| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-02-06 11:43 -0500 (Thu, 06 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" | 4719 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences" | 4480 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2025-01-22 r87618) -- "Unsuffered Consequences" | 4491 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" | 4444 |
| 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 521/2295 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| decoupleR 2.13.0 (landing page) Pau Badia-i-Mompel
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | |||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
|
To the developers/maintainers of the decoupleR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/decoupleR.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: decoupleR |
| Version: 2.13.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:decoupleR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings decoupleR_2.13.0.tar.gz |
| StartedAt: 2025-02-05 18:57:22 -0500 (Wed, 05 Feb 2025) |
| EndedAt: 2025-02-05 19:01:24 -0500 (Wed, 05 Feb 2025) |
| EllapsedTime: 241.8 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: decoupleR.Rcheck |
| Warnings: NA |
##############################################################################
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:decoupleR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings decoupleR_2.13.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/decoupleR.Rcheck’
* using R Under development (unstable) (2025-01-20 r87609)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘decoupleR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘decoupleR’ version ‘2.13.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘decoupleR’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 dependencies in R code ... NOTE
[2025-02-05 18:57:36] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-05 18:57:36] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-05 18:57:36] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-02-05 18:57:36] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2025-02-05 18:57:36] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-02-05
[2025-02-05 18:57:36] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-02-05 20:16:53 UTC; unix
[2025-02-05 18:57:36] [INFO] [OmnipathR] Package `OmnipathR` version: 3.15.6
[2025-02-05 18:57:36] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21
[2025-02-05 18:57:36] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-01-20 r87609); os=macOS Ventura 13.7.1; system=aarch64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-02-05; pandoc=3.1.12.3 @ /opt/homebrew/bin/ (via rmarkdown); quarto=1.4.552 @ /usr/local/bin/quarto]
[2025-02-05 18:57:36] [INFO] [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=; pango=1.50.14; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.5.0; tcl=8.6.13; curl=8.7.1; zlib=1.2.11; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; PCRE=10.42 2022-12-11; ICU=70.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRlapack.dylib; lapack_version=3.12.0]
[2025-02-05 18:57:36] [INFO] [OmnipathR] CURL: version: 8.11.1; headers: 8.11.1; ssl_version: OpenSSL/3.3.2 (SecureTransport); libz_version: 1.2.11; libssh_version: NA; libidn_version: NA; host: aarch64-apple-darwin23.6.0; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE
[2025-02-05 18:57:36] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-02-05 18:57:36] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-02-05 18:57:36] [TRACE] [OmnipathR] Contains 2 files.
[2025-02-05 18:57:36] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-02-05 18:57:36] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-05 18:57:36] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-05 18:57:36] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-02-05 18:57:36] [TRACE] [OmnipathR] Pandoc version: `3.1.12.3`.
[2025-02-05 18:57:36] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-02-05 18:57:36] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-05 18:57:36] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-02-05 18:57:36] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-05 18:57:36] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-02-05 18:57:36] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-05 18:57:36] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-02-05 18:57:36] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-05 18:57:36] [TRACE] [OmnipathR] Cache locked: FALSE
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link(s) in Rd file 'run_gsva.Rd':
‘GSVA::gsva’ ‘GeneSetCollection’
See section 'Cross-references' in the 'Writing R Extensions' manual.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
run_gsva.Rd: GSVA::gsva, GeneSetCollection
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
run_fgsea 9.665 0.338 11.886
get_dorothea 7.553 0.683 19.666
run_aucell 3.227 1.117 5.371
get_collectri 2.856 0.325 9.224
get_progeny 2.601 0.188 11.152
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
[120] 0.112 | 0.112 [120]
[121] 0.991 - 1.000 [121]
[122] 0.991 - 1.000 [122]
[123] 0.123 - 0.126 [123]
[124] 0.123 - 0.126 [124]
[125] 0.156 | 0.156 [125]
[126] 0.156 | 0.156 [126]
[127] 0.592 | 0.592 [127]
`actual$p_value[132:139]`: 0.125 0.592 0.592 0.175 0.175 0.198 0.198 0.592
`expected$p_value[132:139]`: 0.125 0.592 0.592 0.184 0.184 0.198 0.198 0.592
[ FAIL 2 | WARN 9 | SKIP 0 | PASS 33 ]
Error: Test failures
Execution halted
* 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: 1 ERROR, 1 WARNING, 1 NOTE
See
‘/Users/biocbuild/bbs-3.21-bioc/meat/decoupleR.Rcheck/00check.log’
for details.
decoupleR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL decoupleR ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’ * installing *source* package ‘decoupleR’ ... ** this is package ‘decoupleR’ version ‘2.13.0’ ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (decoupleR)
decoupleR.Rcheck/tests/testthat.Rout.fail
R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20
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.
