Re: [gentoo-science] R-3.2.2 and libblas

["François Bissey" <frp.bissey@gmail.com>]

Looks like someone has moved from the main tree blas/lapack to the science overlay one
without reinstalling R afterwards.

You need to reinstall R and potentially all your R packages.

François

> On 7/11/2015, at 02:53, Frederico Moraes Ferreira <ferreirafm@usp.br> wrote:
> 
> Hi there,
> Has anybody experienced such libblas issue? Looks like there are some Bioconductor packages need it to compile.
> 
> Thanks in advance.
> Fred
> 
> mephisto ~ #R
> > install.packages("DESeq2")
> ...
> ...
> 
> * installing *source* package 'DESeq2' ...
> ** libs
> x86_64-pc-linux-gnu-g++ -I/usr/lib64/R/include -DNDEBUG -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/RcppArmadillo/include"   -fpic -march=native  -c DESeq2.cpp -o DESeq2.o
> x86_64-pc-linux-gnu-g++ -I/usr/lib64/R/include -DNDEBUG -I"/usr/lib64/R/library/Rcpp/include" -I"/usr/lib64/R/library/RcppArmadillo/include"   -fpic -march=native  -c RcppExports.cpp -o RcppExports.o
> x86_64-pc-linux-gnu-g++ -shared -L/usr/lib64/R/lib -Wl,--as-needed -o DESeq2.so DESeq2.o RcppExports.o -L/usr/lib64/R/lib -lRlapack -L/usr/lib64/R/lib -lRblas -lgfortran -lm -lquadmath -L/usr/lib64/R/lib -lR
> installing to /usr/lib64/R/library/DESeq2/libs
> ** R
> ** inst
> ** preparing package for lazy loading
> Error in dyn.load(file, DLLpath = DLLpath, ...) :
>  unable to load shared object '/usr/lib64/R/library/RcppArmadillo/libs/RcppArmadillo.so':
>  libblas.so.0: cannot open shared object file: No such file or directory
> 
> 
> 
> This is also happens with other packages too.
> Here goes some information.
> 
> mephisto ~ # R CMD config BLAS_LIBS
> -L/usr/lib64/R/lib -lRblas
> 
> mephisto ~ # ls -l /usr/lib64/R/lib
> total 5264
> -rwxr-xr-x 1 root root  182048 Nov  5 17:08 libRblas.so
> -rwxr-xr-x 1 root root 1815848 Nov  5 17:08 libRlapack.so
> -rwxr-xr-x 1 root root 3384648 Nov  5 17:08 libR.so
> 
> 
> mephisto ~ # revdep-rebuild -i
> * Configuring search environment for revdep-rebuild
> 
> * Checking reverse dependencies
> * Packages containing binaries and libraries broken by a package update
> * will be emerged.
> 
> * Collecting system binaries and libraries
> * Generated new 1_files.rr
> * Collecting complete LD_LIBRARY_PATH
> * Generated new 2_ldpath.rr
> * Checking dynamic linking consistency
> [ 85% ]  *   broken /usr/lib64/R/library/DESeq2/libs/DESeq2.so (requires libblas.so.0)
> *   broken /usr/lib64/R/library/expm/libs/expm.so (requires libblas.so.0)
> [ 86% ]  *   broken /usr/lib64/R/library/mclust/libs/mclust.so (requires libblas.so.0)
> *   broken /usr/lib64/R/library/minpack.lm/libs/minpack.lm.so (requires libblas.so.0)
> *   broken /usr/lib64/R/library/nleqslv/libs/nleqslv.so (requires libblas.so.0)
> *   broken /usr/lib64/R/library/pcaPP/libs/pcaPP.so (requires libblas.so.0)
> [ 87% ]  *   broken /usr/lib64/R/library/quadprog/libs/quadprog.so (requires libblas.so.0)
> *   broken /usr/lib64/R/library/quantreg/libs/quantreg.so (requires libblas.so.0)
> *   broken /usr/lib64/R/library/RcppArmadillo/libs/RcppArmadillo.so (requires libblas.so.0)
> *   broken /usr/lib64/R/library/robustbase/libs/robustbase.so (requires libblas.so.0)
> *   broken /usr/lib64/R/library/rrcov/libs/rrcov.so (requires libblas.so.0)
> [ 100% ]
> * Generated new 3_broken.rr
> * Assigning files to packages
> *  !!! /usr/lib64/R/library/DESeq2/libs/DESeq2.so not owned by any package is broken !!!
> *   /usr/lib64/R/library/DESeq2/libs/DESeq2.so -> (none)
> *  !!! /usr/lib64/R/library/expm/libs/expm.so not owned by any package is broken !!!
> *   /usr/lib64/R/library/expm/libs/expm.so -> (none)
> *  !!! /usr/lib64/R/library/mclust/libs/mclust.so not owned by any package is broken !!!
> *   /usr/lib64/R/library/mclust/libs/mclust.so -> (none)
> *  !!! /usr/lib64/R/library/minpack.lm/libs/minpack.lm.so not owned by any package is broken !!!
> *   /usr/lib64/R/library/minpack.lm/libs/minpack.lm.so -> (none)
> *  !!! /usr/lib64/R/library/nleqslv/libs/nleqslv.so not owned by any package is broken !!!
> *   /usr/lib64/R/library/nleqslv/libs/nleqslv.so -> (none)
> *  !!! /usr/lib64/R/library/pcaPP/libs/pcaPP.so not owned by any package is broken !!!
> *   /usr/lib64/R/library/pcaPP/libs/pcaPP.so -> (none)
> *  !!! /usr/lib64/R/library/quadprog/libs/quadprog.so not owned by any package is broken !!!
