Pau Badia-i-Mompel
| Snapshot Date: 2025-06-12 13:25 -0400 (Thu, 12 Jun 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 2025-06-13 12:08 -0400 (Fri, 13 Jun 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4797 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.0 (2025-04-11 ucrt) -- "How About a Twenty-Six" | 4538 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.0 Patched (2025-04-21 r88169) -- "How About a Twenty-Six" | 4571 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.0 Patched (2025-04-21 r88169) -- "How About a Twenty-Six" | 4515 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4483 |
| 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 528/2309 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| decoupleR 2.15.0 (landing page) Pau Badia-i-Mompel
| nebbiolo2 | Linux (Ubuntu 24.04.2 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: 2025-06-12 20:12:54 -0400 (Thu, 12 Jun 2025) |
| EndedAt: 2025-06-12 20:21:39 -0400 (Thu, 12 Jun 2025) |
| EllapsedTime: 525.3 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: decoupleR.Rcheck |
| Warnings: 1 |
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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_2.15.0.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: x86_64-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 Monterey 12.7.6
* 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
[2025-06-12 20:13:30] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-06-12 20:13:30] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-06-12 20:13:30] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-06-12 20:13:30] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2025-06-12 20:13:30] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-06-12
[2025-06-12 20:13:30] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-06-12 19:18:33 UTC; unix
[2025-06-12 20:13:30] [INFO] [OmnipathR] Package `OmnipathR` version: 3.17.0
[2025-06-12 20:13:30] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-06-12 20:13:30] [INFO] [OmnipathR] Session info: [version=R version 4.5.0 Patched (2025-04-21 r88169); os=macOS Monterey 12.7.6; system=x86_64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-06-12; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown); quarto=NA]
[2025-06-12 20:13:30] [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=70.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1]
[2025-06-12 20:13:31] [INFO] [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); annotate 1.87.0(2025-06-12); AnnotationDbi 1.71.0(2025-06-12); AUCell 1.31.0(2025-06-12); backports 1.5.0(2024-05-23); beachmat 2.25.1(2025-06-12); Biobase 2.69.0(2025-06-12); BiocGenerics 0.55.0(2025-06-12); BiocParallel 1.43.3(2025-06-12); BiocSingular 1.25.0(2025-06-12); Biostrings 2.77.1(2025-06-12); 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 6.3.0(2025-06-06); data.table 1.17.4(2025-05-26); DBI 1.2.3(2024-06-02); decoupleR 2.15.0(2025-06-12); DelayedArray 0.35.1(2025-06-12); DelayedMatrixStats 1.31.0(2025-06-12); 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 0.1.4(2025-05-09); GenomeInfoDb 1.45.4(2025-06-12); GenomicRanges 1.61.0(2025-06-12); glue 1.8.0(2024-09-30); graph 1.87.0(2025-06-12); GSEABase 1.71.0(2025-06-12); GSVA 2.3.1(2025-06-12); h5mread 1.1.1(2025-06-12); HDF5Array 1.37.0(2025-06-12); 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(2025-06-12); irlba 2.3.5.1(2022-10-03); jsonlite 2.0.0(2025-03-27); KEGGREST 1.49.0(2025-06-12); 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(2025-06-12); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); OmnipathR 3.17.0(2025-06-12); parallelly 1.45.0(2025-06-02); 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 1.3.3(2025-05-29); 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 2.53.1(2025-06-12); rhdf5filters 1.21.0(2025-06-12); Rhdf5lib 1.31.0(2025-06-12); rjson 0.2.23(2024-09-16); rlang 1.1.6(2025-04-11); rmarkdown 2.29(2024-11-04); RSQLite 2.4.1(2025-06-08); rsvd 1.0.5(2021-04-16); rvest 1.0.4(2024-02-12); S4Arrays 1.9.1(2025-06-12); S4Vectors 0.47.0(2025-06-12); ScaledMatrix 1.17.0(2025-06-12); sessioninfo 1.2.3(2025-02-05); SingleCellExperiment 1.31.0(2025-06-12); SparseArray 1.9.0(2025-06-12); sparseMatrixStats 1.21.0(2025-06-12); SpatialExperiment 1.19.1(2025-06-12); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); SummarizedExperiment 1.39.0(2025-06-12); tibble 3.3.0(2025-06-08); 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(2025-06-12); 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(2025-06-12); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2025-06-12 20:13:31] [INFO] [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: LibreSSL/3.3.6 (SecureTransport); libz_version: 1.2.11; libssh_version: NA; libidn_version: NA; host: x86_64-apple-darwin22.6.0; 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
[2025-06-12 20:13:31] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-06-12 20:13:31] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-06-12 20:13:31] [TRACE] [OmnipathR] Contains 8 files.
