Denes Turei
| Snapshot Date: 2024-11-19 13:40 -0500 (Tue, 19 Nov 2024) |
| 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 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-11-20 12:02 -0500 (Wed, 20 Nov 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4481 |
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4479 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4359 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4539 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4493 |
| 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
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | ||||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | ERROR | skipped | skipped | |||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / 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: /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_3.14.0.tar.gz |
| StartedAt: 2024-11-20 06:56:16 -0500 (Wed, 20 Nov 2024) |
| EndedAt: 2024-11-20 07:22:50 -0500 (Wed, 20 Nov 2024) |
| EllapsedTime: 1594.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: OmnipathR.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### 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_3.14.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/OmnipathR.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* 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 loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... NOTE
[2024-11-20 06:56:36] [TRACE] [OmnipathR] Reading JSON from `/media/volume/teran2_disk/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-20 06:56:36] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-11-20 06:56:36] [INFO] [OmnipathR] Initialized cache: `/media/volume/teran2_disk/biocbuild/.cache/OmnipathR`.
[2024-11-20 06:56:36] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2024-11-20 06:56:36] [TRACE] [OmnipathR] Cache is at `/media/volume/teran2_disk/biocbuild/.cache/OmnipathR`.
[2024-11-20 06:56:36] [TRACE] [OmnipathR] Contains 1 files.
[2024-11-20 06:56:36] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2024-11-20 06:56:36] [TRACE] [OmnipathR] Reading JSON from `/media/volume/teran2_disk/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-20 06:56:36] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-11-20 06:56:36] [SUCCESS] [OmnipathR] Removing all cache contents from `/media/volume/teran2_disk/biocbuild/.cache/OmnipathR`.
[2024-11-20 06:56:36] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2024-11-20 06:56:36] [TRACE] [OmnipathR] Reading JSON from `/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-11-20 06:56:36] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-11-20 06:56:36] [TRACE] [OmnipathR] Reading JSON from `/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-11-20 06:56:36] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-11-20 06:56:36] [TRACE] [OmnipathR] Reading JSON from `/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-11-20 06:56:36] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-11-20 06:56:36] [TRACE] [OmnipathR] Reading JSON from `/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-11-20 06:56:36] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-11-20 06:56:36] [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
[2024-11-20 06:56:46] [TRACE] [OmnipathR] Reading JSON from `/media/volume/teran2_disk/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-20 06:56:46] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-11-20 06:56:46] [INFO] [OmnipathR] Initialized cache: `/media/volume/teran2_disk/biocbuild/.cache/OmnipathR`.
[2024-11-20 06:56:46] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2024-11-20 06:56:46] [TRACE] [OmnipathR] Cache is at `/media/volume/teran2_disk/biocbuild/.cache/OmnipathR`.
[2024-11-20 06:56:46] [TRACE] [OmnipathR] Contains 1 files.
[2024-11-20 06:56:46] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2024-11-20 06:56:46] [TRACE] [OmnipathR] Reading JSON from `/media/volume/teran2_disk/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-20 06:56:46] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-11-20 06:56:46] [SUCCESS] [OmnipathR] Removing all cache contents from `/media/volume/teran2_disk/biocbuild/.cache/OmnipathR`.
