Pau Badia-i-Mompel
| Snapshot Date: 2025-05-07 13:00 -0400 (Wed, 07 May 2025) |
| git_url: https://git.bioconductor.org/packages/decoupleR |
| git_branch: devel |
| git_last_commit: 6010cb0 |
| git_last_commit_date: 2025-04-15 12:31:44 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-05-08 12:10 -0400 (Thu, 08 May 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4746 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.0 (2025-04-11 ucrt) -- "How About a Twenty-Six" | 4508 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.0 Patched (2025-04-21 r88169) -- "How About a Twenty-Six" | 4547 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.0 Patched (2025-04-21 r88169) -- "How About a Twenty-Six" | 4488 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4441 |
| 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 528/2304 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| decoupleR 2.15.0 (landing page) Pau Badia-i-Mompel
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | ERROR | ||||||||||
|
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: 2.15.0 |
| 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_2.15.0.tar.gz |
| StartedAt: 2025-05-07 19:09:42 -0400 (Wed, 07 May 2025) |
| EndedAt: 2025-05-07 19:14:37 -0400 (Wed, 07 May 2025) |
| EllapsedTime: 294.6 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: decoupleR.Rcheck |
| Warnings: NA |
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###
### Running command:
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### /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_2.15.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/decoupleR.Rcheck’
* using R version 4.5.0 Patched (2025-04-21 r88169)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 16.0.0 (clang-1600.0.26.6)
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 ‘2.15.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking 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
[2025-05-07 19:09:58] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-07 19:09:58] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-05-07 19:09:58] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-05-07 19:09:58] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2025-05-07 19:09:58] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-05-07
[2025-05-07 19:09:58] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-05-07 19:05:17 UTC; unix
[2025-05-07 19:09:58] [INFO] [OmnipathR] Package `OmnipathR` version: 3.17.0
[2025-05-07 19:09:58] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-05-07 19:09:58] [INFO] [OmnipathR] Session info: [version=R version 4.5.0 Patched (2025-04-21 r88169); 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=2025-05-07; pandoc=3.1.12.3 @ /opt/homebrew/bin/ (via rmarkdown); quarto=1.4.552 @ /usr/local/bin/quarto]
[2025-05-07 19:09:58] [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=10.44 2024-06-07; 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=3.12.1]
[2025-05-07 19:09:58] [INFO] [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); annotate 1.87.0(2025-05-07); AnnotationDbi 1.71.0(2025-05-07); AUCell 1.31.0(2025-05-07); backports 1.5.0(2024-05-23); beachmat 2.25.0(2025-05-07); Biobase 2.69.0(2025-05-07); BiocGenerics 0.55.0(2025-05-07); BiocParallel 1.43.0(2025-05-07); BiocSingular 1.25.0(2025-05-07); Biostrings 2.77.0(2025-05-07); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.2(2024-07-29); chromote 0.5.1(2025-04-24); cli 3.6.5(2025-04-23); codetools 0.2-20(2024-03-31); crayon 1.5.3(2024-06-20); curl 6.2.2(2025-03-24); data.table 1.17.0(2025-02-22); DBI 1.2.3(2024-06-02); decoupleR 2.15.0(2025-05-07); DelayedArray 0.35.1(2025-05-07); DelayedMatrixStats 1.31.0(2025-05-07); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.3(2025-01-10); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.3(2022-07-05); GenomeInfoDb 1.45.3(2025-05-07); GenomicRanges 1.61.0(2025-05-07); glue 1.8.0(2024-09-30); graph 1.87.0(2025-05-07); GSEABase 1.71.0(2025-05-07); GSVA 2.3.1(2025-05-07); h5mread 1.1.0(2025-05-07); HDF5Array 1.37.0(2025-05-07); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.1.2(2025-03-26); igraph 2.1.4(2025-01-23); IRanges 2.43.0(2025-05-07); irlba 2.3.5.1(2022-10-03); jsonlite 2.0.0(2025-03-27); KEGGREST 1.49.0(2025-05-07); knitr 1.50(2025-03-16); later 1.4.2(2025-04-08); lattice 0.22-7(2025-04-02); lifecycle 1.0.4(2023-11-07); logger 0.4.0(2024-10-22); lubridate 1.9.4(2024-12-08); magick 2.8.6(2025-03-23); magrittr 2.0.3(2022-03-30); Matrix 1.7-3(2025-03-11); MatrixGenerics 1.21.0(2025-05-07); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); OmnipathR 3.17.0(2025-05-07); parallelly 1.44.0(2025-05-07); pillar 1.10.2(2025-04-05); pkgconfig 2.0.3(2019-09-22); png 0.1-8(2022-11-29); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.3.2(2024-11-28); ps 1.9.1(2025-04-12); purrr 1.0.4(2025-02-05); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.0.14(2025-01-12); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rhdf5 2.53.0(2025-05-07); rhdf5filters 1.21.0(2025-05-07); Rhdf5lib 1.31.0(2025-05-07); rjson 0.2.23(2024-09-16); rlang 1.1.6(2025-04-11); rmarkdown 2.29(2024-11-04); RSQLite 2.3.11(2025-05-04); rsvd 1.0.5(2021-04-16); rvest 1.0.4(2024-02-12); S4Arrays 1.9.0(2025-05-07); S4Vectors 0.47.0(2025-05-07); ScaledMatrix 1.17.0(2025-05-07); sessioninfo 1.2.3(2025-02-05); SingleCellExperiment 1.31.0(2025-05-07); SparseArray 1.9.0(2025-05-07); sparseMatrixStats 1.21.0(2025-05-07); SpatialExperiment 1.19.0(2025-05-07); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); SummarizedExperiment 1.39.0(2025-05-07); tibble 3.2.1(2023-03-20); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); UCSC.utils 1.5.0(2025-05-07); vctrs 0.6.5(2023-12-01); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.52(2025-04-02); XML 3.99-0.18(2025-01-01); xml2 1.3.8(2025-03-14); xtable 1.8-4(2019-04-21); XVector 0.49.0(2025-05-07); yaml 2.3.10(2024-07-26); zip 2.3.2(2025-02-01)
[2025-05-07 19:09:58] [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
[2025-05-07 19:09:58] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-05-07 19:09:58] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-05-07 19:09:58] [TRACE] [OmnipathR] Contains 8 files.
[2025-05-07 19:09:58] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-05-07 19:09:58] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-07 19:09:58] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-05-07 19:09:58] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-05-07 19:09:58] [TRACE] [OmnipathR] Pandoc version: `3.1.12.3`.
