| Summary: | dev-lang/R not linking to correct (Prefix) gfortran library | ||
|---|---|---|---|
| Product: | Gentoo Linux | Reporter: | Robert McGehee <robert.mcgehee> |
| Component: | Current packages | Assignee: | Gentoo Prefix <prefix> |
| Status: | RESOLVED OBSOLETE | ||
| Severity: | normal | ||
| Priority: | Normal | ||
| Version: | unspecified | ||
| Hardware: | AMD64 | ||
| OS: | Linux | ||
| Whiteboard: | |||
| Package list: | Runtime testing required: | --- | |
Please attach the full build log to this bug. Since R and ATLAS both compiled without error, it does not appear that there _is_ a build log for me to send you. If I misunderstand, please let me know where the build log can be found or how to generate it. The contents of $EPREFIX/var/tmp/portage/dev-lang/R-2.15.2-r1/temp was empty. this should be fixed in R-2.15.2-r2 and R-2.15.3. please re-open if not. |
Hello, I use Gentoo Prefix on a Red Hat Enterprise server. I've installed sci-libs/atlas (3.10.1) from the science overlay and the current build of dev-lang/R (2.15.2) from Gentoo linking to the ATLAS blas. Both install without error or warnings. However, I get the following error message when I actually try to start R: [lbos802]~> R /data/gentoo/usr/lib/R/bin/exec/R: /usr/lib64/libgfortran.so.3: version `GFORTRAN_1.4' not found (required by /data/gentoo/usr/lib/libptf77blas.so.3) It seems that R is linking to the Red Hat system libgfortran.so.3 libraries in /usr/lib64/ rather than the Gentoo prefix libgfortran libraries inside my /data/gentoo/ prefix directory. I was able to manually compile R, linking against the Gentoo ATLAS, without any issue. Let me know if you have any questions. --Robert [lbos802]~> emerge --info dev-lang/R !!! Your current profile is deprecated and not supported anymore. !!! Use eselect profile to update your profile. !!! Please upgrade to the following profile if possible: default/linux/amd64/13.0/no-multilib Portage 2.2.01.21688-prefix (prefix/linux/amd64, gcc-4.6.3, unavailable, 2.6.18-308.8.1.0.1.el5 x86_64) ================================================================= System Settings ================================================================= System uname: Linux-2.6.18-308.8.1.0.1.el5-x86_64-Intel-R-_Xeon-R-_CPU_E7440_@_2.40GHz-with-redhat-5.8-Tikanga KiB Mem: 65870840 total, 53690756 free KiB Swap: 67106120 total, 65120712 free Timestamp of tree: Tue, 12 Feb 2013 17:45:03 +0000 ld GNU ld (GNU Binutils) 2.23 app-shells/bash: 4.2_p39-r1::gentoo_prefix dev-java/java-config: 2.1.11-r3::gentoo_prefix dev-lang/python: 2.7.3-r2::gentoo_prefix dev-util/cmake: 2.8.10.2-r1::gentoo_prefix dev-util/pkgconfig: 0.28::gentoo_prefix sys-devel/autoconf: 2.69::gentoo_prefix sys-devel/automake: 1.12.4::gentoo_prefix sys-devel/binutils: 2.23::gentoo_prefix sys-devel/gcc: 4.6.3::gentoo_prefix sys-devel/gcc-config: 1.8-r00.1::gentoo_prefix sys-devel/libtool: 2.4.2::gentoo_prefix sys-devel/make: 3.82-r4::gentoo_prefix sys-kernel/linux-headers: 3.7::gentoo_prefix (virtual/os-headers) Repositories: gentoo_prefix science ACCEPT_KEYWORDS="~amd64-linux" ACCEPT_LICENSE="* -@EULA" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-O2 -march=core2 -mcx16 -msahf -mno-movbe -mno-aes -mno-pclmul -mno-popcnt -mno-abm -mno-lwp -mno-fma -mno-fma4 -mno-xop -mno-bmi -mno-tbm -mno-avx -mno-sse4.2 -mno-sse4.1 --param l1-cache-size=32 --param l1-cache-line-size=64 --param