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Question: Unable to install the package "tissuesGeneExpression"
0
gravatar for mdroog
3 days ago by
mdroog0
mdroog0 wrote:

I am trying to install a package so I can continue a bioconductor course. Unfortunately it's not working. I get the following line:

 

> source("https://bioconductor.org/biocLite.R")
Bioconductor version 3.5 (BiocInstaller 1.26.0), ?biocLite for help
> biocLite("tissuesGeneExpression")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.5 (BiocInstaller 1.26.0), R 3.4.1 (2017-06-30).
Installing package(s) 'tissuesGeneExpression'
Warning: unable to access index for repository https://www.stats.ox.ac.uk/pub/RWin/src/contrib:
  cannot open URL 'https://www.stats.ox.ac.uk/pub/RWin/src/contrib/PACKAGES'
Warning: unable to access index for repository https://www.stats.ox.ac.uk/pub/RWin/bin/windows/contrib/3.4:
  cannot open URL 'https://www.stats.ox.ac.uk/pub/RWin/bin/windows/contrib/3.4/PACKAGES'
Warning: unable to access index for repository https://www.stats.ox.ac.uk/pub/RWin/src/contrib:
  cannot open URL 'https://www.stats.ox.ac.uk/pub/RWin/src/contrib/PACKAGES'
Warning message:
package 'tissuesGeneExpression' is not available (for R version 3.4.1) 
> sessionInfo()
R version 3.4.1 (2017-06-30)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

Matrix products: default

locale:
[1] LC_COLLATE=Dutch_Netherlands.1252  LC_CTYPE=Dutch_Netherlands.1252   
[3] LC_MONETARY=Dutch_Netherlands.1252 LC_NUMERIC=C                      
[5] LC_TIME=Dutch_Netherlands.1252    

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] gwascat_2.8.0                            Homo.sapiens_1.3.1                      
 [3] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2  org.Hs.eg.db_3.4.1                      
 [5] GO.db_3.4.1                              OrganismDbi_1.18.0                      
 [7] GenomicFeatures_1.28.4                   AnnotationDbi_1.38.1                    
 [9] Biobase_2.36.2                           BiocInstaller_1.26.0                    
[11] SNPlocs.Hsapiens.dbSNP144.GRCh37_0.99.20 BSgenome_1.44.0                         
[13] rtracklayer_1.36.4                       Biostrings_2.44.1                       
[15] XVector_0.16.0                           GenomicRanges_1.28.4                    
[17] GenomeInfoDb_1.12.2                      IRanges_2.10.2                          
[19] S4Vectors_0.14.3                         BiocGenerics_0.22.0                     

loaded via a namespace (and not attached):
Error in x[["Version"]] : subscript out of bounds
In addition: Warning message:
In FUN(X[[i]], ...) :
  DESCRIPTION file of package 'Rcpp' is missing or broken

ADD COMMENTlink modified 3 days ago by Mike Smith1.9k • written 3 days ago by mdroog0
0
gravatar for Mike Smith
3 days ago by
Mike Smith1.9k
EMBL Heidelberg / de.NBI
Mike Smith1.9k wrote:

I'm not sure the tissuesGeneExpression package was ever 'officially' in Bioconductor, I think it was created for teaching purposes only.  You can find a Github repository for it at https://github.com/genomicsclass/tissuesGeneExpression and you can try installing it form there using this code:

library(BiocInstaller)
biocLite("genomicsclass/tissuesGeneExpression")

Unrelated, but it looks like you might want to reinstall the Rcpp package too

ADD COMMENTlink written 3 days ago by Mike Smith1.9k
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