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This page was generated on 2024-05-15 13:46:16 -0400 (Wed, 15 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4663
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4480
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 1422/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
OmnipathR 3.13.0  (landing page)
Denes Turei
Snapshot Date: 2024-05-13 14:05:07 -0400 (Mon, 13 May 2024)
git_url: https://git.bioconductor.org/packages/OmnipathR
git_branch: devel
git_last_commit: 8bb9bf7
git_last_commit_date: 2024-04-30 11:18:21 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    ERROR  
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    ERROR  
kjohnson1macOS 13.6.6 Ventura / arm64see weekly results here

CHECK results for OmnipathR on nebbiolo2


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: 3.13.0
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings OmnipathR_3.13.0.tar.gz
StartedAt: 2024-05-14 01:04:01 -0400 (Tue, 14 May 2024)
EndedAt: 2024-05-14 01:28:52 -0400 (Tue, 14 May 2024)
EllapsedTime: 1490.9 seconds
RetCode: 1
Status:   ERROR  
CheckDir: OmnipathR.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings OmnipathR_3.13.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/OmnipathR.Rcheck’
* using R version 4.4.0 RC (2024-04-16 r86468)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘OmnipathR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OmnipathR’ version ‘3.13.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘OmnipathR’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... NOTE
[2024-05-14 01:04:20] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-14 01:04:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-14 01:04:20] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-05-14 01:04:20] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-05-14 01:04:20] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-05-14 01:04:20] [TRACE]   [OmnipathR] Contains 1 files.
[2024-05-14 01:04:20] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-05-14 01:04:20] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-14 01:04:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-14 01:04:20] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-05-14 01:04:20] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-05-14 01:04:20] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-05-14 01:04:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-14 01:04:20] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-05-14 01:04:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-14 01:04:20] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-05-14 01:04:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-14 01:04:20] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-05-14 01:04:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-14 01:04:20] [TRACE]   [OmnipathR] Cache locked: FALSE