l2-cache-size=16384 -mtune=generic" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/env.d/java/ /etc/fonts/fonts.conf /etc/gconf /etc/revdep-rebuild /etc/terminfo /etc/texmf/language.dat.d /etc/texmf/language.def.d /etc/texmf/updmap.d /etc/texmf/web2c" CXXFLAGS="-O2 -march=core2 -mcx16 -msahf -mno-movbe -mno-aes -mno-pclmul -mno-popcnt -mno-abm -mno-lwp -mno-fma -mno-fma4 -mno-xop -mno-bmi -mno-tbm -mno-avx -mno-sse4.2 -mno-sse4.1 --param l1-cache-size=32 --param l1-cache-line-size=64 --param l2-cache-size=16384 -mtune=generic" DISTDIR="/data/gentoo/usr/portage/distfiles" FCFLAGS="-O2 -pipe" FEATURES="assume-digests binpkg-logs collision-protect config-protect-if-modified distlocks ebuild-locks fixlafiles force-prefix merge-sync news parallel-fetch preserve-libs protect-owned sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch" FFLAGS="-O2 -march=core2 -mcx16 -msahf -mno-movbe -mno-aes -mno-pclmul -mno-popcnt -mno-abm -mno-lwp -mno-fma -mno-fma4 -mno-xop -mno-bmi -mno-tbm -mno-avx -mno-sse4.2 -mno-sse4.1 --param l1-cache-size=32 --param l1-cache-line-size=64 --param l2-cache-size=16384 -mtune=generic" GENTOO_MIRRORS="http://distfiles.gentoo.org" LANG="C" LDFLAGS="-Wl,-O1" MAKEOPTS="-j8" PKGDIR="/data/gentoo/usr/portage/packages" PORTAGE_CONFIGROOT="/data/gentoo/" PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --compress --force --whole-file --delete --stats --human-readable --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages" PORTAGE_TMPDIR="/data/gentoo/var/tmp" PORTDIR="/data/gentoo/usr/portage" PORTDIR_OVERLAY="/data/gentoo/var/lib/layman/science" SYNC="rsync://rsync.prefix.freens.org/gentoo-portage-prefix" USE="X amd64 bash-completion berkdb bindist blas bzip2 cairo cli crypt curl curlwrappers cxx emacs flatfile fortran freetds gcj gdbm gtk gzip iconv libcaca mmx modules mpi ncurses nls nptl odbc openmp pango pcre pdf posix postgres prefix readline sasl spell sse sse2 ssl subversion tcl tcpd threads tk truetype unicode xft xml xorg zlib" ABI_X86="64" 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" CAMERAS="ptp2" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" 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 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" PHP_TARGETS="php5-3" PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7" RUBY_TARGETS="ruby18 ruby19" USERLAND="GNU" VIDEO_CARDS="radeon" 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: CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LC_ALL, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, USE_PYTHON ================================================================= Package Settings ================================================================= dev-lang/R-2.15.2-r1 was built with the following: USE="X bash-completion cairo java nls openmp png (prefix) profile readline tiff tk -doc -icu -jpeg -lapack -minimal -perl -static-libs" CFLAGS="-O2 -march=core2 -mcx16 -msahf -mno-movbe -mno-aes -mno-pclmul -mno-popcnt -mno-abm -mno-lwp -mno-fma -mno-fma4 -mno-xop -mno-bmi -mno-tbm -mno-avx -mno-sse4.2 -mno-sse4.1 -mtune=generic -fwrapv" CXXFLAGS="-O2 -march=core2 -mcx16 -msahf -mno-movbe -mno-aes -mno-pclmul -mno-popcnt -mno-abm -mno-lwp -mno-fma -mno-fma4 -mno-xop -mno-bmi -mno-tbm -mno-avx -mno-sse4.2 -mno-sse4.1 -mtune=generic -fwrapv" LDFLAGS="-Wl,-O1 -L/data/gentoo/lib -L/data/gentoo/usr/lib -L/usr/lib64 -L/lib64 -L."