Hi, Just as a quick update. Everything worked yesterday when Richard used another PC computer from his home (another network). So it's definitely not a Bioc problem.
Yet I have no idea how to troubleshoot it beyond burning it all and starting from scratch: re-installing R and everything and checking if that works. Well, or testing using a hotspot wifi connection with one of our phones and seeing if that works to bypass the wifi network from work. Best, Leo On Mon, Jul 30, 2018 at 4:29 PM Tim Triche, Jr. <tim.tri...@gmail.com> wrote: > > are you sure his tmp directory isn't full > > --t > > > On Mon, Jul 30, 2018 at 3:25 PM Leonardo Collado Torres <lcoll...@jhu.edu> > wrote: >> >> From Richard: >> >> > BiocManager::install("DelayedArray") >> >> Bioconductor version 3.7 (BiocManager 1.30.1), R 3.5.0 (2018-04-23) >> >> Installing package(s) 'BiocVersion', 'DelayedArray' >> >> trying URL >> 'https://bioconductor.org/packages/3.7/bioc/bin/windows/contrib/3.5/BiocVersion_3.7.4.zip' >> >> Content type 'application/zip' length 8649 bytes >> >> downloaded 8649 bytes >> >> >> >> package ‘BiocVersion’ successfully unpacked and MD5 sums checked >> >> >> >> The downloaded binary packages are in >> >> C:\Users\Richard >> Straub\AppData\Local\Temp\RtmpQNrgbq\downloaded_packages >> >> installing the source package ‘DelayedArray’ >> >> >> >> trying URL >> 'https://bioconductor.org/packages/3.7/bioc/src/contrib/DelayedArray_0.6.2.tar.gz' >> >> Content type 'application/x-gzip' length 486139 bytes (474 KB) >> >> downloaded 474 KB >> >> >> >> Error in untar2(tarfile, files, list, exdir, restore_times) : >> >> incomplete block on file >> >> In R CMD INSTALL >> >> >> >> The downloaded source packages are in >> >> ‘C:\Users\Richard >> Straub\AppData\Local\Temp\RtmpQNrgbq\downloaded_packages’ >> >> installation path not writeable, unable to update packages: foreign, >> MASS, mgcv, survival >> >> Update old packages: 'openssl', 'stringi' >> >> Update all/some/none? [a/s/n]: >> >> n >> >> Warning message: >> >> In install.packages(pkgs = doing, lib = lib, repos = repos, ...) : >> >> installation of package ‘DelayedArray’ had non-zero exit status >> >> > >> >> >> >> Also, at http://bioconductor.org/packages/release/bioc/html/DelayedArray.html >> I don't see the tar for the Windows binary. >> >> >> >> >> On Mon, Jul 30, 2018 at 2:57 PM Tim Triche, Jr. <tim.tri...@gmail.com> wrote: >> > >> > 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 _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel