Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-08-09 12:08 -0400 (Sat, 09 Aug 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4818 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4553 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4595 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4537 |
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 529/2317 | 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 | |||||||||
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: 2025-08-08 20:27:29 -0400 (Fri, 08 Aug 2025) |
EndedAt: 2025-08-08 20:37:10 -0400 (Fri, 08 Aug 2025) |
EllapsedTime: 581.1 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: decoupleR.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### 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 ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/decoupleR.Rcheck’ * using R version 4.5.1 (2025-06-13) * 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 [2025-08-08 20:28:07] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-08 20:28:07] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-08 20:28:07] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-08-08 20:28:07] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-08-08 20:28:07] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-08-08 [2025-08-08 20:28:07] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-08-08 19:10:26 UTC; unix [2025-08-08 20:28:07] [INFO] [OmnipathR] Package `OmnipathR` version: 3.17.4 [2025-08-08 20:28:07] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22 [2025-08-08 20:28:08] [INFO] [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13); 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=2025-08-08; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown); quarto=1.4.553 @ /usr/local/bin/quarto] [2025-08-08 20:28:08] [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] [2025-08-08 20:28:09] [INFO] [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); annotate 1.87.0(2025-08-08); AnnotationDbi 1.71.1(2025-08-08); AUCell 1.31.0(2025-08-08); backports 1.5.0(2024-05-23); beachmat 2.25.4(2025-08-08); Biobase 2.69.0(2025-08-08); BiocGenerics 0.55.1(2025-08-08); BiocParallel 1.43.4(2025-08-08); BiocSingular 1.25.0(2025-08-08); Biostrings 2.77.2(2025-08-08); 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 6.4.0(2025-06-22); data.table 1.17.8(2025-07-10); DBI 1.2.3(2024-06-02); decoupleR 2.15.0(2025-08-08); DelayedArray 0.35.2(2025-08-08); DelayedMatrixStats 1.31.0(2025-08-08); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.4(2025-06-18); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); GenomicRanges 1.61.1(2025-08-08); glue 1.8.0(2024-09-30); graph 1.87.0(2025-08-08); GSEABase 1.71.0(2025-08-08); GSVA 2.3.1(2025-08-08); h5mread 1.1.1(2025-08-08); HDF5Array 1.37.0(2025-08-08); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.1.4(2025-01-23); IRanges 2.43.0(2025-08-08); irlba 2.3.5.1(2022-10-03); jsonlite 2.0.0(2025-03-27); KEGGREST 1.49.1(2025-08-08); 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 2.8.7(2025-06-06); magrittr 2.0.3(2022-03-30); Matrix 1.7-3(2025-03-11); MatrixGenerics 1.21.0(2025-08-08); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); OmnipathR 3.17.4(2025-08-08); parallelly 1.45.1(2025-07-24); pillar 1.11.0(2025-07-04); 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 1.1.0(2025-07-10); 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 1.1.0(2025-07-02); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rhdf5 2.53.4(2025-08-08); rhdf5filters 1.21.0(2025-08-08); Rhdf5lib 1.31.0(2025-08-08); rjson 0.2.23(2024-09-16); rlang 1.1.6(2025-04-11); rmarkdown 2.29(2024-11-04); RSQLite 2.4.2(2025-07-18); rsvd 1.0.5(2021-04-16); rvest 1.0.4(2024-02-12); S4Arrays 1.9.1(2025-08-08); S4Vectors 0.47.0(2025-08-08); ScaledMatrix 1.17.0(2025-08-08); Seqinfo 0.99.2(2025-08-08); sessioninfo 1.2.3(2025-02-05); SingleCellExperiment 1.31.1(2025-08-08); SparseArray 1.9.1(2025-08-08); sparseMatrixStats 1.21.0(2025-08-08); SpatialExperiment 1.19.1(2025-08-08); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); SummarizedExperiment 1.39.1(2025-08-08); 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); 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(2025-08-08); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13) [2025-08-08 20:28:09] [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 [2025-08-08 20:28:09] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-08-08 20:28:09] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-08-08 20:28:09] [TRACE] [OmnipathR] Contains 9 files. [2025-08-08 20:28:09] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-08-08 20:28:09] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-08 20:28:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-08 20:28:09] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-08-08 20:28:09] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2025-08-08 20:28:09] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-08-08 20:28:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-08 20:28:09] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-08-08 20:28:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-08 20:28:09] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-08-08 20:28:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-08 20:28:09] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-08-08 20:28:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-08 20:28:09] [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_collectri 35.953 4.388 52.401 get_dorothea 26.826 2.024 31.395 run_fgsea 24.782 1.199 26.026 run_aucell 12.925 4.538 17.492 get_progeny 7.498 0.675 15.360 * 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 4.5.1 (2025-06-13) -- "Great Square Root" 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") | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |=================================== | 50% | |======================================================================| 100% | | | 0% | |=================================== | 50% | |======================================================================| 100% | | | 0% | |=================================== | 50% | |======================================================================| 100% | | | 0% | |=================================== | 50% | |======================================================================| 100% | | | 0% | |=================================== | 50% | |======================================================================| 100% | | | 0% | |=================================== | 50% | |======================================================================| 100% | | | 0% | |=================================== | 50% | |======================================================================| 100% | | | 0% | |=================================== | 50% | |======================================================================| 100% | | | 0% | |=================================== | 50% | |======================================================================| 100% | | | 