> library(testthat)
> library(decoupleR)
>
> test_check("decoupleR")
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[2025-02-05 18:59:14] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-05 18:59:14] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-05 18:59:14] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-02-05 18:59:14] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2025-02-05 18:59:14] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-02-05
[2025-02-05 18:59:14] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-02-05 20:16:53 UTC; unix
[2025-02-05 18:59:14] [INFO] [OmnipathR] Package `OmnipathR` version: 3.15.6
[2025-02-05 18:59:14] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21
[2025-02-05 18:59:15] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-01-20 r87609); os=macOS Ventura 13.7.1; system=aarch64, darwin20; ui=X11; language=C; collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-02-05; pandoc=3.1.12.3 @ /opt/homebrew/bin/ (via rmarkdown); quarto=1.4.552 @ /usr/local/bin/quarto]
[2025-02-05 18:59:15] [INFO] [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=; pango=1.50.14; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.5.0; tcl=8.6.13; curl=8.7.1; zlib=1.2.11; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; PCRE=10.42 2022-12-11; ICU=70.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRlapack.dylib; lapack_version=3.12.0]
[2025-02-05 18:59:15] [INFO] [OmnipathR] CURL: version: 8.11.1; headers: 8.11.1; ssl_version: OpenSSL/3.3.2 (SecureTransport); libz_version: 1.2.11; libssh_version: NA; libidn_version: NA; host: aarch64-apple-darwin23.6.0; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE
[2025-02-05 18:59:15] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-02-05 18:59:15] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-02-05 18:59:15] [TRACE] [OmnipathR] Contains 8 files.
[2025-02-05 18:59:15] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-02-05 18:59:15] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-05 18:59:15] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-05 18:59:15] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-02-05 18:59:15] [TRACE] [OmnipathR] Pandoc version: `3.1.12.3`.
[2025-02-05 18:59:15] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-02-05 18:59:15] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-05 18:59:15] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-02-05 18:59:15] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-05 18:59:15] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-02-05 18:59:15] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-05 18:59:15] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-02-05 18:59:15] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-05 18:59:15] [TRACE] [OmnipathR] Cache locked: FALSE
[2025-02-05 18:59:16] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-02-05 18:59:16] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-05 18:59:16] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-02-05 18:59:16] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-05 18:59:16] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2025-02-05 18:59:16] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-05 18:59:16] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-05 18:59:16] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2025-02-05 18:59:16] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-05 18:59:16] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-05 18:59:16] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2025-02-05 18:59:16] [TRACE] [OmnipathR] Cache file path: /Users/biocbuild/Library/Caches/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2025-02-05 18:59:16] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2025-02-05 18:59:16] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2025-02-05 18:59:16] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=13,tcp_keepidle=10,tcp_keepcnt=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-05 18:59:17] [TRACE] [OmnipathR] HTTP 200
[2025-02-05 18:59:18] [INFO] [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1]
[2025-02-05 18:59:18] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-05 18:59:18] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-05 18:59:18] [INFO] [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`.
[2025-02-05 18:59:18] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2025-02-05 18:59:18] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2025-02-05 18:59:18] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2025-02-05 18:59:18] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2025-02-05 18:59:18] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-05 18:59:18] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-05 18:59:18] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-05 18:59:18] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-05 18:59:18] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2025-02-05 18:59:18] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-02-05 18:59:18] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2025-02-05 18:59:18] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2025-02-05 18:59:18] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=13,tcp_keepidle=10,tcp_keepcnt=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-05 18:59:19] [TRACE] [OmnipathR] Downloaded 108 Kb in 1.048699s from omabrowser.org (103 Kb/s); Redirect: 0s, DNS look up: 0.000871s, Connection: 0.001692s, Pretransfer: 0.331077s, First byte at: 0.414224s
[2025-02-05 18:59:20] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-02-05 18:59:20] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1]
[2025-02-05 18:59:20] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-05 18:59:20] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-05 18:59:20] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.
[2025-02-05 18:59:20] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`.
[2025-02-05 18:59:20] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=TFcensus,query_type=annotations]
[2025-02-05 18:59:20] [TRACE] [OmnipathR] Organism(s): 9606
[2025-02-05 18:59:20] [TRACE] [OmnipathR] Orthology targets:
[2025-02-05 18:59:20] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-02-05 18:59:20] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-05 18:59:20] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2025-02-05 18:59:20] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2025-02-05 18:59:20] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2025-02-05 18:59:20] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2025-02-05 18:59:20] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2025-02-05 18:59:20] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2025-02-05 18:59:20] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2025-02-05 18:59:20] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=13,tcp_keepidle=10,tcp_keepcnt=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-05 18:59:21] [TRACE] [OmnipathR] Downloaded 29.2 Kb in 0.522211s from omnipathdb.org (55.8 Kb/s); Redirect: 0s, DNS look up: 0.006301s, Connection: 0.007172s, Pretransfer: 0.164743s, First byte at: 0.446299s
[2025-02-05 18:59:21] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2025-02-05 18:59:21] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-05 18:59:21] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-05 18:59:21] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-05 18:59:21] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-05 18:59:21] [INFO] [OmnipathR] Cache item `6f000d9b5edd9832b1c28754d1c3d9449c1c7490` version 1: status changed from `unknown` to `started`.
[2025-02-05 18:59:21] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/6f000d9b5edd9832b1c28754d1c3d9449c1c7490-1.rds`.
[2025-02-05 18:59:21] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/6f000d9b5edd9832b1c28754d1c3d9449c1c7490-1.rds`.
[2025-02-05 18:59:21] [INFO] [OmnipathR] Download ready [key=6f000d9b5edd9832b1c28754d1c3d9449c1c7490, version=1]
[2025-02-05 18:59:21] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-05 18:59:21] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-05 18:59:21] [INFO] [OmnipathR] Cache item `6f000d9b5edd9832b1c28754d1c3d9449c1c7490` version 1: status changed from `started` to `ready`.
[2025-02-05 18:59:21] [SUCCESS] [OmnipathR] Downloaded 3099 annotation records.