[2024-11-20 06:56:46] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2024-11-20 06:56:46] [TRACE] [OmnipathR] Reading JSON from `/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-11-20 06:56:46] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-11-20 06:56:46] [TRACE] [OmnipathR] Reading JSON from `/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-11-20 06:56:46] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-11-20 06:56:46] [TRACE] [OmnipathR] Reading JSON from `/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-11-20 06:56:46] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-11-20 06:56:46] [TRACE] [OmnipathR] Reading JSON from `/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-11-20 06:56:46] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-11-20 06:56:46] [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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
annotation_categories 74.738 0.039 77.655
curated_ligrec_stats 20.172 0.398 82.500
omnipath-interactions 16.535 0.478 34.338
filter_extra_attrs 12.854 0.008 13.702
nichenet_gr_network_omnipath 7.587 0.105 13.457
extra_attr_values 7.141 0.159 13.200
translate_ids_multi 6.884 0.063 17.282
go_annot_download 6.326 0.578 7.308
extra_attrs_to_cols 6.448 0.006 6.500
pivot_annotations 5.682 0.352 22.004
with_extra_attrs 5.855 0.083 8.283
giant_component 5.851 0.076 7.108
omnipath_for_cosmos 5.230 0.109 14.264
nichenet_signaling_network_omnipath 5.230 0.046 6.374
static_table 3.961 0.124 10.219
filter_intercell 3.273 0.223 5.033
print_interactions 3.399 0.049 6.395
curated_ligand_receptor_interactions 3.152 0.088 11.518
uniprot_full_id_mapping_table 1.653 1.068 155.362
translate_ids 1.381 0.469 399.500
ensembl_id_mapping_table 0.723 0.026 9.855
all_uniprots 0.517 0.055 20.121
biomart_query 0.530 0.040 5.881
* 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: 2 NOTEs
See
‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/OmnipathR.Rcheck/00check.log’
for details.
OmnipathR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL OmnipathR ### ############################################################################## ############################################################################## * installing to library ‘/media/volume/teran2_disk/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 [2024-11-19 16:30:32] [TRACE] [OmnipathR] Reading JSON from `/media/volume/teran2_disk/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-11-19 16:30:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-19 16:30:33] [INFO] [OmnipathR] Initialized cache: `/media/volume/teran2_disk/biocbuild/.cache/OmnipathR`. [2024-11-19 16:30:33] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-11-19 16:30:33] [TRACE] [OmnipathR] Cache is at `/media/volume/teran2_disk/biocbuild/.cache/OmnipathR`. [2024-11-19 16:30:33] [TRACE] [OmnipathR] Contains 8 files. [2024-11-19 16:30:33] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-11-19 16:30:33] [TRACE] [OmnipathR] Reading JSON from `/media/volume/teran2_disk/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-11-19 16:30:33] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-19 16:30:33] [SUCCESS] [OmnipathR] Removing all cache contents from `/media/volume/teran2_disk/biocbuild/.cache/OmnipathR`. [2024-11-19 16:30:33] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2024-11-19 16:30:33] [TRACE] [OmnipathR] Reading JSON from `/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-11-19 16:30:33] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-19 16:30:33] [TRACE] [OmnipathR] Reading JSON from `/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-11-19 16:30:33] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-19 16:30:33] [TRACE] [OmnipathR] Reading JSON from `/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-11-19 16:30:33] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-19 16:30:33] [TRACE] [OmnipathR] Reading JSON from `/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-11-19 16:30:33] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-19 16:30:33] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2024-11-19 16:30:34] [TRACE] [OmnipathR] Reading JSON from `/media/volume/teran2_disk/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-11-19 16:30:34] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-19 16:30:34] [INFO] [OmnipathR] Initialized cache: `/media/volume/teran2_disk/biocbuild/.cache/OmnipathR`. [2024-11-19 16:30:34] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-11-19 16:30:34] [TRACE] [OmnipathR] Cache is at `/media/volume/teran2_disk/biocbuild/.cache/OmnipathR`. [2024-11-19 16:30:34] [TRACE] [OmnipathR] Contains 1 files. [2024-11-19 16:30:34] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-11-19 16:30:34] [TRACE] [OmnipathR] Reading JSON from `/media/volume/teran2_disk/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-11-19 16:30:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-19 16:30:35] [SUCCESS] [OmnipathR] Removing all cache contents from `/media/volume/teran2_disk/biocbuild/.cache/OmnipathR`. [2024-11-19 16:30:35] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2024-11-19 16:30:35] [TRACE] [OmnipathR] Reading JSON from `/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-11-19 16:30:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-19 16:30:35] [TRACE] [OmnipathR] Reading JSON from `/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-11-19 16:30:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-19 16:30:35] [TRACE] [OmnipathR] Reading JSON from `/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-11-19 16:30:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-19 16:30:35] [TRACE] [OmnipathR] Reading JSON from `/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-11-19 16:30:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-11-19 16:30:35] [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 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> #!/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)
[2024-11-20 07:14:09] [TRACE] [OmnipathR] Reading JSON from `/media/volume/teran2_disk/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-20 07:14:09] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-11-20 07:14:09] [INFO] [OmnipathR] Initialized cache: `/media/volume/teran2_disk/biocbuild/.cache/OmnipathR`.