[2025-06-12 20:13:31] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-06-12 20:13:31] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-06-12 20:13:31] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-06-12 20:13:31] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-06-12 20:13:31] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2025-06-12 20:13:31] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-06-12 20:13:31] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-06-12 20:13:31] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-06-12 20:13:31] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-06-12 20:13:31] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-06-12 20:13:31] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-06-12 20:13:31] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-06-12 20:13:31] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-06-12 20:13:31] [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
get_dorothea 25.523 1.977 30.132
run_fgsea 22.432 1.288 23.858
run_aucell 11.381 4.239 15.650
get_collectri 9.045 1.072 23.235
get_progeny 6.365 0.656 13.881
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 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-x86_64/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
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: x86_64-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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[2025-06-12 20:17:12] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-06-12 20:17:12] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-06-12 20:17:12] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-06-12 20:17:12] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2025-06-12 20:17:12] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-06-12
[2025-06-12 20:17:12] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-06-12 19:18:33 UTC; unix
[2025-06-12 20:17:12] [INFO] [OmnipathR] Package `OmnipathR` version: 3.17.0
[2025-06-12 20:17:12] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-06-12 20:17:13] [INFO] [OmnipathR] Session info: [version=R version 4.5.0 Patched (2025-04-21 r88169); os=macOS Monterey 12.7.6; system=x86_64, darwin20; ui=X11; language=C; collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-06-12; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown); quarto=NA]
[2025-06-12 20:17:13] [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=70.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1]
[2025-06-12 20:17:13] [INFO] [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); annotate 1.87.0(2025-06-12); AnnotationDbi 1.71.0(2025-06-12); AUCell 1.31.0(2025-06-12); backports 1.5.0(2024-05-23); beachmat 2.25.1(2025-06-12); Biobase 2.69.0(2025-06-12); BiocGenerics 0.55.0(2025-06-12); BiocParallel 1.43.3(2025-06-12); BiocSingular 1.25.0(2025-06-12); Biostrings 2.77.1(2025-06-12); 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 6.3.0(2025-06-06); data.table 1.17.4(2025-05-26); DBI 1.2.3(2024-06-02); decoupleR 2.15.0(2025-06-12); DelayedArray 0.35.1(2025-06-12); DelayedMatrixStats 1.31.0(2025-06-12); 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 1.35.2(2025-06-12); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); GenomeInfoDb 1.45.4(2025-06-12); GenomicRanges 1.61.0(2025-06-12); ggplot2 3.5.2(2025-04-09); glue 1.8.0(2024-09-30); graph 1.87.0(2025-06-12); GSEABase 1.71.0(2025-06-12); GSVA 2.3.1(2025-06-12); gtable 0.3.6(2024-10-25); h5mread 1.1.1(2025-06-12); HDF5Array 1.37.0(2025-06-12); 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(2025-06-12); irlba 2.3.5.1(2022-10-03); jsonlite 2.0.0(2025-03-27); KEGGREST 1.49.0(2025-06-12); 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(2025-06-12); 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(2025-06-12); parallelly 1.45.0(2025-06-02); 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 1.3.3(2025-05-29); 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 2.53.1(2025-06-12); rhdf5filters 1.21.0(2025-06-12); Rhdf5lib 1.31.0(2025-06-12); 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 2.4.1(2025-06-08); rsvd 1.0.5(2021-04-16); rvest 1.0.4(2024-02-12); S4Arrays 1.9.1(2025-06-12); S4Vectors 0.47.0(2025-06-12); ScaledMatrix 1.17.0(2025-06-12); 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(2025-06-12); SparseArray 1.9.0(2025-06-12); sparseMatrixStats 1.21.0(2025-06-12); SpatialExperiment 1.19.1(2025-06-12); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); SummarizedExperiment 1.39.0(2025-06-12); survival 3.8-3(2024-12-17); testthat 3.2.3(2025-01-13); tibble 3.3.0(2025-06-08); 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(2025-06-12); vctrs 0.6.5(2023-12-01); viper 1.43.0(2025-06-12); 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(2025-06-12); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2025-06-12 20:17:13] [INFO] [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: LibreSSL/3.3.6 (SecureTransport); libz_version: 1.2.11; libssh_version: NA; libidn_version: NA; host: x86_64-apple-darwin22.6.0; 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
[2025-06-12 20:17:13] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-06-12 20:17:13] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-06-12 20:17:13] [TRACE] [OmnipathR] Contains 8 files.
[2025-06-12 20:17:13] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-06-12 20:17:13] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-06-12 20:17:13] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-06-12 20:17:13] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-06-12 20:17:13] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2025-06-12 20:17:13] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-06-12 20:17:13] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-06-12 20:17:13] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-06-12 20:17:13] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-06-12 20:17:13] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-06-12 20:17:13] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-06-12 20:17:13] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-06-12 20:17:13] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-06-12 20:17:13] [TRACE] [OmnipathR] Cache locked: FALSE
[2025-06-12 20:17:14] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-06-12 20:17:14] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-06-12 20:17:15] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-06-12 20:17:15] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-06-12 20:17:15] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2025-06-12 20:17:15] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-06-12 20:17:15] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-06-12 20:17:15] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2025-06-12 20:17:15] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-06-12 20:17:15] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-06-12 20:17:15] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2025-06-12 20:17:15] [TRACE] [OmnipathR] Cache file path: /Users/biocbuild/Library/Caches/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2025-06-12 20:17:15] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2025-06-12 20:17:15] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`.
[2025-06-12 20:17:15] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2025-06-12 20:17:15] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2025-06-12 20:17:15] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-06-12 20:17:15] [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]
[2025-06-12 20:17:15] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-06-12 20:17:15] [TRACE] [OmnipathR] Sending HTTP request.
[2025-06-12 20:17:16] [TRACE] [OmnipathR] HTTP 200 (OK)
[2025-06-12 20:17:16] [TRACE] [OmnipathR] HTTP v2 GET: status 200.
