Pau Badia-i-Mompel
| Snapshot Date: 2025-08-28 13:40 -0400 (Thu, 28 Aug 2025) |
| git_url: https://git.bioconductor.org/packages/decoupleR |
| git_branch: RELEASE_3_21 |
| git_last_commit: 5ed37a4 |
| git_last_commit_date: 2025-04-15 12:31:44 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-09-01 11:38 -0400 (Mon, 01 Sep 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4824 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4606 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4547 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4579 |
| 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 534/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| decoupleR 2.14.0 (landing page) Pau Badia-i-Mompel
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
| kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | ERROR | ||||||||||
|
To the developers/maintainers of the decoupleR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/decoupleR.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: decoupleR |
| Version: 2.14.0 |
| Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:decoupleR.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings decoupleR_2.14.0.tar.gz |
| StartedAt: 2025-08-31 21:42:55 -0400 (Sun, 31 Aug 2025) |
| EndedAt: 2025-08-31 21:52:30 -0400 (Sun, 31 Aug 2025) |
| EllapsedTime: 574.8 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: decoupleR.Rcheck |
| Warnings: 1 |
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###
### Running command:
###
### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:decoupleR.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings decoupleR_2.14.0.tar.gz
###
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##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.21-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 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘decoupleR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘decoupleR’ version ‘2.14.0’
* 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
[2025-08-31 21:43:28] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-31 21:43:28] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-31 21:43:28] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-08-31 21:43:28] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2025-08-31 21:43:28] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-08-31
[2025-08-31 21:43:28] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-08-31 19:12:17 UTC; unix
[2025-08-31 21:43:28] [INFO] [OmnipathR] Package `OmnipathR` version: 3.16.2
[2025-08-31 21:43:28] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21
[2025-08-31 21:43:29] [INFO] [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13); os=Ubuntu 24.04.3 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-08-31; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.5.57 @ /usr/local/bin/quarto]
[2025-08-31 21:43:29] [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-3.21-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-08-31 21:43:29] [INFO] [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); annotate 1.86.1(2025-08-31); AnnotationDbi 1.70.0(2025-08-31); AUCell 1.30.1(2025-08-31); backports 1.5.0(2024-05-23); beachmat 2.24.0(2025-08-31); Biobase 2.68.0(2025-08-31); BiocGenerics 0.54.0(2025-08-31); BiocParallel 1.42.1(2025-08-31); BiocSingular 1.24.0(2025-08-31); Biostrings 2.76.0(2025-08-31); 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 2.3.3(2025-08-18); 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 7.0.0(2025-08-19); data.table 1.17.8(2025-07-10); DBI 1.2.3(2024-06-02); decoupleR 2.14.0(2025-08-31); DelayedArray 0.34.1(2025-08-31); DelayedMatrixStats 1.30.0(2025-08-31); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); GenomeInfoDb 1.44.2(2025-08-31); GenomeInfoDbData 1.2.14(2025-06-19); GenomicRanges 1.60.0(2025-08-31); glue 1.8.0(2024-09-30); graph 1.86.0(2025-08-31); GSEABase 1.70.0(2025-08-31); GSVA 2.2.0(2025-08-31); h5mread 1.0.1(2025-08-31); HDF5Array 1.36.0(2025-08-31); 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 2.42.0(2025-08-31); irlba 2.3.5.1(2022-10-03); jsonlite 2.0.0(2025-03-27); KEGGREST 1.48.1(2025-08-31); knitr 1.50(2025-03-16); later 1.4.4(2025-08-27); 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 1.7-4(2025-08-28); MatrixGenerics 1.20.0(2025-08-31); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); OmnipathR 3.16.2(2025-08-31); 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 2.52.1(2025-08-31); rhdf5filters 1.20.0(2025-08-31); Rhdf5lib 1.30.0(2025-08-31); rjson 0.2.23(2024-09-16); rlang 1.1.6(2025-04-11); rmarkdown 2.29(2024-11-04); RSQLite 2.4.3(2025-08-20); rsvd 1.0.5(2021-04-16); rvest 1.0.5(2025-08-29); S4Arrays 1.8.1(2025-08-31); S4Vectors 0.46.0(2025-08-31); ScaledMatrix 1.16.0(2025-08-31); sessioninfo 1.2.3(2025-02-05); SingleCellExperiment 1.30.1(2025-08-31); SparseArray 1.8.1(2025-08-31); sparseMatrixStats 1.20.0(2025-08-31); SpatialExperiment 1.18.1(2025-08-31); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); SummarizedExperiment 1.38.1(2025-08-31); tibble 3.3.0(2025-06-08); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); UCSC.utils 1.4.0(2025-08-31); vctrs 0.6.5(2023-12-01); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.53(2025-08-19); XML 3.99-0.19(2025-08-22); xml2 1.4.0(2025-08-20); xtable 1.8-4(2019-04-21); XVector 0.48.0(2025-08-31); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2025-08-31 21:43:29] [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
[2025-08-31 21:43:29] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-08-31 21:43:29] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-08-31 21:43:29] [TRACE] [OmnipathR] Contains 8 files.
[2025-08-31 21:43:29] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-08-31 21:43:29] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-31 21:43:29] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-31 21:43:29] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-08-31 21:43:29] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2025-08-31 21:43:29] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-08-31 21:43:29] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-31 21:43:29] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-08-31 21:43:29] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-31 21:43:29] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-08-31 21:43:29] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-31 21:43:29] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-08-31 21:43:29] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-31 21:43:29] [TRACE] [OmnipathR] Cache locked: FALSE
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link(s) in Rd file 'run_gsva.Rd':
‘GSVA::gsva’ ‘GeneSetCollection’
Non-topic package-anchored link(s) in Rd file 'pipe.Rd':
‘[magrittr:pipe]{%>%}’
See section 'Cross-references' in the 'Writing R Extensions' manual.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
run_gsva.Rd: GSVA::gsva, GeneSetCollection
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
run_fgsea 23.561 0.538 24.108
get_dorothea 21.206 1.146 24.504
run_aucell 8.979 1.836 10.834
get_collectri 8.281 0.781 14.514
get_progeny 5.830 0.279 12.395
* 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-3.21-bioc/meat/decoupleR.Rcheck/00check.log’
for details.