[2024-11-20 07:14:09] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2024-11-20 07:14:09] [TRACE] [OmnipathR] Cache is at `/media/volume/teran2_disk/biocbuild/.cache/OmnipathR`.
[2024-11-20 07:14:09] [TRACE] [OmnipathR] Contains 21 files.
[2024-11-20 07:14:09] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2024-11-20 07:14:09] [TRACE] [OmnipathR] Reading JSON from `/media/volume/teran2_disk/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-20 07:14:09] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-11-20 07:14:09] [SUCCESS] [OmnipathR] Removing all cache contents from `/media/volume/teran2_disk/biocbuild/.cache/OmnipathR`.
[2024-11-20 07:14:09] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2024-11-20 07:14:09] [TRACE] [OmnipathR] Reading JSON from `/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-11-20 07:14:09] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-11-20 07:14:09] [TRACE] [OmnipathR] Reading JSON from `/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-11-20 07:14:09] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-11-20 07:14:09] [TRACE] [OmnipathR] Reading JSON from `/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-11-20 07:14:09] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-11-20 07:14:09] [TRACE] [OmnipathR] Reading JSON from `/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-11-20 07:14:09] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-11-20 07:14:09] [TRACE] [OmnipathR] Cache locked: FALSE
>
> test_check('OmnipathR')
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 34 ]
>
> proc.time()
user system elapsed
8.512 0.494 34.549
OmnipathR.Rcheck/OmnipathR-Ex.timings
| name | user | system | elapsed | |
| OmnipathR | 0 | 0 | 0 | |
| all_uniprot_acs | 0.011 | 0.002 | 0.013 | |
| all_uniprots | 0.517 | 0.055 | 20.121 | |
| ancestors | 0.005 | 0.001 | 0.005 | |
| annotated_network | 0.483 | 0.043 | 2.462 | |
| annotation_categories | 74.738 | 0.039 | 77.655 | |
| annotation_resources | 0.055 | 0.002 | 0.641 | |
| annotations | 0.237 | 0.010 | 1.088 | |
| biomart_query | 0.530 | 0.040 | 5.881 | |
| bioplex1 | 0.006 | 0.000 | 0.006 | |
| bioplex2 | 0.006 | 0.000 | 0.006 | |
| bioplex3 | 0.031 | 0.000 | 0.031 | |
| bioplex_all | 0.006 | 0.000 | 0.006 | |
| bioplex_hct116_1 | 0.004 | 0.001 | 0.005 | |
| bma_motif_es | 0.247 | 0.014 | 0.937 | |
| bma_motif_vs | 0.154 | 0.001 | 0.769 | |
| chalmers_gem | 0.005 | 0.001 | 0.005 | |
| chalmers_gem_id_mapping_table | 0.005 | 0.001 | 0.005 | |
| chalmers_gem_id_type | 0.001 | 0.000 | 0.001 | |
| chalmers_gem_metabolites | 0.005 | 0.000 | 0.005 | |
