Denes Turei
| Snapshot Date: 2025-01-31 13:40 -0500 (Fri, 31 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 2025-02-01 11:40 -0500 (Sat, 01 Feb 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" | 4704 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences" | 4467 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2025-01-22 r87618) -- "Unsuffered Consequences" | 4478 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" | 4431 |
| 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 1454/2289 | 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 | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
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: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings OmnipathR_3.15.0.tar.gz |
| StartedAt: 2025-02-01 00:50:31 -0500 (Sat, 01 Feb 2025) |
| EndedAt: 2025-02-01 01:16:18 -0500 (Sat, 01 Feb 2025) |
| EllapsedTime: 1546.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: OmnipathR.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings OmnipathR_3.15.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/OmnipathR.Rcheck’
* using R Under development (unstable) (2025-01-20 r87609)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* 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 ‘3.15.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 33 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable. Move as many as possible to Suggests and
use conditionally.
* 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
[2025-02-01 00:50:55] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-01 00:50:55] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-01 00:50:55] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-02-01 00:50:55] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-02-01 00:50:55] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-02-01 00:50:55] [TRACE] [OmnipathR] Contains 1 files.
[2025-02-01 00:50:55] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-02-01 00:50:55] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-01 00:50:55] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-01 00:50:55] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-02-01 00:50:55] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2025-02-01 00:50:55] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-02-01 00:50:55] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-01 00:50:55] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-02-01 00:50:55] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-01 00:50:55] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-02-01 00:50:55] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-01 00:50:55] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-02-01 00:50:55] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-01 00:50:55] [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
[2025-02-01 00:51:08] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-01 00:51:08] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-01 00:51:08] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-02-01 00:51:08] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-02-01 00:51:08] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-02-01 00:51:08] [TRACE] [OmnipathR] Contains 1 files.
[2025-02-01 00:51:08] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-02-01 00:51:08] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-01 00:51:08] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-01 00:51:08] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-02-01 00:51:08] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2025-02-01 00:51:08] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-02-01 00:51:08] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-01 00:51:08] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-02-01 00:51:08] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-01 00:51:08] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-02-01 00:51:08] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-01 00:51:08] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-02-01 00:51:08] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-01 00:51:08] [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 76.763 0.142 78.477
omnipath-interactions 41.513 2.018 83.369
curated_ligrec_stats 30.491 1.378 105.566
with_extra_attrs 23.832 0.519 40.698
filter_extra_attrs 15.665 0.087 16.530
nichenet_gr_network_omnipath 13.784 0.225 16.241
omnipath_for_cosmos 13.643 0.366 40.199
pivot_annotations 12.739 0.627 25.339
translate_ids_multi 12.257 0.226 38.545
extra_attr_values 10.696 0.522 14.155
nichenet_signaling_network_omnipath 11.059 0.078 13.810
extra_attrs_to_cols 10.478 0.100 10.579
go_annot_download 9.895 0.489 10.659
static_table 9.825 0.360 19.947
print_interactions 9.662 0.159 17.258
giant_component 8.483 0.168 11.363
signed_ptms 7.351 0.107 9.304
omnipath_query 6.806 0.019 7.881
filter_by_resource 6.400 0.226 8.896
pubmed_open 5.737 0.159 5.907
has_extra_attrs 5.479 0.016 5.496
filter_intercell 4.904 0.279 9.191
extra_attrs 5.046 0.076 5.123
resources_in 4.931 0.058 5.204
curated_ligand_receptor_interactions 4.579 0.377 15.218
print_path_vs 3.789 0.183 6.891
translate_ids 3.377 0.110 21.495
uniprot_full_id_mapping_table 1.548 0.142 23.849
ensembl_id_mapping_table 1.140 0.078 18.274
all_uniprots 0.930 0.066 20.645
biomart_query 0.885 0.107 6.184
* 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
‘/home/biocbuild/bbs-3.21-bioc/meat/OmnipathR.Rcheck/00check.log’
for details.
