Created attachment 414766 [details] build.log sci-libs/iml-1.0.4 fails to build: --- checking pkg-config is at least version 0.9.0... yes checking for ATLAS... no configure: error: Package requirements (cblas) were not met: No package 'cblas' found Consider adjusting the PKG_CONFIG_PATH environment variable if you installed software in a non-standard prefix. Alternatively, you may set the environment variables ATLAS_CFLAGS and ATLAS_LIBS to avoid the need to call pkg-config. See the pkg-config man page for more details. --- Apparently there are two eselect modules handling cblas: # eselect ... Alternatives modules: cblas Maintain Alternatives symlinks for cblas Extra modules: alternatives Maintain Alternatives symlinks ... cblas Manage installed CBLAS implementations ... # emerge --info virtual/cblas app-eselect/eselect-cblas sci-libs/iml Portage 2.2.23 (python 3.4.3-final-0, default/linux/amd64/13.0/desktop/plasma/systemd, gcc-4.9.3, glibc-2.21-r1, 4.2.2-gentoo x86_64) ================================================================= System Settings ================================================================= System uname: Linux-4.2.2-gentoo-x86_64-8G-with-gentoo-2.2 KiB Mem: 15381444 total, 8003552 free KiB Swap: 0 total, 0 free Timestamp of repository gentoo: Sat, 17 Oct 2015 08:45:01 +0000 sh bash 4.3_p42 ld GNU ld (Gentoo 2.25.1 p1.1) 2.25.1 ccache version 3.2.4 [disabled] app-shells/bash: 4.3_p42::gentoo dev-java/java-config: 2.2.0::gentoo dev-lang/perl: 5.22.0::gentoo dev-lang/python: 2.7.10::gentoo, 3.3.5-r1::gentoo, 3.4.3::gentoo dev-util/ccache: 3.2.4::gentoo dev-util/cmake: 3.3.2-r1::gentoo dev-util/pkgconfig: 0.29::gentoo sys-apps/baselayout: 2.2::gentoo sys-apps/sandbox: 2.9::gentoo sys-devel/autoconf: 2.13::gentoo, 2.69-r1::gentoo sys-devel/automake: 1.11.6-r1::gentoo, 1.12.6::gentoo, 1.13.4::gentoo, 1.14.1::gentoo, 1.15::gentoo sys-devel/binutils: 2.25.1-r1::gentoo sys-devel/gcc: 4.9.3::gentoo sys-devel/gcc-config: 1.8-r1::gentoo sys-devel/libtool: 2.4.6-r1::gentoo sys-devel/make: 4.1-r1::gentoo sys-kernel/linux-headers: 4.2::gentoo (virtual/os-headers) sys-libs/glibc: 2.21-r1::gentoo Repositories: gentoo location: /var/cache/portage/gentoo sync-type: rsync sync-uri: rsync://rsync.de.gentoo.org/gentoo-portage priority: -1000 aegypius location: /var/lib/layman/aegypius sync-type: laymansync sync-uri: git://github.com/aegypius/overlay.git masters: gentoo priority: 50 kde location: /var/lib/layman/kde sync-type: laymansync sync-uri: git://anongit.gentoo.org/proj/kde.git masters: gentoo priority: 50 sage-on-gentoo location: /var/lib/layman/sage-on-gentoo sync-type: laymansync sync-uri: git://github.com/cschwan/sage-on-gentoo.git masters: gentoo science priority: 50 science location: /var/lib/layman/science sync-type: laymansync sync-uri: git://anongit.gentoo.org/proj/sci.git masters: gentoo priority: 50 local location: /var/cache/portage/local masters: gentoo priority: 100 ACCEPT_KEYWORDS="amd64 ~amd64" ACCEPT_LICENSE="* -@EULA" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-pipe -O2 -march=bdver3" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/lib64/libreoffice/program/sofficerc /usr/share/config /usr/share/gnupg/qualified.txt /usr/share/themes/oxygen-gtk/gtk-2.0 /usr/share/themes/oxygen-gtk/gtk-3.0" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/dconf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/php/apache2-php5.6/ext-active/ /etc/php/cgi-php5.6/ext-active/ /etc/php/cli-php5.6/ext-active/ /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="-pipe -O2 -march=bdver3" DISTDIR="/var/cache/portage/distfiles" EMERGE_DEFAULT_OPTS="--keep-going --nospinner" FCFLAGS="-O2 -pipe" FEATURES="assume-digests binpkg-logs buildsyspkg compressdebug config-protect-if-modified distlocks ebuild-locks fixlafiles merge-sync news parallel-fetch parallel-install preserve-libs protect-owned sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr" FFLAGS="-O2 -pipe" GENTOO_MIRRORS="http://ftp.spline.inf.fu-berlin.de/mirrors/gentoo/ http://ftp-stud.hs-esslingen.de/pub/Mirrors/gentoo/ http://distfiles.gentoo.org" LANG="en_GB.UTF-8" LDFLAGS="-Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu" MAKEOPTS="-j5" PKGDIR="/var/cache/portage/packages" PORTAGE_COMPRESS="xz" 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" PORTAGE_TMPDIR="/var/tmp" USE="X a52 aac aacplus aacs acl acpi alsa amd64 appindicator audit avahi bash-completion bdplus berkdb bluetooth bluray branding bzip2 cairo caps cdda cddb cdio cdr celt cjk cli conntrack cracklib crypt cups cxx dbus declarative dirac dri dts dvb dvd dvdr egl emboss encode exif fam fax ffmpeg firefox flac fontconfig fortran gdbm gif glamor gles gles2 gmp gpm gstreamer gtk ibus iconv ipv6 jpeg jpeg2k kde kipi ladspa latex lcms ldap libnotify libsecret lua_target_lua5-2 lv2 lz4 lzma lzo mad mmx mmxext mng modemmanager modplug modules mp3 mp4 mpeg mplayer mtp multilib multitarget mysql ncurses netlink networkmanager nls nptl ogg openal opencl openexr opengl openmax openmp opus pam pango pch pcre pdf phonon plasma png policykit ppds pulseaudio qml qt3support qt4 qt5 readline rtmp samba scanner schroedinger sctp sdl seccomp semantic-desktop session speex spell sse sse2 ssl startup-notification subversion svg systemd tcpd theora threads tiff truetype udev udisks unicode upnp upnp-av upower usb v4l vaapi vdpau vorbis vpx wavpack wayland webp widgets x264 x265 xattr xcb xcomposite xinerama xml xrandr xscreensaver xv xvid xz zeroconf zlib" ABI_X86="64" ALSA_CARDS="hda-intel" 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="stage words flow sheets gemini" CAMERAS="ptp2" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" CPU_FLAGS_X86="3dnow 3dnowext mmx mmxext sse sse2 sse3" DRACUT_MODULES="btrfs caps systemd" ELIBC="glibc" ENLIGHTENMENT_MODULES="*" GPSD_PROTOCOLS="ashtech aivdm earthmate evermore fv18 garmin garmintxt gpsclock itrax mtk3301 nmea ntrip navcom oceanserver oldstyle oncore rtcm104v2 rtcm104v3 sirf superstar2 timing tsip tripmate tnt ublox ubx" GRUB_PLATFORMS="coreboot efi-64 pc" INPUT_DEVICES="evdev joystick" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" LINGUAS="de en en_GB ar fa" LIRC_DEVICES="devinput" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php5-5" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_4" RUBY_TARGETS="ruby20 ruby21" USERLAND="GNU" VIDEO_CARDS="amdgpu radeon radeonsi" 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, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, USE_PYTHON ================================================================= Package Settings ================================================================= virtual/cblas-2.0-r3::science was built with the following: USE="-int64" ABI_X86="64 -32 -x32" CHOST="" app-eselect/eselect-cblas-0.1::gentoo was built with the following: USE="(policykit)" ABI_X86="64" sci-libs/iml-1.0.4::sage-on-gentoo was built with the following: USE="-static-libs" ABI_X86="64"
Do you have cblas installed? what is the output of "pkg-config --libs cblas"?
(In reply to Justin Lecher from comment #1) > Do you have cblas installed? # eix -e gsl [I] sci-libs/gsl Available versions: 1.14 (~)1.16 (~)1.16-r2[1] {cblas-external static-libs ABI_MIPS="n32 n64 o32" ABI_PPC="32 64" ABI_S390="32 64" ABI_X86="32 64 x32"} Installed versions: 1.16-r2[1](01:37:00 17/10/15)(-cblas-external -static-libs ABI_MIPS="-n32 -n64 -o32" ABI_PPC="-32 -64" ABI_S390="-32 -64" ABI_X86="64 -32 -x32") Homepage: http://www.gnu.org/software/gsl/ Description: GNU Scientific Library [1] "science" /var/lib/layman/science > what is the output of "pkg-config --libs cblas"? # pkg-config --libs cblas Package cblas was not found in the pkg-config search path. Perhaps you should add the directory containing `cblas.pc' to the PKG_CONFIG_PATH environment variable No package 'cblas' found So this is a bug in the gsl ebuild of the science overlay?