[2025-06-12 20:17:16] [TRACE] [OmnipathR] Downloaded 31.2 Kb in 1.132874s from www.ensembl.org (27.6 Kb/s); Redirect: 0.82642s, DNS look up: 0.030156s, Connection: 0.031993s, Pretransfer: 0.707469s, First byte at: 1.10307s
[2025-06-12 20:17:16] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 302 Found; Date: Fri, 13 Jun 2025 00:17:16 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-p1m2-35.ebi.ac.uk; HTTP/2 302 ; date: Fri, 13 Jun 2025 00:17:16 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: Fri, 13 Jun 2025 00:17:16 GMT; content-type: text/html; charset=utf-8; content-length: 31990; server: Apache; set-cookie: redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT; set-cookie: redirect_mirror=no; path=/; expires=Sat, 14 Jun 2025 00:14:15 GMT; set-cookie: ENSEMBL_WWW_SESSION=43ef8b71b67a796a0a2e0562689a8757004ddcf6ee75cc009c485527; 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=Sat, 14 Jun 2025 00:14:15 GMT; set-cookie: ENSEMBL_WWW_SESSION=43ef8b71b67a796a0a2e0562689a8757004ddcf6ee75cc009c485527; 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-10-25-25-73.us-east-2.compute.internal
[2025-06-12 20:17:16] [TRACE] [OmnipathR] Response headers: [date=Fri, 13 Jun 2025 00:17:16 GMT,content-type=text/html; charset=utf-8,content-length=31990,server=Apache,set-cookie=redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT,set-cookie=redirect_mirror=no; path=/; expires=Sat, 14 Jun 2025 00:14:15 GMT,set-cookie=ENSEMBL_WWW_SESSION=43ef8b71b67a796a0a2e0562689a8757004ddcf6ee75cc009c485527; 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=Sat, 14 Jun 2025 00:14:15 GMT,set-cookie=ENSEMBL_WWW_SESSION=43ef8b71b67a796a0a2e0562689a8757004ddcf6ee75cc009c485527; 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-10-25-25-73.us-east-2.compute.internal]
[2025-06-12 20:17:18] [INFO] [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1]
[2025-06-12 20:17:18] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-06-12 20:17:18] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-06-12 20:17:18] [INFO] [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`.
[2025-06-12 20:17:18] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2025-06-12 20:17:18] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2025-06-12 20:17:18] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2025-06-12 20:17:18] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2025-06-12 20:17:18] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-06-12 20:17:18] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-06-12 20:17:18] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-06-12 20:17:18] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-06-12 20:17:18] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2025-06-12 20:17:18] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-06-12 20:17:18] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2025-06-12 20:17:18] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2025-06-12 20:17:18] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2025-06-12 20:17:18] [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]
[2025-06-12 20:17:19] [TRACE] [OmnipathR] HTTP v2 GET: status 200.
[2025-06-12 20:17:19] [TRACE] [OmnipathR] Downloaded 8.7 Kb in 0.422173s from omabrowser.org (20.6 Kb/s); Redirect: 0s, DNS look up: 0.001147s, Connection: 0.002196s, Pretransfer: 0.336515s, First byte at: 0.42185s
[2025-06-12 20:17:19] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; date: Fri, 13 Jun 2025 00:17:19 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
[2025-06-12 20:17:21] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-06-12 20:17:21] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1]
[2025-06-12 20:17:21] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-06-12 20:17:21] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-06-12 20:17:21] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.
[2025-06-12 20:17:21] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`.
[2025-06-12 20:17:21] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-06-12 20:17:21] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=TFcensus,query_type=annotations]
[2025-06-12 20:17:21] [TRACE] [OmnipathR] Organism(s): 9606
[2025-06-12 20:17:21] [TRACE] [OmnipathR] Orthology targets:
[2025-06-12 20:17:21] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-06-12 20:17:21] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-06-12 20:17:21] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2025-06-12 20:17:21] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2025-06-12 20:17:21] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2025-06-12 20:17:21] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2025-06-12 20:17:21] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2025-06-12 20:17:21] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2025-06-12 20:17:21] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2025-06-12 20:17:21] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2025-06-12 20:17:21] [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]
[2025-06-12 20:17:22] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2025-06-12 20:17:22] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.316293s from omnipathdb.org (49.5 Kb/s); Redirect: 0s, DNS look up: 0.001147s, Connection: 0.002156s, Pretransfer: 0.161177s, First byte at: 0.315909s
[2025-06-12 20:17:22] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Fri, 13 Jun 2025 00:17:22 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Fri, 13 Jun 2025 01:17:22 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-06-12 20:17:23] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2025-06-12 20:17:23] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-06-12 20:17:23] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-06-12 20:17:23] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-06-12 20:17:23] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-06-12 20:17:23] [INFO] [OmnipathR] Cache item `6f000d9b5edd9832b1c28754d1c3d9449c1c7490` version 1: status changed from `unknown` to `started`.
[2025-06-12 20:17:23] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/6f000d9b5edd9832b1c28754d1c3d9449c1c7490-1.rds`.
[2025-06-12 20:17:23] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/6f000d9b5edd9832b1c28754d1c3d9449c1c7490-1.rds`.
[2025-06-12 20:17:23] [INFO] [OmnipathR] Download ready [key=6f000d9b5edd9832b1c28754d1c3d9449c1c7490, version=1]
[2025-06-12 20:17:23] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-06-12 20:17:23] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-06-12 20:17:23] [INFO] [OmnipathR] Cache item `6f000d9b5edd9832b1c28754d1c3d9449c1c7490` version 1: status changed from `started` to `ready`.
[2025-06-12 20:17:23] [SUCCESS] [OmnipathR] Downloaded 3099 annotation records.
[2025-06-12 20:17:24] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-06-12 20:17:24] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-06-12 20:17:24] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-06-12 20:17:24] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=PROGENy,query_type=annotations]
[2025-06-12 20:17:24] [TRACE] [OmnipathR] Organism(s): 9606
[2025-06-12 20:17:24] [TRACE] [OmnipathR] Orthology targets:
[2025-06-12 20:17:24] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-06-12 20:17:24] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-06-12 20:17:24] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-06-12 20:17:24] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-06-12 20:17:24] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-06-12 20:17:24] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-06-12 20:17:24] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-06-12 20:17:24] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-06-12 20:17:24] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-06-12 20:17:24] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2025-06-12 20:17:24] [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]
[2025-06-12 20:17:25] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2025-06-12 20:17:25] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.311067s from omnipathdb.org (50.4 Kb/s); Redirect: 0s, DNS look up: 0.000971s, Connection: 0.001911s, Pretransfer: 0.157893s, First byte at: 0.310713s
[2025-06-12 20:17:25] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Fri, 13 Jun 2025 00:17:25 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Fri, 13 Jun 2025 01:17:25 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-06-12 20:17:34] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-06-12 20:17:34] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-06-12 20:17:34] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-06-12 20:17:34] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-06-12 20:17:34] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-06-12 20:17:34] [INFO] [OmnipathR] Cache item `3492392585ba05414edfae46801492076437d7e7` version 1: status changed from `unknown` to `started`.
[2025-06-12 20:17:34] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`.
[2025-06-12 20:17:36] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`.
[2025-06-12 20:17:36] [INFO] [OmnipathR] Download ready [key=3492392585ba05414edfae46801492076437d7e7, version=1]
[2025-06-12 20:17:37] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-06-12 20:17:37] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-06-12 20:17:37] [INFO] [OmnipathR] Cache item `3492392585ba05414edfae46801492076437d7e7` version 1: status changed from `started` to `ready`.
[2025-06-12 20:17:37] [SUCCESS] [OmnipathR] Downloaded 700239 annotation records.
[2025-06-12 20:17:39] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-06-12 20:17:39] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-06-12 20:17:39] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-06-12 20:17:39] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=PROGENy,query_type=annotations]
[2025-06-12 20:17:39] [TRACE] [OmnipathR] Organism(s): 9606
[2025-06-12 20:17:39] [TRACE] [OmnipathR] Orthology targets:
[2025-06-12 20:17:39] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-06-12 20:17:39] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-06-12 20:17:39] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-06-12 20:17:41] [TRACE] [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`.
[2025-06-12 20:17:41] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-06-12 20:17:41] [SUCCESS] [OmnipathR] Loaded 700239 annotation records from cache.
[2025-06-12 20:17:44] [INFO] [OmnipathR] Loading database `Orthologous Matrix (OMA) gene pairs`.
[2025-06-12 20:17:44] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2025-06-12 20:17:44] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2025-06-12 20:17:44] [TRACE] [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-06-12 20:17:44] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2025-06-12 20:17:44] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2025-06-12 20:17:44] [TRACE] [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-06-12 20:17:44] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2025-06-12 20:17:44] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/api/pairs/HUMAN/MOUSE/?format=tsv&xrefs=UniProtKB%2FSwissProt&per_page=2000000`.
[2025-06-12 20:17:44] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/api/pairs/HUMAN/MOUSE/?format=tsv&xrefs=UniProtKB%2FSwissProt&per_page=2000000`
[2025-06-12 20:17:44] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/api/pairs/HUMAN/MOUSE/?format=tsv&xrefs=UniProtKB%2FSwissProt&per_page=2000000`.
[2025-06-12 20:17:44] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-06-12 20:17:44] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-06-12 20:17:44] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-06-12 20:17:44] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-06-12 20:17:44] [INFO] [OmnipathR] Cache item `8f45b25c384d814c7de210e7ca40b7e35894e4f1` version 1: status changed from `unknown` to `started`.
[2025-06-12 20:17:44] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/8f45b25c384d814c7de210e7ca40b7e35894e4f1-1.rds`.
[2025-06-12 20:17:44] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/api/pairs/HUMAN/MOUSE/?format=tsv&xrefs=UniProtKB%2FSwissProt&per_page=2000000`
[2025-06-12 20:17:44] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/api/pairs/HUMAN/MOUSE/?format=tsv&xrefs=UniProtKB%2FSwissProt&per_page=2000000`
[2025-06-12 20:17:44] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2025-06-12 20:17:44] [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]
[2025-06-12 20:18:10] [TRACE] [OmnipathR] HTTP v2 GET: status 200.
[2025-06-12 20:18:10] [TRACE] [OmnipathR] Downloaded 11.1 Kb in 25.612278s from omabrowser.org (442 bytes/s); Redirect: 0s, DNS look up: 0.00137s, Connection: 0.002219s, Pretransfer: 0.170903s, First byte at: 25.612105s
[2025-06-12 20:18:10] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; date: Fri, 13 Jun 2025 00:18:10 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_2025-06-13_001808.tsv; x-frame-options: SAMEORIGIN; set-cookie: __matomo=1227dd34b549e26b; expires=Sun, 13-Jun-2027 00:18:10 UTC; Path=/
[2025-06-12 20:18:13] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/8f45b25c384d814c7de210e7ca40b7e35894e4f1-1.rds`.
[2025-06-12 20:18:13] [INFO] [OmnipathR] Download ready [key=8f45b25c384d814c7de210e7ca40b7e35894e4f1, version=1]
[2025-06-12 20:18:13] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-06-12 20:18:13] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-06-12 20:18:13] [INFO] [OmnipathR] Cache item `8f45b25c384d814c7de210e7ca40b7e35894e4f1` version 1: status changed from `started` to `ready`.
[2025-06-12 20:18:13] [TRACE] [OmnipathR] ID translation table: from `uniprot_entry` to `uniprot`, using `uniprot`.
[2025-06-12 20:18:13] [TRACE] [OmnipathR] Creating ID mapping table from `id` to `accession`, for organism 9606 (only reviewed: TRUE)
[2025-06-12 20:18:13] [TRACE] [OmnipathR] Loading all UniProt records for organism 9606 (only reviewed: TRUE); fields: id,accession
[2025-06-12 20:18:13] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2025-06-12 20:18:13] [TRACE] [OmnipathR] Looking up in cache: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:9606%20AND%20reviewed:true`.
[2025-06-12 20:18:13] [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`
[2025-06-12 20:18:13] [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`.
[2025-06-12 20:18:13] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-06-12 20:18:13] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-06-12 20:18:13] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-06-12 20:18:13] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-06-12 20:18:13] [INFO] [OmnipathR] Cache item `6558a1824894a625b8e3f80538cd3aa6e8a44379` version 1: status changed from `unknown` to `started`.
[2025-06-12 20:18:13] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/6558a1824894a625b8e3f80538cd3aa6e8a44379-1.rds`.
