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This page was generated on 2024-09-27 12:30 -0400 (Fri, 27 Sep 2024).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.1 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4451
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4417
palomino8Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4456
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4489
kjohnson3macOS 13.6.5 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4436
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.1 (2024-06-14) -- "Race for Your Life" 4435
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 1440/2262HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
OmnipathR 3.13.25  (landing page)
Denes Turei
Snapshot Date: 2024-09-26 13:40 -0400 (Thu, 26 Sep 2024)
git_url: https://git.bioconductor.org/packages/OmnipathR
git_branch: devel
git_last_commit: d07da8c
git_last_commit_date: 2024-09-07 11:02:07 -0400 (Sat, 07 Sep 2024)
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    ERROR  skipped
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    ERROR  skipped
palomino8Windows Server 2022 Datacenter / x64  OK    ERROR  skippedskipped
lconwaymacOS 12.7.1 Monterey / x86_64  OK    ERROR  skippedskipped
kjohnson3macOS 13.6.5 Ventura / arm64  OK    ERROR  skippedskipped
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    ERROR  skipped

BUILD results for OmnipathR on lconway

To the developers/maintainers of the OmnipathR package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/OmnipathR.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: OmnipathR
Version: 3.13.25
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data OmnipathR
StartedAt: 2024-09-26 17:58:11 -0400 (Thu, 26 Sep 2024)
EndedAt: 2024-09-26 17:58:55 -0400 (Thu, 26 Sep 2024)
EllapsedTime: 44.7 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data OmnipathR
###
##############################################################################
##############################################################################


* checking for file ‘OmnipathR/DESCRIPTION’ ... OK
* preparing ‘OmnipathR’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘bioc_workshop.Rmd’ using rmarkdown
[2024-09-26 17:58:40] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-09-26 17:58:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-09-26 17:58:40] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-09-26 17:58:40] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-09-26 17:58:40] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-09-26 17:58:40] [TRACE]   [OmnipathR] Contains 1 files.
[2024-09-26 17:58:40] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-09-26 17:58:40] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-09-26 17:58:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-09-26 17:58:40] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-09-26 17:58:40] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-09-26 17:58:40] [TRACE]   [OmnipathR] Reading JSON from `/private/tmp/RtmpIa6yXP/Rinst150eb18b9b43/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-09-26 17:58:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-09-26 17:58:40] [TRACE]   [OmnipathR] Reading JSON from `/private/tmp/RtmpIa6yXP/Rinst150eb18b9b43/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-09-26 17:58:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-09-26 17:58:40] [TRACE]   [OmnipathR] Reading JSON from `/private/tmp/RtmpIa6yXP/Rinst150eb18b9b43/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-09-26 17:58:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-09-26 17:58:40] [TRACE]   [OmnipathR] Reading JSON from `/private/tmp/RtmpIa6yXP/Rinst150eb18b9b43/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-09-26 17:58:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-09-26 17:58:40] [TRACE]   [OmnipathR] Cache locked: FALSE
[2024-09-26 17:58:40] [TRACE]   [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B],query_type=interactions]
[2024-09-26 17:58:40] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2024-09-26 17:58:40] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-09-26 17:58:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-09-26 17:58:40] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2024-09-26 17:58:40] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-09-26 17:58:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-09-26 17:58:40] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2024-09-26 17:58:40] [TRACE]   [OmnipathR] Cache file path: /Users/biocbuild/Library/Caches/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2024-09-26 17:58:40] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2024-09-26 17:58:40] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2024-09-26 17:58:41] [TRACE]   [OmnipathR] HTTP 200
[2024-09-26 17:58:41] [INFO]    [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1]
[2024-09-26 17:58:41] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-09-26 17:58:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-09-26 17:58:41] [INFO]    [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`.
[2024-09-26 17:58:41] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2024-09-26 17:58:42] [INFO]    [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2024-09-26 17:58:42] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2024-09-26 17:58:42] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-09-26 17:58:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-09-26 17:58:42] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-09-26 17:58:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-09-26 17:58:42] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2024-09-26 17:58:42] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2024-09-26 17:58:42] [INFO]    [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2024-09-26 17:58:42] [TRACE]   [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2024-09-26 17:58:43] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2024-09-26 17:58:43] [INFO]    [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1]
[2024-09-26 17:58:43] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-09-26 17:58:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-09-26 17:58:43] [INFO]    [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.

Quitting from lines 216-218 [network] (bioc_workshop.Rmd)
Error: processing vignette 'bioc_workshop.Rmd' failed with diagnostics:
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$ncbi_tax_id` is a <integer>.
ℹ `y$ncbi_tax_id` is a <character>.
--- failed re-building ‘bioc_workshop.Rmd’

--- re-building ‘cosmos.Rmd’ using rmarkdown
[2024-09-26 17:58:44] [TRACE]   [OmnipathR] Bypassing call: `chalmers_gem_raw()`.
[2024-09-26 17:58:44] [TRACE]   [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server.
[2024-09-26 17:58:44] [TRACE]   [OmnipathR] Bypassing call: `chalmers_gem()`.
[2024-09-26 17:58:44] [TRACE]   [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server.
[2024-09-26 17:58:44] [TRACE]   [OmnipathR] Bypassing call: `chalmers_gem_metabolites()`.
[2024-09-26 17:58:44] [TRACE]   [OmnipathR] This behaviour is intended for running R CMD check within limited time and is triggered solely by the user name. Please report if you see this anywhere outside of a Bioconductor build server.
[2024-09-26 17:58:45] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2024-09-26 17:58:45] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, latest version=1.
[2024-09-26 17:58:45] [TRACE]   [OmnipathR] Cache file path: /Users/biocbuild/Library/Caches/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2024-09-26 17:58:45] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2024-09-26 17:58:45] [TRACE]   [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.

