Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-08-07 12:05 -0400 (Thu, 07 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" | 4815 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4550 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4592 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4534 |
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 529/2315 | 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: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:decoupleR.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings decoupleR_2.15.0.tar.gz |
StartedAt: 2025-08-06 21:46:16 -0400 (Wed, 06 Aug 2025) |
EndedAt: 2025-08-06 21:59:25 -0400 (Wed, 06 Aug 2025) |
EllapsedTime: 788.7 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: decoupleR.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:decoupleR.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings decoupleR_2.15.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/decoupleR.Rcheck’ * using R version 4.5.1 (2025-06-13) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 * running under: Ubuntu 24.04.2 LTS * using session charset: UTF-8 * 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 loading without being on the library search path ... OK * checking dependencies in R code ... NOTE [2025-08-06 21:46:52] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-06 21:46:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-06 21:46:52] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2025-08-06 21:46:52] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-08-06 21:46:52] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-08-06 [2025-08-06 21:46:52] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-08-06 19:08:11 UTC; unix [2025-08-06 21:46:52] [INFO] [OmnipathR] Package `OmnipathR` version: 3.17.4 [2025-08-06 21:46:52] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22 [2025-08-06 21:46:52] [INFO] [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13); os=Ubuntu 24.04.2 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-08-06; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto] [2025-08-06 21:46:52] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.22-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0] [2025-08-06 21:46:52] [INFO] [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); annotate 1.87.0(2025-08-06); AnnotationDbi 1.71.1(2025-08-06); AUCell 1.31.0(2025-08-06); backports 1.5.0(2024-05-23); beachmat 2.25.4(2025-08-06); Biobase 2.69.0(2025-08-06); BiocGenerics 0.55.1(2025-08-06); BiocParallel 1.43.4(2025-08-06); BiocSingular 1.25.0(2025-08-06); Biostrings 2.77.2(2025-08-06); 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(2025-08-06); DelayedArray 0.35.2(2025-08-06); DelayedMatrixStats 1.31.0(2025-08-06); 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(2025-08-06); glue 1.8.0(2024-09-30); graph 1.87.0(2025-08-06); GSEABase 1.71.0(2025-08-06); GSVA 2.3.1(2025-08-06); h5mread 1.1.1(2025-08-06); HDF5Array 1.37.0(2025-08-06); 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(2025-08-06); irlba 2.3.5.1(2022-10-03); jsonlite 2.0.0(2025-03-27); KEGGREST 1.49.1(2025-08-06); 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(2025-08-06); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); OmnipathR 3.17.4(2025-08-06); 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(2025-08-06); rhdf5filters 1.21.0(2025-08-06); Rhdf5lib 1.31.0(2025-08-06); 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(2025-08-06); S4Vectors 0.47.0(2025-08-06); ScaledMatrix 1.17.0(2025-08-06); Seqinfo 0.99.2(2025-08-06); sessioninfo 1.2.3(2025-02-05); SingleCellExperiment 1.31.1(2025-08-06); SparseArray 1.9.1(2025-08-06); sparseMatrixStats 1.21.0(2025-08-06); SpatialExperiment 1.19.1(2025-08-06); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); SummarizedExperiment 1.39.1(2025-08-06); 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(2025-08-06); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13) [2025-08-06 21:46:52] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE [2025-08-06 21:46:52] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-08-06 21:46:52] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2025-08-06 21:46:52] [TRACE] [OmnipathR] Contains 9 files. [2025-08-06 21:46:52] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-08-06 21:46:52] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-06 21:46:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-06 21:46:52] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2025-08-06 21:46:52] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2025-08-06 21:46:52] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-08-06 21:46:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-06 21:46:52] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-08-06 21:46:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-06 21:46:52] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-08-06 21:46:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-06 21:46:52] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-08-06 21:46:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-06 21:46:52] [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 31.150 2.382 41.743 run_fgsea 25.263 0.824 26.102 get_dorothea 21.595 1.051 25.100 run_aucell 10.127 1.787 11.958 get_progeny 6.728 0.415 14.631 * 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 re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 WARNING, 1 NOTE See ‘/home/biocbuild/bbs-3.22-bioc/meat/decoupleR.Rcheck/00check.log’ for details.
