August 2017 Update

[mattjeffryes]

It's been a while since the last update (sorry). I'll be updating Yoda and then the EBI cluster over the bank holiday weekend. Here are the anticipated changes for Yoda:

[ebuild     U  ] app-arch/bzip2-1.0.6-r07.1 [1.0.6-r7]
[ebuild     U  ] dev-util/boost-build-1.63.0 [1.62.0-r1]
[ebuild     U *] sci-biology/phyml-2.4.5-r3 [2.4.5-r2]
[ebuild     U  ] sci-libs/geos-3.6.1 [3.5.0-r2]
[ebuild     U  ] sys-apps/file-5.31 [5.29] PYTHON_TARGETS="-python3_6%"
[ebuild     U  ] dev-libs/kpathsea-6.2.3_p20170524 [6.2.1_p20150521-r1]
[ebuild     U  ] sci-libs/htslib-1.5 [1.3.1] USE="bzip2%* lzma%* -curl%"
[ebuild     U  ] sys-apps/less-497 [487]
[ebuild     U  ] app-eselect/eselect-ruby-20170723 [20151229]
[ebuild     U  ] app-shells/bash-completion-2.7 [2.4-r1] USE="{-test%}"
[ebuild     U  ] sys-apps/diffutils-3.6 [3.5]
[ebuild     U  ] sys-devel/make-4.2.1-r1 [4.2.1]
[ebuild     U  ] app-arch/tar-1.29-r3 [1.29-r2]
[ebuild     U  ] sys-apps/man-pages-4.12 [4.09]
[ebuild     U  ] sci-libs/fftw-3.3.6_p2 [3.3.5-r2]
[ebuild     U  ] dev-lang/perl-5.24.2 [5.24.1_rc4]
[ebuild     U  ] dev-lang/python-3.5.2 [3.5.1-r3]
[ebuild  N     ] dev-libs/libpcre2-10.30  USE="bzip2 jit pcre32 readline recursion-limit unicode zlib -libedit -pcre16 -static-libs"
[ebuild     U  ] dev-libs/libuv-1.11.0 [1.9.1-r1]
[ebuild     U  ] app-text/ps2pkm-1.8_p20170524 [1.7_p20150521]
[ebuild     U  ] app-text/dvipsk-5.997_p20170524 [5.995_p20150521]
[ebuild     U  ] dev-tex/bibtexu-3.71_p20170524 [3.71_p20150521]
[ebuild  NS    ] dev-lang/ruby-2.4.1-r2 [2.2.1] USE="berkdb gdbm ipv6 rdoc ssl -debug -doc -examples -jemalloc -libressl -rubytests -socks5 -static-libs -tk -xemacs"
[ebuild     U  ] dev-ruby/rubygems-2.6.12 [2.6.6] RUBY_TARGETS="ruby24%*"
[ebuild     U  ] virtual/rubygems-13 [11] RUBY_TARGETS="ruby24%*"
[ebuild  N    *] dev-ruby/net-telnet-0.1.1-r1  USE="-doc {-test}" RUBY_TARGETS="ruby22 ruby24 -ruby23"
[ebuild     U  ] dev-ruby/rake-12.0.0 [11.2.2-r1] RUBY_TARGETS="ruby24%*"
[ebuild     U  ] dev-ruby/json-2.1.0 [2.0.2] RUBY_TARGETS="ruby24%*"
[ebuild     U  ] dev-ruby/power_assert-1.1.0 [0.2.7] RUBY_TARGETS="ruby24%*"
[ebuild  N    *] dev-ruby/did_you_mean-1.1.2  USE="{-test}" RUBY_TARGETS="ruby24"
[ebuild     U  ] dev-ruby/minitest-5.10.3 [5.9.0] RUBY_TARGETS="ruby24%*"
[ebuild  N    *] dev-ruby/xmlrpc-0.3.0  USE="-doc {-test}" RUBY_TARGETS="ruby24 -ruby23"
[ebuild     U  ] dev-ruby/test-unit-3.2.5 [3.2.1] RUBY_TARGETS="ruby24%*"
[ebuild  N    *] dev-ruby/kpeg-1.1.0  USE="-doc {-test}" RUBY_TARGETS="ruby22 ruby24 -ruby23"
[ebuild   R    ] dev-ruby/racc-1.4.14  RUBY_TARGETS="ruby24%*"
[ebuild     U *] dev-ruby/rdoc-5.1.0 [4.2.2] RUBY_TARGETS="ruby24%*"
[ebuild     U  ] dev-vcs/git-2.14.1 [2.11.0] USE="pcre-jit%*"
[ebuild     U  ] dev-libs/boost-1.63.0 [1.62.0-r1] PYTHON_TARGETS="-python3_6%"
[ebuild  N     ] dev-python/sortedcontainers-1.5.7  USE="{-test}" PYTHON_TARGETS="python2_7 python3_5 (-python3_4) -python3_6"
[ebuild  N    *] dev-python/typing-3.5.3.0  PYTHON_TARGETS="python2_7 python3_5 -pypy -pypy3 (-python3_4) -python3_6"
[ebuild     U  ] media-libs/harfbuzz-1.4.8 [1.3.4] USE="-debug%"
[ebuild     U  ] app-text/texlive-core-2017-r2 [2015-r1]
[ebuild  N     ] virtual/python-enum34-1  PYTHON_TARGETS="python2_7 python3_5 -pypy -pypy3 (-python3_4) -python3_6"
