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EBI-predocs / research-software

:computer: Instructions, tips and issue tracker for the software on the EBI computing cluster
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January update #66

Closed mschubert closed 7 years ago

mschubert commented 7 years ago 
[ebuild     U  ] app-arch/xz-utils-5.2.3 [5.2.2]
[ebuild     U  ] sys-devel/gnuconfig-20170101 [20160402]
[ebuild     U  ] app-arch/tar-1.29-r2 [1.29]
[ebuild   R    ] virtual/libintl-0-r2 
[ebuild     U  ] dev-util/boost-build-1.62.0-r1 [1.61.0]
[ebuild     U  ] sci-biology/hmmer-3.1_beta2 [3.0] USE="(-altivec) {-test%}" 
[ebuild     U  ] sys-apps/file-5.29 [5.24] PYTHON_TARGETS="python3_5%*" 
[ebuild     U  ] sys-apps/net-tools-1.60_p20161110235919 [1.60_p20160215155418]
[ebuild     U  ] app-shells/bash-4.3_p48 [4.3_p39]
[ebuild     U  ] sys-apps/man-pages-4.09 [4.07]
[ebuild     U  ] app-shells/bash-completion-2.4-r1 [2.4]
[ebuild     U  ] app-shells/fish-2.4.0 [2.3.1]
[ebuild     U  ] sys-process/parallel-20160822 [20160222]
[ebuild     U  ] dev-vcs/mercurial-4.0.2 [3.9.2]
[ebuild     U  ] dev-libs/boost-1.62.0-r1 [1.61.0-r1]
[ebuild     U  ] app-portage/gentoolkit-0.3.3 [0.3.2-r1]
[ebuild     U  ] dev-python/cython-0.25.2 [0.24.1]
[ebuild    FU  ] dev-java/oracle-jdk-bin-1.8.0.112 [1.8.0.92]
[ebuild     U  ] dev-python/pip-9.0.1-r1 [8.1.2]
[ebuild     U  ] dev-vcs/bzr-2.7.0 [2.6.0]
[ebuild     U  ] app-editors/vim-core-8.0.0106 [8.0.0005-r1]
[ebuild     U  ] app-editors/vim-8.0.0106 [8.0.0005]
[ebuild     U  ] dev-libs/libpcre-8.39 [8.38]
[ebuild     U  ] dev-python/numpy-1.11.2-r1 [1.11.1]
[ebuild  N     ] sci-libs/amd-2.3.1  USE="fortran -doc -static-libs" 
[ebuild  N     ] sci-libs/colamd-2.8.0  USE="-static-libs" 
[ebuild     U  ] sys-apps/grep-2.27-r1 [2.26]
[ebuild     U  ] sys-apps/less-487 [483-r1]
[ebuild  N     ] sci-libs/cholmod-2.1.2  USE="lapack -cuda -doc -metis -minimal -static-libs" 
[ebuild     U  ] dev-vcs/git-2.11.0 [2.9.0]
[ebuild     U  ] sci-chemistry/pymol-1.8.4.0 [1.7.7.2]
[ebuild  N     ] sci-libs/umfpack-5.6.2  USE="cholmod -doc -static-libs" 
[ebuild     U  ] sci-libs/scipy-0.18.1 [0.17.0] USE="sparse*" 
[ebuild     U  ] dev-python/pandas-0.19.1 [0.17.1]
[ebuild     U  ] dev-python/seaborn-0.7.1 [0.7.0]
[ebuild     U  ] dev-libs/glib-2.50.2 [2.46.2-r1] USE="-xattr*" 
[ebuild     U  ] dev-lang/R-3.3.2 [3.3.1]
[ebuild     U  ] dev-tex/latexmk-448 [445]

@mattjeffryes Do you want to give this a try? Need to exclude lapack until the deps are fixed:

become ...
emerge --ask --update --exclude "seqan" @world
mattjeffryes commented 7 years ago

@mschubert Yes, I'll give it a go. Did you say you usually wait a few days after posting the update issue before executing it? Also, should I be an admin of this repository?

mschubert commented 7 years ago

If there is something controversial (like a major tmux upgrade that breaks running sessions) yes, otherwise use your best judgement.

Generally good to announce it a couple of days before, but then it's also good to do it on the weekend so less stuff is running :wink: (I suspect the first run now will have some issues)