Pau Badia-i-Mompel
| Snapshot Date: 2025-04-22 13:40 -0400 (Tue, 22 Apr 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 2025-04-24 13:02 -0400 (Thu, 24 Apr 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" | 4831 |
| palomino7 | Windows Server 2022 Datacenter | x64 | 4.5.0 RC (2025-04-04 r88126 ucrt) -- "How About a Twenty-Six" | 4573 |
| 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 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | 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: 2.14.0 |
| Command: E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:decoupleR.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings decoupleR_2.14.0.tar.gz |
| StartedAt: 2025-04-23 01:13:24 -0400 (Wed, 23 Apr 2025) |
| EndedAt: 2025-04-23 01:26:39 -0400 (Wed, 23 Apr 2025) |
| EllapsedTime: 794.9 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: decoupleR.Rcheck |
| Warnings: 1 |
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###
### Running command:
###
### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:decoupleR.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings decoupleR_2.14.0.tar.gz
###
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* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/decoupleR.Rcheck'
* using R version 4.5.0 RC (2025-04-04 r88126 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'decoupleR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'decoupleR' version '2.14.0'
* 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 whether package 'decoupleR' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
[2025-04-23 01:14:18] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-23 01:14:21] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-23 01:14:23] [INFO] [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-04-23 01:14:23] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2025-04-23 01:14:23] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-04-22
[2025-04-23 01:14:23] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-04-22 19:35:47 UTC; windows
[2025-04-23 01:14:23] [INFO] [OmnipathR] Package `OmnipathR` version: 3.16.0
[2025-04-23 01:14:23] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21
[2025-04-23 01:14:28] [INFO] [OmnipathR] Session info: [version=R version 4.5.0 RC (2025-04-04 r88126 ucrt); os=Windows Server 2022 x64 (build 20348); system=x86_64, mingw32; ui=RTerm; language=(EN); collate=C; ctype=English_United States.utf8; tz=America/New_York; date=2025-04-23; pandoc=2.7.3 @ C:/PROGRA~1/Pandoc/ (via rmarkdown); quarto=NA]
[2025-04-23 01:14:31] [INFO] [OmnipathR] External libraries: [cairo=1.18.2; cairoFT=; pango=; png=1.6.47; jpeg=9.6; tiff=LIBTIFF, Version 4.7.0; tcl=8.6.16; curl=8.12.1; zlib=1.3.1; bzlib=1.0.8, 13-Jul-2019; xz=5.6.4; deflate=1.23; PCRE=10.45 2025-02-05; ICU=76.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=win_iconv; readline=; BLAS=; lapack=; lapack_version=3.12.1]
[2025-04-23 01:14:32] [INFO] [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); annotate 1.86.0(2025-04-22); AnnotationDbi 1.70.0(2025-04-22); AUCell 1.30.0(2025-04-22); backports 1.5.0(2024-05-23); beachmat 2.24.0(2025-04-22); Biobase 2.68.0(2025-04-22); BiocGenerics 0.54.0(2025-04-22); BiocParallel 1.42.0(2025-04-22); BiocSingular 1.24.0(2025-04-22); Biostrings 2.76.0(2025-04-22); 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 0.5.0(2025-03-21); cli 3.6.4(2025-02-13); codetools 0.2-20(2024-03-31); crayon 1.5.3(2024-06-20); curl 6.2.2(2025-03-24); data.table 1.17.0(2025-02-22); DBI 1.2.3(2024-06-02); decoupleR 2.14.0(2025-04-22); DelayedArray 0.34.1(2025-04-22); DelayedMatrixStats 1.30.0(2025-04-22); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.3(2025-01-10); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.3(2022-07-05); GenomeInfoDb 1.44.0(2025-04-22); GenomeInfoDbData 1.2.14(2025-04-10); GenomicRanges 1.60.0(2025-04-22); glue 1.8.0(2024-09-30); graph 1.86.0(2025-04-22); GSEABase 1.70.0(2025-04-22); GSVA 2.2.0(2025-04-22); h5mread 1.0.0(2025-04-22); HDF5Array 