[ebuild  N    *] net-libs/nghttp2-9999  USE="cxx threads -debug -hpack-tools -jemalloc -libressl -static-libs {-test} -utils -xml"
[ebuild  N    *] sys-devel/llvm-common-9999
[ebuild  N    *] dev-python/snowballstemmer-1.2.1  PYTHON_TARGETS="python2_7 python3_5 -pypy -pypy3 (-python3_4) -python3_6"
[ebuild  N    *] dev-python/pathlib-1.0.1-r1  PYTHON_TARGETS="python2_7 -pypy -pypy3"
[ebuild  N    *] virtual/python-pathlib-1.0  PYTHON_TARGETS="python2_7 python3_5 -pypy -pypy3 (-python3_4) -python3_6"
[ebuild     U  ] dev-python/setuptools-36.0.1 [24.0.2] PYTHON_TARGETS="-python3_6%"
[ebuild     U  ] dev-python/certifi-2017.7.27.1 [2016.8.8] PYTHON_TARGETS="-python3_6%"
[ebuild     U  ] dev-python/numpy-1.13.1 [1.11.2-r1] PYTHON_TARGETS="-python3_6%"
[ebuild     U  ] dev-python/cython-0.26 [0.25.2] PYTHON_TARGETS="-python3_6%"
[ebuild     U  ] sci-libs/scipy-0.19.1 [0.18.1] PYTHON_TARGETS="-python3_6%"
[ebuild     U  ] dev-python/matplotlib-1.5.3-r2 [1.5.3] PYTHON_TARGETS="-python3_6%"
[ebuild  N    *] dev-python/intervaltree-2.1.0  USE="{-test}" PYTHON_TARGETS="python2_7 python3_5 (-python3_4) -python3_6"
[ebuild  N     ] dev-python/pywavelets-0.5.2  USE="-doc -examples {-test}" PYTHON_TARGETS="python2_7 python3_5 (-python3_4) -python3_6"
[ebuild  N     ] dev-python/docutils-0.13.1  PYTHON_TARGETS="python2_7 python3_5 -pypy -pypy3 (-python3_4) -python3_6"
[ebuild  N    *] dev-python/imagesize-0.7.1  USE="{-test}" PYTHON_TARGETS="python2_7 python3_5 -pypy -pypy3 (-python3_4) -python3_6"
[ebuild  N     ] dev-python/sphinx_rtd_theme-0.2.4  PYTHON_TARGETS="python2_7 python3_5 -pypy -pypy3 (-python3_4) -python3_6"
[ebuild  N    *] dev-python/alabaster-0.7.10  PYTHON_TARGETS="python2_7 python3_5 -pypy -pypy3 (-python3_4) -python3_6"
[ebuild  N     ] dev-python/Babel-2.4.0  USE="-doc {-test}" PYTHON_TARGETS="python2_7 python3_5 -pypy -pypy3 (-python3_4) -python3_6"
[ebuild  N    *] dev-python/whoosh-2.7.4  USE="-doc {-test}" PYTHON_TARGETS="python2_7 python3_5 -pypy (-python3_4) -python3_6"
[ebuild  N     ] dev-python/namespace-sphinxcontrib-1.0  PYTHON_TARGETS="python2_7 python3_5 -pypy -pypy3 (-python3_4) -python3_6"
[ebuild  N     ] dev-python/sqlalchemy-1.1.11  USE="sqlite -doc -examples {-test}" PYTHON_TARGETS="python2_7 python3_5 -pypy (-python3_4) -python3_6"
[ebuild     U  ] dev-python/prompt_toolkit-1.0.15 [1.0.3] PYTHON_TARGETS="-python3_6%"
[ebuild     U *] dev-python/jedi-0.10.2 [0.9.0] PYTHON_TARGETS="-python3_6%"
[ebuild     U  ] dev-python/ipython-5.4.1 [4.2.0-r1] USE="-qt5%" PYTHON_TARGETS="-python3_6%"
[ebuild     U  ] dev-db/mariadb-10.2.8 [10.1.20] USE="backup%* -numa% -rocksdb%"
[ebuild  N     ] dev-python/sphinx-1.6.3-r2  USE="-doc -latex -net {-test}" PYTHON_TARGETS="python2_7 python3_5 (-python3_4) -python3_6"
[ebuild  N     ] dev-python/sphinxcontrib-websupport-1.0.1  USE="{-test}" PYTHON_TARGETS="python2_7 python3_5 (-python3_4) -python3_6"
[ebuild  NS   #] sys-devel/llvm-4.0.1 [3.7.1-r3] USE="doc libffi ncurses -debug -gold -libedit {-test}" LLVM_TARGETS="AMDGPU BPF NVPTX (X86) -AArch64 -ARM -Hexagon -Lanai -MSP430 -Mips -PowerPC -RISCV -Sp
arc -SystemZ -XCore"
[ebuild     U  ] dev-python/llvmlite-0.19.0 [0.12.1] PYTHON_TARGETS="-python3_6%"
[ebuild  N     ] perl-core/File-Path-2.130.0
[ebuild     U  ] virtual/perl-File-Path-2.130.0 [2.120.100_rc]
