[Bioc-devel] Is biocLite() working for you right now? Could be a problem on our side. Issue with DelayedArray install with a PC on R 3.5.0

[Tim Triche, Jr.]

are you sure his tmp directory isn't full

--t


On Mon, Jul 30, 2018 at 3:25 PM Leonardo Collado Torres <lcollado using 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 using 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 using 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 using r-project.org mailing list
> >> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

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