0% | |=================================== | 50% | |======================================================================| 100% | | | 0% | |=================================== | 50% | |======================================================================| 100% | | | 0% | |=================================== | 50% | |======================================================================| 100% [2025-08-08 20:32:35] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-08 20:32:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-08 20:32:35] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-08-08 20:32:35] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-08-08 20:32:35] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-08-08 [2025-08-08 20:32:35] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-08-08 19:10:26 UTC; unix [2025-08-08 20:32:35] [INFO] [OmnipathR] Package `OmnipathR` version: 3.17.4 [2025-08-08 20:32:35] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22 [2025-08-08 20:32:36] [INFO] [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13); 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=2025-08-08; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown); quarto=1.4.553 @ /usr/local/bin/quarto] [2025-08-08 20:32:36] [INFO] [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=; pango=1.50.14; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.5.0; tcl=8.6.13; curl=8.7.1; zlib=1.2.11; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; PCRE=10.44 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] [2025-08-08 20:32:37] [INFO] [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); annotate 1.87.0(2025-08-08); AnnotationDbi 1.71.1(2025-08-08); AUCell 1.31.0(2025-08-08); backports 1.5.0(2024-05-23); beachmat 2.25.4(2025-08-08); Biobase 2.69.0(2025-08-08); BiocGenerics 0.55.1(2025-08-08); BiocParallel 1.43.4(2025-08-08); BiocSingular 1.25.0(2025-08-08); Biostrings 2.77.2(2025-08-08); 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 1.0.9(2025-07-28); 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 1.2.0(2025-07-07); crayon 1.5.3(2024-06-20); curl 6.4.0(2025-06-22); data.table 1.17.8(2025-07-10); DBI 1.2.3(2024-06-02); decoupleR 2.15.0(2025-08-08); DelayedArray 0.35.2(2025-08-08); DelayedMatrixStats 1.31.0(2025-08-08); 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 1.0.4(2025-06-18); farver 2.1.2(2024-05-13); fastmap 1.2.0(2024-05-15); fastmatch 1.1-6(2024-12-23); fgsea 1.35.6(2025-08-08); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); GenomicRanges 1.61.1(2025-08-08); ggplot2 3.5.2(2025-04-09); glue 1.8.0(2024-09-30); graph 1.87.0(2025-08-08); GSEABase 1.71.0(2025-08-08); GSVA 2.3.1(2025-08-08); gtable 0.3.6(2024-10-25); h5mread 1.1.1(2025-08-08); HDF5Array 1.37.0(2025-08-08); 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 1.2.1(2025-07-22); igraph 2.1.4(2025-01-23); IRanges 2.43.0(2025-08-08); irlba 2.3.5.1(2022-10-03); jsonlite 2.0.0(2025-03-27); KEGGREST 1.49.1(2025-08-08); 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 2.8.7(2025-06-06); 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(2025-08-08); 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 3.17.4(2025-08-08); parallelly 1.45.1(2025-07-24); pillar 1.11.0(2025-07-04); pkgconfig 2.0.3(2019-09-22); plotly 4.11.0(2025-06-19); 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 1.1.0(2025-07-10); 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 1.1.0(2025-07-02); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rhdf5 2.53.4(2025-08-08); rhdf5filters 1.21.0(2025-08-08); Rhdf5lib 1.31.0(2025-08-08); 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 2.4.2(2025-07-18); rsvd 1.0.5(2021-04-16); rvest 1.0.4(2024-02-12); S4Arrays 1.9.1(2025-08-08); S4Vectors 0.47.0(2025-08-08); ScaledMatrix 1.17.0(2025-08-08); scales 1.4.0(2025-04-24); segmented 2.1-4(2025-02-28); Seqinfo 0.99.2(2025-08-08); sessioninfo 1.2.3(2025-02-05); SingleCellExperiment 1.31.1(2025-08-08); SparseArray 1.9.1(2025-08-08); sparseMatrixStats 1.21.0(2025-08-08); SpatialExperiment 1.19.1(2025-08-08); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); SummarizedExperiment 1.39.1(2025-08-08); 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); vctrs 0.6.5(2023-12-01); viper 1.43.0(2025-08-08); viridisLite 0.4.2(2023-05-02); waldo 0.6.2(2025-07-11); 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(2025-08-08); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13) [2025-08-08 20:32:37] [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 [2025-08-08 20:32:37] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-08-08 20:32:37] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-08-08 20:32:37] [TRACE] [OmnipathR] Contains 9 files. [2025-08-08 20:32:37] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-08-08 20:32:37] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-08 20:32:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-08 20:32:37] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-08-08 20:32:37] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2025-08-08 20:32:37] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-08-08 20:32:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-08 20:32:37] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-08-08 20:32:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-08 20:32:37] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-08-08 20:32:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-08 20:32:37] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-08-08 20:32:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-08 20:32:37] [TRACE] [OmnipathR] Cache locked: FALSE [2025-08-08 20:32:38] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-08-08 20:32:38] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-08 20:32:38] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-08-08 20:32:38] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-08 20:32:38] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2025-08-08 20:32:38] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-08 20:32:38] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-08 20:32:38] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available. [2025-08-08 20:32:38] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-08 20:32:38] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-08 20:32:39] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1. [2025-08-08 20:32:39] [TRACE] [OmnipathR] Cache file path: /Users/biocbuild/Library/Caches/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html [2025-08-08 20:32:39] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html` [2025-08-08 20:32:39] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`. [2025-08-08 20:32:39] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html` [2025-08-08 20:32:39] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`. [2025-08-08 20:32:39] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2025-08-08 20:32:39] [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] [2025-08-08 20:32:39] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2025-08-08 