Back to Multiple platform build/check report for BioC 3.17
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This page was generated on 2023-04-12 10:55:28 -0400 (Wed, 12 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.1 LTS)x86_644.3.0 alpha (2023-04-03 r84154) 4547
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_64R Under development (unstable) (2023-02-14 r83833) -- "Unsuffered Consequences" 4333
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

CHECK results for OmnipathR on nebbiolo1


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.

Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details.

raw results

Package 1413/2207HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
OmnipathR 3.7.15  (landing page)
Denes Turei
Snapshot Date: 2023-04-11 14:00:16 -0400 (Tue, 11 Apr 2023)
git_url: https://git.bioconductor.org/packages/OmnipathR
git_branch: devel
git_last_commit: 394681b
git_last_commit_date: 2023-04-10 12:20:04 -0400 (Mon, 10 Apr 2023)
nebbiolo1Linux (Ubuntu 22.04.1 LTS) / x86_64  OK    OK    OK  
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  

Summary

Package: OmnipathR
Version: 3.7.15
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings OmnipathR_3.7.15.tar.gz
StartedAt: 2023-04-11 22:05:58 -0400 (Tue, 11 Apr 2023)
EndedAt: 2023-04-11 22:35:04 -0400 (Tue, 11 Apr 2023)
EllapsedTime: 1745.7 seconds
RetCode: 0
Status:   OK  
CheckDir: OmnipathR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings OmnipathR_3.7.15.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/OmnipathR.Rcheck’
* using R version 4.3.0 alpha (2023-04-03 r84154)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘OmnipathR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OmnipathR’ version ‘3.7.15’
* 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 R 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 startup messages can be suppressed ... NOTE
[2023-04-11 22:06:15] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-11 22:06:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-04-11 22:06:15] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2023-04-11 22:06:15] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2023-04-11 22:06:15] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2023-04-11 22:06:15] [TRACE]   [OmnipathR] Contains 1 files.
[2023-04-11 22:06:15] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2023-04-11 22:06:15] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-11 22:06:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-04-11 22:06:15] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2023-04-11 22:06:15] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2023-04-11 22:06:15] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2023-04-11 22:06:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-04-11 22:06:15] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2023-04-11 22:06:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-04-11 22:06:15] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2023-04-11 22:06:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-04-11 22:06:15] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2023-04-11 22:06:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-04-11 22:06:15] [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
[2023-04-11 22:06:24] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-11 22:06:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-04-11 22:06:24] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2023-04-11 22:06:24] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2023-04-11 22:06:24] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2023-04-11 22:06:24] [TRACE]   [OmnipathR] Contains 1 files.
[2023-04-11 22:06:24] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2023-04-11 22:06:24] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-11 22:06:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-04-11 22:06:24] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2023-04-11 22:06:24] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2023-04-11 22:06:24] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2023-04-11 22:06:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-04-11 22:06:24] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2023-04-11 22:06:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-04-11 22:06:24] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2023-04-11 22:06:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-04-11 22:06:24] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2023-04-11 22:06:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-04-11 22:06:24] [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                65.143  0.076  66.660
curated_ligrec_stats                 34.484  1.579 111.639
extra_attrs_to_cols                  32.840  0.052  37.548
filter_extra_attrs                   31.392  0.280  37.606
extra_attr_values                    26.131  0.312  30.136
with_extra_attrs                     24.587  0.499  41.532
go_annot_download                    20.076  1.192  33.236
giant_component                      19.603  0.989  31.496
has_extra_attrs                      19.901  0.169  31.165
pivot_annotations                    17.280  1.644  42.469
nichenet_gr_network_omnipath         17.306  0.534  21.776
extra_attrs                          14.376  0.111  16.150
get_signed_ptms                      12.614  0.202  24.519
nichenet_signaling_network_omnipath  10.390  0.803  26.226
print_interactions                    9.932  0.462  19.328
filter_intercell                      9.539  0.600  15.078
pubmed_open                           8.698  0.561  18.925
filter_by_resource                    8.427  0.272  11.372
find_all_paths                        6.120  0.091   6.211
curated_ligand_receptor_interactions  5.634  0.281  16.096
omnipath                              4.675  0.384   6.187
print_path_vs                         4.459  0.340  11.195
import_all_interactions               3.844  0.207   8.669
collectri                             3.909  0.111   5.779
import_transcriptional_interactions   3.799  0.198  10.158
omnipath_cache_download_ready         0.651  3.002   6.299
database_summary                      1.760  1.291   5.538
import_kinaseextra_interactions       2.663  0.259   5.815
hpo_download                          2.618  0.214   6.125
omnipath_cache_load                   0.704  1.787  12.748
import_mirnatarget_interactions       2.113  0.205   5.889
intercell_consensus_filter            2.121  0.159   5.512
obo_parser                            0.169  1.264  19.885
annotated_network                     1.214  0.147   5.140
ensembl_id_mapping_table              1.217  0.037  15.624
biomart_query                         1.175  0.045   5.893
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘bioc_workshop.Rmd’ using ‘UTF-8’... OK
  ‘db_manager.Rmd’ using ‘UTF-8’... OK
  ‘drug_targets.Rmd’ using ‘UTF-8’... OK
  ‘extra_attrs.Rmd’ using ‘UTF-8’... OK
  ‘nichenet.Rmd’ using ‘UTF-8’... OK
  ‘omnipath_intro.Rmd’ using ‘UTF-8’... OK
  ‘paths.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/OmnipathR.Rcheck/00check.log’
for details.

