Thank you for your responses. I have tried the following :
1- From R version 3.0.2 (2013-09-25), still installed on my PC
the command "> source("http://bioconductor.org/biocLite.R")" is working
but the command "> source("https://bioconductor.org/biocLite.R")" is not working issuing in the following error message:
Error in file(filename, "r", encoding = encoding) :
cannot open the connection
In addition: Warning message:
In file(filename, "r", encoding = encoding) : unsupported URL scheme
2- From Firefox
Entering : http://bioconductor.org/packages/3.1/bioc/src/contrib/PACKAGES
give me access to the list of package:
Package: a4
Version: 1.16.0
Depends: a4Base, a4Preproc, a4Classif, a4Core, a4Reporting
Suggests: MLP, nlcv, ALL, Cairo
License: GPL-3
MD5sum: 1bd22944d9e6d7bb2f6c742dcf7e340f
NeedsCompilation: no
Package: a4Base
Version: 1.16.0
Depends: methods, graphics, grid, Biobase, AnnotationDbi, annaffy, mpm,
genefilter, limma, multtest, glmnet, a4Preproc, a4Core, gplots
Suggests: Cairo, ALL
Enhances: gridSVG, JavaGD
License: GPL-3
MD5sum: 0be52bafda21bc84cb17c27376a0b61a
NeedsCompilation: no
etc....
3 - From the newly installed R version:
R version 3.2.2 (2015-08-14) -- "Fire Safety"
Copyright (C) 2015 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)
neither > source("http://bioconductor.org/biocLite.R")
nor > source("https://bioconductor.org/biocLite.R")
are working with different error message.Respectively, for the http command
> source("http://bioconductor.org/biocLite.R")
Warning: unable to access index for repository https://bioconductor.org/packages/3.2/bioc/src/contrib
Warning: unable to access index for repository https://bioconductor.org/packages/3.2/bioc/bin/windows/contrib/3.2
and for the https
> 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: 'An error occurred in the secure channel support'
From the fact that I could get the list of packages from firefox, I am encline to think that the problems are not coming from Windows or some configuration but rather from some thing getting wrong with installation of R 3.2.
Best wishes,
Michel
Folloxing are more info on my R session:
> sessionInfo()
R version 3.2.2 (2015-08-14)
Platform: i386-w64-mingw32/i386 (32-bit)
Running under: Windows XP (build 2600) Service Pack 3
locale:
[1] LC_COLLATE=French_France.1252 LC_CTYPE=French_France.1252
[3] LC_MONETARY=French_France.1252 LC_NUMERIC=C
[5] LC_TIME=French_France.1252
attached base packages:
[1] tcltk stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] survival_2.38-3 lattice_0.20-33 XLConnect_0.2-11
[4] XLConnectJars_0.2-9
loaded via a namespace (and not attached):
[1] splines_3.2.2 grid_3.2.2 rJava_0.9-7
>
Does http:// work on your new R version?
Since you're on Windows XP, you may even run into issues with SSL certificate validation. My understanding is that Windows controls all of this through "Internet Options" in Internet Explorer. To confirm that communication to bioconductor resources works, you could open Internet Explorer and enter "https://bioconductor.org/" in the address bar. Hopefully this works. If not, let us know the outcome. Alternatively, you might try this :