20:32:39] [TRACE] [OmnipathR] Sending HTTP request. [2025-08-08 20:32:46] [TRACE] [OmnipathR] HTTP 200 (OK) [2025-08-08 20:32:46] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2025-08-08 20:32:46] [TRACE] [OmnipathR] Downloaded 31 Kb in 7.232712s from www.ensembl.org (4.3 Kb/s); Redirect: 7.042977s, DNS look up: 6.230193s, Connection: 6.231901s, Pretransfer: 6.919889s, First byte at: 7.200969s [2025-08-08 20:32:46] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 302 Found; Date: Sat, 09 Aug 2025 00:32:39 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-p1m2-31.ebi.ac.uk; HTTP/2 302 ; date: Sat, 09 Aug 2025 00:32:46 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-10-25-25-92.us-east-2.compute.internal; HTTP/2 200 ; date: Sat, 09 Aug 2025 00:32:46 GMT; content-type: text/html; charset=utf-8; content-length: 31700; server: Apache; set-cookie: redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT; set-cookie: redirect_mirror=no; path=/; expires=Sun, 10 Aug 2025 00:30:44 GMT; set-cookie: ENSEMBL_WWW_SESSION=e105034b94a1acad0be67c3068e5b0b406ef7e7c2a7273a21ed194b8; 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=Sun, 10 Aug 2025 00:30:44 GMT; set-cookie: ENSEMBL_WWW_SESSION=e105034b94a1acad0be67c3068e5b0b406ef7e7c2a7273a21ed194b8; 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 [2025-08-08 20:32:46] [TRACE] [OmnipathR] Response headers: [date=Sat, 09 Aug 2025 00:32:46 GMT,content-type=text/html; charset=utf-8,content-length=31700,server=Apache,set-cookie=redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT,set-cookie=redirect_mirror=no; path=/; expires=Sun, 10 Aug 2025 00:30:44 GMT,set-cookie=ENSEMBL_WWW_SESSION=e105034b94a1acad0be67c3068e5b0b406ef7e7c2a7273a21ed194b8; 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=Sun, 10 Aug 2025 00:30:44 GMT,set-cookie=ENSEMBL_WWW_SESSION=e105034b94a1acad0be67c3068e5b0b406ef7e7c2a7273a21ed194b8; 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] [2025-08-08 20:32:47] [INFO] [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1] [2025-08-08 20:32:47] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-08 20:32:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-08 20:32:47] [INFO] [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`. [2025-08-08 20:32:48] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2025-08-08 20:32:48] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2025-08-08 20:32:48] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt` [2025-08-08 20:32:48] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`. [2025-08-08 20:32:48] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-08 20:32:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-08 20:32:48] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-08 20:32:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-08 20:32:48] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`. [2025-08-08 20:32:48] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2025-08-08 20:32:48] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt` [2025-08-08 20:32:48] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt` [2025-08-08 20:32:48] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-08-08 20:32:48] [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] [2025-08-08 20:32:48] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2025-08-08 20:32:48] [TRACE] [OmnipathR] Downloaded 8.7 Kb in 0.456889s from omabrowser.org (19 Kb/s); Redirect: 0s, DNS look up: 0.001146s, Connection: 0.002189s, Pretransfer: 0.362699s, First byte at: 0.456568s [2025-08-08 20:32:48] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; date: Sat, 09 Aug 2025 00:32:48 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 [2025-08-08 20:32:50] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2025-08-08 20:32:50] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1] [2025-08-08 20:32:50] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-08 20:32:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-08 20:32:50] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`. [2025-08-08 20:32:50] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2025-08-08 20:32:50] [TRACE] [OmnipathR] Looking up in cache: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2025-08-08 20:32:50] [INFO] [OmnipathR] Cache record does not exist: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2025-08-08 20:32:50] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2025-08-08 20:32:50] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-08 20:32:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-08 20:32:50] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-08 20:32:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-08 20:32:50] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `unknown` to `started`. [2025-08-08 20:32:50] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2025-08-08 20:32:50] [INFO] [OmnipathR] Retrieving URL: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2025-08-08 20:32:50] [TRACE] [OmnipathR] Attempt 1/3: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2025-08-08 20:33:31] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2025-08-08 20:33:31] [INFO] [OmnipathR] Download ready [key=56ad6544dc07a2222fa6013d8d83e6e5a35fdf33, version=1] [2025-08-08 20:33:31] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-08 20:33:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-08 20:33:31] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `started` to `ready`. [2025-08-08 20:33:31] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`. [2025-08-08 20:33:31] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-08-08 20:33:31] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=TFcensus,query_type=annotations] [2025-08-08 20:33:31] [TRACE] [OmnipathR] Organism(s): 9606 [2025-08-08 20:33:31] [TRACE] [OmnipathR] Orthology targets: [2025-08-08 20:33:32] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-08-08 20:33:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-08 20:33:32] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic` [2025-08-08 20:33:32] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic` [2025-08-08 20:33:32] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=TFcensus&license=academic` [2025-08-08 20:33:32] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=TFcensus&license=academic` [2025-08-08 20:33:32] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=TFcensus&license=academic` [2025-08-08 20:33:32] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic` [2025-08-08 20:33:32] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic` [2025-08-08 20:33:32] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-08-08 20:33:32] [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] [2025-08-08 20:33:33] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-08-08 20:33:33] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.460787s from omnipathdb.org (34 Kb/s); Redirect: 0s, DNS look up: 0.001314s, Connection: 0.002342s, Pretransfer: 0.307699s, First byte at: 0.460297s [2025-08-08 20:33:33] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 09 