Denes Turei
| Snapshot Date: 2025-01-03 13:40 -0500 (Fri, 03 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 2025-01-04 11:47 -0500 (Sat, 04 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" | 4756 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4475 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4435 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4390 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4383 |
| 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 1449/2275 | 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 | OK | WARNINGS | ||||||||||
|
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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: OmnipathR |
| Version: 3.15.0 |
| Command: /home/biocbuild/R/R/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings OmnipathR_3.15.0.tar.gz |
| StartedAt: 2025-01-04 08:59:39 -0000 (Sat, 04 Jan 2025) |
| EndedAt: 2025-01-04 09:17:46 -0000 (Sat, 04 Jan 2025) |
| EllapsedTime: 1087.1 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: OmnipathR.Rcheck |
| Warnings: 5 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings OmnipathR_3.15.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/OmnipathR.Rcheck’
* using R Under development (unstable) (2024-11-24 r87369)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* 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 ... 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 ... WARNING
Found the following significant warnings:
Warning: program compiled against libxml 212 using older 211
See ‘/home/biocbuild/bbs-3.21-bioc/meat/OmnipathR.Rcheck/00install.out’ for details.
* 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 ...Warning: program compiled against libxml 212 using older 211
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 ... NOTE
Warning: program compiled against libxml 212 using older 211
[2025-01-04 08:59:56] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-04 08:59:56] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-04 08:59:56] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-01-04 08:59:56] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-01-04 08:59:56] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-01-04 08:59:56] [TRACE] [OmnipathR] Contains 1 files.
[2025-01-04 08:59:56] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-01-04 08:59:56] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-04 08:59:56] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-04 08:59:56] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-01-04 08:59:56] [TRACE] [OmnipathR] Pandoc version: `2.12`.
[2025-01-04 08:59:56] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-01-04 08:59:56] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-04 08:59:56] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-01-04 08:59:56] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-04 08:59:56] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-01-04 08:59:56] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-04 08:59:56] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-01-04 08:59:56] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-04 08:59:56] [TRACE] [OmnipathR] Cache locked: FALSE
A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.
Probably some imports need to be declared in the NAMESPACE file.
* 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
Warning: program compiled against libxml 212 using older 211
[2025-01-04 09:00:09] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-04 09:00:09] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-04 09:00:09] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-01-04 09:00:09] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-01-04 09:00:09] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-01-04 09:00:09] [TRACE] [OmnipathR] Contains 1 files.
[2025-01-04 09:00:09] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-01-04 09:00:09] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-04 09:00:09] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-04 09:00:09] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-01-04 09:00:09] [TRACE] [OmnipathR] Pandoc version: `2.12`.
[2025-01-04 09:00:09] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-01-04 09:00:09] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-04 09:00:09] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-01-04 09:00:09] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-04 09:00:09] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-01-04 09:00:09] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-04 09:00:09] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-01-04 09:00:09] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-04 09:00:09] [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 ... NOTE
Warning: program compiled against libxml 212 using older 211
* checking S3 generic/method consistency ... WARNING
Warning: program compiled against libxml 212 using older 211
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
* checking replacement functions ... WARNING
Warning: program compiled against libxml 212 using older 211
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
* checking foreign function calls ... NOTE
Warning: program compiled against libxml 212 using older 211
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... NOTE
Warning: program compiled against libxml 212 using older 211
[2025-01-04 09:00:26] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-04 09:00:26] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-04 09:00:26] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-01-04 09:00:26] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-01-04 09:00:26] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-01-04 09:00:26] [TRACE] [OmnipathR] Contains 1 files.
[2025-01-04 09:00:26] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-01-04 09:00:26] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-04 09:00:26] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-04 09:00:26] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-01-04 09:00:26] [TRACE] [OmnipathR] Pandoc version: `2.12`.