[2025-05-07 19:09:58] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-05-07 19:09:58] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-05-07 19:09:58] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-05-07 19:09:58] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-05-07 19:09:58] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-05-07 19:09:58] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-05-07 19:09:58] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-05-07 19:09:58] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-05-07 19:09:58] [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’
Non-topic package-anchored link(s) in Rd file 'pipe.Rd':
‘[magrittr:pipe]{%>%}’
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 12.485 0.731 15.595
get_dorothea 8.139 0.610 14.825
run_aucell 4.710 1.903 9.900
get_collectri 3.305 0.409 9.522
get_progeny 2.909 0.252 10.959
* 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 1 | WARN 18 | SKIP 0 | PASS 34 ]
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-3.22-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 ‘2.15.0’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** 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 version 4.5.0 Patched (2025-04-21 r88169) -- "How About a Twenty-Six"
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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[2025-05-07 19:11:52] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-07 19:11:52] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-05-07 19:11:52] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-05-07 19:11:52] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2025-05-07 19:11:52] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-05-07
[2025-05-07 19:11:52] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-05-07 19:05:17 UTC; unix
[2025-05-07 19:11:52] [INFO] [OmnipathR] Package `OmnipathR` version: 3.17.0
[2025-05-07 19:11:52] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-05-07 19:11:53] [INFO] [OmnipathR] Session info: [version=R version 4.5.0 Patched (2025-04-21 r88169); 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=2025-05-07; pandoc=3.1.12.3 @ /opt/homebrew/bin/ (via rmarkdown); quarto=1.4.552 @ /usr/local/bin/quarto]
[2025-05-07 19:11:53] [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=10.44 2024-06-07; 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=3.12.1]
[2025-05-07 19:11:53] [INFO] [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); annotate 1.87.0(2025-05-07); AnnotationDbi 1.71.0(2025-05-07); AUCell 1.31.0(2025-05-07); backports 1.5.0(2024-05-23); beachmat 2.25.0(2025-05-07); Biobase 2.69.0(2025-05-07); BiocGenerics 0.55.0(2025-05-07); BiocParallel 1.43.0(2025-05-07); BiocSingular 1.25.0(2025-05-07); Biostrings 2.77.0(2025-05-07); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); brio 1.1.5(2024-04-24); broom 1.0.8(2025-03-28); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.2(2024-07-29); chromote 0.5.1(2025-04-24); class 7.3-23(2025-01-01); cli 3.6.5(2025-04-23); codetools 0.2-20(2024-03-31); cowplot 1.1.3(2024-01-22); crayon 1.5.3(2024-06-20); curl 6.2.2(2025-03-24); data.table 1.17.0(2025-02-22); DBI 1.2.3(2024-06-02); decoupleR 2.15.0(2025-05-07); DelayedArray 0.35.1(2025-05-07); DelayedMatrixStats 1.31.0(2025-05-07); desc 1.4.3(2023-12-10); dichromat 2.0-0.1(2022-05-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); e1071 1.7-16(2024-09-16); evaluate 1.0.3(2025-01-10); farver 2.1.2(2024-05-13); fastmap 1.2.0(2024-05-15); fastmatch 1.1-6(2024-12-23); fgsea 1.35.0(2025-05-07); fs 1.6.6(2025-04-12); generics 0.1.3(2022-07-05); GenomeInfoDb 1.45.3(2025-05-07); GenomicRanges 1.61.0(2025-05-07); ggplot2 3.5.2(2025-04-09); glue 1.8.0(2024-09-30); graph 1.87.0(2025-05-07); GSEABase 1.71.0(2025-05-07); GSVA 2.3.1(2025-05-07); gtable 0.3.6(2024-10-25); h5mread 1.1.0(2025-05-07); HDF5Array 1.37.0(2025-05-07); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); htmlwidgets 1.6.4(2023-12-06); httr 1.4.7(2023-08-15); httr2 1.1.2(2025-03-26); igraph 2.1.4(2025-01-23); IRanges 2.43.0(2025-05-07); irlba 2.3.5.1(2022-10-03); jsonlite 2.0.0(2025-03-27); KEGGREST 1.49.0(2025-05-07); kernlab 0.9-33(2024-08-13); KernSmooth 2.23-26(2025-01-01); knitr 1.50(2025-03-16); later 1.4.2(2025-04-08); lattice 0.22-7(2025-04-02); lazyeval 0.2.2(2019-03-15); lifecycle 1.0.4(2023-11-07); logger 0.4.0(2024-10-22); lubridate 1.9.4(2024-12-08); magick 2.8.6(2025-03-23); magrittr 2.0.3(2022-03-30); MASS 7.3-65(2025-02-28); Matrix 1.7-3(2025-03-11); MatrixGenerics 1.21.0(2025-05-07); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); mixtools 2.0.0.1(2025-03-08); nlme 3.1-168(2025-03-31); OmnipathR 3.17.0(2025-05-07); parallelly 1.44.0(2025-05-07); pillar 1.10.2(2025-04-05); pkgconfig 2.0.3(2019-09-22); plotly 4.10.4(2024-01-13); png 0.1-8(2022-11-29); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.3.2(2024-11-28); proxy 0.4-27(2022-06-09); ps 1.9.1(2025-04-12); purrr 1.0.4(2025-02-05); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); ranger 0.17.0(2024-11-08); rappdirs 0.3.3(2021-01-31); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.0.14(2025-01-12); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rhdf5 2.53.0(2025-05-07); rhdf5filters 1.21.0(2025-05-07); Rhdf5lib 1.31.0(2025-05-07); rjson 0.2.23(2024-09-16); rlang 1.1.6(2025-04-11); rmarkdown 2.29(2024-11-04); rpart 4.1.24(2025-01-07); RSQLite 2.3.11(2025-05-04); rsvd 1.0.5(2021-04-16); rvest 1.0.4(2024-02-12); S4Arrays 1.9.0(2025-05-07); S4Vectors 0.47.0(2025-05-07); ScaledMatrix 1.17.0(2025-05-07); scales 1.4.0(2025-04-24); segmented 2.1-4(2025-02-28); sessioninfo 1.2.3(2025-02-05); SingleCellExperiment 1.31.0(2025-05-07); SparseArray 1.9.0(2025-05-07); sparseMatrixStats 1.21.0(2025-05-07); SpatialExperiment 1.19.0(2025-05-07); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); SummarizedExperiment 1.39.0(2025-05-07); survival 3.8-3(2024-12-17); testthat 3.2.3(2025-01-13); tibble 3.2.1(2023-03-20); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); UCSC.utils 1.5.0(2025-05-07); vctrs 0.6.5(2023-12-01); viper 1.43.0(2025-05-07); viridisLite 0.4.2(2023-05-02); waldo 0.6.1(2024-11-07); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.52(2025-04-02); XML 3.99-0.18(2025-01-01); xml2 1.3.8(2025-03-14); xtable 1.8-4(2019-04-21); XVector 0.49.0(2025-05-07); yaml 2.3.10(2024-07-26); zip 2.3.2(2025-02-01)
[2025-05-07 19:11:53] [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
[2025-05-07 19:11:53] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-05-07 19:11:53] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-05-07 19:11:53] [TRACE] [OmnipathR] Contains 8 files.
[2025-05-07 19:11:53] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-05-07 19:11:53] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-07 19:11:53] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-05-07 19:11:53] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-05-07 19:11:53] [TRACE] [OmnipathR] Pandoc version: `3.1.12.3`.
