Denes Turei
| Snapshot Date: 2025-01-10 13:40 -0500 (Fri, 10 Jan 2025) |
| git_url: https://git.bioconductor.org/packages/OmnipathR |
| git_branch: devel |
| git_last_commit: bc4d2dd |
| git_last_commit_date: 2024-10-29 10:41:00 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-01-11 11:42 -0500 (Sat, 11 Jan 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4760 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4479 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4443 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4398 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4391 |
| 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 1450/2277 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| OmnipathR 3.15.0 (landing page) Denes Turei
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | ERROR | skipped | skipped | |||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | ERROR | skipped | skipped | |||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | TIMEOUT | skipped | ||||||||||
|
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: 3.15.0 |
| Command: E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:OmnipathR.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings OmnipathR_3.15.0.tar.gz |
| StartedAt: 2025-01-11 03:46:28 -0500 (Sat, 11 Jan 2025) |
| EndedAt: 2025-01-11 04:01:36 -0500 (Sat, 11 Jan 2025) |
| EllapsedTime: 907.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: OmnipathR.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:OmnipathR.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings OmnipathR_3.15.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/OmnipathR.Rcheck'
* using R Under development (unstable) (2024-10-26 r87273 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 13.2.0
GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'OmnipathR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'OmnipathR' version '3.15.0'
* 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 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
[2025-01-11 03:47:01] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-11 03:47:01] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-11 03:47:01] [INFO] [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-01-11 03:47:01] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-01-11 03:47:01] [TRACE] [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-01-11 03:47:01] [TRACE] [OmnipathR] Contains 1 files.
[2025-01-11 03:47:01] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-01-11 03:47:02] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-11 03:47:02] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-11 03:47:02] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-01-11 03:47:02] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2025-01-11 03:47:02] [TRACE] [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-01-11 03:47:02] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-11 03:47:02] [TRACE] [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-01-11 03:47:02] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-11 03:47:02] [TRACE] [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-01-11 03:47:02] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-11 03:47:02] [TRACE] [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-01-11 03:47:02] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-11 03:47:02] [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
[2025-01-11 03:47:20] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-11 03:47:20] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-11 03:47:20] [INFO] [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-01-11 03:47:20] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-01-11 03:47:20] [TRACE] [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-01-11 03:47:20] [TRACE] [OmnipathR] Contains 1 files.
[2025-01-11 03:47:20] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-01-11 03:47:20] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-11 03:47:20] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-11 03:47:20] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-01-11 03:47:21] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2025-01-11 03:47:21] [TRACE] [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-01-11 03:47:21] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-11 03:47:21] [TRACE] [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-01-11 03:47:21] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-11 03:47:21] [TRACE] [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-01-11 03:47:21] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-11 03:47:21] [TRACE] [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-01-11 03:47:21] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-11 03:47:21] [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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
annotation_categories 59.88 0.03 60.59
omnipath-interactions 33.28 1.46 75.54
curated_ligrec_stats 31.70 1.31 80.18
filter_extra_attrs 20.66 0.09 21.19
nichenet_gr_network_omnipath 16.18 1.13 17.82
go_annot_download 13.31 0.87 12.47
pivot_annotations 12.02 0.89 22.31
extra_attr_values 11.97 0.26 12.76
with_extra_attrs 11.77 0.27 12.80
nichenet_signaling_network_omnipath 10.81 0.82 12.54
extra_attrs_to_cols 10.87 0.13 11.02
giant_component 10.48 0.35 11.29
omnipath_for_cosmos 10.11 0.30 60.97
translate_ids_multi 8.27 0.12 60.47
static_table 7.31 0.42 22.97
filter_by_resource 7.25 0.22 7.98
has_extra_attrs 7.10 0.06 7.17
filter_intercell 6.70 0.36 7.27
print_interactions 6.49 0.24 9.06
extra_attrs 6.63 0.09 6.73
find_all_paths 6.19 0.13 6.33
signed_ptms 6.20 0.00 6.79
curated_ligand_receptor_interactions 5.75 0.41 12.22
resources_in 5.13 0.04 5.32
print_path_vs 3.00 0.11 5.37
ensembl_id_mapping_table 1.67 0.08 36.63
translate_ids 1.03 0.19 17.76
uniprot_full_id_mapping_table 1.05 0.14 23.03
all_uniprots 0.90 0.11 20.74
resources_colname 0.76 0.05 6.25
print_path_es 0.64 0.06 6.94
* 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: 2 NOTEs
See
'E:/biocbuild/bbs-3.21-bioc/meat/OmnipathR.Rcheck/00check.log'
for details.