[blocks b      ] >perl-core/File-Path-2.120.100_rc-r999 (">perl-core/File-Path-2.120.100_rc-r999" is blocking virtual/perl-File-Path-2.120.100_rc)
[ebuild     U  ] sys-apps/grep-3.1 [2.27-r1]
[ebuild     U  ] dev-perl/DBD-mysql-4.41.0-r1 [4.32.0-r1] USE="ssl%*"
[ebuild     U  ] media-gfx/graphviz-2.40.1 [2.38.0-r1]
[ebuild     U  ] dev-python/sympy-1.1.1 [1.0-r1] USE="-symengine%" PYTHON_TARGETS="-python3_6%"
[ebuild     U  ] app-misc/jq-1.5-r3 [1.5-r2] USE="valgrind%*"
[ebuild     U  ] dev-lang/R-3.4.1 [3.3.2]
[ebuild     U  ] app-misc/colordiff-1.0.18 [1.0.16]
[ebuild     U  ] app-portage/gentoolkit-0.4.0 [0.3.3]
[ebuild     U  ] app-portage/eix-0.32.9 [0.32.5-r1]
[ebuild     U  ] app-portage/layman-2.4.2 [2.2.0-r7] USE="-gpg% -sqlite% -sync-plugin-portage%" PYTHON_TARGETS="python3_5%* -python3_6%"
[ebuild     U  ] app-misc/tmux-2.5-r2 [2.3]
[ebuild     U  ] dev-python/numba-0.34.0 [0.26.0] PYTHON_TARGETS="-python3_6%"
[ebuild     U  ] dev-lang/ghc-8.0.2 [7.10.3] USE="profile%*"
[ebuild     U  ] sci-libs/scikits_image-0.13.0 [0.12.3] PYTHON_TARGETS="-python3_6%"
[ebuild     U  ] app-editors/emacs-25.2 [25.1] USE="-dynamic-loading%"
[ebuild     U  ] dev-vcs/subversion-1.9.7 [1.9.4] USE="-kwallet%"
[ebuild     U  ] media-gfx/imagemagick-7.0.6.9 [6.9.8.3]
[ebuild     U *] sci-biology/tophat-2.1.1-r4 [2.1.1-r3]
[ebuild     U  ] sci-biology/cd-hit-4.6.6 [4.6]
[ebuild     U  ] sci-mathematics/glpk-4.63 [4.61-r1]
[ebuild     U  ] net-libs/nodejs-8.4.0 [7.3.0]
[ebuild     U  ] dev-python/pip-9.0.1-r2 [9.0.1-r1] USE="-vanilla%" PYTHON_TARGETS="-python3_6%"
[ebuild     U  ] sci-libs/scikits_learn-0.19.0 [0.17.1] PYTHON_TARGETS="-python3_6%"
[ebuild     U  ] app-text/dos2unix-7.3.5 [7.3.4]
[ebuild     U  ] sci-visualization/gnuplot-5.0.6 [5.0.4]
[ebuild     U  ] dev-python/pandas-0.20.3 [0.19.1] PYTHON_TARGETS="-python3_6%"
[ebuild     U  ] app-shells/fish-2.6.0 [2.4.0] USE="nls%*"
[ebuild     U  ] dev-vcs/mercurial-4.3.1 [4.0.1]
[ebuild     U  ] sci-chemistry/pymol-1.8.6.0 [1.8.4.0]
[ebuild     U  ] dev-tex/latexmk-452c [448]
[ebuild     U  ] dev-texlive/texlive-basic-2017-r1 [2015]
[ebuild     U  ] dev-texlive/texlive-fontsrecommended-2017 [2015]
[ebuild     U  ] dev-texlive/texlive-fontutils-2017 [2015]
[ebuild  N     ] dev-texlive/texlive-plaingeneric-2017  USE="-doc -source"
[ebuild  N     ] dev-texlive/texlive-mathscience-2017  USE="-doc -source"
[uninstall     ] dev-texlive/texlive-science-2015
[blocks b      ] dev-texlive/texlive-science ("dev-texlive/texlive-science" is blocking dev-texlive/texlive-mathscience-2017)
[ebuild     U  ] dev-texlive/texlive-latexrecommended-2017 [2015-r1]
[uninstall     ] dev-texlive/texlive-latexextra-2015-r1
[blocks b      ] <dev-texlive/texlive-latexextra-2017 ("<dev-texlive/texlive-latexextra-2017" is blocking dev-texlive/texlive-mathscience-2017, dev-texlive/texlive-latexrecommended-2017)
[uninstall     ] dev-texlive/texlive-mathextra-2015
[blocks b      ] dev-texlive/texlive-mathextra ("dev-texlive/texlive-mathextra" is blocking dev-texlive/texlive-mathscience-2017, dev-texlive/texlive-latexrecommended-2017)
[uninstall     ] dev-texlive/texlive-xetex-2015
[blocks b      ] <dev-texlive/texlive-xetex-2016 ("<dev-texlive/texlive-xetex-2016" is blocking dev-texlive/texlive-latexrecommended-2017)
[ebuild     U  ] dev-texlive/texlive-luatex-2017 [2015]
[ebuild     U  ] app-text/texlive-2017 [2015]