decoupleR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL decoupleR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’ * installing *source* package ‘decoupleR’ ... ** this is package ‘decoupleR’ version ‘2.14.0’ ** 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")
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[2025-08-31 21:46:30] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-31 21:46:30] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-31 21:46:30] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-08-31 21:46:30] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2025-08-31 21:46:30] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-08-31
[2025-08-31 21:46:30] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-08-31 19:12:17 UTC; unix
[2025-08-31 21:46:30] [INFO] [OmnipathR] Package `OmnipathR` version: 3.16.2
[2025-08-31 21:46:30] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21
[2025-08-31 21:46:30] [INFO] [OmnipathR] Session info: [version=R version 4.5.1 (2025-06-13); os=Ubuntu 24.04.3 LTS; system=x86_64, linux-gnu; ui=X11; language=C; collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-08-31; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.5.57 @ /usr/local/bin/quarto]
[2025-08-31 21:46:30] [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-3.21-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-08-31 21:46:31] [INFO] [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); annotate 1.86.1(2025-08-31); AnnotationDbi 1.70.0(2025-08-31); AUCell 1.30.1(2025-08-31); backports 1.5.0(2024-05-23); beachmat 2.24.0(2025-08-31); Biobase 2.68.0(2025-08-31); BiocGenerics 0.54.0(2025-08-31); BiocParallel 1.42.1(2025-08-31); BiocSingular 1.24.0(2025-08-31); Biostrings 2.76.0(2025-08-31); 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 2.3.3(2025-08-18); 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 7.0.0(2025-08-19); data.table 1.17.8(2025-07-10); DBI 1.2.3(2024-06-02); decoupleR 2.14.0(2025-08-31); DelayedArray 0.34.1(2025-08-31); DelayedMatrixStats 1.30.0(2025-08-31); 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 1.0.5(2025-08-27); farver 2.1.2(2024-05-13); fastmap 1.2.0(2024-05-15); fastmatch 1.1-6(2024-12-23); fgsea 1.34.2(2025-08-31); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); GenomeInfoDb 1.44.2(2025-08-31); GenomeInfoDbData 1.2.14(2025-06-19); GenomicRanges 1.60.0(2025-08-31); ggplot2 3.5.2(2025-04-09); glue 1.8.0(2024-09-30); graph 1.86.0(2025-08-31); GSEABase 1.70.0(2025-08-31); GSVA 2.2.0(2025-08-31); gtable 0.3.6(2024-10-25); h5mread 1.0.1(2025-08-31); HDF5Array 1.36.0(2025-08-31); 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 2.42.0(2025-08-31); irlba 2.3.5.1(2022-10-03); jsonlite 2.0.0(2025-03-27); KEGGREST 1.48.1(2025-08-31); kernlab 0.9-33(2024-08-13); KernSmooth 2.23-26(2025-01-01); knitr 1.50(2025-03-16); later 1.4.4(2025-08-27); 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 1.7-4(2025-08-28); MatrixGenerics 1.20.0(2025-08-31); 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 3.16.2(2025-08-31); 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 2.52.1(2025-08-31); rhdf5filters 1.20.0(2025-08-31); Rhdf5lib 1.30.0(2025-08-31); 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 2.4.3(2025-08-20); rsvd 1.0.5(2021-04-16); rvest 1.0.5(2025-08-29); S4Arrays 1.8.1(2025-08-31); S4Vectors 0.46.0(2025-08-31); ScaledMatrix 1.16.0(2025-08-31); scales 1.4.0(2025-04-24); segmented 2.1-4(2025-02-28); sessioninfo 1.2.3(2025-02-05); SingleCellExperiment 1.30.1(2025-08-31); SparseArray 1.8.1(2025-08-31); sparseMatrixStats 1.20.0(2025-08-31); SpatialExperiment 1.18.1(2025-08-31); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); SummarizedExperiment 1.38.1(2025-08-31); survival 3.8-3(2024-12-17); testthat 3.2.3(2025-01-13); tibble 3.3.0(2025-06-08); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); UCSC.utils 1.4.0(2025-08-31); vctrs 0.6.5(2023-12-01); viper 1.42.0(2025-08-31); viridisLite 0.4.2(2023-05-02); waldo 0.6.2(2025-07-11); withr 3.0.2(2024-10-28); xfun 0.53(2025-08-19); XML 3.99-0.19(2025-08-22); xml2 1.4.0(2025-08-20); xtable 1.8-4(2019-04-21); XVector 0.48.0(2025-08-31); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2025-08-31 21:46:31] [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
[2025-08-31 21:46:31] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-08-31 21:46:31] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-08-31 21:46:31] [TRACE] [OmnipathR] Contains 8 files.
[2025-08-31 21:46:31] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-08-31 21:46:31] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-31 21:46:31] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-31 21:46:31] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-08-31 21:46:31] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2025-08-31 21:46:31] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-08-31 21:46:31] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-31 21:46:31] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-08-31 21:46:31] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-31 21:46:31] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-08-31 21:46:31] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-31 21:46:31] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-08-31 21:46:31] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-31 21:46:31] [TRACE] [OmnipathR] Cache locked: FALSE
[2025-08-31 21:46:31] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-08-31 21:46:31] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-31 21:46:32] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-08-31 21:46:32] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-31 21:46:32] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2025-08-31 21:46:32] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-31 21:46:32] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-31 21:46:32] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2025-08-31 21:46:32] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-31 21:46:32] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-31 21:46:32] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2025-08-31 21:46:32] [TRACE] [OmnipathR] Cache file path: /home/biocbuild/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2025-08-31 21:46:32] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2025-08-31 21:46:32] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`.
[2025-08-31 21:46:32] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2025-08-31 21:46:32] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2025-08-31 21:46:32] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0]
[2025-08-31 21:46:32] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-08-31 21:46:32] [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]
[2025-08-31 21:46:32] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:120.0) Gecko/20100101 Firefox/120.0]
[2025-08-31 21:46:32] [TRACE] [OmnipathR] Sending HTTP request.
[2025-08-31 21:46:54] [TRACE] [OmnipathR] HTTP 200 (OK)
[2025-08-31 21:46:54] [TRACE] [OmnipathR] HTTP v2 GET: status 200.