Installation output

OmnipathR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL OmnipathR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-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
[2023-04-11 15:24:33] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-11 15:24:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-04-11 15:24:33] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2023-04-11 15:24:33] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2023-04-11 15:24:33] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2023-04-11 15:24:33] [TRACE]   [OmnipathR] Contains 6 files.
[2023-04-11 15:24:33] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2023-04-11 15:24:33] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-11 15:24:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-04-11 15:24:33] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2023-04-11 15:24:33] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2023-04-11 15:24:33] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2023-04-11 15:24:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-04-11 15:24:33] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2023-04-11 15:24:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-04-11 15:24:33] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2023-04-11 15:24:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-04-11 15:24:33] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2023-04-11 15:24:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-04-11 15:24:33] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2023-04-11 15:24:34] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-11 15:24:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-04-11 15:24:34] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2023-04-11 15:24:34] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2023-04-11 15:24:34] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2023-04-11 15:24:34] [TRACE]   [OmnipathR] Contains 1 files.
[2023-04-11 15:24:34] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2023-04-11 15:24:34] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-11 15:24:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-04-11 15:24:34] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2023-04-11 15:24:34] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2023-04-11 15:24:34] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2023-04-11 15:24:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-04-11 15:24:34] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2023-04-11 15:24:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-04-11 15:24:34] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2023-04-11 15:24:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-04-11 15:24:34] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2023-04-11 15:24:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-04-11 15:24:34] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package keeps a record of temporary installation path
* DONE (OmnipathR)

Tests output

OmnipathR.Rcheck/tests/testthat.Rout


R version 4.3.0 alpha (2023-04-03 r84154)
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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
> #  2018-2023
> #  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)
[2023-04-11 22:21:26] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-11 22:21:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-04-11 22:21:26] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2023-04-11 22:21:26] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2023-04-11 22:21:26] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2023-04-11 22:21:26] [TRACE]   [OmnipathR] Contains 15 files.
[2023-04-11 22:21:26] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2023-04-11 22:21:26] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-11 22:21:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-04-11 22:21:27] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2023-04-11 22:21:27] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2023-04-11 22:21:27] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2023-04-11 22:21:27] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-04-11 22:21:27] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2023-04-11 22:21:27] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-04-11 22:21:27] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2023-04-11 22:21:27] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-04-11 22:21:27] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2023-04-11 22:21:27] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-04-11 22:21:27] [TRACE]   [OmnipathR] Cache locked: FALSE
> 
> test_check('OmnipathR')
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 34 ]
> 
> proc.time()
   user  system elapsed 
 21.695   1.523  64.902