[2025-02-05 18:59:22] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-02-05 18:59:22] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-05 18:59:22] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=PROGENy,query_type=annotations]
[2025-02-05 18:59:22] [TRACE] [OmnipathR] Organism(s): 9606
[2025-02-05 18:59:22] [TRACE] [OmnipathR] Orthology targets:
[2025-02-05 18:59:23] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-02-05 18:59:23] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-05 18:59:23] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-02-05 18:59:23] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-02-05 18:59:23] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-02-05 18:59:23] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-02-05 18:59:23] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-02-05 18:59:23] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-02-05 18:59:23] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-02-05 18:59:23] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=13,tcp_keepidle=10,tcp_keepcnt=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-05 18:59:30] [TRACE] [OmnipathR] Downloaded 8.9 Mb in 6.893185s from omnipathdb.org (1.3 Mb/s); Redirect: 0s, DNS look up: 0.004862s, Connection: 0.005539s, Pretransfer: 0.170662s, First byte at: 0.335387s
[2025-02-05 18:59:31] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-02-05 18:59:31] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-05 18:59:31] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-05 18:59:31] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-05 18:59:31] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-05 18:59:31] [INFO] [OmnipathR] Cache item `3492392585ba05414edfae46801492076437d7e7` version 1: status changed from `unknown` to `started`.
[2025-02-05 18:59:31] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`.
[2025-02-05 18:59:32] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`.
[2025-02-05 18:59:32] [INFO] [OmnipathR] Download ready [key=3492392585ba05414edfae46801492076437d7e7, version=1]
[2025-02-05 18:59:32] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-05 18:59:32] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-05 18:59:32] [INFO] [OmnipathR] Cache item `3492392585ba05414edfae46801492076437d7e7` version 1: status changed from `started` to `ready`.
[2025-02-05 18:59:32] [SUCCESS] [OmnipathR] Downloaded 700239 annotation records.
[2025-02-05 18:59:33] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-02-05 18:59:33] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-05 18:59:33] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=PROGENy,query_type=annotations]
[2025-02-05 18:59:33] [TRACE] [OmnipathR] Organism(s): 9606
[2025-02-05 18:59:33] [TRACE] [OmnipathR] Orthology targets:
[2025-02-05 18:59:34] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-02-05 18:59:34] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-05 18:59:34] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-02-05 18:59:35] [TRACE] [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`.
[2025-02-05 18:59:35] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-02-05 18:59:35] [SUCCESS] [OmnipathR] Loaded 700239 annotation records from cache.
[2025-02-05 18:59:36] [INFO] [OmnipathR] Loading database `Orthologous Matrix (OMA) gene pairs`.
[2025-02-05 18:59:36] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2025-02-05 18:59:36] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2025-02-05 18:59:36] [TRACE] [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-02-05 18:59:36] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2025-02-05 18:59:36] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2025-02-05 18:59:36] [TRACE] [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-02-05 18:59:36] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2025-02-05 18:59:36] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/api/pairs/HUMAN/MOUSE/?format=tsv&xrefs=UniProtKB%2FSwissProt&per_page=2000000`.
[2025-02-05 18:59:36] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/api/pairs/HUMAN/MOUSE/?format=tsv&xrefs=UniProtKB%2FSwissProt&per_page=2000000`
[2025-02-05 18:59:36] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/api/pairs/HUMAN/MOUSE/?format=tsv&xrefs=UniProtKB%2FSwissProt&per_page=2000000`.
[2025-02-05 18:59:36] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-05 18:59:36] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-05 18:59:36] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-05 18:59:36] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-05 18:59:36] [INFO] [OmnipathR] Cache item `8f45b25c384d814c7de210e7ca40b7e35894e4f1` version 1: status changed from `unknown` to `started`.
[2025-02-05 18:59:36] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/8f45b25c384d814c7de210e7ca40b7e35894e4f1-1.rds`.
[2025-02-05 18:59:36] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/api/pairs/HUMAN/MOUSE/?format=tsv&xrefs=UniProtKB%2FSwissProt&per_page=2000000`
[2025-02-05 18:59:36] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/api/pairs/HUMAN/MOUSE/?format=tsv&xrefs=UniProtKB%2FSwissProt&per_page=2000000`
[2025-02-05 18:59:36] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=13,tcp_keepidle=10,tcp_keepcnt=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-05 19:00:03] [TRACE] [OmnipathR] Downloaded 1.1 Mb in 27.533262s from omabrowser.org (42.1 Kb/s); Redirect: 0s, DNS look up: 0.000991s, Connection: 0.00164s, Pretransfer: 0.167846s, First byte at: 25.871655s
[2025-02-05 19:00:04] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/8f45b25c384d814c7de210e7ca40b7e35894e4f1-1.rds`.
[2025-02-05 19:00:04] [INFO] [OmnipathR] Download ready [key=8f45b25c384d814c7de210e7ca40b7e35894e4f1, version=1]
[2025-02-05 19:00:04] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-05 19:00:04] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-05 19:00:04] [INFO] [OmnipathR] Cache item `8f45b25c384d814c7de210e7ca40b7e35894e4f1` version 1: status changed from `started` to `ready`.
[2025-02-05 19:00:04] [TRACE] [OmnipathR] ID translation table: from `uniprot_entry` to `uniprot`, using `uniprot`.
[2025-02-05 19:00:04] [TRACE] [OmnipathR] Creating ID mapping table from `id` to `accession`, for organism 9606 (only reviewed: TRUE)
[2025-02-05 19:00:04] [TRACE] [OmnipathR] Loading all UniProt records for organism 9606 (only reviewed: TRUE); fields: id,accession
[2025-02-05 19:00:04] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2025-02-05 19:00:04] [TRACE] [OmnipathR] Looking up in cache: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:9606%20AND%20reviewed:true`.