| chalmers_gem_network | 0.006 | 0.000 | 0.006 | |
| chalmers_gem_raw | 0.006 | 0.000 | 0.006 | |
| chalmers_gem_reactions | 0.004 | 0.001 | 0.005 | |
| common_name | 0.046 | 0.000 | 0.045 | |
| complex_genes | 0.321 | 0.005 | 1.805 | |
| complex_resources | 0.085 | 0.000 | 0.733 | |
| complexes | 0.113 | 0.003 | 0.789 | |
| consensuspathdb_download | 0.001 | 0.000 | 0.000 | |
| consensuspathdb_raw_table | 0.006 | 0.000 | 0.011 | |
| cosmos_pkn | 0 | 0 | 0 | |
| curated_ligand_receptor_interactions | 3.152 | 0.088 | 11.518 | |
| curated_ligrec_stats | 20.172 | 0.398 | 82.500 | |
| database_summary | 0.989 | 0.008 | 2.380 | |
| descendants | 0.006 | 0.002 | 0.008 | |
| ensembl_dataset | 0.009 | 0.000 | 0.008 | |
| ensembl_id_mapping_table | 0.723 | 0.026 | 9.855 | |
| ensembl_id_type | 0.002 | 0.000 | 0.001 | |
| ensembl_name | 0.038 | 0.000 | 0.037 | |
| ensembl_organisms | 0.107 | 0.000 | 0.106 | |
| ensembl_organisms_raw | 0.079 | 0.001 | 0.079 | |
| ensembl_orthology | 0.001 | 0.000 | 0.000 | |
| enzsub_graph | 1.323 | 0.020 | 2.654 | |
| enzsub_resources | 0.059 | 0.001 | 0.677 | |
| enzyme_substrate | 0.658 | 0.002 | 1.133 | |
| evex_download | 0.006 | 0.000 | 0.006 | |
| evidences | 0 | 0 | 0 | |
| extra_attr_values | 7.141 | 0.159 | 13.200 | |
| extra_attrs | 4.408 | 0.017 | 4.470 | |
| extra_attrs_to_cols | 6.448 | 0.006 | 6.500 | |
| filter_by_resource | 3.760 | 0.063 | 4.978 | |
| filter_extra_attrs | 12.854 | 0.008 | 13.702 | |
| filter_intercell | 3.273 | 0.223 | 5.033 | |
| filter_intercell_network | 0.013 | 0.000 | 0.012 | |
| find_all_paths | 3.525 | 0.002 | 3.579 | |
| from_evidences | 0 | 0 | 0 | |
| get_db | 0.001 | 0.000 | 0.000 | |
| get_ontology_db | 0.005 | 0.000 | 0.006 | |
| giant_component | 5.851 | 0.076 | 7.108 | |
| go_annot_download | 6.326 | 0.578 | 7.308 | |
| go_annot_slim | 0 | 0 | 0 | |
| go_ontology_download | 0.005 | 0.001 | 0.006 | |
| guide2pharma_download | 0.004 | 0.001 | 0.005 | |
| harmonizome_download | 0.005 | 0.000 | 0.005 | |
| has_extra_attrs | 3.854 | 0.014 | 3.873 | |
| hmdb_id_mapping_table | 0.005 | 0.000 | 0.005 | |
| hmdb_id_type | 0.001 | 0.000 | 0.001 | |
| hmdb_metabolite_fields | 0.001 | 0.000 | 0.000 | |
| hmdb_protein_fields | 0 | 0 | 0 | |
| hmdb_table | 0.006 | 0.000 | 0.005 | |
| homologene_download | 0.006 | 0.000 | 0.006 | |
| homologene_raw | 0.013 | 0.000 | 0.013 | |
| homologene_uniprot_orthology | 0.005 | 0.000 | 0.005 | |
| hpo_download | 1.218 | 0.102 | 1.908 | |
| htridb_download | 0.006 | 0.000 | 0.006 | |
| id_translation_resources | 0.000 | 0.000 | 0.001 | |
| id_types | 0.034 | 0.000 | 0.034 | |