OmnipathR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL OmnipathR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’ * installing *source* package ‘OmnipathR’ ... ** this is package ‘OmnipathR’ version ‘3.15.0’ ** 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 [2025-01-31 15:39:08] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-01-31 15:39:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-31 15:39:08] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2025-01-31 15:39:08] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-01-31 15:39:08] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2025-01-31 15:39:08] [TRACE] [OmnipathR] Contains 8 files. [2025-01-31 15:39:08] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-01-31 15:39:08] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-01-31 15:39:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-31 15:39:08] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2025-01-31 15:39:08] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2025-01-31 15:39:08] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-01-31 15:39:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-31 15:39:08] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-01-31 15:39:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-31 15:39:08] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-01-31 15:39:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-31 15:39:08] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-01-31 15:39:08] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-31 15:39:08] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2025-01-31 15:39:10] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-01-31 15:39:10] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-31 15:39:10] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2025-01-31 15:39:10] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-01-31 15:39:10] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2025-01-31 15:39:10] [TRACE] [OmnipathR] Contains 1 files. [2025-01-31 15:39:10] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-01-31 15:39:10] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-01-31 15:39:10] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-31 15:39:10] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2025-01-31 15:39:10] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2025-01-31 15:39:10] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-01-31 15:39:10] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-31 15:39:10] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-01-31 15:39:10] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-31 15:39:10] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-01-31 15:39:10] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-31 15:39:10] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-01-31 15:39:10] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-31 15:39:10] [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) (2025-01-20 r87609) -- "Unsuffered Consequences"
Copyright (C) 2025 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)
