| 1 |
Hi there, |
| 2 |
Has anybody experienced such libblas issue? Looks like there are some |
| 3 |
Bioconductor packages need it to compile. |
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|
| 5 |
Thanks in advance. |
| 6 |
Fred |
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|
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mephisto ~ #R |
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> install.packages("DESeq2") |
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... |
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... |
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|
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* installing *source* package 'DESeq2' ... |
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** libs |
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x86_64-pc-linux-gnu-g++ -I/usr/lib64/R/include -DNDEBUG |
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-I"/usr/lib64/R/library/Rcpp/include" |
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-I"/usr/lib64/R/library/RcppArmadillo/include" -fpic -march=native -c |
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DESeq2.cpp -o DESeq2.o |
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x86_64-pc-linux-gnu-g++ -I/usr/lib64/R/include -DNDEBUG |
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-I"/usr/lib64/R/library/Rcpp/include" |
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-I"/usr/lib64/R/library/RcppArmadillo/include" -fpic -march=native -c |
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RcppExports.cpp -o RcppExports.o |
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x86_64-pc-linux-gnu-g++ -shared -L/usr/lib64/R/lib -Wl,--as-needed -o |
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DESeq2.so DESeq2.o RcppExports.o -L/usr/lib64/R/lib -lRlapack |
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-L/usr/lib64/R/lib -lRblas -lgfortran -lm -lquadmath -L/usr/lib64/R/lib -lR |
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installing to /usr/lib64/R/library/DESeq2/libs |
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** R |
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** inst |
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** preparing package for lazy loading |
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Error in dyn.load(file, DLLpath = DLLpath, ...) : |
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unable to load shared object |
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'/usr/lib64/R/library/RcppArmadillo/libs/RcppArmadillo.so': |
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libblas.so.0: cannot open shared object file: No such file or directory |
| 34 |
|
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|
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|
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This is also happens with other packages too. |
| 38 |
Here goes some information. |
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|
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mephisto ~ # R CMD config BLAS_LIBS |
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-L/usr/lib64/R/lib -lRblas |
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|
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mephisto ~ # ls -l /usr/lib64/R/lib |
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total 5264 |
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-rwxr-xr-x 1 root root 182048 Nov 5 17:08 libRblas.so |
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-rwxr-xr-x 1 root root 1815848 Nov 5 17:08 libRlapack.so |
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-rwxr-xr-x 1 root root 3384648 Nov 5 17:08 libR.so |
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|
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|
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mephisto ~ # revdep-rebuild -i |
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* Configuring search environment for revdep-rebuild |
| 52 |
|
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* Checking reverse dependencies |
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* Packages containing binaries and libraries broken by a package update |