[2025-06-12 20:18:13] [INFO] [OmnipathR] Retrieving URL: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:9606%20AND%20reviewed:true`
[2025-06-12 20:18:13] [TRACE] [OmnipathR] Attempt 1/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:9606%20AND%20reviewed:true`
[2025-06-12 20:18:13] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2025-06-12 20:18:13] [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]
[2025-06-12 20:18:14] [TRACE] [OmnipathR] HTTP v2 GET: status 200.
[2025-06-12 20:18:14] [TRACE] [OmnipathR] Downloaded 31 bytes in 1.321814s from rest.uniprot.org (23 bytes/s); Redirect: 0s, DNS look up: 0.015682s, Connection: 0.016588s, Pretransfer: 0.543374s, First byte at: 1.31145s
[2025-06-12 20:18:15] [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: Fri, 13 Jun 2025 00:18:15 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
[2025-06-12 20:18:42] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/6558a1824894a625b8e3f80538cd3aa6e8a44379-1.rds`.
[2025-06-12 20:18:42] [INFO] [OmnipathR] Download ready [key=6558a1824894a625b8e3f80538cd3aa6e8a44379, version=1]
[2025-06-12 20:18:42] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-06-12 20:18:42] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-06-12 20:18:42] [INFO] [OmnipathR] Cache item `6558a1824894a625b8e3f80538cd3aa6e8a44379` version 1: status changed from `started` to `ready`.
[2025-06-12 20:18:42] [SUCCESS] [OmnipathR] UniProt (rest.uniprot.org): downloaded 20421 records
[2025-06-12 20:18:42] [TRACE] [OmnipathR] Translating complexes: 0 complexes in data.
[2025-06-12 20:18:42] [TRACE] [OmnipathR] 0 complexes after removing the ones mapping to more than 1 items in target identifier space.
[2025-06-12 20:18:42] [TRACE] [OmnipathR] Translated 0 complexes to 0.
[2025-06-12 20:18:42] [TRACE] [OmnipathR] 13774 rows before translation, 13774 uniprot_entry IDs in column `id_organism_a`.
[2025-06-12 20:18:42] [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`.
[2025-06-12 20:18:42] [TRACE] [OmnipathR] ID translation table: from `uniprot_entry` to `uniprot`, using `uniprot`.
[2025-06-12 20:18:43] [TRACE] [OmnipathR] Creating ID mapping table from `id` to `accession`, for organism 10090 (only reviewed: TRUE)
[2025-06-12 20:18:43] [TRACE] [OmnipathR] Loading all UniProt records for organism 10090 (only reviewed: TRUE); fields: id,accession
[2025-06-12 20:18:43] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2025-06-12 20:18:43] [TRACE] [OmnipathR] Looking up in cache: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:10090%20AND%20reviewed:true`.
[2025-06-12 20:18:43] [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`
[2025-06-12 20:18:43] [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`.
[2025-06-12 20:18:43] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-06-12 20:18:43] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-06-12 20:18:43] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-06-12 20:18:43] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-06-12 20:18:43] [INFO] [OmnipathR] Cache item `43ea5f2cdaa9ac7e0e114371af97235cdddd776f` version 1: status changed from `unknown` to `started`.
[2025-06-12 20:18:43] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/43ea5f2cdaa9ac7e0e114371af97235cdddd776f-1.rds`.
[2025-06-12 20:18:43] [INFO] [OmnipathR] Retrieving URL: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:10090%20AND%20reviewed:true`
[2025-06-12 20:18:43] [TRACE] [OmnipathR] Attempt 1/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:10090%20AND%20reviewed:true`
[2025-06-12 20:18:43] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2025-06-12 20:18:43] [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]
[2025-06-12 20:18:44] [TRACE] [OmnipathR] HTTP v2 GET: status 200.
[2025-06-12 20:18:44] [TRACE] [OmnipathR] Downloaded 31 bytes in 1.641403s from rest.uniprot.org (18 bytes/s); Redirect: 0s, DNS look up: 0.001182s, Connection: 0.002084s, Pretransfer: 0.492395s, First byte at: 1.641266s
[2025-06-12 20:18:44] [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: Fri, 13 Jun 2025 00:18:44 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
[2025-06-12 20:19:07] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/43ea5f2cdaa9ac7e0e114371af97235cdddd776f-1.rds`.
[2025-06-12 20:19:07] [INFO] [OmnipathR] Download ready [key=43ea5f2cdaa9ac7e0e114371af97235cdddd776f, version=1]
[2025-06-12 20:19:07] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-06-12 20:19:07] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-06-12 20:19:07] [INFO] [OmnipathR] Cache item `43ea5f2cdaa9ac7e0e114371af97235cdddd776f` version 1: status changed from `started` to `ready`.
[2025-06-12 20:19:07] [SUCCESS] [OmnipathR] UniProt (rest.uniprot.org): downloaded 17230 records
[2025-06-12 20:19:07] [TRACE] [OmnipathR] Translating complexes: 0 complexes in data.
[2025-06-12 20:19:07] [TRACE] [OmnipathR] 0 complexes after removing the ones mapping to more than 1 items in target identifier space.
[2025-06-12 20:19:07] [TRACE] [OmnipathR] Translated 0 complexes to 0.
[2025-06-12 20:19:08] [TRACE] [OmnipathR] 13774 rows before translation, 13773 uniprot_entry IDs in column `id_organism_b`.
[2025-06-12 20:19:08] [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`.
[2025-06-12 20:19:08] [INFO] [OmnipathR] Loaded database `Orthologous Matrix (OMA) gene pairs`.
[2025-06-12 20:19:08] [TRACE] [OmnipathR] ID translation table: from `uniprot` to `genesymbol`, using `uniprot`.