[2025-01-04 09:00:26] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-01-04 09:00:26] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-04 09:00:26] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-01-04 09:00:26] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-04 09:00:26] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-01-04 09:00:26] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-04 09:00:26] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-01-04 09:00:26] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-04 09:00:26] [TRACE] [OmnipathR] Cache locked: FALSE
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Warning: program compiled against libxml 212 using older 211
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... WARNING
Warning: program compiled against libxml 212 using older 211
Warning: program compiled against libxml 212 using older 211
Warning: program compiled against libxml 212 using older 211
* checking Rd \usage sections ... NOTE
Warning: program compiled against libxml 212 using older 211
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 102.255 0.034 108.460
curated_ligrec_stats 35.213 2.096 164.039
omnipath-interactions 31.731 1.042 82.463
filter_extra_attrs 25.295 0.182 28.750
nichenet_gr_network_omnipath 17.599 0.359 35.304
extra_attrs_to_cols 14.569 0.018 15.921
extra_attr_values 14.062 0.071 18.070
go_annot_download 12.599 0.226 24.405
with_extra_attrs 12.631 0.102 14.512
nichenet_signaling_network_omnipath 12.500 0.068 28.277
giant_component 11.517 0.140 16.664
pivot_annotations 11.223 0.340 21.533
omnipath_for_cosmos 10.484 0.287 28.416
filter_by_resource 8.621 0.235 12.435
has_extra_attrs 7.776 0.028 8.463
translate_ids_multi 7.682 0.057 30.820
extra_attrs 7.697 0.034 8.498
print_interactions 6.628 0.240 11.193
find_all_paths 6.511 0.150 8.093
static_table 6.480 0.172 12.970
curated_ligand_receptor_interactions 5.931 0.619 22.135
filter_intercell 6.087 0.082 12.665
signed_ptms 5.697 0.060 6.727
print_path_vs 2.369 0.147 5.682
enzsub_graph 2.466 0.031 5.240
hpo_download 2.264 0.061 21.698
ensembl_id_mapping_table 1.383 0.024 29.024
translate_ids 1.281 0.020 19.161
uniprot_full_id_mapping_table 1.120 0.004 22.392
all_uniprots 0.870 0.067 22.446
annotated_network 0.850 0.080 5.145
print_bma_motif_vs 0.157 0.024 5.795
* 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: 5 WARNINGs, 6 NOTEs
See
‘/home/biocbuild/bbs-3.21-bioc/meat/OmnipathR.Rcheck/00check.log’
for details.
OmnipathR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL OmnipathR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’ * installing *source* package ‘OmnipathR’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading Warning: program compiled against libxml 212 using older 211 ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning: program compiled against libxml 212 using older 211 [2025-01-03 20:07:28] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-01-03 20:07:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-03 20:07:28] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2025-01-03 20:07:28] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-01-03 20:07:28] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2025-01-03 20:07:28] [TRACE] [OmnipathR] Contains 6 files. [2025-01-03 20:07:28] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-01-03 20:07:28] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-01-03 20:07:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-03 20:07:28] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2025-01-03 20:07:28] [TRACE] [OmnipathR] Pandoc version: `2.12`. [2025-01-03 20:07:28] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/00LOCK-OmnipathR/00new/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-01-03 20:07:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-03 20:07:28] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-01-03 20:07:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-03 20:07:28] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-01-03 20:07:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-03 20:07:28] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/00LOCK-OmnipathR/00new/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-01-03 20:07:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-03 20:07:28] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location Warning: program compiled against libxml 212 using older 211 [2025-01-03 20:07:31] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-01-03 20:07:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-03 20:07:31] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2025-01-03 20:07:31] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-01-03 20:07:31] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2025-01-03 20:07:31] [TRACE] [OmnipathR] Contains 1 files. [2025-01-03 20:07:31] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-01-03 20:07:31] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-01-03 20:07:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-03 20:07:31] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2025-01-03 20:07:31] [TRACE] [OmnipathR] Pandoc version: `2.12`. [2025-01-03 20:07:31] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-01-03 20:07:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-03 20:07:31] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-01-03 20:07:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-03 20:07:31] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-01-03 20:07:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-03 20:07:31] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-01-03 20:07:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-01-03 20:07:31] [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) (2024-11-24 r87369) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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)
Warning: program compiled against libxml 212 using older 211
[2025-01-04 09:16:44] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-04 09:16:44] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-04 09:16:44] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-01-04 09:16:44] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-01-04 09:16:44] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-01-04 09:16:44] [TRACE] [OmnipathR] Contains 21 files.
[2025-01-04 09:16:44] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-01-04 09:16:44] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-04 09:16:44] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-04 09:16:44] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-01-04 09:16:45] [TRACE] [OmnipathR] Pandoc version: `2.12`.