[2025-08-31 21:46:54] [TRACE] [OmnipathR] Downloaded 31.2 Kb in 21.59085s from www.ensembl.org (1.4 Kb/s); Redirect: 1.497863s, DNS look up: 0.010439s, Connection: 0.011885s, Pretransfer: 0.699598s, First byte at: 21.560474s
[2025-08-31 21:46:54] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 302 Found; Date: Mon, 01 Sep 2025 01:46:33 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: Mon, 01 Sep 2025 01:46:34 GMT; content-type: text/html; charset=iso-8859-1; content-length: 208; server: Apache; set-cookie: redirected_from_url=%2F%2Fwww.ensembl.org%252Finfo%252Fabout%252Fspecies.html; path=/; expires=Thu, 31-Dec-2037 23:59:59 GMT; location: /info/about/species.html; x-nginx-machine: ip-10-25-25-86.us-east-2.compute.internal; HTTP/2 200 ; date: Mon, 01 Sep 2025 01:46:54 GMT; content-type: text/html; charset=utf-8; content-length: 31909; server: Apache; set-cookie: redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT; set-cookie: redirect_mirror=no; path=/; expires=Tue, 02 Sep 2025 01:42:41 GMT; set-cookie: ENSEMBL_WWW_SESSION=803685513b4a34680e10ae6a690414170012b27ee6c82a760d812203; 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=Tue, 02 Sep 2025 01:42:41 GMT; set-cookie: ENSEMBL_WWW_SESSION=803685513b4a34680e10ae6a690414170012b27ee6c82a760d812203; path=/; expires=Thu, 31-Dec-2037 23:59:59 GMT; HttpOnly; vary: Accept-Encoding; content-encoding: gzip; x-frame-options: SAMEORIGIN; content-security-policy: frame-ancestors 'self'; x-nginx-machine: ip-10-25-25-73.us-east-2.compute.internal
[2025-08-31 21:46:54] [TRACE] [OmnipathR] Response headers: [date=Mon, 01 Sep 2025 01:46:54 GMT,content-type=text/html; charset=utf-8,content-length=31909,server=Apache,set-cookie=redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT,set-cookie=redirect_mirror=no; path=/; expires=Tue, 02 Sep 2025 01:42:41 GMT,set-cookie=ENSEMBL_WWW_SESSION=803685513b4a34680e10ae6a690414170012b27ee6c82a760d812203; 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=Tue, 02 Sep 2025 01:42:41 GMT,set-cookie=ENSEMBL_WWW_SESSION=803685513b4a34680e10ae6a690414170012b27ee6c82a760d812203; path=/; expires=Thu, 31-Dec-2037 23:59:59 GMT; HttpOnly,vary=Accept-Encoding,content-encoding=gzip,x-frame-options=SAMEORIGIN,content-security-policy=frame-ancestors 'self',x-nginx-machine=ip-10-25-25-73.us-east-2.compute.internal]
[2025-08-31 21:46:55] [INFO] [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1]
[2025-08-31 21:46:55] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-31 21:46:55] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-31 21:46:55] [INFO] [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`.
[2025-08-31 21:46:56] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2025-08-31 21:46:56] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2025-08-31 21:46:56] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2025-08-31 21:46:56] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2025-08-31 21:46:56] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-31 21:46:56] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-31 21:46:56] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-31 21:46:56] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-31 21:46:56] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2025-08-31 21:46:56] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-08-31 21:46:56] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2025-08-31 21:46:56] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2025-08-31 21:46:56] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2025-08-31 21:46:56] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-08-31 21:46:56] [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]
[2025-08-31 21:46:56] [TRACE] [OmnipathR] HTTP v2 GET: status 200.
[2025-08-31 21:46:56] [TRACE] [OmnipathR] Downloaded 8.7 Kb in 0.420252s from omabrowser.org (20.7 Kb/s); Redirect: 0s, DNS look up: 0.001854s, Connection: 0.002549s, Pretransfer: 0.335102s, First byte at: 0.419938s
[2025-08-31 21:46:56] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; date: Mon, 01 Sep 2025 01:46:56 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
[2025-08-31 21:46:58] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-08-31 21:46:58] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1]
[2025-08-31 21:46:58] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-31 21:46:58] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-31 21:46:58] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.
[2025-08-31 21:46:58] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`.
[2025-08-31 21:46:58] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-08-31 21:46:58] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=TFcensus,query_type=annotations]
[2025-08-31 21:46:58] [TRACE] [OmnipathR] Organism(s): 9606
[2025-08-31 21:46:58] [TRACE] [OmnipathR] Orthology targets:
[2025-08-31 21:46:59] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-08-31 21:46:59] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-31 21:46:59] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2025-08-31 21:46:59] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2025-08-31 21:46:59] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2025-08-31 21:46:59] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2025-08-31 21:46:59] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2025-08-31 21:46:59] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2025-08-31 21:46:59] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2025-08-31 21:46:59] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2025-08-31 21:46:59] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-08-31 21:46:59] [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]
[2025-08-31 21:46:59] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2025-08-31 21:46:59] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.278077s from omnipathdb.org (56.3 Kb/s); Redirect: 0s, DNS look up: 0.001675s, Connection: 0.002481s, Pretransfer: 0.14278s, First byte at: 0.277662s
[2025-08-31 21:46:59] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 01 Sep 2025 01:46:59 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Mon, 01 Sep 2025 02:46:59 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-08-31 21:47:00] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2025-08-31 21:47:00] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-31 21:47:00] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-31 21:47:00] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-31 21:47:00] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-31 21:47:00] [INFO] [OmnipathR] Cache item `6f000d9b5edd9832b1c28754d1c3d9449c1c7490` version 1: status changed from `unknown` to `started`.
[2025-08-31 21:47:00] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/6f000d9b5edd9832b1c28754d1c3d9449c1c7490-1.rds`.
[2025-08-31 21:47:00] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/6f000d9b5edd9832b1c28754d1c3d9449c1c7490-1.rds`.
[2025-08-31 21:47:00] [INFO] [OmnipathR] Download ready [key=6f000d9b5edd9832b1c28754d1c3d9449c1c7490, version=1]
[2025-08-31 21:47:00] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-31 21:47:01] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-31 21:47:01] [INFO] [OmnipathR] Cache item `6f000d9b5edd9832b1c28754d1c3d9449c1c7490` version 1: status changed from `started` to `ready`.