[2025-06-12 20:19:08] [TRACE] [OmnipathR] Creating ID mapping table from `accession` to `gene_primary`, for organism 10090 (only reviewed: TRUE)
[2025-06-12 20:19:08] [TRACE] [OmnipathR] Loading all UniProt records for organism 10090 (only reviewed: TRUE); fields: accession,gene_primary
[2025-06-12 20:19:08] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2025-06-12 20:19:08] [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`.
[2025-06-12 20:19:08] [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`
[2025-06-12 20:19:08] [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`.
[2025-06-12 20:19:08] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-06-12 20:19:08] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-06-12 20:19:08] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-06-12 20:19:08] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-06-12 20:19:08] [INFO] [OmnipathR] Cache item `3ec84ba713c02573704adb50f1a94dab684df34b` version 1: status changed from `unknown` to `started`.
[2025-06-12 20:19:08] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/3ec84ba713c02573704adb50f1a94dab684df34b-1.rds`.
[2025-06-12 20:19:08] [INFO] [OmnipathR] Retrieving URL: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:10090%20AND%20reviewed:true`
[2025-06-12 20:19:08] [TRACE] [OmnipathR] Attempt 1/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:10090%20AND%20reviewed:true`
[2025-06-12 20:19:08] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2025-06-12 20:19:08] [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]
[2025-06-12 20:19:09] [TRACE] [OmnipathR] HTTP v2 GET: status 200.
[2025-06-12 20:19:09] [TRACE] [OmnipathR] Downloaded 43 bytes in 1.489524s from rest.uniprot.org (28 bytes/s); Redirect: 0s, DNS look up: 0.001245s, Connection: 0.002298s, Pretransfer: 0.488924s, First byte at: 1.489387s
[2025-06-12 20:19:09] [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: Fri, 13 Jun 2025 00:19:09 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
[2025-06-12 20:19:33] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/3ec84ba713c02573704adb50f1a94dab684df34b-1.rds`.
[2025-06-12 20:19:33] [INFO] [OmnipathR] Download ready [key=3ec84ba713c02573704adb50f1a94dab684df34b, version=1]
[2025-06-12 20:19:33] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-06-12 20:19:33] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-06-12 20:19:33] [INFO] [OmnipathR] Cache item `3ec84ba713c02573704adb50f1a94dab684df34b` version 1: status changed from `started` to `ready`.
[2025-06-12 20:19:33] [SUCCESS] [OmnipathR] UniProt (rest.uniprot.org): downloaded 17230 records
[2025-06-12 20:19:34] [TRACE] [OmnipathR] Translating complexes: 0 complexes in data.
[2025-06-12 20:19:34] [TRACE] [OmnipathR] 0 complexes after removing the ones mapping to more than 1 items in target identifier space.
[2025-06-12 20:19:34] [TRACE] [OmnipathR] Translated 0 complexes to 0.
[2025-06-12 20:19:34] [TRACE] [OmnipathR] 164123 rows before translation, 12872 uniprot IDs in column `uniprot`.
[2025-06-12 20:19:34] [TRACE] [OmnipathR] 164123 rows after translation; translated 12872 `uniprot` IDs in column `uniprot` to 12786 `genesymbol` IDs in column `genesymbol`.
[2025-06-12 20:19:34] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-06-12 20:19:34] [TRACE] [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B,C,D],genesymbols=TRUE,organisms=9606,query_type=interactions,datasets=dorothea]
[2025-06-12 20:19:34] [TRACE] [OmnipathR] Organism(s): 9606
[2025-06-12 20:19:34] [TRACE] [OmnipathR] Orthology targets:
[2025-06-12 20:19:34] [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`
[2025-06-12 20:19:34] [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`
[2025-06-12 20:19:34] [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`
[2025-06-12 20:19:34] [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`
[2025-06-12 20:19:34] [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`
[2025-06-12 20:19:34] [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`
[2025-06-12 20:19:34] [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`
[2025-06-12 20:19:34] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2025-06-12 20:19:34] [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]
[2025-06-12 20:19:35] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2025-06-12 20:19:35] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.480798s from omnipathdb.org (32.6 Kb/s); Redirect: 0s, DNS look up: 0.001176s, Connection: 0.002031s, Pretransfer: 0.325846s, First byte at: 0.480421s
[2025-06-12 20:19:35] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Fri, 13 Jun 2025 00:19:35 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Fri, 13 Jun 2025 01:19:35 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-06-12 20:19:39] [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`
[2025-06-12 20:19:39] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-06-12 20:19:39] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-06-12 20:19:39] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-06-12 20:19:39] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-06-12 20:19:39] [INFO] [OmnipathR] Cache item `46d37339bbc3f9a05bb89ccb79278cf1233f5cdf` version 1: status changed from `unknown` to `started`.
[2025-06-12 20:19:39] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/46d37339bbc3f9a05bb89ccb79278cf1233f5cdf-1.rds`.
[2025-06-12 20:19:41] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/46d37339bbc3f9a05bb89ccb79278cf1233f5cdf-1.rds`.
[2025-06-12 20:19:41] [INFO] [OmnipathR] Download ready [key=46d37339bbc3f9a05bb89ccb79278cf1233f5cdf, version=1]
[2025-06-12 20:19:41] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-06-12 20:19:41] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-06-12 20:19:41] [INFO] [OmnipathR] Cache item `46d37339bbc3f9a05bb89ccb79278cf1233f5cdf` version 1: status changed from `started` to `ready`.
[2025-06-12 20:19:52] [SUCCESS] [OmnipathR] Downloaded 278830 interactions.