And for the EBI cluster:

[ebuild     U  ] app-arch/bzip2-1.0.6-r07.1 [1.0.6-r7]
[ebuild     U  ] sys-devel/make-4.2.1-r1 [4.2.1]
[ebuild  N     ] app-crypt/rhash-1.3.5  USE="-debug -nls -openssl -static-libs"
[ebuild     U  ] sys-apps/diffutils-3.6 [3.5]
[ebuild  N     ] app-portage/elt-patches-20170815
[ebuild     U  ] sys-apps/file-5.31 [5.29] PYTHON_TARGETS="(-python3_4*) -python3_6%"
[ebuild     U  ] dev-libs/kpathsea-6.2.3_p20170524 [6.2.1_p20150521]
[ebuild     U  ] app-shells/bash-completion-2.7 [2.4-r1] USE="{-test%}"
[ebuild     U  ] app-shells/fish-2.6.0 [2.4.0-r1] USE="-nls%"
[ebuild     U  ] sys-apps/man-pages-4.12 [4.09]
[ebuild     U  ] app-misc/colordiff-1.0.18 [1.0.16]
[ebuild     U  ] sys-process/parallel-20170422 [20160222]
[ebuild  N    *] media-gfx/sam2p-0.49.3  USE="-examples -gif"
[ebuild     U  ] dev-lang/ghc-8.0.2 [7.10.3] USE="profile%*"
[ebuild     U  ] app-editors/vim-core-8.0.0983 [8.0.0106]
[ebuild     U  ] app-editors/vim-8.0.0983 [8.0.0106] USE="-terminal%" PYTHON_SINGLE_TARGET="python3_5%* -python2_7% (-python3_4) -python3_6%" PYTHON_TARGETS="-python3_6%"
[ebuild  N     ] app-eselect/eselect-lapack-0.1
[ebuild  N     ] app-eselect/eselect-cblas-0.1
[ebuild  N     ] app-eselect/eselect-blas-0.1
[ebuild  N    *] dev-python/typing-3.5.3.0  PYTHON_TARGETS="python2_7 python3_5 -pypy -pypy3 (-python3_4) -python3_6"
[ebuild  N    *] dev-python/snowballstemmer-1.2.1  PYTHON_TARGETS="python2_7 python3_5 -pypy -pypy3 (-python3_4) -python3_6"
[ebuild  N    *] dev-python/pathlib-1.0.1-r1  PYTHON_TARGETS="python2_7 -pypy -pypy3"
[ebuild  N    *] virtual/python-pathlib-1.0  PYTHON_TARGETS="python2_7 python3_5 -pypy -pypy3 (-python3_4) -python3_6"
[ebuild     U *] dev-python/traitlets-4.3.2 [4.1.0] PYTHON_TARGETS="(-python3_4*) -python3_6%"
[ebuild     U  ] app-portage/gentoolkit-0.4.0 [0.3.3] PYTHON_TARGETS="(-python3_4*)"
[ebuild  N     ] dev-python/pygments-2.2.0  USE="-doc {-test}" PYTHON_TARGETS="python2_7 python3_5 -pypy -pypy3 (-python3_4) -python3_6"
[ebuild  N     ] dev-python/backports-shutil_get_terminal_size-1.0.0-r1  PYTHON_TARGETS="python2_7"
[ebuild     U *] dev-python/jedi-0.10.2 [0.9.0] PYTHON_TARGETS="(-python3_4*) -python3_6%"
[ebuild  N     ] dev-python/wcwidth-0.1.7-r1  USE="{-test}" PYTHON_TARGETS="python2_7 python3_5 (-python3_4) -python3_6"
[ebuild  N    *] dev-python/alabaster-0.7.10  PYTHON_TARGETS="python2_7 python3_5 -pypy -pypy3 (-python3_4) -python3_6"
[ebuild  N     ] dev-python/sphinx_rtd_theme-0.2.4  PYTHON_TARGETS="python2_7 python3_5 -pypy -pypy3 (-python3_4) -python3_6"
[ebuild  N    *] dev-python/imagesize-0.7.1  USE="{-test}" PYTHON_TARGETS="python2_7 python3_5 -pypy -pypy3 (-python3_4) -python3_6"
[ebuild  N     ] dev-python/sqlalchemy-1.1.11  USE="sqlite -doc -examples {-test}" PYTHON_TARGETS="python2_7 python3_5 -pypy (-python3_4) -python3_6"