1.36.0(2025-04-22); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.1.2(2025-03-26); igraph 2.1.4(2025-01-23); IRanges 2.42.0(2025-04-22); irlba 2.3.5.1(2022-10-03); jsonlite 2.0.0(2025-03-27); KEGGREST 1.48.0(2025-04-22); knitr 1.50(2025-03-16); later 1.4.2(2025-04-08); lattice 0.22-7(2025-04-02); lifecycle 1.0.4(2023-11-07); logger 0.4.0(2024-10-22); lubridate 1.9.4(2024-12-08); magick 2.8.6(2025-03-23); magrittr 2.0.3(2022-03-30); Matrix 1.7-3(2025-03-11); MatrixGenerics 1.20.0(2025-04-22); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); OmnipathR 3.16.0(2025-04-22); parallelly 1.43.0(2025-03-24); pillar 1.10.2(2025-04-05); pkgconfig 2.0.3(2019-09-22); png 0.1-8(2022-11-29); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.3.2(2024-11-28); ps 1.9.1(2025-04-12); purrr 1.0.4(2025-02-05); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.0(2024-11-01); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.0.14(2025-01-12); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rhdf5 2.52.0(2025-04-22); rhdf5filters 1.20.0(2025-04-22); Rhdf5lib 1.30.0(2025-04-22); rjson 0.2.23(2024-09-16); rlang 1.1.6(2025-04-11); rmarkdown 2.29(2024-11-04); RSQLite 2.3.9(2024-12-03); rsvd 1.0.5(2021-04-16); rvest 1.0.4(2024-02-12); S4Arrays 1.8.0(2025-04-22); S4Vectors 0.46.0(2025-04-22); ScaledMatrix 1.16.0(2025-04-22); sessioninfo 1.2.3(2025-02-05); SingleCellExperiment 1.30.0(2025-04-22); SparseArray 1.8.0(2025-04-22); sparseMatrixStats 1.20.0(2025-04-22); SpatialExperiment 1.18.0(2025-04-22); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); SummarizedExperiment 1.38.0(2025-04-22); tibble 3.2.1(2023-03-20); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); UCSC.utils 1.4.0(2025-04-22); 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 0.48.0(2025-04-22); yaml 2.3.10(2024-07-26); zip 2.3.2(2025-02-01)
[2025-04-23 01:14:32] [INFO] [OmnipathR] CURL: version: 8.10.1; headers: 8.10.1; ssl_version: (OpenSSL/3.4.0) Schannel; libz_version: 1.3; libssh_version: libssh2/1.11.0; libidn_version: NA; host: x86_64-w64-mingw32; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2025-04-23 01:14:32] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-04-23 01:14:32] [TRACE] [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-04-23 01:14:32] [TRACE] [OmnipathR] Contains 8 files.
[2025-04-23 01:14:32] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-04-23 01:14:32] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-23 01:14:32] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-23 01:14:32] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-04-23 01:14:32] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2025-04-23 01:14:32] [TRACE] [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-04-23 01:14:32] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-23 01:14:33] [TRACE] [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-04-23 01:14:33] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-23 01:14:33] [TRACE] [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-04-23 01:14:33] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-23 01:14:33] [TRACE] [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-04-23 01:14:33] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-23 01:14:34] [TRACE] [OmnipathR] Cache locked: FALSE
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link(s) in Rd file 'run_gsva.Rd':
'GSVA::gsva' 'GeneSetCollection'
Non-topic package-anchored link(s) in Rd file 'pipe.Rd':
'[magrittr:pipe]{%>%}'
See section 'Cross-references' in the 'Writing R Extensions' manual.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
run_gsva.Rd: GSVA::gsva, GeneSetCollection
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
get_dorothea 24.78 0.53 26.21
run_fgsea 23.02 0.04 23.08
get_collectri 9.22 0.79 16.58
run_aucell 8.70 0.70 9.49
get_progeny 6.38 0.49 8.85
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
Running 'testthat.R'
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING, 1 NOTE
See
'E:/biocbuild/bbs-3.21-bioc/meat/decoupleR.Rcheck/00check.log'
for details.
