BiocManager::install(whatever) doesn't work? biocLite is supposed to die, you see...
--t On Mon, Jul 30, 2018 at 2:45 PM Leonardo Collado Torres <lcoll...@jhu.edu> wrote: > Hi bioc-devel, > > A co-worker of mine (Richard) tried several times to install the > DelayedArray package. We got a couple of errors but it ultimately > looks like it's an internet connection problem. The truth is that > might be something affecting us on our side since I can't access > http://www.comunidadbioinfo.org/ either but collaborators in Mexico > (cc'ed) can right now. Me (on a Mac) and Emily (on a PC) on the same > network can't access that website. > > One of the errors we saw with Richard (on a PC) was about a missing > tar block. We failed to save that error message (for what's it's > worth, that was using RStudio). We then tried again and ran into this > error: > > > ## try http:// if https:// URLs are not supported > > > source("https://bioconductor.org/biocLite.R") > > Error in file(filename, "r", encoding = encoding) : > > cannot open the connection > > In addition: Warning message: > > In file(filename, "r", encoding = encoding) : > > InternetOpenUrl failed: 'A connection with the server could not be > established' > > > source("http://bioconductor.org/biocLite.R") > > Error in file(filename, "r", encoding = encoding) : > > cannot open the connection > > In addition: Warning message: > > In file(filename, "r", encoding = encoding) : > > InternetOpenUrl failed: 'A connection with the server could not be > established' > > > sessionInfo() > > R version 3.5.0 (2018-04-23) > > Platform: x86_64-w64-mingw32/x64 (64-bit) > > Running under: Windows 10 x64 (build 17134) > > > > Matrix products: default > > > > locale: > > [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United > States.1252 LC_MONETARY=English_United States.1252 > > [4] LC_NUMERIC=C LC_TIME=English_United > States.1252 > > > > attached base packages: > > [1] stats graphics grDevices utils datasets methods base > > > > loaded via a namespace (and not attached): > > [1] compiler_3.5.0 > > > > > On my Mac however, I can install DelayedArray. > > > source('http://bioconductor.org/biocLite.R') > Bioconductor version 3.7 (BiocInstaller 1.30.0), ?biocLite for help > > biocLite('DelayedArray') > BioC_mirror: https://bioconductor.org > Using Bioconductor 3.7 (BiocInstaller 1.30.0), R 3.5.1 (2018-07-02). > Installing package(s) ‘DelayedArray’ > trying URL ' > https://bioconductor.org/packages/3.7/bioc/bin/macosx/el-capitan/contrib/3.5/DelayedArray_0.6.2.tgz > ' > Content type 'application/x-gzip' length 1308365 bytes (1.2 MB) > ================================================== > downloaded 1.2 MB > > sessionInfo() > R version 3.5.1 (2018-07-02) > Platform: x86_64-apple-darwin15.6.0 (64-bit) > Running under: macOS High Sierra 10.13.6 > > Matrix products: default > BLAS: > /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib > LAPACK: > /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib > > locale: > [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] BiocInstaller_1.30.0 > > loaded via a namespace (and not attached): > [1] compiler_3.5.1 tools_3.5.1 > > > So, I have no idea how to approach this and just wanted to double > check that things are ok from your side. > > > Thanks, > Leo > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel