Question: workflowInstall issues; missing Windows binary
0
gravatar for anoll2
4.2 years ago by
anoll20
anoll20 wrote:

Hello I am interested in using the bioconductor 3.1 workflow for annotation.  It appears as though the windows binary is missing from the bioconductor repository?  Perhaps it just needs to be uploaded or is not yet available?  (http://master.bioconductor.org/help/workflows/annotation/annotation_0.99.103323.zip)

> source("http://bioconductor.org/biocLite.R")
Bioconductor version 3.1 (BiocInstaller 1.18.2), ?biocLite for help

> workflowInstall("annotation")
Installing package into ‘C:/Users/anoll2/Documents/R/win-library/3.2’
(as ‘lib’ is unspecified)
Warning in install.packages :
  cannot open: HTTP status was '404 Not Found'
Warning in install.packages :
  cannot open: HTTP status was '404 Not Found'
Warning in install.packages :
  unable to access index for repository http://bioconductor.org/packages/3.1/workflows/src/contrib
Warning in install.packages :
  package ‘annotation’ is not available (for R version 3.2.0)
Warning in install.packages :
  cannot open: HTTP status was '404 Not Found'
Warning in install.packages :
  cannot open: HTTP status was '404 Not Found'
Warning in install.packages :
  unable to access index for repository http://bioconductor.org/packages/3.1/workflows/bin/windows/contrib/3.2

> sessionInfo()
R version 3.2.0 (2015-04-16)
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] parallel  stats4    stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
 [1] GO.db_3.1.2          RSQLite_1.0.0        DBI_0.3.1           
 [4] AnnotationDbi_1.30.1 GenomeInfoDb_1.4.0   IRanges_2.2.1       
 [7] S4Vectors_0.6.0      Biobase_2.28.0       BiocGenerics_0.14.0 
[10] BiocInstaller_1.18.2

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

ADD COMMENTlink modified 4.2 years ago • written 4.2 years ago by anoll20

Something was misconfigured; please try again in a fresh R session (it just worked for me in windows).

ADD REPLYlink written 4.2 years ago by Dan Tenenbaum8.2k
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