Aug 2025 00:33:33 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Sat, 09 Aug 2025 01:33:33 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-08-08 20:33:34] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic` [2025-08-08 20:33:34] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-08 20:33:34] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-08 20:33:34] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-08 20:33:34] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-08 20:33:34] [INFO] [OmnipathR] Cache item `6f000d9b5edd9832b1c28754d1c3d9449c1c7490` version 1: status changed from `unknown` to `started`. [2025-08-08 20:33:34] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/6f000d9b5edd9832b1c28754d1c3d9449c1c7490-1.rds`. [2025-08-08 20:33:34] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/6f000d9b5edd9832b1c28754d1c3d9449c1c7490-1.rds`. [2025-08-08 20:33:34] [INFO] [OmnipathR] Download ready [key=6f000d9b5edd9832b1c28754d1c3d9449c1c7490, version=1] [2025-08-08 20:33:34] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-08 20:33:34] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-08 20:33:34] [INFO] [OmnipathR] Cache item `6f000d9b5edd9832b1c28754d1c3d9449c1c7490` version 1: status changed from `started` to `ready`. [2025-08-08 20:33:34] [SUCCESS] [OmnipathR] Downloaded 3099 annotation records. [2025-08-08 20:33:35] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-08-08 20:33:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-08 20:33:35] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-08-08 20:33:35] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=PROGENy,query_type=annotations] [2025-08-08 20:33:35] [TRACE] [OmnipathR] Organism(s): 9606 [2025-08-08 20:33:35] [TRACE] [OmnipathR] Orthology targets: [2025-08-08 20:33:35] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-08-08 20:33:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-08 20:33:36] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` [2025-08-08 20:33:36] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` [2025-08-08 20:33:36] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=PROGENy&license=academic` [2025-08-08 20:33:36] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=PROGENy&license=academic` [2025-08-08 20:33:36] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` [2025-08-08 20:33:36] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` [2025-08-08 20:33:36] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` [2025-08-08 20:33:36] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-08-08 20:33:36] [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] [2025-08-08 20:33:36] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-08-08 20:33:36] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.316853s from omnipathdb.org (49.4 Kb/s); Redirect: 0s, DNS look up: 0.001194s, Connection: 0.002111s, Pretransfer: 0.164963s, First byte at: 0.316464s [2025-08-08 20:33:36] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 09 Aug 2025 00:33:36 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Sat, 09 Aug 2025 01:33:36 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-08-08 20:33:45] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` [2025-08-08 20:33:45] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-08 20:33:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-08 20:33:45] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-08 20:33:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-08 20:33:45] [INFO] [OmnipathR] Cache item `3492392585ba05414edfae46801492076437d7e7` version 1: status changed from `unknown` to `started`. [2025-08-08 20:33:45] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`. [2025-08-08 20:33:48] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`. [2025-08-08 20:33:48] [INFO] [OmnipathR] Download ready [key=3492392585ba05414edfae46801492076437d7e7, version=1] [2025-08-08 20:33:48] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-08 20:33:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-08 20:33:48] [INFO] [OmnipathR] Cache item `3492392585ba05414edfae46801492076437d7e7` version 1: status changed from `started` to `ready`. [2025-08-08 20:33:48] [SUCCESS] [OmnipathR] Downloaded 700239 annotation records. [2025-08-08 20:33:50] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-08-08 20:33:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-08 20:33:50] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-08-08 20:33:50] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=PROGENy,query_type=annotations] [2025-08-08 20:33:50] [TRACE] [OmnipathR] Organism(s): 9606 [2025-08-08 20:33:50] [TRACE] [OmnipathR] Orthology targets: [2025-08-08 20:33:51] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-08-08 20:33:51] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-08 20:33:51] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` [2025-08-08 20:33:53] [TRACE] [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`. [2025-08-08 20:33:53] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` [2025-08-08 20:33:53] [SUCCESS] [OmnipathR] Loaded 700239 annotation records from cache. [2025-08-08 20:33:56] [INFO] [OmnipathR] Loading database `Orthologous Matrix (OMA) gene pairs`. [2025-08-08 20:33:56] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2025-08-08 20:33:56] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2025-08-08 20:33:56] [TRACE] [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2025-08-08 20:33:56] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2025-08-08 20:33:56] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2025-08-08 20:33:56] [TRACE] [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2025-08-08 20:33:56] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2025-08-08 20:33:56] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/api/pairs/HUMAN/MOUSE/?format=tsv&xrefs=UniProtKB%2FSwissProt&per_page=2000000`. [2025-08-08 20:33:56] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/api/pairs/HUMAN/MOUSE/?format=tsv&xrefs=UniProtKB%2FSwissProt&per_page=2000000` [2025-08-08 20:33:56] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/api/pairs/HUMAN/MOUSE/?format=tsv&xrefs=UniProtKB%2FSwissProt&per_page=2000000`. [2025-08-08 20:33:56] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-08 20:33:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-08 20:33:56] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-08 20:33:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-08 20:33:56] [INFO] [OmnipathR] Cache item `8f45b25c384d814c7de210e7ca40b7e35894e4f1` version 1: status changed from `unknown` to `started`. [2025-08-08 20:33:56] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/8f45b25c384d814c7de210e7ca40b7e35894e4f1-1.rds`. [2025-08-08 20:33:56] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/api/pairs/HUMAN/MOUSE/?format=tsv&xrefs=UniProtKB%2FSwissProt&per_page=2000000` [2025-08-08 20:33:56] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/api/pairs/HUMAN/MOUSE/?format=tsv&xrefs=UniProtKB%2FSwissProt&per_page=2000000` [2025-08-08 