[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.]

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
>
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> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

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