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* will be emerged. |
| 56 |
|
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* Collecting system binaries and libraries |
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* Generated new 1_files.rr |
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* Collecting complete LD_LIBRARY_PATH |
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* Generated new 2_ldpath.rr |
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* Checking dynamic linking consistency |
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[ 85% ] * broken /usr/lib64/R/library/DESeq2/libs/DESeq2.so (requires |
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libblas.so.0) |
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* broken /usr/lib64/R/library/expm/libs/expm.so (requires libblas.so.0) |
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[ 86% ] * broken /usr/lib64/R/library/mclust/libs/mclust.so (requires |
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libblas.so.0) |
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* broken /usr/lib64/R/library/minpack.lm/libs/minpack.lm.so |
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(requires libblas.so.0) |
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* broken /usr/lib64/R/library/nleqslv/libs/nleqslv.so (requires |
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libblas.so.0) |
| 71 |
* broken /usr/lib64/R/library/pcaPP/libs/pcaPP.so (requires |
| 72 |
libblas.so.0) |
| 73 |
[ 87% ] * broken /usr/lib64/R/library/quadprog/libs/quadprog.so |
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(requires libblas.so.0) |
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* broken /usr/lib64/R/library/quantreg/libs/quantreg.so (requires |
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libblas.so.0) |
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* broken /usr/lib64/R/library/RcppArmadillo/libs/RcppArmadillo.so |
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(requires libblas.so.0) |
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* broken /usr/lib64/R/library/robustbase/libs/robustbase.so |
| 80 |
(requires libblas.so.0) |
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* broken /usr/lib64/R/library/rrcov/libs/rrcov.so (requires |
| 82 |
libblas.so.0) |
| 83 |
[ 100% ] |
| 84 |
* Generated new 3_broken.rr |
| 85 |
* Assigning files to packages |
| 86 |
* !!! /usr/lib64/R/library/DESeq2/libs/DESeq2.so not owned by any |
| 87 |
package is broken !!! |
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* /usr/lib64/R/library/DESeq2/libs/DESeq2.so -> (none) |
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* !!! /usr/lib64/R/library/expm/libs/expm.so not owned by any package |
| 90 |
is broken !!! |
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* /usr/lib64/R/library/expm/libs/expm.so -> (none) |
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* !!! /usr/lib64/R/library/mclust/libs/mclust.so not owned by any |
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package is broken !!! |
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* /usr/lib64/R/library/mclust/libs/mclust.so -> (none) |
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* !!! /usr/lib64/R/library/minpack.lm/libs/minpack.lm.so not owned by |
| 96 |
any package is broken !!! |
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* /usr/lib64/R/library/minpack.lm/libs/minpack.lm.so -> (none) |
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* !!! /usr/lib64/R/library/nleqslv/libs/nleqslv.so not owned by any |
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package is broken !!! |
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* /usr/lib64/R/library/nleqslv/libs/nleqslv.so -> (none) |
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* !!! /usr/lib64/R/library/pcaPP/libs/pcaPP.so not owned by any |
| 102 |
package is broken !!! |
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* /usr/lib64/R/library/pcaPP/libs/pcaPP.so -> (none) |
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* !!! /usr/lib64/R/library/quadprog/libs/quadprog.so not owned by any |
