Error: Error installing package 'OmnipathR': when trying to install LianaR

[maximelepetit]

Hi,
I'm having an issue with OmnipathR when i try to install liana R wrapper 👍

renv::install("saezlab/liana")
# Downloading packages -------------------------------------------------------
- Downloading liana from GitHub ...             OK [6.9 Mb in 0.73s]
- Downloading OmnipathR from GitHub ...         OK [6.9 Mb in 0.9s]
- Downloading basilisk.utils from GitHub ...    OK [32.9 Kb in 0.63s]
- Downloading basilisk from GitHub ...          OK [48.9 Kb in 0.48s]
Successfully downloaded 4 packages in 12 seconds.

The following package(s) will be installed:
- basilisk       [LTLA/basilisk]
- basilisk.utils [LTLA/basilisk.utils]
- liana          [saezlab/liana]
- OmnipathR      [saezlab/OmnipathR]
These packages will be installed into "~/Projects/liana/renv/library/R-4.2/x86_64-pc-linux-gnu".

Do you want to proceed? [Y/n]: Y

# Installing packages --------------------------------------------------------
- Installing OmnipathR ...                      FAILED
Error: Error installing package 'OmnipathR':
=====================================

Warning in untar2(tarfile, files, list, exdir, restore_times) :
  skipping pax global extended headers
* installing *source* package ‘OmnipathR’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : 
  there is no package called ‘metaboliteIDmapping’
Calls: <Anonymous> ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
ERROR: lazy loading failed for package ‘OmnipathR’
* removing ‘/home/labex-cortex/Projects/liana/renv/library/R-4.2/x86_64-pc-linux-gnu/.renv/1/OmnipathR’
install of package 'OmnipathR' failed [error code 1]
Traceback (most recent calls last):
12: renv::install("saezlab/liana")
11: renv_install_impl(records)
10: renv_install_staged(records)
 9: renv_install_default(records)
 8: handler(package, renv_install_package(record))
 7: renv_install_package(record)
 6: withCallingHandlers(renv_install_package_impl(record), error = function(e) writef("FAILED"))
 5: renv_install_package_impl(record)
 4: r_cmd_install(package, path) 
 3: r_exec_error(package, output, "install", status)
 2: abort(all)
 1: stop(fallback)

This error also appear when i manually install OmnipathR from Github:

renv::install("saezlab/OmnipathR")
# Downloading packages -------------------------------------------------------
- Downloading OmnipathR from GitHub ...         OK [6.9 Mb in 0.95s]
Successfully downloaded 1 package in 1.8 seconds.

The following package(s) will be installed:
- OmnipathR [saezlab/OmnipathR]
These packages will be installed into "~/Projects/liana/renv/library/R-4.2/x86_64-pc-linux-gnu".

Do you want to proceed? [Y/n]: Y

# Installing packages --------------------------------------------------------
- Installing OmnipathR ...                      FAILED
Error: Error installing package 'OmnipathR':
=====================================

Warning in untar2(tarfile, files, list, exdir, restore_times) :
  skipping pax global extended headers
* installing *source* package ‘OmnipathR’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : 
  there is no package called ‘metaboliteIDmapping’
Calls: <Anonymous> ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
ERROR: lazy loading failed for package ‘OmnipathR’
* removing ‘/home/labex-cortex/Projects/liana/renv/library/R-4.2/x86_64-pc-linux-gnu/.renv/1/OmnipathR’
install of package 'OmnipathR' failed [error code 1]
Traceback (most recent calls last):
12: renv::install("saezlab/OmnipathR")
11: renv_install_impl(records)
10: renv_install_staged(records)
 9: renv_install_default(records)
 8: handler(package, renv_install_package(record))
 7: renv_install_package(record)
 6: withCallingHandlers(renv_install_package_impl(record), error = function(e) writef("FAILED"))
 5: renv_install_package_impl(record)
 4: r_cmd_install(package, path)
 3: r_exec_error(package, output, "install", status)
 2: abort(all)
 1: stop(fallback)

I try to install manually metaboliteIDmapping and i have also an error :

renv::install("Bioc::metaboliteIDmapping")
# Downloading packages -------------------------------------------------------
- Downloading metaboliteIDmapping from BioCann ... OK [file is up to date]
Successfully downloaded 1 package in 1.6 seconds.