[2025-08-31 21:47:01] [SUCCESS] [OmnipathR] Downloaded 3497 annotation records.
[2025-08-31 21:47:01] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-08-31 21:47:01] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-31 21:47:01] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-08-31 21:47:01] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=PROGENy,query_type=annotations]
[2025-08-31 21:47:01] [TRACE] [OmnipathR] Organism(s): 9606
[2025-08-31 21:47:01] [TRACE] [OmnipathR] Orthology targets:
[2025-08-31 21:47:02] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-08-31 21:47:02] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-31 21:47:02] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-08-31 21:47:02] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-08-31 21:47:02] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-08-31 21:47:02] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-08-31 21:47:02] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-08-31 21:47:02] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-08-31 21:47:02] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-08-31 21:47:02] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2025-08-31 21:47:02] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-08-31 21:47:02] [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]
[2025-08-31 21:47:02] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2025-08-31 21:47:02] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.273388s from omnipathdb.org (57.3 Kb/s); Redirect: 0s, DNS look up: 0.001676s, Connection: 0.002357s, Pretransfer: 0.13945s, First byte at: 0.272517s
[2025-08-31 21:47:02] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 01 Sep 2025 01:47:02 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Mon, 01 Sep 2025 02:47:02 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-08-31 21:47:11] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-08-31 21:47:11] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-31 21:47:11] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-31 21:47:11] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-31 21:47:11] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-31 21:47:11] [INFO] [OmnipathR] Cache item `3492392585ba05414edfae46801492076437d7e7` version 1: status changed from `unknown` to `started`.
[2025-08-31 21:47:11] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`.
[2025-08-31 21:47:14] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`.
[2025-08-31 21:47:14] [INFO] [OmnipathR] Download ready [key=3492392585ba05414edfae46801492076437d7e7, version=1]
[2025-08-31 21:47:14] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-31 21:47:14] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-31 21:47:14] [INFO] [OmnipathR] Cache item `3492392585ba05414edfae46801492076437d7e7` version 1: status changed from `started` to `ready`.
[2025-08-31 21:47:14] [SUCCESS] [OmnipathR] Downloaded 699831 annotation records.
[2025-08-31 21:47:15] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-08-31 21:47:15] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-31 21:47:16] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-08-31 21:47:16] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=PROGENy,query_type=annotations]
[2025-08-31 21:47:16] [TRACE] [OmnipathR] Organism(s): 9606
[2025-08-31 21:47:16] [TRACE] [OmnipathR] Orthology targets:
[2025-08-31 21:47:16] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-08-31 21:47:16] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-31 21:47:16] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-08-31 21:47:18] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`.
[2025-08-31 21:47:18] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-08-31 21:47:18] [SUCCESS] [OmnipathR] Loaded 699831 annotation records from cache.
[2025-08-31 21:47:20] [INFO] [OmnipathR] Loading database `Orthologous Matrix (OMA) gene pairs`.
[2025-08-31 21:47:20] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2025-08-31 21:47:20] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2025-08-31 21:47:20] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-08-31 21:47:20] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2025-08-31 21:47:20] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2025-08-31 21:47:20] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-08-31 21:47:20] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2025-08-31 21:47:20] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/api/pairs/HUMAN/MOUSE/?format=tsv&xrefs=UniProtKB%2FSwissProt&per_page=2000000`.
[2025-08-31 21:47:20] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/api/pairs/HUMAN/MOUSE/?format=tsv&xrefs=UniProtKB%2FSwissProt&per_page=2000000`
[2025-08-31 21:47:20] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/api/pairs/HUMAN/MOUSE/?format=tsv&xrefs=UniProtKB%2FSwissProt&per_page=2000000`.
[2025-08-31 21:47:20] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-31 21:47:20] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-31 21:47:20] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-31 21:47:20] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-31 21:47:20] [INFO] [OmnipathR] Cache item `8f45b25c384d814c7de210e7ca40b7e35894e4f1` version 1: status changed from `unknown` to `started`.
[2025-08-31 21:47:20] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/8f45b25c384d814c7de210e7ca40b7e35894e4f1-1.rds`.
[2025-08-31 21:47:20] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/api/pairs/HUMAN/MOUSE/?format=tsv&xrefs=UniProtKB%2FSwissProt&per_page=2000000`
[2025-08-31 21:47:20] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/api/pairs/HUMAN/MOUSE/?format=tsv&xrefs=UniProtKB%2FSwissProt&per_page=2000000`
[2025-08-31 21:47:20] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2025-08-31 21:47:20] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-08-31 21:47:20] [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]
[2025-08-31 21:47:49] [TRACE] [OmnipathR] HTTP v2 GET: status 200.
[2025-08-31 21:47:49] [TRACE] [OmnipathR] Downloaded 11.1 Kb in 28.600647s from omabrowser.org (396 bytes/s); Redirect: 0s, DNS look up: 0.001849s, Connection: 0.002604s, Pretransfer: 0.169047s, First byte at: 28.600455s
[2025-08-31 21:47:49] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; date: Mon, 01 Sep 2025 01:47:49 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_2025-09-01_014747.tsv; x-frame-options: SAMEORIGIN; set-cookie: __matomo=73d0113761fa7ad3; expires=Wed, 01-Sep-2027 01:47:49 UTC; Path=/
[2025-08-31 21:47:52] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/8f45b25c384d814c7de210e7ca40b7e35894e4f1-1.rds`.
[2025-08-31 21:47:52] [INFO] [OmnipathR] Download ready [key=8f45b25c384d814c7de210e7ca40b7e35894e4f1, version=1]
[2025-08-31 21:47:52] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-31 21:47:52] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-31 21:47:52] [INFO] [OmnipathR] Cache item `8f45b25c384d814c7de210e7ca40b7e35894e4f1` version 1: status changed from `started` to `ready`.
[2025-08-31 21:47:52] [TRACE] [OmnipathR] ID translation table: from `uniprot_entry` to `uniprot`, using `uniprot`.