[ebuild  N    *] dev-python/whoosh-2.7.4  USE="-doc {-test}" PYTHON_TARGETS="python2_7 python3_5 -pypy (-python3_4) -python3_6"
[ebuild  N     ] dev-python/namespace-sphinxcontrib-1.0  PYTHON_TARGETS="python2_7 python3_5 -pypy -pypy3 (-python3_4) -python3_6"
[ebuild  N     ] dev-python/markupsafe-0.23  PYTHON_TARGETS="python2_7 python3_5 -pypy -pypy3 (-python3_4) -python3_6"
[ebuild     U  ] dev-python/pip-9.0.1-r2 [9.0.1-r1] USE="-vanilla%" PYTHON_TARGETS="(-python3_4*) -python3_6%"
[ebuild  N     ] dev-python/prompt_toolkit-1.0.15  USE="{-test}" PYTHON_TARGETS="python2_7 python3_5 (-python3_4) -python3_6"
[ebuild  N     ] dev-python/Babel-2.4.0  USE="-doc {-test}" PYTHON_TARGETS="python2_7 python3_5 -pypy -pypy3 (-python3_4) -python3_6"
[ebuild  N     ] dev-python/docutils-0.13.1  PYTHON_TARGETS="python2_7 python3_5 -pypy -pypy3 (-python3_4) -python3_6"
[ebuild  N     ] dev-python/jinja-2.9.6  USE="-doc -examples {-test}" PYTHON_TARGETS="python2_7 python3_5 -pypy -pypy3 (-python3_4) -python3_6"
[ebuild  N     ] dev-python/sphinx-1.6.3-r2  USE="-doc -latex -net {-test}" PYTHON_TARGETS="python2_7 python3_5 (-python3_4) -python3_6"
[ebuild  N     ] dev-python/sphinxcontrib-websupport-1.0.1  USE="{-test}" PYTHON_TARGETS="python2_7 python3_5 (-python3_4) -python3_6"
[ebuild     U  ] dev-python/ipython-5.4.1 [4.1.1] USE="-qt5%" PYTHON_TARGETS="(-python3_4*) -python3_6%"
[ebuild     U  ] dev-libs/libpcre-8.41 [8.38]
[ebuild     U  ] media-libs/freetype-2.8 [2.6.3] USE="cleartype_hinting%*"
[ebuild     U  ] dev-util/cmake-3.9.1 [3.5.0] USE="-server%"
[ebuild     U  ] dev-libs/icu-58.2 [55.1]
[ebuild     U  ] dev-vcs/git-2.14.1 [2.9.0] USE="pcre-jit%*"
[ebuild     U  ] app-text/dvipsk-5.997_p20170524 [5.995_p20150521]
[ebuild     U  ] app-text/ps2pkm-1.8_p20170524 [1.7_p20150521]
[ebuild     U  ] app-misc/tmux-2.5-r2 [2.3]
[ebuild     U  ] sys-apps/grep-3.1 [2.27-r1]
[ebuild     U  ] sys-apps/less-497 [487]
[ebuild     U  ] media-gfx/graphite2-1.3.10 [1.3.7]
[ebuild     U  ] sci-libs/blas-reference-20161223 [20151113-r100] USE="-doc%"
[ebuild  N    *] sys-devel/llvm-common-9999
[ebuild  N     ] sys-libs/libomp-3.9.1  USE="-hwloc -ompt"
[ebuild  N     ] dev-libs/msgpack-2.0.0  USE="cxx -static-libs {-test}"
[ebuild     U  ] dev-tex/bibtexu-3.71_p20170524 [3.71_p20150521]
[ebuild     U  ] app-portage/layman-2.4.2 [2.2.0-r7] USE="-gpg% -sqlite% -sync-plugin-portage%" PYTHON_TARGETS="python3_5%* (-python3_4*) -python3_6%"
[ebuild     U  ] virtual/blas-3.7 [3.6]
[ebuild  NS   *] sys-devel/llvm-4.0.1 [3.8.1-r2] USE="doc libffi ncurses -debug -gold -libedit {-test}" LLVM_TARGETS="AMDGPU BPF NVPTX (X86) -AArch64 -ARM -Hexagon -Lanai -MSP430 -Mips -PowerPC -RISCV -Sp
arc -SystemZ -XCore"
