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:computer: Instructions, tips and issue tracker for the software on the EBI computing cluster
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Update February 2019 #76

Closed lafita closed 5 years ago

lafita commented 5 years ago

We have not updated the software in a while, so I am planning to run periodical updates every month starting this Friday (1st February).

This is the long list of anticipated changes on the EBI cluster (will post the Yoda ones soon):

[ebuild     U  ] app-arch/bzip2-1.0.6-r10:0/1::gentoo [1.0.6-r8:0/1::gentoo] USE="-static -static-libs" 0 KiB
[ebuild     U  ] sys-devel/patch-2.7.6-r2::gentoo [2.7.6-r1::gentoo] USE="-static {-test} -xattr" 0 KiB
[ebuild  N     ] dev-java/byaccj-1.15-r1::gentoo  53 KiB
[ebuild  N     ] dev-util/gperf-3.1::gentoo  1,188 KiB
[ebuild     U  ] virtual/os-headers-0-r1::gentoo [0::gentoo] 0 KiB
[ebuild     U  ] net-dns/libidn2-2.1.0:0/4.0.0::gentoo [2.0.4:0/0::gentoo] USE="-static-libs" 2,054 KiB
[ebuild     U  ] sys-libs/glibc-2.28-r5:2.2::gentoo [2.26-r6:2.2::gentoo] USE="multiarch%* -audit -caps (-cet) (-compile-locales) -doc -gd -headers-only (-multilib) -nscd -profile (-selinux) -suid -systemtap {-test%} (-vanilla) (-debug%) (-hardened%)" 16,194 KiB
[ebuild     U  ] app-arch/gzip-1.10::gentoo [1.9::gentoo] USE="-pic -static" 757 KiB
[ebuild     U  ] sys-apps/less-548::gentoo [530::gentoo] USE="pcre unicode" 339 KiB
[ebuild     U  ] sys-apps/baselayout-2.6-r1::gentoo [2.4.1-r2::gentoo] USE="split-usr%* -build" 32 KiB
[ebuild     U  ] app-arch/xz-utils-5.2.4-r2::gentoo [5.2.3::gentoo] USE="extra-filters nls threads -static-libs" 1,536 KiB
[ebuild     U  ] sys-apps/file-5.35::gentoo [5.32::gentoo] USE="zlib -python -static-libs" PYTHON_TARGETS="python2_7 python3_6* -pypy -python3_4 -python3_5* -python3_7%" 846 KiB
[ebuild     U  ] sys-apps/coreutils-8.30::gentoo [8.29::gentoo] USE="acl nls split-usr%* -caps -gmp -hostname -kill -multicall (-selinux) -static {-test} -vanilla -xattr" 5,240 KiB
[ebuild     U  ] sys-apps/net-tools-1.60_p20180626073013::gentoo [1.60_p20170221182432::gentoo] USE="arp hostname ipv6 nls -nis -plipconfig (-selinux) -slattach -static" 223 KiB
[ebuild     U  ] sci-libs/htslib-1.9:0/2::gentoo [1.5:0/2::gentoo] USE="bzip2 lzma -curl -static-libs" 1,152 KiB
[ebuild     U  ] sys-libs/readline-8.0:0/8::gentoo [7.0_p3:0/7::gentoo] USE="-static-libs -utils" 2,907 KiB
[ebuild     U  ] sys-process/procps-3.3.15-r1:0/6::gentoo [3.3.12-r1:0/5::gentoo] USE="kill ncurses nls unicode -elogind -modern-top (-selinux) -static-libs -systemd {-test}" 884 KiB
[ebuild     U  ] sys-process/htop-2.2.0::gentoo [2.1.0-r1::gentoo] USE="unicode -openvz -vserver" PYTHON_SINGLE_TARGET="python3_6* -python2_7 -python3_4 -python3_5* -python3_7%" PYTHON_TARGETS="python2_7 python3_6* -python3_4 -python3_5* -python3_7%" 301 KiB
[ebuild     U  ] app-shells/bash-5.0_p2::gentoo [4.4_p19::gentoo] USE="net nls (readline) -afs -bashlogger -examples -mem-scramble -plugins" 9,906 KiB
[ebuild     U  ] app-shells/bash-completion-2.8::gentoo [2.7-r2::gentoo] USE="{-test}" 280 KiB
[ebuild     U  ] sys-devel/make-4.2.1-r4::gentoo [4.2.1-r2::gentoo] USE="nls -guile -static" 0 KiB
[ebuild     U  ] sys-apps/sed-4.7::gentoo [4.4::gentoo] USE="acl nls -forced-sandbox% (-selinux) -static" 1,268 KiB
[ebuild     U  ] sys-apps/util-linux-2.33.1::gentoo [2.31.1::gentoo] USE="cramfs ncurses nls readline suid unicode -build -caps -fdformat -kill (-pam) -python (-selinux) -slang -static-libs -systemd {-test} -tty-helpers (-udev)" PYTHON_SINGLE_TARGET="(-python2_7%) (-python3_4%) (-python3_5%*) (-python3_6%)" PYTHON_TARGETS="python2_7 python3_6* -python3_4 -python3_5* -python3_7%" 4,542 KiB