OmnipathR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL OmnipathR ### ############################################################################## ############################################################################## * installing to library 'E:/biocbuild/bbs-3.21-bioc/R/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 [2025-01-10 15:53:58] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8). [2025-01-10 15:53:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-10 15:53:58] [INFO] [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2025-01-10 15:53:58] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-01-10 15:53:58] [TRACE] [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2025-01-10 15:53:58] [TRACE] [OmnipathR] Contains 1 files. [2025-01-10 15:53:58] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-01-10 15:53:58] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8). [2025-01-10 15:53:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-10 15:53:58] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2025-01-10 15:53:58] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2025-01-10 15:53:58] [TRACE] [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/00LOCK-OmnipathR/00new/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-01-10 15:53:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-10 15:53:58] [TRACE] [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/00LOCK-OmnipathR/00new/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-01-10 15:53:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-10 15:53:58] [TRACE] [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-01-10 15:53:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-10 15:53:58] [TRACE] [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/00LOCK-OmnipathR/00new/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-01-10 15:53:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-10 15:53:58] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2025-01-10 15:54:00] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8). [2025-01-10 15:54:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-10 15:54:00] [INFO] [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2025-01-10 15:54:00] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-01-10 15:54:00] [TRACE] [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2025-01-10 15:54:00] [TRACE] [OmnipathR] Contains 1 files. [2025-01-10 15:54:00] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-01-10 15:54:00] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8). [2025-01-10 15:54:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-10 15:54:00] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2025-01-10 15:54:01] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2025-01-10 15:54:01] [TRACE] [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-01-10 15:54:01] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-10 15:54:01] [TRACE] [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-01-10 15:54:01] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-10 15:54:01] [TRACE] [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-01-10 15:54:01] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-10 15:54:01] [TRACE] [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-01-10 15:54:01] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-10 15:54:01] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package keeps a record of temporary installation path * DONE (OmnipathR)