[2025-01-04 09:16:45] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-01-04 09:16:45] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-04 09:16:45] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-01-04 09:16:45] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-04 09:16:45] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-01-04 09:16:45] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-04 09:16:45] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-01-04 09:16:45] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-01-04 09:16:45] [TRACE] [OmnipathR] Cache locked: FALSE
>
> test_check('OmnipathR')
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 34 ]
>
> proc.time()
user system elapsed
12.967 1.151 51.724
OmnipathR.Rcheck/OmnipathR-Ex.timings
| name | user | system | elapsed | |
| OmnipathR | 0 | 0 | 0 | |
| all_uniprot_acs | 0.021 | 0.004 | 0.025 | |
| all_uniprots | 0.870 | 0.067 | 22.446 | |
| ancestors | 0.013 | 0.001 | 0.012 | |
| annotated_network | 0.850 | 0.080 | 5.145 | |
| annotation_categories | 102.255 | 0.034 | 108.460 | |
| annotation_resources | 0.088 | 0.012 | 1.057 | |
| annotations | 0.330 | 0.012 | 2.113 | |
| biomart_query | 0.943 | 0.024 | 3.329 | |
| bioplex1 | 0.010 | 0.000 | 0.011 | |
| bioplex2 | 0.011 | 0.000 | 0.011 | |
| bioplex3 | 0.012 | 0.000 | 0.011 | |
| bioplex_all | 0.055 | 0.000 | 0.054 | |
| bioplex_hct116_1 | 0.011 | 0.000 | 0.011 | |
| bma_motif_es | 0.428 | 0.175 | 2.379 | |
| bma_motif_vs | 0.258 | 0.004 | 1.453 | |
| chalmers_gem | 0.013 | 0.000 | 0.013 | |
| chalmers_gem_id_mapping_table | 0.012 | 0.000 | 0.012 | |
| chalmers_gem_id_type | 0.003 | 0.000 | 0.003 | |
| chalmers_gem_metabolites | 0.012 | 0.000 | 0.012 | |
| chalmers_gem_network | 0.013 | 0.000 | 0.021 | |
| chalmers_gem_raw | 0.013 | 0.000 | 0.024 | |
| chalmers_gem_reactions | 0.012 | 0.000 | 0.030 | |
| common_name | 0.040 | 0.000 | 0.062 | |
| complex_genes | 0.580 | 0.088 | 3.225 | |
| complex_resources | 0.101 | 0.008 | 1.157 | |
| complexes | 0.222 | 0.036 | 1.444 | |
| consensuspathdb_download | 0.000 | 0.000 | 0.001 | |
| consensuspathdb_raw_table | 0.016 | 0.000 | 0.032 | |
| cosmos_pkn | 0 | 0 | 0 | |
| curated_ligand_receptor_interactions | 5.931 | 0.619 | 22.135 | |
| curated_ligrec_stats | 35.213 | 2.096 | 164.039 | |
| database_summary | 1.687 | 0.016 | 3.614 | |
| descendants | 0.011 | 0.000 | 0.012 | |
| ensembl_dataset | 0.012 | 0.000 | 0.012 | |
| ensembl_id_mapping_table | 1.383 | 0.024 | 29.024 | |
| ensembl_id_type | 0.003 | 0.000 | 0.004 | |
| ensembl_name | 0.08 | 0.00 | 0.08 | |
| ensembl_organisms | 0.186 | 0.012 | 0.198 | |
| ensembl_organisms_raw | 0.136 | 0.000 | 0.137 | |
| ensembl_orthology | 0 | 0 | 0 | |
| enzsub_graph | 2.466 | 0.031 | 5.240 | |
| enzsub_resources | 0.097 | 0.000 | 1.097 | |
| enzyme_substrate | 1.461 | 0.048 | 2.961 | |
| evex_download | 0.011 | 0.000 | 0.011 | |
| evidences | 0.001 | 0.000 | 0.000 | |
| extra_attr_values | 14.062 | 0.071 | 18.070 | |
| extra_attrs | 7.697 | 0.034 | 8.498 | |
