[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]

>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