decoupleR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL decoupleR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-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-pc-linux-gnu R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > 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% [2025-08-06 21:50:34] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-06 21:50:34] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-06 21:50:34] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2025-08-06 21:50:34] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-08-06 21:50:34] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-08-06 [2025-08-06 21:50:34] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-08-06 19:08:11 UTC; unix [2025-08-06 21:50:34] [INFO] [OmnipathR] Package `OmnipathR` version: 3.17.4 [2025-08-06 21:50:34] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22 [2025-08-06 21:50:35] [INFO] [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13); os=Ubuntu 24.04.2 LTS; system=x86_64, linux-gnu; ui=X11; language=C; collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-08-06; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto] [2025-08-06 21:50:35] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.22-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0] [2025-08-06 21:50:35] [INFO] [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); annotate 1.87.0(2025-08-06); AnnotationDbi 1.71.1(2025-08-06); AUCell 1.31.0(2025-08-06); backports 1.5.0(2024-05-23); beachmat 2.25.4(2025-08-06); Biobase 2.69.0(2025-08-06); BiocGenerics 0.55.1(2025-08-06); BiocParallel 1.43.4(2025-08-06); BiocSingular 1.25.0(2025-08-06); Biostrings 2.77.2(2025-08-06); 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); 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(2025-08-06); DelayedArray 0.35.2(2025-08-06); DelayedMatrixStats 1.31.0(2025-08-06); desc 1.4.3(2023-12-10); 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(2025-08-06); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); GenomicRanges 1.61.1(2025-08-06); ggplot2 3.5.2(2025-04-09); glue 1.8.0(2024-09-30); graph 1.87.0(2025-08-06); GSEABase 1.71.0(2025-08-06); GSVA 2.3.1(2025-08-06); gtable 0.3.6(2024-10-25); h5mread 1.1.1(2025-08-06); HDF5Array 1.37.0(2025-08-06); 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(2025-08-06); irlba 2.3.5.1(2022-10-03); jsonlite 2.0.0(2025-03-27); KEGGREST 1.49.1(2025-08-06); 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(2025-08-06); 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(2025-08-06); 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); progress 1.2.3(2023-12-06); proxy 0.4-27(2022-06-09); 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(2025-08-06); rhdf5filters 1.21.0(2025-08-06); Rhdf5lib 1.31.0(2025-08-06); 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(2025-08-06); S4Vectors 0.47.0(2025-08-06); ScaledMatrix 1.17.0(2025-08-06); scales 1.4.0(2025-04-24); segmented 2.1-4(2025-02-28); Seqinfo 0.99.2(2025-08-06); sessioninfo 1.2.3(2025-02-05); SingleCellExperiment 1.31.1(2025-08-06); SparseArray 1.9.1(2025-08-06); sparseMatrixStats 1.21.0(2025-08-06); SpatialExperiment 1.19.1(2025-08-06); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); SummarizedExperiment 1.39.1(2025-08-06); 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(2025-08-06); viridisLite 0.4.2(2023-05-02); waldo 0.6.2(2025-07-11); 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(2025-08-06); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13) [2025-08-06 21:50:35] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE [2025-08-06 21:50:35] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-08-06 21:50:35] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2025-08-06 21:50:35] [TRACE] [OmnipathR] Contains 9 files. [2025-08-06 21:50:35] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-08-06 21:50:35] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-06 21:50:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-06 21:50:35] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2025-08-06 21:50:35] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2025-08-06 21:50:35] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-08-06 21:50:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-06 21:50:35] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-08-06 21:50:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-06 21:50:35] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-08-06 21:50:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-06 21:50:35] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-08-06 21:50:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-06 21:50:35] [TRACE] [OmnipathR] Cache locked: FALSE [2025-08-06 21:50:36] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-08-06 21:50:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-06 21:50:37] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-08-06 21:50:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-06 21:50:37] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`. [2025-08-06 21:50:37] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-06 21:50:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-06 21:50:37] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available. [2025-08-06 21:50:37] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-06 21:50:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-06 21:50:37] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1. [2025-08-06 21:50:37] [TRACE] [OmnipathR] Cache file path: /home/biocbuild/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html [2025-08-06 21:50:37] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html` [2025-08-06 21:50:37] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`. [2025-08-06 21:50:37] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html` [2025-08-06 21:50:37] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`. [2025-08-06 21:50:37] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2025-08-06 21:50:37] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-08-06 21:50:37] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-08-06 21:50:37] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0] [2025-08-06 21:50:37] [TRACE] [OmnipathR] Sending HTTP request. [2025-08-06 21:50:38] [TRACE] [OmnipathR] HTTP 200 (OK) [2025-08-06 21:50:38] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2025-08-06 21:50:38] [TRACE] [OmnipathR] Downloaded 31 Kb in 1.030512s from www.ensembl.org (30.1 Kb/s); Redirect: 0.782797s, DNS look up: 0.006506s, Connection: 0.007884s, Pretransfer: 0.665091s, First byte at: 1.005454s [2025-08-06 21:50:38] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 302 Found; Date: Thu, 07 Aug 2025 01:50:37 GMT; Content-Type: text/html; charset=iso-8859-1; Content-Length: 