20:33:56] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-08-08 20:33:56] [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] [2025-08-08 20:34:32] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2025-08-08 20:34:32] [TRACE] [OmnipathR] Downloaded 11.1 Kb in 35.62506s from omabrowser.org (318 bytes/s); Redirect: 0s, DNS look up: 0.001303s, Connection: 0.002272s, Pretransfer: 0.364374s, First byte at: 35.624893s [2025-08-08 20:34:32] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; date: Sat, 09 Aug 2025 00:34:32 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_2025-08-09_003430.tsv; x-frame-options: SAMEORIGIN; set-cookie: __matomo=1227dd34b549e26b; expires=Mon, 09-Aug-2027 00:34:32 UTC; Path=/ [2025-08-08 20:34:35] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/8f45b25c384d814c7de210e7ca40b7e35894e4f1-1.rds`. [2025-08-08 20:34:35] [INFO] [OmnipathR] Download ready [key=8f45b25c384d814c7de210e7ca40b7e35894e4f1, version=1] [2025-08-08 20:34:35] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-08 20:34:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-08 20:34:35] [INFO] [OmnipathR] Cache item `8f45b25c384d814c7de210e7ca40b7e35894e4f1` version 1: status changed from `started` to `ready`. [2025-08-08 20:34:35] [TRACE] [OmnipathR] ID translation table: from `uniprot_entry` to `uniprot`, using `uniprot`. [2025-08-08 20:34:35] [TRACE] [OmnipathR] Creating ID mapping table from `id` to `accession`, for organism 9606 (only reviewed: TRUE) [2025-08-08 20:34:35] [TRACE] [OmnipathR] Loading all UniProt records for organism 9606 (only reviewed: TRUE); fields: id,accession [2025-08-08 20:34:35] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2025-08-08 20:34:35] [TRACE] [OmnipathR] Looking up in cache: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:9606%20AND%20reviewed:true`. [2025-08-08 20:34:35] [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` [2025-08-08 20:34:35] [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`. [2025-08-08 20:34:35] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-08 20:34:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-08 20:34:35] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-08 20:34:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-08 20:34:35] [INFO] [OmnipathR] Cache item `6558a1824894a625b8e3f80538cd3aa6e8a44379` version 1: status changed from `unknown` to `started`. [2025-08-08 20:34:35] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/6558a1824894a625b8e3f80538cd3aa6e8a44379-1.rds`. [2025-08-08 20:34:35] [INFO] [OmnipathR] Retrieving URL: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:9606%20AND%20reviewed:true` [2025-08-08 20:34:35] [TRACE] [OmnipathR] Attempt 1/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:9606%20AND%20reviewed:true` [2025-08-08 20:34:35] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-08-08 20:34:36] [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] [2025-08-08 20:34:36] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2025-08-08 20:34:36] [TRACE] [OmnipathR] Downloaded 31 bytes in 0.8793s from rest.uniprot.org (35 bytes/s); Redirect: 0s, DNS look up: 0.014408s, Connection: 0.015458s, Pretransfer: 0.546133s, First byte at: 0.879127s [2025-08-08 20:34:36] [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: 08-August-2025; strict-transport-security: max-age=31536000; includeSubDomains; date: Sat, 09 Aug 2025 00:34:36 GMT; access-control-max-age: 1728000; x-uniprot-release: 2025_03; 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: 18-June-2025 [2025-08-08 20:34:46] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/6558a1824894a625b8e3f80538cd3aa6e8a44379-1.rds`. [2025-08-08 20:34:46] [INFO] [OmnipathR] Download ready [key=6558a1824894a625b8e3f80538cd3aa6e8a44379, version=1] [2025-08-08 20:34:46] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-08 20:34:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-08 20:34:46] [INFO] [OmnipathR] Cache item `6558a1824894a625b8e3f80538cd3aa6e8a44379` version 1: status changed from `started` to `ready`. [2025-08-08 20:34:46] [SUCCESS] [OmnipathR] UniProt (rest.uniprot.org): downloaded 20420 records [2025-08-08 20:34:47] [TRACE] [OmnipathR] Translating complexes: 0 complexes in data. [2025-08-08 20:34:47] [TRACE] [OmnipathR] 0 complexes after removing the ones mapping to more than 1 items in target identifier space. [2025-08-08 20:34:47] [TRACE] [OmnipathR] Translated 0 complexes to 0. [2025-08-08 20:34:47] [TRACE] [OmnipathR] 13774 rows before translation, 13774 uniprot_entry IDs in column `id_organism_a`. [2025-08-08 20:34:47] [TRACE] [OmnipathR] 13774 rows after translation; translated 13550 `uniprot_entry` IDs in column `id_organism_a` to 13550 `uniprot` IDs in column `id_organism_a`. [2025-08-08 20:34:47] [TRACE] [OmnipathR] ID translation table: from `uniprot_entry` to `uniprot`, using `uniprot`. [2025-08-08 20:34:47] [TRACE] [OmnipathR] Creating ID mapping table from `id` to `accession`, for organism 10090 (only reviewed: TRUE) [2025-08-08 20:34:47] [TRACE] [OmnipathR] Loading all UniProt records for organism 10090 (only reviewed: TRUE); fields: id,accession [2025-08-08 20:34:47] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2025-08-08 20:34:47] [TRACE] [OmnipathR] Looking up in cache: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:10090%20AND%20reviewed:true`. [2025-08-08 20:34:47] [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` [2025-08-08 20:34:47] [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`. [2025-08-08 20:34:47] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-08 20:34:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-08 20:34:47] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-08 20:34:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-08 20:34:47] [INFO] [OmnipathR] Cache item `43ea5f2cdaa9ac7e0e114371af97235cdddd776f` version 1: status changed from `unknown` to `started`. [2025-08-08 20:34:47] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/43ea5f2cdaa9ac7e0e114371af97235cdddd776f-1.rds`. [2025-08-08 20:34:47] [INFO] [OmnipathR] Retrieving URL: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:10090%20AND%20reviewed:true` [2025-08-08 20:34:47] [TRACE] [OmnipathR] Attempt 1/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:10090%20AND%20reviewed:true` [2025-08-08 20:34:47] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-08-08 20:34:47] [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] [2025-08-08 20:34:48] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2025-08-08 20:34:48] [TRACE] [OmnipathR] Downloaded 31 bytes in 0.775957s from rest.uniprot.org (39 bytes/s); Redirect: 0s, DNS look up: 0.001162s, Connection: 0.002205s, Pretransfer: 0.492388s, First byte at: 0.775798s [2025-08-08 20:34:48] [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: 08-August-2025; strict-transport-security: max-age=31536000; includeSubDomains; date: Sat, 09 Aug 2025 00:34:48 GMT; access-control-max-age: 1728000; x-uniprot-release: 2025_03; 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: 18-June-2025 [2025-08-08 