# emerge --info blas-reference cblas-reference lapack-reference gsl virtual/blas virtual/cblas eselect eselect-blas eselect-cblas Portage 2.2.23 (python 3.4.3-final-0, default/linux/amd64/13.0/desktop/plasma/systemd, gcc-4.9.3, glibc-2.22-r1, 4.2.5-gentoo x86_64) ================================================================= System Settings ================================================================= System uname: Linux-4.2.5-gentoo-x86_64-AMD_A10-7800_Radeon_R7,_12_Compute_Cores_4C+8G-with-gentoo-2.2 KiB Mem: 15381424 total, 6777000 free KiB Swap: 0 total, 0 free Timestamp of repository gentoo: Sat, 31 Oct 2015 08:15:01 +0000 sh bash 4.3_p42 ld GNU ld (Gentoo 2.25 p1.2) 2.25 ccache version 3.2.4 [disabled] app-shells/bash: 4.3_p42::gentoo dev-java/java-config: 2.2.0::gentoo dev-lang/perl: 5.22.0::gentoo dev-lang/python: 2.7.10::gentoo, 3.3.5-r1::gentoo, 3.4.3::gentoo dev-util/ccache: 3.2.4::gentoo dev-util/cmake: 3.3.2-r1::gentoo dev-util/pkgconfig: 0.29::gentoo sys-apps/baselayout: 2.2::gentoo sys-apps/sandbox: 2.9::gentoo sys-devel/autoconf: 2.13::gentoo, 2.69-r1::gentoo sys-devel/automake: 1.11.6-r1::gentoo, 1.12.6::gentoo, 1.13.4::gentoo, 1.14.1::gentoo, 1.15::gentoo sys-devel/binutils: 2.25-r1::gentoo sys-devel/gcc: 4.9.3::gentoo sys-devel/gcc-config: 1.8-r1::gentoo sys-devel/libtool: 2.4.6-r1::gentoo sys-devel/make: 4.1-r1::gentoo sys-kernel/linux-headers: 4.2::gentoo (virtual/os-headers) sys-libs/glibc: 2.22-r1::gentoo Repositories: gentoo location: /var/cache/portage/gentoo sync-type: rsync sync-uri: rsync://rsync.de.gentoo.org/gentoo-portage priority: -1000 aegypius location: /var/lib/layman/aegypius sync-type: laymansync sync-uri: git://github.com/aegypius/overlay.git masters: gentoo priority: 50 kde location: /var/lib/layman/kde sync-type: laymansync sync-uri: git://anongit.gentoo.org/proj/kde.git masters: gentoo priority: 50 sage-on-gentoo location: /var/lib/layman/sage-on-gentoo sync-type: laymansync sync-uri: git://github.com/cschwan/sage-on-gentoo.git masters: gentoo science priority: 50 science location: /var/lib/layman/science sync-type: laymansync sync-uri: git://anongit.gentoo.org/proj/sci.git masters: gentoo priority: 50 local location: /var/cache/portage/local masters: gentoo priority: 100 ACCEPT_KEYWORDS="amd64 ~amd64" ACCEPT_LICENSE="* -@EULA" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-pipe -O2 -march=bdver3" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/lib64/libreoffice/program/sofficerc /usr/share/config /usr/share/gnupg/qualified.txt /usr/share/themes/oxygen-gtk/gtk-2.0 /usr/share/themes/oxygen-gtk/gtk-3.0" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/dconf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/php/apache2-php5.6/ext-active/ /etc/php/cgi-php5.6/ext-active/ /etc/php/cli-php5.6/ext-active/ /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="-pipe -O2 -march=bdver3" DISTDIR="/var/cache/portage/distfiles" EMERGE_DEFAULT_OPTS="--keep-going --nospinner" FCFLAGS="-O2 -pipe" FEATURES="assume-digests binpkg-logs buildsyspkg compressdebug config-protect-if-modified distlocks ebuild-locks fixlafiles merge-sync news parallel-fetch parallel-install preserve-libs protect-owned sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr" FFLAGS="-O2 -pipe" GENTOO_MIRRORS="http://ftp.spline.inf.fu-berlin.de/mirrors/gentoo/ http://ftp-stud.hs-esslingen.de/pub/Mirrors/gentoo/ http://distfiles.gentoo.org" LANG="en_GB.UTF-8" LDFLAGS="-Wl,-O1 -Wl,--as-needed -Wl,--hash-style=gnu" MAKEOPTS="-j5" PKGDIR="/var/cache/portage/packages" PORTAGE_COMPRESS="xz" 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" PORTAGE_TMPDIR="/var/tmp" USE="X a52 aac aacplus aacs acl acpi alsa amd64 appindicator audit avahi bash-completion bdplus berkdb bluetooth bluray branding bzip2 cairo caps cdda cddb cdio cdr celt cjk cli conntrack cracklib crypt cups cxx dbus declarative dirac dri dts dvb dvd dvdr egl emboss encode exif fam fax ffmpeg firefox flac fontconfig fortran gdbm gif glamor gles gles2 