The current "sci-mathematics/petsc-3.13.0" package needs "suitesparse" at least 5.6.0 to compile when sparse use flag is enabled. I temporarily disabled the "sparse" use flag to keep going. The error message is: ======================================================== TESTING: checkVersion from config.packages.SuiteSparse(/var/tmp/portage/sci-mathematics/petsc-3.13.0/work/petsc-3.13.0/config/BuildSystem/config/package.py:992) ******************************************************************************* UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for details): ------------------------------------------------------------------------------- suitesparse version is 5.4.0 this version of PETSc needs at least 5.6.0 Suggest using --download-suitesparse for a compatible SuiteSparse ******************************************************************************* * ERROR: sci-mathematics/petsc-3.13.0::gentoo failed (configure phase): * econf failed * * Call stack: * ebuild.sh, line 125: Called src_configure * environment, line 2764: Called econf 'scrollOutput=1' 'FFLAGS=-O2 -pipe -fPIC' 'CFLAGS=-march=native -O2 -pipe -fPIC' 'CXXFLAGS=-march=native -O2 -pipe -fPIC' 'LDFLAGS=-Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0' '--prefix=/usr/lib64/petsc' '--with-shared-libraries' '--with-single-library' '--with-clanguage=c' '--with-petsc-arch=linux-gnu-c-opt' '--with-precision=double' '--with-gnu-compilers' '--with-blas-lapack-lib=-lblas -llapack' '--with-debugging=0' '--with-mpi=1' '--with-cc=mpicc' '--with-cxx=mpicxx' '--with-fortran=1' '--with-fc=mpif77' '--with-mpi-compilers=1' '--with-scalar-type=complex' '--with-windows-graphics=0' '--with-matlab=0' '--with-cmake:BOOL=1' '--with-pthread=0' '--with-afterimage=0' '--without-hdf5' '--with-hypre=0' '--with-suitesparse' '--with-superlu=0' '--with-x' '--with-x11' '--with-ptscotch=0' '--with-scalapack=0' '--without-mumps' '--with-imagemagick=0' '--with-python=0' '--with-boost' '--with-fftw' * phase-helpers.sh, line 681: Called __helpers_die 'econf failed' * isolated-functions.sh, line 112: Called die * The specific snippet of code: * die "$@" * * If you need support, post the output of `emerge --info '=sci-mathematics/petsc-3.13.0::gentoo'`, * the complete build log and the output of `emerge -pqv '=sci-mathematics/petsc-3.13.0::gentoo'`. * The complete build log is located at '/var/tmp/portage/sci-mathematics/petsc-3.13.0/temp/build.log'. * The ebuild environment file is located at '/var/tmp/portage/sci-mathematics/petsc-3.13.0/temp/environment'. * Working directory: '/var/tmp/portage/sci-mathematics/petsc-3.13.0/work/petsc-3.13.0' * S: '/var/tmp/portage/sci-mathematics/petsc-3.13.0/work/petsc-3.13.0' ===================================================== There's no ">=sci-libs/suitesparse-5.6.0" in the portage right now, but I still think it's a good idea to specify the version requirement in the RDEPEND entry in the ebuild file. Meanwhile, we can use "--download-suitesparse" as suggested in "src_configure" function.
Thank you for the report. We need to have all information at hand before ticket assignment. That is why I ask you to * attach the logs and * paste the emerge info as described on https://wiki.gentoo.org/wiki/Attach_the_logs_to_the_bug_ticket Please reopen this ticket (Status:UNCONFIRMED) afterwards.