20:34:54] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/43ea5f2cdaa9ac7e0e114371af97235cdddd776f-1.rds`. [2025-08-08 20:34:54] [INFO] [OmnipathR] Download ready [key=43ea5f2cdaa9ac7e0e114371af97235cdddd776f, version=1] [2025-08-08 20:34:54] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-08 20:34:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-08 20:34:54] [INFO] [OmnipathR] Cache item `43ea5f2cdaa9ac7e0e114371af97235cdddd776f` version 1: status changed from `started` to `ready`. [2025-08-08 20:34:54] [SUCCESS] [OmnipathR] UniProt (rest.uniprot.org): downloaded 17240 records [2025-08-08 20:34:55] [TRACE] [OmnipathR] Translating complexes: 0 complexes in data. [2025-08-08 20:34:55] [TRACE] [OmnipathR] 0 complexes after removing the ones mapping to more than 1 items in target identifier space. [2025-08-08 20:34:55] [TRACE] [OmnipathR] Translated 0 complexes to 0. [2025-08-08 20:34:55] [TRACE] [OmnipathR] 13774 rows before translation, 13773 uniprot_entry IDs in column `id_organism_b`. [2025-08-08 20:34:55] [TRACE] [OmnipathR] 13774 rows after translation; translated 13253 `uniprot_entry` IDs in column `id_organism_b` to 13253 `uniprot` IDs in column `id_organism_b`. [2025-08-08 20:34:55] [INFO] [OmnipathR] Loaded database `Orthologous Matrix (OMA) gene pairs`. [2025-08-08 20:34:55] [TRACE] [OmnipathR] ID translation table: from `uniprot` to `genesymbol`, using `uniprot`. [2025-08-08 20:34:55] [TRACE] [OmnipathR] Creating ID mapping table from `accession` to `gene_primary`, for organism 10090 (only reviewed: TRUE) [2025-08-08 20:34:55] [TRACE] [OmnipathR] Loading all UniProt records for organism 10090 (only reviewed: TRUE); fields: accession,gene_primary [2025-08-08 20:34:55] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2025-08-08 20:34:55] [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`. [2025-08-08 20:34:55] [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` [2025-08-08 20:34:55] [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`. [2025-08-08 20:34:55] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-08 20:34:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-08 20:34:55] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-08 20:34:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-08 20:34:55] [INFO] [OmnipathR] Cache item `3ec84ba713c02573704adb50f1a94dab684df34b` version 1: status changed from `unknown` to `started`. [2025-08-08 20:34:55] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/3ec84ba713c02573704adb50f1a94dab684df34b-1.rds`. [2025-08-08 20:34:55] [INFO] [OmnipathR] Retrieving URL: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:10090%20AND%20reviewed:true` [2025-08-08 20:34:55] [TRACE] [OmnipathR] Attempt 1/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:10090%20AND%20reviewed:true` [2025-08-08 20:34:55] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-08-08 20:34:55] [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] [2025-08-08 20:34:56] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2025-08-08 20:34:56] [TRACE] [OmnipathR] Downloaded 43 bytes in 0.535132s from rest.uniprot.org (80 bytes/s); Redirect: 0s, DNS look up: 0.001138s, Connection: 0.002198s, Pretransfer: 0.248848s, First byte at: 0.534957s [2025-08-08 20:34:56] [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: 08-August-2025; strict-transport-security: max-age=31536000; includeSubDomains; date: Sat, 09 Aug 2025 00:34:56 GMT; access-control-max-age: 1728000; x-uniprot-release: 2025_03; 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: 18-June-2025 [2025-08-08 20:35:03] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/3ec84ba713c02573704adb50f1a94dab684df34b-1.rds`. [2025-08-08 20:35:03] [INFO] [OmnipathR] Download ready [key=3ec84ba713c02573704adb50f1a94dab684df34b, version=1] [2025-08-08 20:35:03] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-08 20:35:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-08 20:35:03] [INFO] [OmnipathR] Cache item `3ec84ba713c02573704adb50f1a94dab684df34b` version 1: status changed from `started` to `ready`. [2025-08-08 20:35:03] [SUCCESS] [OmnipathR] UniProt (rest.uniprot.org): downloaded 17240 records [2025-08-08 20:35:05] [TRACE] [OmnipathR] Translating complexes: 0 complexes in data. [2025-08-08 20:35:05] [TRACE] [OmnipathR] 0 complexes after removing the ones mapping to more than 1 items in target identifier space. [2025-08-08 20:35:05] [TRACE] [OmnipathR] Translated 0 complexes to 0. [2025-08-08 20:35:05] [TRACE] [OmnipathR] 163950 rows before translation, 12858 uniprot IDs in column `uniprot`. [2025-08-08 20:35:05] [TRACE] [OmnipathR] 163950 rows after translation; translated 12858 `uniprot` IDs in column `uniprot` to 12772 `genesymbol` IDs in column `genesymbol`. [2025-08-08 20:35:06] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-08-08 20:35:06] [TRACE] [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B,C,D],genesymbols=TRUE,organisms=9606,query_type=interactions,datasets=dorothea] [2025-08-08 20:35:06] [TRACE] [OmnipathR] Organism(s): 9606 [2025-08-08 20:35:06] [TRACE] [OmnipathR] Orthology targets: [2025-08-08 20:35:06] [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` [2025-08-08 20:35:06] [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` [2025-08-08 20:35:06] [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` [2025-08-08 20:35:06] [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` [2025-08-08 20:35:06] [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` [2025-08-08 20:35:06] [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` [2025-08-08 20:35:06] [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` [2025-08-08 20:35:06] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-08-08 20:35:06] [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] [2025-08-08 20:35:06] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-08-08 20:35:06] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.325243s from omnipathdb.org (48.2 Kb/s); Redirect: 0s, DNS look up: 0.00684s, Connection: 0.007915s, Pretransfer: 0.172789s, First byte at: 0.3249s [2025-08-08 20:35:06] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 09 Aug 2025 00:35:06 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Sat, 09 Aug 2025 01:35:06 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-08-08 20:35:11] [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` [2025-08-08 20:35:11] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-08 20:35:11] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-08 20:35:11] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-08 20:35:11] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-08 20:35:11] [INFO] [OmnipathR] Cache item `46d37339bbc3f9a05bb89ccb79278cf1233f5cdf` version 1: status changed from `unknown` to `started`. [2025-08-08 20:35:11] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/46d37339bbc3f9a05bb89ccb79278cf1233f5cdf-1.rds`. [2025-08-08 20:35:13] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/46d37339bbc3f9a05bb89ccb79278cf1233f5cdf-1.rds`. [2025-08-08 20:35:13] [INFO] [OmnipathR] Download ready [key=46d37339bbc3f9a05bb89ccb79278cf1233f5cdf, version=1] [2025-08-08 