| inbiomap_download | 0 | 0 | 0 | |
| inbiomap_raw | 0 | 0 | 0 | |
| interaction_datasets | 0.295 | 0.007 | 0.705 | |
| interaction_graph | 0.224 | 0.001 | 0.807 | |
| interaction_resources | 0.064 | 0.003 | 0.647 | |
| interaction_types | 0.026 | 0.001 | 0.027 | |
| intercell | 0.260 | 0.019 | 0.699 | |
| intercell_categories | 0.229 | 0.015 | 0.494 | |
| intercell_consensus_filter | 0.664 | 0.036 | 1.553 | |
| intercell_generic_categories | 0.031 | 0.000 | 0.030 | |
| intercell_network | 0.006 | 0.000 | 0.006 | |
| intercell_resources | 0.067 | 0.003 | 0.648 | |
| intercell_summary | 0.032 | 0.002 | 0.035 | |
| is_ontology_id | 0 | 0 | 0 | |
| is_swissprot | 0.018 | 0.000 | 0.017 | |
| is_trembl | 0.017 | 0.000 | 0.017 | |
| is_uniprot | 0.007 | 0.001 | 0.007 | |
| kegg_info | 0.005 | 0.000 | 0.006 | |
| kegg_open | 0.005 | 0.000 | 0.005 | |
| kegg_pathway_annotations | 0 | 0 | 0 | |
| kegg_pathway_download | 0.006 | 0.000 | 0.006 | |
| kegg_pathway_list | 0.005 | 0.000 | 0.006 | |
| kegg_pathways_download | 0.000 | 0.000 | 0.001 | |
| kegg_picture | 0.093 | 0.002 | 2.017 | |
| kegg_process | 0.011 | 0.001 | 0.016 | |
| latin_name | 0.036 | 0.000 | 0.039 | |
| load_db | 0.048 | 0.001 | 0.049 | |
| ncbi_taxid | 0.038 | 0.001 | 0.038 | |
| nichenet_build_model | 0 | 0 | 0 | |
| nichenet_expression_data | 0.007 | 0.000 | 0.007 | |
| nichenet_gr_network | 0.017 | 0.000 | 0.017 | |
| nichenet_gr_network_evex | 0.006 | 0.000 | 0.006 | |
| nichenet_gr_network_harmonizome | 0.006 | 0.000 | 0.006 | |
| nichenet_gr_network_htridb | 0.006 | 0.000 | 0.006 | |
| nichenet_gr_network_omnipath | 7.587 | 0.105 | 13.457 | |
| nichenet_gr_network_pathwaycommons | 0.006 | 0.001 | 0.006 | |
| nichenet_gr_network_regnetwork | 0.005 | 0.000 | 0.005 | |
| nichenet_gr_network_remap | 0.005 | 0.000 | 0.005 | |
| nichenet_gr_network_trrust | 0.005 | 0.000 | 0.005 | |
| nichenet_ligand_activities | 0 | 0 | 0 | |
| nichenet_ligand_target_links | 0 | 0 | 0 | |
| nichenet_ligand_target_matrix | 0.000 | 0.000 | 0.001 | |
| nichenet_lr_network | 0.013 | 0.002 | 0.015 | |
| nichenet_lr_network_guide2pharma | 0.028 | 0.001 | 0.029 | |
| nichenet_lr_network_omnipath | 0.015 | 0.000 | 0.016 | |
| nichenet_lr_network_ramilowski | 0.005 | 0.001 | 0.005 | |
| nichenet_main | 0 | 0 | 0 | |
| nichenet_networks | 0.024 | 0.001 | 0.026 | |
| nichenet_optimization | 0 | 0 | 0 | |
| nichenet_remove_orphan_ligands | 0.015 | 0.000 | 0.015 | |
| nichenet_results_dir | 0.001 | 0.000 | 0.000 | |
| nichenet_signaling_network | 0.015 | 0.000 | 0.016 | |
| nichenet_signaling_network_cpdb | 0.005 | 0.001 | 0.005 | |
