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.triche at 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 <lcollado at 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.triche at 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 <lcollado at 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
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