[2025-08-31 21:47:52] [TRACE] [OmnipathR] Creating ID mapping table from `id` to `accession`, for organism 9606 (only reviewed: TRUE)
[2025-08-31 21:47:52] [TRACE] [OmnipathR] Loading all UniProt records for organism 9606 (only reviewed: TRUE); fields: id,accession
[2025-08-31 21:47:52] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2025-08-31 21:47:52] [TRACE] [OmnipathR] Looking up in cache: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:9606%20AND%20reviewed:true`.
[2025-08-31 21:47:52] [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`
[2025-08-31 21:47:52] [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`.
[2025-08-31 21:47:52] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-31 21:47:52] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-31 21:47:52] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-31 21:47:52] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-31 21:47:52] [INFO] [OmnipathR] Cache item `6558a1824894a625b8e3f80538cd3aa6e8a44379` version 1: status changed from `unknown` to `started`.
[2025-08-31 21:47:52] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/6558a1824894a625b8e3f80538cd3aa6e8a44379-1.rds`.
[2025-08-31 21:47:52] [INFO] [OmnipathR] Retrieving URL: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:9606%20AND%20reviewed:true`
[2025-08-31 21:47:52] [TRACE] [OmnipathR] Attempt 1/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:9606%20AND%20reviewed:true`
[2025-08-31 21:47:52] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2025-08-31 21:47:52] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-08-31 21:47:52] [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]
[2025-08-31 21:47:53] [TRACE] [OmnipathR] HTTP v2 GET: status 200.
[2025-08-31 21:47:53] [TRACE] [OmnipathR] Downloaded 31 bytes in 0.91203s from rest.uniprot.org (33 bytes/s); Redirect: 0s, DNS look up: 0.003146s, Connection: 0.003875s, Pretransfer: 0.529854s, First byte at: 0.911969s
[2025-08-31 21:47:53] [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: Mon, 01 Sep 2025 01:47:53 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
[2025-08-31 21:48:03] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/6558a1824894a625b8e3f80538cd3aa6e8a44379-1.rds`.
[2025-08-31 21:48:03] [INFO] [OmnipathR] Download ready [key=6558a1824894a625b8e3f80538cd3aa6e8a44379, version=1]
[2025-08-31 21:48:03] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-31 21:48:03] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-31 21:48:03] [INFO] [OmnipathR] Cache item `6558a1824894a625b8e3f80538cd3aa6e8a44379` version 1: status changed from `started` to `ready`.
[2025-08-31 21:48:03] [SUCCESS] [OmnipathR] UniProt (rest.uniprot.org): downloaded 20420 records
[2025-08-31 21:48:03] [TRACE] [OmnipathR] Translating complexes: 0 complexes in data.
[2025-08-31 21:48:03] [TRACE] [OmnipathR] 0 complexes after removing the ones mapping to more than 1 items in target identifier space.
[2025-08-31 21:48:03] [TRACE] [OmnipathR] Translated 0 complexes to 0.
[2025-08-31 21:48:03] [TRACE] [OmnipathR] 13774 rows before translation, 13774 uniprot_entry IDs in column `id_organism_a`.
[2025-08-31 21:48:03] [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`.
[2025-08-31 21:48:03] [TRACE] [OmnipathR] ID translation table: from `uniprot_entry` to `uniprot`, using `uniprot`.
[2025-08-31 21:48:03] [TRACE] [OmnipathR] Creating ID mapping table from `id` to `accession`, for organism 10090 (only reviewed: TRUE)
[2025-08-31 21:48:03] [TRACE] [OmnipathR] Loading all UniProt records for organism 10090 (only reviewed: TRUE); fields: id,accession
[2025-08-31 21:48:03] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2025-08-31 21:48:03] [TRACE] [OmnipathR] Looking up in cache: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:10090%20AND%20reviewed:true`.
[2025-08-31 21:48:03] [INFO] [OmnipathR] Cache record does not exist: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:10090%20AND%20reviewed:true`
[2025-08-31 21:48:03] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:10090%20AND%20reviewed:true`.
[2025-08-31 21:48:03] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-31 21:48:03] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-31 21:48:03] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-31 21:48:03] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-31 21:48:03] [INFO] [OmnipathR] Cache item `43ea5f2cdaa9ac7e0e114371af97235cdddd776f` version 1: status changed from `unknown` to `started`.
[2025-08-31 21:48:03] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/43ea5f2cdaa9ac7e0e114371af97235cdddd776f-1.rds`.
[2025-08-31 21:48:03] [INFO] [OmnipathR] Retrieving URL: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:10090%20AND%20reviewed:true`
[2025-08-31 21:48:03] [TRACE] [OmnipathR] Attempt 1/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:10090%20AND%20reviewed:true`
[2025-08-31 21:48:03] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2025-08-31 21:48:03] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-08-31 21:48:03] [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]
[2025-08-31 21:48:04] [TRACE] [OmnipathR] HTTP v2 GET: status 200.
[2025-08-31 21:48:04] [TRACE] [OmnipathR] Downloaded 31 bytes in 0.762125s from rest.uniprot.org (40 bytes/s); Redirect: 0s, DNS look up: 0.002372s, Connection: 0.003079s, Pretransfer: 0.485392s, First byte at: 0.762038s
[2025-08-31 21:48:04] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; vary: accept,accept-encoding,x-uniprot-release,x-api-deployment-date; vary: User-Agent; cache-control: public, max-age=43200; content-type: text/plain;format=tsv; content-encoding: gzip; access-control-allow-credentials: true; access-control-expose-headers: Link, X-Total-Results, X-UniProt-Release, X-UniProt-Release-Date, X-API-Deployment-Date; x-api-deployment-date: 08-August-2025; strict-transport-security: max-age=31536000; includeSubDomains; date: Mon, 01 Sep 2025 01:48:04 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
[2025-08-31 21:48:11] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/43ea5f2cdaa9ac7e0e114371af97235cdddd776f-1.rds`.
[2025-08-31 21:48:11] [INFO] [OmnipathR] Download ready [key=43ea5f2cdaa9ac7e0e114371af97235cdddd776f, version=1]
[2025-08-31 21:48:11] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-31 21:48:11] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-31 21:48:11] [INFO] [OmnipathR] Cache item `43ea5f2cdaa9ac7e0e114371af97235cdddd776f` version 1: status changed from `started` to `ready`.