| nichenet_signaling_network_evex | 0.003 | 0.002 | 0.006 | |
| nichenet_signaling_network_harmonizome | 0.005 | 0.000 | 0.005 | |
| nichenet_signaling_network_inbiomap | 0 | 0 | 0 | |
| nichenet_signaling_network_omnipath | 5.230 | 0.046 | 6.374 | |
| nichenet_signaling_network_pathwaycommons | 0.004 | 0.002 | 0.006 | |
| nichenet_signaling_network_vinayagam | 0.006 | 0.000 | 0.006 | |
| nichenet_test | 0 | 0 | 0 | |
| nichenet_workarounds | 0.001 | 0.000 | 0.000 | |
| obo_parser | 0.057 | 0.001 | 0.130 | |
| oma_code | 0.049 | 0.000 | 0.049 | |
| oma_organisms | 0.045 | 0.001 | 0.046 | |
| oma_pairwise | 0.007 | 0.000 | 0.007 | |
| oma_pairwise_genesymbols | 0.005 | 0.001 | 0.006 | |
| oma_pairwise_translated | 0.005 | 0.001 | 0.006 | |
| omnipath-interactions | 16.535 | 0.478 | 34.338 | |
| omnipath_cache_autoclean | 0 | 0 | 0 | |
| omnipath_cache_clean | 0.005 | 0.000 | 0.004 | |
| omnipath_cache_clean_db | 0.075 | 0.003 | 0.080 | |
| omnipath_cache_download_ready | 0.292 | 0.029 | 0.424 | |
| omnipath_cache_filter_versions | 0.056 | 0.003 | 0.077 | |
| omnipath_cache_get | 0.044 | 0.002 | 0.047 | |
| omnipath_cache_key | 0.001 | 0.000 | 0.001 | |
| omnipath_cache_latest_or_new | 0.033 | 0.001 | 0.034 | |
| omnipath_cache_load | 0.340 | 0.015 | 1.797 | |
| omnipath_cache_move_in | 0.108 | 0.008 | 0.130 | |
| omnipath_cache_remove | 0.056 | 0.001 | 0.071 | |
| omnipath_cache_save | 0.098 | 0.007 | 0.239 | |
| omnipath_cache_search | 0 | 0 | 0 | |
| omnipath_cache_set_ext | 0.041 | 0.004 | 0.060 | |
| omnipath_cache_update_status | 0.046 | 0.003 | 0.049 | |
| omnipath_cache_wipe | 0.000 | 0.000 | 0.001 | |
| omnipath_config_path | 0 | 0 | 0 | |
| omnipath_for_cosmos | 5.230 | 0.109 | 14.264 | |
| omnipath_load_config | 0 | 0 | 0 | |
| omnipath_log | 0 | 0 | 0 | |
| omnipath_logfile | 0.001 | 0.000 | 0.001 | |
| omnipath_msg | 0.003 | 0.000 | 0.003 | |
| omnipath_query | 2.053 | 0.000 | 2.133 | |
| omnipath_reset_config | 0.000 | 0.000 | 0.001 | |
| omnipath_save_config | 0 | 0 | 0 | |
| omnipath_set_cachedir | 0.013 | 0.001 | 0.015 | |
| omnipath_set_console_loglevel | 0.002 | 0.000 | 0.002 | |
| omnipath_set_logfile_loglevel | 0.002 | 0.000 | 0.002 | |
| omnipath_set_loglevel | 0.002 | 0.000 | 0.001 | |
| omnipath_show_db | 0.034 | 0.000 | 0.034 | |
| omnipath_unlock_cache_db | 0.001 | 0.000 | 0.000 | |
| only_from | 0 | 0 | 0 | |
| ontology_ensure_id | 0.001 | 0.000 | 0.000 | |
| ontology_ensure_name | 0.000 | 0.000 | 0.001 | |
| ontology_name_id | 0.000 | 0.001 | 0.001 | |
| organism_for | 0.026 | 0.000 | 0.026 | |
| pathwaycommons_download | 0 | 0 | 0 | |