Quitting from lines 176-179 [omnipath] (cosmos.Rmd)
Error: processing vignette 'cosmos.Rmd' failed with diagnostics:
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$ncbi_tax_id` is a <integer>.
ℹ `y$ncbi_tax_id` is a <character>.
--- failed re-building ‘cosmos.Rmd’

--- re-building ‘db_manager.Rmd’ using rmarkdown
[2024-09-26 17:58:46] [INFO]    [OmnipathR] Loading database `UniProt-GeneSymbol table`.
[2024-09-26 17:58:46] [TRACE]   [OmnipathR] Creating ID mapping table from `accession` to `gene_primary`, for organism 9606 (only reviewed: TRUE)
[2024-09-26 17:58:46] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2024-09-26 17:58:46] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, latest version=1.
[2024-09-26 17:58:46] [TRACE]   [OmnipathR] Cache file path: /Users/biocbuild/Library/Caches/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2024-09-26 17:58:46] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2024-09-26 17:58:46] [TRACE]   [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.

Quitting from lines 67-69 [get] (db_manager.Rmd)
Error: processing vignette 'db_manager.Rmd' failed with diagnostics:
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$ncbi_tax_id` is a <integer>.
ℹ `y$ncbi_tax_id` is a <character>.
--- failed re-building ‘db_manager.Rmd’

--- re-building ‘drug_targets.Rmd’ using rmarkdown
[2024-09-26 17:58:47] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath]
[2024-09-26 17:58:47] [TRACE]   [OmnipathR] Arguments for OmniPath query: [datasets=omnipath,query_type=interactions]
[2024-09-26 17:58:47] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2024-09-26 17:58:47] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, latest version=1.
[2024-09-26 17:58:47] [TRACE]   [OmnipathR] Cache file path: /Users/biocbuild/Library/Caches/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2024-09-26 17:58:47] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2024-09-26 17:58:47] [TRACE]   [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.

Quitting from lines 46-51 [unnamed-chunk-2] (drug_targets.Rmd)
Error: processing vignette 'drug_targets.Rmd' failed with diagnostics:
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$ncbi_tax_id` is a <integer>.
ℹ `y$ncbi_tax_id` is a <character>.
--- failed re-building ‘drug_targets.Rmd’

--- re-building ‘extra_attrs.Rmd’ using rmarkdown
[2024-09-26 17:58:47] [TRACE]   [OmnipathR] Arguments for OmniPath query: [fields=extra_attrs,query_type=interactions]
[2024-09-26 17:58:47] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2024-09-26 17:58:47] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, latest version=1.
[2024-09-26 17:58:47] [TRACE]   [OmnipathR] Cache file path: /Users/biocbuild/Library/Caches/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2024-09-26 17:58:47] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2024-09-26 17:58:47] [TRACE]   [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.

Quitting from lines 56-58 [load-interactions] (extra_attrs.Rmd)
Error: processing vignette 'extra_attrs.Rmd' failed with diagnostics:
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$ncbi_tax_id` is a <integer>.
ℹ `y$ncbi_tax_id` is a <character>.
--- failed re-building ‘extra_attrs.Rmd’

--- re-building ‘nichenet.Rmd’ using rmarkdown
--- finished re-building ‘nichenet.Rmd’

--- re-building ‘omnipath_intro.Rmd’ using rmarkdown
[2024-09-26 17:58:53] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2024-09-26 17:58:53] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-09-26 17:58:53] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[SignaLink3,PhosphoSite,SIGNOR],datasets=omnipath]
[2024-09-26 17:58:53] [TRACE]   [OmnipathR] Arguments for OmniPath query: [resources=[SignaLink3,PhosphoSite,SIGNOR],datasets=omnipath,query_type=interactions]
[2024-09-26 17:58:53] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2024-09-26 17:58:53] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, latest version=1.
[2024-09-26 17:58:53] [TRACE]   [OmnipathR] Cache file path: /Users/biocbuild/Library/Caches/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2024-09-26 17:58:53] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2024-09-26 17:58:53] [TRACE]   [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.

Quitting from lines 167-175 [interactions] (omnipath_intro.Rmd)
Error: processing vignette 'omnipath_intro.Rmd' failed with diagnostics:
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$ncbi_tax_id` is a <integer>.
ℹ `y$ncbi_tax_id` is a <character>.
--- failed re-building ‘omnipath_intro.Rmd’

--- re-building ‘paths.Rmd’ using rmarkdown
[2024-09-26 17:58:54] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=FALSE,resources=TFcensus,entity_types=protein,query_type=annotations]
[2024-09-26 17:58:54] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2024-09-26 17:58:54] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, latest version=1.
[2024-09-26 17:58:54] [TRACE]   [OmnipathR] Cache file path: /Users/biocbuild/Library/Caches/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2024-09-26 17:58:54] [TRACE]   [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2024-09-26 17:58:54] [TRACE]   [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.

Quitting from lines 56-67 [tfcensus-op] (paths.Rmd)
Error: processing vignette 'paths.Rmd' failed with diagnostics:
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$ncbi_tax_id` is a <integer>.
ℹ `y$ncbi_tax_id` is a <character>.
--- failed re-building ‘paths.Rmd’

SUMMARY: processing the following files failed:
  ‘bioc_workshop.Rmd’ ‘cosmos.Rmd’ ‘db_manager.Rmd’ ‘drug_targets.Rmd’ ‘extra_attrs.Rmd’
  ‘omnipath_intro.Rmd’ ‘paths.Rmd’

Error: Vignette re-building failed.
Execution halted