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Question: edgeR reinstall failure: edgeR.rdb' is corrupt
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gravatar for afreedman405
5 months ago by
Harvard University, Cambridge, Massachusetts, USA
afreedman4050 wrote:

Running R ver. 3.4.0, after generating an error message with an edgeR load, I updated bioconductor and then re-installed, i.e. via biocLite("edgeR")

library(edgeR) produced the following error:

Error: package or namespace load failed for ‘edgeR’ in get(Info[i, 1], envir = env):
 lazy-load database '/Users/adamfreedman/Library/R/3.4/library/edgeR/R/edgeR.rdb' is corrupt
In addition: Warning message:
In get(Info[i, 1], envir = env) : internal error -3 in R_decompress1

I cleared out the edgeR dir and tried it again .... same result.

ideas as to what's going on here?

 

ADD COMMENTlink modified 5 months ago by Aaron Lun17k • written 5 months ago by afreedman4050
1
gravatar for Aaron Lun
5 months ago by
Aaron Lun17k
Cambridge, United Kingdom
Aaron Lun17k wrote:

This usually happens to me when I try to install a package (e.g., via the command line, or with a separate R session) that's being used in a current R session. To fix this, I would restart the R session completely and run biocLite("edgeR"). If that doesn't work, try running remove.packages("edgeR") beforehand. But whatever you do, don't manually change the contents of the installation directory.

ADD COMMENTlink modified 5 months ago • written 5 months ago by Aaron Lun17k
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