decoupleR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL decoupleR ### ############################################################################## ############################################################################## * installing to library 'E:/biocbuild/bbs-3.21-bioc/R/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 4.5.0 RC (2025-04-04 r88126 ucrt) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64
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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[2025-04-23 01:19:43] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-23 01:19:43] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-23 01:19:43] [INFO] [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-04-23 01:19:43] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2025-04-23 01:19:43] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-04-22
[2025-04-23 01:19:43] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-04-22 19:35:47 UTC; windows
[2025-04-23 01:19:43] [INFO] [OmnipathR] Package `OmnipathR` version: 3.16.0
[2025-04-23 01:19:43] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21
[2025-04-23 01:19:45] [INFO] [OmnipathR] Session info: [version=R version 4.5.0 RC (2025-04-04 r88126 ucrt); os=Windows Server 2022 x64 (build 20348); system=x86_64, mingw32; ui=RTerm; language=C; collate=C; ctype=English_United States.utf8; tz=America/New_York; date=2025-04-23; pandoc=2.7.3 @ C:/PROGRA~1/Pandoc/ (via rmarkdown); quarto=NA]
[2025-04-23 01:19:45] [INFO] [OmnipathR] External libraries: [cairo=1.18.2; cairoFT=; pango=; png=1.6.47; jpeg=9.6; tiff=LIBTIFF, Version 4.7.0; tcl=8.6.16; curl=8.12.1; zlib=1.3.1; bzlib=1.0.8, 13-Jul-2019; xz=5.6.4; deflate=1.23; PCRE=10.45 2025-02-05; ICU=76.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=win_iconv; readline=; BLAS=; lapack=; lapack_version=3.12.1]
[2025-04-23 01:19:46] [INFO] [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); annotate 1.86.0(2025-04-22); AnnotationDbi 1.70.0(2025-04-22); AUCell 1.30.0(2025-04-22); backports 1.5.0(2024-05-23); beachmat 2.24.0(2025-04-22); Biobase 2.68.0(2025-04-22); BiocGenerics 0.54.0(2025-04-22); BiocParallel 1.42.0(2025-04-22); BiocSingular 1.24.0(2025-04-22); Biostrings 2.76.0(2025-04-22); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); brio 1.1.5(2024-04-24); broom 1.0.8(2025-03-28); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.2(2024-07-29); chromote 0.5.0(2025-03-21); class 7.3-23(2025-01-01); cli 3.6.4(2025-02-13); codetools 0.2-20(2024-03-31); colorspace 2.1-1(2024-07-26); cowplot 1.1.3(2024-01-22); crayon 1.5.3(2024-06-20); curl 6.2.2(2025-03-24); data.table 1.17.0(2025-02-22); DBI 1.2.3(2024-06-02); decoupleR 2.14.0(2025-04-22); DelayedArray 0.34.1(2025-04-22); DelayedMatrixStats 1.30.0(2025-04-22); 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 1.0.3(2025-01-10); fastmap 1.2.0(2024-05-15); fastmatch 1.1-6(2024-12-23); fgsea 1.34.0(2025-04-22); fs 1.6.6(2025-04-12); generics 0.1.3(2022-07-05); GenomeInfoDb 1.44.0(2025-04-22); GenomeInfoDbData 1.2.14(2025-04-10); GenomicRanges 1.60.0(2025-04-22); ggplot2 3.5.2(2025-04-09); glue 1.8.0(2024-09-30); graph 1.86.0(2025-04-22); GSEABase 1.70.0(2025-04-22); GSVA 2.2.0(2025-04-22); gtable 0.3.6(2024-10-25); h5mread 1.0.0(2025-04-22); HDF5Array 1.36.0(2025-04-22); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); htmlwidgets 1.6.4(2023-12-06); httr 1.4.7(2023-08-15); httr2 1.1.2(2025-03-26); igraph 2.1.4(2025-01-23); IRanges 2.42.0(2025-04-22); irlba 2.3.5.1(2022-10-03); jsonlite 2.0.0(2025-03-27); KEGGREST 1.48.0(2025-04-22); kernlab 0.9-33(2024-08-13); KernSmooth 2.23-26(2025-01-01); knitr 1.50(2025-03-16); later 1.4.2(2025-04-08); lattice 0.22-7(2025-04-02); lazyeval 0.2.2(2019-03-15); lifecycle 1.0.4(2023-11-07); logger 0.4.0(2024-10-22); lubridate 1.9.4(2024-12-08); magick 2.8.6(2025-03-23); magrittr 2.0.3(2022-03-30); MASS 7.3-65(2025-02-28); Matrix 1.7-3(2025-03-11); MatrixGenerics 1.20.0(2025-04-22); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); mixtools 2.0.0.1(2025-03-08); munsell 0.5.1(2024-04-01); nlme 3.1-168(2025-03-31); OmnipathR 3.16.0(2025-04-22); parallelly 