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Question: Problems installing S4Vectors using Bioconductor version 3.0 (BiocInstaller 1.16.5), R version 3.2.1.
0
gravatar for tresch
2.4 years ago by
tresch0
Germany
tresch0 wrote:

Dear BioConductor team,

I am having problems installing the package "S4Vectors" using the latest versions of R and BioC (see below). Judging from the posts here, this seems to be a recurrent problem. Thanks for any help, Best,

Achim

 

> biocLite("S4Vectors")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 3.0 (BiocInstaller 1.16.5), R version 3.2.1.
Installing package(s) 'S4Vectors'
Warning: unable to access index for repository http://bioconductor.org/packages/3.0/bioc/bin/windows/contrib/3.2
Warning: unable to access index for repository http://bioconductor.org/packages/3.0/data/annotation/bin/windows/contrib/3.2
Warning: unable to access index for repository http://bioconductor.org/packages/3.0/data/experiment/bin/windows/contrib/3.2
Package which is only available in source form, and may need compilation of C/C++/Fortran:
  ‘S4Vectors’
  These will not be installed
Old packages: 'Biobase', 'Biostrings', 'biovizBase', 'GenomicAlignments', 'GenomicRanges', 'IRanges',
  'Matrix', 'Rsamtools', 'rtracklayer', 'STAN', 'VariantAnnotation', 'XVector', 'zlibbioc'
Update all/some/none? [a/s/n]: n
Warning message:
installed directory not writable, cannot update packages 'boot', 'class', 'cluster', 'foreign',
  'KernSmooth', 'MASS', 'Matrix', 'nlme', 'nnet', 'rpart', 'spatial', 'survival' 

> sessionInfo()
R version 3.2.1 (2015-06-18)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

locale:
[1] LC_COLLATE=German_Germany.1252  LC_CTYPE=German_Germany.1252    LC_MONETARY=German_Germany.1252
[4] LC_NUMERIC=C                    LC_TIME=German_Germany.1252    

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

other attached packages:
[1] BiocGenerics_0.12.1  BiocInstaller_1.16.5

loaded via a namespace (and not attached):
[1] tools_3.2.1
 

 

ADD COMMENTlink written 2.4 years ago by tresch0
1
gravatar for Martin Morgan
2.4 years ago by
Martin Morgan ♦♦ 20k
United States
Martin Morgan ♦♦ 20k wrote:

Earlier in your session, when you first ran source("http://bioconductor.org/biocLite.R") or perhaps library(BiocInstaller), did you see a message

BiocInstaller version 3.0 is too old for R version 3.2.1;
  remove.packages("BiocInstaller") then
  source("http://bioconductor.org/biocLite.R") 

Try following these instructions in a new R session. If remove.packages() fails with some kind of error message, try and trouble shoot why that is. If the problem remains. Start a fresh R session and paste the entire output from the following commands

remove.pacakges("BiocInstaller")
source("http://bioconductor.org/biocLite.R")
BiocInstaller::biocVersion()
.libPaths()
​sessionInfo()

 

 

ADD COMMENTlink written 2.4 years ago by Martin Morgan ♦♦ 20k
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