[2025-02-05 19:00:04] [INFO] [OmnipathR] Cache record does not exist: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:9606%20AND%20reviewed:true`
[2025-02-05 19:00:04] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:9606%20AND%20reviewed:true`.
[2025-02-05 19:00:04] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-05 19:00:04] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-05 19:00:04] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-05 19:00:04] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-05 19:00:04] [INFO] [OmnipathR] Cache item `6558a1824894a625b8e3f80538cd3aa6e8a44379` version 1: status changed from `unknown` to `started`.
[2025-02-05 19:00:04] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/6558a1824894a625b8e3f80538cd3aa6e8a44379-1.rds`.
[2025-02-05 19:00:04] [INFO] [OmnipathR] Retrieving URL: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:9606%20AND%20reviewed:true`
[2025-02-05 19:00:04] [TRACE] [OmnipathR] Attempt 1/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:9606%20AND%20reviewed:true`
[2025-02-05 19:00:04] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=13,tcp_keepidle=10,tcp_keepcnt=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-05 19:00:22] [TRACE] [OmnipathR] Downloaded 128.7 Kb in 18.014083s from rest.uniprot.org (7.1 Kb/s); Redirect: 0s, DNS look up: 0.009752s, Connection: 0.01142s, Pretransfer: 0.538363s, First byte at: 1.117772s
[2025-02-05 19:00:23] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/6558a1824894a625b8e3f80538cd3aa6e8a44379-1.rds`.
[2025-02-05 19:00:23] [INFO] [OmnipathR] Download ready [key=6558a1824894a625b8e3f80538cd3aa6e8a44379, version=1]
[2025-02-05 19:00:23] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-05 19:00:23] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-05 19:00:23] [INFO] [OmnipathR] Cache item `6558a1824894a625b8e3f80538cd3aa6e8a44379` version 1: status changed from `started` to `ready`.
[2025-02-05 19:00:23] [SUCCESS] [OmnipathR] UniProt (rest.uniprot.org): downloaded 20417 records
[2025-02-05 19:00:23] [TRACE] [OmnipathR] Translating complexes: 0 complexes in data.
[2025-02-05 19:00:23] [TRACE] [OmnipathR] 0 complexes after removing the ones mapping to more than 1 items in target identifier space.
[2025-02-05 19:00:23] [TRACE] [OmnipathR] Translated 0 complexes to 0.
[2025-02-05 19:00:23] [TRACE] [OmnipathR] 13774 rows before translation, 13774 uniprot_entry IDs in column `id_organism_a`.
[2025-02-05 19:00:23] [TRACE] [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B,C,D],genesymbols=TRUE,organisms=9606,query_type=interactions,datasets=dorothea]
[2025-02-05 19:00:23] [TRACE] [OmnipathR] Organism(s): 9606
[2025-02-05 19:00:23] [TRACE] [OmnipathR] Orthology targets:
[2025-02-05 19:00:23] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2025-02-05 19:00:23] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2025-02-05 19:00:23] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2025-02-05 19:00:23] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2025-02-05 19:00:23] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2025-02-05 19:00:23] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2025-02-05 19:00:23] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2025-02-05 19:00:23] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=13,tcp_keepidle=10,tcp_keepcnt=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-05 19:00:27] [TRACE] [OmnipathR] Downloaded 3.3 Mb in 3.4651s from omnipathdb.org (982.7 Kb/s); Redirect: 0s, DNS look up: 0.001337s, Connection: 0.002194s, Pretransfer: 0.3366s, First byte at: 0.49208s
[2025-02-05 19:00:27] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2025-02-05 19:00:27] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-05 19:00:27] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-05 19:00:27] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-05 19:00:27] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-05 19:00:27] [INFO] [OmnipathR] Cache item `46d37339bbc3f9a05bb89ccb79278cf1233f5cdf` version 1: status changed from `unknown` to `started`.
[2025-02-05 19:00:27] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/46d37339bbc3f9a05bb89ccb79278cf1233f5cdf-1.rds`.
[2025-02-05 19:00:28] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/46d37339bbc3f9a05bb89ccb79278cf1233f5cdf-1.rds`.
[2025-02-05 19:00:28] [INFO] [OmnipathR] Download ready [key=46d37339bbc3f9a05bb89ccb79278cf1233f5cdf, version=1]
[2025-02-05 19:00:28] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-05 19:00:28] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-05 19:00:28] [INFO] [OmnipathR] Cache item `46d37339bbc3f9a05bb89ccb79278cf1233f5cdf` version 1: status changed from `started` to `ready`.
[2025-02-05 19:00:31] [SUCCESS] [OmnipathR] Downloaded 278830 interactions.