It looks like this package (or a package it requires) has a startup
message which cannot be suppressed: see ?packageStartupMessage.
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
[2024-05-14 01:04:30] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-14 01:04:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-14 01:04:30] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-05-14 01:04:30] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-05-14 01:04:30] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-05-14 01:04:30] [TRACE]   [OmnipathR] Contains 1 files.
[2024-05-14 01:04:30] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-05-14 01:04:30] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-14 01:04:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-14 01:04:30] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-05-14 01:04:30] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-05-14 01:04:30] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-05-14 01:04:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-14 01:04:30] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-05-14 01:04:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-14 01:04:30] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-05-14 01:04:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-14 01:04:30] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-05-14 01:04:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-14 01:04:30] [TRACE]   [OmnipathR] Cache locked: FALSE
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘oma_pairwise_translated’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘OmnipathR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ensembl_id_mapping_table
> ### Title: Identifier translation table from Ensembl
> ### Aliases: ensembl_id_mapping_table
> 
> ### ** Examples
> 
> ensp_up <- ensembl_id_mapping_table("ensp")
[2024-05-14 01:13:16] [TRACE]   [OmnipathR] Creating ID mapping table from `uniprotswissprot` to `ensembl_peptide_id`, for organism hsapiens
[2024-05-14 01:13:16] [TRACE]   [OmnipathR] BioMart query: <?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE Query>
<Query  virtualSchemaName="default" formatter="TSV" header="0" uniqueRows="0" count="" datasetConfigVersion="0.6" completionStamp="1" >
    <Dataset name="hsapiens_gene_ensembl" interface="default" >
        <Attribute name="uniprotswissprot"/>
        <Attribute name="ensembl_peptide_id"/>
    </Dataset>
</Query>
[2024-05-14 01:13:16] [TRACE]   [OmnipathR] Looking up in cache: `http://www.ensembl.org/biomart/martservice?query=%3C?xml%20version=%221.0%22%20encoding=%22UTF-8%22?%3E%0A%3C!DOCTYPE%20Query%3E%0A%3CQuery%20%20virtualSchemaName=%22default%22%20formatter=%22TSV%22%20header=%220%22%20uniqueRows=%220%22%20count=%22%22%20datasetConfigVersion=%220.6%22%20completionStamp=%221%22%20%3E%0A%20%20%20%20%3CDataset%20name=%22hsapiens_gene_ensembl%22%20interface=%22default%22%20%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22uniprotswissprot%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22ensembl_peptide_id%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A`.
[2024-05-14 01:13:16] [INFO]    [OmnipathR] Cache record does not exist: `http://www.ensembl.org/biomart/martservice?query=%3C?xml%20version=%221.0%22%20encoding=%22UTF-8%22?%3E%0A%3C!DOCTYPE%20Query%3E%0A%3CQuery%20%20virtualSchemaName=%22default%22%20formatter=%22TSV%22%20header=%220%22%20uniqueRows=%220%22%20count=%22%22%20datasetConfigVersion=%220.6%22%20completionStamp=%221%22%20%3E%0A%20%20%20%20%3CDataset%20name=%22hsapiens_gene_ensembl%22%20interface=%22default%22%20%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22uniprotswissprot%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22ensembl_peptide_id%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A`
[2024-05-14 01:13:16] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `http://www.ensembl.org/biomart/martservice?query=%3C?xml%20version=%221.0%22%20encoding=%22UTF-8%22?%3E%0A%3C!DOCTYPE%20Query%3E%0A%3CQuery%20%20virtualSchemaName=%22default%22%20formatter=%22TSV%22%20header=%220%22%20uniqueRows=%220%22%20count=%22%22%20datasetConfigVersion=%220.6%22%20completionStamp=%221%22%20%3E%0A%20%20%20%20%3CDataset%20name=%22hsapiens_gene_ensembl%22%20interface=%22default%22%20%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22uniprotswissprot%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22ensembl_peptide_id%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A`.
[2024-05-14 01:13:16] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-14 01:13:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-14 01:13:16] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-14 01:13:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-14 01:13:16] [INFO]    [OmnipathR] Cache item `5146291739ab7fee3dd9b2830721d4357888383d` version 1: status changed from `unknown` to `started`.
[2024-05-14 01:13:16] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/5146291739ab7fee3dd9b2830721d4357888383d-1.rds`.
[2024-05-14 01:13:16] [INFO]    [OmnipathR] Retrieving URL: `http://www.ensembl.org/biomart/martservice?query=%3C?xml%20version=%221.0%22%20encoding=%22UTF-8%22?%3E%0A%3C!DOCTYPE%20Query%3E%0A%3CQuery%20%20virtualSchemaName=%22default%22%20formatter=%22TSV%22%20header=%220%22%20uniqueRows=%220%22%20count=%22%22%20datasetConfigVersion=%220.6%22%20completionStamp=%221%22%20%3E%0A%20%20%20%20%3CDataset%20name=%22hsapiens_gene_ensembl%22%20interface=%22default%22%20%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22uniprotswissprot%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22ensembl_peptide_id%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A`
[2024-05-14 01:13:16] [TRACE]   [OmnipathR] Attempt 1/3: `http://www.ensembl.org/biomart/martservice?query=%3C?xml%20version=%221.0%22%20encoding=%22UTF-8%22?%3E%0A%3C!DOCTYPE%20Query%3E%0A%3CQuery%20%20virtualSchemaName=%22default%22%20formatter=%22TSV%22%20header=%220%22%20uniqueRows=%220%22%20count=%22%22%20datasetConfigVersion=%220.6%22%20completionStamp=%221%22%20%3E%0A%20%20%20%20%3CDataset%20name=%22hsapiens_gene_ensembl%22%20interface=%22default%22%20%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22uniprotswissprot%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22ensembl_peptide_id%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A`
[2024-05-14 01:13:17] [TRACE]   [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/5146291739ab7fee3dd9b2830721d4357888383d-1.rds`.
[2024-05-14 01:13:17] [INFO]    [OmnipathR] Download ready [key=5146291739ab7fee3dd9b2830721d4357888383d, version=1]
[2024-05-14 01:13:17] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-14 01:13:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-14 01:13:17] [INFO]    [OmnipathR] Cache item `5146291739ab7fee3dd9b2830721d4357888383d` version 1: status changed from `started` to `ready`.
[2024-05-14 01:13:17] [WARN]    [OmnipathR] BioMart: missing success flag, data might be incomplete or contain error message!
[2024-05-14 01:13:17] [WARN]    [OmnipathR] Query ERROR: caught BioMart::Exception::Database: Error during query execution: Table 'ensembl_mart_112.hsapiens_gene_ensembl__ox_uniprotswissprot__dm' doesn't exist
[2024-05-14 01:13:17] [SUCCESS] [OmnipathR] www.ensembl.org: downloaded 1 records
Error in `set_names()`:
! The size of `nm` (2) must be compatible with the size of `x` (1).
Backtrace:
    ▆
 1. ├─OmnipathR::ensembl_id_mapping_table("ensp")
 2. │ └─... %>% trim_and_distinct
 3. ├─OmnipathR:::trim_and_distinct(.)
 4. │ └─d %>% mutate(across(everything(), str_trim)) %>% distinct
 5. ├─dplyr::distinct(.)
 6. ├─dplyr::mutate(., across(everything(), str_trim))
 7. ├─rlang::set_names(., c("From", "To"))
 8. └─rlang::abort(message = message)
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 WARNING, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/OmnipathR.Rcheck/00check.log’
for details.

Installation output

OmnipathR.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL OmnipathR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘OmnipathR’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
[2024-05-13 15:34:59] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-13 15:34:59] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-13 15:34:59] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-05-13 15:34:59] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-05-13 15:34:59] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-05-13 15:34:59] [TRACE]   [OmnipathR] Contains 8 files.
[2024-05-13 15:34:59] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-05-13 15:34:59] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-13 15:34:59] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-13 15:34:59] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-05-13 15:34:59] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-05-13 15:34:59] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-05-13 15:34:59] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-13 15:34:59] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-05-13 15:34:59] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-13 15:34:59] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-05-13 15:34:59] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-13 15:34:59] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-05-13 15:34:59] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-13 15:34:59] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2024-05-13 15:35:01] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-13 15:35:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-13 15:35:01] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-05-13 15:35:01] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-05-13 15:35:01] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-05-13 15:35:01] [TRACE]   [OmnipathR] Contains 1 files.
[2024-05-13 15:35:01] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-05-13 15:35:01] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-13 15:35:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-13 15:35:01] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-05-13 15:35:01] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-05-13 15:35:01] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-05-13 15:35:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-13 15:35:01] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-05-13 15:35:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-13 15:35:01] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-05-13 15:35:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-13 15:35:01] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-05-13 15:35:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-13 15:35:01] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package keeps a record of temporary installation path
* DONE (OmnipathR)

Tests output

OmnipathR.Rcheck/tests/testthat.Rout


R version 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup"
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> #!/usr/bin/env Rscript
> 
> #
> #  This file is part of the `OmnipathR` R package
> #
> #  Copyright
> #  2018-2024
> #  Saez Lab, Uniklinik RWTH Aachen, Heidelberg University
> #
> #  File author(s): Alberto Valdeolivas
> #                  Dénes Türei (turei.denes@gmail.com)
> #                  Attila Gábor
> #
> #  Distributed under the MIT (Expat) License.
> #  See accompanying file `LICENSE` or find a copy at
> #      https://directory.fsf.org/wiki/License:Expat
> #
> #  Website: https://r.omnipathdb.org/
> #  Git repo: https://github.com/saezlab/OmnipathR
> #
> 
> 
> library(testthat)
> library(OmnipathR)
[2024-05-14 01:13:21] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-14 01:13:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-14 01:13:21] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-05-14 01:13:21] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-05-14 01:13:21] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-05-14 01:13:21] [TRACE]   [OmnipathR] Contains 37 files.
[2024-05-14 01:13:21] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-05-14 01:13:21] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-14 01:13:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-14 01:13:22] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-05-14 01:13:22] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-05-14 01:13:22] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-05-14 01:13:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-14 01:13:22] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-05-14 01:13:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-14 01:13:22] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-05-14 01:13:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-14 01:13:22] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-05-14 01:13:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-14 01:13:22] [TRACE]   [OmnipathR] Cache locked: FALSE
> 
> test_check('OmnipathR')
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 34 ]

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 34 ]
> 
> proc.time()
   user  system elapsed 
 20.095   1.542  58.385

Example timings

OmnipathR.Rcheck/OmnipathR-Ex.timings

nameusersystemelapsed
OmnipathR0.0010.0000.000
all_uniprot_acs0.0210.0010.020
all_uniprots0.0100.0000.011
ancestors0.0090.0000.010
annotated_network1.8870.2537.904
annotation_categories85.902 0.05187.557
biomart_query0.6160.0204.358
bioplex10.0120.0000.012
bioplex20.010.000.01
bioplex30.0100.0000.009
bioplex_all0.0090.0000.009
bioplex_hct116_10.0090.0000.009
bma_motif_es0.4090.0481.369
bma_motif_vs0.1770.0120.873
collectri145.219 2.254154.225
common_name0.0180.0000.018
consensuspathdb_download0.0000.0000.001
consensuspathdb_raw_table0.010.000.01
curated_ligand_receptor_interactions 5.643 0.50017.064
curated_ligrec_stats 46.796 3.941133.628
database_summary1.5340.1244.286
descendants0.0140.0000.014
dorothea86.143 2.20491.320
ensembl_dataset0.0060.0040.009