[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
Leonardo Collado Torres
lcoll@do @ending from jhu@edu
Wed Aug 1 23:23:02 CEST 2018
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 using 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 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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