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dan.gatti
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@dangatti-7637
Last seen 7.4 years ago
I just installed R 3.3 and was trying to upgrade my Bioconductor packages. But I ran into an odd "404 file not found" error with the BiocInstaller file.
> source("http://bioconductor.org/biocLite.R")
Bioconductor version 2.14 (BiocInstaller 1.14.3), ?biocLite for help
A newer version of Bioconductor is available for this version of R, ?BiocUpgrade for help
> biocLite("BiocUpgrade")
Upgrade all packages to Bioconductor version 3.0? [y/n]: y
Installing package into ‘C:/Program Files/R/library’
(as ‘lib’ is unspecified)
trying URL 'http://bioconductor.org/packages/3.0/bioc/src/contrib/BiocInstaller_1.16.5.zip'
Error in download.file(url, destfile, method, mode = "wb", ...) :
cannot open URL 'http://bioconductor.org/packages/3.0/bioc/src/contrib/BiocInstaller_1.16.5.zip'
Bioconductor version 2.14 (BiocInstaller 1.14.3), ?biocLite for help
A newer version of Bioconductor is available for this version of R, ?BiocUpgrade for help
'BiocInstaller' changed to version 1.14.3
BioC_mirror: http://bioconductor.org
Using Bioconductor version 2.14 (BiocInstaller 1.14.3), R version 3.3.0.
Temporarily using Bioconductor version 2.14
I found another post from an earlier version of Bioconductor that suggested modifying the method that R uses to download files. I tried all of the options in the 'method' argument of download.files().
> url = "http://bioconductor.org/packages/3.0/bioc/src/contrib/BiocInstaller_1.16.5.zip" > download.file(url = url, destfile = tempfile()) trying URL 'http://bioconductor.org/packages/3.0/bioc/src/contrib/BiocInstaller_1.16.5.zip' Error in download.file(url = url, destfile = tempfile()) : cannot open URL 'http://bioconductor.org/packages/3.0/bioc/src/contrib/BiocInstaller_1.16.5.zip' In addition: Warning message: In download.file(url = url, destfile = tempfile()) : cannot open URL 'http://bioconductor.org/packages/3.0/bioc/src/contrib/BiocInstaller_1.16.5.zip': HTTP status was '404 Not Found' > download.file(url = url, destfile = tempfile(), method = "wget") Warning messages: 1: running command 'wget "http://bioconductor.org/packages/3.0/bioc/src/contrib/BiocInstaller_1.16.5.zip" -O "C:\Users\dgatti\AppData\Local\Temp\Rtmp4U20cX\file12147eab173b"' had status 127 2: In download.file(url = url, destfile = tempfile(), method = "wget") : download had nonzero exit status
I'm omitting the similar results from the other methods that I tried. I can see http://bioconductor.org/packages/3.0/bioc/ in my web browser just fine.
Any thoughts here? From my end, it looks like BiocInstaller_1.16.5.zip isn't in http://bioconductor.org/packages/3.0/bioc/src/contrib/, but that seems like an unlikely oversight on the part of the Bioconductor team.
Thanks,
Dan
> sessionInfo() R version 3.3.0 (2016-05-03) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 7 x64 (build 7601) Service Pack 1 locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] BiocInstaller_1.14.3 loaded via a namespace (and not attached): [1] tools_3.3.0
Do this: Start an R session like this
then
remove.packages("BiocInstaller") # keep doing this till R says there is no such package source("https://bioconductor.org/biocLite.R") biocLite() # to update all outdated pkgs, answer 'a' when prompted