[ebuild  N     ] sys-devel/clang-runtime-3.9.1  USE="openmp -libcxx"
[ebuild     U  ] sci-libs/cblas-reference-20161223 [20151113-r100]
[ebuild     U  ] sci-libs/lapack-reference-3.7.0 [3.6.0-r100]
[blocks b      ] app-eselect/eselect-blas ("app-eselect/eselect-blas" is blocking sci-libs/blas-reference-20151113-r100, sci-libs/cblas-reference-20151113-r100, sci-libs/lapack-reference-3.6.0-r100)
[blocks b      ] app-eselect/eselect-lapack ("app-eselect/eselect-lapack" is blocking sci-libs/blas-reference-20151113-r100, sci-libs/cblas-reference-20151113-r100, sci-libs/lapack-reference-3.6.0-r100)
[blocks b      ] app-eselect/eselect-cblas ("app-eselect/eselect-cblas" is blocking sci-libs/blas-reference-20151113-r100, sci-libs/cblas-reference-20151113-r100, sci-libs/lapack-reference-3.6.0-r100)
[ebuild     U  ] dev-python/llvmlite-0.19.0 [0.15.0] PYTHON_TARGETS="(-python3_4*) -python3_6%"
[ebuild     U  ] sci-chemistry/pymol-1.8.6.0 [1.8.4.0]
[ebuild     U  ] dev-python/numba-0.34.0 [0.30.0] PYTHON_TARGETS="(-python3_4*) -python3_6%"
[ebuild     UD ] dev-python/symengine-0.3.0 [9999] USE="{-test%}" PYTHON_TARGETS="(-python3_4*) -python3_6%"
[ebuild    fU  ] dev-java/oracle-jdk-bin-1.8.0.144 [1.8.0.112] USE="-commercial% -visualvm%"
[ebuild     U  ] dev-libs/glib-2.50.2 [2.46.2-r1] USE="doc%* -xattr*"
[ebuild     U  ] media-libs/harfbuzz-1.4.8 [1.2.4] USE="-debug%"
[ebuild     U  ] app-text/texlive-core-2017-r2 [2015]
[ebuild     U  ] dev-lang/R-3.4.1 [3.3.2]
[ebuild     U  ] sys-devel/llvm-3.9.1-r1 [3.8.1-r2] USE="-multitarget*" LLVM_TARGETS="AMDGPU%* BPF%* NVPTX%* (X86%*) -AArch64% -ARM% -Hexagon% -MSP430% -Mips% -PowerPC% -Sparc% -SystemZ% -XCore%"
[ebuild     U  ] sys-devel/clang-3.9.1-r100 [3.8.1-r100] LLVM_TARGETS="AMDGPU%* BPF%* NVPTX%* (X86%*) -AArch64% -ARM% -Hexagon% -MSP430% -Mips% -PowerPC% -Sparc% -SystemZ% -XCore%"
[ebuild     U  ] dev-tex/latexmk-452c [448]
[ebuild     U  ] dev-texlive/texlive-basic-2017-r1 [2015]
[ebuild     U  ] dev-texlive/texlive-latex-2017 [2015]
[ebuild     U  ] dev-texlive/texlive-fontsrecommended-2017 [2015]
[ebuild     U  ] dev-texlive/texlive-fontutils-2017 [2015]
[ebuild  N     ] dev-texlive/texlive-plaingeneric-2017  USE="-doc -source"
[ebuild     U  ] dev-texlive/texlive-latexrecommended-2017 [2015-r1]
[ebuild  N     ] dev-texlive/texlive-mathscience-2017  USE="-doc -source"
[ebuild     U  ] dev-texlive/texlive-luatex-2017 [2015]
[ebuild     U  ] app-text/texlive-2017 [2015] L10N="-af% -ar% -as% -bg% -bn% -br% -ca% -cs% -cy% -da% -de% -el% -en% -en-GB% -eo% -es% -et% -eu% -fa% -fi% -fr% -ga% -gl% -gu% -he% -hi% -hr% -hsb% -hu% -hy% -ia% -id% -is% -it% -ja% -kn% -ko% -la% -lo% -lt% -lv% -ml% -mn% -mr% -nb% -nl% -nn% -no% -or% -pa% -pl% -pt% -rm% -ro% -ru% -sa% -sco% -sk% -sl% -sq% -sr% -sv% -ta% -te% -th% -tk% -tr% -uk% -vi% -zh%"