[ebuild     U  ] app-arch/tar-1.31-r1::gentoo [1.30::gentoo] USE="acl nls -minimal (-selinux) -static -xattr" 2,877 KiB
[ebuild  NS    ] sys-devel/binutils-2.31.1-r3:2.31::gentoo [2.30:2.30::gentoo] USE="cxx nls -doc -multitarget -static-libs {-test}" 20,053 KiB
[ebuild     U  ] sys-apps/gawk-4.2.1-r1::gentoo [4.2.1::gentoo] USE="nls readline -forced-sandbox% -mpfr" 0 KiB
[ebuild     U  ] sys-apps/grep-3.3-r1::gentoo [3.1::gentoo] USE="nls pcre -static" 1,439 KiB
[ebuild     U  ] sys-apps/diffutils-3.7::gentoo [3.6::gentoo] USE="nls -static" 1,415 KiB
[ebuild     U  ] net-misc/wget-1.20.1::gentoo [1.19.4::gentoo] USE="ipv6 nls pcre ssl zlib -debug -gnutls -idn -libressl -ntlm -static {-test} -uuid" 4,290 KiB
[ebuild  NS    ] sys-devel/gcc-8.2.0-r6:8.2.0::gentoo [5.4.0-r4:5.4.0::gentoo, 7.3.0:7.3.0::gentoo] USE="cxx fortran nls nptl openmp pch (pie) sanitize ssp vtv (-altivec) -debug -doc (-fixed-point) -go -graphite (-hardened) (-jit) (-libssp) -mpx (-multilib) -objc -objc++ -objc-gc -pgo -regression-test -systemtap (-vanilla)" 61,992 KiB
[ebuild     U  ] app-shells/fish-3.0.0-r1::gentoo [2.7.1::gentoo] USE="nls -doc% {-test}" 6,321 KiB
[ebuild     U  ] sys-libs/libomp-7.0.1::gentoo [5.0.1::gentoo] USE="-cuda% -hwloc -offload% -ompt {-test}" 889 KiB
[ebuild  N     ] dev-perl/TimeDate-2.300.0::gentoo  31 KiB
[ebuild     U  ] sci-biology/bwa-0.7.17::science [0.7.16a::gentoo] 187 KiB
[ebuild  N     ] dev-perl/MailTools-2.190.0::gentoo  USE="-examples {-test}" 55 KiB
[ebuild     U  ] sys-process/parallel-20190122::gentoo [20180222::gentoo] 1,752 KiB
[ebuild     U  ] app-admin/eselect-1.4.13-r101::science [1.4.10-r100::science] USE="-doc -emacs -vim-syntax" 174 KiB
[ebuild     U  ] sys-process/psmisc-23.2-r1::gentoo [23.1::gentoo] USE="ipv6 nls -X (-selinux)" 297 KiB
[ebuild  N     ] net-libs/libtirpc-1.1.4:0/3::gentoo  USE="ipv6 -kerberos -static-libs" 508 KiB
[ebuild     U  ] net-libs/zeromq-4.3.1:0/5::gentoo [4.2.3:0/5::gentoo] USE="drafts%* sodium -doc -pgm -static-libs {-test} -unwind" 1,456 KiB
[ebuild     U  ] app-misc/tmux-2.8::gentoo [2.6::gentoo] USE="-debug (-selinux) -utempter -vim-syntax" 623 KiB
[ebuild     U  ] app-portage/eix-0.33.6::gentoo [0.33.2::gentoo] USE="nls -debug -doc -sqlite" 611 KiB
[ebuild     U  ] sci-libs/blas-reference-20171112-r100:0/3.8.0::science [20161223-r100:0/3.7.0::science] USE="-int64 -static-libs {-test}" 7,253 KiB
[ebuild   R    ] dev-lang/python-3.6.6:3.6/3.6m::gentoo  USE="gdbm ipv6 ncurses readline sqlite* ssl (threads) xml -bluetooth -build -examples -hardened -libressl {-test} -tk -wininst" 0 KiB
[ebuild     U  ] sci-libs/lapack-reference-3.8.0-r100:0/3.8.0::science [3.7.0-r100:0/3.7.0::science] USE="deprecated -int64 -static-libs {-test} -xblas" 0 KiB
[ebuild     U  ] media-libs/fontconfig-2.13.1-r2:1.0::gentoo [2.13.0-r4:1.0::gentoo] USE="-doc -static-libs" 1,684 KiB
[ebuild  N     ] dev-java/javatoolkit-0.3.0-r9::gentoo  PYTHON_TARGETS="python2_7" 17 KiB
[ebuild  NS    ] sys-devel/llvm-7.0.1:7::gentoo [5.0.1:5::gentoo] USE="libffi ncurses -debug -doc -exegesis -gold -libedit {-test} -xar -xml" LLVM_TARGETS="AMDGPU BPF NVPTX (X86) -AArch64 -ARM -Hexagon -Lanai -MSP430 -Mips -PowerPC -Sparc -SystemZ -XCore" 27,766 KiB
[ebuild   R    ] dev-python/ipython_genutils-0.2.0::gentoo  USE="{-test}" PYTHON_TARGETS="python2_7 python3_6* -python3_4 -python3_5* -python3_7%" 0 KiB
[ebuild   R    ] dev-python/ptyprocess-0.5.2::gentoo  USE="{-test}" PYTHON_TARGETS="python2_7 python3_6* -pypy -pypy3 -python3_4 -python3_5* -python3_7%" 0 KiB
[ebuild     U  ] dev-vcs/git-2.20.1::gentoo [2.16.2::gentoo] USE="blksha1 curl gpg iconv nls pcre pcre-jit perl python threads webdav -cgi -cvs -doc -emacs -gnome-keyring -highlight -libressl -mediawiki -mediawiki-experimental (-ppcsha1) -subversion {-test} -tk -xinetd" PYTHON_TARGETS="python2_7" 5,664 KiB