[2025-06-12 20:20:04] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-06-12 20:20:04] [TRACE] [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B,C,D],genesymbols=TRUE,organisms=10090,query_type=interactions,datasets=dorothea]
[2025-06-12 20:20:04] [TRACE] [OmnipathR] Organism(s): 10090
[2025-06-12 20:20:04] [TRACE] [OmnipathR] Orthology targets:
[2025-06-12 20:20:04] [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`
[2025-06-12 20:20:04] [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`
[2025-06-12 20:20:04] [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`
[2025-06-12 20:20:04] [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`
[2025-06-12 20:20:04] [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`
[2025-06-12 20:20:04] [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`
[2025-06-12 20:20:04] [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`
[2025-06-12 20:20:04] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2025-06-12 20:20:04] [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]
[2025-06-12 20:20:04] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2025-06-12 20:20:04] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.32126s from omnipathdb.org (48.8 Kb/s); Redirect: 0s, DNS look up: 0.00118s, Connection: 0.002133s, Pretransfer: 0.163145s, First byte at: 0.32092s
[2025-06-12 20:20:04] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Fri, 13 Jun 2025 00:20:04 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Fri, 13 Jun 2025 01:20:04 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-06-12 20:20:09] [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`
[2025-06-12 20:20:09] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-06-12 20:20:09] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-06-12 20:20:09] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-06-12 20:20:09] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-06-12 20:20:09] [INFO] [OmnipathR] Cache item `ff347dedf78ef5e38c9c6d8eed291fa901aa3791` version 1: status changed from `unknown` to `started`.
[2025-06-12 20:20:09] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/ff347dedf78ef5e38c9c6d8eed291fa901aa3791-1.rds`.
[2025-06-12 20:20:10] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/ff347dedf78ef5e38c9c6d8eed291fa901aa3791-1.rds`.
[2025-06-12 20:20:10] [INFO] [OmnipathR] Download ready [key=ff347dedf78ef5e38c9c6d8eed291fa901aa3791, version=1]
[2025-06-12 20:20:10] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-06-12 20:20:10] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-06-12 20:20:10] [INFO] [OmnipathR] Cache item `ff347dedf78ef5e38c9c6d8eed291fa901aa3791` version 1: status changed from `started` to `ready`.
[2025-06-12 20:20:20] [SUCCESS] [OmnipathR] Downloaded 234298 interactions.
[2025-06-12 20:20:30] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-06-12 20:20:30] [TRACE] [OmnipathR] Arguments for OmniPath query: [loops=TRUE,organisms=9606,genesymbols=TRUE,query_type=interactions,datasets=collectri]
[2025-06-12 20:20:30] [TRACE] [OmnipathR] Organism(s): 9606
[2025-06-12 20:20:30] [TRACE] [OmnipathR] Orthology targets:
[2025-06-12 20:20:30] [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`
[2025-06-12 20:20:30] [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`
[2025-06-12 20:20:30] [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`
[2025-06-12 20:20:30] [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`
[2025-06-12 20:20:30] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2025-06-12 20:20:30] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2025-06-12 20:20:30] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2025-06-12 20:20:30] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2025-06-12 20:20:30] [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]
[2025-06-12 20:20:31] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2025-06-12 20:20:31] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.469999s from omnipathdb.org (33.3 Kb/s); Redirect: 0s, DNS look up: 0.000991s, Connection: 0.001961s, Pretransfer: 0.31514s, First byte at: 0.469585s
[2025-06-12 20:20:31] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Fri, 13 Jun 2025 00:20:31 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Fri, 13 Jun 2025 01:20:31 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-06-12 20:20:34] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2025-06-12 20:20:34] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-06-12 20:20:34] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-06-12 20:20:34] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-06-12 20:20:34] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-06-12 20:20:34] [INFO] [OmnipathR] Cache item `b10176737ba43d460b13709623189f3911123779` version 1: status changed from `unknown` to `started`.
[2025-06-12 20:20:34] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/b10176737ba43d460b13709623189f3911123779-1.rds`.
[2025-06-12 20:20:35] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/b10176737ba43d460b13709623189f3911123779-1.rds`.
[2025-06-12 20:20:35] [INFO] [OmnipathR] Download ready [key=b10176737ba43d460b13709623189f3911123779, version=1]
[2025-06-12 20:20:35] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-06-12 20:20:35] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-06-12 20:20:35] [INFO] [OmnipathR] Cache item `b10176737ba43d460b13709623189f3911123779` version 1: status changed from `started` to `ready`.
[2025-06-12 20:20:38] [SUCCESS] [OmnipathR] Downloaded 64958 interactions.
[2025-06-12 20:20:38] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-06-12 20:20:38] [TRACE] [OmnipathR] Arguments for OmniPath query: [genesymbols=TRUE,resources=CollecTRI,strict_evidences=TRUE,query_type=interactions,datasets=tf_mirna]
[2025-06-12 20:20:38] [TRACE] [OmnipathR] Organism(s): 9606
[2025-06-12 20:20:38] [TRACE] [OmnipathR] Orthology targets:
[2025-06-12 20:20:38] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-06-12 20:20:38] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-06-12 20:20:38] [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`
[2025-06-12 20:20:38] [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`
[2025-06-12 20:20:38] [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`
[2025-06-12 20:20:38] [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`
[2025-06-12 20:20:38] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2025-06-12 20:20:38] [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`
[2025-06-12 20:20:38] [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`
[2025-06-12 20:20:38] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2025-06-12 20:20:38] [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]
[2025-06-12 20:20:39] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2025-06-12 20:20:39] [TRACE] [OmnipathR] Downloaded 9.5 Kb in 0.235333s from omnipathdb.org (40.3 Kb/s); Redirect: 0s, DNS look up: 0.001056s, Connection: 0.002004s, Pretransfer: 0.157903s, First byte at: 0.235032s
[2025-06-12 20:20:39] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Fri, 13 Jun 2025 00:20:39 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Fri, 13 Jun 2025 01:20:39 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-06-12 20:20:40] [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`
[2025-06-12 20:20:40] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-06-12 20:20:40] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-06-12 20:20:40] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-06-12 20:20:40] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-06-12 20:20:40] [INFO] [OmnipathR] Cache item `f7d34500401ba98803b7d2b26c48f64cee1eea1b` version 1: status changed from `unknown` to `started`.
