R Cloud System Install Request of "msa" package (path not writeable)

[emmabueren]

Hello! I am working with a group to get a bioinformatics class up and running for next semester but we are unable to install msa into posit cloud (error output below).

This seems to be because it requires a system library as described here: RStudio Education.

Is it possible for the support team to install msa into the R studio cloud?

Thanks!

input:

 if(!require("msa", quietly = TRUE)) {
   BiocManager::install("msa") 
   }

error output:

'getOption("repos")' replaces Bioconductor standard repositories, see
'help("repositories", package = "BiocManager")' for details.
Replacement repositories:
    CRAN: http://rspm/default/__linux__/focal/latest
Bioconductor version 3.20 (BiocManager 1.30.25), R 4.4.1 (2024-06-14)
Installing package(s) 'msa'
also installing the dependencies ‘XVector’, ‘GenomeInfoDb’, ‘Biostrings’, ‘IRanges’

trying URL 'https://bioconductor.org/packages/3.20/bioc/src/contrib/XVector_0.46.0.tar.gz'
Content type 'application/x-gzip' length 70185 bytes (68 KB)
==================================================
downloaded 68 KB

trying URL 'https://bioconductor.org/packages/3.20/bioc/src/contrib/GenomeInfoDb_1.42.0.tar.gz'
Content type 'application/x-gzip' length 3589936 bytes (3.4 MB)
==================================================
downloaded 3.4 MB

trying URL 'https://bioconductor.org/packages/3.20/bioc/src/contrib/Biostrings_2.74.0.tar.gz'
Content type 'application/x-gzip' length 12812595 bytes (12.2 MB)
==================================================
downloaded 12.2 MB

trying URL 'https://bioconductor.org/packages/3.20/bioc/src/contrib/IRanges_2.40.0.tar.gz'
Content type 'application/x-gzip' length 486878 bytes (475 KB)
==================================================
downloaded 475 KB

trying URL 'https://bioconductor.org/packages/3.20/bioc/src/contrib/msa_1.38.0.tar.gz'
Content type 'application/x-gzip' length 4107247 bytes (3.9 MB)
==================================================
downloaded 3.9 MB

ERROR: failed to lock directory ‘/cloud/lib/x86_64-pc-linux-gnu-library/4.4’ for modifying
Try removing ‘/cloud/lib/x86_64-pc-linux-gnu-library/4.4/00LOCK-IRanges’
ERROR: dependency ‘IRanges’ is not available for package ‘XVector’
* removing ‘/cloud/lib/x86_64-pc-linux-gnu-library/4.4/XVector’
ERROR: dependency ‘IRanges’ is not available for package ‘GenomeInfoDb’
* removing ‘/cloud/lib/x86_64-pc-linux-gnu-library/4.4/GenomeInfoDb’
ERROR: dependencies ‘IRanges’, ‘XVector’, ‘GenomeInfoDb’ are not available for package ‘Biostrings’
* removing ‘/cloud/lib/x86_64-pc-linux-gnu-library/4.4/Biostrings’
ERROR: dependencies ‘Biostrings’, ‘IRanges’ are not available for package ‘msa’
* removing ‘/cloud/lib/x86_64-pc-linux-gnu-library/4.4/msa’

The downloaded source packages are in
	‘/tmp/RtmpnSkMED/downloaded_packages’
Installation paths not writeable, unable to update packages
  path: /opt/R/4.4.1/lib/R/library
  packages:
    boot, foreign, MASS, Matrix, nlme, survival
Warning messages:
1: In install.packages(...) :
  installation of package ‘IRanges’ had non-zero exit status
2: In install.packages(...) :
  installation of package ‘XVector’ had non-zero exit status
3: In install.packages(...) :
  installation of package ‘GenomeInfoDb’ had non-zero exit status
4: In install.packages(...) :
  installation of package ‘Biostrings’ had non-zero exit status
5: In install.packages(...) :
  installation of package ‘msa’ had non-zero exit status

[randyzwitch]

@emmabueren

ERROR: failed to lock directory ‘/cloud/lib/x86_64-pc-linux-gnu-library/4.4’ for modifying
Try removing ‘/cloud/lib/x86_64-pc-linux-gnu-library/4.4/00LOCK-IRanges’

HI @emmabueren, welcome to the community!

The quoted section above tells you that the issue is that the directory is locked. This can either occur because of a failed installation in the past (where the lockfile didn't get deleted) or someone else on your system is currently installing something.

You might try using pak for installing, I believe it might use its own directory for packages. Or, if you can contact support, I'm sure someone can resolve the lockfile issue (if that is actually the issue)

Best,
Randy

[emmabueren]

I tried deleting the lockfiles and they simply returned after each installation attempt, but pak seems to have solved the problem and msa is now installed and functioning correctly!

Thank you!