[ebuild     U  ] dev-python/pycurl-7.43.0.2::gentoo [7.43.0::gentoo] USE="ssl -examples {-test}" CURL_SSL="openssl -gnutls -libressl -nss" PYTHON_TARGETS="python2_7 python3_6* -python3_4 -python3_5* -python3_7%" 210 KiB
[ebuild   R    ] dev-python/testpath-0.3.1::gentoo  USE="-doc {-test}" PYTHON_TARGETS="python2_7 python3_6* -pypy% -pypy3% -python3_4 -python3_5* -python3_7%" 0 KiB
[ebuild   R    ] dev-python/pandocfilters-1.4.2-r1::gentoo  PYTHON_TARGETS="python2_7 python3_6* -python3_4 -python3_5* -python3_7%" 0 KiB
[ebuild   R    ] dev-python/strict-rfc3339-0.7::gentoo  PYTHON_TARGETS="python2_7 python3_6* -pypy -pypy3 -python3_4 -python3_5* -python3_7%" 0 KiB
[ebuild     U  ] dev-python/regex-2017.04.05-r1::gentoo [2017.04.05::gentoo] USE="-doc" PYTHON_TARGETS="python2_7 python3_6* -pypy -pypy3% -python3_4 -python3_5* -python3_7%" 0 KiB
[ebuild   R    ] dev-python/appdirs-1.4.3::gentoo  PYTHON_TARGETS="python2_7 python3_6* -pypy -pypy3 -python3_4 -python3_5* -python3_7%" 0 KiB
[ebuild     U  ] dev-python/olefile-0.46::gentoo [0.44::gentoo] USE="-doc" PYTHON_TARGETS="python2_7 python3_6* -pypy% -pypy3% -python3_4 -python3_5* -python3_7%" 96 KiB
[ebuild     U  ] dev-python/pyyaml-3.13::gentoo [3.12::gentoo] USE="-examples -libyaml" PYTHON_TARGETS="python2_7 python3_6* -pypy -pypy3 -python3_4 -python3_5* -python3_7%" 265 KiB
[ebuild     U  ] sci-biology/samtools-1.9::gentoo [1.5::gentoo] USE="-examples" PYTHON_TARGETS="python2_7" 4,337 KiB
[ebuild  N     ] virtual/python-typing-0-r1::gentoo  PYTHON_TARGETS="python2_7 python3_6 -pypy -pypy3 -python3_4 -python3_5 -python3_7" 0 KiB
[ebuild     U  ] dev-python/pexpect-4.6.0::gentoo [4.2.1::gentoo] USE="-doc -examples {-test}" PYTHON_TARGETS="python2_7 python3_6* -pypy -pypy3 -python3_4 -python3_5* -python3_7%" 146 KiB
[ebuild   R    ] virtual/python-backports_abc-0::gentoo  PYTHON_TARGETS="python2_7 python3_6* -pypy -python3_4 -python3_5* -python3_7%" 0 KiB
[ebuild   R    ] virtual/python-pathlib-1.0::gentoo  PYTHON_TARGETS="python2_7 python3_6* -pypy -pypy3 -python3_4 -python3_5* -python3_7%" 0 KiB
[ebuild     U  ] virtual/python-funcsigs-2::gentoo [1::gentoo] PYTHON_TARGETS="python2_7 python3_6* -pypy -pypy3 -python3_4 -python3_5* -python3_7%" 0 KiB
[ebuild   R    ] virtual/python-enum34-1::gentoo  PYTHON_TARGETS="python2_7 python3_6* -pypy -pypy3 -python3_4 -python3_5* -python3_7%" 0 KiB
[ebuild     U  ] virtual/python-futures-1::gentoo [0::gentoo] PYTHON_TARGETS="python2_7 python3_6* -pypy -pypy3% -python3_4 -python3_5* -python3_7%" 0 KiB
[ebuild   R    ] virtual/python-ipaddress-1.0-r1::gentoo  PYTHON_TARGETS="python2_7 python3_6* -pypy -pypy3 -python3_4 -python3_5* -python3_7%" 0 KiB
[ebuild   R    ] dev-python/entrypoints-0.2.3::gentoo  USE="-doc {-test}" PYTHON_TARGETS="python2_7 python3_6* -pypy% -pypy3% -python3_4 -python3_5* -python3_7%" 0 KiB
[ebuild  NSF   ] dev-java/oracle-jdk-bin-11.0.2:11::gentoo [9.0.4-r2:9::gentoo] USE="fontconfig -alsa -commercial (-cups) -doc (-gentoo-vm) -gtk2 -gtk3 -headless-awt -javafx -nsplugin (-selinux) -source" 175,431 KiB
[ebuild     U  ] app-editors/vim-core-8.1.0648::gentoo [8.0.1428::gentoo] USE="acl nls -minimal" 13,733 KiB
[ebuild     U  ] app-editors/vim-8.1.0648-r1::gentoo [8.0.1428::gentoo] USE="X acl nls python -cscope -debug (-gpm) -lua -luajit -minimal -perl -racket -ruby (-selinux) -tcl -terminal -vim-pager" PYTHON_SINGLE_TARGET="python3_6* -python2_7 -python3_4 -python3_5* -python3_7%" PYTHON_TARGETS="python2_7 python3_5 python3_6* -python3_4 -python3_7%" 0 KiB
[ebuild     U  ] virtual/editor-0-r2::gentoo [0::gentoo] 0 KiB
