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Question: BiocInstaller_1.16.5.zip not found when using biocLite("BiocUpgrade")
0
gravatar for dan.gatti
18 months ago by
dan.gatti0
dan.gatti0 wrote:

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
ADD COMMENTlink modified 18 months ago by Martin Morgan ♦♦ 20k • written 18 months ago by dan.gatti0

Do this: Start an R session like this

R --vanilla

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
ADD REPLYlink modified 18 months ago by Martin Morgan ♦♦ 20k • written 18 months ago by Dan Tenenbaum ♦♦ 8.2k
0
gravatar for dan.gatti
18 months ago by
dan.gatti0
dan.gatti0 wrote:

That worked.  Awesome.  Thanks.

ADD COMMENTlink written 18 months ago by dan.gatti0
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