[2025-08-31 21:48:11] [SUCCESS] [OmnipathR] UniProt (rest.uniprot.org): downloaded 17240 records
[2025-08-31 21:48:11] [TRACE] [OmnipathR] Translating complexes: 0 complexes in data.
[2025-08-31 21:48:11] [TRACE] [OmnipathR] 0 complexes after removing the ones mapping to more than 1 items in target identifier space.
[2025-08-31 21:48:11] [TRACE] [OmnipathR] Translated 0 complexes to 0.
[2025-08-31 21:48:11] [TRACE] [OmnipathR] 13774 rows before translation, 13773 uniprot_entry IDs in column `id_organism_b`.
[2025-08-31 21:48:11] [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`.
[2025-08-31 21:48:11] [INFO] [OmnipathR] Loaded database `Orthologous Matrix (OMA) gene pairs`.
[2025-08-31 21:48:11] [TRACE] [OmnipathR] ID translation table: from `uniprot` to `genesymbol`, using `uniprot`.
[2025-08-31 21:48:11] [TRACE] [OmnipathR] Creating ID mapping table from `accession` to `gene_primary`, for organism 10090 (only reviewed: TRUE)
[2025-08-31 21:48:11] [TRACE] [OmnipathR] Loading all UniProt records for organism 10090 (only reviewed: TRUE); fields: accession,gene_primary
[2025-08-31 21:48:11] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2025-08-31 21:48:11] [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`.
[2025-08-31 21:48:11] [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`
[2025-08-31 21:48:11] [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`.
[2025-08-31 21:48:11] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-31 21:48:11] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-31 21:48:11] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-31 21:48:11] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-31 21:48:11] [INFO] [OmnipathR] Cache item `3ec84ba713c02573704adb50f1a94dab684df34b` version 1: status changed from `unknown` to `started`.
[2025-08-31 21:48:11] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/3ec84ba713c02573704adb50f1a94dab684df34b-1.rds`.
[2025-08-31 21:48:11] [INFO] [OmnipathR] Retrieving URL: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:10090%20AND%20reviewed:true`
[2025-08-31 21:48:11] [TRACE] [OmnipathR] Attempt 1/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:10090%20AND%20reviewed:true`
[2025-08-31 21:48:11] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2025-08-31 21:48:11] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-08-31 21:48:11] [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]
[2025-08-31 21:48:12] [TRACE] [OmnipathR] HTTP v2 GET: status 200.
[2025-08-31 21:48:12] [TRACE] [OmnipathR] Downloaded 43 bytes in 0.567448s from rest.uniprot.org (75 bytes/s); Redirect: 0s, DNS look up: 0.003182s, Connection: 0.003918s, Pretransfer: 0.246056s, First byte at: 0.567391s
[2025-08-31 21:48:12] [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: Mon, 01 Sep 2025 01:48:12 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
[2025-08-31 21:48:19] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/3ec84ba713c02573704adb50f1a94dab684df34b-1.rds`.
[2025-08-31 21:48:19] [INFO] [OmnipathR] Download ready [key=3ec84ba713c02573704adb50f1a94dab684df34b, version=1]
[2025-08-31 21:48:19] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-31 21:48:19] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-31 21:48:19] [INFO] [OmnipathR] Cache item `3ec84ba713c02573704adb50f1a94dab684df34b` version 1: status changed from `started` to `ready`.
[2025-08-31 21:48:19] [SUCCESS] [OmnipathR] UniProt (rest.uniprot.org): downloaded 17240 records
[2025-08-31 21:48:19] [TRACE] [OmnipathR] Translating complexes: 0 complexes in data.
[2025-08-31 21:48:19] [TRACE] [OmnipathR] 0 complexes after removing the ones mapping to more than 1 items in target identifier space.
[2025-08-31 21:48:19] [TRACE] [OmnipathR] Translated 0 complexes to 0.
[2025-08-31 21:48:19] [TRACE] [OmnipathR] 163908 rows before translation, 12855 uniprot IDs in column `uniprot`.
[2025-08-31 21:48:19] [TRACE] [OmnipathR] 163908 rows after translation; translated 12855 `uniprot` IDs in column `uniprot` to 12769 `genesymbol` IDs in column `genesymbol`.
[2025-08-31 21:48:19] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-08-31 21:48:19] [TRACE] [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B,C,D],genesymbols=TRUE,organisms=9606,query_type=interactions,datasets=dorothea]
[2025-08-31 21:48:19] [TRACE] [OmnipathR] Organism(s): 9606
[2025-08-31 21:48:19] [TRACE] [OmnipathR] Orthology targets:
[2025-08-31 21:48:19] [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`
[2025-08-31 21:48:19] [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`
[2025-08-31 21:48:19] [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`
[2025-08-31 21:48:19] [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`
[2025-08-31 21:48:19] [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`
[2025-08-31 21:48:19] [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`
[2025-08-31 21:48:19] [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`
[2025-08-31 21:48:19] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2025-08-31 21:48:19] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-08-31 21:48:19] [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]
[2025-08-31 21:48:20] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2025-08-31 21:48:20] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.274152s from omnipathdb.org (57.1 Kb/s); Redirect: 0s, DNS look up: 0.001694s, Connection: 0.002314s, Pretransfer: 0.140691s, First byte at: 0.273392s
[2025-08-31 21:48:20] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 01 Sep 2025 01:48:20 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Mon, 01 Sep 2025 02:48:20 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-08-31 21:48:24] [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`
[2025-08-31 21:48:24] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-31 21:48:24] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-31 21:48:24] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-31 21:48:24] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-31 21:48:24] [INFO] [OmnipathR] Cache item `46d37339bbc3f9a05bb89ccb79278cf1233f5cdf` version 1: status changed from `unknown` to `started`.
[2025-08-31 21:48:24] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/46d37339bbc3f9a05bb89ccb79278cf1233f5cdf-1.rds`.
[2025-08-31 21:48:25] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/46d37339bbc3f9a05bb89ccb79278cf1233f5cdf-1.rds`.
[2025-08-31 21:48:25] [INFO] [OmnipathR] Download ready [key=46d37339bbc3f9a05bb89ccb79278cf1233f5cdf, version=1]
[2025-08-31 21:48:25] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-31 21:48:25] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-31 21:48:25] [INFO] [OmnipathR] Cache item `46d37339bbc3f9a05bb89ccb79278cf1233f5cdf` version 1: status changed from `started` to `ready`.