> *   /usr/lib64/R/library/quadprog/libs/quadprog.so -> (none)
> *  !!! /usr/lib64/R/library/quantreg/libs/quantreg.so not owned by any package is broken !!!
> *   /usr/lib64/R/library/quantreg/libs/quantreg.so -> (none)
> *  !!! /usr/lib64/R/library/RcppArmadillo/libs/RcppArmadillo.so not owned by any package is broken !!!
> *   /usr/lib64/R/library/RcppArmadillo/libs/RcppArmadillo.so -> (none)
> *  !!! /usr/lib64/R/library/robustbase/libs/robustbase.so not owned by any package is broken !!!
> *   /usr/lib64/R/library/robustbase/libs/robustbase.so -> (none)
> *  !!! /usr/lib64/R/library/rrcov/libs/rrcov.so not owned by any package is broken !!!
> *   /usr/lib64/R/library/rrcov/libs/rrcov.so -> (none)
> * Generated new 4_raw.rr and 4_owners.rr
> * Found some broken files, but none of them were associated with known packages
> * Unable to proceed with automatic repairs.
> * The broken files are listed in 4_owners.rr
> 
> 
> mephisto ~ # emerge --info
> Portage 2.2.24 (python 3.4.3-final-0, default/linux/amd64/13.0/desktop/gnome/systemd, gcc-4.9.3, glibc-2.22-r1, 4.0.0-gentoo x86_64) ================================================================= System uname: Linux-4.0.0-gentoo-x86_64-Intel-R-_Core-TM-_i7-5960X_CPU_@_3.00GHz-with-gentoo-2.2 KiB Mem: 16346068 total, 5356644 free KiB Swap: 524284 total, 362228 free Timestamp of repository gentoo: Fri, 06 Nov 2015 07:00:01 +0000 sh bash 4.3_p42 ld GNU ld (Gentoo 2.25.1 p1.1) 2.25.1 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-r2::gentoo, 3.4.3::gentoo, 3.5.0-r1::gentoo dev-util/cmake: 3.3.2-r1::gentoo dev-util/pkgconfig: 0.29::gentoo sys-apps/baselayout: 2.2::gentoo sys-apps/openrc: 0.18.3::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, 1.13.4::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::gentoo sys-devel/libtool: 2.4.6-r1::gentoo sys-devel/make: 4.1-r1::gentoo sys-kernel/linux-headers: 4.3::gentoo (virtual/os-headers) sys-libs/glibc: 2.22-r1::gentoo Repositories: gentoo location: /usr/portage sync-type: rsync sync-uri: rsync://rsync.gentoo.org/gentoo-portage priority: -1000 local_overlay location: /usr/local/portage masters: gentoo science location: /var/lib/layman/science masters: gentoo priority: 50 ACCEPT_KEYWORDS="amd64 ~amd64" ACCEPT_LICENSE="*" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-march=native" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/lib64/libreoffice/program/sofficerc /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" DISTDIR="/usr/portage/distfiles" FCFLAGS="-O2 -pipe" FEATURES="assume-digests binpkg-logs config-protect-if-modified distlocks ebuild-locks fixlafiles merge-sync news parallel-fetch preserve-libs sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr" FFLAGS="-O2 -pipe" GENTOO_MIRRORS="ftp://ftp.las.ic.unicamp.br/pub/gentoo/ http://www.las.ic.unicamp.br/pub/gentoo/ ftp://ftp.ussg.iu.edu/pub/linux/gentoo ftp://mirror.iawnet.sandia.gov/pub/gentoo/" LANG="pt_BR.utf8" LDFLAGS="-Wl,--as-needed" PKGDIR="/usr/portage/packages" 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 acl acpi alsa amd64 berkdb bluetooth branding bzip2 cairo cdda cdr cli colord cracklib crypt cups cxx dbus dri dts dvd dvdr eds emboss encode evo exif fam firefox flac fortran gdbm gif glamor gnome gnome-keyring gnome-online-accounts gpm gstreamer gtk iconv introspection ipv6 jpeg lcms ldap libnotify libsecret mad mmx mmxext mng modules mp3 mp4 mpeg multilib nautilus ncurses nls nptl ogg opengl openmp pam pango pcre pdf png policykit ppds pulseaudio qt3support readline sdl seccomp session spell sse sse2 ssl startup-notification svg systemd tcpd tiff tracker truetype udev udisks unicode upower usb uvm vorbis wxwidgets x264 xattr xcb xml xv xvid zlib" ABI_X86="64 32" 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="mmx mmxext sse sse2" 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" GRUB_PLATFORMS="efi-64" INPUT_DEVICES="evdev" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console presenter-minimizer" LINGUAS="pt_BR en" 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="nvidia" 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, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LC_ALL, MAKEOPTS, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, USE_PYTHON
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