gmp gpm gstreamer gtk ibus iconv ipv6 jpeg jpeg2k kde kipi ladspa latex lcms ldap libinput libnotify libproxy libsecret lua_target_lua5-2 lv2 lz4 lzma lzo mad mmx mmxext mng modemmanager modplug modules mp3 mp4 mpeg mplayer mtp multilib multitarget mysql ncurses netlink networkmanager nls nptl ogg openal opencl openexr opengl openmax openmp opus pam pango pch pcre pdf phonon plasma png policykit ppds pulseaudio qml qt3support qt4 qt5 readline rtmp samba scanner schroedinger sctp sdl seccomp semantic-desktop session speex spell sse sse2 ssl startup-notification subversion svg systemd tcpd theora threads tiff truetype udev udisks unicode upnp upnp-av upower usb v4l vaapi vdpau vorbis vpx wavpack wayland webp widgets x264 x265 xattr xcb xcomposite xinerama xml xrandr xscreensaver xv xvid xz zeroconf zlib" ABI_X86="64" ALSA_CARDS="hda-intel" 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="stage words flow sheets gemini" CAMERAS="ptp2" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" CPU_FLAGS_X86="3dnow 3dnowext mmx mmxext sse sse2 sse3" DRACUT_MODULES="btrfs caps systemd" ELIBC="glibc" ENLIGHTENMENT_MODULES="*" GPSD_PROTOCOLS="ashtech aivdm earthmate evermore fv18 garmin garmintxt gpsclock itrax mtk3301 nmea ntrip navcom oceanserver oldstyle oncore rtcm104v2 rtcm104v3 sirf superstar2 timing tsip tripmate tnt ublox ubx" GRUB_PLATFORMS="coreboot efi-64 pc" INPUT_DEVICES="evdev joystick" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" LINGUAS="de en en_GB ar fa" LIRC_DEVICES="devinput" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php5-5" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_4" RUBY_TARGETS="ruby20 ruby21" USERLAND="GNU" VIDEO_CARDS="amdgpu radeon radeonsi" 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, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, USE_PYTHON ================================================================= Package Settings ================================================================= sci-libs/blas-reference-20131116-r1::science was built with the following: USE="-int64 -static-libs -test" ABI_X86="64 -32 -x32" sci-libs/lapack-reference-3.2.1-r1::gentoo was built with the following: USE="(policykit) -doc" ABI_X86="64" sci-libs/gsl-1.16-r2::science was built with the following: USE="-cblas-external -static-libs" ABI_X86="64 -32 -x32" virtual/blas-2.1-r3::science was built with the following: USE="-doc -int64" ABI_X86="64" CHOST="" virtual/cblas-2.0-r3::science was built with the following: USE="-int64" ABI_X86="64 -32 -x32" CHOST="" app-admin/eselect-1.4.5-r101::science was built with the following: USE="-doc -emacs -vim-syntax" ABI_X86="64" app-eselect/eselect-blas-0.1::gentoo was built with the following: USE="(policykit)" ABI_X86="64" app-eselect/eselect-cblas-0.1::gentoo was built with the following: USE="(policykit)" ABI_X86="64"
There shound't be two eselect modules handling cblas. Uninstall 'app-eselect/eselect-cblas'[1]. Using the science overlay, there only should be the 'Alternatives module'. Furthermore, if I remember correctly after installing gsl you still need to select the cblas implementation to be used utilizing 'eselect cblas set'. [1] https://wiki.gentoo.org/wiki/User_talk:Houseofsuns
The bug has been closed via the following commit(s): https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=77dd20308b4aca8c18f3964196af7252aa85bbc1 commit 77dd20308b4aca8c18f3964196af7252aa85bbc1 Author: Benda Xu <heroxbd@gentoo.org> AuthorDate: 2019-08-19 07:49:21 +0000 Commit: Benda Xu <heroxbd@gentoo.org> CommitDate: 2019-08-19 07:49:51 +0000 sci-libs/iml: import from the science overlay and bump to EAPI 7. Closes: https://bugs.gentoo.org/563288 Package-Manager: Portage-2.3.69, Repoman-2.3.12 Signed-off-by: Benda Xu <heroxbd@gentoo.org> sci-libs/iml/Manifest | 1 + .../iml-1.0.4-use-any-cblas-implementation.patch | 22 +++++++++++++ sci-libs/iml/iml-1.0.5.ebuild | 38 ++++++++++++++++++++++ sci-libs/iml/metadata.xml | 9 +++++ 4 files changed, 70 insertions(+)