Example timings

OmnipathR.Rcheck/OmnipathR-Ex.timings

nameusersystemelapsed
OmnipathR0.0010.0000.001
all_uniprot_acs0.0240.0000.024
all_uniprots0.0110.0000.011
ancestors0.010.000.01
annotated_network1.2140.1475.140
annotation_categories65.143 0.07666.660
biomart_query1.1750.0455.893
bioplex10.0100.0080.018
bioplex20.0150.0000.015
bioplex30.0150.0000.015
bioplex_all0.0080.0040.013
bioplex_hct116_10.0110.0000.011
bma_motif_es0.4790.0281.416
bma_motif_vs0.2600.0041.020
collectri3.9090.1115.779
common_name0.0320.0000.032
consensuspathdb_download0.0010.0000.001
consensuspathdb_raw_table0.0100.0040.013
curated_ligand_receptor_interactions 5.634 0.28116.096
curated_ligrec_stats 34.484 1.579111.639
database_summary1.7601.2915.538
descendants0.0130.0040.016
dorothea2.2740.0534.283
ensembl_dataset0.0120.0000.013
ensembl_id_mapping_table 1.217 0.03715.624
ensembl_id_type0.0060.0000.007
ensembl_name0.060.000.06
ensembl_organisms0.2450.0110.256
ensembl_organisms_raw0.2750.0000.294
ensembl_orthology0.0000.0010.000
enzsub_graph2.3630.1384.609
evex_download0.0110.0000.010
extra_attr_values26.131 0.31230.136
extra_attrs14.376 0.11116.150
extra_attrs_to_cols32.840 0.05237.548
filter_by_resource 8.427 0.27211.372
filter_extra_attrs31.392 0.28037.606
filter_intercell 9.539 0.60015.078
filter_intercell_network0.0330.0000.034
find_all_paths6.1200.0916.211
get_annotation_resources0.1910.0080.882
get_complex_genes1.3510.0613.325
get_complex_resources0.1720.0041.049
get_db0.0000.0000.001
get_enzsub_resources0.2940.0441.191
get_interaction_resources0.2110.0081.191
get_intercell_categories0.5510.0521.044
get_intercell_generic_categories0.0400.0040.043
get_intercell_resources0.2760.0161.326
get_ontology_db0.0210.0040.040
get_resources0.1970.0081.060
get_signed_ptms12.614 0.20224.519
giant_component19.603 0.98931.496
go_annot_download20.076 1.19233.236
go_annot_slim0.0000.0010.001
go_ontology_download0.0160.0030.018
guide2pharma_download0.0150.0030.018
harmonizome_download0.0190.0000.019
has_extra_attrs19.901 0.16931.165
homologene_download0.0290.0040.084
homologene_raw0.0570.0040.136
homologene_uniprot_orthology0.0280.0040.064
homology_translate0.0000.0000.001
hpo_download2.6180.2146.125
htridb_download0.0350.0000.035
import_all_interactions3.8440.2078.669
import_intercell_network0.0270.0000.028
import_kinaseextra_interactions2.6630.2595.815
import_ligrecextra_interactions1.4240.1153.697
import_lncrna_mrna_interactions1.0100.1152.888
import_mirnatarget_interactions2.1130.2055.889
import_omnipath_annotations1.1200.0852.627
import_omnipath_complexes1.0400.0763.285
import_omnipath_enzsub1.3890.0282.092
import_omnipath_interactions0.4510.0611.248
import_omnipath_intercell0.4710.0441.040
import_pathwayextra_interactions1.3600.1463.458
import_post_translational_interactions1.5740.1144.106
import_small_molecule_protein_interactions0.8420.1011.304
import_tf_mirna_interactions1.3580.1022.894
import_tf_target_interactions2.0270.1404.251
import_transcriptional_interactions 3.799 0.19810.158
inbiomap_download0.0010.0000.001
inbiomap_raw000
interaction_datasets1.1470.0361.956
interaction_graph0.6390.0532.077
interaction_types0.0430.0000.091
intercell_categories0.0740.0040.202
intercell_consensus_filter2.1210.1595.512
is_ontology_id000
is_swissprot0.0790.0050.189
is_trembl0.0810.0000.210
is_uniprot0.0300.0040.081
kegg_info0.0320.0160.101
kegg_open0.0330.0000.073
kegg_pathway_annotations000
kegg_pathway_download0.1000.0080.297
kegg_pathway_list0.0210.0090.069
kegg_pathways_download0.0000.0000.001
kegg_picture0.3050.0224.724
kegg_process0.0510.0000.050
latin_name0.1530.0040.172
load_db0.1860.0160.262
ncbi_taxid0.1610.0000.162
nichenet_build_model0.0000.0000.001
nichenet_expression_data0.0330.0000.032
nichenet_gr_network0.0820.0040.088
nichenet_gr_network_evex0.0930.0000.092
