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Question: bioconductor not available for R 3.2.2
0
gravatar for r01ced13
2.9 years ago by
r01ced130
r01ced130 wrote:

Hi all,

I am aware that a question about this error message was posted before, but following the recommendations has still not gotten me much further.

Please find my code and error message below:

> source("http://www.bioconductor.org/biocLite.R")
  Installing package into ‘C:/Users/r01ced13/Documents/R/win-library/3.2’
   (as ‘lib’ is unspecified)
   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
   'biocLite.R' failed to install 'BiocInstaller', use
     'install.packages("BiocInstaller",
    repos="https://bioconductor.org/packages/3.1/bioc")' or
    'install.packages("BiocInstaller",
    repos="http://bioconductor.org/packages/3.1/bioc")'
    Warning message:
     package ‘BiocInstaller’ is not available (for R version 3.2.2)

I then followed the advise to try downloading the url as temporary file:

> url="http://bioconductor.org/packages/3.1/bioc/src/contrib/PACKAGES"
> t=tempfile()
> download.file(url,t)
trying URL 'http://bioconductor.org/packages/3.1/bioc/src/contrib/PACKAGES'
Content type '' length 278574 bytes (272 KB)
downloaded 272 KB

which appears to download a file of expected size as stated in the previous post. I looked at the file t to see if it is functional:

[7611] "Version: 1.16.0"                                                                                           
[7612] "Depends: R (>= 2.15), methods, igraph"                                                                     
[7613] "Imports: RCurl, XML"                                                                                       
[7614] "Suggests: PANR, pvclust"                                                                                   
[7615] "License: GPL (>= 2)"                                                                                       
[7616] "MD5sum: 685e7d91565b3c3916396990a4227bdc"                                                                  
[7617] "NeedsCompilation: no"                                                                                      
[7618] ""                                                                                                          
[7619] "Package: REDseq"                                                                                           
[7620] "Version: 1.14.1"                                                                                           
[7621] "Depends: R (>= 2.15.0), BiocGenerics (>= 0.1.0),"                                                          
[7622] "        BSgenome.Celegans.UCSC.ce2, multtest, Biostrings, BSgenome,"                                       
[7623] "        ChIPpeakAnno"                                                                                      
[7624] "Imports: BiocGenerics, AnnotationDbi, Biostrings, ChIPpeakAnno,"                                           
[7625] "        graphics, IRanges (>= 1.13.5), multtest, stats, utils" 

which appears to be sensible output.

I then tried source("http://www.bioconductor.org/biocLite.R") again but get the same error message as before:

> source("http://www.bioconductor.org/biocLite.R")
Installing package into ‘C:/Users/r01ced13/Documents/R/win-library/3.2’
(as ‘lib’ is unspecified)
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
'biocLite.R' failed to install 'BiocInstaller', use 'install.packages("BiocInstaller", repos="https://bioconductor.org/packages/3.1/bioc")' or
  'install.packages("BiocInstaller", repos="http://bioconductor.org/packages/3.1/bioc")'
Warning message:
package ‘BiocInstaller’ is not available (for R version 3.2.2)

Could someone suggest a solution please? Any suggestions welcome!

Thanks!

 

ADD COMMENTlink modified 2.9 years ago • written 2.9 years ago by r01ced130
0
gravatar for Martin Morgan
2.9 years ago by
Martin Morgan ♦♦ 22k
United States
Martin Morgan ♦♦ 22k wrote:

Try options(useHTTPS=FALSE) before source("http://bioconductor.org/biocLite.R").

ADD COMMENTlink written 2.9 years ago by Martin Morgan ♦♦ 22k
0
gravatar for r01ced13
2.9 years ago by
r01ced130
r01ced130 wrote:

Thanks for your reply Martin, unfortunately that did not work either

ADD COMMENTlink written 2.9 years ago by r01ced130

If you could please update your response to include the session showing your attempt that would be very helpful. Martin

ADD REPLYlink modified 2.9 years ago • written 2.9 years ago by Martin Morgan ♦♦ 22k
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