1.43.0(2025-03-24); pillar 1.10.2(2025-04-05); pkgconfig 2.0.3(2019-09-22); plotly 4.10.4(2024-01-13); png 0.1-8(2022-11-29); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.3.2(2024-11-28); proxy 0.4-27(2022-06-09); ps 1.9.1(2025-04-12); purrr 1.0.4(2025-02-05); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.0(2024-11-01); 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); Rcpp 1.0.14(2025-01-12); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rhdf5 2.52.0(2025-04-22); rhdf5filters 1.20.0(2025-04-22); Rhdf5lib 1.30.0(2025-04-22); rjson 0.2.23(2024-09-16); rlang 1.1.6(2025-04-11); rmarkdown 2.29(2024-11-04); rpart 4.1.24(2025-01-07); RSQLite 2.3.9(2024-12-03); rsvd 1.0.5(2021-04-16); rvest 1.0.4(2024-02-12); S4Arrays 1.8.0(2025-04-22); S4Vectors 0.46.0(2025-04-22); ScaledMatrix 1.16.0(2025-04-22); scales 1.3.0(2023-11-28); segmented 2.1-4(2025-02-28); sessioninfo 1.2.3(2025-02-05); SingleCellExperiment 1.30.0(2025-04-22); snow 0.4-4(2021-10-27); SparseArray 1.8.0(2025-04-22); sparseMatrixStats 1.20.0(2025-04-22); SpatialExperiment 1.18.0(2025-04-22); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); SummarizedExperiment 1.38.0(2025-04-22); survival 3.8-3(2024-12-17); testthat 3.2.3(2025-01-13); tibble 3.2.1(2023-03-20); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); UCSC.utils 1.4.0(2025-04-22); vctrs 0.6.5(2023-12-01); viper 1.42.0(2025-04-22); viridisLite 0.4.2(2023-05-02); waldo 0.6.1(2024-11-07); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.52(2025-04-02); XML 3.99-0.18(2025-01-01); xml2 1.3.8(2025-03-14); xtable 1.8-4(2019-04-21); XVector 0.48.0(2025-04-22); yaml 2.3.10(2024-07-26); zip 2.3.2(2025-02-01)
[2025-04-23 01:19:46] [INFO] [OmnipathR] CURL: version: 8.10.1; headers: 8.10.1; ssl_version: (OpenSSL/3.4.0) Schannel; libz_version: 1.3; libssh_version: libssh2/1.11.0; libidn_version: NA; host: x86_64-w64-mingw32; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2025-04-23 01:19:46] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-04-23 01:19:46] [TRACE] [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-04-23 01:19:46] [TRACE] [OmnipathR] Contains 8 files.
[2025-04-23 01:19:46] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-04-23 01:19:46] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-23 01:19:46] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-23 01:19:46] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-04-23 01:19:46] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2025-04-23 01:19:46] [TRACE] [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-04-23 01:19:47] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-23 01:19:47] [TRACE] [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-04-23 01:19:47] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-23 01:19:47] [TRACE] [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-04-23 01:19:47] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-23 01:19:47] [TRACE] [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-04-23 01:19:47] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-23 01:19:47] [TRACE] [OmnipathR] Cache locked: FALSE
[2025-04-23 01:19:47] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-04-23 01:19:47] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-23 01:19:48] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-04-23 01:19:48] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-23 01:19:48] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2025-04-23 01:19:48] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-23 01:19:48] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-23 01:19:48] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2025-04-23 01:19:48] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-23 01:19:48] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-23 01:19:48] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2025-04-23 01:19:48] [TRACE] [OmnipathR] Cache file path: C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2025-04-23 01:19:48] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2025-04-23 01:19:48] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`.