[2025-05-07 19:11:53] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-05-07 19:11:53] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-05-07 19:11:53] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-05-07 19:11:53] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-05-07 19:11:53] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-05-07 19:11:53] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-05-07 19:11:53] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-05-07 19:11:53] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-05-07 19:11:53] [TRACE] [OmnipathR] Cache locked: FALSE
[2025-05-07 19:11:54] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-05-07 19:11:54] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-05-07 19:11:54] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-05-07 19:11:54] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-05-07 19:11:54] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2025-05-07 19:11:54] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-07 19:11:54] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-05-07 19:11:54] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2025-05-07 19:11:54] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-07 19:11:55] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-05-07 19:11:55] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2025-05-07 19:11:55] [TRACE] [OmnipathR] Cache file path: /Users/biocbuild/Library/Caches/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2025-05-07 19:11:55] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2025-05-07 19:11:55] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`.
[2025-05-07 19:11:55] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2025-05-07 19:11:55] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2025-05-07 19:11:55] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-05-07 19:11:55] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-05-07 19:11:55] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-05-07 19:11:55] [TRACE] [OmnipathR] Sending HTTP request.
[2025-05-07 19:11:55] [TRACE] [OmnipathR] HTTP 200 (OK)
[2025-05-07 19:11:55] [TRACE] [OmnipathR] HTTP v2 GET: status 200.
[2025-05-07 19:11:55] [TRACE] [OmnipathR] Downloaded 31.2 Kb in 0.706053s from www.ensembl.org (44.2 Kb/s); Redirect: 0.535328s, DNS look up: 0.011243s, Connection: 0.012952s, Pretransfer: 0.416901s, First byte at: 0.677355s
[2025-05-07 19:11:55] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 302 Found; Date: Wed, 07 May 2025 23:11:55 GMT; Content-Type: text/html; charset=iso-8859-1; Content-Length: 288; Connection: keep-alive; Server: Apache; Set-cookie: redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT; Location: //useast.ensembl.org/info/about/species.html?redirectsrc=//www.ensembl.org%2Finfo%2Fabout%2Fspecies.html; X-NGINX-MACHINE: wp-p1m2-33.ebi.ac.uk; HTTP/2 302 ; date: Wed, 07 May 2025 23:11:55 GMT; content-type: text/html; charset=iso-8859-1; content-length: 208; server: Apache; set-cookie: redirected_from_url=%2F%2Fwww.ensembl.org%252Finfo%252Fabout%252Fspecies.html; path=/; expires=Thu, 31-Dec-2037 23:59:59 GMT; location: /info/about/species.html; x-nginx-machine: ip-10-25-25-86.us-east-2.compute.internal; HTTP/2 200 ; date: Wed, 07 May 2025 23:11:55 GMT; content-type: text/html; charset=utf-8; content-length: 31969; server: Apache; set-cookie: redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT; set-cookie: redirect_mirror=no; path=/; expires=Thu, 08 May 2025 23:11:48 GMT; set-cookie: ENSEMBL_WWW_SESSION=1300546d132bac630fa890b8686b02b406c82ea85194858aded3c8eb; path=/; expires=Thu, 31-Dec-2037 23:59:59 GMT; HttpOnly; set-cookie: redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT; set-cookie: redirect_mirror=no; path=/; expires=Thu, 08 May 2025 23:11:48 GMT; set-cookie: ENSEMBL_WWW_SESSION=1300546d132bac630fa890b8686b02b406c82ea85194858aded3c8eb; path=/; expires=Thu, 31-Dec-2037 23:59:59 GMT; HttpOnly; vary: Accept-Encoding; content-encoding: gzip; x-frame-options: SAMEORIGIN; content-security-policy: frame-ancestors 'self'; x-nginx-machine: ip-10-25-25-86.us-east-2.compute.internal
[2025-05-07 19:11:55] [TRACE] [OmnipathR] Response headers: [date=Wed, 07 May 2025 23:11:55 GMT,content-type=text/html; charset=utf-8,content-length=31969,server=Apache,set-cookie=redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT,set-cookie=redirect_mirror=no; path=/; expires=Thu, 08 May 2025 23:11:48 GMT,set-cookie=ENSEMBL_WWW_SESSION=1300546d132bac630fa890b8686b02b406c82ea85194858aded3c8eb; path=/; expires=Thu, 31-Dec-2037 23:59:59 GMT; HttpOnly,set-cookie=redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT,set-cookie=redirect_mirror=no; path=/; expires=Thu, 08 May 2025 23:11:48 GMT,set-cookie=ENSEMBL_WWW_SESSION=1300546d132bac630fa890b8686b02b406c82ea85194858aded3c8eb; path=/; expires=Thu, 31-Dec-2037 23:59:59 GMT; HttpOnly,vary=Accept-Encoding,content-encoding=gzip,x-frame-options=SAMEORIGIN,content-security-policy=frame-ancestors 'self',x-nginx-machine=ip-10-25-25-86.us-east-2.compute.internal]
[2025-05-07 19:11:56] [INFO] [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1]
[2025-05-07 19:11:56] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-07 19:11:56] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-05-07 19:11:56] [INFO] [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`.
[2025-05-07 19:11:56] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2025-05-07 19:11:56] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2025-05-07 19:11:56] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2025-05-07 19:11:56] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2025-05-07 19:11:56] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-07 19:11:56] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-05-07 19:11:56] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-07 19:11:56] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-05-07 19:11:56] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2025-05-07 19:11:56] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-05-07 19:11:56] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2025-05-07 19:11:56] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2025-05-07 19:11:56] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2025-05-07 19:11:56] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-05-07 19:11:57] [TRACE] [OmnipathR] HTTP v2 GET: status 200.
[2025-05-07 19:11:57] [TRACE] [OmnipathR] Downloaded 8.7 Kb in 0.41491s from omabrowser.org (20.9 Kb/s); Redirect: 0s, DNS look up: 0.001045s, Connection: 0.001996s, Pretransfer: 0.330987s, First byte at: 0.414725s
[2025-05-07 19:11:57] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; date: Wed, 07 May 2025 23:11:57 GMT; server: nginx; strict-transport-security: max-age=31536000; includeSubDomains; content-type: text/plain; charset=UTF-8; last-modified: Wed, 20 Nov 2024 10:20:02 GMT; etag: W/"673db7d2-6517f"; access-control-allow-origin: *; content-encoding: gzip
[2025-05-07 19:11:58] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-05-07 19:11:58] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1]
[2025-05-07 19:11:58] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-07 19:11:58] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-05-07 19:11:58] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.
[2025-05-07 19:11:58] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`.