The following package(s) will be installed:
- AnnotationDbi          [1.60.2]
- AnnotationHub          [3.6.0]
- BiocFileCache          [2.6.1]
- Biostrings             [2.66.0]
- blob                   [1.2.4]
- DBI                    [1.2.1]
- dbplyr                 [2.4.0]
- DT                     [0.31]
- interactiveDisplayBase [1.36.0]
- KEGGREST               [1.38.0]
- metaboliteIDmapping    [1.0.0]
- plogr                  [0.2.0]
- RSQLite                [2.3.4]
These packages will be installed into "~/Projects/liana/renv/library/R-4.2/x86_64-pc-linux-gnu".

Do you want to proceed? [Y/n]: Y

# Installing packages --------------------------------------------------------
- Installing blob ...                           OK [linked from cache]
- Installing DBI ...                            OK [linked from cache]
- Installing dbplyr ...                         OK [linked from cache]
- Installing plogr ...                          OK [linked from cache]
- Installing RSQLite ...                        OK [linked from cache]
- Installing BiocFileCache ...                  OK [linked from cache]
- Installing Biostrings ...                     OK [linked from cache]
- Installing KEGGREST ...                       OK [linked from cache]
- Installing AnnotationDbi ...                  OK [linked from cache]
- Installing DT ...                             OK [linked from cache]
- Installing interactiveDisplayBase ...         OK [linked from cache]
- Installing AnnotationHub ...                  OK [linked from cache]
- Installing metaboliteIDmapping ...            FAILED
Error: Error installing package 'metaboliteIDmapping':
===============================================

* installing *source* package ‘metaboliteIDmapping’ ...
** 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: package or namespace load failed for ‘metaboliteIDmapping’:
 .onLoad failed in loadNamespace() for 'metaboliteIDmapping', details:
  call: collect(., Inf)
  error: Failed to collect lazy table.
Caused by error in `db_collect()`:
! Arguments in `...` must be used.
✖ Problematic argument:
• ..1 = Inf
ℹ Did you misspell an argument name?
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/home/labex-cortex/Projects/liana/renv/library/R-4.2/x86_64-pc-linux-gnu/.renv/1/metaboliteIDmapping’
install of package 'metaboliteIDmapping' failed [error code 1]
Traceback (most recent calls last):
12: renv::install("Bioc::metaboliteIDmapping")
11: renv_install_impl(records)
10: renv_install_staged(records)
 9: renv_install_default(records)
 8: handler(package, renv_install_package(record))
 7: renv_install_package(record)
 6: withCallingHandlers(renv_install_package_impl(record), error = function(e) writef("FAILED"))
 5: renv_install_package_impl(record)
 4: r_cmd_install(package, path)
 3: r_exec_error(package, output, "install", status)
 2: abort(all)
 1: stop(fallback)

Best regards

Maxime

[maximelepetit]

My session Info :

sessionInfo()
R version 4.2.3 (2023-03-15)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.6 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=fr_FR.UTF-8        LC_COLLATE=en_US.UTF-8     LC_MONETARY=fr_FR.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=fr_FR.UTF-8       LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=fr_FR.UTF-8 LC_IDENTIFICATION=C       

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

loaded via a namespace (and not attached):
 [1] gitcreds_0.1.2      crayon_1.5.2        withr_2.5.2         lifecycle_1.0.4     magrittr_2.0.3      rlang_1.1.3         cli_3.6.2           renv_1.0.3          curl_5.2.0         
[10] remotes_2.4.2.1     rstudioapi_0.15.0   fs_1.6.3            vctrs_0.6.5         tools_4.2.3         glue_1.7.0          purrr_1.0.2         compiler_4.2.3      BiocManager_1.30.22
[19] usethis_2.2.2      

[deeenes]

Hi Maxime,

I'm about to fix this right now, until then a few commits older version should work:

library(remotes)
remotes::install_github('saezlab/OmnipathR', ref = '4b83e3c')

Apologies for the inconvenience.

Best,

Denes

[maximelepetit]

Thanks a lot the installation of OmnipathR from Github work with your suggestions!!

[enblacar]

Hi @deeenes,

Thank you for the work towards fixing the error!

What is the current status of the hotfix implementation? My R package is failing in all CI tests due to Omnipath not being installed correctly.

Best,
Enrique