[ebuild     U  ] dev-python/setuptools-40.7.1::gentoo [38.5.1::gentoo] USE="{-test}" PYTHON_TARGETS="python2_7 python3_6* -pypy -pypy3 -python3_4 -python3_5* -python3_7%" 824 KiB
[ebuild     U  ] dev-python/certifi-2018.11.29::gentoo [2017.11.5::gentoo] PYTHON_TARGETS="python2_7 python3_6* -pypy -pypy3 -python3_4 -python3_5* -python3_7%" 151 KiB
[ebuild     U  ] dev-python/six-1.12.0::gentoo [1.11.0::gentoo] USE="-doc {-test}" PYTHON_TARGETS="python2_7 python3_6* -pypy -pypy3 -python3_4 -python3_5* -python3_7%" 32 KiB
[ebuild     U  ] dev-python/numpy-1.15.4::gentoo [1.13.3::gentoo] USE="lapack -doc {-test}" PYTHON_TARGETS="python2_7 python3_6* -python3_4 -python3_5* -python3_7%" 4,369 KiB
[ebuild     U  ] dev-python/cython-0.29.3::gentoo [0.26.1::gentoo] USE="-doc -emacs {-test}" PYTHON_TARGETS="python2_7 python3_6* -python3_4 -python3_5* -python3_7%" 1,995 KiB
[ebuild     U  ] dev-python/idna-2.8::gentoo [2.6::gentoo] PYTHON_TARGETS="python2_7 python3_6* -pypy -pypy3 -python3_4 -python3_5* -python3_7%" 171 KiB
[ebuild     U  ] dev-python/setuptools_scm-3.2.0::gentoo [1.15.6-r1::gentoo] USE="{-test} (-git%) (-mercurial%)" PYTHON_TARGETS="python2_7 python3_6* -pypy -pypy3 -python3_4 -python3_5* -python3_7%" 39 KiB
[ebuild     U  ] dev-python/decorator-4.3.0::gentoo [4.2.1::gentoo] USE="-doc" PYTHON_TARGETS="python2_7 python3_6* -pypy -pypy3 -python3_4 -python3_5* -python3_7%" 33 KiB
[ebuild     U  ] dev-python/pyparsing-2.3.0::gentoo [2.2.0::gentoo] USE="-examples (-doc%)" PYTHON_TARGETS="python2_7 python3_6* -pypy -pypy3 -python3_4 -python3_5* -python3_7%" 610 KiB
[ebuild     U  ] dev-python/pytz-2018.4::gentoo [2017.2::gentoo] PYTHON_TARGETS="python2_7 python3_6* -pypy -pypy3 -python3_4 -python3_5* -python3_7%" 301 KiB
[ebuild     U  ] dev-python/pyasn1-0.4.2::gentoo [0.3.7::gentoo] USE="-doc" PYTHON_TARGETS="python2_7 python3_6* -pypy -pypy3 -python3_4 -python3_5* -python3_7%" 116 KiB
[ebuild     U  ] dev-python/pygments-2.3.1::gentoo [2.2.0::gentoo] USE="-doc {-test}" PYTHON_TARGETS="python2_7 python3_6* -pypy -pypy3 -python3_4 -python3_5* -python3_7%" 3,051 KiB
[ebuild     U  ] dev-util/meson-0.49.1::gentoo [0.44.1::gentoo] USE="{-test%}" PYTHON_TARGETS="python3_6* -python3_5* -python3_7% (-python3_4%)" 1,310 KiB
[ebuild  N     ] dev-python/kiwisolver-1.0.1::gentoo  PYTHON_TARGETS="python2_7 python3_6 -python3_4 -python3_5 -python3_7" 34 KiB
[ebuild   R    ] dev-python/versioneer-0.16::gentoo  PYTHON_TARGETS="python2_7 python3_6* -pypy -python3_4 -python3_5* -python3_7%" 0 KiB
[ebuild   R    ] dev-python/chardet-3.0.4::gentoo  USE="{-test}" PYTHON_TARGETS="python2_7 python3_6* -pypy -pypy3 -python3_4 -python3_5* -python3_7%" 0 KiB
[ebuild   R    ] dev-python/asn1crypto-0.24.0::gentoo  USE="{-test}" PYTHON_TARGETS="python2_7 python3_6* -pypy -pypy3 -python3_4 -python3_5* -python3_7%" 0 KiB
[ebuild   R    ] dev-python/ply-3.11:0/3.11::gentoo  USE="-examples" PYTHON_TARGETS="python2_7 python3_6* -pypy -pypy3 -python3_4 -python3_5* -python3_7%" 0 KiB
[ebuild     U  ] dev-python/PySocks-1.6.8::gentoo [1.6.7::gentoo] USE="{-test%}" PYTHON_TARGETS="python2_7 python3_6* -pypy -pypy3 -python3_4 -python3_5* -python3_7%" 277 KiB
[ebuild   R    ] dev-python/simplegeneric-0.8.1-r1::gentoo  PYTHON_TARGETS="python2_7 python3_6* -pypy -python3_4 -python3_5* -python3_7%" 0 KiB
[ebuild   R    ] dev-python/incremental-17.5.0::gentoo  PYTHON_TARGETS="python2_7 python3_6* -pypy -python3_4 -python3_5* -python3_7%" 0 KiB
[ebuild   R    ] dev-python/constantly-15.1.0-r1::gentoo  USE="{-test}" PYTHON_TARGETS="python2_7 python3_6* -python3_4 -python3_5* -python3_7%" 0 KiB
[ebuild   R    ] dev-python/namespace-zope-1::gentoo  PYTHON_TARGETS="python2_7 python3_6* -pypy -pypy3 -python3_4 -python3_5* -python3_7%" 0 KiB
[ebuild  N     ] dev-python/send2trash-1.5.0::gentoo  PYTHON_TARGETS="python2_7 python3_6 -pypy -python3_5 -python3_7" 11 KiB
