Closed lcoombe closed 5 years ago
lcoombe
commented
5 years ago lcoombe
commented
5 years ago Remove libdivsufsort, do temporary uninstall:
=> Installing sdsl-lite from brewsci/bio
==> Downloading https://linuxbrew.bintray.com/bottles-bio/sdsl-lite-2.1.1_2.x86_64_linux.bottle.tar.gz
==> Downloading from https://akamai.bintray.com/34/34182f95fd635533ba8f686b5ebafe411204dbcb3969a6b2e92f2e22c4d778bb?__gda__=exp=1556661789~hmac=6140bf77d18acb1fb06e0980a107cd5dc18d5468b59b30526d1e669df03bf753&response-content-disposition=attachment%3Bfilename%3D%22sdsl-lite-2.1.1_2.x86_64_linux.bottle.tar.gz%22&response-content-type=application%2Fgzip&requestInfo=U2FsdGVkX1-l6aoPG4qogMiecwVa06E9ldjj4vF6VbO_qBO1aub-sXuuhwTK8tvBOUZ-1BHH8c0W4Dz5V4VIemNPyzSoqwapjyb0uqw29glcf7FFolalWqRvwNXAlcJ2XHkTrh7pEpSKrPjm1azCkLWkSUxVBb6bE7IgwR_6xC4&response-X-Checksum-Sha1=29d79f9d6d5e005c9172e7c70ea5719f663d4ab6&response-X-Checksum-Sha2=34182f95fd635533ba8f686b5ebafe411204dbcb3969a6b2e92f2e22c4d778bb
==> Pouring sdsl-lite-2.1.1_2.x86_64_linux.bottle.tar.gz
Error: The `brew link` step did not complete successfully
The formula built, but is not symlinked into /home/linuxbrew/.linuxbrew
Could not symlink include/divsufsort.h
Target /home/linuxbrew/.linuxbrew/include/divsufsort.h
is a symlink belonging to libdivsufsort. You can unlink it:brew uninstall libdivsufsort to orca-6 Dockerfile lcoombe
commented
5 years ago Temporary uninstall of ruby
Docker error:
==> Installing brewsci/bio/uniqtag dependency: ruby
==> Downloading https://linuxbrew.bintray.com/bottles/ruby-2.6.3.x86_64_linux.bottle.tar.gz
==> Downloading from https://akamai.bintray.com/b5/b5be8d6c3c3bed4ae5ee9e6600716d35fff328d3480de0a84c213afa2e35ce4a?__gda__=exp=1556663110~hmac=17bdf314ac6a76e76b3c49030b6b07b01fccc7e4ebec6711a99bd4c7ca284510&response-content-disposition=attachment%3Bfilename%3D%22ruby-2.6.3.x86_64_linux.bottle.tar.gz%22&response-content-type=application%2Fgzip&requestInfo=U2FsdGVkX19RaGol5puvSD_1uekJY8S6zD3RxgwOg5tus-64v4hVNiG6JU5EOaKDtEjhIcqo7gtlN6sohOiauO_r0rLJ6Eo7QbYf4tIpEwwiqVmTMdbLOgZqdn9KRK-oPZ0M5l17a2zg0V7gPugCcQ&response-X-Checksum-Sha1=01658e18ba010d7d090bedfa9512ee8fa238df1a&response-X-Checksum-Sha2=b5be8d6c3c3bed4ae5ee9e6600716d35fff328d3480de0a84c213afa2e35ce4a
==> Pouring ruby-2.6.3.x86_64_linux.bottle.tar.gz
Error: The `brew link` step did not complete successfully
The formula built, but is not symlinked into /home/linuxbrew/.linuxbrew
Could not symlink bin/bundle
Target /home/linuxbrew/.linuxbrew/bin/bundle
is a symlink belonging to ruby. You can unlink it:
brew unlink rubySeems to be a bug related to the updated version of Ruby. As a work-around uninstalled ruby (and vim, which depends on it) so they can re-install cleanly.
lcoombe
commented
5 years ago Remove brewsci/science/weblogo
Docker error:
=> Installing brewsci/science/weblogo dependency: libomp
==> Downloading https://linuxbrew.bintray.com/bottles/libomp-7.0.0.x86_64_linux.bottle.tar.gz
==> Downloading from https://akamai.bintray.com/99/99dd838e3fdcfebde01929dd521a145e972955a78f959ecb00f8a59772568dd2?__gda__=exp=1556663609~hmac=564d1218247bd6dab4656000058f21257df263508503df919f9638180e76e60e&response-content-disposition=attachment%3Bfilename%3D%22libomp-7.0.0.x86_64_linux.bottle.tar.gz%22&response-content-type=application%2Fgzip&requestInfo=U2FsdGVkX19Nfvo4pkFsaSI-Fo5zMQ-4JYoJExkbGPD4vhpMJPknJKrLB8xjOZAtLdNWfRQqJAhqEyN2ZIbyHPby8An5ZSQJ6EXEw1pMcwAA16CvxlO7ST4r2zpILnS3jtBWeNgMxMnicAO1BVGpdQ&response-X-Checksum-Sha1=8845ff3d7eafbcc42b1f9be0d6109f52d5a46dde&response-X-Checksum-Sha2=99dd838e3fdcfebde01929dd521a145e972955a78f959ecb00f8a59772568dd2
==> Pouring libomp-7.0.0.x86_64_linux.bottle.tar.gz
Error: The `brew link` step did not complete successfully
The formula built, but is not symlinked into /home/linuxbrew/.linuxbrew
Could not symlink lib/libgomp.a
Target /home/linuxbrew/.linuxbrew/lib/libgomp.a
is a symlink belonging to gcc. You can unlink it:
brew unlink gccTemporary uninstall of libbigwig
Docker error:
Error: libbigwig is already installed from brewsci/science!
Please `brew uninstall libbigwig` first."Due to libbigwig being migrated to brewsci/bio since the orca-4 build. Temporarily uninstall so it can be re-installed cleanly.