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Question: reactome.db installation problem
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gravatar for Jan-Jaap
6 months ago by
Jan-Jaap0
Jan-Jaap0 wrote:

Hi,

I am having trouble installing reactome.db when using, when I definitely do have space left on the device and I have write permissions. Any help would be much appreciated. The command and error messages are pasted below,

Thank you,

JJ

 

biocLite("reactome.db", lib="..path/to/R/site-library")

Warning in writeBin(block[seq_len(min(512L, remain))], out) :
  problem writing to connection
Warning in dir.create(path, showWarnings = TRUE, recursive = TRUE, ...) :
  cannot create dir 'reactome.db/man', reason 'No space left on device'
Error in mydir.create(name) : 
  failed to create directory ‘reactome.db/man’

 sessionInfo()
R version 3.3.2 (2016-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.5 LTS

locale:
 [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8    
 [5] LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.UTF-8   
 [7] LC_PAPER=en_GB.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] BiocInstaller_1.24.0

loaded via a namespace (and not attached):
[1] tools_3.3.2

 

ADD COMMENTlink written 6 months ago by Jan-Jaap0

Can you clarify what the library path is, e.g., to a network drive? I'm wondering if the error message is entirely accurate.

ADD REPLYlink written 6 months ago by Martin Morgan ♦♦ 20k

Hi Martin, 

No, the library path is to a physical drive and there is disk space and I have writing permissions.

Best,

Jan-Jaap

ADD REPLYlink written 6 months ago by Jan-Jaap0

This is highly unlikely to be related to the package.
Did you try to install it on another machine?
What filesystem is the disk you are trying to install to?
I notice you are on linux, but if you are writhing to a shared disk between windows and linux (FAT/NTFS) you might run into path length issues.

My first test would be to try to install into another location.

ADD REPLYlink written 6 months ago by willem.ligtenberg150

mydir.create is used when R tries to untar the archive, probably into the temporary directory. Is there space there, e.g., in the location returned by tempfile(). If no space, and no way to get more in that location, using biocLite("reactome.db", destdir="path/to/more/space") might work (I'm not 100% sure that it would).

ADD REPLYlink written 6 months ago by Martin Morgan ♦♦ 20k

This worked, thank you very much! I removed some data from /tmp , which was the output of tempfile() and then biocLite("reactome.db", destdir="path/to/more/space") worked. Thanks again!

JJ

ADD REPLYlink written 6 months ago by Jan-Jaap0
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