| pivot_annotations | 5.682 | 0.352 | 22.004 | |
| preppi_download | 0.000 | 0.000 | 0.001 | |
| preppi_filter | 0.001 | 0.001 | 0.001 | |
| print_bma_motif_es | 0.165 | 0.007 | 1.104 | |
| print_bma_motif_vs | 0.095 | 0.003 | 0.740 | |
| print_interactions | 3.399 | 0.049 | 6.395 | |
| print_path_es | 0.299 | 0.008 | 1.526 | |
| print_path_vs | 1.274 | 0.018 | 4.187 | |
| pubmed_open | 2.460 | 0.003 | 2.471 | |
| query_info | 0.077 | 0.006 | 0.515 | |
| ramilowski_download | 0.001 | 0.000 | 0.001 | |
| ramp_id_mapping_table | 0.001 | 0.000 | 0.000 | |
| ramp_id_type | 0.001 | 0.000 | 0.003 | |
| ramp_sqlite | 0.000 | 0.000 | 0.001 | |
| ramp_table | 0 | 0 | 0 | |
| ramp_tables | 0.001 | 0.000 | 0.000 | |
| regnetwork_directions | 0 | 0 | 0 | |
| regnetwork_download | 0.000 | 0.000 | 0.001 | |
| relations_list_to_table | 0.056 | 0.000 | 0.140 | |
| relations_table_to_graph | 0 | 0 | 0 | |
| relations_table_to_list | 0.045 | 0.000 | 0.202 | |
| remap_dorothea_download | 0.001 | 0.000 | 0.000 | |
| remap_filtered | 0 | 0 | 0 | |
| remap_tf_target_download | 0 | 0 | 0 | |
| resource_info | 0.105 | 0.012 | 0.730 | |
| resources | 0.053 | 0.001 | 0.474 | |
| resources_colname | 0.381 | 0.020 | 1.515 | |
| resources_in | 2.192 | 0.001 | 2.203 | |
| show_network | 0 | 0 | 0 | |
| signed_ptms | 2.824 | 0.016 | 4.159 | |
| simplify_intercell_network | 0.001 | 0.000 | 0.004 | |
| static_table | 3.961 | 0.124 | 10.219 | |
| static_tables | 0.036 | 0.001 | 0.162 | |
| stitch_actions | 0.001 | 0.000 | 0.000 | |
| stitch_links | 0 | 0 | 0 | |
| stitch_network | 0.000 | 0.000 | 0.001 | |
| stitch_remove_prefixes | 0.005 | 0.000 | 0.010 | |
| swap_relations | 0.092 | 0.003 | 0.200 | |
| swissprots_only | 0.02 | 0.00 | 0.04 | |
| tfcensus_download | 0.113 | 0.006 | 0.433 | |
| translate_ids | 1.381 | 0.469 | 399.500 | |
| translate_ids_multi | 6.884 | 0.063 | 17.282 | |
| trembls_only | 0.022 | 0.000 | 0.022 | |
| trrust_download | 0.000 | 0.000 | 0.001 | |
| uniprot_full_id_mapping_table | 1.653 | 1.068 | 155.362 | |
| uniprot_genesymbol_cleanup | 0.000 | 0.000 | 0.001 | |
| uniprot_id_mapping_table | 0.001 | 0.000 | 0.001 | |
| uniprot_id_type | 0.001 | 0.001 | 0.007 | |
| uniprot_idmapping_id_types | 0.136 | 0.005 | 0.882 | |
| unique_intercell_network | 0.001 | 0.000 | 0.001 | |
| unnest_evidences | 0 | 0 | 0 | |
| uploadlists_id_type | 0.002 | 0.000 | 0.002 | |
| vinayagam_download | 0.000 | 0.001 | 0.000 | |
| walk_ontology_tree | 0.000 | 0.001 | 0.005 | |
| with_extra_attrs | 5.855 | 0.083 | 8.283 | |
| with_references | 0.289 | 0.011 | 1.324 | |
| zenodo_download | 0.001 | 0.000 | 0.001 | |