Question

Help with error install csaw

0

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Chris • 0

@3fdb6f97

Last seen 9 hours ago

United States

Hi all,

Would you have a suggestion how to fix the error below? Thank you so much!

if (!require("BiocManager", quietly = TRUE))
  install.packages("BiocManager")

BiocManager::install("csaw")
library(csaw)

Error in library(csaw) : there is no package called ‘csaw’

ChIPSeq ATACSeq • 989 views

ADD COMMENT • link written 12 months ago by Chris • 0

1

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You don't show the results from running BiocManager::install("csaw")

ADD REPLY • link 12 months ago James W. MacDonald 65k

0

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Sorry for that. I assumed it was not helpful in this case.

BiocManager::install("csaw")

'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package
= "BiocManager")' for details.
Replacement repositories:
    CRAN: https://cran.rstudio.com/
Bioconductor version 3.16 (BiocManager 1.30.20), R 4.2.2 (2022-10-31)
Installing package(s) 'csaw'
Warning in install.packages(...) :
  'lib = "/scg/apps/software/r/4.2.2/lib"' is not writable
Would you like to use a personal library instead? (yes/No/cancel) Yes
trying URL 'https://bioconductor.org/packages/3.16/bioc/src/contrib/csaw_1.32.0.tar.gz'
Content type 'application/x-gzip' length 398305 bytes (388 KB)
==================================================
downloaded 388 KB

Error: ERROR: no permission to install to directory ‘/scg/apps/software/r/4.2.2/lib’

The downloaded source packages are in
    ‘/tmp/RtmpCYqA2u/downloaded_packages’
Warning message:
In install.packages(...) :
  installation of package ‘csaw’ had non-zero exit status

Seem I don't have permission to install to directory ‘/scg/apps/software/r/4.2.2/lib’, so I should contact server admin or I can install somewhere else?

ADD REPLY • link 12 months ago Chris • 0

score 2 · Answer 1 · 2023-03-27

2

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James W. MacDonald 65k

@james-w-macdonald-5106

Last seen 1 day ago

United States

I am not sure why you didn't think that was helpful? I mean it says

Error: ERROR: no permission to install to directory ‘/scg/apps/software/r/4.2.2/lib’

The downloaded source packages are in
    ‘/tmp/RtmpCYqA2u/downloaded_packages’
Warning message:
In install.packages(...) :
  installation of package ‘csaw’ had non-zero exit status

Which is pretty explanatory, no?

ADD COMMENT • link 12 months ago James W. MacDonald 65k

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Thank you. So seem the packages downloaded at ‘/tmp/RtmpCYqA2u/downloaded_packages’. But module avail, I don't see csaw. Would you tell me how to load this package?

ADD REPLY • link 12 months ago Chris • 0

1

Entering edit mode

Yes, it was downloaded, but you cannot install in a library directory for which you have no permissions. You could do

.libPaths(<path to somewhere that you do have permissions>)
install("csaw")

Normally BiocManager::install will tell you that you don't have permissions and ask if you want to install in a different directory that you do have permissions for. Did that not happen?

ADD REPLY • link 12 months ago James W. MacDonald 65k

0

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Thank you for your help.

.libPaths(<path to somewhere that you do have permissions>)
install("csaw")

There is no error but Rstudio still running and print a lot of output on the console which I think there is something wrong. It took a lot longer than usual to install a package.

Update: after about 30 minutes, it finished. Do you think it is normal?

ADD REPLY • link 12 months ago Chris • 0