[2025-05-07 19:11:58] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-05-07 19:11:58] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=TFcensus,query_type=annotations]
[2025-05-07 19:11:58] [TRACE] [OmnipathR] Organism(s): 9606
[2025-05-07 19:11:58] [TRACE] [OmnipathR] Orthology targets:
[2025-05-07 19:11:59] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-05-07 19:11:59] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-05-07 19:11:59] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2025-05-07 19:11:59] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2025-05-07 19:11:59] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2025-05-07 19:11:59] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2025-05-07 19:11:59] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2025-05-07 19:11:59] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2025-05-07 19:11:59] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2025-05-07 19:11:59] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2025-05-07 19:11:59] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-05-07 19:11:59] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2025-05-07 19:11:59] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.402439s from omnipathdb.org (38.9 Kb/s); Redirect: 0s, DNS look up: 0.000978s, Connection: 0.0017s, Pretransfer: 0.148259s, First byte at: 0.398977s
[2025-05-07 19:11:59] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 07 May 2025 23:11:59 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Thu, 08 May 2025 00:11:59 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-05-07 19:12:00] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2025-05-07 19:12:00] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-07 19:12:00] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-05-07 19:12:00] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-07 19:12:00] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-05-07 19:12:00] [INFO] [OmnipathR] Cache item `6f000d9b5edd9832b1c28754d1c3d9449c1c7490` version 1: status changed from `unknown` to `started`.
[2025-05-07 19:12:00] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/6f000d9b5edd9832b1c28754d1c3d9449c1c7490-1.rds`.
[2025-05-07 19:12:00] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/6f000d9b5edd9832b1c28754d1c3d9449c1c7490-1.rds`.
[2025-05-07 19:12:00] [INFO] [OmnipathR] Download ready [key=6f000d9b5edd9832b1c28754d1c3d9449c1c7490, version=1]
[2025-05-07 19:12:00] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-07 19:12:00] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-05-07 19:12:00] [INFO] [OmnipathR] Cache item `6f000d9b5edd9832b1c28754d1c3d9449c1c7490` version 1: status changed from `started` to `ready`.
[2025-05-07 19:12:00] [SUCCESS] [OmnipathR] Downloaded 3099 annotation records.
[2025-05-07 19:12:01] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-05-07 19:12:01] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-05-07 19:12:01] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-05-07 19:12:01] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=PROGENy,query_type=annotations]
[2025-05-07 19:12:01] [TRACE] [OmnipathR] Organism(s): 9606
[2025-05-07 19:12:01] [TRACE] [OmnipathR] Orthology targets:
[2025-05-07 19:12:01] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-05-07 19:12:01] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-05-07 19:12:01] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-05-07 19:12:01] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-05-07 19:12:01] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-05-07 19:12:01] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-05-07 19:12:01] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-05-07 19:12:01] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-05-07 19:12:01] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-05-07 19:12:01] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2025-05-07 19:12:01] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-05-07 19:12:02] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2025-05-07 19:12:02] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.327047s from omnipathdb.org (47.9 Kb/s); Redirect: 0s, DNS look up: 0.0011s, Connection: 0.003713s, Pretransfer: 0.163772s, First byte at: 0.323965s
[2025-05-07 19:12:02] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 07 May 2025 23:12:02 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Thu, 08 May 2025 00:12:02 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-05-07 19:12:10] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-05-07 19:12:10] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-07 19:12:10] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-05-07 19:12:10] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-07 19:12:10] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-05-07 19:12:10] [INFO] [OmnipathR] Cache item `3492392585ba05414edfae46801492076437d7e7` version 1: status changed from `unknown` to `started`.
[2025-05-07 19:12:10] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`.
[2025-05-07 19:12:11] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`.
[2025-05-07 19:12:11] [INFO] [OmnipathR] Download ready [key=3492392585ba05414edfae46801492076437d7e7, version=1]
[2025-05-07 19:12:11] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-07 19:12:11] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-05-07 19:12:11] [INFO] [OmnipathR] Cache item `3492392585ba05414edfae46801492076437d7e7` version 1: status changed from `started` to `ready`.
[2025-05-07 19:12:11] [SUCCESS] [OmnipathR] Downloaded 700239 annotation records.
[2025-05-07 19:12:13] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-05-07 19:12:13] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-05-07 19:12:13] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-05-07 19:12:13] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=PROGENy,query_type=annotations]
[2025-05-07 19:12:13] [TRACE] [OmnipathR] Organism(s): 9606
[2025-05-07 19:12:13] [TRACE] [OmnipathR] Orthology targets:
[2025-05-07 19:12:13] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-05-07 19:12:13] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-05-07 19:12:13] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-05-07 19:12:14] [TRACE] [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`.
[2025-05-07 19:12:14] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-05-07 19:12:14] [SUCCESS] [OmnipathR] Loaded 700239 annotation records from cache.
[2025-05-07 19:12:15] [INFO] [OmnipathR] Loading database `Orthologous Matrix (OMA) gene pairs`.
[2025-05-07 19:12:15] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2025-05-07 19:12:15] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2025-05-07 19:12:15] [TRACE] [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-05-07 19:12:15] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2025-05-07 19:12:15] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2025-05-07 19:12:15] [TRACE] [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-05-07 19:12:15] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2025-05-07 19:12:15] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/api/pairs/HUMAN/MOUSE/?format=tsv&xrefs=UniProtKB%2FSwissProt&per_page=2000000`.
[2025-05-07 19:12:15] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/api/pairs/HUMAN/MOUSE/?format=tsv&xrefs=UniProtKB%2FSwissProt&per_page=2000000`
[2025-05-07 19:12:15] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/api/pairs/HUMAN/MOUSE/?format=tsv&xrefs=UniProtKB%2FSwissProt&per_page=2000000`.
[2025-05-07 19:12:15] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-07 19:12:15] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-05-07 19:12:15] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-07 19:12:15] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-05-07 19:12:15] [INFO] [OmnipathR] Cache item `8f45b25c384d814c7de210e7ca40b7e35894e4f1` version 1: status changed from `unknown` to `started`.
[2025-05-07 19:12:15] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/8f45b25c384d814c7de210e7ca40b7e35894e4f1-1.rds`.
[2025-05-07 19:12:15] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/api/pairs/HUMAN/MOUSE/?format=tsv&xrefs=UniProtKB%2FSwissProt&per_page=2000000`
[2025-05-07 19:12:15] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/api/pairs/HUMAN/MOUSE/?format=tsv&xrefs=UniProtKB%2FSwissProt&per_page=2000000`
[2025-05-07 19:12:15] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2025-05-07 19:12:15] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-05-07 19:12:41] [TRACE] [OmnipathR] HTTP v2 GET: status 200.
[2025-05-07 19:12:41] [TRACE] [OmnipathR] Downloaded 11.1 Kb in 25.829283s from omabrowser.org (439 bytes/s); Redirect: 0s, DNS look up: 0.001041s, Connection: 0.001852s, Pretransfer: 0.329292s, First byte at: 25.829173s
[2025-05-07 19:12:41] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; date: Wed, 07 May 2025 23:12:41 GMT; server: nginx; strict-transport-security: max-age=31536000; includeSubDomains; content-type: text/tsv; charset=utf-8; content-length: 1187278; x-total-count: 22374; vary: Accept,Origin,Cookie; allow: GET, HEAD, OPTIONS; content-disposition: attachment; filename=OMA-Pairs_HUMAN-MOUSE_2025-05-07_231239.tsv; x-frame-options: SAMEORIGIN; set-cookie: __matomo=1a5495fd28391a38; expires=Fri, 07-May-2027 23:12:41 UTC; Path=/
[2025-05-07 19:12:44] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/8f45b25c384d814c7de210e7ca40b7e35894e4f1-1.rds`.