OmnipathR.Rcheck/tests/testthat.Rout
R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64
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)
[2025-01-11 04:00:41] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-11 04:00:41] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-11 04:00:41] [INFO] [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-01-11 04:00:41] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-01-11 04:00:41] [TRACE] [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-01-11 04:00:41] [TRACE] [OmnipathR] Contains 21 files.
[2025-01-11 04:00:41] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-01-11 04:00:41] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-11 04:00:41] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-11 04:00:41] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-01-11 04:00:42] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2025-01-11 04:00:42] [TRACE] [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-01-11 04:00:42] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-11 04:00:42] [TRACE] [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-01-11 04:00:42] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-11 04:00:42] [TRACE] [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-01-11 04:00:42] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-11 04:00:42] [TRACE] [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-01-11 04:00:42] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-11 04:00:42] [TRACE] [OmnipathR] Cache locked: FALSE
>
> test_check('OmnipathR')
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 34 ]
>
> proc.time()
user system elapsed
11.78 1.54 31.12
OmnipathR.Rcheck/OmnipathR-Ex.timings
| name | user | system | elapsed | |
| OmnipathR | 0 | 0 | 0 | |
| all_uniprot_acs | 0.01 | 0.02 | 0.04 | |
| all_uniprots | 0.90 | 0.11 | 20.74 | |
| ancestors | 0.02 | 0.00 | 0.01 | |
| annotated_network | 0.84 | 0.11 | 2.94 | |
| annotation_categories | 59.88 | 0.03 | 60.59 | |
| annotation_resources | 0.04 | 0.00 | 0.47 | |
| annotations | 0.23 | 0.03 | 0.97 | |
| biomart_query | 1.15 | 0.03 | 3.54 | |
| bioplex1 | 0.01 | 0.00 | 0.02 | |
| bioplex2 | 0.02 | 0.00 | 0.01 | |
| bioplex3 | 0.04 | 0.00 | 0.05 | |
| bioplex_all | 0.02 | 0.00 | 0.02 | |
| bioplex_hct116_1 | 0.01 | 0.00 | 0.01 | |
| bma_motif_es | 0.44 | 0.13 | 1.14 | |
| bma_motif_vs | 0.22 | 0.03 | 0.66 | |
| chalmers_gem | 0.02 | 0.00 | 0.01 | |
| chalmers_gem_id_mapping_table | 0.01 | 0.00 | 0.02 | |
| chalmers_gem_id_type | 0 | 0 | 0 | |
| chalmers_gem_metabolites | 0.02 | 0.00 | 0.01 | |
| chalmers_gem_network | 0.01 | 0.00 | 0.02 | |
| chalmers_gem_raw | 0.02 | 0.00 | 0.01 | |
| chalmers_gem_reactions | 0.01 | 0.00 | 0.02 | |