[2025-02-01 01:04:50] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-01 01:04:50] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-01 01:04:50] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-02-01 01:04:50] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-02-01 01:04:50] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-02-01 01:04:50] [TRACE] [OmnipathR] Contains 21 files.
[2025-02-01 01:04:50] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-02-01 01:04:50] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-01 01:04:50] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-01 01:04:50] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-02-01 01:04:50] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2025-02-01 01:04:50] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-02-01 01:04:50] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-01 01:04:50] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-02-01 01:04:50] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-01 01:04:50] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-02-01 01:04:50] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-01 01:04:50] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-02-01 01:04:50] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-01 01:04:50] [TRACE] [OmnipathR] Cache locked: FALSE
>
> test_check('OmnipathR')
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 34 ]
>
> proc.time()
user system elapsed
16.325 1.366 52.200
OmnipathR.Rcheck/OmnipathR-Ex.timings
| name | user | system | elapsed | |
| OmnipathR | 0.001 | 0.000 | 0.001 | |
| all_uniprot_acs | 0.011 | 0.007 | 0.018 | |
| all_uniprots | 0.930 | 0.066 | 20.645 | |
| ancestors | 0.009 | 0.000 | 0.009 | |
| annotated_network | 0.913 | 0.175 | 4.356 | |
| annotation_categories | 76.763 | 0.142 | 78.477 | |
| annotation_resources | 0.122 | 0.026 | 0.838 | |
| annotations | 0.419 | 0.054 | 1.303 | |
| biomart_query | 0.885 | 0.107 | 6.184 | |
| bioplex1 | 0.008 | 0.002 | 0.010 | |
| bioplex2 | 0.006 | 0.003 | 0.009 | |
| bioplex3 | 0.008 | 0.001 | 0.009 | |
| bioplex_all | 0.007 | 0.001 | 0.009 | |
| bioplex_hct116_1 | 0.009 | 0.001 | 0.010 | |
| bma_motif_es | 0.412 | 0.063 | 1.444 | |
| bma_motif_vs | 0.224 | 0.003 | 0.914 | |
| chalmers_gem | 0.01 | 0.00 | 0.01 | |
| chalmers_gem_id_mapping_table | 0.008 | 0.000 | 0.008 | |
| chalmers_gem_id_type | 0.002 | 0.000 | 0.002 | |
| chalmers_gem_metabolites | 0.008 | 0.000 | 0.008 | |
| chalmers_gem_network | 0.007 | 0.001 | 0.009 | |
| chalmers_gem_raw | 0.007 | 0.001 | 0.008 | |
| chalmers_gem_reactions | 0.008 | 0.000 | 0.008 | |
| common_name | 0.035 | 0.001 | 0.035 | |
| complex_genes | 0.551 | 0.014 | 2.349 | |
| complex_resources | 0.142 | 0.005 | 0.834 | |
| complexes | 0.257 | 0.004 | 0.938 | |
| consensuspathdb_download | 0.000 | 0.000 | 0.001 | |
| consensuspathdb_raw_table | 0.013 | 0.000 | 0.012 | |
| cosmos_pkn | 0.001 | 0.000 | 0.000 | |
| curated_ligand_receptor_interactions | 4.579 | 0.377 | 15.218 | |
| curated_ligrec_stats | 30.491 | 1.378 | 105.566 | |
| database_summary | 1.256 | 0.021 | 4.021 | |
| descendants | 0.008 | 0.001 | 0.009 | |
| ensembl_dataset | 0.011 | 0.001 | 0.011 | |
| ensembl_id_mapping_table | 1.140 | 0.078 | 18.274 | |
| ensembl_id_type | 0.002 | 0.000 | 0.002 | |
