Denes Turei
| Snapshot Date: 2025-03-17 13:00 -0400 (Mon, 17 Mar 2025) |
| git_url: https://git.bioconductor.org/packages/OmnipathR |
| git_branch: RELEASE_3_20 |
| git_last_commit: 3c7d7f1 |
| git_last_commit_date: 2024-10-29 10:41:00 -0400 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2025-03-20 12:09 -0400 (Thu, 20 Mar 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4756 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.3 (2025-02-28 ucrt) -- "Trophy Case" | 4487 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4514 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4441 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4406 |
| 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 1456/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| OmnipathR 3.14.0 (landing page) Denes Turei
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | ERROR | ||||||||||
|
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. |
| Package: OmnipathR |
| Version: 3.14.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings OmnipathR_3.14.0.tar.gz |
| StartedAt: 2025-03-18 07:29:06 -0400 (Tue, 18 Mar 2025) |
| EndedAt: 2025-03-18 07:37:31 -0400 (Tue, 18 Mar 2025) |
| EllapsedTime: 504.9 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: OmnipathR.Rcheck |
| Warnings: NA |
##############################################################################
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings OmnipathR_3.14.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/OmnipathR.Rcheck’
* using R version 4.4.3 (2025-02-28)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘OmnipathR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OmnipathR’ version ‘3.14.0’
* 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 ... OK
* 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 whether startup messages can be suppressed ... NOTE
[2025-03-18 07:29:51] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 07:29:51] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-18 07:29:51] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-03-18 07:29:51] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-03-18 07:29:51] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-03-18 07:29:51] [TRACE] [OmnipathR] Contains 1 files.
[2025-03-18 07:29:51] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-03-18 07:29:51] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 07:29:51] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-18 07:29:51] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-03-18 07:29:51] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2025-03-18 07:29:51] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-03-18 07:29:51] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-18 07:29:51] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-03-18 07:29:51] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-18 07:29:51] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-03-18 07:29:51] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-18 07:29:51] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-03-18 07:29:51] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-18 07:29:51] [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
[2025-03-18 07:30:20] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 07:30:20] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-18 07:30:20] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-03-18 07:30:20] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-03-18 07:30:20] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-03-18 07:30:20] [TRACE] [OmnipathR] Contains 1 files.
[2025-03-18 07:30:20] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-03-18 07:30:20] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 07:30:20] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-18 07:30:20] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-03-18 07:30:21] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2025-03-18 07:30:21] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-03-18 07:30:21] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-18 07:30:21] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-03-18 07:30:21] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-18 07:30:21] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-03-18 07:30:21] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-18 07:30:21] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-03-18 07:30:21] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-18 07:30:21] [TRACE] [OmnipathR] Cache locked: FALSE
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* 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")
[2025-03-18 07:36:10] [TRACE] [OmnipathR] Creating ID mapping table from `uniprotswissprot` to `ensembl_peptide_id`, for organism hsapiens
[2025-03-18 07:36:10] [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>
[2025-03-18 07:36:10] [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`.
[2025-03-18 07:36:10] [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`
[2025-03-18 07:36:10] [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`.
[2025-03-18 07:36:10] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 07:36:10] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-18 07:36:10] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 07:36:10] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-18 07:36:10] [INFO] [OmnipathR] Cache item `5146291739ab7fee3dd9b2830721d4357888383d` version 1: status changed from `unknown` to `started`.
[2025-03-18 07:36:10] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/5146291739ab7fee3dd9b2830721d4357888383d-1.rds`.
[2025-03-18 07:36:10] [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`
[2025-03-18 07:36:10] [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`
[2025-03-18 07:36:11] [TRACE] [OmnipathR] HTTP 200
[2025-03-18 07:36:11] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/5146291739ab7fee3dd9b2830721d4357888383d-1.rds`.
[2025-03-18 07:36:11] [INFO] [OmnipathR] Download ready [key=5146291739ab7fee3dd9b2830721d4357888383d, version=1]
[2025-03-18 07:36:11] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 07:36:11] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-18 07:36:11] [INFO] [OmnipathR] Cache item `5146291739ab7fee3dd9b2830721d4357888383d` version 1: status changed from `started` to `ready`.
[2025-03-18 07:36:11] [WARN] [OmnipathR] BioMart: missing success flag, data might be incomplete or contain error message!
[2025-03-18 07:36:11] [WARN] [OmnipathR] Query ERROR: caught BioMart::Exception::Database: Could not connect to mysql database ensembl_mart_113: DBI connect('database=ensembl_mart_113;host=127.0.0.1;port=5316','ensro',...) failed: Can't connect to MySQL server on '127.0.0.1' (111) at /nfs/public/ro/ensweb/live/mart/www_113/biomart-perl/lib/BioMart/Configuration/DBLocation.pm line 98.
[2025-03-18 07:36:11] [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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 2 NOTEs
See
‘/Users/biocbuild/bbs-3.20-bioc/meat/OmnipathR.Rcheck/00check.log’
for details.