[2025-08-31 21:48:34] [SUCCESS] [OmnipathR] Downloaded 278677 interactions.
[2025-08-31 21:48:43] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-08-31 21:48:43] [TRACE] [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B,C,D],genesymbols=TRUE,organisms=10090,query_type=interactions,datasets=dorothea]
[2025-08-31 21:48:43] [TRACE] [OmnipathR] Organism(s): 10090
[2025-08-31 21:48:43] [TRACE] [OmnipathR] Orthology targets:
[2025-08-31 21:48:43] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=10090&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2025-08-31 21:48:43] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=10090&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2025-08-31 21:48:43] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=10090&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2025-08-31 21:48:43] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=10090&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2025-08-31 21:48:43] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=10090&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2025-08-31 21:48:43] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=10090&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2025-08-31 21:48:43] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=10090&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2025-08-31 21:48:43] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2025-08-31 21:48:43] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-08-31 21:48:43] [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]
[2025-08-31 21:48:44] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2025-08-31 21:48:44] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.411282s from omnipathdb.org (38.1 Kb/s); Redirect: 0s, DNS look up: 0.001701s, Connection: 0.002509s, Pretransfer: 0.274765s, First byte at: 0.410671s
[2025-08-31 21:48:44] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 01 Sep 2025 01:48:43 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Mon, 01 Sep 2025 02:48:43 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-08-31 21:48:48] [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`
[2025-08-31 21:48:48] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-31 21:48:48] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-31 21:48:48] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-31 21:48:48] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-31 21:48:48] [INFO] [OmnipathR] Cache item `ff347dedf78ef5e38c9c6d8eed291fa901aa3791` version 1: status changed from `unknown` to `started`.
[2025-08-31 21:48:48] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/ff347dedf78ef5e38c9c6d8eed291fa901aa3791-1.rds`.
[2025-08-31 21:48:49] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/ff347dedf78ef5e38c9c6d8eed291fa901aa3791-1.rds`.
[2025-08-31 21:48:49] [INFO] [OmnipathR] Download ready [key=ff347dedf78ef5e38c9c6d8eed291fa901aa3791, version=1]
[2025-08-31 21:48:49] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-31 21:48:49] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-31 21:48:49] [INFO] [OmnipathR] Cache item `ff347dedf78ef5e38c9c6d8eed291fa901aa3791` version 1: status changed from `started` to `ready`.
[2025-08-31 21:48:58] [SUCCESS] [OmnipathR] Downloaded 249440 interactions.
[2025-08-31 21:49:06] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-08-31 21:49:06] [TRACE] [OmnipathR] Arguments for OmniPath query: [loops=TRUE,organisms=9606,genesymbols=TRUE,query_type=interactions,datasets=collectri]
[2025-08-31 21:49:06] [TRACE] [OmnipathR] Organism(s): 9606
[2025-08-31 21:49:06] [TRACE] [OmnipathR] Orthology targets:
[2025-08-31 21:49:06] [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`
[2025-08-31 21:49:06] [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`
[2025-08-31 21:49:06] [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`
[2025-08-31 21:49:06] [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`
[2025-08-31 21:49:06] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2025-08-31 21:49:06] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2025-08-31 21:49:06] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2025-08-31 21:49:06] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2025-08-31 21:49:06] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-08-31 21:49:06] [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]
[2025-08-31 21:49:06] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2025-08-31 21:49:06] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.276139s from omnipathdb.org (56.7 Kb/s); Redirect: 0s, DNS look up: 0.001878s, Connection: 0.002601s, Pretransfer: 0.140795s, First byte at: 0.275278s
[2025-08-31 21:49:06] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 01 Sep 2025 01:49:06 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Mon, 01 Sep 2025 02:49:06 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-08-31 21:49:09] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2025-08-31 21:49:09] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-31 21:49:09] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-31 21:49:09] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-31 21:49:09] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-31 21:49:09] [INFO] [OmnipathR] Cache item `b10176737ba43d460b13709623189f3911123779` version 1: status changed from `unknown` to `started`.
[2025-08-31 21:49:09] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/b10176737ba43d460b13709623189f3911123779-1.rds`.
[2025-08-31 21:49:10] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/b10176737ba43d460b13709623189f3911123779-1.rds`.
[2025-08-31 21:49:10] [INFO] [OmnipathR] Download ready [key=b10176737ba43d460b13709623189f3911123779, version=1]
[2025-08-31 21:49:10] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-31 21:49:10] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-31 21:49:10] [INFO] [OmnipathR] Cache item `b10176737ba43d460b13709623189f3911123779` version 1: status changed from `started` to `ready`.
[2025-08-31 21:49:12] [SUCCESS] [OmnipathR] Downloaded 64979 interactions.
[2025-08-31 21:49:12] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-08-31 21:49:12] [TRACE] [OmnipathR] Arguments for OmniPath query: [genesymbols=TRUE,resources=CollecTRI,strict_evidences=TRUE,query_type=interactions,datasets=tf_mirna]
[2025-08-31 21:49:12] [TRACE] [OmnipathR] Organism(s): 9606
[2025-08-31 21:49:12] [TRACE] [OmnipathR] Orthology targets:
[2025-08-31 21:49:13] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-08-31 21:49:13] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-31 21:49:13] [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`
[2025-08-31 21:49:13] [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`
[2025-08-31 21:49:13] [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`
[2025-08-31 21:49:13] [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`
[2025-08-31 21:49:13] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2025-08-31 21:49:13] [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`
[2025-08-31 21:49:13] [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`
[2025-08-31 21:49:13] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2025-08-31 21:49:13] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-08-31 21:49:13] [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]
[2025-08-31 21:49:13] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2025-08-31 21:49:13] [TRACE] [OmnipathR] Downloaded 9 Kb in 0.2081s from omnipathdb.org (43.5 Kb/s); Redirect: 0s, DNS look up: 0.001811s, Connection: 0.002564s, Pretransfer: 0.139719s, First byte at: 0.207388s
[2025-08-31 21:49:13] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Mon, 01 Sep 2025 01:49:13 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Mon, 01 Sep 2025 02:49:13 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-08-31 21:49:14] [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`
[2025-08-31 21:49:14] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-31 21:49:14] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-31 21:49:14] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-31 21:49:14] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-31 21:49:14] [INFO] [OmnipathR] Cache item `f7d34500401ba98803b7d2b26c48f64cee1eea1b` version 1: status changed from `unknown` to `started`.
