Question: GO.db won't install for using goseq package
gravatar for veerle
2.1 years ago by
veerle0 wrote:

Hej, I am trying to install the Goseq package, but I keep getting this error. I tried downloading the GO.db package, but then I get a new error. See below.
I have update both R and RStudio to the latest version. 


Anyone has some advice on how to get it running? 

Thank you,


> library(goseq)

Indlæser krævet pakke: BiasedUrn

Indlæser krævet pakke: geneLenDataBase

Error: package or namespace load failed for ‘goseq’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):

 der er ingen pakke med navn ‘GO.db’

> source("")

Bioconductor version 3.5 (BiocInstaller 1.26.1), ?biocLite for help

> biocLite("goseq")


Using Bioconductor 3.5 (BiocInstaller 1.26.1), R 3.4.1 (2017-06-30).

Installing package(s) ‘goseq’

also installing the dependency ‘GO.db’


trying URL ''

Content type 'application/zip' length 1613819 bytes (1.5 MB)

downloaded 1.5 MB


package ‘goseq’ successfully unpacked and MD5 sums checked


The downloaded binary packages are in


installing the source package ‘GO.db’


trying URL ''

Content type 'application/x-gzip' length 32989255 bytes (31.5 MB)

downloaded 31.5 MB



CMD.EXE was started with the above path as the current directory.

UNC paths are not supported.  Defaulting to Windows directory.

* installing *source* package 'GO.db' ...

** R

** inst

** preparing package for lazy loading

Error: package or namespace load failed for 'Biobase' in inDL(x, as.logical(local), as.logical(now), ...):

 kan ikke indlæse delt objekt '//':

  LoadLibrary failure:  This file is currently not available for use on this computer.


Error : package 'Biobase' could not be loaded

ERROR: lazy loading failed for package 'GO.db'

* removing '\\'


The downloaded source packages are in


installation path not writeable, unable to update packages: boot, Matrix, mgcv

Warning messages:

1: running command '"C:/PROGRA~1/R/R-34~1.1/bin/x64/R" CMD INSTALL -l "\\\Users\AU346588\Documents\R\win-library\3.4" C:\Users\au346588\AppData\Local\Temp\RtmpeO0wQ3/downloaded_packages/GO.db_3.4.1.tar.gz' had status 1 

2: In install.packages(pkgs = doing, lib = lib, ...) :

  installation of package ‘GO.db’ had non-zero exit status



> 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

[1] LC_COLLATE=Danish_Denmark.1252  LC_CTYPE=Danish_Denmark.1252    LC_MONETARY=Danish_Denmark.1252 LC_NUMERIC=C                   
[5] LC_TIME=Danish_Denmark.1252    

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

other attached packages:
[1] BiocInstaller_1.26.1   geneLenDataBase_1.12.0 BiasedUrn_1.07        

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.12               compiler_3.4.1             GenomeInfoDb_1.12.2        XVector_0.16.0             GenomicFeatures_1.28.4    
 [6] bitops_1.0-6               tools_3.4.1                zlibbioc_1.22.0            biomaRt_2.32.1             digest_0.6.12             
[11] bit_1.1-12                 nlme_3.1-131               RSQLite_2.0                memoise_1.1.0              tibble_1.3.4              
[16] lattice_0.20-35            mgcv_1.8-17                rlang_0.1.2                Matrix_1.2-10              DelayedArray_0.2.7        
[21] DBI_0.7                    parallel_3.4.1             GenomeInfoDbData_0.99.0    rtracklayer_1.36.4         Biostrings_2.44.2         
[26] S4Vectors_0.14.4           IRanges_2.10.3             stats4_3.4.1               bit64_0.9-7                grid_3.4.1                
[31] Biobase_2.36.2             AnnotationDbi_1.38.2       XML_3.98-1.9               BiocParallel_1.10.1        blob_1.1.0                
[36] Rsamtools_1.28.0           matrixStats_0.52.2         GenomicAlignments_1.12.2   BiocGenerics_0.22.0        GenomicRanges_1.28.5      
[41] SummarizedExperiment_1.6.3 RCurl_1.95-4.8            

ADD COMMENTlink modified 2.1 years ago by Martin Morgan ♦♦ 23k • written 2.1 years ago by veerle0
Answer: GO.db won't install for using goseq package
gravatar for Martin Morgan
2.1 years ago by
Martin Morgan ♦♦ 23k
United States
Martin Morgan ♦♦ 23k wrote:

Avoid 'UNC' paths like \\\Users... by mapping the path to a network drive (e.g., here) and using that to launch R.

ADD COMMENTlink written 2.1 years ago by Martin Morgan ♦♦ 23k
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