[2025-06-12 20:20:40] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/f7d34500401ba98803b7d2b26c48f64cee1eea1b-1.rds`.
[2025-06-12 20:20:40] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/f7d34500401ba98803b7d2b26c48f64cee1eea1b-1.rds`.
[2025-06-12 20:20:40] [INFO] [OmnipathR] Download ready [key=f7d34500401ba98803b7d2b26c48f64cee1eea1b, version=1]
[2025-06-12 20:20:40] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-06-12 20:20:40] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-06-12 20:20:40] [INFO] [OmnipathR] Cache item `f7d34500401ba98803b7d2b26c48f64cee1eea1b` version 1: status changed from `started` to `ready`.
[2025-06-12 20:20:40] [TRACE] [OmnipathR] Converting JSON column `evidences` to list.
[2025-06-12 20:20:40] [TRACE] [OmnipathR] Restricting interaction records to datasets: tf_mirna; and resources: CollecTRI
[2025-06-12 20:20:40] [TRACE] [OmnipathR] Filtering evidence columns: positive, negative, directed, undirected; to datasets: tf_mirna; and resources: CollecTRI; excluding resources: none
[2025-06-12 20:20:41] [SUCCESS] [OmnipathR] Downloaded 232 interactions.
[2025-06-12 20:20:41] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-06-12 20:20:41] [TRACE] [OmnipathR] Arguments for OmniPath query: [loops=TRUE,organisms=9606,genesymbols=TRUE,query_type=interactions,datasets=collectri]
[2025-06-12 20:20:41] [TRACE] [OmnipathR] Organism(s): 9606
[2025-06-12 20:20:41] [TRACE] [OmnipathR] Orthology targets:
[2025-06-12 20:20:41] [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`
[2025-06-12 20:20:41] [TRACE] [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/b10176737ba43d460b13709623189f3911123779-1.rds`.
[2025-06-12 20:20:41] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2025-06-12 20:20:46] [SUCCESS] [OmnipathR] Loaded 64958 interactions from cache.
[2025-06-12 20:20:46] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-06-12 20:20:46] [TRACE] [OmnipathR] Arguments for OmniPath query: [genesymbols=TRUE,resources=CollecTRI,strict_evidences=TRUE,query_type=interactions,datasets=tf_mirna]
[2025-06-12 20:20:46] [TRACE] [OmnipathR] Organism(s): 9606
[2025-06-12 20:20:46] [TRACE] [OmnipathR] Orthology targets:
[2025-06-12 20:20:46] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-06-12 20:20:46] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-06-12 20:20:46] [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`
[2025-06-12 20:20:46] [TRACE] [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/f7d34500401ba98803b7d2b26c48f64cee1eea1b-1.rds`.
[2025-06-12 20:20:46] [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`
[2025-06-12 20:20:46] [TRACE] [OmnipathR] Converting JSON column `evidences` to list.
[2025-06-12 20:20:47] [TRACE] [OmnipathR] Restricting interaction records to datasets: tf_mirna; and resources: CollecTRI
[2025-06-12 20:20:47] [TRACE] [OmnipathR] Filtering evidence columns: positive, negative, directed, undirected; to datasets: tf_mirna; and resources: CollecTRI; excluding resources: none
[2025-06-12 20:20:48] [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 0 | WARN 18 | SKIP 0 | PASS 35 ]
[ FAIL 0 | WARN 18 | SKIP 0 | PASS 35 ]
>
> proc.time()
user system elapsed
171.854 19.710 319.642
decoupleR.Rcheck/decoupleR-Ex.timings
| name | user | system | elapsed | |
| check_corr | 0.095 | 0.016 | 0.111 | |
| convert_f_defaults | 0.031 | 0.004 | 0.034 | |
| decouple | 0.001 | 0.001 | 0.002 | |
| dot-fit_preprocessing | 0.022 | 0.003 | 0.025 | |
| extract_sets | 0.027 | 0.001 | 0.029 | |
| filt_minsize | 0.043 | 0.001 | 0.044 | |
| get_collectri | 9.045 | 1.072 | 23.235 | |
| get_dorothea | 25.523 | 1.977 | 30.132 | |
| get_profile_of | 0.000 | 0.001 | 0.000 | |
| get_progeny | 6.365 | 0.656 | 13.881 | |
| get_resource | 0.824 | 0.093 | 2.602 | |
| get_toy_data | 0.003 | 0.001 | 0.004 | |
| intersect_regulons | 0.035 | 0.008 | 0.043 | |
| pipe | 0.000 | 0.000 | 0.001 | |
| pivot_wider_profile | 0.000 | 0.001 | 0.000 | |
| randomize_matrix | 0.000 | 0.000 | 0.001 | |
| rename_net | 0.05 | 0.01 | 0.06 | |
| run_aucell | 11.381 | 4.239 | 15.650 | |
| run_consensus | 2.661 | 0.737 | 3.451 | |
| run_fgsea | 22.432 | 1.288 | 23.858 | |
| run_gsva | 2.517 | 1.084 | 4.071 | |
| run_mdt | 0.252 | 0.072 | 0.462 | |
| run_mlm | 0.098 | 0.017 | 0.115 | |
| run_ora | 0.518 | 0.088 | 0.651 | |
| run_udt | 0.385 | 0.066 | 0.525 | |
| run_ulm | 0.097 | 0.019 | 0.115 | |
| run_viper | 1.188 | 0.555 | 1.766 | |
| run_wmean | 1.003 | 0.126 | 1.136 | |
| run_wsum | 1.057 | 0.127 | 1.188 | |
| show_methods | 0.065 | 0.016 | 0.089 | |
| show_resources | 0.072 | 0.010 | 0.715 | |
| tidyeval | 0.000 | 0.001 | 0.000 | |