eix scipy [U] dev-python/scipy Available versions: 1.8.1(stable) ~1.9.1 1.9.2(stable) ~1.9.3 Installed versions: 1.8.1 (00:50:11 27/09/2022)(-doc -pythran -sparse -test PYTHON_TARGETS="python3_9 -python3_8 -python3_10") Reproducible: Always Steps to Reproduce: USE="python_targets_python3_9 -pythran" emerge -1 =dev-python/scipy-1.9.2 Actual Results: Build type: native build Project name: SciPy Project version: 1.9.2 C compiler for the host machine: x86_64-pc-linux-gnu-gcc (gcc 12.2.1 "x86_64-pc-linux-gnu-gcc (Gentoo 12.2.1_p20221008 p1) 12.2.1 20221008") C linker for the host machine: x86_64-pc-linux-gnu-gcc ld.bfd 2.38 C++ compiler for the host machine: x86_64-pc-linux-gnu-g++ (gcc 12.2.1 "x86_64-pc-linux-gnu-g++ (Gentoo 12.2.1_p20221008 p1) 12.2.1 20221008") C++ linker for the host machine: x86_64-pc-linux-gnu-g++ ld.bfd 2.38 Host machine cpu family: x86_64 Host machine cpu: x86_64 Compiler for C supports arguments -Wno-unused-but-set-variable: YES Compiler for C supports arguments -Wno-unused-but-set-variable: YES (cached) Compiler for C supports arguments -Wno-unused-function: YES Compiler for C supports arguments -Wno-conversion: YES Compiler for C supports arguments -Wno-misleading-indentation: YES Compiler for C supports arguments -Wno-incompatible-pointer-types: YES Library m found: YES Fortran compiler for the host machine: x86_64-pc-linux-gnu-gfortran (gcc 12.2.1 "GNU Fortran (Gentoo 12.2.1_p20221008 p1) 12.2.1 20221008") Fortran linker for the host machine: x86_64-pc-linux-gnu-gfortran ld.bfd 2.38 Compiler for Fortran supports arguments -Wno-conversion: YES Program cython found: YES (/usr/bin/cython) Program pythran found: NO ../../meson.build:64:0: ERROR: Program 'pythran' not found or not executable A full log can be found at /var/tmp/portage/dev-python/scipy-1.9.2/work/scipy-1.9.2/.mesonpy-lwnawibq/build/meson-logs/meson-log.txt Traceback (most recent call last): pythran : Use dev-python/pythran to accelerate runtime USE="python_targets_python3_9 pythran" emerge -1 =dev-python/scipy-1.9.2 is queued here. I expect it to build and will likely remain configured.
Please attach the full build.log and emerge --info.
(And attach the referenced meson-log.txt)
Created attachment 825489 [details] build log
Portage 3.0.38.1 (python 3.9.15-final-0, default/linux/amd64/17.1/desktop/gnome, gcc-12, glibc-2.35-r8, 6.0.3-gentoo-classic x86_64) ================================================================= System Settings ================================================================= System uname: Linux-6.0.3-gentoo-classic-x86_64-Intel-R-_Core-TM-_i3-6100_CPU_@_3.70GHz-with-glibc2.35 KiB Mem: 3935620 total, 624592 free KiB Swap: 65535996 total, 62903376 free Timestamp of repository FireBurn: Mon, 24 Oct 2022 15:04:31 +0000 Head commit of repository FireBurn: c7c541dad912c67b07605fec84da46e44a21037c Timestamp of repository ace: Fri, 21 Oct 2022 23:01:55 +0000 Head commit of repository ace: 38be4878ddada51df2fb09cec13c72aef8d9c484 Timestamp of repository argent-main: Sat, 03 Sep 2022 14:17:00 +0000 Head commit of repository argent-main: f65ef9f6336782ae1048e2a0a6190899ffa36da9 Timestamp of repository audio-overlay: Thu, 20 Oct 2022 06:32:22 +0000 Head commit of repository audio-overlay: 37b53f73598b6e7c4ed724ae2a5aadd43826f1d2 Timestamp of repository booboo: Thu, 20 Oct 2022 06:32:07 +0000 