* Package: sci-biology/plink-1.90_pre140514 * Repository: gentoo * Maintainer: sci-biology@gentoo.org * USE: abi_x86_64 amd64 elibc_glibc kernel_linux prefix userland_GNU * FEATURES: nostrip preserve-libs splitdebug userpriv >>> Unpacking source... >>> Unpacking plink-1.90_pre140514.zip to /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/plink-1.90_pre140514/work >>> Source unpacked in /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/plink-1.90_pre140514/work >>> Preparing source in /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/plink-1.90_pre140514/work ... >>> Source prepared. >>> Configuring source in /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/plink-1.90_pre140514/work ... >>> Source configured. >>> Compiling source in /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/plink-1.90_pre140514/work ... make -j8 CXX=x86_64-pc-linux-gnu-g++ 'CFLAGS=-O2 -pipe -O2 -pipe -march=native' ZLIB=-lz 'BLASFLAGS=-lreflapack -lrefblas -lgsl' x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native plink.c plink_assoc.c plink_calc.c plink_cluster.c plink_cnv.c plink_common.c plink_data.c plink_family.c plink_filter.c plink_glm.c plink_help.c plink_homozyg.c plink_lasso.c plink_ld.c plink_matrix.c plink_misc.c plink_set.c plink_stats.c SFMT.c dcdflib.c pigz.c yarn.c -o plink -lreflapack -lrefblas -lgsl -lm -lpthread -L. -lz In file included from plink_stats.h:4:0, from plink.c:43: plink_matrix.h:52:19: fatal error: cblas.h: No such file or directory compilation terminated. $ equery files cblas.h * Searching for cblas.h ... !!! No installed packages matching 'cblas.h' $ emerge -pv sci-libs/atlas sci-libs/cblas-reference sci-libs/gsl These are the packages that would be merged, in order: Calculating dependencies... done! [ebuild N ] sci-libs/atlas-3.11.38-r1::science USE="deprecated fortran lapack threads -doc -generic -ifko -static-libs" 5273 KiB [ebuild R ] sci-libs/gsl-2.1:0/19::science USE="-cblas-external -int64 -static-libs" 0 KiB [ebuild N ] sci-libs/cblas-reference-20151113-r3:0/3.6.0::science USE="-int64 -static-libs {-test}" 0 KiB Total: 3 packages (2 new, 1 reinstall), Size of downloads: 5273 KiB $ So, somehow the dependency on Further to say, on another host I have a cblas.h-related files here: # equery belongs cblas.h * Searching for cblas.h ... sci-libs/atlas-3.10.1-r2 (/etc/env.d/alternatives/cblas/atlas/usr/include/cblas.h -> ../../../../../../../usr/include/atlas/cblas.h) sci-libs/atlas-3.10.1-r2 (/usr/include/atlas/cblas.h) sci-libs/atlas-3.10.1-r2 (/etc/env.d/alternatives/cblas/atlas-threads/usr/include/cblas.h -> ../../../../../../../usr/include/atlas/cblas.h) sci-libs/cblas-reference-20110218-r1 (/etc/env.d/alternatives/cblas/reference/usr/include/cblas.h -> ../../../../../../../usr/include/cblas/cblas.h) sci-libs/cblas-reference-20110218-r1 (/usr/include/cblas/cblas.h) sci-libs/gsl-1.16-r2 (/etc/env.d/alternatives/cblas/gsl/usr/include/cblas.h -> ../../../../../../../usr/include/gsl/gsl_cblas.h) So, may the include line needs a patch as well, or -I/usr/include/cblas to added specifically.
Please provide emerge --info.
$ emerge --info Portage 2.3.0 (python 2.7.11-final-0, prefix/linux-standalone/amd64, gcc-5.4.0, unavailable, 2.6.32-573.12.1.el6.Bull.88.x86_64 x86_64) ================================================================= System uname: Linux-2.6.32-573.12.1.el6.Bull.88.x86_64-x86_64-Intel-R-_Xeon-R-_CPU_E5-2670_0_@_2.60GHz-with-redhat-6.4-Santiago KiB Mem: 131942764 total, 56985848 free KiB Swap: 65536128 total, 65536128 free Timestamp of repository gentoo: Fri, 15 Jul 2016 09:30:01 +0000 sh bash 4.3_p46 ld GNU ld (Gentoo 2.26) 2.26.20160125 app-shells/bash: 4.3_p46::rap dev-lang/perl: 5.24.0-r1::gentoo dev-lang/python: 2.7.11-r2::gentoo, 3.4.4::gentoo dev-util/cmake: 3.5.2-r1::gentoo dev-util/pkgconfig: 0.29.1::gentoo sys-apps/baselayout: 2.2::rap sys-apps/sandbox: 2.10-r2::gentoo sys-devel/autoconf: 2.69-r2::gentoo sys-devel/automake: 1.13.4-r1::gentoo, 1.14.1-r1::gentoo, 1.15-r2::gentoo sys-devel/binutils: 2.26::rap sys-devel/gcc: 4.2.4-r1::gentoo, 5.4.0::gentoo sys-devel/gcc-config: 1.8_p20160608::rap sys-devel/libtool: 2.4.6-r2::gentoo sys-devel/make: 4.2.1::gentoo sys-kernel/linux-headers: 4.6::gentoo (virtual/os-headers) sys-libs/glibc: 2.23-r2::rap Repositories: gentoo location: /scratch/mmokrejs/gentoo_rap/usr/portage sync-type: rsync sync-uri: rsync://rsync.gentoo.org/gentoo-portage priority: -1000 eclass-overrides: rap layman location: /scratch/mmokrejs/gentoo_rap/var/lib/layman masters: gentoo priority: 0 eclass-overrides: rap rap location: /scratch/mmokrejs/gentoo_rap/usr/portage-stage sync-type: git sync-uri: https://anongit.gentoo.org/git/proj/android.git masters: gentoo eclass-overrides: rap haskell location: /scratch/mmokrejs/gentoo_rap/var/lib/layman/haskell masters: gentoo priority: 50 eclass-overrides: rap science location: /scratch/mmokrejs/gentoo_rap/var/lib/layman/science masters: gentoo priority: 50 eclass-overrides: rap ACCEPT_KEYWORDS="amd64 ~amd64 ~amd64-linux" ACCEPT_LICENSE="* -@EULA" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-O2 -pipe -O2 -pipe -march=native" 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="-O2 -pipe -O2 -pipe -march=native" DISTDIR="/scratch/mmokrejs/gentoo_rap/usr/portage/distfiles" FCFLAGS="-O2 -pipe" FEATURES="assume-digests binpkg-logs config-protect-if-modified distlocks ebuild-locks fixlafiles force-prefix merge-sync news nostrip parallel-fetch preserve-libs protect-owned sfperms splitdebug strict unknown-features-warn unmerge-logs unmerge-orphans unprivileged userfetch userpriv usersync" FFLAGS="-O2 -pipe" GENTOO_MIRRORS="http://gentoo.wheel.sk/ 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" MAKEOPTS="-j8" PKGDIR="/scratch/mmokrejs/gentoo_rap/usr/portage/packages" PORTAGE_CONFIGROOT="/scratch/mmokrejs/gentoo_rap/" 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="/scratch/mmokrejs/gentoo_rap/var/tmp" USE="X amd64 apache apache2 avx avx2 berkdb bindist boost bzip2 cairo cgi cli coin consolekit 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 java javascript jce jpeg jpg js jscript keymap ladspa lapack lcms libnotify lm_sensors mad mmx mmxext modules mpi mpich2 mysql ncurses nfs nls nptl nptlonly nscd openmp pcre pdf perl php png policykit polkit 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" CAMERAS="ptp2" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" CPU_FLAGS_X86="aes avx mmx mmxext popcnt sse sse2 sse3 sse4_1 sse4_2 ssse3" ELIBC="glibc" 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" INPUT_DEVICES="keyboard mouse evdev" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" LINGUAS="en en_US cs cz" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php5-5" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7" RUBY_TARGETS="ruby20 ruby21" 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" USE_PYTHON="2.7" 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
I introduced in science overlay sci-biology/plink-1.90_pre160731::science which has this issue as well. However, I at least rescued USE=lapack logick from the old 1.07 ebuild. It brought me to a difference: On machine where it works is: >>> Compiling source in /scratch/var/tmp/portage/sci-biology/plink-1.90_pre160731/work ... make -j2 CXX=x86_64-pc-linux-gnu-g++ 'CFLAGS=-O2 -pipe -maes -mpclmul -mpopcnt -mavx -march=native' 'ZLIB=-lz ' 'BLASFLAGS=-latllapack -lf77blas -latlcblas ' x86_64-pc-linux-gnu-g++ -O2 -pipe -maes -mpclmul -mpopcnt -mavx -march=native plink.c plink_assoc.c plink_calc.c plink_cluster.c plink_cnv.c plink_common.c plink_data.c plink_dosage.c plink_family.c plink_filter.c plink_glm.c plink_help.c plink_homozyg.c plink_lasso.c plink_ld.c plink_matrix.c plink_misc.c plink_perm.c plink_rserve.c plink_set.c plink_stats.c SFMT.c dcdflib.c pigz.c yarn.c Rconnection.cc hfile.c bgzf.c -o plink -latllapack -lf77blas -latlcblas -lm -lpthread -ldl -L. -lz >>> Source compiled. On the one where it fails: >>> Compiling source in /scratch/mmokrejs/gentoo_rap/var/tmp/portage/sci-biology/plink-1.90_pre160731/work ... make -j8 CXX=x86_64-pc-linux-gnu-g++ 'CFLAGS=-O2 -pipe -O2 -pipe -march=native' ZLIB=-lz 'BLASFLAGS=-lreflapack -lrefblas -lgsl' x86_64-pc-linux-gnu-g++ -O2 -pipe -O2 -pipe -march=native plink.c plink_assoc.c plink_calc.c plink_cluster.c plink_cnv.c plink_common.c plink_data.c plink_dosage.c plink_family.c plink_filter.c plink_glm.c plink_help.c plink_homozyg.c plink_lasso.c plink_ld.c plink_matrix.c plink_misc.c plink_perm.c plink_rserve.c plink_set.c plink_stats.c SFMT.c dcdflib.c pigz.c yarn.c Rconnection.cc hfile.c bgzf.c -o plink -lreflapack -lrefblas -lgsl -lm -lpthread -ldl -L. -lz In file included from plink_glm.h:4:0, from plink_dosage.h:4, from plink.c:34: plink_matrix.h:59:19: fatal error: cblas.h: No such file or directory So, the real cause could be the DEPENDency on virtuals while the simple Makefile and code requires maybe just one implementation? I am lost in this lapack/blas/atlas/you_know_them_all libraries. Please fix eventually all the ebuilds in the main tree and in science overlay. Thank you. ;-)
*** Bug 689096 has been marked as a duplicate of this bug. ***
