Hi all, I`m trying to install some packages like DESeq, GenomicRanges etc with R 2.14. I am getting error like the following. Same with dependent packages like RCurl, rtracklayer. Can someone help me with correct installation instructions here? > source("http://www.bioconductor.org/biocLite.R") > biocLite("GenomicRanges") BioC_mirror: 'http://www.bioconductor.org' Using R version 2.14, BiocInstaller version 1.2.1. Installing package(s) 'GenomicRanges' also installing the dependency ‘IRanges’ trying URL ' http://www.bioconductor.org/packages/2.9/bioc/bin/windows/contrib/2.14 /IRanges_1.12.5.zip ' Error in download.file(url, destfile, method, mode = "wb", ...) : cannot open URL ' http://www.bioconductor.org/packages/2.9/bioc/bin/windows/contrib/2.14 /IRanges_1.12.5.zip ' In addition: Warning message: In download.file(url, destfile, method, mode = "wb", ...) : cannot open: HTTP status was '404 Not Found' Warning in download.packages(pkgs, destdir = tmpd, available = available, : download of package ‘IRanges’ failed trying URL ' http://www.bioconductor.org/packages/2.9/bioc/bin/windows/contrib/2.14 /GenomicRanges_1.6.6.zip ' Error in download.file(url, destfile, method, mode = "wb", ...) : cannot open URL ' http://www.bioconductor.org/packages/2.9/bioc/bin/windows/contrib/2.14 /GenomicRanges_1.6.6.zip ' In addition: Warning message: In download.file(url, destfile, method, mode = "wb", ...) : cannot open: HTTP status was '404 Not Found' Warning in download.packages(pkgs, destdir = tmpd, available = available, : download of package ‘GenomicRanges’ failed > sessionInfo() R version 2.14.1 (2011-12-22) Platform: i386-pc-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] splines stats graphics grDevices utils datasets methods base other attached packages: [1] Biostrings_2.22.0 locfit_1.5-6 lattice_0.20-0 akima_0.5-7 DEXSeq_1.0.2 Biobase_2.14.0 GenomicRanges_1.6.7 IRanges_1.12.6 [9] edgeR_2.4.3 limma_3.10.2 BiocInstaller_1.2.1 loaded via a namespace (and not attached): [1] bitops_1.0-4.1 grid_2.14.1 hwriter_1.3 plyr_1.7.1 statmod_1.4.14 stringr_0.6 tools_2.14.1 zlibbioc_1.0.0 Many thanks [[alternative HTML version deleted]]

On 02/18/2012 04:18 PM, Alpesh Querer wrote: > Hi all, > > I`m trying to install some packages like DESeq, GenomicRanges etc with R > 2.14. > I am getting error like the following. Same with dependent packages like > RCurl, rtracklayer. > Can someone help me with correct installation instructions here? > > >> source("http://www.bioconductor.org/biocLite.R") >> biocLite("GenomicRanges") > BioC_mirror: 'http://www.bioconductor.org' > Using R version 2.14, BiocInstaller version 1.2.1. > Installing package(s) 'GenomicRanges' > also installing the dependency ?IRanges? > > trying URL ' > http://www.bioconductor.org/packages/2.9/bioc/bin/windows/contrib/2. 14/IRanges_1.12.5.zip > ' > Error in download.file(url, destfile, method, mode = "wb", ...) : > cannot open URL ' > http://www.bioconductor.org/packages/2.9/bioc/bin/windows/contrib/2. 14/IRanges_1.12.5.zip I'm not sure exactly why you're seeing this, but the problem is that the current version of IRanges is 1.12.6, but biocLite is pointing you toward 1.12.5. I would suggest starting a new R session and trying again. In particular, open a DOS prompt and run Rgui --vanilla perhaps proving the full path to Rgui, along the lines of "c:\Program Files\R\R-2.14.1\bin\i386\Rgui.exe" --vanilla Martin > ' > In addition: Warning message: > In download.file(url, destfile, method, mode = "wb", ...) : > cannot open: HTTP status was '404 Not Found' > Warning in download.packages(pkgs, destdir = tmpd, available = available, : > download of package ?IRanges? failed > trying URL ' > http://www.bioconductor.org/packages/2.9/bioc/bin/windows/contrib/2. 14/GenomicRanges_1.6.6.zip > ' > Error in download.file(url, destfile, method, mode = "wb", ...) : > cannot open URL ' > http://www.bioconductor.org/packages/2.9/bioc/bin/windows/contrib/2. 14/GenomicRanges_1.6.6.zip > ' > In addition: Warning message: > In download.file(url, destfile, method, mode = "wb", ...) : > cannot open: HTTP status was '404 Not Found' > Warning in download.packages(pkgs, destdir = tmpd, available = available, : > download of package ?GenomicRanges? failed > > > >> sessionInfo() > R version 2.14.1 (2011-12-22) > Platform: i386-pc-mingw32/i386 (32-bit) > > locale: > [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United > States.1252 LC_MONETARY=English_United States.1252 LC_NUMERIC=C > > [5] LC_TIME=English_United States.1252 > > attached base packages: > [1] splines stats graphics grDevices utils datasets methods > base > > other attached packages: > [1] Biostrings_2.22.0 locfit_1.5-6 lattice_0.20-0 > akima_0.5-7 DEXSeq_1.0.2 Biobase_2.14.0 > GenomicRanges_1.6.7 IRanges_1.12.6 > [9] edgeR_2.4.3 limma_3.10.2 BiocInstaller_1.2.1 > > loaded via a namespace (and not attached): > [1] bitops_1.0-4.1 grid_2.14.1 hwriter_1.3 plyr_1.7.1 > statmod_1.4.14 stringr_0.6 tools_2.14.1 zlibbioc_1.0.0 > > Many thanks > > [[alternative HTML version deleted]] > > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793