| ensembl_name | 0.056 | 0.001 | 0.057 | |
| ensembl_organisms | 0.104 | 0.001 | 0.105 | |
| ensembl_organisms_raw | 0.123 | 0.004 | 0.127 | |
| ensembl_orthology | 0.001 | 0.000 | 0.000 | |
| enzsub_graph | 1.887 | 0.045 | 4.161 | |
| enzsub_resources | 0.120 | 0.001 | 0.832 | |
| enzyme_substrate | 0.931 | 0.061 | 1.707 | |
| evex_download | 0.007 | 0.001 | 0.008 | |
| evidences | 0.001 | 0.000 | 0.000 | |
| extra_attr_values | 10.696 | 0.522 | 14.155 | |
| extra_attrs | 5.046 | 0.076 | 5.123 | |
| extra_attrs_to_cols | 10.478 | 0.100 | 10.579 | |
| filter_by_resource | 6.400 | 0.226 | 8.896 | |
| filter_extra_attrs | 15.665 | 0.087 | 16.530 | |
| filter_intercell | 4.904 | 0.279 | 9.191 | |
| filter_intercell_network | 0.015 | 0.001 | 0.016 | |
| find_all_paths | 4.445 | 0.052 | 4.498 | |
| from_evidences | 0.000 | 0.000 | 0.001 | |
| get_db | 0.000 | 0.000 | 0.001 | |
| get_ontology_db | 0.007 | 0.001 | 0.009 | |
| giant_component | 8.483 | 0.168 | 11.363 | |
| go_annot_download | 9.895 | 0.489 | 10.659 | |
| go_annot_slim | 0 | 0 | 0 | |
| go_ontology_download | 0.008 | 0.000 | 0.009 | |
| guide2pharma_download | 0.007 | 0.001 | 0.009 | |
| harmonizome_download | 0.008 | 0.000 | 0.008 | |
| has_extra_attrs | 5.479 | 0.016 | 5.496 | |
| hmdb_id_mapping_table | 0.008 | 0.000 | 0.009 | |
| hmdb_id_type | 0.002 | 0.001 | 0.002 | |
| hmdb_metabolite_fields | 0.000 | 0.001 | 0.001 | |
| hmdb_protein_fields | 0.000 | 0.001 | 0.001 | |
| hmdb_table | 0.008 | 0.000 | 0.008 | |
| homologene_download | 0.007 | 0.000 | 0.008 | |
| homologene_raw | 0.018 | 0.000 | 0.018 | |
| homologene_uniprot_orthology | 0.008 | 0.000 | 0.008 | |
| hpo_download | 1.898 | 0.112 | 2.481 | |
| htridb_download | 0.007 | 0.001 | 0.008 | |
| id_translation_resources | 0 | 0 | 0 | |
| id_types | 0.036 | 0.000 | 0.037 | |
| inbiomap_download | 0.000 | 0.001 | 0.001 | |
| inbiomap_raw | 0 | 0 | 0 | |
| interaction_datasets | 0.340 | 0.010 | 0.734 | |
| interaction_graph | 0.413 | 0.006 | 0.967 | |
| interaction_resources | 0.127 | 0.004 | 0.909 | |
| interaction_types | 0.037 | 0.001 | 0.038 | |
| intercell | 0.363 | 0.048 | 0.841 | |
| intercell_categories | 0.330 | 0.024 | 0.550 | |
| intercell_consensus_filter | 1.065 | 0.079 | 2.700 | |
| intercell_generic_categories | 0.06 | 0.00 | 0.06 | |
| intercell_network | 0.037 | 0.001 | 0.039 | |
| intercell_resources | 0.088 | 0.002 | 0.790 | |
| intercell_summary | 0.048 | 0.011 | 0.059 | |
| is_ontology_id | 0 | 0 | 0 | |
| is_swissprot | 0.027 | 0.002 | 0.029 | |
| is_trembl | 0.029 | 0.001 | 0.030 | |
| is_uniprot | 0.01 | 0.00 | 0.01 | |
| kegg_info | 0.009 | 0.000 | 0.009 | |
| kegg_open | 0.007 | 0.000 | 0.008 | |
| kegg_pathway_annotations | 0.000 | 0.000 | 0.001 | |
| kegg_pathway_download | 0.008 | 0.000 | 0.008 | |
| kegg_pathway_list | 0.008 | 0.000 | 0.008 | |
| kegg_pathways_download | 0 | 0 | 0 | |
| kegg_picture | 0.178 | 0.008 | 4.841 | |
| kegg_process | 0.029 | 0.000 | 0.030 | |
| latin_name | 0.118 | 0.000 | 0.117 | |
| load_db | 0.066 | 0.000 | 0.065 | |
| ncbi_taxid | 0.059 | 0.000 | 0.060 | |
| nichenet_build_model | 0.000 | 0.000 | 0.001 | |
| nichenet_expression_data | 0.008 | 0.001 | 0.009 | |
| nichenet_gr_network | 0.021 | 0.001 | 0.022 | |