[2025-02-05 19:00:34] [TRACE] [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B,C,D],genesymbols=TRUE,organisms=10090,query_type=interactions,datasets=dorothea]
[2025-02-05 19:00:34] [TRACE] [OmnipathR] Organism(s): 10090
[2025-02-05 19:00:34] [TRACE] [OmnipathR] Orthology targets:
[2025-02-05 19:00:34] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=10090&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2025-02-05 19:00:34] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=10090&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2025-02-05 19:00:34] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=10090&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2025-02-05 19:00:34] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=10090&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2025-02-05 19:00:34] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=10090&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2025-02-05 19:00:34] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=10090&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2025-02-05 19:00:34] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=10090&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2025-02-05 19:00:34] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=13,tcp_keepidle=10,tcp_keepcnt=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-05 19:00:44] [TRACE] [OmnipathR] Downloaded 2.9 Mb in 9.667667s from omnipathdb.org (303.3 Kb/s); Redirect: 0s, DNS look up: 0.000813s, Connection: 0.001499s, Pretransfer: 0.162514s, First byte at: 7.012477s
[2025-02-05 19:00:45] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=10090&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2025-02-05 19:00:45] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-05 19:00:45] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-05 19:00:45] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-05 19:00:45] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-05 19:00:45] [INFO] [OmnipathR] Cache item `ff347dedf78ef5e38c9c6d8eed291fa901aa3791` version 1: status changed from `unknown` to `started`.
[2025-02-05 19:00:45] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/ff347dedf78ef5e38c9c6d8eed291fa901aa3791-1.rds`.
[2025-02-05 19:00:45] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/ff347dedf78ef5e38c9c6d8eed291fa901aa3791-1.rds`.
[2025-02-05 19:00:45] [INFO] [OmnipathR] Download ready [key=ff347dedf78ef5e38c9c6d8eed291fa901aa3791, version=1]
[2025-02-05 19:00:45] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-05 19:00:45] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-05 19:00:45] [INFO] [OmnipathR] Cache item `ff347dedf78ef5e38c9c6d8eed291fa901aa3791` version 1: status changed from `started` to `ready`.
[2025-02-05 19:00:50] [SUCCESS] [OmnipathR] Downloaded 234298 interactions.
[2025-02-05 19:00:54] [TRACE] [OmnipathR] Arguments for OmniPath query: [loops=TRUE,organisms=9606,genesymbols=TRUE,query_type=interactions,datasets=collectri]
[2025-02-05 19:00:54] [TRACE] [OmnipathR] Organism(s): 9606
[2025-02-05 19:00:54] [TRACE] [OmnipathR] Orthology targets:
[2025-02-05 19:00:54] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2025-02-05 19:00:54] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2025-02-05 19:00:54] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2025-02-05 19:00:54] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2025-02-05 19:00:54] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2025-02-05 19:00:54] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2025-02-05 19:00:54] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2025-02-05 19:00:54] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=13,tcp_keepidle=10,tcp_keepcnt=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-05 19:00:56] [TRACE] [OmnipathR] Downloaded 1.5 Mb in 2.197534s from omnipathdb.org (678.2 Kb/s); Redirect: 0s, DNS look up: 0.00085s, Connection: 0.001624s, Pretransfer: 0.170371s, First byte at: 0.336784s
[2025-02-05 19:00:57] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2025-02-05 19:00:57] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-05 19:00:57] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-05 19:00:57] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-05 19:00:57] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-05 19:00:57] [INFO] [OmnipathR] Cache item `b10176737ba43d460b13709623189f3911123779` version 1: status changed from `unknown` to `started`.
[2025-02-05 19:00:57] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/b10176737ba43d460b13709623189f3911123779-1.rds`.
[2025-02-05 19:00:57] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/b10176737ba43d460b13709623189f3911123779-1.rds`.
[2025-02-05 19:00:57] [INFO] [OmnipathR] Download ready [key=b10176737ba43d460b13709623189f3911123779, version=1]
[2025-02-05 19:00:57] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-05 19:00:57] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-05 19:00:57] [INFO] [OmnipathR] Cache item `b10176737ba43d460b13709623189f3911123779` version 1: status changed from `started` to `ready`.
[2025-02-05 19:00:59] [SUCCESS] [OmnipathR] Downloaded 64958 interactions.
[2025-02-05 19:00:59] [TRACE] [OmnipathR] Arguments for OmniPath query: [genesymbols=TRUE,resources=CollecTRI,strict_evidences=TRUE,query_type=interactions,datasets=tf_mirna]
[2025-02-05 19:00:59] [TRACE] [OmnipathR] Organism(s): 9606
[2025-02-05 19:00:59] [TRACE] [OmnipathR] Orthology targets:
[2025-02-05 19:01:00] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-02-05 19:01:00] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-05 19:01:00] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2025-02-05 19:01:00] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2025-02-05 19:01:00] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2025-02-05 19:01:00] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2025-02-05 19:01:00] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2025-02-05 19:01:00] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2025-02-05 19:01:00] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2025-02-05 19:01:00] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=13,tcp_keepidle=10,tcp_keepcnt=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-05 19:01:00] [TRACE] [OmnipathR] Downloaded 9.5 Kb in 0.23596s from omnipathdb.org (40.2 Kb/s); Redirect: 0s, DNS look up: 0.000915s, Connection: 0.001791s, Pretransfer: 0.157359s, First byte at: 0.235809s
[2025-02-05 19:01:01] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2025-02-05 19:01:01] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-05 19:01:01] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-05 19:01:01] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-05 19:01:01] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-05 19:01:01] [INFO] [OmnipathR] Cache item `f7d34500401ba98803b7d2b26c48f64cee1eea1b` version 1: status changed from `unknown` to `started`.
[2025-02-05 19:01:01] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/f7d34500401ba98803b7d2b26c48f64cee1eea1b-1.rds`.
[2025-02-05 19:01:01] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/f7d34500401ba98803b7d2b26c48f64cee1eea1b-1.rds`.