| common_name | 0.04 | 0.00 | 0.03 | |
| complex_genes | 0.56 | 0.00 | 1.58 | |
| complex_resources | 0.05 | 0.02 | 0.48 | |
| complexes | 0.12 | 0.03 | 0.75 | |
| consensuspathdb_download | 0 | 0 | 0 | |
| consensuspathdb_raw_table | 0 | 0 | 0 | |
| cosmos_pkn | 0 | 0 | 0 | |
| curated_ligand_receptor_interactions | 5.75 | 0.41 | 12.22 | |
| curated_ligrec_stats | 31.70 | 1.31 | 80.18 | |
| database_summary | 1.58 | 0.02 | 3.02 | |
| descendants | 0.01 | 0.00 | 0.01 | |
| ensembl_dataset | 0.00 | 0.01 | 0.02 | |
| ensembl_id_mapping_table | 1.67 | 0.08 | 36.63 | |
| ensembl_id_type | 0 | 0 | 0 | |
| ensembl_name | 0.10 | 0.00 | 0.09 | |
| ensembl_organisms | 0.28 | 0.01 | 0.30 | |
| ensembl_organisms_raw | 0.11 | 0.02 | 0.12 | |
| ensembl_orthology | 0 | 0 | 0 | |
| enzsub_graph | 2.09 | 0.09 | 3.24 | |
| enzsub_resources | 0.08 | 0.00 | 0.50 | |
| enzyme_substrate | 1.11 | 0.04 | 1.56 | |
| evex_download | 0 | 0 | 0 | |
| evidences | 0 | 0 | 0 | |
| extra_attr_values | 11.97 | 0.26 | 12.76 | |
| extra_attrs | 6.63 | 0.09 | 6.73 | |
| extra_attrs_to_cols | 10.87 | 0.13 | 11.02 | |
| filter_by_resource | 7.25 | 0.22 | 7.98 | |
| filter_extra_attrs | 20.66 | 0.09 | 21.19 | |
| filter_intercell | 6.70 | 0.36 | 7.27 | |
| filter_intercell_network | 0.02 | 0.00 | 0.01 | |
| find_all_paths | 6.19 | 0.13 | 6.33 | |
| from_evidences | 0 | 0 | 0 | |
| get_db | 0 | 0 | 0 | |
| get_ontology_db | 0 | 0 | 0 | |
| giant_component | 10.48 | 0.35 | 11.29 | |
| go_annot_download | 13.31 | 0.87 | 12.47 | |
| go_annot_slim | 0 | 0 | 0 | |
| go_ontology_download | 0.00 | 0.00 | 0.02 | |
| guide2pharma_download | 0.02 | 0.00 | 0.01 | |
| harmonizome_download | 0.02 | 0.00 | 0.02 | |
| has_extra_attrs | 7.10 | 0.06 | 7.17 | |
| hmdb_id_mapping_table | 0.02 | 0.00 | 0.02 | |
| hmdb_id_type | 0 | 0 | 0 | |
| hmdb_metabolite_fields | 0 | 0 | 0 | |
| hmdb_protein_fields | 0 | 0 | 0 | |
| hmdb_table | 0.02 | 0.00 | 0.01 | |
| homologene_download | 0.00 | 0.02 | 0.02 | |
| homologene_raw | 0.03 | 0.00 | 0.03 | |
| homologene_uniprot_orthology | 0 | 0 | 0 | |
| hpo_download | 2.15 | 0.19 | 2.42 | |
| htridb_download | 0.02 | 0.00 | 0.02 | |
| id_translation_resources | 0 | 0 | 0 | |
| id_types | 0.01 | 0.01 | 0.03 | |
| inbiomap_download | 0 | 0 | 0 | |
| inbiomap_raw | 0 | 0 | 0 | |
| interaction_datasets | 0.38 | 0.05 | 0.72 | |
| interaction_graph | 0.37 | 0.00 | 0.80 | |
| interaction_resources | 0.03 | 0.00 | 0.45 | |
| interaction_types | 0.05 | 0.00 | 0.05 | |
| intercell | 0.48 | 0.05 | 0.94 | |
| intercell_categories | 0.42 | 0.01 | 0.75 | |
| intercell_consensus_filter | 1.38 | 0.08 | 1.98 | |
| intercell_generic_categories | 0.05 | 0.02 | 0.06 | |
| intercell_network | 0.01 | 0.00 | 0.01 | |
| intercell_resources | 0.13 | 0.00 | 0.54 | |
| intercell_summary | 0.04 | 0.02 | 0.06 | |
| is_ontology_id | 0 | 0 | 0 | |
| is_swissprot | 0.04 | 0.00 | 0.03 | |
| is_trembl | 0.04 | 0.00 | 0.05 | |
| is_uniprot | 0.02 | 0.00 | 0.01 | |
| kegg_info | 0.01 | 0.00 | 0.02 | |
| kegg_open | 0 | 0 | 0 | |
| kegg_pathway_annotations | 0 | 0 | 0 | |
| kegg_pathway_download | 0.02 | 0.00 | 0.01 | |