| 105 |
package is broken !!! |
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* /usr/lib64/R/library/quadprog/libs/quadprog.so -> (none) |
| 107 |
* !!! /usr/lib64/R/library/quantreg/libs/quantreg.so not owned by any |
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package is broken !!! |
| 109 |
* /usr/lib64/R/library/quantreg/libs/quantreg.so -> (none) |
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* !!! /usr/lib64/R/library/RcppArmadillo/libs/RcppArmadillo.so not |
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owned by any package is broken !!! |
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* /usr/lib64/R/library/RcppArmadillo/libs/RcppArmadillo.so -> (none) |
| 113 |
* !!! /usr/lib64/R/library/robustbase/libs/robustbase.so not owned by |
| 114 |
any package is broken !!! |
| 115 |
* /usr/lib64/R/library/robustbase/libs/robustbase.so -> (none) |
| 116 |
* !!! /usr/lib64/R/library/rrcov/libs/rrcov.so not owned by any |
| 117 |
package is broken !!! |
| 118 |
* /usr/lib64/R/library/rrcov/libs/rrcov.so -> (none) |
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* Generated new 4_raw.rr and 4_owners.rr |
| 120 |
* Found some broken files, but none of them were associated with known |
| 121 |
packages |
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* Unable to proceed with automatic repairs. |
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* The broken files are listed in 4_owners.rr |
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|
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|
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mephisto ~ # emerge --info |
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Portage 2.2.24 (python 3.4.3-final-0, |
| 128 |
default/linux/amd64/13.0/desktop/gnome/systemd, gcc-4.9.3, |
| 129 |
glibc-2.22-r1, 4.0.0-gentoo x86_64) |
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================================================================= System |
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uname: |
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Linux-4.0.0-gentoo-x86_64-Intel-R-_Core-TM-_i7-5960X_CPU_@_3.00GHz-with-gentoo-2.2 |
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KiB Mem: 16346068 total, 5356644 free KiB Swap: 524284 total, 362228 |
| 134 |
free Timestamp of repository gentoo: Fri, 06 Nov 2015 07:00:01 +0000 sh |
| 135 |
bash 4.3_p42 ld GNU ld (Gentoo 2.25.1 p1.1) 2.25.1 app-shells/bash: |
| 136 |
4.3_p42::gentoo dev-java/java-config: 2.2.0::gentoo dev-lang/perl: |
| 137 |
5.22.0::gentoo dev-lang/python: 2.7.10::gentoo, 3.3.5-r2::gentoo, |
| 138 |
3.4.3::gentoo, 3.5.0-r1::gentoo dev-util/cmake: 3.3.2-r1::gentoo |
| 139 |
dev-util/pkgconfig: 0.29::gentoo sys-apps/baselayout: 2.2::gentoo |
| 140 |
sys-apps/openrc: 0.18.3::gentoo sys-apps/sandbox: 2.9::gentoo |
| 141 |
sys-devel/autoconf: 2.13::gentoo, 2.69-r1::gentoo sys-devel/automake: |
| 142 |
1.11.6-r1::gentoo, 1.13.4::gentoo, 1.14.1::gentoo, 1.15::gentoo |
| 143 |
sys-devel/binutils: 2.25.1-r1::gentoo sys-devel/gcc: 4.9.3::gentoo |
| 144 |
sys-devel/gcc-config: 1.8::gentoo sys-devel/libtool: 2.4.6-r1::gentoo |
| 145 |
sys-devel/make: 4.1-r1::gentoo sys-kernel/linux-headers: 4.3::gentoo |
| 146 |
(virtual/os-headers) sys-libs/glibc: 2.22-r1::gentoo Repositories: |
| 147 |
gentoo location: /usr/portage sync-type: rsync sync-uri: |
| 148 |
rsync://rsync.gentoo.org/gentoo-portage priority: -1000 local_overlay |
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location: /usr/local/portage masters: gentoo science location: |
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/var/lib/layman/science masters: gentoo priority: 50 |
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ACCEPT_KEYWORDS="amd64 ~amd64" ACCEPT_LICENSE="*" |
| 152 |
CBUILD="x86_64-pc-linux-gnu" CFLAGS="-march=native" |
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CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc |
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/usr/lib64/libreoffice/program/sofficerc /usr/share/gnupg/qualified.txt" |
| 155 |
CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/dconf /etc/env.d |
| 156 |
/etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/revdep-rebuild |
| 157 |
/etc/sandbox.d /etc/terminfo /etc/texmf/language.dat.d |
| 158 |
/etc/texmf/language.def.d /etc/texmf/updmap.d /etc/texmf/web2c" |
| 159 |
CXXFLAGS="-march=native" DISTDIR="/usr/portage/distfiles" FCFLAGS="-O2 |
| 160 |
-pipe" FEATURES="assume-digests binpkg-logs config-protect-if-modified |
| 161 |
distlocks ebuild-locks fixlafiles merge-sync news parallel-fetch |
| 162 |
preserve-libs sandbox sfperms strict unknown-features-warn unmerge-logs |
| 163 |
unmerge-orphans userfetch userpriv usersandbox usersync xattr" |
| 164 |
FFLAGS="-O2 -pipe" |
| 165 |
GENTOO_MIRRORS="ftp://ftp.las.ic.unicamp.br/pub/gentoo/ |
| 166 |
http://www.las.ic.unicamp.br/pub/gentoo/ |
| 167 |
ftp://ftp.ussg.iu.edu/pub/linux/gentoo |
| 168 |
ftp://mirror.iawnet.sandia.gov/pub/gentoo/" LANG="pt_BR.utf8" |
| 169 |
LDFLAGS="-Wl,--as-needed" PKGDIR="/usr/portage/packages" |
| 170 |
PORTAGE_CONFIGROOT="/" PORTAGE_RSYNC_OPTS="--recursive --links |
| 171 |
--safe-links --perms --times --omit-dir-times --compress --force |
| 172 |
--whole-file --delete --stats --human-readable --timeout=180 |
| 173 |
--exclude=/distfiles --exclude=/local --exclude=/packages" |
| 174 |
PORTAGE_TMPDIR="/var/tmp" USE="X a52 aac acl acpi alsa amd64 berkdb |
| 175 |
bluetooth branding bzip2 cairo cdda cdr cli colord cracklib crypt cups |
| 176 |
cxx dbus dri dts dvd dvdr eds emboss encode evo exif fam firefox flac |
| 177 |
fortran gdbm gif glamor gnome gnome-keyring gnome-online-accounts gpm |
| 178 |
gstreamer gtk iconv introspection ipv6 jpeg lcms ldap libnotify |
| 179 |
libsecret mad mmx mmxext mng modules mp3 mp4 mpeg multilib nautilus |
| 180 |
ncurses nls nptl ogg opengl openmp pam pango pcre pdf png policykit ppds |
| 181 |
pulseaudio qt3support readline sdl seccomp session spell sse sse2 ssl |
| 182 |
startup-notification svg systemd tcpd tiff tracker truetype udev udisks |
| 183 |
unicode upower usb uvm vorbis wxwidgets x264 xattr xcb xml xv xvid zlib" |
| 184 |
ABI_X86="64 32" ALSA_CARDS="ali5451 als4000 atiixp atiixp-modem bt87x |
| 185 |
ca0106 cmipci emu10k1x ens1370 ens1371 es1938 es1968 fm801 hda-intel |
| 186 |
intel8x0 intel8x0m maestro3 trident usb-audio via82xx via82xx-modem |
| 187 |
ymfpci" APACHE2_MODULES="authn_core authz_core socache_shmcb unixd |
| 188 |
actions alias auth_basic authn_alias authn_anon authn_dbm authn_default |
| 189 |
authn_file authz_dbm authz_default authz_groupfile authz_host |
| 190 |
authz_owner authz_user autoindex cache cgi cgid dav dav_fs dav_lock |
| 191 |
deflate dir disk_cache env expires ext_filter file_cache filter headers |
| 192 |
include info log_config logio mem_cache mime mime_magic negotiation |
| 193 |
rewrite setenvif speling status unique_id userdir usertrack vhost_alias" |
| 194 |
CALLIGRA_FEATURES="kexi words flow plan sheets stage tables krita karbon |
| 195 |
braindump author" CAMERAS="ptp2" COLLECTD_PLUGINS="df interface irq load |
| 196 |
memory rrdtool swap syslog" CPU_FLAGS_X86="mmx mmxext sse sse2" |
| 197 |
ELIBC="glibc" GPSD_PROTOCOLS="ashtech aivdm earthmate evermore fv18 |
| 198 |
garmin garmintxt gpsclock itrax mtk3301 nmea ntrip navcom oceanserver |
| 199 |
oldstyle oncore rtcm104v2 rtcm104v3 sirf superstar2 timing tsip tripmate |
| 200 |
tnt ublox ubx" GRUB_PLATFORMS="efi-64" INPUT_DEVICES="evdev" |
| 201 |
KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 |
| 202 |
lcdm001 mtxorb ncurses text" LIBREOFFICE_EXTENSIONS="presenter-console |
| 203 |
presenter-minimizer" LINGUAS="pt_BR en" |
| 204 |
OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php5-5" |
| 205 |
PYTHON_SINGLE_TARGET="python2_7" PYTHON_TARGETS="python2_7 python3_4" |
| 206 |
RUBY_TARGETS="ruby20 ruby21" USERLAND="GNU" VIDEO_CARDS="nvidia" |
| 207 |
XTABLES_ADDONS="quota2 psd pknock lscan length2 ipv4options ipset ipp2p |
| 208 |
iface geoip fuzzy condition tee tarpit sysrq steal rawnat logmark ipmark |
| 209 |
dhcpmac delude chaos account" Unset: CC, CPPFLAGS, CTARGET, CXX, |
| 210 |
EMERGE_DEFAULT_OPTS, INSTALL_MASK, LC_ALL, MAKEOPTS, |
| 211 |
PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, |
| 212 |
PORTAGE_RSYNC_EXTRA_OPTS, USE_PYTHON |
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