[2025-02-05 19:01:01] [INFO] [OmnipathR] Download ready [key=f7d34500401ba98803b7d2b26c48f64cee1eea1b, version=1]
[2025-02-05 19:01:01] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-05 19:01:01] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-05 19:01:01] [INFO] [OmnipathR] Cache item `f7d34500401ba98803b7d2b26c48f64cee1eea1b` version 1: status changed from `started` to `ready`.
[2025-02-05 19:01:01] [TRACE] [OmnipathR] Converting JSON column `evidences` to list.
[2025-02-05 19:01:01] [TRACE] [OmnipathR] Restricting interaction records to datasets: tf_mirna; and resources: CollecTRI
[2025-02-05 19:01:01] [TRACE] [OmnipathR] Filtering evidence columns: positive, negative, directed, undirected; to datasets: tf_mirna; and resources: CollecTRI; excluding resources: none
[2025-02-05 19:01:01] [SUCCESS] [OmnipathR] Downloaded 232 interactions.
[2025-02-05 19:01:01] [TRACE] [OmnipathR] Arguments for OmniPath query: [loops=TRUE,organisms=9606,genesymbols=TRUE,query_type=interactions,datasets=collectri]
[2025-02-05 19:01:01] [TRACE] [OmnipathR] Organism(s): 9606
[2025-02-05 19:01:01] [TRACE] [OmnipathR] Orthology targets:
[2025-02-05 19:01:01] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2025-02-05 19:01:01] [TRACE] [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/b10176737ba43d460b13709623189f3911123779-1.rds`.
[2025-02-05 19:01:01] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2025-02-05 19:01:02] [SUCCESS] [OmnipathR] Loaded 64958 interactions from cache.
[2025-02-05 19:01:02] [TRACE] [OmnipathR] Arguments for OmniPath query: [genesymbols=TRUE,resources=CollecTRI,strict_evidences=TRUE,query_type=interactions,datasets=tf_mirna]
[2025-02-05 19:01:02] [TRACE] [OmnipathR] Organism(s): 9606
[2025-02-05 19:01:02] [TRACE] [OmnipathR] Orthology targets:
[2025-02-05 19:01:03] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-02-05 19:01:03] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-05 19:01:03] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2025-02-05 19:01:03] [TRACE] [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/f7d34500401ba98803b7d2b26c48f64cee1eea1b-1.rds`.
[2025-02-05 19:01:03] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2025-02-05 19:01:03] [TRACE] [OmnipathR] Converting JSON column `evidences` to list.
[2025-02-05 19:01:03] [TRACE] [OmnipathR] Restricting interaction records to datasets: tf_mirna; and resources: CollecTRI
[2025-02-05 19:01:03] [TRACE] [OmnipathR] Filtering evidence columns: positive, negative, directed, undirected; to datasets: tf_mirna; and resources: CollecTRI; excluding resources: none
[2025-02-05 19:01:03] [SUCCESS] [OmnipathR] Loaded 232 interactions from cache.
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Attaching package: 'dplyr'
The following object is masked from 'package:testthat':
matches
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
[ FAIL 2 | WARN 9 | SKIP 0 | PASS 33 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-omnipath.R:19:3'): test get_progeny mouse ──────────────────────
<vctrs_error_names_must_be_unique/vctrs_error_names/vctrs_error/rlang_error/error/condition>
Error in `rename(., `:=`(!!sym(to_col), To))`: Names must be unique.
x These names are duplicated:
* "id_organism_a" at locations 1 and 3.
Backtrace:
▆
1. ├─decoupleR::get_progeny(organism = "mouse") at test-omnipath.R:19:3
2. │ ├─... %>% ...
3. │ └─decoupleR::get_resource("PROGENy", organism = organism)
4. │ └─... %>% ...
5. ├─rlang::set_names(., c("source", "target", "weight", "p_value"))
6. ├─dplyr::select(., pathway, genesymbol, weight, p_value)
7. ├─dplyr::bind_rows(.)
8. │ └─rlang::list2(...)
9. ├─purrr::map(...)
10. │ └─purrr:::map_("list", .x, .f, ..., .progress = .progress)
11. │ └─purrr:::vctrs_vec_compat(.x, .purrr_user_env)
12. ├─dplyr::group_split(.)
13. ├─dplyr::group_by(., pathway)
14. ├─dplyr::select(., genesymbol, p_value, pathway, weight)
15. ├─dplyr::mutate(., weight = as.double(weight), p_value = as.double(p_value))
16. ├─dplyr::distinct(., pathway, genesymbol, .keep_all = TRUE)
17. ├─... %>% ...
18. ├─OmnipathR::translate_ids(., uniprot, genesymbol, organism = organism)
19. ├─OmnipathR::orthology_translate_column(...)
20. │ ├─... %>% ...
21. │ └─OmnipathR::get_db(db_name, param = orthology_param)
22. │ └─OmnipathR::load_db(key, param = param)
23. │ ├─rlang::exec(loader, !!!param)
24. │ └─OmnipathR (local) `<fn>`(organism_a = 9606L, organism_b = 10090L)
25. │ └─environment() %>% as.list %>% ...
26. ├─rlang::set_names(., c(ORTHO_SOURCE_COL, ORTHO_TARGET_COL))
27. ├─dplyr::select(., -any_of("hgroup"))
28. ├─rlang::exec(oma_pairwise_translated, !!!.)
29. ├─OmnipathR (local) `<fn>`(...)
30. │ └─... %>% ...
31. ├─dplyr::filter(., !is.na(id_organism_a) & !is.na(id_organism_b))
32. ├─OmnipathR::translate_ids(...)