20:35:13] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-08 20:35:13] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-08 20:35:13] [INFO] [OmnipathR] Cache item `46d37339bbc3f9a05bb89ccb79278cf1233f5cdf` version 1: status changed from `started` to `ready`. [2025-08-08 20:35:24] [SUCCESS] [OmnipathR] Downloaded 278830 interactions. [2025-08-08 20:35:39] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-08-08 20:35:39] [TRACE] [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B,C,D],genesymbols=TRUE,organisms=10090,query_type=interactions,datasets=dorothea] [2025-08-08 20:35:39] [TRACE] [OmnipathR] Organism(s): 10090 [2025-08-08 20:35:39] [TRACE] [OmnipathR] Orthology targets: [2025-08-08 20:35:39] [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` [2025-08-08 20:35:39] [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` [2025-08-08 20:35:39] [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` [2025-08-08 20:35:39] [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` [2025-08-08 20:35:39] [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` [2025-08-08 20:35:39] [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` [2025-08-08 20:35:39] [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` [2025-08-08 20:35:39] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-08-08 20:35:39] [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] [2025-08-08 20:35:39] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-08-08 20:35:39] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.476507s from omnipathdb.org (32.9 Kb/s); Redirect: 0s, DNS look up: 0.001181s, Connection: 0.00214s, Pretransfer: 0.321829s, First byte at: 0.476137s [2025-08-08 20:35:39] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 09 Aug 2025 00:35:39 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Sat, 09 Aug 2025 01:35:39 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-08-08 20:35:44] [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` [2025-08-08 20:35:44] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-08 20:35:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-08 20:35:44] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-08 20:35:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-08 20:35:44] [INFO] [OmnipathR] Cache item `ff347dedf78ef5e38c9c6d8eed291fa901aa3791` version 1: status changed from `unknown` to `started`. [2025-08-08 20:35:44] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/ff347dedf78ef5e38c9c6d8eed291fa901aa3791-1.rds`. [2025-08-08 20:35:45] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/ff347dedf78ef5e38c9c6d8eed291fa901aa3791-1.rds`. [2025-08-08 20:35:45] [INFO] [OmnipathR] Download ready [key=ff347dedf78ef5e38c9c6d8eed291fa901aa3791, version=1] [2025-08-08 20:35:45] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-08 20:35:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-08 20:35:45] [INFO] [OmnipathR] Cache item `ff347dedf78ef5e38c9c6d8eed291fa901aa3791` version 1: status changed from `started` to `ready`. [2025-08-08 20:35:54] [SUCCESS] [OmnipathR] Downloaded 234298 interactions. [2025-08-08 20:36:05] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-08-08 20:36:05] [TRACE] [OmnipathR] Arguments for OmniPath query: [loops=TRUE,organisms=9606,genesymbols=TRUE,query_type=interactions,datasets=collectri] [2025-08-08 20:36:05] [TRACE] [OmnipathR] Organism(s): 9606 [2025-08-08 20:36:05] [TRACE] [OmnipathR] Orthology targets: [2025-08-08 20:36:05] [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` [2025-08-08 20:36:05] [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` [2025-08-08 20:36:05] [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` [2025-08-08 20:36:05] [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` [2025-08-08 20:36:05] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic` [2025-08-08 20:36:05] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic` [2025-08-08 20:36:05] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic` [2025-08-08 20:36:05] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-08-08 20:36:05] [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] [2025-08-08 20:36:06] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-08-08 20:36:06] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.308931s from omnipathdb.org (50.7 Kb/s); Redirect: 0s, DNS look up: 0.001082s, Connection: 0.002059s, Pretransfer: 0.156375s, First byte at: 0.308248s [2025-08-08 20:36:06] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 09 Aug 2025 00:36:06 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Sat, 09 Aug 2025 01:36:06 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-08-08 20:36:09] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic` [2025-08-08 20:36:09] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-08 20:36:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-08 20:36:09] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-08 20:36:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-08 20:36:09] [INFO] [OmnipathR] Cache item `b10176737ba43d460b13709623189f3911123779` version 1: status changed from `unknown` to `started`. [2025-08-08 20:36:09] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/b10176737ba43d460b13709623189f3911123779-1.rds`. [2025-08-08 20:36:09] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/b10176737ba43d460b13709623189f3911123779-1.rds`. [2025-08-08 20:36:09] [INFO] [OmnipathR] Download ready [key=b10176737ba43d460b13709623189f3911123779, version=1] [2025-08-08 20:36:09] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-08 20:36:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-08 20:36:09] [INFO] [OmnipathR] Cache item `b10176737ba43d460b13709623189f3911123779` version 1: status changed from `started` to `ready`. [2025-08-08 20:36:12] [SUCCESS] [OmnipathR] Downloaded 64958 interactions. [2025-08-08 20:36:12] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-08-08 20:36:12] [TRACE] [OmnipathR] Arguments for OmniPath query: [genesymbols=TRUE,resources=CollecTRI,strict_evidences=TRUE,query_type=interactions,datasets=tf_mirna] [2025-08-08 20:36:12] [TRACE] [OmnipathR] Organism(s): 9606 [2025-08-08 20:36:12] [TRACE] [OmnipathR] Orthology targets: [2025-08-08 20:36:13] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-08-08 20:36:13] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-08 20:36:13] [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` [2025-08-08 20:36:13] [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` [2025-08-08 20:36:13] [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` [2025-08-08 20:36:13] [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` [2025-08-08 20:36:13] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic` [2025-08-08 20:36:13] [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` [2025-08-08 20:36:13] [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` [2025-08-08 20:36:13] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-08-08 20:36:13] [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] [2025-08-08 20:36:13] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-08-08 