Head commit of repository booboo: 1f261dc1e52311a0d28eaac1558157d9f013b184 Timestamp of repository eclipse: Thu, 20 Oct 2022 06:32:20 +0000 Head commit of repository eclipse: 9af00d52ee8f0a9c7521a12ac5247f9f488e2329 Timestamp of repository fol4: Thu, 20 Oct 2022 06:32:25 +0000 Head commit of repository fol4: daace42159705da4170d6c35f38b549b9385fdc5 Timestamp of repository go-overlay: Wed, 11 Nov 2020 05:35:23 +0000 Head commit of repository go-overlay: 6c5883fb73ef12b56309dcaf00a46b65f7c091a3 Timestamp of repository guru: Fri, 21 Oct 2022 23:01:56 +0000 Head commit of repository guru: afbe8ecaf776b282dc3a64f0bcf4eb7660476cc4 Timestamp of repository haskell: Thu, 20 Oct 2022 06:32:10 +0000 Head commit of repository haskell: d6b0cb3599ec938fabb0bb76e39484aebad4025a Timestamp of repository linuxunderground-overlay: Thu, 20 Oct 2022 06:32:23 +0000 Head commit of repository linuxunderground-overlay: c3d8d1be8f0d962ffbc3fa3c46cf2173433446ed Timestamp of repository luke-jr: Thu, 20 Oct 2022 06:32:11 +0000 Head commit of repository luke-jr: 2d2f544f30903cf3d6fb30b28e0becac11537df5 Timestamp of repository mv: Thu, 20 Oct 2022 06:32:12 +0000 Head commit of repository mv: ab19d6f0e57761a12a4ba1c17ae736e70f159225 Timestamp of repository nymphos: Fri, 21 Oct 2022 23:01:58 +0000 Head commit of repository nymphos: 3166c78bfda38b38a6465cc5631b7071d189d337 Timestamp of repository palemoon: Thu, 20 Oct 2022 06:32:12 +0000 Head commit of repository palemoon: 2cf616377bc5ecf8d8b7063b00ccba3f94771a44 Timestamp of repository pentoo: Tue, 25 Oct 2022 04:01:55 +0000 Head commit of repository pentoo: b5ca641cc52e3475b8fab523766e205f9be88dcd Timestamp of repository qt: Thu, 20 Oct 2022 06:32:12 +0000 Head commit of repository qt: e93a66b15f7fffffaa53141431d37a9e74ef3a86 Timestamp of repository ricerlay: Wed, 19 Oct 2022 03:16:52 +0000 Head commit of repository ricerlay: f6052bd12fe1507fd1dfd29b9fb64dc2bab9ceab Timestamp of repository robert7k: Fri, 21 Oct 2022 23:01:53 +0000 Head commit of repository robert7k: 6ff215facc38b692a7dad589365c199aa5109487 Timestamp of repository rukruk: Thu, 20 Oct 2022 06:32:18 +0000 Head commit of repository rukruk: de5cf1c57b512fb0be0146b42a1eaa3c7ec0451b Timestamp of repository sage-on-gentoo: Mon, 24 Oct 2022 23:16:46 +0000 Head commit of repository sage-on-gentoo: 458b800d50c37f6421a8f47b6ad9d9b6f766020b Timestamp of repository science: Fri, 21 Oct 2022 10:46:45 +0000 Head commit of repository science: 8bdb59ef21614a64071a7b5ae18d966fcc8e0223 Timestamp of repository seden: Tue, 25 Oct 2022 05:46:43 +0000 Head commit of repository seden: 7f1be8999eac134181f8359c9b6985779f90d4f1 Timestamp of repository src_prepare-overlay: Sun, 23 Oct 2022 00:01:56 +0000 Head commit of repository src_prepare-overlay: 7f1cd2d5124f2e24932b51b7c4dc8608fbdf0428 Timestamp of repository ssnb: Thu, 20 Oct 2022 06:32:18 +0000 Head commit of repository ssnb: ca75f2cb8b63a89fe2d7c5fdbf79f61eab98bf78 Timestamp of repository third-party-certbot-plugins: Mon, 17 Oct 2022 19:03:39 +0000 Head commit of repository third-party-certbot-plugins: 10e69a30f69c6ff1650ea0294cbbda9485e65f42 Timestamp of repository torbrowser: Fri, 21 Oct 2022 23:01:53 +0000 Head commit of repository torbrowser: 5b5499df9ec3364c0a0e33a66f5077dc07cfbd3f Timestamp of repository waebbl: Thu, 20 Oct 2022 06:32:23 +0000 Head commit of repository