[2025-04-23 01:19:48] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2025-04-23 01:19:48] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2025-04-23 01:19:48] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-04-23 01:19:48] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-04-23 01:19:48] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-04-23 01:19:48] [TRACE] [OmnipathR] Sending HTTP request.
[2025-04-23 01:19:49] [TRACE] [OmnipathR] HTTP 200 (OK)
[2025-04-23 01:19:49] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2025-04-23 01:19:49] [TRACE] [OmnipathR] Downloaded 31 Kb in 0.829145s from www.ensembl.org (37.4 Kb/s); Redirect: 0s, DNS look up: 0.381367s, Connection: 0.463237s, Pretransfer: 0.557991s, First byte at: 0.726497s
[2025-04-23 01:19:49] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Date: Wed, 23 Apr 2025 05:19:49 GMT; Content-Type: text/html; charset=utf-8; Content-Length: 31741; Connection: keep-alive; Server: Apache; Set-cookie: redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT; Set-cookie: redirect_mirror=no; path=/; expires=Thu, 24 Apr 2025 05:19:49 GMT; Set-cookie: ENSEMBL_HINX_SESSION=53bed67048406fb3096d3eb5685792750b78c6d6824429242b6d0bc7; path=/; expires=Thu, 31-Dec-2037 23:59:59 GMT; HttpOnly; Set-cookie: redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT; Set-cookie: redirect_mirror=no; path=/; expires=Thu, 24 Apr 2025 05:19:49 GMT; Set-cookie: ENSEMBL_HINX_SESSION=53bed67048406fb3096d3eb5685792750b78c6d6824429242b6d0bc7; 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: wp-p1m2-33.ebi.ac.uk
[2025-04-23 01:19:49] [TRACE] [OmnipathR] Response headers: [Date=Wed, 23 Apr 2025 05:19:49 GMT,Content-Type=text/html; charset=utf-8,Content-Length=31741,Connection=keep-alive,Server=Apache,Set-cookie=redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT,Set-cookie=redirect_mirror=no; path=/; expires=Thu, 24 Apr 2025 05:19:49 GMT,Set-cookie=ENSEMBL_HINX_SESSION=53bed67048406fb3096d3eb5685792750b78c6d6824429242b6d0bc7; path=/; expires=Thu, 31-Dec-2037 23:59:59 GMT; HttpOnly,Set-cookie=redirect_mirror=; path=/; expires=Mon, 01-Jan-2001 00:00:01 GMT,Set-cookie=redirect_mirror=no; path=/; expires=Thu, 24 Apr 2025 05:19:49 GMT,Set-cookie=ENSEMBL_HINX_SESSION=53bed67048406fb3096d3eb5685792750b78c6d6824429242b6d0bc7; 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=wp-p1m2-33.ebi.ac.uk]
[2025-04-23 01:19:51] [INFO] [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1]
[2025-04-23 01:19:51] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-23 01:19:51] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-23 01:19:51] [INFO] [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`.
[2025-04-23 01:19:51] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2025-04-23 01:19:51] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2025-04-23 01:19:51] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2025-04-23 01:19:51] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2025-04-23 01:19:51] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-23 01:19:51] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-23 01:19:51] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-23 01:19:51] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-23 01:19:51] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2025-04-23 01:19:51] [TRACE] [OmnipathR] Exporting object to RDS: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-04-23 01:19:51] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2025-04-23 01:19:51] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2025-04-23 01:19:51] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2025-04-23 01:19:52] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-04-23 01:19:52] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2025-04-23 01:19:52] [TRACE] [OmnipathR] Downloaded 8 Kb in 0.298402s from omabrowser.org (26.8 Kb/s); Redirect: 0s, DNS look up: 0.002136s, Connection: 0.095346s, Pretransfer: 0.20204s, First byte at: 0.298127s
[2025-04-23 01:19:52] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Date: Wed, 23 Apr 2025 05:19:52 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; Transfer-Encoding: chunked
[2025-04-23 01:19:53] [TRACE] [OmnipathR] Exported RDS to `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-04-23 01:19:53] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1]
[2025-04-23 01:19:53] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-23 01:19:53] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-23 01:19:53] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.
[2025-04-23 01:19:53] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`.