288; Connection: keep-alive; Server: Apache; Set-cookie: redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT; Location: //useast.ensembl.org/info/about/species.html?redirectsrc=//www.ensembl.org%2Finfo%2Fabout%2Fspecies.html; X-NGINX-MACHINE: wp-p1m2-35.ebi.ac.uk; HTTP/2 302 ; date: Thu, 07 Aug 2025 01:50:38 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-10-25-25-73.us-east-2.compute.internal; HTTP/2 200 ; date: Thu, 07 Aug 2025 01:50:38 GMT; content-type: text/html; charset=utf-8; content-length: 31787; server: Apache; set-cookie: redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT; set-cookie: redirect_mirror=no; path=/; expires=Fri, 08 Aug 2025 01:49:23 GMT; set-cookie: ENSEMBL_WWW_SESSION=26fc6d57202a16fa0c27d64368e3202400d37e5feb4b423c16481fa6; 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=Fri, 08 Aug 2025 01:49:23 GMT; set-cookie: ENSEMBL_WWW_SESSION=26fc6d57202a16fa0c27d64368e3202400d37e5feb4b423c16481fa6; 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-10-25-25-92.us-east-2.compute.internal [2025-08-06 21:50:38] [TRACE] [OmnipathR] Response headers: [date=Thu, 07 Aug 2025 01:50:38 GMT,content-type=text/html; charset=utf-8,content-length=31787,server=Apache,set-cookie=redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT,set-cookie=redirect_mirror=no; path=/; expires=Fri, 08 Aug 2025 01:49:23 GMT,set-cookie=ENSEMBL_WWW_SESSION=26fc6d57202a16fa0c27d64368e3202400d37e5feb4b423c16481fa6; 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=Fri, 08 Aug 2025 01:49:23 GMT,set-cookie=ENSEMBL_WWW_SESSION=26fc6d57202a16fa0c27d64368e3202400d37e5feb4b423c16481fa6; 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-10-25-25-92.us-east-2.compute.internal] [2025-08-06 21:50:39] [INFO] [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1] [2025-08-06 21:50:39] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-06 21:50:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-06 21:50:39] [INFO] [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`. [2025-08-06 21:50:40] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2025-08-06 21:50:40] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2025-08-06 21:50:40] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt` [2025-08-06 21:50:40] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`. [2025-08-06 21:50:40] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-06 21:50:40] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-06 21:50:40] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-06 21:50:40] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-06 21:50:40] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`. [2025-08-06 21:50:40] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2025-08-06 21:50:40] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt` [2025-08-06 21:50:40] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt` [2025-08-06 21:50:40] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-08-06 21:50:40] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-08-06 21:50:40] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-08-06 21:50:40] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2025-08-06 21:50:40] [TRACE] [OmnipathR] Downloaded 8.7 Kb in 0.465113s from omabrowser.org (18.7 Kb/s); Redirect: 0s, DNS look up: 0.001562s, Connection: 0.002291s, Pretransfer: 0.37309s, First byte at: 0.464868s [2025-08-06 21:50:40] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; date: Thu, 07 Aug 2025 01:50:40 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 [2025-08-06 21:50:42] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2025-08-06 21:50:42] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1] [2025-08-06 21:50:42] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-06 21:50:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-06 21:50:42] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`. [2025-08-06 21:50:42] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2025-08-06 21:50:42] [TRACE] [OmnipathR] Looking up in cache: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2025-08-06 21:50:42] [INFO] [OmnipathR] Cache record does not exist: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2025-08-06 21:50:42] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`. [2025-08-06 21:50:42] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-06 21:50:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-06 21:50:42] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-06 21:50:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-06 21:50:42] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `unknown` to `started`. [2025-08-06 21:50:42] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2025-08-06 21:50:42] [INFO] [OmnipathR] Retrieving URL: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2025-08-06 21:50:42] [TRACE] [OmnipathR] Attempt 1/3: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt` [2025-08-06 21:51:11] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`. [2025-08-06 21:51:11] [INFO] [OmnipathR] Download ready [key=56ad6544dc07a2222fa6013d8d83e6e5a35fdf33, version=1] [2025-08-06 21:51:11] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-06 21:51:11] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-06 21:51:11] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `started` to `ready`. [2025-08-06 21:51:11] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`. [2025-08-06 21:51:11] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-08-06 21:51:11] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=TFcensus,query_type=annotations] [2025-08-06 21:51:11] [TRACE] [OmnipathR] Organism(s): 9606 [2025-08-06 21:51:11] [TRACE] [OmnipathR] Orthology targets: [2025-08-06 21:51:12] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-08-06 21:51:12] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-06 21:51:12] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic` [2025-08-06 21:51:12] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic` [2025-08-06 21:51:12] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=TFcensus&license=academic` [2025-08-06 21:51:12] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=TFcensus&license=academic` [2025-08-06 21:51:12] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=TFcensus&license=academic` [2025-08-06 21:51:12] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic` [2025-08-06 21:51:12] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic` [2025-08-06 21:51:12] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-08-06 21:51:12] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-08-06 21:51:12] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-08-06 21:51:13] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-08-06 21:51:13] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.312055s