[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]

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