map_int() error

[gabrigammal]

Hi deeenes, I cant seem to be able to use OmnipathR. I clearly have the most recent version, but keep getting this error, no matter what I try...

library(remotes)
remotes::install_github('saezlab/OmnipathR',force=TRUE)
Downloading GitHub repo saezlab/OmnipathR@HEAD
── R CMD build ─────────────────────────────────────────────────────────────────
✔ checking for file 'C:\Users\gabri\AppData\Local\Temp\RtmpEvdNxT\remotes40d893b5afb\saezlab-OmnipathR-a7f3b9d/DESCRIPTION' (355ms)
─ preparing 'OmnipathR': (22.2s)
checking DESCRIPTION meta-information ...
checking DESCRIPTION meta-information ...
✔ checking DESCRIPTION meta-information
checking for LF line-endings in source and make files and shell scripts
─ checking for LF line-endings in source and make files and shell scripts (1.2s)
─ checking for empty or unneeded directories
Removed empty directory 'OmnipathR/.github'
─ looking to see if a 'data/datalist' file should be added
─ building 'OmnipathR_3.17.4.tar.gz'
Installing package into ‘C:/Users/gabri/AppData/Local/R/win-library/4.4’
(as ‘lib’ is unspecified)

• installing source package 'OmnipathR' ...
  ** using staged installation
  ** R
  ** inst
  ** byte-compile and prepare package for lazy loading
  ** help
  *** installing help indices
  ** building package indices
  ** installing vignettes
  ** testing if installed package can be loaded from temporary location
  ERROR: Unknown command "TMPDIR=C:/Users/gabri/AppData/Local/Temp/RtmpisJVxu/filecea84cc97594". Did you mean command "install"?
  Warning in system2("quarto", "-V", stdout = TRUE, env = paste0("TMPDIR=", :
  running command '"quarto" TMPDIR=C:/Users/gabri/AppData/Local/Temp/RtmpisJVxu/filecea84cc97594 -V' had status 1
  ** testing if installed package can be loaded from final location
  ERROR: Unknown command "TMPDIR=C:/Users/gabri/AppData/Local/Temp/RtmpmoHNM4/filefe9c43ed1988". Did you mean command "remove"?
  Warning in system2("quarto", "-V", stdout = TRUE, env = paste0("TMPDIR=", :
  running command '"quarto" TMPDIR=C:/Users/gabri/AppData/Local/Temp/RtmpmoHNM4/filefe9c43ed1988 -V' had status 1
  ** testing if installed package keeps a record of temporary installation path
• DONE (OmnipathR)

library(OmnipathR)
ERROR: Unknown command "TMPDIR=C:/Users/gabri/AppData/Local/Temp/RtmpEvdNxT/file40d815b42d71". Did you mean command "preview"?
Warning message:
In system2("quarto", "-V", stdout = TRUE, env = paste0("TMPDIR=", :
running command '"quarto" TMPDIR=C:/Users/gabri/AppData/Local/Temp/RtmpEvdNxT/file40d815b42d71 -V' had status 1

gri <- transcriptional()
Error in map_int():
ℹ In index: 1.
Caused by error in map_int():
ℹ In index: 1.
Caused by error in full_join():
! Can't join x$ncbi_tax_id with y$ncbi_tax_id due to incompatible
types.
ℹ x$ncbi_tax_id is a .
ℹ y$ncbi_tax_id is a .
Run rlang::last_trace() to see where the error occurred.

packageVersion("OmnipathR")
[1] ‘3.17.4’

[deeenes]

Hello, This happens because in your current cache directory the data frame downloaded by a version before 3.17.4 is dumped as an rds, and it contains the ncbi_tax_id column with the wrong type. The solution is to remove this outdated cache file. Maybe the easiest is to empty the whole cache, then everything will be freshly downloaded. You can do this by calling omnipath_cache_wipe(). Let me know whether it works.

---

_{Free Palestine!}

[yesitsjess]

Hello, This happens because in your current cache directory the data frame downloaded by a version before 3.17.4 is dumped as an rds, and it contains the ncbi_tax_id column with the wrong type. The solution is to remove this outdated cache file. Maybe the easiest is to empty the whole cache, then everything will be freshly downloaded. You can do this by calling omnipath_cache_wipe(). Let me know whether it works.

Free Palestine!

This worked for me, many thanks!