from omnipathdb.org (50.2 Kb/s); Redirect: 0s, DNS look up: 0.002014s, Connection: 0.002866s, Pretransfer: 0.159426s, First byte at: 0.311442s [2025-08-06 21:51:13] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 07 Aug 2025 01:51:13 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Thu, 07 Aug 2025 02:51:13 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-08-06 21:51:14] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic` [2025-08-06 21:51:14] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-06 21:51:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-06 21:51:14] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-06 21:51:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-06 21:51:14] [INFO] [OmnipathR] Cache item `6f000d9b5edd9832b1c28754d1c3d9449c1c7490` version 1: status changed from `unknown` to `started`. [2025-08-06 21:51:14] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/6f000d9b5edd9832b1c28754d1c3d9449c1c7490-1.rds`. [2025-08-06 21:51:14] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/6f000d9b5edd9832b1c28754d1c3d9449c1c7490-1.rds`. [2025-08-06 21:51:14] [INFO] [OmnipathR] Download ready [key=6f000d9b5edd9832b1c28754d1c3d9449c1c7490, version=1] [2025-08-06 21:51:14] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-06 21:51:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-06 21:51:14] [INFO] [OmnipathR] Cache item `6f000d9b5edd9832b1c28754d1c3d9449c1c7490` version 1: status changed from `started` to `ready`. [2025-08-06 21:51:14] [SUCCESS] [OmnipathR] Downloaded 3099 annotation records. [2025-08-06 21:51:15] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-08-06 21:51:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-06 21:51:15] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-08-06 21:51:15] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=PROGENy,query_type=annotations] [2025-08-06 21:51:15] [TRACE] [OmnipathR] Organism(s): 9606 [2025-08-06 21:51:15] [TRACE] [OmnipathR] Orthology targets: [2025-08-06 21:51:16] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-08-06 21:51:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-06 21:51:16] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` [2025-08-06 21:51:16] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` [2025-08-06 21:51:16] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=PROGENy&license=academic` [2025-08-06 21:51:16] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=PROGENy&license=academic` [2025-08-06 21:51:16] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` [2025-08-06 21:51:16] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` [2025-08-06 21:51:16] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` [2025-08-06 21:51:16] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-08-06 21:51:16] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-08-06 21:51:16] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-08-06 21:51:16] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-08-06 21:51:16] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.321352s from omnipathdb.org (48.8 Kb/s); Redirect: 0s, DNS look up: 0.002431s, Connection: 0.003134s, Pretransfer: 0.169713s, First byte at: 0.320882s [2025-08-06 21:51:16] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 07 Aug 2025 01:51:16 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Thu, 07 Aug 2025 02:51:16 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-08-06 21:51:26] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` [2025-08-06 21:51:26] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-06 21:51:26] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-06 21:51:26] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-06 21:51:26] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-06 21:51:26] [INFO] [OmnipathR] Cache item `3492392585ba05414edfae46801492076437d7e7` version 1: status changed from `unknown` to `started`. [2025-08-06 21:51:26] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`. [2025-08-06 21:51:28] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`. [2025-08-06 21:51:28] [INFO] [OmnipathR] Download ready [key=3492392585ba05414edfae46801492076437d7e7, version=1] [2025-08-06 21:51:28] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-06 21:51:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-06 21:51:28] [INFO] [OmnipathR] Cache item `3492392585ba05414edfae46801492076437d7e7` version 1: status changed from `started` to `ready`. [2025-08-06 21:51:28] [SUCCESS] [OmnipathR] Downloaded 700239 annotation records. [2025-08-06 21:51:30] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-08-06 21:51:30] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-06 21:51:30] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-08-06 21:51:30] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=PROGENy,query_type=annotations] [2025-08-06 21:51:30] [TRACE] [OmnipathR] Organism(s): 9606 [2025-08-06 21:51:30] [TRACE] [OmnipathR] Orthology targets: [2025-08-06 21:51:31] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-08-06 21:51:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-06 21:51:31] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` [2025-08-06 21:51:33] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`. [2025-08-06 21:51:33] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` [2025-08-06 21:51:33] [SUCCESS] [OmnipathR] Loaded 700239 annotation records from cache. [2025-08-06 21:51:35] [INFO] [OmnipathR] Loading database `Orthologous Matrix (OMA) gene pairs`. [2025-08-06 21:51:35] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2025-08-06 21:51:35] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2025-08-06 21:51:35] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2025-08-06 21:51:35] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2025-08-06 21:51:35] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`. [2025-08-06 21:51:35] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`. [2025-08-06 21:51:35] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2025-08-06 21:51:35] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/api/pairs/HUMAN/MOUSE/?format=tsv&xrefs=UniProtKB%2FSwissProt&per_page=2000000`. [2025-08-06 21:51:35] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/api/pairs/HUMAN/MOUSE/?format=tsv&xrefs=UniProtKB%2FSwissProt&per_page=2000000` [2025-08-06 21:51:35] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/api/pairs/HUMAN/MOUSE/?format=tsv&xrefs=UniProtKB%2FSwissProt&per_page=2000000`. [2025-08-06 21:51:35] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-06 21:51:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-06 21:51:35] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-06 21:51:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-06 21:51:36] [INFO] [OmnipathR] Cache item `8f45b25c384d814c7de210e7ca40b7e35894e4f1` version 1: status changed from `unknown` to `started`. [2025-08-06 21:51:36] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/8f45b25c384d814c7de210e7ca40b7e35894e4f1-1.rds`. [2025-08-06 21:51:36] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/api/pairs/HUMAN/MOUSE/?format=tsv&xrefs=UniProtKB%2FSwissProt&per_page=2000000` [2025-08-06 21:51:36] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/api/pairs/HUMAN/MOUSE/?format=tsv&xrefs=UniProtKB%2FSwissProt&per_page=2000000` [2025-08-06 21:51:36] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-08-06 21:51:36] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-08-06 21:51:36] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-08-06 21:52:27] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2025-08-06 21:52:27] [TRACE] [OmnipathR] Downloaded 11.1 Kb in 50.964486s from omabrowser.org (222 bytes/s); Redirect: 0s, DNS look up: 0.001541s, Connection: 0.002258s, Pretransfer: 0.375039s, First byte at: 50.964216s [2025-08-06 21:52:27] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; date: Thu, 07 Aug 2025 01:52:26 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_2025-08-07_015225.tsv; x-frame-options: SAMEORIGIN; set-cookie: __matomo=8244793c6b91d491; expires=Sat, 07-Aug-2027 01:52:26 UTC; Path=/ [2025-08-06 21:52:30] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/8f45b25c384d814c7de210e7ca40b7e35894e4f1-1.rds`. [2025-08-06 21:52:30] [INFO] [OmnipathR] Download ready [key=8f45b25c384d814c7de210e7ca40b7e35894e4f1, version=1] [2025-08-06 21:52:30] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-06 21:52:30] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-06 21:52:30] [INFO] [OmnipathR] Cache item `8f45b25c384d814c7de210e7ca40b7e35894e4f1` version 1: status changed from `started` to `ready`. [2025-08-06 21:52:30] [TRACE] [OmnipathR] ID translation table: from `uniprot_entry` to `uniprot`, using `uniprot`. [2025-08-06 21:52:30] [TRACE] [OmnipathR] Creating ID mapping table from `id` to `accession`, for organism 9606 (only reviewed: TRUE) [2025-08-06 21:52:30] [TRACE] [OmnipathR] Loading all UniProt records for organism 9606 (only reviewed: TRUE); fields: id,accession [2025-08-06 21:52:30] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2025-08-06 21:52:30] [TRACE] [OmnipathR] Looking up in cache: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:9606%20AND%20reviewed:true`. [2025-08-06 21:52:30] [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` [2025-08-06 21:52:30] [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`. [2025-08-06 21:52:30] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-06 21:52:30] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-06 21:52:30] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-06 21:52:30] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-06 21:52:30] [INFO] [OmnipathR] Cache item `6558a1824894a625b8e3f80538cd3aa6e8a44379` version 1: status changed from `unknown` to `started`. [2025-08-06 21:52:30] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/6558a1824894a625b8e3f80538cd3aa6e8a44379-1.rds`. [2025-08-06 21:52:30] [INFO] [OmnipathR] Retrieving URL: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:9606%20AND%20reviewed:true` [2025-08-06 21:52:30] [TRACE] [OmnipathR] Attempt 1/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:9606%20AND%20reviewed:true` [2025-08-06 21:52:30] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-08-06 21:52:30] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-08-06 21:52:30] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-08-06 21:52:31] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2025-08-06 21:52:31] [TRACE] [OmnipathR] Downloaded 31 bytes in 0.884178s from rest.uniprot.org (35 bytes/s); Redirect: 0s, DNS look up: 0.017924s, Connection: 0.018657s, Pretransfer: 0.541331s, First byte at: 0.884093s [2025-08-06 21:52:31] [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: 18-June-2025; strict-transport-security: max-age=31536000; includeSubDomains; date: Thu, 07 Aug 2025 01:52:31 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 [2025-08-06 21:52:41] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/6558a1824894a625b8e3f80538cd3aa6e8a44379-1.rds`. [2025-08-06 21:52:41] [INFO] [OmnipathR] Download ready [key=6558a1824894a625b8e3f80538cd3aa6e8a44379, version=1] [2025-08-06 21:52:41] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-06 21:52:41] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-06 21:52:41] [INFO] [OmnipathR] Cache item `6558a1824894a625b8e3f80538cd3aa6e8a44379` version 1: status changed from `started` to `ready`. [2025-08-06 21:52:41] [SUCCESS] [OmnipathR] UniProt (rest.uniprot.org): downloaded 20420 records [2025-08-06 21:52:42] [TRACE] [OmnipathR] Translating complexes: 0 complexes in data. [2025-08-06 21:52:42] [TRACE] [OmnipathR] 0 complexes after removing the ones mapping to more than 1 items in target identifier space. [2025-08-06 21:52:42] [TRACE] [OmnipathR] Translated 0 complexes to 0. [2025-08-06 21:52:42] [TRACE] [OmnipathR] 13774 rows before translation, 13774 uniprot_entry IDs in column `id_organism_a`. [2025-08-06 21:52:42] [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`. [2025-08-06 21:52:42] [TRACE] [OmnipathR] ID translation table: from `uniprot_entry` to `uniprot`, using `uniprot`. [2025-08-06 21:52:42] [TRACE] [OmnipathR] Creating ID mapping table from `id` to `accession`, for organism 10090 (only reviewed: TRUE) [2025-08-06 21:52:42] [TRACE] [OmnipathR] Loading all UniProt records for organism 10090 (only reviewed: TRUE); fields: id,accession [2025-08-06 21:52:42] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2025-08-06 21:52:42] [TRACE] [OmnipathR] Looking up in cache: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:10090%20AND%20reviewed:true`. [2025-08-06 21:52:42] [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` [2025-08-06 21:52:42] [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`. [2025-08-06 21:52:42] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-06 21:52:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-06 21:52:42] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-06 21:52:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-06 21:52:42] [INFO] [OmnipathR] Cache item `43ea5f2cdaa9ac7e0e114371af97235cdddd776f` version 1: status changed from `unknown` to `started`. [2025-08-06 21:52:42] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/43ea5f2cdaa9ac7e0e114371af97235cdddd776f-1.rds`. [2025-08-06 21:52:42] [INFO] [OmnipathR] Retrieving URL: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:10090%20AND%20reviewed:true` [2025-08-06 21:52:42] [TRACE] [OmnipathR] Attempt 1/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:10090%20AND%20reviewed:true` [2025-08-06 