[2025-05-07 19:12:44] [INFO] [OmnipathR] Download ready [key=8f45b25c384d814c7de210e7ca40b7e35894e4f1, version=1]
[2025-05-07 19:12:44] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-07 19:12:44] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-05-07 19:12:44] [INFO] [OmnipathR] Cache item `8f45b25c384d814c7de210e7ca40b7e35894e4f1` version 1: status changed from `started` to `ready`.
[2025-05-07 19:12:44] [TRACE] [OmnipathR] ID translation table: from `uniprot_entry` to `uniprot`, using `uniprot`.
[2025-05-07 19:12:44] [TRACE] [OmnipathR] Creating ID mapping table from `id` to `accession`, for organism 9606 (only reviewed: TRUE)
[2025-05-07 19:12:44] [TRACE] [OmnipathR] Loading all UniProt records for organism 9606 (only reviewed: TRUE); fields: id,accession
[2025-05-07 19:12:44] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2025-05-07 19:12:44] [TRACE] [OmnipathR] Looking up in cache: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:9606%20AND%20reviewed:true`.
[2025-05-07 19:12:44] [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`
[2025-05-07 19:12:44] [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`.
[2025-05-07 19:12:44] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-07 19:12:44] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-05-07 19:12:44] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-07 19:12:44] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-05-07 19:12:44] [INFO] [OmnipathR] Cache item `6558a1824894a625b8e3f80538cd3aa6e8a44379` version 1: status changed from `unknown` to `started`.
[2025-05-07 19:12:44] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/6558a1824894a625b8e3f80538cd3aa6e8a44379-1.rds`.
[2025-05-07 19:12:44] [INFO] [OmnipathR] Retrieving URL: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:9606%20AND%20reviewed:true`
[2025-05-07 19:12:44] [TRACE] [OmnipathR] Attempt 1/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:9606%20AND%20reviewed:true`
[2025-05-07 19:12:44] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2025-05-07 19:12:44] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-05-07 19:12:45] [TRACE] [OmnipathR] HTTP v2 GET: status 200.
[2025-05-07 19:12:45] [TRACE] [OmnipathR] Downloaded 31 bytes in 1.099301s from rest.uniprot.org (28 bytes/s); Redirect: 0s, DNS look up: 0.006242s, Connection: 0.010684s, Pretransfer: 0.489089s, First byte at: 1.099196s
[2025-05-07 19:12:45] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; vary: accept,accept-encoding,x-uniprot-release,x-api-deployment-date; vary: User-Agent; cache-control: public, max-age=43200; content-type: text/plain;format=tsv; content-encoding: gzip; access-control-allow-credentials: true; access-control-expose-headers: Link, X-Total-Results, X-UniProt-Release, X-UniProt-Release-Date, X-API-Deployment-Date; x-api-deployment-date: 30-April-2025; strict-transport-security: max-age=31536000; includeSubDomains; date: Wed, 07 May 2025 23:12:45 GMT; access-control-max-age: 1728000; x-uniprot-release: 2025_02; access-control-allow-origin: *; access-control-allow-methods: GET, PUT, POST, DELETE, PATCH, OPTIONS; access-control-allow-headers: DNT,Keep-Alive,User-Agent,X-Requested-With,If-Modified-Since,Cache-Control,Content-Type,Range,Authorization; x-uniprot-release-date: 23-April-2025
[2025-05-07 19:13:02] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/6558a1824894a625b8e3f80538cd3aa6e8a44379-1.rds`.
[2025-05-07 19:13:02] [INFO] [OmnipathR] Download ready [key=6558a1824894a625b8e3f80538cd3aa6e8a44379, version=1]
[2025-05-07 19:13:02] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-07 19:13:02] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-05-07 19:13:02] [INFO] [OmnipathR] Cache item `6558a1824894a625b8e3f80538cd3aa6e8a44379` version 1: status changed from `started` to `ready`.
[2025-05-07 19:13:02] [SUCCESS] [OmnipathR] UniProt (rest.uniprot.org): downloaded 20421 records
[2025-05-07 19:13:03] [TRACE] [OmnipathR] Translating complexes: 0 complexes in data.
[2025-05-07 19:13:03] [TRACE] [OmnipathR] 0 complexes after removing the ones mapping to more than 1 items in target identifier space.
[2025-05-07 19:13:03] [TRACE] [OmnipathR] Translated 0 complexes to 0.
[2025-05-07 19:13:03] [TRACE] [OmnipathR] 13774 rows before translation, 13774 uniprot_entry IDs in column `id_organism_a`.
[2025-05-07 19:13:03] [TRACE] [OmnipathR] 13774 rows after translation; translated 13565 `uniprot_entry` IDs in column `id_organism_a` to 13565 `uniprot` IDs in column `id_organism_a`.
[2025-05-07 19:13:03] [TRACE] [OmnipathR] ID translation table: from `uniprot_entry` to `uniprot`, using `uniprot`.
[2025-05-07 19:13:03] [TRACE] [OmnipathR] Creating ID mapping table from `id` to `accession`, for organism 10090 (only reviewed: TRUE)
[2025-05-07 19:13:03] [TRACE] [OmnipathR] Loading all UniProt records for organism 10090 (only reviewed: TRUE); fields: id,accession
[2025-05-07 19:13:03] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2025-05-07 19:13:03] [TRACE] [OmnipathR] Looking up in cache: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:10090%20AND%20reviewed:true`.
[2025-05-07 19:13:03] [INFO] [OmnipathR] Cache record does not exist: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:10090%20AND%20reviewed:true`
[2025-05-07 19:13:03] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:10090%20AND%20reviewed:true`.
[2025-05-07 19:13:03] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-07 19:13:03] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-05-07 19:13:03] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-07 19:13:03] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-05-07 19:13:03] [INFO] [OmnipathR] Cache item `43ea5f2cdaa9ac7e0e114371af97235cdddd776f` version 1: status changed from `unknown` to `started`.
[2025-05-07 19:13:03] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/43ea5f2cdaa9ac7e0e114371af97235cdddd776f-1.rds`.
[2025-05-07 19:13:03] [INFO] [OmnipathR] Retrieving URL: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:10090%20AND%20reviewed:true`
[2025-05-07 19:13:03] [TRACE] [OmnipathR] Attempt 1/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:10090%20AND%20reviewed:true`
[2025-05-07 19:13:03] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2025-05-07 19:13:03] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-05-07 19:13:04] [TRACE] [OmnipathR] HTTP v2 GET: status 200.