[2025-08-31 21:49:14] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/f7d34500401ba98803b7d2b26c48f64cee1eea1b-1.rds`.
[2025-08-31 21:49:14] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/f7d34500401ba98803b7d2b26c48f64cee1eea1b-1.rds`.
[2025-08-31 21:49:14] [INFO] [OmnipathR] Download ready [key=f7d34500401ba98803b7d2b26c48f64cee1eea1b, version=1]
[2025-08-31 21:49:14] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-31 21:49:14] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-31 21:49:14] [INFO] [OmnipathR] Cache item `f7d34500401ba98803b7d2b26c48f64cee1eea1b` version 1: status changed from `started` to `ready`.
[2025-08-31 21:49:14] [TRACE] [OmnipathR] Converting JSON column `evidences` to list.
[2025-08-31 21:49:14] [TRACE] [OmnipathR] Restricting interaction records to datasets: tf_mirna; and resources: CollecTRI
[2025-08-31 21:49:14] [TRACE] [OmnipathR] Filtering evidence columns: positive, negative, directed, undirected; to datasets: tf_mirna; and resources: CollecTRI; excluding resources: none
[2025-08-31 21:49:15] [SUCCESS] [OmnipathR] Downloaded 207 interactions.
[2025-08-31 21:49:15] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-08-31 21:49:15] [TRACE] [OmnipathR] Arguments for OmniPath query: [loops=TRUE,organisms=9606,genesymbols=TRUE,query_type=interactions,datasets=collectri]
[2025-08-31 21:49:15] [TRACE] [OmnipathR] Organism(s): 9606
[2025-08-31 21:49:15] [TRACE] [OmnipathR] Orthology targets:
[2025-08-31 21:49:15] [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`
[2025-08-31 21:49:15] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/b10176737ba43d460b13709623189f3911123779-1.rds`.
[2025-08-31 21:49:15] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2025-08-31 21:49:17] [SUCCESS] [OmnipathR] Loaded 64979 interactions from cache.
[2025-08-31 21:49:17] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-08-31 21:49:17] [TRACE] [OmnipathR] Arguments for OmniPath query: [genesymbols=TRUE,resources=CollecTRI,strict_evidences=TRUE,query_type=interactions,datasets=tf_mirna]
[2025-08-31 21:49:17] [TRACE] [OmnipathR] Organism(s): 9606
[2025-08-31 21:49:17] [TRACE] [OmnipathR] Orthology targets:
[2025-08-31 21:49:18] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-08-31 21:49:18] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-31 21:49:18] [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`
[2025-08-31 21:49:18] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/f7d34500401ba98803b7d2b26c48f64cee1eea1b-1.rds`.
[2025-08-31 21:49:18] [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`
[2025-08-31 21:49:18] [TRACE] [OmnipathR] Converting JSON column `evidences` to list.
[2025-08-31 21:49:18] [TRACE] [OmnipathR] Restricting interaction records to datasets: tf_mirna; and resources: CollecTRI
[2025-08-31 21:49:18] [TRACE] [OmnipathR] Filtering evidence columns: positive, negative, directed, undirected; to datasets: tf_mirna; and resources: CollecTRI; excluding resources: none
[2025-08-31 21:49:18] [SUCCESS] [OmnipathR] Loaded 207 interactions from cache.
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Attaching package: 'dplyr'
The following object is masked from 'package:testthat':
matches
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
[ FAIL 0 | WARN 18 | SKIP 0 | PASS 35 ]
[ FAIL 0 | WARN 18 | SKIP 0 | PASS 35 ]
>
> proc.time()
user system elapsed
148.418 16.434 254.745
decoupleR.Rcheck/decoupleR-Ex.timings
| name | user | system | elapsed | |
| check_corr | 0.076 | 0.018 | 0.094 | |
| convert_f_defaults | 0.049 | 0.015 | 0.063 | |
| decouple | 0.000 | 0.000 | 0.001 | |
| dot-fit_preprocessing | 0.024 | 0.001 | 0.026 | |
| extract_sets | 0.023 | 0.000 | 0.024 | |
| filt_minsize | 0.043 | 0.003 | 0.045 | |
| get_collectri | 8.281 | 0.781 | 14.514 | |
| get_dorothea | 21.206 | 1.146 | 24.504 | |
| get_profile_of | 0.000 | 0.000 | 0.001 | |
| get_progeny | 5.830 | 0.279 | 12.395 | |
| get_resource | 0.943 | 0.077 | 2.457 | |
| get_toy_data | 0.002 | 0.000 | 0.002 | |
| intersect_regulons | 0.026 | 0.003 | 0.029 | |
| pipe | 0.000 | 0.000 | 0.001 | |
| pivot_wider_profile | 0.001 | 0.000 | 0.001 | |
| randomize_matrix | 0.001 | 0.000 | 0.000 | |
| rename_net | 0.035 | 0.008 | 0.043 | |
| run_aucell | 8.979 | 1.836 | 10.834 | |
| run_consensus | 1.958 | 0.381 | 2.340 | |
| run_fgsea | 23.561 | 0.538 | 24.108 | |
| run_gsva | 1.790 | 0.529 | 2.321 | |
| run_mdt | 0.182 | 0.029 | 0.209 | |
| run_mlm | 0.083 | 0.013 | 0.096 | |
| run_ora | 0.467 | 0.046 | 0.513 | |
| run_udt | 0.266 | 0.033 | 0.298 | |
| run_ulm | 0.077 | 0.009 | 0.085 | |
| run_viper | 0.805 | 0.244 | 1.050 | |
| run_wmean | 0.670 | 0.038 | 0.706 | |
| run_wsum | 0.694 | 0.049 | 0.741 | |
| show_methods | 0.048 | 0.002 | 0.051 | |
| show_resources | 0.168 | 0.005 | 0.794 | |
| tidyeval | 0.001 | 0.000 | 0.000 | |