file_cache filter headers include info log_config logio mem_cache mime mime_magic negotiation rewrite setenvif speling status unique_id userdir usertrack vhost_alias" CALLIGRA_FEATURES="kexi words flow plan sheets stage tables krita karbon braindump author" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" CPU_FLAGS_X86="avx avx2 fma3 mmx mmxext popcnt sse sse2 sse3 sse4_1 sse4_2 ssse3" ELIBC="glibc" GPSD_PROTOCOLS="ashtech aivdm earthmate evermore fv18 garmin garmintxt gpsclock isync itrax mtk3301 nmea ntrip navcom oceanserver oldstyle oncore rtcm104v2 rtcm104v3 sirf skytraq superstar2 timing tsip tripmate tnt ublox ubx" INPUT_DEVICES="libinput keyboard mouse" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php5-6 php7-0" POSTGRES_TARGETS="postgres9_5" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_5" RUBY_TARGETS="ruby24 ruby25" USERLAND="GNU" VIDEO_CARDS="amdgpu fbdev intel nouveau radeon radeonsi vesa dummy v4l" XTABLES_ADDONS="quota2 psd pknock lscan length2 ipv4options ipset ipp2p iface geoip fuzzy condition tee tarpit sysrq steal rawnat logmark ipmark dhcpmac delude chaos account" Unset: CC, CPPFLAGS, CTARGET, CXX, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LANG, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS
Created attachment 518712 [details] numpy-1.9.2-no-hardcode-blas.patch.out
$ cat numpy/distutils/system_info.py.rej --- numpy/distutils/system_info.py +++ numpy/distutils/system_info.py @@ -303,26 +303,7 @@ def get_info(name, notfound_action=0): 1 - display warning message 2 - raise error """ - cl = {'atlas': atlas_info, # use lapack_opt or blas_opt instead - 'atlas_threads': atlas_threads_info, # ditto - 'atlas_blas': atlas_blas_info, - 'atlas_blas_threads': atlas_blas_threads_info, - 'lapack_atlas': lapack_atlas_info, # use lapack_opt instead - 'lapack_atlas_threads': lapack_atlas_threads_info, # ditto - 'atlas_3_10': atlas_3_10_info, # use lapack_opt or blas_opt instead - 'atlas_3_10_threads': atlas_3_10_threads_info, # ditto - 'atlas_3_10_blas': atlas_3_10_blas_info, - 'atlas_3_10_blas_threads': atlas_3_10_blas_threads_info, - 'lapack_atlas_3_10': lapack_atlas_3_10_info, # use lapack_opt instead - 'lapack_atlas_3_10_threads': lapack_atlas_3_10_threads_info, # ditto - 'mkl': mkl_info, - # openblas which may or may not have embedded lapack - 'openblas': openblas_info, # use blas_opt instead - # openblas with embedded lapack - 'openblas_lapack': openblas_lapack_info, # use blas_opt instead - 'lapack_mkl': lapack_mkl_info, # use lapack_opt instead - 'blas_mkl': blas_mkl_info, # use blas_opt instead - 'x11': x11_info, + cl = {'x11': x11_info, 'fft_opt': fft_opt_info, 'fftw': fftw_info, 'fftw2': fftw2_info, $
This ebuild has more problems: >>> Compiling source in /var/tmp/portage/dev-python/numpy-9999/work/numpy-9999 ... * python2_7: running distutils-r1_run_phase python_compile python2.7 setup.py build -j 1 Traceback (most recent call last): File "setup.py", line 31, in <module> raise RuntimeError("Python version >= 3.5 required.") python3.6 setup.py build -j 1 Processing numpy/random/mtrand/randint_helpers.pxi.in Processing numpy/random/mtrand/mtrand.pyx Traceback (most recent call last): File "/var/tmp/portage/dev-python/numpy-9999/work/numpy-9999-python3_6/tools/cythonize.py", line 61, in process_pyx from Cython.Compiler.Version import version as cython_version ModuleNotFoundError: No module named 'Cython' During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/var/tmp/portage/dev-python/numpy-9999/work/numpy-9999-python3_6/tools/cythonize.py", line 67, in process_pyx ['cython'] + flags + ["-o", tofile, fromfile]) File "/usr/lib/python3.6/subprocess.py", line 286, in check_call retcode = call(*popenargs, **kwargs) File "/usr/lib/python3.6/subprocess.py", line 267, in call with Popen(*popenargs, **kwargs) as p: File "/usr/lib/python3.6/subprocess.py", line 709, in __init__ restore_signals, start_new_session) File "/usr/lib/python3.6/subprocess.py", line 1344, in _execute_child raise child_exception_type(errno_num, err_msg, err_filename) FileNotFoundError: [Errno 2] No such file or directory: 'cython': 'cython' During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/var/tmp/portage/dev-python/numpy-9999/work/numpy-9999-python3_6/tools/cythonize.py", line 224, in <module> main() File "/var/tmp/portage/dev-python/numpy-9999/work/numpy-9999-python3_6/tools/cythonize.py", line 220, in main find_process_files(root_dir) File "/var/tmp/portage/dev-python/numpy-9999/work/numpy-9999-python3_6/tools/cythonize.py", line 212, in find_process_files process(cur_dir, fromfile, tofile, function, hash_db) File "/var/tmp/portage/dev-python/numpy-9999/work/numpy-9999-python3_6/tools/cythonize.py", line 171, in process processor_function(fromfile, tofile) File "/var/tmp/portage/dev-python/numpy-9999/work/numpy-9999-python3_6/tools/cythonize.py", line 69, in process_pyx raise OSError('Cython needs to be installed') OSError: Cython needs to be installed Running from numpy source directory. Cythonizing sources Traceback (most recent call last): File "setup.py", line 409, in <module> setup_package() File "setup.py", line 392, in setup_package generate_cython() File "setup.py", line 205, in generate_cython raise RuntimeError("Running cythonize failed!") RuntimeError: Running cythonize failed!
The bug has been referenced in the following commit(s): https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=4a58f0a1115c689cbde65388efc97cbe74cb147b commit 4a58f0a1115c689cbde65388efc97cbe74cb147b Author: Rolf Eike Beer <eike@sf-mail.de> AuthorDate: 2019-01-01 13:44:56 +0000 Commit: Sergei Trofimovich <slyfox@gentoo.org> CommitDate: 2019-01-02 10:30:25 +0000 dev-python/numpy-9999: fix python requirement Bug: https://bugs.gentoo.org/647072 Signed-off-by: Rolf Eike Beer <eike@sf-mail.de> Package-Manager: Portage-2.3.51, Repoman-2.3.11 Signed-off-by: Sergei Trofimovich <slyfox@gentoo.org> dev-python/numpy/numpy-9999.ebuild | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-)
The bug has been closed via the following commit(s): https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=f5c71a4aa9615c8c14caa8e7076519ab2a4b9824 commit f5c71a4aa9615c8c14caa8e7076519ab2a4b9824 Author: Benda Xu <heroxbd@gentoo.org> AuthorDate: 2019-06-23 12:46:21 +0000 Commit: Benda Xu <heroxbd@gentoo.org> CommitDate: 2019-06-23 12:47:37 +0000 dev-python/numpy: fix cblas detection. Drop old ebuilds versionator eclass. Drop live ebuild. It has not been taken care of since numpy-1.9. Suggested-By: Zongyu Zhang <zzy2529420793@gmail.com> Closes: https://bugs.gentoo.org/647072 Closes: https://bugs.gentoo.org/688392 Package-Manager: Portage-2.3.52, Repoman-2.3.12 Signed-off-by: Benda Xu <heroxbd@gentoo.org> dev-python/numpy/Manifest | 16 -- .../files/numpy-1.10.2-no-hardcode-blas.patch | 64 -------- .../files/numpy-1.12.1-no-hardcode-blas.patch | 72 --------- .../numpy/files/numpy-1.8.0-no-hardcode-blas.patch | 25 --- .../numpy/files/numpy-1.9.2-no-hardcode-blas.patch | 35 ----- dev-python/numpy/numpy-1.10.4.ebuild | 154 ------------------- dev-python/numpy/numpy-1.13.3.ebuild | 167 --------------------- dev-python/numpy/numpy-1.14.5.ebuild | 3 +- dev-python/numpy/numpy-1.15.4.ebuild | 3 +- dev-python/numpy/numpy-1.16.1.ebuild | 3 +- dev-python/numpy/numpy-1.8.2.ebuild | 145 ------------------ dev-python/numpy/numpy-1.9.2.ebuild | 146 ------------------ dev-python/numpy/numpy-9999.ebuild | 134 ----------------- 13 files changed, 6 insertions(+), 961 deletions(-)
