[gentoo-science] R-3.2.2 and libblas

[Frederico Moraes Ferreira <ferreirafm@usp.br>]

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