Unable to install the package "tissuesGeneExpression"
2
1
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mdroog ▴ 10
@mdroog-13422
Last seen 5.5 years ago

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

bioconductor • 4.6k views
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1
Entering edit mode
Mike Smith ★ 6.5k
@mike-smith
Last seen 2 hours ago
EMBL Heidelberg

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

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0
Entering edit mode
@151be250
Last seen 14 days ago
Pakistan

For packages which are not available, you have to then install these packages directly from its source like its Github repository. To install packages from their "source", you must have rtools installed available at https://cran.r-project.org/bin/windows/Rtools/. While installing Rtools make sure you install the Rtools for the same version of the R which you intend to use. For example, if your R version is 4.4.1, then the Rtools to be installed will be Rtools 4.4. Similarly for R version 4.2.1, the Rtools version will be 4.2. After installing you need to restart R and/or Rstudio. After restarting R, make sure you are using the right version of R for which you installed Rtools. After this is done, you are good to install any package from its source and there are plenty of methods available like the one which I followed and installed this package.

library(devtools)

# after downloading and extracting the github repo to your downloads directory (C:/Users/{YOUR USERNAME}/Downloads)

install. Packages("C:/Users/{YOUR USERNAME}/Downloads/tissuesGeneExpression-master", repos = NULL, type = "source")

# check installation
library("tissuesGeneExpression")
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