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Question: GO.db won't install for using goseq package
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gravatar for veerle
9 weeks ago by
veerle0
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("https://bioconductor.org/biocLite.R")

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

> biocLite("goseq")

BioC_mirror: https://bioconductor.org

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 'https://bioconductor.org/packages/3.5/bioc/bin/windows/contrib/3.4/goseq_1.28.0.zip'

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

C:\Users\au346588\AppData\Local\Temp\RtmpeO0wQ3\downloaded_packages

installing the source package ‘GO.db’

 

trying URL 'https://bioconductor.org/packages/3.5/data/annotation/src/contrib/GO.db_3.4.1.tar.gz'

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

downloaded 31.5 MB

 

'\\uni.au.dk\Users\au346588\Documents'

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 '//uni.au.dk/Users/AU346588/Documents/R/win-library/3.4/Biobase/libs/x64/Biobase.dll':

  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 '\\uni.au.dk/Users/AU346588/Documents/R/win-library/3.4/GO.db'

 

The downloaded source packages are in

‘C:\Users\au346588\AppData\Local\Temp\RtmpeO0wQ3\downloaded_packages’

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 "\\uni.au.dk\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

locale:
[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 9 weeks ago by Martin Morgan ♦♦ 20k • written 9 weeks ago by veerle0
0
gravatar for Martin Morgan
9 weeks ago by
Martin Morgan ♦♦ 20k
United States
Martin Morgan ♦♦ 20k wrote:

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

ADD COMMENTlink written 9 weeks ago by Martin Morgan ♦♦ 20k
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