21:52:42] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-08-06 21:52:42] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-08-06 21:52:42] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-08-06 21:52:43] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2025-08-06 21:52:43] [TRACE] [OmnipathR] Downloaded 31 bytes in 0.77688s from rest.uniprot.org (39 bytes/s); Redirect: 0s, DNS look up: 0.001661s, Connection: 0.002355s, Pretransfer: 0.489885s, First byte at: 0.776781s [2025-08-06 21:52:43] [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: 18-June-2025; strict-transport-security: max-age=31536000; includeSubDomains; date: Thu, 07 Aug 2025 01:52:43 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 [2025-08-06 21:52:49] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/43ea5f2cdaa9ac7e0e114371af97235cdddd776f-1.rds`. [2025-08-06 21:52:49] [INFO] [OmnipathR] Download ready [key=43ea5f2cdaa9ac7e0e114371af97235cdddd776f, version=1] [2025-08-06 21:52:49] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-06 21:52:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-06 21:52:49] [INFO] [OmnipathR] Cache item `43ea5f2cdaa9ac7e0e114371af97235cdddd776f` version 1: status changed from `started` to `ready`. [2025-08-06 21:52:49] [SUCCESS] [OmnipathR] UniProt (rest.uniprot.org): downloaded 17240 records [2025-08-06 21:52:50] [TRACE] [OmnipathR] Translating complexes: 0 complexes in data. [2025-08-06 21:52:50] [TRACE] [OmnipathR] 0 complexes after removing the ones mapping to more than 1 items in target identifier space. [2025-08-06 21:52:50] [TRACE] [OmnipathR] Translated 0 complexes to 0. [2025-08-06 21:52:50] [TRACE] [OmnipathR] 13774 rows before translation, 13773 uniprot_entry IDs in column `id_organism_b`. [2025-08-06 21:52:50] [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`. [2025-08-06 21:52:50] [INFO] [OmnipathR] Loaded database `Orthologous Matrix (OMA) gene pairs`. [2025-08-06 21:52:50] [TRACE] [OmnipathR] ID translation table: from `uniprot` to `genesymbol`, using `uniprot`. [2025-08-06 21:52:50] [TRACE] [OmnipathR] Creating ID mapping table from `accession` to `gene_primary`, for organism 10090 (only reviewed: TRUE) [2025-08-06 21:52:50] [TRACE] [OmnipathR] Loading all UniProt records for organism 10090 (only reviewed: TRUE); fields: accession,gene_primary [2025-08-06 21:52:50] [TRACE] [OmnipathR] Downloading by `generic_downloader`. [2025-08-06 21:52:50] [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`. [2025-08-06 21:52:50] [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` [2025-08-06 21:52:50] [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`. [2025-08-06 21:52:50] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-06 21:52:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-06 21:52:50] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-06 21:52:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-06 21:52:50] [INFO] [OmnipathR] Cache item `3ec84ba713c02573704adb50f1a94dab684df34b` version 1: status changed from `unknown` to `started`. [2025-08-06 21:52:50] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/3ec84ba713c02573704adb50f1a94dab684df34b-1.rds`. [2025-08-06 21:52:50] [INFO] [OmnipathR] Retrieving URL: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:10090%20AND%20reviewed:true` [2025-08-06 21:52:50] [TRACE] [OmnipathR] Attempt 1/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:10090%20AND%20reviewed:true` [2025-08-06 21:52:50] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-08-06 21:52:50] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-08-06 21:52:50] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-08-06 21:52:51] [TRACE] [OmnipathR] HTTP v2 GET: status 200. [2025-08-06 21:52:51] [TRACE] [OmnipathR] Downloaded 43 bytes in 0.543122s from rest.uniprot.org (79 bytes/s); Redirect: 0s, DNS look up: 0.002051s, Connection: 0.002768s, Pretransfer: 0.257544s, First byte at: 0.543058s [2025-08-06 21:52:51] [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: 18-June-2025; strict-transport-security: max-age=31536000; includeSubDomains; date: Thu, 07 Aug 2025 01:52:51 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 [2025-08-06 21:52:57] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/3ec84ba713c02573704adb50f1a94dab684df34b-1.rds`. [2025-08-06 21:52:57] [INFO] [OmnipathR] Download ready [key=3ec84ba713c02573704adb50f1a94dab684df34b, version=1] [2025-08-06 21:52:57] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-06 21:52:57] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-06 21:52:57] [INFO] [OmnipathR] Cache item `3ec84ba713c02573704adb50f1a94dab684df34b` version 1: status changed from `started` to `ready`. [2025-08-06 21:52:57] [SUCCESS] [OmnipathR] UniProt (rest.uniprot.org): downloaded 17240 records [2025-08-06 21:52:57] [TRACE] [OmnipathR] Translating complexes: 0 complexes in data. [2025-08-06 21:52:57] [TRACE] [OmnipathR] 0 complexes after removing the ones mapping to more than 1 items in target identifier space. [2025-08-06 21:52:57] [TRACE] [OmnipathR] Translated 0 complexes to 0. [2025-08-06 21:52:57] [TRACE] [OmnipathR] 163950 rows before translation, 12858 uniprot IDs in column `uniprot`. [2025-08-06 21:52:58] [TRACE] [OmnipathR] 163950 rows after translation; translated 12858 `uniprot` IDs in column `uniprot` to 12772 `genesymbol` IDs in column `genesymbol`. [2025-08-06 21:52:58] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-08-06 21:52:58] [TRACE] [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B,C,D],genesymbols=TRUE,organisms=9606,query_type=interactions,datasets=dorothea] [2025-08-06 21:52:58] [TRACE] [OmnipathR] Organism(s): 9606 [2025-08-06 21:52:58] [TRACE] [OmnipathR] Orthology targets: [2025-08-06 21:52:58] [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` [2025-08-06 21:52:58] [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` [2025-08-06 21:52:58] [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` [2025-08-06 21:52:58] [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` [2025-08-06 21:52:58] [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` [2025-08-06 21:52:58] [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` [2025-08-06 21:52:58] [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` [2025-08-06 21:52:58] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-08-06 21:52:58] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-08-06 21:52:58] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-08-06 21:52:58] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-08-06 21:52:58] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.462427s from omnipathdb.org (33.9 Kb/s); Redirect: 0s, DNS look up: 0.00176s, Connection: 0.002418s, Pretransfer: 0.309761s, First byte at: 0.461617s [2025-08-06 21:52:58] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 07 Aug 2025 