OmnipathR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL OmnipathR ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/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 [2025-03-17 16:53:38] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-17 16:53:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-17 16:53:39] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-03-17 16:53:39] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-03-17 16:53:39] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-03-17 16:53:39] [TRACE] [OmnipathR] Contains 1 files. [2025-03-17 16:53:39] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-03-17 16:53:39] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-17 16:53:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-17 16:53:39] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-03-17 16:53:39] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2025-03-17 16:53:39] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-03-17 16:53:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-17 16:53:39] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-03-17 16:53:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-17 16:53:39] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-03-17 16:53:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-17 16:53:39] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/00LOCK-OmnipathR/00new/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-03-17 16:53:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-17 16:53:39] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2025-03-17 16:53:44] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-17 16:53:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-17 16:53:44] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-03-17 16:53:44] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-03-17 16:53:44] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-03-17 16:53:44] [TRACE] [OmnipathR] Contains 1 files. [2025-03-17 16:53:44] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-03-17 16:53:44] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-03-17 16:53:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-17 16:53:44] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-03-17 16:53:44] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2025-03-17 16:53:44] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-03-17 16:53:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-17 16:53:44] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-03-17 16:53:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-17 16:53:44] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-03-17 16:53:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-17 16:53:44] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-03-17 16:53:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-03-17 16:53:44] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package keeps a record of temporary installation path * DONE (OmnipathR)
OmnipathR.Rcheck/tests/testthat.Rout
R version 4.4.3 (2025-02-28) -- "Trophy Case"
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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)
[2025-03-18 07:36:18] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 07:36:18] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-18 07:36:18] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-03-18 07:36:18] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-03-18 07:36:18] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-03-18 07:36:18] [TRACE] [OmnipathR] Contains 38 files.
[2025-03-18 07:36:18] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-03-18 07:36:18] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 07:36:18] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-18 07:36:18] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-03-18 07:36:18] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2025-03-18 07:36:18] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-03-18 07:36:18] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-18 07:36:18] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-03-18 07:36:18] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-18 07:36:18] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-03-18 07:36:18] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-18 07:36:18] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-03-18 07:36:18] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-03-18 07:36:18] [TRACE] [OmnipathR] Cache locked: FALSE
>
> test_check('OmnipathR')
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 34 ]
>
> proc.time()
user system elapsed
21.735 1.601 45.362
OmnipathR.Rcheck/OmnipathR-Ex.timings
| name | user | system | elapsed | |
| OmnipathR | 0.001 | 0.001 | 0.001 | |
| all_uniprot_acs | 0.037 | 0.006 | 0.044 | |
| all_uniprots | 1.452 | 0.141 | 21.279 | |
| ancestors | 0.018 | 0.002 | 0.019 | |
| annotated_network | 1.354 | 0.090 | 3.898 | |
| annotation_categories | 102.103 | 0.308 | 104.770 | |
| annotation_resources | 0.128 | 0.006 | 0.607 | |
| annotations | 0.483 | 0.026 | 1.289 | |
| biomart_query | 0.411 | 0.027 | 0.734 | |
| bioplex1 | 0.017 | 0.001 | 0.018 | |
| bioplex2 | 0.018 | 0.001 | 0.018 | |
| bioplex3 | 0.017 | 0.001 | 0.018 | |
| bioplex_all | 0.018 | 0.002 | 0.020 | |
| bioplex_hct116_1 | 0.018 | 0.001 | 0.020 | |
| bma_motif_es | 0.609 | 0.041 | 1.562 | |
| bma_motif_vs | 0.343 | 0.010 | 0.867 | |
| chalmers_gem | 0.017 | 0.002 | 0.019 | |
| chalmers_gem_id_mapping_table | 0.017 | 0.001 | 0.018 | |
| chalmers_gem_id_type | 0.004 | 0.000 | 0.004 | |
| chalmers_gem_metabolites | 0.018 | 0.001 | 0.020 | |
| chalmers_gem_network | 0.019 | 0.001 | 0.020 | |
| chalmers_gem_raw | 0.017 | 0.001 | 0.020 | |
| chalmers_gem_reactions | 0.018 | 0.001 | 0.019 | |
| common_name | 0.054 | 0.001 | 0.056 | |
| complex_genes | 0.759 | 0.043 | 1.982 | |
| complex_resources | 0.127 | 0.005 | 0.611 | |
| complexes | 0.291 | 0.009 | 1.095 | |
| consensuspathdb_download | 0.000 | 0.001 | 0.001 | |
| consensuspathdb_raw_table | 0.018 | 0.001 | 0.019 | |
| cosmos_pkn | 0.000 | 0.001 | 0.001 | |
| curated_ligand_receptor_interactions | 9.372 | 0.392 | 16.852 | |
| curated_ligrec_stats | 57.498 | 1.638 | 117.286 | |
| database_summary | 2.754 | 0.058 | 3.775 | |
| descendants | 0.018 | 0.001 | 0.027 | |
| ensembl_dataset | 0.019 | 0.000 | 0.020 | |