[demh]

Hi Matt !!

It looks like Numpy doesn't work in the EBI cluster after the update. This is the error I get:

import numpy Traceback (most recent call last): File "", line 1, in File "/nfs/research2/software/prefix/usr/lib/python2.7/site-packages/numpy/init.py", line 142, in from . import add_newdocs File "/nfs/research2/software/prefix/usr/lib/python2.7/site-packages/numpy/add_newdocs.py", line 13, in from numpy.lib import add_newdoc File "/nfs/research2/software/prefix/usr/lib/python2.7/site-packages/numpy/lib/init.py", line 8, in from .type_check import * File "/nfs/research2/software/prefix/usr/lib/python2.7/site-packages/numpy/lib/type_check.py", line 11, in import numpy.core.numeric as _nx File "/nfs/research2/software/prefix/usr/lib/python2.7/site-packages/numpy/core/init.py", line 14, in from . import multiarray ImportError: librefblas.so.3: cannot open shared object file: No such file or directory

Could you please have a look at it?

Thanks !!

Dani

[mschubert]

@demh err, that might have been my fault - fixed now

[demh]

@mschubert It is working now. Thanks for the quick fix !!

[mattjeffryes]

The EBI cluster has been updated. Please post a new issue if you have any problems. I will update the Yoda cluster next weekend.

[demh]

Hey guys !!

I have some issues again. I am trying to install an R package in the EBI cluster and get the following error:

install.packages('mclust') Installing package into ‘/homes/dem44/R’ (as ‘lib’ is unspecified) trying URL 'http://mirrors.ebi.ac.uk/CRAN/src/contrib/mclust_5.3.tar.gz' Content type 'application/x-gzip' length 2792962 bytes (2.7 MB)

downloaded 2.7 MB

• installing source package ‘mclust’ ... package ‘mclust’ successfully unpacked and MD5 sums checked libs x86_64-pc-linux-gnu-gcc -I/nfs/research2/software/prefix/usr/lib/R/include -DNDEBUG -fpic -O2 -pipe -O2 -pipe -c init.c -o init.o x86_64-pc-linux-gnu-gfortran -fpic -O2 -pipe -c mclust.f -o mclust.o x86_64-pc-linux-gnu-gfortran -fpic -O2 -pipe -c mclustaddson.f -o mclustaddson.o x86_64-pc-linux-gnu-gcc -shared -L/nfs/research2/software/prefix/usr/lib/R/lib -Wl,-O1 -Wl,-rpath=/nfs/research2/software/prefix/usr/lib/R/lib -o mclust.so init.o mclust.o mclustaddson.o -llapack -lblas -lblas -lgfortran -lm -lquadmath -lgfortran -lm -lquadmath -L/nfs/research2/software/prefix/usr/lib/R/lib -lR ld: cannot find -llapack ld: cannot find -lblas ld: cannot find -lblas collect2: error: ld returned 1 exit status make: *** [/nfs/research2/software/prefix/usr/lib/R/share/make/shlib.mk:6: mclust.so] Error 1 ERROR: compilation failed for package ‘mclust’
• removing ‘/homes/dem44/R/mclust’

The downloaded source packages are in ‘/tmp/RtmpXjpEL5/downloaded_packages’ Warning message: In install.packages("mclust") : installation of package ‘mclust’ had non-zero exit status

I think it may have something to do with the llapack / lblas libraries after the update. Any ideas?

Thanks !!

Dani

[mattjeffryes]

@demh This should be fixed now.

[demh]

@mattjeffryes It is working now. Thanks Matt !!