waebbl: 295f6af36044574621fd2e6a0f90994d5ee26315 Timestamp of repository wayland-desktop: Fri, 21 Oct 2022 13:16:46 +0000 Head commit of repository wayland-desktop: 56f3b260c69b31516b7f46ef3720d6e23c04ead4 Timestamp of repository zGentoo: Fri, 21 Oct 2022 23:01:58 +0000 Head commit of repository zGentoo: 02d420b57a88ab63555f5fc4165f8f229c5988ac Timestamp of repository gentoo: Tue, 25 Oct 2022 16:15:01 +0000 Head commit of repository gentoo: ac6bd67e437c096edbb3a656ae9566e9658bdcf0 sh bash 5.0_p18 ld GNU ld (Gentoo 2.38 p4) 2.38 distcc 3.4 x86_64-pc-linux-gnu [disabled] app-misc/pax-utils: 1.3.5::gentoo app-shells/bash: 5.0_p18::gentoo dev-java/java-config: 2.3.1::gentoo dev-lang/perl: 5.34.1-r3::gentoo dev-lang/python: 2.7.18_p15-r1::gentoo, 3.9.15::gentoo, 3.10.8::gentoo, 3.11.0::gentoo dev-lang/rust: 1.64.0-r1::gentoo dev-util/cmake: 3.24.2::gentoo dev-util/meson: 0.63.2-r1::gentoo sys-apps/baselayout: 2.8::gentoo sys-apps/openrc: 0.45.2-r1::gentoo sys-apps/sandbox: 2.29::gentoo sys-devel/autoconf: 2.13-r2::gentoo, 2.71-r1::gentoo sys-devel/automake: 1.16.5::gentoo sys-devel/binutils: 2.38-r2::gentoo sys-devel/binutils-config: 5.4.1::gentoo sys-devel/clang: 14.0.6-r1::gentoo, 15.0.3::gentoo sys-devel/gcc: 10.4.0::gentoo, 11.3.0::gentoo, 12.2.1_p20221008::gentoo sys-devel/gcc-config: 2.6::gentoo sys-devel/libtool: 2.4.7::gentoo sys-devel/lld: 14.0.6-r1::gentoo sys-devel/llvm: 14.0.6-r2::gentoo, 15.0.3::gentoo sys-devel/make: 4.3::gentoo sys-kernel/linux-headers: 5.19::gentoo (virtual/os-headers) sys-libs/glibc: 2.35-r8::gentoo Repositories: gentoo location: /var/db/repos/gentoo sync-type: rsync sync-uri: rsync://rsync.europe.gentoo.org/gentoo-portage priority: -1000 sync-rsync-verify-jobs: 1 sync-rsync-verify-max-age: 24 sync-rsync-verify-metamanifest: no sync-rsync-extra-opts: gnu-elpa location: /var/lib/layman/gnu-elpa sync-type: laymansync sync-uri: gs-elpa gnu-elpa masters: gentoo priority: 50 melpa location: /var/lib/layman/melpa sync-type: laymansync sync-uri: gs-elpa melpa masters: gnu-elpa gentoo priority: 50 local-repo location: /var/db/repos/local-repo masters: gentoo priority: 10000 ACCEPT_KEYWORDS="amd64" ACCEPT_LICENSE="* -@EULA" AR="gcc-ar" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-march=native -O2 -pipe -Wa,-mbranches-within-32B-boundaries " CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/share/config /usr/share/gnupg/qualified.txt /usr/share/maven-bin-3.8/conf" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/dconf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/php/apache2-php8.1/ext-active/ /etc/php/cgi-php8.1/ext-active/ /etc/php/cli-php8.1/ext-active/ /etc/php/fpm-php8.1/ext-active/ /etc/php/phpdbg-php8.1/ext-active/ /etc/revdep-rebuild /etc/sandbox.d /etc/splash /etc/terminfo /etc/texmf/language.dat.d /etc/texmf/language.def.d /etc/texmf/updmap.d /etc/texmf/web2c" CXXFLAGS="-march=native -O2 -pipe -Wa,-mbranches-within-32B-boundaries " DISTDIR="/var/cache/distfiles" EMERGE_DEFAULT_OPTS="--alert y --alphabetical --ask-enter-invalid --autounmask y --autounmask-only n --autounmask-unrestricted-atoms y --autounmask-write y --misspell-suggestions n --noconfmem --nospinner --tree --with-bdeps y" 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 XDG_STATE_HOME" FCFLAGS="-march=native -O2 -pipe -Wa,-mbranches-within-32B-boundaries " FEATURES="assume-digests binpkg-docompress binpkg-dostrip binpkg-logs buildpkg-live compress-build-logs 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 split-elog strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync" FFLAGS="-march=native -O2 -pipe -Wa,-mbranches-within-32B-boundaries " GENTOO_MIRRORS="http://ftp-stud.hs-esslingen.de/pub/Mirrors/gentoo/ http://ftp.halifax.rwth-aachen.de/gentoo/ http://gentoo.mirrors.ovh.net/gentoo-distfiles/ http://ftp.leg.uct.ac.za/pub/linux/gentoo/ http://ftp.free.fr/mirrors/ftp.gentoo.org/ http://mirrors.soeasyto.com/distfiles.gentoo.org/ http://mirror.eu.oneandone.net/linux/distributions/gentoo/gentoo/ http://ftp.fau.de/gentoo http://ftp.gwdg.de/pub/linux/gentoo/ http://ftp.belnet.be/pub/rsync.gentoo.org/gentoo/" LANG="fr_FR.utf8" LDFLAGS="-Wl,-O1 -Wl,-fuse-ld=bfd " LINGUAS="fr" MAKEOPTS="-j3 -l3" NM="gcc-nm" PKGDIR="/var/cache/binpkgs" PORTAGE_COMPRESS="lzma" PORTAGE_COMPRESS_FLAGS="-9" 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" RANLIB="gcc-ranlib" SHELL="/bin/bash" USE="amd64 asm emacs gtk-doc libglvnd minimal split-usr test-rust verify-sig" ABI_X86="64" ALSA_CARDS="hda-intel" CPU_FLAGS_X86="aes avx avx2 f16c fma3 mmx mmxext pclmul popcnt rdrand sse sse2 sse3 sse4_1 sse4_2 ssse3" ELIBC="glibc" GRUB_PLATFORMS="efi-64" INPUT_DEVICES="libinput" KERNEL="linux" L10N="fr" LUA_SINGLE_TARGET="lua5-4" LUA_TARGETS="lua5-4" PHP_TARGETS="php8-1" PYTHON_SINGLE_TARGET="python3_9" PYTHON_TARGETS="python3_9" QEMU_USER_TARGETS="aarch64" RUBY_TARGETS="ruby27" USERLAND="GNU" VIDEO_CARDS="intel" Unset: ADDR2LINE, ARFLAGS, AS, ASFLAGS, CC, CCLD, CONFIG_SHELL, CPP, CPPFLAGS, CTARGET, CXX, CXXFILT, ELFEDIT, EXTRA_ECONF, F77FLAGS, FC, GCOV, GPROF, INSTALL_MASK, LC_ALL, LD, LEX, LFLAGS, LIBTOOL, MAKE, MAKEFLAGS, OBJCOPY, OBJDUMP, PORTAGE_BINHOST, PORTAGE_BUNZIP2_COMMAND, PORTAGE_RSYNC_EXTRA_OPTS, READELF, RUSTFLAGS, SIZE, STRINGS, STRIP, YACC, YFLAGS ================================================================= Package Settings ================================================================= dev-python/scipy-1.8.1::gentoo was built with the following: USE="-doc -pythran -sparse -test" ABI_X86="(64)" PYTHON_TARGETS="-python3_10 -python3_8 python3_9" CFLAGS="-march=native -O2 -flto -fuse-linker-plugin -fno-fat-lto-objects -pipe -Wa,-mbranches-within-32B-boundaries" CXXFLAGS="-march=native -O2 -flto -fuse-linker-plugin -fno-fat-lto-objects -pipe -Wa,-mbranches-within-32B-boundaries" FEATURES="binpkg-dostrip binpkg-logs compress-build-logs unmerge-orphans config-protect-if-modified multilib-strict binpkg-docompress userfetch sandbox distlocks unknown-features-warn sfperms buildpkg-live parallel-fetch qa-unresolved-soname-deps merge-sync unmerge-logs split-elog userpriv assume-digests ipc-sandbox news network-sandbox usersync fixlafiles strict usersandbox ebuild-locks preserve-libs protect-owned pid-sandbox" LDFLAGS="-Wl,-O1 -Wl,-fuse-ld=bfd -shared"
(In reply to Sam James from comment #2) > (And attach the referenced meson-log.txt) amd64 ~ # ll /var/tmp/portage/dev-python/scipy-1.9.2/work/scipy-1.9.2/.mesonpy-lwnawibq/build/meson-logs/meson-log.txt ls: cannot access '/var/tmp/portage/dev-python/scipy-1.9.2/work/scipy-1.9.2/.mesonpy-lwnawibq/build/meson-logs/meson-log.txt' amd64 ~ # find /var/tmp/portage/dev-python/scipy-1.9.2 -name meson-log.txt Sorry.
