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Question: .onLoad failed in loadNamespace() for 'org.Hs.eg.db'
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gravatar for dsp35
14 days ago by
dsp350
dsp350 wrote:

I would like to install the package org.Hs.eg.db version 3.5 in R 3.4.0 and Bioconductor 3.6 (BiocInstaller 1.28.0). I have tried to install the package version 3.4.1, and also tried to use R.3.4.2. The error is always the same, as follows. Any help would be greatly appreciated!

> biocLite("org.Hs.eg.db")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.0 (2017-04-21).
Installing package(s) ‘org.Hs.eg.db’
installing the source package ‘org.Hs.eg.db’

trying URL 'https://bioconductor.org/packages/3.6/data/annotation/src/contrib/org.Hs.eg.db_3.5.0.tar.gz'
Content type 'application/x-gzip' length 75219292 bytes (71.7 MB)
downloaded 71.7 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 'org.Hs.eg.db' ...
** R
** inst
** preparing package for lazy loading
Warning: package 'AnnotationDbi' was built under R version 3.4.2
Warning: package 'BiocGenerics' was built under R version 3.4.2
Warning: package 'Biobase' was built under R version 3.4.2
Warning: package 'IRanges' was built under R version 3.4.2
Warning: package 'S4Vectors' was built under R version 3.4.2
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
*** arch - i386
Warning: package 'AnnotationDbi' was built under R version 3.4.2
Warning: package 'BiocGenerics' was built under R version 3.4.2
Warning: package 'Biobase' was built under R version 3.4.2
Warning: package 'IRanges' was built under R version 3.4.2
Warning: package 'S4Vectors' was built under R version 3.4.2
Error: package or namespace load failed for 'org.Hs.eg.db':
 .onLoad failed in loadNamespace() for 'org.Hs.eg.db', details:
  call: dbFileConnect(dbfile)
  error: DB file '' not found
Error: loading failed
Execution halted
*** arch - x64
Warning: package 'AnnotationDbi' was built under R version 3.4.2
Warning: package 'BiocGenerics' was built under R version 3.4.2
Warning: package 'Biobase' was built under R version 3.4.2
Warning: package 'IRanges' was built under R version 3.4.2
Warning: package 'S4Vectors' was built under R version 3.4.2
Error: package or namespace load failed for 'org.Hs.eg.db':
 .onLoad failed in loadNamespace() for 'org.Hs.eg.db', details:
  call: dbFileConnect(dbfile)
  error: DB file '' not found
Error: loading failed
Execution halted
ERROR: loading failed for 'i386', 'x64'

Here is my SessionInfo():

> sessionInfo()
R version 3.4.0 (2017-04-21)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 14393)

Matrix products: default

locale:
[1] LC_COLLATE=English_United Kingdom.1252  LC_CTYPE=English_United Kingdom.1252    LC_MONETARY=English_United Kingdom.1252 LC_NUMERIC=C                           
[5] LC_TIME=English_United Kingdom.1252    

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

other attached packages:
[1] BiocInstaller_1.28.0

loaded via a namespace (and not attached):
[1] compiler_3.4.0 tools_3.4.0
ADD COMMENTlink modified 14 days ago by James W. MacDonald45k • written 14 days ago by dsp350
0
gravatar for James W. MacDonald
14 days ago by
United States
James W. MacDonald45k wrote:

This usually comes up when you are trying to use a network directory for your library path. That's not (IMO) usually worth the effort, so the quick fix is to set your .libPaths to somewhere on your computer's hard drive. An alternative might be to map the directory share to a drive path, like Z:, but like I said, usually not worth the effort...
 

ADD COMMENTlink written 14 days ago by James W. MacDonald45k

Thank you, James! I was actually not intending to use a network directory. How can I set the .libPaths when installing the library from Bioconductor in this case? Thanks so much for your help!

ADD REPLYlink written 14 days ago by dsp350

Have you looked at the help page for .libPaths? It's pretty comprehensive.

ADD REPLYlink written 14 days ago by James W. MacDonald45k
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