[2025-05-07 19:13:04] [TRACE] [OmnipathR] Downloaded 31 bytes in 1.009571s from rest.uniprot.org (30 bytes/s); Redirect: 0s, DNS look up: 0.005762s, Connection: 0.01035s, Pretransfer: 0.486973s, First byte at: 1.009463s
[2025-05-07 19:13:04] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; vary: accept,accept-encoding,x-uniprot-release,x-api-deployment-date; vary: User-Agent; cache-control: public, max-age=43200; content-type: text/plain;format=tsv; content-encoding: gzip; access-control-allow-credentials: true; access-control-expose-headers: Link, X-Total-Results, X-UniProt-Release, X-UniProt-Release-Date, X-API-Deployment-Date; x-api-deployment-date: 30-April-2025; strict-transport-security: max-age=31536000; includeSubDomains; date: Wed, 07 May 2025 23:13:04 GMT; access-control-max-age: 1728000; x-uniprot-release: 2025_02; access-control-allow-origin: *; access-control-allow-methods: GET, PUT, POST, DELETE, PATCH, OPTIONS; access-control-allow-headers: DNT,Keep-Alive,User-Agent,X-Requested-With,If-Modified-Since,Cache-Control,Content-Type,Range,Authorization; x-uniprot-release-date: 23-April-2025
[2025-05-07 19:13:16] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/43ea5f2cdaa9ac7e0e114371af97235cdddd776f-1.rds`.
[2025-05-07 19:13:16] [INFO] [OmnipathR] Download ready [key=43ea5f2cdaa9ac7e0e114371af97235cdddd776f, version=1]
[2025-05-07 19:13:16] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-07 19:13:16] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-05-07 19:13:16] [INFO] [OmnipathR] Cache item `43ea5f2cdaa9ac7e0e114371af97235cdddd776f` version 1: status changed from `started` to `ready`.
[2025-05-07 19:13:16] [SUCCESS] [OmnipathR] UniProt (rest.uniprot.org): downloaded 17230 records
[2025-05-07 19:13:16] [TRACE] [OmnipathR] Translating complexes: 0 complexes in data.
[2025-05-07 19:13:16] [TRACE] [OmnipathR] 0 complexes after removing the ones mapping to more than 1 items in target identifier space.
[2025-05-07 19:13:16] [TRACE] [OmnipathR] Translated 0 complexes to 0.
[2025-05-07 19:13:16] [TRACE] [OmnipathR] 13774 rows before translation, 13773 uniprot_entry IDs in column `id_organism_b`.
[2025-05-07 19:13:16] [TRACE] [OmnipathR] 13774 rows after translation; translated 13268 `uniprot_entry` IDs in column `id_organism_b` to 13268 `uniprot` IDs in column `id_organism_b`.
[2025-05-07 19:13:16] [INFO] [OmnipathR] Loaded database `Orthologous Matrix (OMA) gene pairs`.
[2025-05-07 19:13:16] [TRACE] [OmnipathR] ID translation table: from `uniprot` to `genesymbol`, using `uniprot`.
[2025-05-07 19:13:16] [TRACE] [OmnipathR] Creating ID mapping table from `accession` to `gene_primary`, for organism 10090 (only reviewed: TRUE)
[2025-05-07 19:13:16] [TRACE] [OmnipathR] Loading all UniProt records for organism 10090 (only reviewed: TRUE); fields: accession,gene_primary
[2025-05-07 19:13:16] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2025-05-07 19:13:16] [TRACE] [OmnipathR] Looking up in cache: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:10090%20AND%20reviewed:true`.
[2025-05-07 19:13:16] [INFO] [OmnipathR] Cache record does not exist: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:10090%20AND%20reviewed:true`
[2025-05-07 19:13:16] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:10090%20AND%20reviewed:true`.
[2025-05-07 19:13:16] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-07 19:13:16] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-05-07 19:13:16] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-07 19:13:16] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-05-07 19:13:16] [INFO] [OmnipathR] Cache item `3ec84ba713c02573704adb50f1a94dab684df34b` version 1: status changed from `unknown` to `started`.
[2025-05-07 19:13:16] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/3ec84ba713c02573704adb50f1a94dab684df34b-1.rds`.
[2025-05-07 19:13:16] [INFO] [OmnipathR] Retrieving URL: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:10090%20AND%20reviewed:true`
[2025-05-07 19:13:16] [TRACE] [OmnipathR] Attempt 1/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:10090%20AND%20reviewed:true`
[2025-05-07 19:13:16] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2025-05-07 19:13:16] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-05-07 19:13:17] [TRACE] [OmnipathR] HTTP v2 GET: status 200.
[2025-05-07 19:13:17] [TRACE] [OmnipathR] Downloaded 43 bytes in 0.740374s from rest.uniprot.org (58 bytes/s); Redirect: 0s, DNS look up: 0.001214s, Connection: 0.002181s, Pretransfer: 0.260713s, First byte at: 0.740271s
[2025-05-07 19:13:17] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; vary: accept,accept-encoding,x-uniprot-release,x-api-deployment-date; vary: User-Agent; cache-control: public, max-age=43200; content-type: text/plain;format=tsv; content-encoding: gzip; access-control-allow-credentials: true; access-control-expose-headers: Link, X-Total-Results, X-UniProt-Release, X-UniProt-Release-Date, X-API-Deployment-Date; x-api-deployment-date: 30-April-2025; strict-transport-security: max-age=31536000; includeSubDomains; date: Wed, 07 May 2025 23:13:17 GMT; access-control-max-age: 1728000; x-uniprot-release: 2025_02; access-control-allow-origin: *; access-control-allow-methods: GET, PUT, POST, DELETE, PATCH, OPTIONS; access-control-allow-headers: DNT,Keep-Alive,User-Agent,X-Requested-With,If-Modified-Since,Cache-Control,Content-Type,Range,Authorization; x-uniprot-release-date: 23-April-2025
[2025-05-07 19:13:28] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/3ec84ba713c02573704adb50f1a94dab684df34b-1.rds`.
[2025-05-07 19:13:28] [INFO] [OmnipathR] Download ready [key=3ec84ba713c02573704adb50f1a94dab684df34b, version=1]
[2025-05-07 19:13:28] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-07 19:13:28] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-05-07 19:13:28] [INFO] [OmnipathR] Cache item `3ec84ba713c02573704adb50f1a94dab684df34b` version 1: status changed from `started` to `ready`.
[2025-05-07 19:13:28] [SUCCESS] [OmnipathR] UniProt (rest.uniprot.org): downloaded 17230 records
[2025-05-07 19:13:28] [TRACE] [OmnipathR] Translating complexes: 0 complexes in data.
[2025-05-07 19:13:28] [TRACE] [OmnipathR] 0 complexes after removing the ones mapping to more than 1 items in target identifier space.
[2025-05-07 19:13:28] [TRACE] [OmnipathR] Translated 0 complexes to 0.
[2025-05-07 19:13:28] [TRACE] [OmnipathR] 164123 rows before translation, 12872 uniprot IDs in column `uniprot`.
[2025-05-07 19:13:28] [TRACE] [OmnipathR] 164123 rows after translation; translated 12872 `uniprot` IDs in column `uniprot` to 12786 `genesymbol` IDs in column `genesymbol`.