01:52:58 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Thu, 07 Aug 2025 02:52:58 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-08-06 21:53:03] [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` [2025-08-06 21:53:03] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-06 21:53:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-06 21:53:03] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-06 21:53:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-06 21:53:03] [INFO] [OmnipathR] Cache item `46d37339bbc3f9a05bb89ccb79278cf1233f5cdf` version 1: status changed from `unknown` to `started`. [2025-08-06 21:53:03] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/46d37339bbc3f9a05bb89ccb79278cf1233f5cdf-1.rds`. [2025-08-06 21:53:04] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/46d37339bbc3f9a05bb89ccb79278cf1233f5cdf-1.rds`. [2025-08-06 21:53:04] [INFO] [OmnipathR] Download ready [key=46d37339bbc3f9a05bb89ccb79278cf1233f5cdf, version=1] [2025-08-06 21:53:04] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-06 21:53:04] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-06 21:53:04] [INFO] [OmnipathR] Cache item `46d37339bbc3f9a05bb89ccb79278cf1233f5cdf` version 1: status changed from `started` to `ready`. [2025-08-06 21:53:13] [SUCCESS] [OmnipathR] Downloaded 278830 interactions. [2025-08-06 21:53:22] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-08-06 21:53:22] [TRACE] [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B,C,D],genesymbols=TRUE,organisms=10090,query_type=interactions,datasets=dorothea] [2025-08-06 21:53:22] [TRACE] [OmnipathR] Organism(s): 10090 [2025-08-06 21:53:22] [TRACE] [OmnipathR] Orthology targets: [2025-08-06 21:53:22] [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` [2025-08-06 21:53:22] [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` [2025-08-06 21:53:22] [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` [2025-08-06 21:53:22] [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` [2025-08-06 21:53:22] [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` [2025-08-06 21:53:22] [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` [2025-08-06 21:53:22] [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` [2025-08-06 21:53:22] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-08-06 21:53:22] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-08-06 21:53:22] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-08-06 21:53:23] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-08-06 21:53:23] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.46299s from omnipathdb.org (33.8 Kb/s); Redirect: 0s, DNS look up: 0.002078s, Connection: 0.00281s, Pretransfer: 0.312158s, First byte at: 0.462544s [2025-08-06 21:53:23] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 07 Aug 2025 01:53:23 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Thu, 07 Aug 2025 02:53:23 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-08-06 21:53:28] [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` [2025-08-06 21:53:28] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-06 21:53:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-06 21:53:28] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-06 21:53:28] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-06 21:53:28] [INFO] [OmnipathR] Cache item `ff347dedf78ef5e38c9c6d8eed291fa901aa3791` version 1: status changed from `unknown` to `started`. [2025-08-06 21:53:28] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/ff347dedf78ef5e38c9c6d8eed291fa901aa3791-1.rds`. [2025-08-06 21:53:29] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/ff347dedf78ef5e38c9c6d8eed291fa901aa3791-1.rds`. [2025-08-06 21:53:29] [INFO] [OmnipathR] Download ready [key=ff347dedf78ef5e38c9c6d8eed291fa901aa3791, version=1] [2025-08-06 21:53:29] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-06 21:53:29] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-06 21:53:29] [INFO] [OmnipathR] Cache item `ff347dedf78ef5e38c9c6d8eed291fa901aa3791` version 1: status changed from `started` to `ready`. [2025-08-06 21:53:36] [SUCCESS] [OmnipathR] Downloaded 234298 interactions. [2025-08-06 21:53:44] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-08-06 21:53:44] [TRACE] [OmnipathR] Arguments for OmniPath query: [loops=TRUE,organisms=9606,genesymbols=TRUE,query_type=interactions,datasets=collectri] [2025-08-06 21:53:44] [TRACE] [OmnipathR] Organism(s): 9606 [2025-08-06 21:53:44] [TRACE] [OmnipathR] Orthology targets: [2025-08-06 21:53:44] [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` [2025-08-06 21:53:44] [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` [2025-08-06 21:53:44] [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` [2025-08-06 21:53:44] [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` [2025-08-06 21:53:44] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic` [2025-08-06 21:53:44] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic` [2025-08-06 21:53:44] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic` [2025-08-06 21:53:44] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-08-06 21:53:44] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-08-06 21:53:44] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-08-06 21:53:45] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-08-06 21:53:45] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.316032s from omnipathdb.org (49.6 Kb/s); Redirect: 0s, DNS look up: 0.002443s, Connection: 0.003276s, Pretransfer: 0.161874s, First byte at: 0.314954s [2025-08-06 21:53:45] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 07 Aug 2025 01:53:45 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Thu, 07 Aug 2025 02:53:45 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-08-06 21:53:48] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic` [2025-08-06 21:53:48] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-06 21:53:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-06 21:53:48] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-06 21:53:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-06 21:53:48] [INFO] [OmnipathR] Cache item `b10176737ba43d460b13709623189f3911123779` version 1: status changed from `unknown` to `started`. [2025-08-06 21:53:48] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/b10176737ba43d460b13709623189f3911123779-1.rds`. [2025-08-06 21:53:49] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/b10176737ba43d460b13709623189f3911123779-1.rds`. [2025-08-06 21:53:49] [INFO] [OmnipathR] Download ready [key=b10176737ba43d460b13709623189f3911123779, version=1] [2025-08-06 21:53:49] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-06 21:53:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-06 21:53:49] [INFO] [OmnipathR] Cache item `b10176737ba43d460b13709623189f3911123779` version 