When I try to install the hightrokghput assays workflow The following happens:
> source("https://bioconductor.org/workflows.R") Bioconductor version 3.4 (BiocInstaller 1.24.0), ?biocLite for help > workflowInstall("highthroughputassays") Installing package into ‘/Users/johansenkh/Library/R/3.3/library’ (as ‘lib’ is unspecified) Warning in install.packages : URL 'https://bioconductor.org/packages/3.4/workflows/bin/macosx/mavericks/contrib/3.3/PACKAGES.gz': status was '404 Not Found' Warning in install.packages : URL 'https://bioconductor.org/packages/3.4/workflows/bin/macosx/mavericks/contrib/3.3/PACKAGES': status was '404 Not Found' Warning in install.packages : unable to access index for repository https://bioconductor.org/packages/3.4/workflows/bin/macosx/mavericks/contrib/3.3: cannot download all files installing the source package ‘highthroughputassays’ trying URL 'https://bioconductor.org/packages/3.4/workflows/src/contrib/highthroughputassays_0.99.120889.tar.gz' Content type 'application/x-gzip' length 441585 bytes (431 KB) ================================================== downloaded 431 KB * installing *source* package ‘highthroughputassays’ ... ** inst ** help No man pages found in package ‘highthroughputassays’ *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded Error : .onLoad failed in loadNamespace() for 'rgl', details: call: dyn.load(file, DLLpath = DLLpath, ...) error: unable to load shared object '/Users/johansenkh/Library/R/3.3/library/rgl/libs/rgl.so': dlopen(/Users/johansenkh/Library/R/3.3/library/rgl/libs/rgl.so, 6): Library not loaded: /opt/X11/lib/libGLU.1.dylib Referenced from: /Users/johansenkh/Library/R/3.3/library/rgl/libs/rgl.so Reason: image not found Error: loading failed Execution halted ERROR: loading failed * removing ‘/Users/johansenkh/Library/R/3.3/library/highthroughputassays’ Warning in install.packages : installation of package ‘highthroughputassays’ had non-zero exit status The downloaded source packages are in ‘/private/var/folders/hb/sc3x6vtj0ys009qnyplbp2_h1g5hgm/T/RtmptgIUo5/downloaded_packages’
What should I do about it? I have tried on 3 computers (Mac).
I assume you previously had a working installation of rgl, but probably because of some system changes (?) it stopped loading. The easiest thing to try is to re-install the package.
It gives the exact same error after doing that. Further, I have tried on 2 other macs, and it wouldn't work there either.