[2025-05-07 19:13:28] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-05-07 19:13:28] [TRACE] [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B,C,D],genesymbols=TRUE,organisms=9606,query_type=interactions,datasets=dorothea]
[2025-05-07 19:13:28] [TRACE] [OmnipathR] Organism(s): 9606
[2025-05-07 19:13:28] [TRACE] [OmnipathR] Orthology targets:
[2025-05-07 19:13:28] [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`
[2025-05-07 19:13:28] [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`
[2025-05-07 19:13:28] [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`
[2025-05-07 19:13:28] [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`
[2025-05-07 19:13:28] [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`
[2025-05-07 19:13:28] [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`
[2025-05-07 19:13:28] [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`
[2025-05-07 19:13:28] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2025-05-07 19:13:28] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-05-07 19:13:29] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2025-05-07 19:13:29] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.462211s from omnipathdb.org (33.9 Kb/s); Redirect: 0s, DNS look up: 0.001046s, Connection: 0.002016s, Pretransfer: 0.305821s, First byte at: 0.462019s
[2025-05-07 19:13:29] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 07 May 2025 23:13:28 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Thu, 08 May 2025 00:13:28 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-05-07 19:13:32] [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`
[2025-05-07 19:13:32] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-07 19:13:32] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-05-07 19:13:32] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-07 19:13:32] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-05-07 19:13:32] [INFO] [OmnipathR] Cache item `46d37339bbc3f9a05bb89ccb79278cf1233f5cdf` version 1: status changed from `unknown` to `started`.
[2025-05-07 19:13:32] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/46d37339bbc3f9a05bb89ccb79278cf1233f5cdf-1.rds`.
[2025-05-07 19:13:33] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/46d37339bbc3f9a05bb89ccb79278cf1233f5cdf-1.rds`.
[2025-05-07 19:13:33] [INFO] [OmnipathR] Download ready [key=46d37339bbc3f9a05bb89ccb79278cf1233f5cdf, version=1]
[2025-05-07 19:13:33] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-07 19:13:33] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-05-07 19:13:33] [INFO] [OmnipathR] Cache item `46d37339bbc3f9a05bb89ccb79278cf1233f5cdf` version 1: status changed from `started` to `ready`.
[2025-05-07 19:13:38] [SUCCESS] [OmnipathR] Downloaded 278830 interactions.
[2025-05-07 19:13:43] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-05-07 19:13:43] [TRACE] [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B,C,D],genesymbols=TRUE,organisms=10090,query_type=interactions,datasets=dorothea]
[2025-05-07 19:13:43] [TRACE] [OmnipathR] Organism(s): 10090
[2025-05-07 19:13:43] [TRACE] [OmnipathR] Orthology targets:
[2025-05-07 19:13:43] [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`
[2025-05-07 19:13:43] [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`
[2025-05-07 19:13:43] [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`
[2025-05-07 19:13:43] [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`
[2025-05-07 19:13:43] [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`
[2025-05-07 19:13:43] [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`
[2025-05-07 19:13:43] [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`
[2025-05-07 19:13:43] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2025-05-07 19:13:43] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-05-07 19:13:47] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2025-05-07 19:13:47] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 4.070949s from omnipathdb.org (3.8 Kb/s); Redirect: 0s, DNS look up: 0.001018s, Connection: 0.002235s, Pretransfer: 0.167164s, First byte at: 4.070727s
[2025-05-07 19:13:47] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 07 May 2025 23:13:47 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Thu, 08 May 2025 00:13:47 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-05-07 19:13:51] [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`
[2025-05-07 19:13:51] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-07 19:13:51] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-05-07 19:13:51] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-07 19:13:51] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-05-07 19:13:51] [INFO] [OmnipathR] Cache item `ff347dedf78ef5e38c9c6d8eed291fa901aa3791` version 1: status changed from `unknown` to `started`.
[2025-05-07 19:13:51] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/ff347dedf78ef5e38c9c6d8eed291fa901aa3791-1.rds`.
[2025-05-07 19:13:51] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/ff347dedf78ef5e38c9c6d8eed291fa901aa3791-1.rds`.
[2025-05-07 19:13:51] [INFO] [OmnipathR] Download ready [key=ff347dedf78ef5e38c9c6d8eed291fa901aa3791, version=1]
[2025-05-07 19:13:51] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-07 19:13:51] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-05-07 19:13:51] [INFO] [OmnipathR] Cache item `ff347dedf78ef5e38c9c6d8eed291fa901aa3791` version 1: status changed from `started` to `ready`.
[2025-05-07 19:13:57] [SUCCESS] [OmnipathR] Downloaded 234298 interactions.
[2025-05-07 19:14:00] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-05-07 19:14:00] [TRACE] [OmnipathR] Arguments for OmniPath query: [loops=TRUE,organisms=9606,genesymbols=TRUE,query_type=interactions,datasets=collectri]
[2025-05-07 19:14:00] [TRACE] [OmnipathR] Organism(s): 9606
[2025-05-07 19:14:00] [TRACE] [OmnipathR] Orthology targets:
[2025-05-07 19:14:00] [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`
[2025-05-07 19:14:00] [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`
[2025-05-07 19:14:00] [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`
[2025-05-07 19:14:00] [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`
[2025-05-07 19:14:00] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2025-05-07 19:14:00] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2025-05-07 19:14:00] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2025-05-07 19:14:00] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2025-05-07 19:14:00] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-05-07 19:14:00] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2025-05-07 19:14:00] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.311355s from omnipathdb.org (50.3 Kb/s); Redirect: 0s, DNS look up: 0.000974s, Connection: 0.001815s, Pretransfer: 0.155432s, First byte at: 0.311071s
[2025-05-07 19:14:00] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 07 May 2025 23:14:00 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Thu, 08 May 2025 00:14:00 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-05-07 19:14:03] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2025-05-07 19:14:03] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-07 19:14:03] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-05-07 19:14:03] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-07 19:14:03] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-05-07 19:14:03] [INFO] [OmnipathR] Cache item `b10176737ba43d460b13709623189f3911123779` version 1: status changed from `unknown` to `started`.
[2025-05-07 19:14:03] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/b10176737ba43d460b13709623189f3911123779-1.rds`.
[2025-05-07 19:14:03] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/b10176737ba43d460b13709623189f3911123779-1.rds`.
[2025-05-07 19:14:03] [INFO] [OmnipathR] Download ready [key=b10176737ba43d460b13709623189f3911123779, version=1]
[2025-05-07 19:14:03] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-07 19:14:03] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-05-07 19:14:03] [INFO] [OmnipathR] Cache item `b10176737ba43d460b13709623189f3911123779` version 1: status changed from `started` to `ready`.
[2025-05-07 19:14:04] [SUCCESS] [OmnipathR] Downloaded 64958 interactions.