[ebuild     U  ] dev-python/markupsafe-1.0::gentoo [0.23::gentoo] PYTHON_TARGETS="python2_7 python3_6* -pypy -pypy3 -python3_4 -python3_5* -python3_7%" 15 KiB
[ebuild   R    ] dev-python/webencodings-0.5.1::gentoo  USE="{-test}" PYTHON_TARGETS="python2_7 python3_6* -pypy -pypy3 -python3_4 -python3_5* -python3_7%" 0 KiB
[ebuild     U  ] dev-python/rfc3987-1.3.8::gentoo [1.3.7::gentoo] PYTHON_TARGETS="python2_7 python3_6* -pypy -pypy3 -python3_4 -python3_5* -python3_7%" 21 KiB
[ebuild     U  ] dev-python/webcolors-1.8.1::gentoo [1.5::gentoo] USE="{-test}" PYTHON_TARGETS="python2_7 python3_6* -pypy -pypy3 -python3_4 -python3_5* -python3_7%" 33 KiB
[ebuild   R    ] dev-python/vcversioner-2.16.0.0::gentoo  USE="{-test}" PYTHON_TARGETS="python2_7 python3_6* -pypy -pypy3 -python3_4 -python3_5* -python3_7%" 0 KiB
[ebuild     U  ] dev-python/parso-0.3.1::gentoo [0.1.1::gentoo] USE="-doc {-test}" PYTHON_TARGETS="python2_7 python3_6* -python3_4 -python3_5* -python3_7%" 367 KiB
[ebuild     U  ] dev-python/path-py-11.0.1::gentoo [10.3.1::gentoo] USE="{-test}" PYTHON_TARGETS="python2_7 python3_6* -pypy -pypy3 -python3_4 -python3_5* -python3_7%" 38 KiB
[ebuild   R    ] dev-python/wcwidth-0.1.7-r1::gentoo  USE="{-test}" PYTHON_TARGETS="python2_7 python3_6* -python3_4 -python3_5* -python3_7%" 0 KiB
[ebuild     U  ] dev-python/pillow-5.4.1::gentoo [4.3.0::gentoo] USE="zlib -doc -examples -imagequant -jpeg% -jpeg2k -lcms {-test} -tiff -tk -truetype -webp" PYTHON_TARGETS="python2_7 python3_6* -pypy% -python3_4 -python3_5* -python3_7%" 15,430 KiB
[ebuild     U  ] dev-python/pip-10.0.1::gentoo [9.0.1-r2::gentoo] USE="-vanilla" PYTHON_TARGETS="python2_7 python3_6* -pypy -pypy3 -python3_4 -python3_5* -python3_7%" 1,217 KiB
[ebuild   R    ] dev-python/traitlets-4.3.2::gentoo  USE="-doc {-test}" PYTHON_TARGETS="python2_7 python3_6* -python3_4 -python3_5* -python3_7%" 0 KiB
[ebuild     U  ] sci-libs/scipy-1.1.0::gentoo [1.0.0::gentoo] USE="-doc -sparse {-test}" PYTHON_TARGETS="python2_7 python3_6* -python3_4 -python3_5* -python3_7%" 15,219 KiB
[ebuild     U  ] dev-python/python-dateutil-2.7.5::gentoo [2.6.1::gentoo] USE="{-test%}" PYTHON_TARGETS="python2_7 python3_6* -pypy -pypy3 -python3_4 -python3_5* -python3_7%" 309 KiB
[ebuild     U  ] dev-python/zope-interface-4.6.0::gentoo [4.4.3::gentoo] USE="{-test}" PYTHON_TARGETS="python2_7 python3_6* -pypy -pypy3 -python3_4 -python3_5* -python3_7%" 148 KiB
[ebuild     U  ] dev-python/mistune-0.8.3::gentoo [0.7.4::gentoo] USE="{-test}" PYTHON_TARGETS="python2_7 python3_6* -pypy -pypy3 -python3_4 -python3_5* -python3_7%" 58 KiB
[ebuild   R    ] dev-python/docutils-0.14::gentoo  PYTHON_TARGETS="python2_7 python3_6* -pypy -pypy3 -python3_4 -python3_5* -python3_7%" 0 KiB
[ebuild   R    ] dev-python/jinja-2.10::gentoo  USE="-doc -examples {-test}" PYTHON_TARGETS="python2_7 python3_6* -pypy -pypy3 -python3_4 -python3_5* -python3_7%" 0 KiB
[ebuild     U  ] x11-libs/libdrm-2.4.97::gentoo [2.4.90::gentoo] USE="-libkms -valgrind (-static-libs%)" VIDEO_CARDS="amdgpu intel nouveau radeon (-exynos) (-freedreno) (-omap) (-tegra) (-vc4) (-vivante) -vmware" 818 KiB
[ebuild   R    ] dev-python/cycler-0.10.0::gentoo  USE="{-test}" PYTHON_TARGETS="python2_7 python3_6* -python3_4 -python3_5* -python3_7%" 0 KiB
[ebuild     U  ] dev-python/pycparser-2.19::gentoo [2.18-r1::gentoo] USE="{-test}" PYTHON_TARGETS="python2_7 python3_6* -pypy -pypy3 -python3_4 -python3_5* -python3_7%" 155 KiB
[ebuild     U  ] dev-python/llvmlite-0.27.0::gentoo [0.22.0::gentoo] USE="-examples" PYTHON_TARGETS="python2_7 python3_6* -python3_4 -python3_5* -python3_7%" 183 KiB
[ebuild     U  ] dev-python/numexpr-2.6.8::gentoo [2.6.2::gentoo] USE="(-mkl)" PYTHON_TARGETS="python2_7 python3_6* -python3_4 -python3_5* -python3_7%" 93 KiB