1: status changed from `started` to `ready`. [2025-08-06 21:53:51] [SUCCESS] [OmnipathR] Downloaded 64958 interactions. [2025-08-06 21:53:51] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-08-06 21:53:51] [TRACE] [OmnipathR] Arguments for OmniPath query: [genesymbols=TRUE,resources=CollecTRI,strict_evidences=TRUE,query_type=interactions,datasets=tf_mirna] [2025-08-06 21:53:51] [TRACE] [OmnipathR] Organism(s): 9606 [2025-08-06 21:53:51] [TRACE] [OmnipathR] Orthology targets: [2025-08-06 21:53:52] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-08-06 21:53:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-06 21:53:52] [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` [2025-08-06 21:53:52] [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` [2025-08-06 21:53:52] [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` [2025-08-06 21:53:52] [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` [2025-08-06 21:53:52] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic` [2025-08-06 21:53:52] [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` [2025-08-06 21:53:52] [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` [2025-08-06 21:53:52] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`. [2025-08-06 21:53:52] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt [2025-08-06 21:53:52] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2] [2025-08-06 21:53:52] [TRACE] [OmnipathR] HTTP v1 GET: status 200. [2025-08-06 21:53:52] [TRACE] [OmnipathR] Downloaded 9.5 Kb in 0.234496s from omnipathdb.org (40.5 Kb/s); Redirect: 0s, DNS look up: 0.001872s, Connection: 0.002596s, Pretransfer: 0.158244s, First byte at: 0.234112s [2025-08-06 21:53:52] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Thu, 07 Aug 2025 01:53:52 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Thu, 07 Aug 2025 02:53:52 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip [2025-08-06 21:53:54] [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` [2025-08-06 21:53:54] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-06 21:53:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-06 21:53:54] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-06 21:53:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-06 21:53:54] [INFO] [OmnipathR] Cache item `f7d34500401ba98803b7d2b26c48f64cee1eea1b` version 1: status changed from `unknown` to `started`. [2025-08-06 21:53:54] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/f7d34500401ba98803b7d2b26c48f64cee1eea1b-1.rds`. [2025-08-06 21:53:54] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/f7d34500401ba98803b7d2b26c48f64cee1eea1b-1.rds`. [2025-08-06 21:53:54] [INFO] [OmnipathR] Download ready [key=f7d34500401ba98803b7d2b26c48f64cee1eea1b, version=1] [2025-08-06 21:53:54] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-06 21:53:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-06 21:53:54] [INFO] [OmnipathR] Cache item `f7d34500401ba98803b7d2b26c48f64cee1eea1b` version 1: status changed from `started` to `ready`. [2025-08-06 21:53:54] [TRACE] [OmnipathR] Converting JSON column `evidences` to list. [2025-08-06 21:53:54] [TRACE] [OmnipathR] Restricting interaction records to datasets: tf_mirna; and resources: CollecTRI [2025-08-06 21:53:54] [TRACE] [OmnipathR] Filtering evidence columns: positive, negative, directed, undirected; to datasets: tf_mirna; and resources: CollecTRI; excluding resources: none [2025-08-06 21:53:54] [SUCCESS] [OmnipathR] Downloaded 232 interactions. [2025-08-06 21:53:55] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-08-06 21:53:55] [TRACE] [OmnipathR] Arguments for OmniPath query: [loops=TRUE,organisms=9606,genesymbols=TRUE,query_type=interactions,datasets=collectri] [2025-08-06 21:53:55] [TRACE] [OmnipathR] Organism(s): 9606 [2025-08-06 21:53:55] [TRACE] [OmnipathR] Orthology targets: [2025-08-06 21:53:55] [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` [2025-08-06 21:53:55] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/b10176737ba43d460b13709623189f3911123779-1.rds`. [2025-08-06 21:53:55] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic` [2025-08-06 21:53:57] [SUCCESS] [OmnipathR] Loaded 64958 interactions from cache. [2025-08-06 21:53:57] [TRACE] [OmnipathR] Processing args for OmniPath query [2025-08-06 21:53:57] [TRACE] [OmnipathR] Arguments for OmniPath query: [genesymbols=TRUE,resources=CollecTRI,strict_evidences=TRUE,query_type=interactions,datasets=tf_mirna] [2025-08-06 21:53:57] [TRACE] [OmnipathR] Organism(s): 9606 [2025-08-06 21:53:57] [TRACE] [OmnipathR] Orthology targets: [2025-08-06 21:53:58] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8). [2025-08-06 21:53:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-06 21:53:58] [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` [2025-08-06 21:53:58] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/f7d34500401ba98803b7d2b26c48f64cee1eea1b-1.rds`. [2025-08-06 21:53:58] [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` [2025-08-06 21:53:58] [TRACE] [OmnipathR] Converting JSON column `evidences` to list. [2025-08-06 21:53:58] [TRACE] [OmnipathR] Restricting interaction records to datasets: tf_mirna; and resources: CollecTRI [2025-08-06 21:53:58] [TRACE] [OmnipathR] Filtering evidence columns: positive, negative, directed, undirected; to datasets: tf_mirna; and resources: CollecTRI; excluding resources: none [2025-08-06 21:53:59] [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 179.205 25.983 301.751
decoupleR.Rcheck/decoupleR-Ex.timings
name | user | system | elapsed | |
check_corr | 0.072 | 0.026 | 0.098 | |
convert_f_defaults | 0.058 | 0.012 | 0.070 | |
decouple | 0.001 | 0.000 | 0.001 | |
dot-fit_preprocessing | 0.026 | 0.001 | 0.028 | |
extract_sets | 0.025 | 0.002 | 0.027 | |
filt_minsize | 0.045 | 0.003 | 0.048 | |
get_collectri | 31.150 | 2.382 | 41.743 | |
get_dorothea | 21.595 | 1.051 | 25.100 | |
get_profile_of | 0 | 0 | 0 | |
get_progeny | 6.728 | 0.415 | 14.631 | |
get_resource | 1.65 | 0.12 | 3.40 | |
get_toy_data | 0.003 | 0.000 | 0.002 | |
intersect_regulons | 0.023 | 0.005 | 0.027 | |
pipe | 0 | 0 | 0 | |
pivot_wider_profile | 0.001 | 0.000 | 0.000 | |
randomize_matrix | 0 | 0 | 0 | |
rename_net | 0.036 | 0.004 | 0.040 | |
run_aucell | 10.127 | 1.787 | 11.958 | |
run_consensus | 1.922 | 0.445 | 2.375 | |
run_fgsea | 25.263 | 0.824 | 26.102 | |
run_gsva | 1.941 | 0.448 | 2.401 | |
run_mdt | 0.153 | 0.020 | 0.169 | |
run_mlm | 0.087 | 0.023 | 0.110 | |
run_ora | 0.483 | 0.058 | 0.542 | |
run_udt | 0.264 | 0.036 | 0.300 | |
run_ulm | 0.076 | 0.010 | 0.087 | |
run_viper | 0.942 | 0.277 | 1.223 | |
run_wmean | 0.789 | 0.100 | 0.889 | |
run_wsum | 0.819 | 0.095 | 0.916 | |
show_methods | 0.047 | 0.008 | 0.055 | |
show_resources | 0.163 | 0.029 | 0.801 | |
tidyeval | 0.000 | 0.000 | 0.001 | |