33. ├─OmnipathR::translate_ids(...)
34. │ └─... %>% ...
35. ├─purrr::reduce2(...)
36. │ └─purrr:::reduce2_impl(.x, .y, .f, ..., .init = .init, .left = TRUE)
37. │ └─OmnipathR (local) .f(out, .x[[x_i]], .y[[y_i]], ...)
38. │ └─... %>% ...
39. ├─dplyr::rename(., `:=`(!!sym(to_col), To))
40. └─dplyr:::rename.data.frame(., `:=`(!!sym(to_col), To))
41. └─tidyselect::eval_rename(expr(c(...)), .data)
42. └─tidyselect:::rename_impl(...)
43. ├─tidyselect:::with_subscript_errors(...)
44. │ └─base::withCallingHandlers(...)
45. └─vctrs::vec_as_names(names, repair = "check_unique", call = error_call)
46. └─vctrs (local) `<fn>`()
47. └─vctrs:::validate_unique(names = names, arg = arg, call = call)
48. └─vctrs:::stop_names_must_be_unique(names, arg, call = call)
49. └─vctrs:::stop_names(...)
50. └─vctrs:::stop_vctrs(...)
51. └─rlang::abort(message, class = c(class, "vctrs_error"), ..., call = call)
── Failure ('test-statistic-fgsea.R:26:3'): test run_fgsea ─────────────────────
`res_1` (`actual`) not equal to `exp_1` (`expected`).
actual vs expected
p_value
actual[1, ] 0.075479709
actual[2, ] 0.075479709
- actual[3, ] 0.511687342
+ expected[3, ] 0.548454870
- actual[4, ] 0.511687342
+ expected[4, ] 0.548454870
actual[5, ] 0.010000000
actual[6, ] 0.010000000
actual[7, ] 0.076411558
actual vs expected
p_value
actual[12, ] 0.010000000
actual[13, ] 0.114238030
actual[14, ] 0.114238030
- actual[15, ] 0.510665738
+ expected[15, ] 0.522337972
- actual[16, ] 0.510665738
+ expected[16, ] 0.522337972
actual[17, ] 0.010000000
actual[18, ] 0.010000000
actual[19, ] 0.004682543
actual[20, ] 0.004682543
- actual[21, ] 0.219233595
+ expected[21, ] 0.294730294
and 10 more ...
actual vs expected
p_value
actual[34, ] 1.000000000
actual[35, ] 0.010000000
actual[36, ] 0.010000000
- actual[37, ] 0.091542106
+ expected[37, ] 0.103646587
- actual[38, ] 0.091542106
+ expected[38, ] 0.103646587
actual[39, ] 0.592371428
actual[40, ] 0.592371428
actual[41, ] 0.010000000
actual vs expected
p_value
actual[52, ] 0.976649086
actual[53, ] 0.010000000
actual[54, ] 0.010000000
- actual[55, ] 0.066624941
+ expected[55, ] 0.076411558
- actual[56, ] 0.066624941
+ expected[56, ] 0.076411558
actual[57, ] 0.592371428
actual[58, ] 0.592371428
actual[59, ] 0.010000000
actual[60, ] 0.010000000
- actual[61, ] 0.111211902
+ expected[61, ] 0.108185775
and 4 more ...
actual vs expected
p_value
actual[70, ] 1.000000000
actual[71, ] 0.010000000
actual[72, ] 0.010000000
- actual[73, ] 0.256981914
+ expected[73, ] 0.469812943
- actual[74, ] 0.256981914
+ expected[74, ] 0.469812943
- actual[75, ] 0.133907888
+ expected[75, ] 0.132394821
- actual[76, ] 0.133907888
+ expected[76, ] 0.132394821
actual[77, ] 0.123204721
actual[78, ] 0.123204721
- actual[79, ] 0.146641013
+ expected[79, ] 0.207618744
and 4 more ...
actual vs expected
p_value
actual[88, ] 0.177906190
actual[89, ] 0.154281338
actual[90, ] 0.154281338
- actual[91, ] 0.434796297
+ expected[91, ] 0.487321278
- actual[92, ] 0.434796297
+ expected[92, ] 0.487321278
actual[93, ] 0.009411332
actual[94, ] 0.009411332
actual[95, ] 0.005020222
actual[96, ] 0.005020222
- actual[97, ] 0.294730294
+ expected[97, ] 0.493157392
and 16 more ...
actual vs expected
p_value
actual[118, ] 0.126342554
actual[119, ] 0.111593916
actual[120, ] 0.111593916
- actual[121, ] 0.991185346
+ expected[121, ] 1.000000000
- actual[122, ] 0.991185346
+ expected[122, ] 1.000000000
- actual[123, ] 0.123316421
+ expected[123, ] 0.126342554
- actual[124, ] 0.123316421
+ expected[124, ] 0.126342554
actual[125, ] 0.155922629
actual[126, ] 0.155922629
actual[127, ] 0.592371428
actual vs expected
p_value
actual[132, ] 0.124515409
actual[133, ] 0.592371428
actual[134, ] 0.592371428
- actual[135, ] 0.174865133
+ expected[135, ] 0.183988307
- actual[136, ] 0.174865133
+ expected[136, ] 0.183988307
actual[137, ] 0.198360798
actual[138, ] 0.198360798
actual[139, ] 0.592371428
`actual$p_value[1:7]`: 0.075 0.075 0.512 0.512 0.010 0.010 0.076
`expected$p_value[1:7]`: 0.075 0.075 0.548 0.548 0.010 0.010 0.076
actual$p_value | expected$p_value
[12] 0.010 | 0.010 [12]
[13] 0.114 | 0.114 [13]
[14] 0.114 | 0.114 [14]
[15] 0.511 - 0.522 [15]
[16] 0.511 - 0.522 [16]
[17] 0.010 | 0.010 [17]
[18] 0.010 | 0.010 [18]
[19] 0.005 | 0.005 [19]
[20] 0.005 | 0.005 [20]
[21] 0.219 - 0.295 [21]
... ... ... and 10 more ...