[ebuild   R    ] dev-python/prompt_toolkit-1.0.15::gentoo  USE="{-test}" PYTHON_TARGETS="python2_7 python3_6* -python3_4 -python3_5* -python3_7%" 0 KiB
[ebuild   R    ] dev-python/pickleshare-0.7.4-r1::gentoo  USE="{-test}" PYTHON_TARGETS="python2_7 python3_6* -python3_4 -python3_5* -python3_7%" 0 KiB
[ebuild     U  ] dev-python/jedi-0.12.1::gentoo [0.11.1::gentoo] USE="-doc {-test}" PYTHON_TARGETS="python2_7 python3_6* -python3_4 -python3_5* -python3_7%" 349 KiB
[ebuild     U  ] dev-python/py-1.5.4::gentoo [1.5.2::gentoo] USE="-doc {-test}" PYTHON_TARGETS="python2_7 python3_6* -pypy -pypy3 -python3_4 -python3_5* -python3_7%" 197 KiB
[ebuild     U  ] dev-python/hyperlink-18.0.0::gentoo [17.3.1::gentoo] USE="{-test}" PYTHON_TARGETS="python2_7 python3_6* -pypy -python3_4 -python3_5* -python3_7%" 96 KiB
[ebuild  N     ] dev-python/pyhamcrest-1.9.0-r1::gentoo  USE="-doc -examples {-test}" PYTHON_TARGETS="python2_7 python3_6 -python3_4 -python3_5 -python3_7" 57 KiB
[ebuild     U  ] dev-python/pyasn1-modules-0.2.1::gentoo [0.1.5::gentoo] USE="{-test}" PYTHON_TARGETS="python2_7 python3_6* -pypy -pypy3 -python3_4 -python3_5* -python3_7%" 65 KiB
[ebuild     U  ] dev-python/bleach-3.1.0::gentoo [2.1.1::gentoo] USE="{-test}" PYTHON_TARGETS="python2_7 python3_6* -pypy -pypy3 -python3_4 -python3_5* -python3_7%" 164 KiB
[ebuild   R    ] dev-python/jsonschema-2.6.0::gentoo  USE="{-test}" PYTHON_TARGETS="python2_7 python3_6* -pypy -pypy3 -python3_4 -python3_5* -python3_7%" 0 KiB
[ebuild     U  ] dev-python/lxml-4.3.0::gentoo [4.2.0::gentoo] USE="threads -doc -examples {-test}" PYTHON_TARGETS="python2_7 python3_6* -pypy -python3_4 -python3_5* -python3_7%" 2,425 KiB
[ebuild   R    ] dev-python/jupyter_core-4.4.0::gentoo  USE="-doc {-test}" PYTHON_TARGETS="python2_7 python3_6* -python3_4 -python3_5* -python3_7%" 0 KiB
[ebuild     U  ] dev-python/attrs-18.2.0::gentoo [17.4.0::gentoo] USE="{-test}" PYTHON_TARGETS="python2_7 python3_6* -pypy -pypy3 -python3_4 -python3_5* -python3_7%" 115 KiB
[ebuild     U  ] dev-python/cffi-1.11.5:0/1.11.5::gentoo [1.11.4:0/1.11.4::gentoo] USE="-doc {-test}" PYTHON_TARGETS="python2_7 python3_6* -python3_4 -python3_5* -python3_7%" 429 KiB
[ebuild   R    ] dev-python/patsy-0.4.1::gentoo  USE="-doc {-test}" PYTHON_TARGETS="python2_7 python3_6* -python3_4 -python3_5*" 0 KiB
[ebuild   R    ] virtual/python-singledispatch-0::gentoo  PYTHON_TARGETS="python2_7 python3_6* -pypy -python3_4 -python3_5* -python3_7%" 0 KiB
[ebuild     U  ] dev-python/matplotlib-2.2.2-r1::gentoo [2.1.2-r1::gentoo] USE="-cairo -doc -examples -excel -gtk2 -gtk3 -latex -qt5 {-test} -tk -wxwidgets (-pyside%)" PYTHON_TARGETS="python2_7 python3_6* -python3_4 -python3_5* -python3_7%" 36,443 KiB
[ebuild     U  ] dev-python/bottleneck-1.2.1::gentoo [1.0.0::gentoo] USE="{-test%}" PYTHON_TARGETS="python2_7 python3_6* -python3_4 -python3_5*" 97 KiB
[ebuild     U  ] dev-python/m2r-0.1.14::gentoo [0.1.12::gentoo] USE="{-test}" PYTHON_TARGETS="python2_7 python3_6* -pypy -python3_4 -python3_5* -python3_7%" 16 KiB
[ebuild     U  ] dev-python/cryptography-2.4.2::gentoo [2.1.4::gentoo] USE="-libressl {-test}" PYTHON_TARGETS="python2_7 python3_6* -pypy -pypy3 -python3_4 -python3_5* -python3_7%" 458 KiB
[ebuild     U  ] dev-python/pyzmq-17.1.0::gentoo [16.0.2::gentoo] USE="-doc {-test}" PYTHON_TARGETS="python2_7 python3_6* -python3_4 -python3_5* -python3_7%" 1,058 KiB
[ebuild     U  ] dev-python/pandas-0.23.4::gentoo [0.20.3::gentoo] USE="-X -doc -full-support -minimal {-test}" PYTHON_TARGETS="python2_7 python3_6* -python3_5* (-python3_4%)" 10,245 KiB
[ebuild   R    ] dev-python/nbformat-4.4.0::gentoo  USE="-doc {-test}" PYTHON_TARGETS="python2_7 python3_6* -python3_4 -python3_5* -python3_7%" 0 KiB