[nvolkova]

Hi guys, I was trying to re-install all the necessary R packages and I keep getting this or similar errors:

> install.packages('plyr')
Installing package into ‘/homes/nvolkova/R’
(as ‘lib’ is unspecified)
also installing the dependency ‘Rcpp’

trying URL 'http://mirrors.ebi.ac.uk/CRAN/src/contrib/Rcpp_0.12.12.tar.gz'
Content type 'application/x-gzip' length 2421289 bytes (2.3 MB)
==================================================
downloaded 2.3 MB

trying URL 'http://mirrors.ebi.ac.uk/CRAN/src/contrib/plyr_1.8.4.tar.gz'
Content type 'application/x-gzip' length 392451 bytes (383 KB)
==================================================
downloaded 383 KB

* installing *source* package ‘Rcpp’ ...
** package ‘Rcpp’ successfully unpacked and MD5 sums checked
** libs
x86_64-pc-linux-gnu-g++  -I/nfs/research2/software/prefix/usr/lib/R/include -DNDEBUG -I../inst/include/     -fpic  -O2 -pipe -O2 -pipe  -c Date.cpp -o Date.o
x86_64-pc-linux-gnu-g++  -I/nfs/research2/software/prefix/usr/lib/R/include -DNDEBUG -I../inst/include/     -fpic  -O2 -pipe -O2 -pipe  -c Module.cpp -o Module.o
x86_64-pc-linux-gnu-g++  -I/nfs/research2/software/prefix/usr/lib/R/include -DNDEBUG -I../inst/include/     -fpic  -O2 -pipe -O2 -pipe  -c Rcpp_init.cpp -o Rcpp_init.o
x86_64-pc-linux-gnu-g++  -I/nfs/research2/software/prefix/usr/lib/R/include -DNDEBUG -I../inst/include/     -fpic  -O2 -pipe -O2 -pipe  -c api.cpp -o api.o
x86_64-pc-linux-gnu-g++  -I/nfs/research2/software/prefix/usr/lib/R/include -DNDEBUG -I../inst/include/     -fpic  -O2 -pipe -O2 -pipe  -c attributes.cpp -o attributes.o
x86_64-pc-linux-gnu-g++  -I/nfs/research2/software/prefix/usr/lib/R/include -DNDEBUG -I../inst/include/     -fpic  -O2 -pipe -O2 -pipe  -c barrier.cpp -o barrier.o
x86_64-pc-linux-gnu-g++ -shared -L/nfs/research2/software/prefix/usr/lib/R/lib -Wl,-O1 -Wl,-rpath=/nfs/research2/software/prefix/usr/lib/R/lib -o Rcpp.so Date.o Module.o Rcpp_init.o api.o attributes.o barrier.o -L/nfs/research2/software/prefix/usr/lib/R/lib -lR
installing to /homes/nvolkova/R/Rcpp/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (Rcpp)
* installing *source* package ‘plyr’ ...
** package ‘plyr’ successfully unpacked and MD5 sums checked
** libs
x86_64-pc-linux-gnu-g++  -I/nfs/research2/software/prefix/usr/lib/R/include -DNDEBUG  -I"/homes/nvolkova/R/Rcpp/include"    -fpic  -O2 -pipe -O2 -pipe  -c RcppExports.cpp -o RcppExports.o
x86_64-pc-linux-gnu-gcc -I/nfs/research2/software/prefix/usr/lib/R/include -DNDEBUG  -I"/homes/nvolkova/R/Rcpp/include"    -fpic  -O2 -pipe -O2 -pipe  -c loop_apply.c -o loop_apply.o
loop_apply.c: In function 'loop_apply_':
loop_apply.c:15:3: error: 'for' loop initial declarations are only allowed in C99 mode
   for(int i = 0; i < n1; i++) {
   ^
loop_apply.c:15:3: note: use option -std=c99 or -std=gnu99 to compile your code
make: *** [/nfs/research2/software/prefix/usr/lib/R/etc/Makeconf:159: loop_apply.o] Error 1
ERROR: compilation failed for package ‘plyr’
* removing ‘/homes/nvolkova/R/plyr’

The downloaded source packages are in
    ‘/tmp/RtmpmcqI88/downloaded_packages’
Warning message:
In install.packages("plyr") :
  installation of package ‘plyr’ had non-zero exit status

How do I get around that compilation flag? Thanks in advance for any advice!

[mattjeffryes]

@nvolkova Hi Nadia, I'm not seeing this issue myself, but I've found some discussion of this problem. I've added the -std=gnu99 flag to GCC in $PREFIX/usr/lib/R/etc/Makeconf. Please try installing the package now. Maybe @mschubert can advise on how ill-advised my solution is.

[mschubert]

Err, don't. That will add the flag to all R packages compiled by the prefix gcc, which will sooner or later break other packages - and then the error message will not be as helpful.

Likely something borked in your environment, have you tried starting R from the prefix shell? Otherwise, much better to set CFLAGS environment temporarily.