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