| extra_attrs_to_cols | 14.569 | 0.018 | 15.921 | |
| filter_by_resource | 8.621 | 0.235 | 12.435 | |
| filter_extra_attrs | 25.295 | 0.182 | 28.750 | |
| filter_intercell | 6.087 | 0.082 | 12.665 | |
| filter_intercell_network | 0.022 | 0.000 | 0.023 | |
| find_all_paths | 6.511 | 0.150 | 8.093 | |
| from_evidences | 0 | 0 | 0 | |
| get_db | 0 | 0 | 0 | |
| get_ontology_db | 0.011 | 0.000 | 0.011 | |
| giant_component | 11.517 | 0.140 | 16.664 | |
| go_annot_download | 12.599 | 0.226 | 24.405 | |
| go_annot_slim | 0 | 0 | 0 | |
| go_ontology_download | 0.011 | 0.000 | 0.011 | |
| guide2pharma_download | 0.011 | 0.000 | 0.011 | |
| harmonizome_download | 0.01 | 0.00 | 0.01 | |
| has_extra_attrs | 7.776 | 0.028 | 8.463 | |
| hmdb_id_mapping_table | 0.012 | 0.000 | 0.011 | |
| hmdb_id_type | 0.003 | 0.000 | 0.003 | |
| hmdb_metabolite_fields | 0.000 | 0.000 | 0.001 | |
| hmdb_protein_fields | 0 | 0 | 0 | |
| hmdb_table | 0.012 | 0.000 | 0.012 | |
| homologene_download | 0.011 | 0.000 | 0.012 | |
| homologene_raw | 0.024 | 0.000 | 0.024 | |
| homologene_uniprot_orthology | 0.012 | 0.000 | 0.012 | |
| hpo_download | 2.264 | 0.061 | 21.698 | |
| htridb_download | 0.011 | 0.000 | 0.011 | |
| id_translation_resources | 0.001 | 0.000 | 0.000 | |
| id_types | 0.05 | 0.00 | 0.05 | |
| inbiomap_download | 0.000 | 0.000 | 0.001 | |
| inbiomap_raw | 0 | 0 | 0 | |
| interaction_datasets | 0.426 | 0.004 | 1.177 | |
| interaction_graph | 0.382 | 0.004 | 1.713 | |
| interaction_resources | 0.137 | 0.004 | 1.292 | |
| interaction_types | 0.050 | 0.000 | 0.058 | |
| intercell | 0.473 | 0.008 | 1.704 | |
| intercell_categories | 0.425 | 0.008 | 1.044 | |
| intercell_consensus_filter | 1.289 | 0.045 | 3.440 | |
| intercell_generic_categories | 0.054 | 0.000 | 0.054 | |
| intercell_network | 0.007 | 0.004 | 0.012 | |
| intercell_resources | 0.096 | 0.000 | 1.236 | |
| intercell_summary | 0.054 | 0.003 | 0.113 | |
| is_ontology_id | 0 | 0 | 0 | |
| is_swissprot | 0.035 | 0.001 | 0.067 | |
| is_trembl | 0.032 | 0.004 | 0.072 | |
| is_uniprot | 0.014 | 0.000 | 0.026 | |
| kegg_info | 0.011 | 0.000 | 0.013 | |
| kegg_open | 0.011 | 0.000 | 0.010 | |
| kegg_pathway_annotations | 0 | 0 | 0 | |
| kegg_pathway_download | 0.011 | 0.000 | 0.011 | |
| kegg_pathway_list | 0.011 | 0.000 | 0.011 | |
| kegg_pathways_download | 0 | 0 | 0 | |
| kegg_picture | 0.117 | 0.008 | 1.479 | |
| kegg_process | 0.024 | 0.000 | 0.049 | |
| latin_name | 0.075 | 0.000 | 0.090 | |
| load_db | 0.095 | 0.000 | 0.202 | |
| ncbi_taxid | 0.075 | 0.000 | 0.140 | |
| nichenet_build_model | 0 | 0 | 0 | |
| nichenet_expression_data | 0.013 | 0.000 | 0.024 | |
| nichenet_gr_network | 0.036 | 0.000 | 0.066 | |
| nichenet_gr_network_evex | 0.011 | 0.000 | 0.024 | |
| nichenet_gr_network_harmonizome | 0.013 | 0.000 | 0.025 | |
| nichenet_gr_network_htridb | 0.012 | 0.000 | 0.024 | |
| nichenet_gr_network_omnipath | 17.599 | 0.359 | 35.304 | |
| nichenet_gr_network_pathwaycommons | 0.013 | 0.000 | 0.042 | |
| nichenet_gr_network_regnetwork | 0.012 | 0.000 | 0.024 | |
| nichenet_gr_network_remap | 0.011 | 0.000 | 0.029 | |