Created attachment 637818 [details] build log
awesome /etc/portage # emerge --info Portage 2.3.99 (python 3.6.10-final-0, default/linux/amd64/17.1, gcc-8.3.0, glibc-2.31-r2, 5.4.7-gentoo x86_64) ================================================================= System uname: Linux-5.4.7-gentoo-x86_64-Intel-R-_Core-TM-_i7-9700_CPU_@_3.00GHz-with-gentoo-2.7 KiB Mem: 32696748 total, 717384 free KiB Swap: 0 total, 0 free Timestamp of repository gentoo: Sun, 10 May 2020 23:09:04 +0000 Head commit of repository gentoo: 9ca0ff6a2e63e627f01d91b37f456a8e5a60f33e Timestamp of repository gamerlay: Fri, 01 May 2020 10:40:18 +0000 Head commit of repository gamerlay: e56525c8338b674548e55e0afea3391a921fe593 Timestamp of repository haskell: Thu, 07 May 2020 21:35:19 +0000 Head commit of repository haskell: 496566ce98f84edf122c9d591f568449fb61b92d Timestamp of repository jorgicio: Sun, 10 May 2020 20:35:26 +0000 Head commit of repository jorgicio: 7b09ffbac7d88872a2319ba97b3b4fbbcd0f0262 Timestamp of repository libressl: Sun, 10 May 2020 20:35:26 +0000 Head commit of repository libressl: 5a346117de3318f3c53b34884e2902f1bfb7eeeb Timestamp of repository palemoon: Fri, 08 May 2020 16:05:13 +0000 Head commit of repository palemoon: 740618405656e2491d18cd72fcf266453cc861f6 Timestamp of repository python: Thu, 30 Apr 2020 06:12:57 +0000 Head commit of repository python: 1751a47d1c83592a1efac39860ce9efc7aae01a1 Timestamp of repository raiagent: Sun, 10 May 2020 17:05:31 +0000 Head commit of repository raiagent: cf558f721862ba73935273c4f274cea4bc61a96f Timestamp of repository science: Sun, 10 May 2020 17:05:52 +0000 Head commit of repository science: a07727463df84bffd5cc9fc4366a9b9244d3a677 sh bash 5.0_p17 ld GNU ld (Gentoo 2.33.1 p2) 2.33.1 app-shells/bash: 5.0_p17::gentoo dev-lang/perl: 5.30.1::gentoo dev-lang/python: 2.7.18::gentoo, 3.6.10-r2::gentoo, 3.7.7-r2::gentoo, 3.8.2-r2::gentoo dev-util/cmake: 3.17.1::gentoo sys-apps/baselayout: 2.7::gentoo sys-apps/openrc: 0.42.1::gentoo sys-apps/sandbox: 2.18::gentoo sys-devel/autoconf: 2.13-r1::gentoo, 2.69-r5::gentoo sys-devel/automake: 1.16.2::gentoo sys-devel/binutils: 2.33.1-r1::gentoo, 2.34::gentoo sys-devel/gcc: 8.3.0-r3::gentoo, 9.2.0-r2::gentoo sys-devel/gcc-config: 2.2.1::gentoo sys-devel/libtool: 2.4.6-r6::gentoo sys-devel/make: 4.3::gentoo sys-kernel/linux-headers: 5.6::gentoo (virtual/os-headers) sys-libs/glibc: 2.31-r2::gentoo Repositories: gentoo location: /var/db/repos/gentoo sync-type: git sync-uri: https://github.com/gentoo-mirror/gentoo.git priority: -1000 daq location: /var/db/repos/daq masters: gentoo gamerlay location: /var/db/repos/gamerlay sync-type: git sync-uri: https://github.com/gentoo-mirror/gamerlay.git masters: gentoo haskell location: /var/db/repos/haskell sync-type: git sync-uri: https://github.com/gentoo-mirror/haskell.git masters: gentoo jorgicio location: /var/db/repos/jorgicio sync-type: git sync-uri: https://github.com/gentoo-mirror/jorgicio.git masters: gentoo libressl location: /var/db/repos/libressl sync-type: git sync-uri: https://github.com/gentoo-mirror/libressl.git masters: gentoo palemoon location: /var/db/repos/palemoon sync-type: git sync-uri: https://github.com/gentoo-mirror/palemoon.git masters: gentoo python location: /var/db/repos/python sync-type: git sync-uri: https://github.com/gentoo-mirror/python.git masters: gentoo raiagent location: /var/db/repos/raiagent sync-type: git sync-uri: https://github.com/gentoo-mirror/raiagent.git masters: gentoo science location: /var/db/repos/science sync-type: git sync-uri: https://github.com/gentoo-mirror/science.git masters: gentoo Installed sets: @fonts, @sci-comp, @tools ACCEPT_KEYWORDS="amd64 ~amd64" ACCEPT_LICENSE="* -@EULA freedist qlogic-fibre-channel-firmware Amazon sun-jlfgr MaxMind2 vlgothic man-pages man-pages-posix-2013 BitstreamVera man-pages-posix CC-BY-SA-1.0 BAEKMUK LDP-1 LDP-1a Texinfo-manual mplus-fonts quake1-textures UbuntuFontLicense-1.0 CC-PD CC-SA-1.0 myspell-en_CA-KevinAtkinson wxWinFDL-3 FreeArt GPL-1+ CC-BY-SA-3.0 Arphic OPL FDL-1.3+ FDL-1.2+ FDL-1.1 CC-BY-2.0 OFL-1.1 FDL-1.1+ CC-BY-SA-4.0 GPL-3+ CC-BY-4.0 CC-BY-3.0 IPAfont GPL-2+ GPL-2 GPL-3 CC-BY-2.5 OFL GPL-1 CC-BY-SA-2.5 FDL-1.2 FDL-1.3 CC-BY-SA-2.0 matplotlib ZSH CeCILL-B LPPL-1.3b FVWM IDPL Toyoda docbook HTML-Tidy libpng otter freetts Old-MIT ErlPL-1.1 imagemagick File-MMagic mpich2 Khronos-CLHPP pngnq xvt libtiff tablelist BSD-with-attribution Mail-Sendmail pngcrush CPL-0.5 xtrs xbatt LambdaMOO DES gsm CAOSL Time-Format xboing CMake torque-2.5 alternate CDDL-1.1 x2x VTK Emacs Time-modules tm-align Flashpix JNIC Mini-XML BZIP2 wm2 tcp_wrappers_license ipadic BSD-with-disclosure rc SMAIL shrimp CRACKLIB Crypt-IDEA eGenixPublic-1.1 Subversion ipx-utils PHP-2.02 canfep JDOM TeX MIT-with-advertising totd perforce tcltk photopc Sendmail-Open-Source SSLeay SVFL feh par gd boehm-gc NCSA-HDF LIBGLOSS rwpng symlinks FLTK repoze iASL dom4j tumbolia lsof icu rdisc URT minpack AMPAS JOVE libmng ngrep Xdebug Openwall netcat XC AIFFWriter.m LPPL-1.3 TeX-other-free NEWLIB buddy BEER-WARE LLVM-Grant the-Click-license sdlsasteroids bufexplorer.vim Snd sash regexp-UofT DUMB-0.9.3 CeCILL-C UCAR-Unidata w3m openafs-krb5-a FLEX ElementTree htmlc PCRE inner-net Interbase-1.0 libpng2 flexmock BSD-1 Sendmail CDDL-Schily Ispell Princeton psutils scanlogd mm RSA FastCGI Allegro Info-ZIP bea.ri.jsr173 Watcom-1.0 AFL-3.0 GPL-1+ UoI-NCSA LGPL-3 Apache-2.0 POSTGRESQL W3C CDDL PSF-2 OSL-2.1 ZLIB AGPL-3+ APL-1.0 MIT BSD LGPL-2.1 Artistic-2 APSL-2 CNRI ISC EPL-2.0 EPL-1.0 OFL-1.1 EUPL-1.1 ECL-2.0 LGPL-2.1+ PHP-3 MPL-1.1 AGPL-3 ZPL CPAL-1.0 GPL-3+ HPND Ms-PL LGPL-3+ nethack NOSA PHP-3.01 QPL IPAfont Sleepycat GPL-2+ GPL-2 GPL-3 MPL-2.0 LGPL-2+ CPL-1.0 MPL-1.0 Apache-1.1 Artistic Boost-1.0 IBM LPPL-1.3c wxWinLL-3 BSD-2 gnuplot AFL-3.0 OSL-1.1 CDDL NPL-1.1 OSL-2.1 FraunhoferFDK AFL-2.1 Apache-1.0 APSL-2 BSD-4 CNRI EPL-2.0 OSL-2.0 EPL-1.0 EUPL-1.1 MPL-1.1 CPAL-1.0 openssl Ms-PL Zend-2.0 Transmission-OpenSSL-exception libgcc PSF-2.4 wxWinLL-3.1 GPL-1+ UoI-NCSA LGPL-3 metapackage UPX-exception FTL Apache-2.0 GPL-2-with-font-exception W3C LGPL-2-with-linking-exception PSF-2 PSF-2.2 vim AGPL-3+ MIT public-domain unicode ZLIB BSD GPL-3+-with-cuda-openssl-exception LGPL-2.1 GPL-3+-with-cuda-exception GPL-3-with-font-exception PYTHON Apache-2.0-with-LLVM-exceptions Artistic-2 gcc-runtime-library-exception-3.1 OPENLDAP GPL-3-with-openssl-exception Clear-BSD GPL-2-with-MySQL-FLOSS-exception GPL-2-with-classpath-exception ISC ECL-2.0 LGPL-2.1+ tanuki-community ZPL AGPL-3 GPL-3+ qwt HPND LGPL-3+ libstdc++ CeCILL-2 WTFPL-2 IJG