[ebuild     U  ] dev-python/automat-0.7.0::gentoo [0.6.0::gentoo] USE="-examples {-test}" PYTHON_TARGETS="python2_7 python3_6* -pypy -python3_4 -python3_5* -python3_7%" 61 KiB
[ebuild     U  ] dev-python/numba-0.39.0::gentoo [0.35.0::gentoo] USE="-examples {-test}" PYTHON_TARGETS="python2_7 python3_6* -python3_4 -python3_5*" 1,741 KiB
[ebuild     U  ] dev-python/pyopenssl-18.0.0::gentoo [17.5.0::gentoo] USE="-doc -examples {-test}" PYTHON_TARGETS="python2_7 python3_6* -pypy -pypy3 -python3_4 -python3_5* -python3_7%" 164 KiB
[ebuild     U  ] dev-python/jupyter_client-5.2.3::gentoo [5.1.0-r1::gentoo] USE="{-test}" PYTHON_TARGETS="python2_7 python3_6* -python3_4 -python3_5* -python3_7%" 266 KiB
[ebuild     U  ] dev-python/statsmodels-0.9.0::gentoo [0.8.0::gentoo] USE="-doc -examples {-test}" PYTHON_TARGETS="python2_7 python3_6* -python3_5* (-python3_4%)" 12,362 KiB
[ebuild  N     ] media-libs/glm-0.9.9.3::gentoo  USE="{-test}" CPU_FLAGS_X86="sse2 -avx -avx2 -sse3" 4,470 KiB
[ebuild     U  ] dev-python/urllib3-1.24.1::gentoo [1.22::gentoo] USE="-doc {-test}" PYTHON_TARGETS="python2_7 python3_6* -pypy -pypy3 -python3_4 -python3_5* -python3_7%" 225 KiB
[ebuild   R    ] dev-python/service_identity-17.0.0-r1::gentoo  USE="-doc {-test}" PYTHON_TARGETS="python2_7 python3_6* -pypy -python3_4 -python3_5* -python3_7%" 0 KiB
[ebuild     U  ] dev-python/seaborn-0.9.0::gentoo [0.7.1::gentoo] USE="{-test}" PYTHON_TARGETS="python2_7 python3_6%* -python3_4 -python3_5*" 194 KiB
[ebuild     U  ] dev-python/twisted-18.7.0::gentoo [17.9.0::gentoo] USE="crypt soap -conch -http2 -serial {-test}" PYTHON_TARGETS="python2_7 python3_6* -python3_4 -python3_5* -python3_7%" 2,993 KiB
[ebuild     U  ] dev-python/requests-2.21.0-r1::gentoo [2.18.4::gentoo] USE="ssl -socks5" PYTHON_TARGETS="python2_7 python3_6* -pypy -pypy3 -python3_4 -python3_5* -python3_7%" 109 KiB
[ebuild     U  ] www-servers/tornado-5.1::gentoo [4.5.1::gentoo] USE="-doc -examples {-test}" PYTHON_TARGETS="python2_7 python3_6* -python3_4 -python3_5* -python3_7%" 505 KiB
[ebuild   R    ] dev-python/ssl-fetch-0.4::gentoo  PYTHON_TARGETS="python2_7 python3_6* -pypy -python3_4 -python3_5* -python3_7%" 0 KiB
[ebuild  N     ] dev-python/prometheus_client-0.5.0::gentoo  USE="{-test}" PYTHON_TARGETS="python2_7 python3_6 -python3_4 -python3_5 -python3_7" 59 KiB
[ebuild   R    ] dev-python/nbconvert-5.2.1::gentoo  USE="-doc {-test}" PYTHON_TARGETS="python2_7 python3_6* -python3_4 -python3_5* -python3_7%" 0 KiB
[ebuild   R    ] dev-python/terminado-0.8.1::gentoo  USE="{-test}" PYTHON_TARGETS="python2_7 python3_6* -python3_4 -python3_5* -python3_7%" 0 KiB
[ebuild     U  ] sci-chemistry/pymol-2.2.0::gentoo [1.8.6.0::gentoo] USE="-web" PYTHON_TARGETS="python2_7" 10,269 KiB
[ebuild     U  ] dev-tex/latexmk-456::gentoo [453a::gentoo] 416 KiB
[ebuild  NS    ] sys-devel/clang-7.0.1:7::gentoo [5.0.1:5::gentoo] USE="static-analyzer -debug -default-compiler-rt -default-libcxx -doc {-test} -xml (-z3)" LLVM_TARGETS="AMDGPU BPF NVPTX (X86) -AArch64 -ARM -Hexagon -Lanai -MSP430 -Mips -PowerPC -Sparc -SystemZ -XCore" PYTHON_TARGETS="python2_7" 13,077 KiB
[ebuild  N     ] sys-devel/clang-common-7.0.1::gentoo  0 KiB
[ebuild  NS    ] sys-libs/compiler-rt-7.0.1:7.0.1::gentoo [5.0.1:5.0.1::gentoo] USE="clang {-test}" 1,821 KiB
[ebuild  NS    ] sys-libs/compiler-rt-sanitizers-7.0.1:7.0.1::gentoo [5.0.1:5.0.1::gentoo] USE="clang libfuzzer profile sanitize xray {-test}" 0 KiB
[ebuild  NS    ] sys-devel/clang-runtime-7.0.1:7.0.1::gentoo [5.0.1:5.0.1::gentoo] USE="compiler-rt openmp sanitize -crt -libcxx" 0 KiB
[ebuild     U  ] dev-lang/R-3.5.1::gentoo [3.4.1::gentoo] USE="X cairo jpeg lapack nls openmp png (prefix) readline tiff -doc -icu -java -minimal -perl -profile -static-libs -tk" 29,115 KiB
