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