[2025-05-07 19:14:04] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-05-07 19:14:04] [TRACE] [OmnipathR] Arguments for OmniPath query: [genesymbols=TRUE,resources=CollecTRI,strict_evidences=TRUE,query_type=interactions,datasets=tf_mirna]
[2025-05-07 19:14:05] [TRACE] [OmnipathR] Organism(s): 9606
[2025-05-07 19:14:05] [TRACE] [OmnipathR] Orthology targets:
[2025-05-07 19:14:05] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-05-07 19:14:05] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-05-07 19:14:05] [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`
[2025-05-07 19:14:05] [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`
[2025-05-07 19:14:05] [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`
[2025-05-07 19:14:05] [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`
[2025-05-07 19:14:05] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2025-05-07 19:14:05] [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`
[2025-05-07 19:14:05] [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`
[2025-05-07 19:14:05] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2025-05-07 19:14:05] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-05-07 19:14:06] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2025-05-07 19:14:06] [TRACE] [OmnipathR] Downloaded 9.5 Kb in 0.233537s from omnipathdb.org (40.6 Kb/s); Redirect: 0s, DNS look up: 0.00124s, Connection: 0.002249s, Pretransfer: 0.15631s, First byte at: 0.233382s
[2025-05-07 19:14:06] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 07 May 2025 23:14:06 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Thu, 08 May 2025 00:14:06 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-05-07 19:14:06] [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`
[2025-05-07 19:14:06] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-07 19:14:06] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-05-07 19:14:06] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-07 19:14:06] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-05-07 19:14:06] [INFO] [OmnipathR] Cache item `f7d34500401ba98803b7d2b26c48f64cee1eea1b` version 1: status changed from `unknown` to `started`.
[2025-05-07 19:14:06] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/f7d34500401ba98803b7d2b26c48f64cee1eea1b-1.rds`.
[2025-05-07 19:14:06] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/f7d34500401ba98803b7d2b26c48f64cee1eea1b-1.rds`.
[2025-05-07 19:14:06] [INFO] [OmnipathR] Download ready [key=f7d34500401ba98803b7d2b26c48f64cee1eea1b, version=1]
[2025-05-07 19:14:06] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-07 19:14:06] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-05-07 19:14:06] [INFO] [OmnipathR] Cache item `f7d34500401ba98803b7d2b26c48f64cee1eea1b` version 1: status changed from `started` to `ready`.
[2025-05-07 19:14:06] [TRACE] [OmnipathR] Converting JSON column `evidences` to list.
[2025-05-07 19:14:06] [TRACE] [OmnipathR] Restricting interaction records to datasets: tf_mirna; and resources: CollecTRI
[2025-05-07 19:14:06] [TRACE] [OmnipathR] Filtering evidence columns: positive, negative, directed, undirected; to datasets: tf_mirna; and resources: CollecTRI; excluding resources: none
[2025-05-07 19:14:07] [SUCCESS] [OmnipathR] Downloaded 232 interactions.
[2025-05-07 19:14:07] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-05-07 19:14:07] [TRACE] [OmnipathR] Arguments for OmniPath query: [loops=TRUE,organisms=9606,genesymbols=TRUE,query_type=interactions,datasets=collectri]
[2025-05-07 19:14:07] [TRACE] [OmnipathR] Organism(s): 9606
[2025-05-07 19:14:07] [TRACE] [OmnipathR] Orthology targets:
[2025-05-07 19:14:07] [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`
[2025-05-07 19:14:07] [TRACE] [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/b10176737ba43d460b13709623189f3911123779-1.rds`.
[2025-05-07 19:14:07] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2025-05-07 19:14:08] [SUCCESS] [OmnipathR] Loaded 64958 interactions from cache.
[2025-05-07 19:14:08] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-05-07 19:14:08] [TRACE] [OmnipathR] Arguments for OmniPath query: [genesymbols=TRUE,resources=CollecTRI,strict_evidences=TRUE,query_type=interactions,datasets=tf_mirna]
[2025-05-07 19:14:08] [TRACE] [OmnipathR] Organism(s): 9606
[2025-05-07 19:14:08] [TRACE] [OmnipathR] Orthology targets:
[2025-05-07 19:14:09] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-05-07 19:14:09] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-05-07 19:14:09] [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`
[2025-05-07 19:14:09] [TRACE] [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/f7d34500401ba98803b7d2b26c48f64cee1eea1b-1.rds`.
[2025-05-07 19:14:09] [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`
[2025-05-07 19:14:09] [TRACE] [OmnipathR] Converting JSON column `evidences` to list.
[2025-05-07 19:14:09] [TRACE] [OmnipathR] Restricting interaction records to datasets: tf_mirna; and resources: CollecTRI
[2025-05-07 19:14:09] [TRACE] [OmnipathR] Filtering evidence columns: positive, negative, directed, undirected; to datasets: tf_mirna; and resources: CollecTRI; excluding resources: none
[2025-05-07 19:14:09] [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 1 | WARN 18 | SKIP 0 | PASS 34 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── 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 1 | WARN 18 | SKIP 0 | PASS 34 ]
Error: Test failures
Execution halted
decoupleR.Rcheck/decoupleR-Ex.timings
| name | user | system | elapsed | |
| check_corr | 0.032 | 0.006 | 0.037 | |
| convert_f_defaults | 0.020 | 0.008 | 0.028 | |
| decouple | 0 | 0 | 0 | |
| dot-fit_preprocessing | 0.008 | 0.001 | 0.009 | |
| extract_sets | 0.007 | 0.000 | 0.007 | |
| filt_minsize | 0.011 | 0.001 | 0.012 | |
| get_collectri | 3.305 | 0.409 | 9.522 | |
| get_dorothea | 8.139 | 0.610 | 14.825 | |
| get_profile_of | 0 | 0 | 0 | |
| get_progeny | 2.909 | 0.252 | 10.959 | |
| get_resource | 0.444 | 0.057 | 2.413 | |
| get_toy_data | 0.001 | 0.000 | 0.001 | |
| intersect_regulons | 0.016 | 0.005 | 0.023 | |
| pipe | 0 | 0 | 0 | |
| pivot_wider_profile | 0.000 | 0.000 | 0.001 | |
| randomize_matrix | 0 | 0 | 0 | |
| rename_net | 0.023 | 0.006 | 0.030 | |
| run_aucell | 4.710 | 1.903 | 9.900 | |
| run_consensus | 0.670 | 0.253 | 1.335 | |
| run_fgsea | 12.485 | 0.731 | 15.595 | |
| run_gsva | 0.857 | 0.717 | 3.388 | |
| run_mdt | 0.089 | 0.038 | 0.219 | |
| run_mlm | 0.042 | 0.015 | 0.081 | |
| run_ora | 0.213 | 0.080 | 0.484 | |
| run_udt | 0.114 | 0.034 | 0.279 | |
| run_ulm | 0.034 | 0.013 | 0.077 | |
| run_viper | 0.383 | 0.368 | 1.149 | |
| run_wmean | 0.246 | 0.062 | 0.390 | |
| run_wsum | 0.277 | 0.072 | 0.409 | |
| show_methods | 0.020 | 0.007 | 0.039 | |
| show_resources | 0.021 | 0.006 | 0.753 | |
| tidyeval | 0 | 0 | 0 | |