nichenet_gr_network_harmonizome0.0260.0040.029
nichenet_gr_network_htridb0.0270.0000.027
nichenet_gr_network_omnipath17.306 0.53421.776
nichenet_gr_network_pathwaycommons0.0170.0080.025
nichenet_gr_network_regnetwork0.0530.0330.133
nichenet_gr_network_remap0.0140.0040.034
nichenet_gr_network_trrust0.0140.0040.050
nichenet_ligand_activities0.0010.0000.001
nichenet_ligand_target_links0.0000.0010.001
nichenet_ligand_target_matrix000
nichenet_lr_network0.0480.0090.105
nichenet_lr_network_guide2pharma0.0190.0000.018
nichenet_lr_network_omnipath0.0470.0040.068
nichenet_lr_network_ramilowski0.0100.0080.018
nichenet_main0.0010.0000.001
nichenet_networks0.1080.0080.117
nichenet_optimization0.0000.0010.001
nichenet_remove_orphan_ligands0.0800.0110.091
nichenet_results_dir0.0000.0000.001
nichenet_signaling_network0.0390.0080.047
nichenet_signaling_network_cpdb0.0160.0000.015
nichenet_signaling_network_evex0.0110.0040.016
nichenet_signaling_network_harmonizome0.0110.0050.015
nichenet_signaling_network_inbiomap0.0010.0000.001
nichenet_signaling_network_omnipath10.390 0.80326.226
nichenet_signaling_network_pathwaycommons0.0110.0000.011
nichenet_signaling_network_vinayagam0.0100.0000.009
nichenet_test000
nichenet_workarounds000
obo_parser 0.169 1.26419.885
omnipath4.6750.3846.187
omnipath_cache_autoclean0.0000.0000.001
omnipath_cache_clean0.0130.0000.038
omnipath_cache_clean_db0.0590.0120.071
omnipath_cache_download_ready0.6513.0026.299
omnipath_cache_filter_versions0.1390.0120.178
omnipath_cache_get0.1460.0000.146
omnipath_cache_key0.0020.0000.001
omnipath_cache_latest_or_new0.0730.0040.076
omnipath_cache_load 0.704 1.78712.748
omnipath_cache_move_in0.1810.0480.257
omnipath_cache_remove0.1060.0030.113
omnipath_cache_save0.3190.0120.557
omnipath_cache_search0.0010.0000.001
omnipath_cache_set_ext0.1150.0090.127
omnipath_cache_update_status0.1220.0160.139
omnipath_cache_wipe0.0000.0000.001
omnipath_get_config_path0.0010.0000.002
omnipath_load_config0.0000.0000.001
omnipath_log000
omnipath_logfile0.0000.0020.004
omnipath_msg0.0060.0050.010
omnipath_reset_config0.0000.0000.001
omnipath_save_config0.0000.0000.001
omnipath_set_cachedir0.0600.0320.093
omnipath_set_console_loglevel0.0000.0010.001
omnipath_set_logfile_loglevel0.0000.0010.001
omnipath_set_loglevel000
omnipath_show_db0.0820.0000.083
omnipath_unlock_cache_db0.0000.0000.001
ontology_ensure_id0.0010.0000.001
ontology_ensure_name0.0010.0000.001
ontology_name_id0.0010.0000.001
pathwaycommons_download000
pivot_annotations17.280 1.64442.469
preppi_download0.0010.0010.001
preppi_filter0.0000.0020.002
print_bma_motif_es0.6000.0232.694
print_bma_motif_vs0.3510.0321.925
print_interactions 9.932 0.46219.328
print_path_es1.0210.0493.024
print_path_vs 4.459 0.34011.195
pubmed_open 8.698 0.56118.925
query_info0.2120.0110.816
ramilowski_download0.0020.0000.007
regnetwork_directions0.0010.0000.001
regnetwork_download0.0020.0000.002
relations_list_to_table0.2200.0040.465
relations_table_to_graph0.0010.0000.000
relations_table_to_list0.1680.0070.331
remap_dorothea_download0.0010.0000.001
remap_filtered0.0010.0000.000
remap_tf_target_download0.0010.0000.001
resource_info0.3340.0651.685
resources_colname0.9860.0773.635
simplify_intercell_network0.0020.0000.006
swap_relations0.2740.0240.754
swissprots_only0.0730.0040.221
tfcensus_download0.3850.0382.332
translate_ids0.0030.0000.034
trembls_only0.0840.0200.420
trrust_download0.0000.0010.002
uniprot_full_id_mapping_table0.0020.0000.026
uniprot_genesymbol_cleanup0.0010.0000.000
uniprot_id_mapping_table0.0010.0000.009
uniprot_id_type0.0060.0080.038
unique_intercell_network0.0010.0000.001
uploadlists_id_type0.0180.0000.099
vinayagam_download0.0020.0000.010
walk_ontology_tree0.0030.0000.027
with_extra_attrs24.587 0.49941.532
with_references0.8640.0313.958
zenodo_download0.0000.0020.018