| nichenet_gr_network_evex | 0.007 | 0.000 | 0.008 | |
| nichenet_gr_network_harmonizome | 0.007 | 0.001 | 0.008 | |
| nichenet_gr_network_htridb | 0.008 | 0.000 | 0.007 | |
| nichenet_gr_network_omnipath | 13.784 | 0.225 | 16.241 | |
| nichenet_gr_network_pathwaycommons | 0.008 | 0.001 | 0.009 | |
| nichenet_gr_network_regnetwork | 0.008 | 0.000 | 0.008 | |
| nichenet_gr_network_remap | 0.008 | 0.000 | 0.008 | |
| nichenet_gr_network_trrust | 0.007 | 0.001 | 0.008 | |
| nichenet_ligand_activities | 0.001 | 0.000 | 0.001 | |
| nichenet_ligand_target_links | 0.000 | 0.001 | 0.001 | |
| nichenet_ligand_target_matrix | 0.001 | 0.000 | 0.001 | |
| nichenet_lr_network | 0.021 | 0.002 | 0.023 | |
| nichenet_lr_network_guide2pharma | 0.008 | 0.000 | 0.008 | |
| nichenet_lr_network_omnipath | 0.056 | 0.001 | 0.057 | |
| nichenet_lr_network_ramilowski | 0.008 | 0.001 | 0.009 | |
| nichenet_main | 0.000 | 0.000 | 0.001 | |
| nichenet_networks | 0.042 | 0.004 | 0.046 | |
| nichenet_optimization | 0 | 0 | 0 | |
| nichenet_remove_orphan_ligands | 0.023 | 0.001 | 0.024 | |
| nichenet_results_dir | 0 | 0 | 0 | |
| nichenet_signaling_network | 0.022 | 0.002 | 0.024 | |
| nichenet_signaling_network_cpdb | 0.008 | 0.000 | 0.008 | |
| nichenet_signaling_network_evex | 0.007 | 0.001 | 0.008 | |
| nichenet_signaling_network_harmonizome | 0.008 | 0.000 | 0.008 | |
| nichenet_signaling_network_inbiomap | 0 | 0 | 0 | |
| nichenet_signaling_network_omnipath | 11.059 | 0.078 | 13.810 | |
| nichenet_signaling_network_pathwaycommons | 0.012 | 0.000 | 0.012 | |
| nichenet_signaling_network_vinayagam | 0.011 | 0.000 | 0.010 | |
| nichenet_test | 0 | 0 | 0 | |
| nichenet_workarounds | 0.001 | 0.000 | 0.001 | |
| obo_parser | 0.851 | 0.008 | 0.899 | |
| oma_code | 0.066 | 0.001 | 0.067 | |
| oma_organisms | 0.105 | 0.000 | 0.105 | |
| oma_pairwise | 0.018 | 0.000 | 0.018 | |
| oma_pairwise_genesymbols | 0.014 | 0.001 | 0.016 | |
| oma_pairwise_translated | 0.017 | 0.000 | 0.017 | |
| omnipath-interactions | 41.513 | 2.018 | 83.369 | |
| omnipath_cache_autoclean | 0 | 0 | 0 | |
| omnipath_cache_clean | 0.007 | 0.000 | 0.006 | |
| omnipath_cache_clean_db | 0.075 | 0.006 | 0.081 | |
| omnipath_cache_download_ready | 0.436 | 0.016 | 0.478 | |
| omnipath_cache_filter_versions | 0.105 | 0.003 | 0.129 | |
| omnipath_cache_get | 0.081 | 0.005 | 0.087 | |
| omnipath_cache_key | 0.002 | 0.000 | 0.001 | |
| omnipath_cache_latest_or_new | 0.054 | 0.003 | 0.057 | |
| omnipath_cache_load | 0.859 | 0.020 | 4.000 | |
| omnipath_cache_move_in | 0.299 | 0.016 | 0.523 | |
| omnipath_cache_remove | 0.253 | 0.010 | 0.402 | |
| omnipath_cache_save | 0.385 | 0.038 | 0.867 | |
| omnipath_cache_search | 0.000 | 0.001 | 0.001 | |
| omnipath_cache_set_ext | 0.164 | 0.019 | 0.440 | |
| omnipath_cache_update_status | 0.200 | 0.020 | 0.634 | |
| omnipath_cache_wipe | 0 | 0 | 0 | |
| omnipath_config_path | 0.001 | 0.001 | 0.009 | |
| omnipath_for_cosmos | 13.643 | 0.366 | 40.199 | |
| omnipath_load_config | 0 | 0 | 0 | |
| omnipath_log | 0.000 | 0.001 | 0.001 | |
| omnipath_logfile | 0.003 | 0.000 | 0.003 | |
| omnipath_msg | 0.010 | 0.002 | 0.012 | |
| omnipath_query | 6.806 | 0.019 | 7.881 | |