| kegg_pathway_list | 0.01 | 0.00 | 0.02 | |
| kegg_pathways_download | 0 | 0 | 0 | |
| kegg_picture | 0.07 | 0.01 | 2.58 | |
| kegg_process | 0.03 | 0.00 | 0.03 | |
| latin_name | 0.09 | 0.00 | 0.09 | |
| load_db | 0.06 | 0.00 | 0.06 | |
| ncbi_taxid | 0.11 | 0.02 | 0.13 | |
| nichenet_build_model | 0 | 0 | 0 | |
| nichenet_expression_data | 0 | 0 | 0 | |
| nichenet_gr_network | 0.05 | 0.00 | 0.05 | |
| nichenet_gr_network_evex | 0.01 | 0.00 | 0.01 | |
| nichenet_gr_network_harmonizome | 0.02 | 0.00 | 0.02 | |
| nichenet_gr_network_htridb | 0.01 | 0.00 | 0.01 | |
| nichenet_gr_network_omnipath | 16.18 | 1.13 | 17.82 | |
| nichenet_gr_network_pathwaycommons | 0.01 | 0.00 | 0.01 | |
| nichenet_gr_network_regnetwork | 0 | 0 | 0 | |
| nichenet_gr_network_remap | 0 | 0 | 0 | |
| nichenet_gr_network_trrust | 0.02 | 0.00 | 0.01 | |
| nichenet_ligand_activities | 0 | 0 | 0 | |
| nichenet_ligand_target_links | 0.00 | 0.02 | 0.02 | |
| nichenet_ligand_target_matrix | 0 | 0 | 0 | |
| nichenet_lr_network | 0.03 | 0.00 | 0.03 | |
| nichenet_lr_network_guide2pharma | 0.01 | 0.00 | 0.02 | |
| nichenet_lr_network_omnipath | 0.05 | 0.00 | 0.04 | |
| nichenet_lr_network_ramilowski | 0 | 0 | 0 | |
| nichenet_main | 0 | 0 | 0 | |
| nichenet_networks | 0.06 | 0.00 | 0.07 | |
| nichenet_optimization | 0 | 0 | 0 | |
| nichenet_remove_orphan_ligands | 0.05 | 0.00 | 0.05 | |
| nichenet_results_dir | 0 | 0 | 0 | |
| nichenet_signaling_network | 0.04 | 0.00 | 0.05 | |
| nichenet_signaling_network_cpdb | 0.00 | 0.02 | 0.01 | |
| nichenet_signaling_network_evex | 0 | 0 | 0 | |
| nichenet_signaling_network_harmonizome | 0.02 | 0.00 | 0.02 | |
| nichenet_signaling_network_inbiomap | 0 | 0 | 0 | |
| nichenet_signaling_network_omnipath | 10.81 | 0.82 | 12.54 | |
| nichenet_signaling_network_pathwaycommons | 0.02 | 0.00 | 0.02 | |
| nichenet_signaling_network_vinayagam | 0.01 | 0.00 | 0.02 | |
| nichenet_test | 0 | 0 | 0 | |
| nichenet_workarounds | 0 | 0 | 0 | |
| obo_parser | 0.12 | 0.00 | 0.32 | |
| oma_code | 0.05 | 0.00 | 0.05 | |
| oma_organisms | 0.15 | 0.00 | 0.19 | |
| oma_pairwise | 0.02 | 0.00 | 0.01 | |
| oma_pairwise_genesymbols | 0.01 | 0.00 | 0.02 | |
| oma_pairwise_translated | 0.02 | 0.00 | 0.02 | |
| omnipath-interactions | 33.28 | 1.46 | 75.54 | |
| omnipath_cache_autoclean | 0 | 0 | 0 | |
| omnipath_cache_clean | 0.02 | 0.00 | 0.02 | |
| omnipath_cache_clean_db | 0.12 | 0.01 | 0.14 | |
| omnipath_cache_download_ready | 0.66 | 0.05 | 2.27 | |
| omnipath_cache_filter_versions | 0.17 | 0.01 | 0.46 | |
| omnipath_cache_get | 0.12 | 0.00 | 0.35 | |
| omnipath_cache_key | 0.02 | 0.00 | 0.01 | |
| omnipath_cache_latest_or_new | 0.06 | 0.02 | 0.27 | |
| omnipath_cache_load | 0.73 | 0.05 | 2.11 | |
| omnipath_cache_move_in | 0.19 | 0.06 | 0.93 | |
| omnipath_cache_remove | 0.14 | 0.03 | 0.53 | |
| omnipath_cache_save | 0.16 | 0.06 | 0.65 | |
| omnipath_cache_search | 0 | 0 | 0 | |
| omnipath_cache_set_ext | 0.14 | 0.00 | 0.48 | |
| omnipath_cache_update_status | 0.19 | 0.03 | 0.58 | |
| omnipath_cache_wipe | 0 | 0 | 0 | |
| omnipath_config_path | 0 | 0 | 0 | |