| nichenet_gr_network_trrust | 0.011 | 0.000 | 0.020 | |
| nichenet_ligand_activities | 0.00 | 0.00 | 0.01 | |
| nichenet_ligand_target_links | 0.000 | 0.000 | 0.001 | |
| nichenet_ligand_target_matrix | 0 | 0 | 0 | |
| nichenet_lr_network | 0.031 | 0.004 | 0.076 | |
| nichenet_lr_network_guide2pharma | 0.012 | 0.000 | 0.025 | |
| nichenet_lr_network_omnipath | 0.033 | 0.004 | 0.074 | |
| nichenet_lr_network_ramilowski | 0.012 | 0.000 | 0.029 | |
| nichenet_main | 0 | 0 | 0 | |
| nichenet_networks | 0.057 | 0.004 | 0.121 | |
| nichenet_optimization | 0 | 0 | 0 | |
| nichenet_remove_orphan_ligands | 0.036 | 0.000 | 0.077 | |
| nichenet_results_dir | 0.001 | 0.000 | 0.001 | |
| nichenet_signaling_network | 0.037 | 0.000 | 0.073 | |
| nichenet_signaling_network_cpdb | 0.012 | 0.000 | 0.023 | |
| nichenet_signaling_network_evex | 0.012 | 0.000 | 0.029 | |
| nichenet_signaling_network_harmonizome | 0.012 | 0.000 | 0.020 | |
| nichenet_signaling_network_inbiomap | 0.000 | 0.000 | 0.001 | |
| nichenet_signaling_network_omnipath | 12.500 | 0.068 | 28.277 | |
| nichenet_signaling_network_pathwaycommons | 0.014 | 0.000 | 0.031 | |
| nichenet_signaling_network_vinayagam | 0.067 | 0.000 | 0.135 | |
| nichenet_test | 0 | 0 | 0 | |
| nichenet_workarounds | 0 | 0 | 0 | |
| obo_parser | 0.112 | 0.008 | 1.208 | |
| oma_code | 0.041 | 0.000 | 0.081 | |
| oma_organisms | 0.069 | 0.000 | 0.140 | |
| oma_pairwise | 0.013 | 0.000 | 0.025 | |
| oma_pairwise_genesymbols | 0.012 | 0.000 | 0.014 | |
| oma_pairwise_translated | 0.013 | 0.000 | 0.025 | |
| omnipath-interactions | 31.731 | 1.042 | 82.463 | |
| omnipath_cache_autoclean | 0 | 0 | 0 | |
| omnipath_cache_clean | 0.008 | 0.000 | 0.008 | |
| omnipath_cache_clean_db | 0.115 | 0.004 | 0.122 | |
| omnipath_cache_download_ready | 0.550 | 0.036 | 1.072 | |
| omnipath_cache_filter_versions | 0.119 | 0.000 | 0.129 | |
| omnipath_cache_get | 0.095 | 0.008 | 0.104 | |
| omnipath_cache_key | 0.002 | 0.000 | 0.002 | |
| omnipath_cache_latest_or_new | 0.124 | 0.000 | 0.124 | |
| omnipath_cache_load | 0.557 | 0.047 | 2.549 | |
| omnipath_cache_move_in | 0.184 | 0.016 | 0.208 | |
| omnipath_cache_remove | 0.119 | 0.016 | 0.285 | |
| omnipath_cache_save | 0.255 | 0.032 | 0.731 | |
| omnipath_cache_search | 0.001 | 0.000 | 0.001 | |
| omnipath_cache_set_ext | 0.096 | 0.008 | 0.170 | |
| omnipath_cache_update_status | 0.113 | 0.012 | 0.239 | |
| omnipath_cache_wipe | 0 | 0 | 0 | |
| omnipath_config_path | 0.001 | 0.000 | 0.000 | |
| omnipath_for_cosmos | 10.484 | 0.287 | 28.416 | |
| omnipath_load_config | 0 | 0 | 0 | |
| omnipath_log | 0.001 | 0.000 | 0.000 | |
| omnipath_logfile | 0.002 | 0.000 | 0.002 | |
| omnipath_msg | 0.006 | 0.000 | 0.007 | |
| omnipath_query | 4.568 | 0.020 | 4.726 | |
| omnipath_reset_config | 0 | 0 | 0 | |
| omnipath_save_config | 0 | 0 | 0 | |
| omnipath_set_cachedir | 0.034 | 0.000 | 0.034 | |
| omnipath_set_console_loglevel | 0.006 | 0.000 | 0.005 | |
| omnipath_set_logfile_loglevel | 0.005 | 0.000 | 0.005 | |