| omnipath_reset_config | 0.000 | 0.001 | 0.001 | |
| omnipath_save_config | 0 | 0 | 0 | |
| omnipath_set_cachedir | 0.037 | 0.001 | 0.038 | |
| omnipath_set_console_loglevel | 0.006 | 0.000 | 0.006 | |
| omnipath_set_logfile_loglevel | 0.004 | 0.001 | 0.005 | |
| omnipath_set_loglevel | 0.002 | 0.001 | 0.003 | |
| omnipath_show_db | 0.074 | 0.000 | 0.074 | |
| 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 | 0.001 | 0.000 | 0.001 | |
| organism_for | 0.05 | 0.00 | 0.05 | |
| pathwaycommons_download | 0.001 | 0.000 | 0.001 | |
| pivot_annotations | 12.739 | 0.627 | 25.339 | |
| preppi_download | 0.002 | 0.001 | 0.005 | |
| preppi_filter | 0.002 | 0.000 | 0.006 | |
| print_bma_motif_es | 0.451 | 0.048 | 1.718 | |
| print_bma_motif_vs | 0.293 | 0.015 | 1.029 | |
| print_interactions | 9.662 | 0.159 | 17.258 | |
| print_path_es | 1.017 | 0.053 | 3.132 | |
| print_path_vs | 3.789 | 0.183 | 6.891 | |
| pubmed_open | 5.737 | 0.159 | 5.907 | |
| query_info | 0.177 | 0.030 | 0.499 | |
| ramilowski_download | 0.002 | 0.000 | 0.002 | |
| ramp_id_mapping_table | 0.001 | 0.000 | 0.001 | |
| ramp_id_type | 0.005 | 0.000 | 0.004 | |
| ramp_sqlite | 0.000 | 0.000 | 0.001 | |
| ramp_table | 0.001 | 0.000 | 0.001 | |
| ramp_tables | 0.000 | 0.000 | 0.001 | |
| regnetwork_directions | 0.001 | 0.000 | 0.001 | |
| regnetwork_download | 0.001 | 0.000 | 0.002 | |
| relations_list_to_table | 0.142 | 0.011 | 0.270 | |
| relations_table_to_graph | 0 | 0 | 0 | |
| relations_table_to_list | 0.113 | 0.004 | 0.140 | |
| remap_dorothea_download | 0.000 | 0.001 | 0.002 | |
| remap_filtered | 0 | 0 | 0 | |
| remap_tf_target_download | 0.001 | 0.000 | 0.001 | |
| resource_info | 0.272 | 0.073 | 1.046 | |
| resources | 0.131 | 0.007 | 0.981 | |
| resources_colname | 0.797 | 0.045 | 3.365 | |
| resources_in | 4.931 | 0.058 | 5.204 | |
| show_network | 0.001 | 0.000 | 0.000 | |
| signed_ptms | 7.351 | 0.107 | 9.304 | |
| simplify_intercell_network | 0.002 | 0.000 | 0.002 | |
| static_table | 9.825 | 0.360 | 19.947 | |
| static_tables | 0.113 | 0.000 | 0.252 | |
| stitch_actions | 0.000 | 0.001 | 0.003 | |
| stitch_links | 0.002 | 0.000 | 0.001 | |
| stitch_network | 0.001 | 0.001 | 0.004 | |
| stitch_remove_prefixes | 0.016 | 0.000 | 0.034 | |
| swap_relations | 0.166 | 0.002 | 0.312 | |
| swissprots_only | 0.065 | 0.000 | 0.065 | |
| tfcensus_download | 0.346 | 0.009 | 0.677 | |
| translate_ids | 3.377 | 0.110 | 21.495 | |
| translate_ids_multi | 12.257 | 0.226 | 38.545 | |
| trembls_only | 0.128 | 0.000 | 0.127 | |
| trrust_download | 0.002 | 0.001 | 0.003 | |
| uniprot_full_id_mapping_table | 1.548 | 0.142 | 23.849 | |
| uniprot_genesymbol_cleanup | 0.001 | 0.000 | 0.000 | |
| uniprot_id_mapping_table | 0.000 | 0.001 | 0.002 | |
| uniprot_id_type | 0.004 | 0.000 | 0.004 | |
| uniprot_idmapping_id_types | 0.354 | 0.044 | 1.152 | |
| unique_intercell_network | 0.002 | 0.000 | 0.002 | |
| unnest_evidences | 0 | 0 | 0 | |
| uploadlists_id_type | 0.004 | 0.001 | 0.009 | |
| vinayagam_download | 0.002 | 0.000 | 0.002 | |
| walk_ontology_tree | 0.002 | 0.001 | 0.006 | |
| with_extra_attrs | 23.832 | 0.519 | 40.698 | |
| with_references | 0.659 | 0.049 | 2.224 | |
| zenodo_download | 0.001 | 0.002 | 0.002 | |