| omnipath_for_cosmos | 10.11 | 0.30 | 60.97 | |
| omnipath_load_config | 0 | 0 | 0 | |
| omnipath_log | 0 | 0 | 0 | |
| omnipath_logfile | 0 | 0 | 0 | |
| omnipath_msg | 0 | 0 | 0 | |
| omnipath_query | 3.81 | 0.02 | 3.82 | |
| omnipath_reset_config | 0 | 0 | 0 | |
| omnipath_save_config | 0 | 0 | 0 | |
| omnipath_set_cachedir | 0.03 | 0.00 | 0.04 | |
| omnipath_set_console_loglevel | 0 | 0 | 0 | |
| omnipath_set_logfile_loglevel | 0.01 | 0.00 | 0.01 | |
| omnipath_set_loglevel | 0 | 0 | 0 | |
| omnipath_show_db | 0.08 | 0.00 | 0.08 | |
| omnipath_unlock_cache_db | 0 | 0 | 0 | |
| only_from | 0 | 0 | 0 | |
| ontology_ensure_id | 0 | 0 | 0 | |
| ontology_ensure_name | 0.02 | 0.00 | 0.01 | |
| ontology_name_id | 0 | 0 | 0 | |
| organism_for | 0.06 | 0.00 | 0.07 | |
| pathwaycommons_download | 0 | 0 | 0 | |
| pivot_annotations | 12.02 | 0.89 | 22.31 | |
| preppi_download | 0 | 0 | 0 | |
| preppi_filter | 0 | 0 | 0 | |
| print_bma_motif_es | 0.22 | 0.03 | 0.98 | |
| print_bma_motif_vs | 0.10 | 0.01 | 0.52 | |
| print_interactions | 6.49 | 0.24 | 9.06 | |
| print_path_es | 0.64 | 0.06 | 6.94 | |
| print_path_vs | 3.00 | 0.11 | 5.37 | |
| pubmed_open | 4.22 | 0.05 | 4.35 | |
| query_info | 0.14 | 0.00 | 0.40 | |
| ramilowski_download | 0 | 0 | 0 | |
| ramp_id_mapping_table | 0 | 0 | 0 | |
| ramp_id_type | 0 | 0 | 0 | |
| ramp_sqlite | 0.01 | 0.00 | 0.02 | |
| ramp_table | 0 | 0 | 0 | |
| ramp_tables | 0 | 0 | 0 | |
| regnetwork_directions | 0 | 0 | 0 | |
| regnetwork_download | 0 | 0 | 0 | |
| relations_list_to_table | 0.18 | 0.01 | 0.47 | |
| relations_table_to_graph | 0 | 0 | 0 | |
| relations_table_to_list | 0.09 | 0.00 | 0.34 | |
| remap_dorothea_download | 0 | 0 | 0 | |
| remap_filtered | 0 | 0 | 0 | |
| remap_tf_target_download | 0 | 0 | 0 | |
| resource_info | 0.22 | 0.05 | 0.71 | |
| resources | 0.05 | 0.00 | 0.46 | |
| resources_colname | 0.76 | 0.05 | 6.25 | |
| resources_in | 5.13 | 0.04 | 5.32 | |
| show_network | 0 | 0 | 0 | |
| signed_ptms | 6.20 | 0.00 | 6.79 | |
| simplify_intercell_network | 0.00 | 0.02 | 0.02 | |
| static_table | 7.31 | 0.42 | 22.97 | |
| static_tables | 0.06 | 0.00 | 0.14 | |
| stitch_actions | 0 | 0 | 0 | |
| stitch_links | 0 | 0 | 0 | |
| stitch_network | 0 | 0 | 0 | |
| stitch_remove_prefixes | 0 | 0 | 0 | |
| swap_relations | 0.14 | 0.00 | 0.18 | |
| swissprots_only | 0.04 | 0.00 | 0.04 | |
| tfcensus_download | 0.16 | 0.06 | 0.41 | |
| translate_ids | 1.03 | 0.19 | 17.76 | |
| translate_ids_multi | 8.27 | 0.12 | 60.47 | |
| trembls_only | 0.04 | 0.00 | 0.05 | |
| trrust_download | 0 | 0 | 0 | |
| uniprot_full_id_mapping_table | 1.05 | 0.14 | 23.03 | |
| uniprot_genesymbol_cleanup | 0.02 | 0.00 | 0.02 | |
| uniprot_id_mapping_table | 0 | 0 | 0 | |
| uniprot_id_type | 0 | 0 | 0 | |
| uniprot_idmapping_id_types | 0.20 | 0.00 | 0.53 | |
| unique_intercell_network | 0 | 0 | 0 | |
| unnest_evidences | 0 | 0 | 0 | |
| uploadlists_id_type | 0 | 0 | 0 | |
| vinayagam_download | 0 | 0 | 0 | |
| walk_ontology_tree | 0 | 0 | 0 | |
| with_extra_attrs | 11.77 | 0.27 | 12.80 | |
| with_references | 0.58 | 0.03 | 1.50 | |
| zenodo_download | 0 | 0 | 0 | |