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 <[email protected]> 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 > > >