| omnipath_set_loglevel | 0.003 | 0.000 | 0.002 | |
| omnipath_show_db | 0.116 | 0.024 | 0.141 | |
| omnipath_unlock_cache_db | 0 | 0 | 0 | |
| only_from | 0.000 | 0.000 | 0.001 | |
| ontology_ensure_id | 0.000 | 0.001 | 0.001 | |
| ontology_ensure_name | 0.000 | 0.000 | 0.001 | |
| ontology_name_id | 0.000 | 0.001 | 0.001 | |
| organism_for | 0.050 | 0.004 | 0.054 | |
| pathwaycommons_download | 0.001 | 0.000 | 0.000 | |
| pivot_annotations | 11.223 | 0.340 | 21.533 | |
| preppi_download | 0.001 | 0.000 | 0.000 | |
| preppi_filter | 0.000 | 0.001 | 0.001 | |
| print_bma_motif_es | 0.245 | 0.023 | 1.900 | |
| print_bma_motif_vs | 0.157 | 0.024 | 5.795 | |
| print_interactions | 6.628 | 0.240 | 11.193 | |
| print_path_es | 0.504 | 0.024 | 2.516 | |
| print_path_vs | 2.369 | 0.147 | 5.682 | |
| pubmed_open | 4.649 | 0.144 | 4.812 | |
| query_info | 0.104 | 0.012 | 0.717 | |
| ramilowski_download | 0.001 | 0.000 | 0.001 | |
| ramp_id_mapping_table | 0.001 | 0.000 | 0.001 | |
| ramp_id_type | 0.003 | 0.000 | 0.002 | |
| ramp_sqlite | 0.001 | 0.000 | 0.001 | |
| ramp_table | 0.001 | 0.000 | 0.000 | |
| ramp_tables | 0.001 | 0.000 | 0.000 | |
| regnetwork_directions | 0.001 | 0.000 | 0.001 | |
| regnetwork_download | 0.001 | 0.000 | 0.000 | |
| relations_list_to_table | 0.096 | 0.004 | 0.763 | |
| relations_table_to_graph | 0 | 0 | 0 | |
| relations_table_to_list | 0.080 | 0.019 | 0.332 | |
| remap_dorothea_download | 0.001 | 0.000 | 0.001 | |
| remap_filtered | 0 | 0 | 0 | |
| remap_tf_target_download | 0.001 | 0.000 | 0.000 | |
| resource_info | 0.150 | 0.036 | 1.142 | |
| resources | 0.079 | 0.000 | 0.978 | |
| resources_colname | 0.618 | 0.035 | 2.629 | |
| resources_in | 4.347 | 0.112 | 4.477 | |
| show_network | 0 | 0 | 0 | |
| signed_ptms | 5.697 | 0.060 | 6.727 | |
| simplify_intercell_network | 0.001 | 0.000 | 0.001 | |
| static_table | 6.480 | 0.172 | 12.970 | |
| static_tables | 0.058 | 0.000 | 0.242 | |
| stitch_actions | 0.001 | 0.000 | 0.001 | |
| stitch_links | 0.001 | 0.000 | 0.000 | |
| stitch_network | 0.001 | 0.000 | 0.000 | |
| stitch_remove_prefixes | 0.076 | 0.000 | 0.076 | |
| swap_relations | 0.092 | 0.000 | 0.317 | |
| swissprots_only | 0.040 | 0.000 | 0.041 | |
| tfcensus_download | 0.195 | 0.004 | 0.224 | |
| translate_ids | 1.281 | 0.020 | 19.161 | |
| translate_ids_multi | 7.682 | 0.057 | 30.820 | |
| trembls_only | 0.039 | 0.000 | 0.039 | |
| trrust_download | 0.001 | 0.000 | 0.001 | |
| uniprot_full_id_mapping_table | 1.120 | 0.004 | 22.392 | |
| uniprot_genesymbol_cleanup | 0 | 0 | 0 | |
| uniprot_id_mapping_table | 0.001 | 0.000 | 0.001 | |
| uniprot_id_type | 0.002 | 0.000 | 0.002 | |
| uniprot_idmapping_id_types | 0.192 | 0.008 | 1.070 | |
| unique_intercell_network | 0.001 | 0.000 | 0.001 | |
| unnest_evidences | 0 | 0 | 0 | |
| uploadlists_id_type | 0.003 | 0.000 | 0.003 | |
| vinayagam_download | 0 | 0 | 0 | |
| walk_ontology_tree | 0.000 | 0.002 | 0.001 | |
| with_extra_attrs | 12.631 | 0.102 | 14.512 | |
| with_references | 0.457 | 0.032 | 2.288 | |
| zenodo_download | 0.000 | 0.001 | 0.002 | |