Clarified-Artistic Sleepycat GPL-3+-with-opencl-exception GPL-2+ GPL-2 GPL-3 LGPL-3-with-linking-exception MPL-2.0 GPL-2-with-linking-exception PSF-2.3 Nokia-Qt-LGPL-Exception-1.1 LGPL-2+ Ruby Unlicense LGPL-2 GPL-1 GPL-2-with-exceptions Ruby-BSD Boost-1.0 SGI-B-2.0 CC0-1.0 GPL-3+-with-opencl-openssl-exception BSD-2 GPL-2+-with-openssl-exception LGPL-2.1-with-linking-exception PHP-3.01 QPL QPL-1.0 CPL-1.0 MPL-1.0 Apache-1.1 IBM LPPL-1.2 shmux unRAR Mellanox-AS-IS SmartLabs bh-luxi LSI-tw_cli ISSL intel-ucode ipw2200-fw JSON Broadcom linux-fw-redistributable NVIDIA-r1 AVASYS Atmel no-source-code ipw3945 bonnie ipw2100-fw MicroChip-SDCC" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-march=native -O2 -pipe" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/share/gnupg/qualified.txt" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/dconf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /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="-march=native -O2 -pipe" DISTDIR="/var/cache/distfiles" EMERGE_DEFAULT_OPTS="--verbose-conflicts --quiet" ENV_UNSET="DBUS_SESSION_BUS_ADDRESS DISPLAY GOBIN 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="-march=native -O2 -pipe" FEATURES="assume-digests binpkg-docompress binpkg-dostrip binpkg-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 strict strict-keepdir unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr" FFLAGS="-march=native -O2 -pipe" GENTOO_MIRRORS="http://mirrors.163.com/gentoo/" LANG="en_US.utf8" LDFLAGS="-Wl,-O1 -Wl,--as-needed" MAKEOPTS="-j8" PKGDIR="/var/cache/binpkgs" 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="X acl amd64 berkdb bzip2 cleartype cli corefonts crypt dri elogind fontforge fortran gdbm harfbuzz iconv icu idm infinality ipv6 jpeg libressl libtirpc multilib ncurses nls nptl opengl openmp pam pcre png qt4 qt5 readline savedconfig seccomp split-usr ssl svg tcpd truetype type1 unicode urandom x264 xattr zlib" ABI_X86="64" ADA_TARGET="gnat_2018" 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="karbon sheets words" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" CPU_FLAGS_X86="mmx mmxext sse sse2" CURL_SSL="libressl" ELIBC="glibc" GPSD_PROTOCOLS="ashtech aivdm earthmate evermore fv18 garmin garmintxt gpsclock greis isync itrax mtk3301 nmea ntrip navcom oceanserver oldstyle oncore rtcm104v2 rtcm104v3 sirf skytraq superstar2 timing tsip tripmate tnt ublox ubx" INPUT_DEVICES="libinput" 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="php7-2" POSTGRES_TARGETS="postgres10 postgres11" PYTHON_SINGLE_TARGET="python3_7" PYTHON_TARGETS="python3_6 python3_7 python3_8" RUBY_TARGETS="ruby27 ruby26 ruby25" USERLAND="GNU" VIDEO_CARDS="intel i965" 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, INSTALL_MASK, LC_ALL, LINGUAS, PORTAGE_BINHOST, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS
I can confirm this.
Here too. Also in petsc-3.13.1.ebuild.
I can confirm this for 3.13.1 too. Additionally I'm having sandbox violations for /dev/nvidiactl (see attached build log)
Created attachment 687669 [details] petsc-3.13.1:20210219-195522.log build log with configuration failure and sandbox violations.
Opening a new bug for the sandbox violations, as it's independent from this bug.
USE=sparse had been removed in 3.15.0-r1 and later.