`actual$p_value[34:41]`: 1.000 0.010 0.010 0.092 0.092 0.592 0.592 0.010
`expected$p_value[34:41]`: 1.000 0.010 0.010 0.104 0.104 0.592 0.592 0.010
actual$p_value | expected$p_value
[52] 0.977 | 0.977 [52]
[53] 0.010 | 0.010 [53]
[54] 0.010 | 0.010 [54]
[55] 0.067 - 0.076 [55]
[56] 0.067 - 0.076 [56]
[57] 0.592 | 0.592 [57]
[58] 0.592 | 0.592 [58]
[59] 0.010 | 0.010 [59]
[60] 0.010 | 0.010 [60]
[61] 0.111 - 0.108 [61]
... ... ... and 4 more ...
actual$p_value | expected$p_value
[70] 1.000 | 1.000 [70]
[71] 0.010 | 0.010 [71]
[72] 0.010 | 0.010 [72]
[73] 0.257 - 0.470 [73]
[74] 0.257 - 0.470 [74]
[75] 0.134 - 0.132 [75]
[76] 0.134 - 0.132 [76]
[77] 0.123 | 0.123 [77]
[78] 0.123 | 0.123 [78]
[79] 0.147 - 0.208 [79]
... ... ... and 4 more ...
actual$p_value | expected$p_value
[88] 0.178 | 0.178 [88]
[89] 0.154 | 0.154 [89]
[90] 0.154 | 0.154 [90]
[91] 0.435 - 0.487 [91]
[92] 0.435 - 0.487 [92]
[93] 0.009 | 0.009 [93]
[94] 0.009 | 0.009 [94]
[95] 0.005 | 0.005 [95]
[96] 0.005 | 0.005 [96]
[97] 0.295 - 0.493 [97]
... ... ... and 16 more ...
actual$p_value | expected$p_value
[118] 0.126 | 0.126 [118]
[119] 0.112 | 0.112 [119]
[120] 0.112 | 0.112 [120]
[121] 0.991 - 1.000 [121]
[122] 0.991 - 1.000 [122]
[123] 0.123 - 0.126 [123]
[124] 0.123 - 0.126 [124]
[125] 0.156 | 0.156 [125]
[126] 0.156 | 0.156 [126]
[127] 0.592 | 0.592 [127]
`actual$p_value[132:139]`: 0.125 0.592 0.592 0.175 0.175 0.198 0.198 0.592
`expected$p_value[132:139]`: 0.125 0.592 0.592 0.184 0.184 0.198 0.198 0.592
[ FAIL 2 | WARN 9 | SKIP 0 | PASS 33 ]
Error: Test failures
Execution halted
decoupleR.Rcheck/decoupleR-Ex.timings
| name | user | system | elapsed | |
| check_corr | 0.029 | 0.003 | 0.034 | |
| convert_f_defaults | 0.008 | 0.002 | 0.010 | |
| decouple | 0.000 | 0.000 | 0.001 | |
| dot-fit_preprocessing | 0.007 | 0.000 | 0.009 | |
| extract_sets | 0.006 | 0.000 | 0.007 | |
| filt_minsize | 0.011 | 0.001 | 0.011 | |
| get_collectri | 2.856 | 0.325 | 9.224 | |
| get_dorothea | 7.553 | 0.683 | 19.666 | |
| get_profile_of | 0.000 | 0.001 | 0.000 | |
| get_progeny | 2.601 | 0.188 | 11.152 | |
| get_resource | 0.296 | 0.033 | 2.292 | |
| get_toy_data | 0.001 | 0.000 | 0.001 | |
| intersect_regulons | 0.008 | 0.004 | 0.011 | |
| pipe | 0.001 | 0.000 | 0.000 | |
| pivot_wider_profile | 0.000 | 0.001 | 0.000 | |
| randomize_matrix | 0.000 | 0.000 | 0.001 | |
| rename_net | 0.012 | 0.004 | 0.018 | |
| run_aucell | 3.227 | 1.117 | 5.371 | |
| run_consensus | 0.612 | 0.138 | 1.340 | |
| run_fgsea | 9.665 | 0.338 | 11.886 | |
| run_gsva | 0.648 | 0.245 | 0.924 | |
| run_mdt | 0.063 | 0.018 | 0.083 | |
| run_mlm | 0.026 | 0.005 | 0.032 | |
| run_ora | 0.140 | 0.025 | 0.180 | |
| run_udt | 0.085 | 0.013 | 0.165 | |
| run_ulm | 0.024 | 0.004 | 0.045 | |
| run_viper | 0.302 | 0.133 | 0.870 | |
| run_wmean | 0.200 | 0.022 | 0.224 | |
| run_wsum | 0.215 | 0.024 | 0.238 | |
| show_methods | 0.016 | 0.003 | 0.019 | |
| show_resources | 0.020 | 0.003 | 0.626 | |
| tidyeval | 0 | 0 | 0 | |