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Question: Couldn't install GenomicRanges packages after update bioconductor to 3.2 version ?
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gravatar for Jurat Shahidin
21 months ago by
Italy
Jurat Shahidin60 wrote:

Dear member of this group:

I got strange error when I update bioconductor to latest version 3.2, and I could not install GenomicRanges, IRanges packages. Here is the error what I ran into: 

 

> sessionInfo()
R version 3.2.0 (2015-04-16)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 8 x64 (build 9200)

locale:
[1] LC_COLLATE=Uyghur_China.1256  LC_CTYPE=Uyghur_China.1256   
[3] LC_MONETARY=Uyghur_China.1256 LC_NUMERIC=C                 
[5] LC_TIME=Uyghur_China.1256    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] BiocInstaller_1.20.1

loaded via a namespace (and not attached):
[1] tools_3.2.0

 

then, I tried to install GenomicRanges packages but can not have it. I got error like this:

install.packages("GenomicRanges")
Installing package into ‘C:/Users/Jvret/Documents/R/win-library/3.2’
(as ‘lib’ is unspecified)
Warning in install.packages :
  package ‘GenomicRanges’ is not available (for R version 3.2.0)

 

why this happens ? How can I fix this bug? Please help me out !!

 

ADD COMMENTlink written 21 months ago by Jurat Shahidin60

You can see that R is reporting version 3.2.0. The current release version of R is 3.2.3.

The way to install any Bioconductor package is listed on its landing page, e.g., for GenomicRanges

biocLite("GenomicRanges")
ADD REPLYlink written 21 months ago by Martin Morgan ♦♦ 20k

Dear Martin Morgan:

I have tried this already but did not work. I got same error like this:

biocLite("GenomicRanges")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.2 (BiocInstaller 1.20.1), R 3.2.0 (2015-04-16).
Installing package(s) ‘GenomicRanges’
also installing the dependencies ‘zlibbioc’, ‘S4Vectors’, ‘IRanges’, ‘XVector’

  There is a binary version available but the source version is
  later:
              binary source needs_compilation
GenomicRanges 1.22.3 1.22.4              TRUE

  Binaries will be installed
trying URL 'https://bioconductor.org/packages/3.2/bioc/bin/windows/contrib/3.2/zlibbioc_1.16.0.zip'
Content type 'application/zip' length 693613 bytes (677 KB)
downloaded 677 KB

trying URL 'https://bioconductor.org/packages/3.2/bioc/bin/windows/contrib/3.2/S4Vectors_0.8.11.zip'
Content type 'application/zip' length 1755464 bytes (1.7 MB)
downloaded 1.7 MB

trying URL 'https://bioconductor.org/packages/3.2/bioc/bin/windows/contrib/3.2/IRanges_2.4.6.zip'
Content type 'application/zip' length 3088977 bytes (2.9 MB)
downloaded 2.9 MB

trying URL 'https://bioconductor.org/packages/3.2/bioc/bin/windows/contrib/3.2/XVector_0.10.0.zip'
Content type 'application/zip' length 749339 bytes (731 KB)
downloaded 731 KB

trying URL 'https://bioconductor.org/packages/3.2/bioc/bin/windows/contrib/3.2/GenomicRanges_1.22.3.zip'
Content type 'application/zip' length 3028504 bytes (2.9 MB)
downloaded 2.9 MB

package ‘zlibbioc’ successfully unpacked and MD5 sums checked
Warning: cannot remove prior installation of package ‘zlibbioc’
package ‘S4Vectors’ successfully unpacked and MD5 sums checked
Warning: cannot remove prior installation of package ‘S4Vectors’
package ‘IRanges’ successfully unpacked and MD5 sums checked
Warning: cannot remove prior installation of package ‘IRanges’
package ‘XVector’ successfully unpacked and MD5 sums checked
Warning: cannot remove prior installation of package ‘XVector’
package ‘GenomicRanges’ successfully unpacked and MD5 sums checked
Warning: cannot remove prior installation of package ‘GenomicRanges’

The downloaded binary packages are in
    C:\Users\Jvret\AppData\Local\Temp\Rtmp0GNchN\downloaded_packages
Old packages: 'TxDb.Dmelanogaster.UCSC.dm3.ensGene', 'boot', 'class',
  'cluster', 'codetools', 'foreign', 'KernSmooth', 'lattice', 'MASS',
  'Matrix', 'mgcv', 'nlme', 'nnet', 'rpart', 'spatial', 'survival'
Update all/some/none? [a/s/n]: 

 

then, I did like this:

 install.packages("GenomicRanges")
Installing package into ‘C:/Users/Jvret/Documents/R/win-library/3.2’
(as ‘lib’ is unspecified)
Warning in install.packages :
  package ‘GenomicRanges’ is not available (for R version 3.2.0)
> library(GenomicRanges)
Error in library(GenomicRanges) : 
  there is no package called ‘GenomicRanges’

before, I used old version of biocondutor package and it works perfectly, I could install both GenomicRanges and IRanges packages. Now, I have updated new bioconductor but GenomicRanges package cannot be installed. Thanks a lot !

ADD REPLYlink modified 21 months ago • written 21 months ago by Jurat Shahidin60
1

So instead of the error "there is no package called 'GenomicRanges'", the recommended procedure leads to the warning that R could not "remove prior installation of package 'GenomicRanges'".

This means that one user (maybe 'Administrator') installed GenomicRanges, but another (non-administrator) user tried to update it. Your computer is in a mess, and needs to be cleaned up. There are many ways to do this.

I suggest that as administrator you start R and run the command .libPaths(). Then quit R, remove the version of R that you have installed, and remove the directories reported by .libPaths().

As your regular user, install R version 3.2.3. Start that version of R, and run the command

source("http://bioconductor.org/biocLite.R")

Install any other packages, from Bioconductor or CRAN, using biocLite(), e.g,.

biocLite(c("GenomicRanges", "TxDb.Dmelanogaster.UCSC.dm3.ensGene"))

 

ADD REPLYlink modified 21 months ago • written 21 months ago by Martin Morgan ♦♦ 20k

Dear Martin Morgan:

Thanks a lot for your help. I have cleared all mass from the past. Now problem solved. Thanks a lot !!

ADD REPLYlink written 21 months ago by Jurat Shahidin60
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