(In reply to Sam James from comment #1) > Please attach the full build.log and emerge --info. Providing build is fine here. I don't see any way to post any attachment along with the first bug post. Was RESOLVED switching less than a minute after initial post really necessary?
There is a kind of hidden Expert Mode in the bugzilla menu look in the title line for "Home | New–[Ex]" Ex enables to do more in the initial ticket. Besides that its all fine. Do not take it personal, we close tickets as RESOLVED/NEEDINFO. Just forgot to leave a comment for explanation.
(In reply to Jonas Stein from comment #7) > There is a kind of hidden Expert Mode in the bugzilla menu look in the title > line for "Home | New–[Ex]" Ex enables to do more in the initial ticket. Interesting, Never tried [Ex] as it didn't make any sense to me, i.e. no obvious meaning. > Besides that its all fine. Do not take it personal, we close tickets as > RESOLVED/NEEDINFO. Just forgot to leave a comment for explanation. Sounds more like an under pressure behaviour indeed. Happens to often here too.
Interestingly, USE="python_targets_python3_9 -pythran" emerge -1 =dev-python/scipy-1.9.2 doesn't fail when dev-python/pythran is already intalled.
The bug has been referenced in the following commit(s): https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=8852406a7b12e2ad7024b0db7e16ea53d0f5f73c commit 8852406a7b12e2ad7024b0db7e16ea53d0f5f73c Author: Sam James <sam@gentoo.org> AuthorDate: 2022-10-27 01:18:12 +0000 Commit: Sam James <sam@gentoo.org> CommitDate: 2022-10-27 01:18:12 +0000 dev-python/scipy: switch to python_configure_all I don't think this is sufficient though. Bug: https://bugs.gentoo.org/878361 Signed-off-by: Sam James <sam@gentoo.org> dev-python/scipy/scipy-1.9.3.ebuild | 2 +- dev-python/scipy/scipy-1.9.9999.ebuild | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-)
Created attachment 825549 [details] post-patch ebuild log Failing here still.
Created attachment 825551 [details] post patch ebuild 1.9.3 log Didn't notice patch is on 1.9.3... whereas bug report is on 1.9.2 Fails here still.
The bug has been referenced in the following commit(s): https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=c6e1c019205cf536a6522e9d99acbaa05873d8a7 commit c6e1c019205cf536a6522e9d99acbaa05873d8a7 Author: Sam James <sam@gentoo.org> AuthorDate: 2022-11-04 00:22:56 +0000 Commit: Sam James <sam@gentoo.org> CommitDate: 2022-11-04 00:23:25 +0000 dev-python/scipy: fix pkg_setup optionality for fortran, rename USE=pythran This still doesn't fix USE=-fortran builds, but reported that upstream now. Bug: https://bugs.gentoo.org/878361 Signed-off-by: Sam James <sam@gentoo.org> dev-python/scipy/scipy-1.9.3.ebuild | 7 ++++--- dev-python/scipy/scipy-1.9.9999.ebuild | 7 ++++--- 2 files changed, 8 insertions(+), 6 deletions(-)
(In reply to CaptainBlood from comment #12) > Created attachment 825551 [details] > post patch ebuild 1.9.3 log > > Didn't notice patch is on 1.9.3... whereas bug report is on 1.9.2 > Fails here still. I did mention that in the commit message that it's not enough :) Anyway, I've reported upstream at https://github.com/scipy/scipy/issues/17336.
*** Bug 890487 has been marked as a duplicate of this bug. ***
Fixed in 1.10.x.
*** Bug 890827 has been marked as a duplicate of this bug. ***
*** Bug 892361 has been marked as a duplicate of this bug. ***
*** Bug 892483 has been marked as a duplicate of this bug. ***