[ebuild     U  ] dev-python/ipython-5.8.0-r1::gentoo [5.4.1::gentoo] USE="smp -doc -examples -matplotlib -nbconvert -notebook -qt5 {-test} -wxwidgets" PYTHON_TARGETS="python2_7 python3_6* -python3_4 -python3_5*" 4,862 KiB
[ebuild     U  ] dev-python/ipykernel-4.8.2::gentoo [4.6.1-r2::gentoo] USE="{-test}" PYTHON_TARGETS="python2_7 python3_6* -python3_4 -python3_5*" 93 KiB
[ebuild     U  ] dev-python/notebook-5.7.0::gentoo [5.0.0::gentoo] USE="-doc {-test}" PYTHON_TARGETS="python2_7 python3_6* -python3_4 -python3_5* -python3_7%" 13,081 KiB
[ebuild   R    ] dev-python/ipyparallel-6.0.2-r1::gentoo  USE="-doc {-test}" PYTHON_TARGETS="python2_7 python3_6* -python3_4 -python3_5* -python3_7%" 0 KiB
[ebuild  N     ] dev-java/ant-core-1.10.5-r1::gentoo  USE="-doc -source" 4,367 KiB
[ebuild  N     ] dev-java/bcprov-1.52-r2::gentoo  USE="-doc -source {-test}" 6,187 KiB
[ebuild  N     ] dev-java/commons-io-2.4:1::gentoo  USE="-doc -source {-test}" 324 KiB
[ebuild  N     ] dev-java/objenesis-1.3::gentoo  USE="-doc -source" 281 KiB
[ebuild  N     ] dev-java/asm-5.1:4::gentoo  USE="-doc -source" 1,508 KiB
[ebuild  N     ] dev-java/junit-3.8.2-r2::gentoo  USE="-doc -source" 451 KiB
[ebuild  N     ] dev-java/cglib-3.1:3::gentoo  USE="-doc -examples -source {-test}" 1,506 KiB
[ebuild  N     ] dev-java/jmock-1.2.0-r1:1.0::gentoo  USE="-doc -source" 150 KiB
[ebuild  N     ] dev-java/jflex-1.6.1::gentoo  USE="-doc -examples -source {-test} -vim-syntax" 2,957 KiB
[ebuild  N     ] dev-java/javacup-0.11b_p20151001::gentoo  USE="-doc -source" 307 KiB
[ebuild  N     ] dev-java/qdox-1.12.1-r1:1.12::gentoo  USE="-doc -source {-test}" 508 KiB
[ebuild  N     ] dev-java/hamcrest-generator-1.3-r1:1.3::gentoo  USE="-source {-test}" 3,600 KiB
[ebuild  N     ] dev-java/hamcrest-core-1.3:1.3::gentoo  USE="-doc -source" 0 KiB
[ebuild  N     ] dev-java/junit-4.12-r1:4::gentoo  USE="-doc -examples -source" 434 KiB
[ebuild  N     ] dev-java/easymock-3.3.1:3.2::gentoo  USE="-doc -examples -source" 992 KiB
[ebuild  N     ] dev-java/commons-lang-3.6:3.6::gentoo  USE="-doc -source {-test}" 833 KiB
[ebuild     U  ] app-text/pdftk-3.0.0::gentoo [2.02::gentoo] 535 KiB
[ebuild     U  ] sys-apps/portage-2.3.59-r1::gentoo [2.3.33::gentoo] USE="(ipc) -build -doc -epydoc -gentoo-dev (-native-extensions*) -rsync-verify* (-selinux) -xattr" PYTHON_TARGETS="python2_7 python3_6* -pypy -python3_4 -python3_5* -python3_7%" 996 KiB
[ebuild     U  ] virtual/package-manager-1::gentoo [0::gentoo] 0 KiB
[ebuild     U  ] app-portage/repoman-2.3.12::gentoo [2.3.9::gentoo] PYTHON_TARGETS="python2_7 python3_6* -python3_4 -python3_5* -python3_7%" 85 KiB
[blocks b      ] <app-portage/repoman-2.3.10 ("<app-portage/repoman-2.3.10" is blocking sys-apps/portage-2.3.59-r1)
[ebuild     U  ] app-portage/gentoolkit-0.4.2-r1::gentoo [0.4.2::gentoo] PYTHON_TARGETS="python2_7 python3_6* -pypy -python3_4 -python3_5* -python3_7%" 0 KiB
[ebuild     U  ] app-portage/layman-2.4.2-r2::gentoo [2.4.2::gentoo] USE="git -bazaar -cvs -darcs -g-sorcery -gpg -mercurial -sqlite -squashfs -subversion -sync-plugin-portage {-test}" PYTHON_TARGETS="python2_7 python3_6* -pypy -python3_4 -python3_5* -python3_7%" 0 KiB

Total: 191 packages (115 upgrades, 29 new, 8 in new slots, 39 reinstalls), Size of downloads: 612,752 KiB
Fetch Restriction: 1 package (1 unsatisfied)
Conflict: 1 block
lafita commented 5 years ago

Yoda users: there were too many problems updating the packages so I am re-installing the prefix from scratch. You may experience problems connecting to the cluster or running some of the software, which can be temporarily fixed by changing your login shell to /bin/bash.

Thank you and sorry for the inconvenience.