20:36:13] [TRACE] [OmnipathR] Downloaded 9.5 Kb in 0.233119s from omnipathdb.org (40.7 Kb/s); Redirect: 0s, DNS look up: 0.001234s, Connection: 0.00231s, Pretransfer: 0.156312s, First byte at: 0.232854s [2025-08-08 20:36:13] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Sat, 09 Aug 2025 00:36:13 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Sat, 09 Aug 2025 01:36:13 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-08-08 20:36:15] [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` [2025-08-08 20:36:15] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-08 20:36:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-08 20:36:15] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-08 20:36:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-08 20:36:15] [INFO] [OmnipathR] Cache item `f7d34500401ba98803b7d2b26c48f64cee1eea1b` version 1: status changed from `unknown` to `started`. [2025-08-08 20:36:15] [TRACE] [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/f7d34500401ba98803b7d2b26c48f64cee1eea1b-1.rds`. [2025-08-08 20:36:15] [TRACE] [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/f7d34500401ba98803b7d2b26c48f64cee1eea1b-1.rds`. [2025-08-08 20:36:15] [INFO] [OmnipathR] Download ready [key=f7d34500401ba98803b7d2b26c48f64cee1eea1b, version=1] [2025-08-08 20:36:15] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-08 20:36:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-08 20:36:15] [INFO] [OmnipathR] Cache item `f7d34500401ba98803b7d2b26c48f64cee1eea1b` version 1: status changed from `started` to `ready`. [2025-08-08 20:36:15] [TRACE] [OmnipathR] Converting JSON column `evidences` to list. [2025-08-08 20:36:15] [TRACE] [OmnipathR] Restricting interaction records to datasets: tf_mirna; and resources: CollecTRI [2025-08-08 20:36:15] [TRACE] [OmnipathR] Filtering evidence columns: positive, negative, directed, undirected; to datasets: tf_mirna; and resources: CollecTRI; excluding resources: none [2025-08-08 20:36:16] [SUCCESS] [OmnipathR] Downloaded 232 interactions. [2025-08-08 20:36:16] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-08-08 20:36:16] [TRACE] [OmnipathR] Arguments for OmniPath query: [loops=TRUE,organisms=9606,genesymbols=TRUE,query_type=interactions,datasets=collectri] [2025-08-08 20:36:16] [TRACE] [OmnipathR] Organism(s): 9606 [2025-08-08 20:36:16] [TRACE] [OmnipathR] Orthology targets: [2025-08-08 20:36:16] [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` [2025-08-08 20:36:16] [TRACE] [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/b10176737ba43d460b13709623189f3911123779-1.rds`. [2025-08-08 20:36:16] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic` [2025-08-08 20:36:19] [SUCCESS] [OmnipathR] Loaded 64958 interactions from cache. [2025-08-08 20:36:19] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-08-08 20:36:19] [TRACE] [OmnipathR] Arguments for OmniPath query: [genesymbols=TRUE,resources=CollecTRI,strict_evidences=TRUE,query_type=interactions,datasets=tf_mirna] [2025-08-08 20:36:19] [TRACE] [OmnipathR] Organism(s): 9606 [2025-08-08 20:36:19] [TRACE] [OmnipathR] Orthology targets: [2025-08-08 20:36:20] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-08-08 20:36:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-08 20:36:20] [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` [2025-08-08 20:36:20] [TRACE] [OmnipathR] Loaded data from RDS `/Users/biocbuild/Library/Caches/OmnipathR/f7d34500401ba98803b7d2b26c48f64cee1eea1b-1.rds`. [2025-08-08 20:36:20] [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` [2025-08-08 20:36:20] [TRACE] [OmnipathR] Converting JSON column `evidences` to list. [2025-08-08 20:36:20] [TRACE] [OmnipathR] Restricting interaction records to datasets: tf_mirna; and resources: CollecTRI [2025-08-08 20:36:20] [TRACE] [OmnipathR] Filtering evidence columns: positive, negative, directed, undirected; to datasets: tf_mirna; and resources: CollecTRI; excluding resources: none [2025-08-08 20:36:21] [SUCCESS] [OmnipathR] Loaded 232 interactions from cache. | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |=================================== | 50% | |======================================================================| 100% | | | 0% | |=================================== | 50% | |======================================================================| 100% | | | 0% | |=================================== | 50% | |======================================================================| 100% | | | 0% | |=================================== | 50% | |======================================================================| 100% | | | 0% | |=================================== | 50% | |======================================================================| 100% | | | 0% | |=================================== | 50% | |======================================================================| 100% | | | 0% | |=================================== | 50% | |======================================================================| 100% | | | 0% | |=================================== | 50% | |======================================================================| 100% | | | 0% | |=================================== | 50% | |======================================================================| 100% | | | 0% | |=================================== | 50% | |======================================================================| 100% | | | 0% | |=================================== | 50% | |======================================================================| 100% | | | 0% | |=================================== | 50% | |======================================================================| 100% 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 209.594 25.806 333.824
decoupleR.Rcheck/decoupleR-Ex.timings
name | user | system | elapsed | |
check_corr | 0.093 | 0.015 | 0.108 | |
convert_f_defaults | 0.031 | 0.004 | 0.035 | |
decouple | 0.001 | 0.001 | 0.002 | |
dot-fit_preprocessing | 0.031 | 0.003 | 0.035 | |
extract_sets | 0.027 | 0.001 | 0.028 | |
filt_minsize | 0.042 | 0.002 | 0.045 | |
get_collectri | 35.953 | 4.388 | 52.401 | |
get_dorothea | 26.826 | 2.024 | 31.395 | |
get_profile_of | 0.001 | 0.000 | 0.001 | |
get_progeny | 7.498 | 0.675 | 15.360 | |
get_resource | 0.875 | 0.082 | 2.386 | |
get_toy_data | 0.003 | 0.000 | 0.003 | |
intersect_regulons | 0.037 | 0.009 | 0.046 | |
pipe | 0.000 | 0.000 | 0.001 | |
pivot_wider_profile | 0.000 | 0.001 | 0.000 | |
randomize_matrix | 0 | 0 | 0 | |
rename_net | 0.059 | 0.013 | 0.074 | |
run_aucell | 12.925 | 4.538 | 17.492 | |
run_consensus | 2.769 | 0.659 | 3.431 | |
run_fgsea | 24.782 | 1.199 | 26.026 | |
run_gsva | 2.970 | 1.296 | 4.268 | |
run_mdt | 0.209 | 0.056 | 0.273 | |
run_mlm | 0.139 | 0.024 | 0.164 | |
run_ora | 0.761 | 0.123 | 0.886 | |
run_udt | 0.442 | 0.069 | 0.512 | |
run_ulm | 0.114 | 0.024 | 0.137 | |
run_viper | 1.282 | 0.562 | 1.847 | |
run_wmean | 1.074 | 0.142 | 1.220 | |
run_wsum | 1.150 | 0.148 | 1.305 | |
show_methods | 0.069 | 0.016 | 0.085 | |
show_resources | 0.070 | 0.010 | 0.663 | |
tidyeval | 0.000 | 0.001 | 0.000 | |