[2025-04-23 01:19:53] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-04-23 01:19:54] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=TFcensus,query_type=annotations]
[2025-04-23 01:19:54] [TRACE] [OmnipathR] Organism(s): 9606
[2025-04-23 01:19:54] [TRACE] [OmnipathR] Orthology targets:
[2025-04-23 01:19:54] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-04-23 01:19:54] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-23 01:19:54] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2025-04-23 01:19:54] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2025-04-23 01:19:54] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2025-04-23 01:19:54] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2025-04-23 01:19:54] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2025-04-23 01:19:54] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2025-04-23 01:19:54] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2025-04-23 01:19:54] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2025-04-23 01:19:54] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-04-23 01:19:55] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2025-04-23 01:19:55] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.33878s from omnipathdb.org (46.2 Kb/s); Redirect: 0s, DNS look up: 0.002083s, Connection: 0.083836s, Pretransfer: 0.175842s, First byte at: 0.338198s
[2025-04-23 01:19:55] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 23 Apr 2025 05:19:55 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Wed, 23 Apr 2025 06:19:55 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-04-23 01:19:56] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2025-04-23 01:19:56] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-23 01:19:56] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-23 01:19:56] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-23 01:19:56] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-23 01:19:56] [INFO] [OmnipathR] Cache item `6f000d9b5edd9832b1c28754d1c3d9449c1c7490` version 1: status changed from `unknown` to `started`.
[2025-04-23 01:19:56] [TRACE] [OmnipathR] Exporting object to RDS: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/6f000d9b5edd9832b1c28754d1c3d9449c1c7490-1.rds`.
[2025-04-23 01:19:56] [TRACE] [OmnipathR] Exported RDS to `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/6f000d9b5edd9832b1c28754d1c3d9449c1c7490-1.rds`.
[2025-04-23 01:19:56] [INFO] [OmnipathR] Download ready [key=6f000d9b5edd9832b1c28754d1c3d9449c1c7490, version=1]
[2025-04-23 01:19:56] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-23 01:19:56] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-23 01:19:56] [INFO] [OmnipathR] Cache item `6f000d9b5edd9832b1c28754d1c3d9449c1c7490` version 1: status changed from `started` to `ready`.
[2025-04-23 01:19:56] [SUCCESS] [OmnipathR] Downloaded 3099 annotation records.
[2025-04-23 01:19:57] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-04-23 01:19:57] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-23 01:19:57] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-04-23 01:19:57] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=PROGENy,query_type=annotations]
[2025-04-23 01:19:57] [TRACE] [OmnipathR] Organism(s): 9606
[2025-04-23 01:19:57] [TRACE] [OmnipathR] Orthology targets:
[2025-04-23 01:19:58] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-04-23 01:19:58] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-23 01:19:58] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-04-23 01:19:58] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-04-23 01:19:58] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-04-23 01:19:58] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-04-23 01:19:58] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-04-23 01:19:58] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-04-23 01:19:58] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-04-23 01:19:58] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2025-04-23 01:19:58] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-04-23 01:19:59] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2025-04-23 01:19:59] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.336079s from omnipathdb.org (46.6 Kb/s); Redirect: 0s, DNS look up: 0.002266s, Connection: 0.082956s, Pretransfer: 0.174271s, First byte at: 0.335599s
[2025-04-23 01:19:59] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 23 Apr 2025 05:19:58 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Wed, 23 Apr 2025 06:19:58 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-04-23 01:20:02] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-04-23 01:20:02] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-23 01:20:02] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-23 01:20:02] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-23 01:20:02] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-23 01:20:02] [INFO] [OmnipathR] Cache item `3492392585ba05414edfae46801492076437d7e7` version 1: status changed from `unknown` to `started`.
[2025-04-23 01:20:02] [TRACE] [OmnipathR] Exporting object to RDS: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`.
[2025-04-23 01:20:05] [TRACE] [OmnipathR] Exported RDS to `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`.
[2025-04-23 01:20:05] [INFO] [OmnipathR] Download ready [key=3492392585ba05414edfae46801492076437d7e7, version=1]
[2025-04-23 01:20:05] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-23 01:20:05] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-23 01:20:05] [INFO] [OmnipathR] Cache item `3492392585ba05414edfae46801492076437d7e7` version 1: status changed from `started` to `ready`.
[2025-04-23 01:20:05] [SUCCESS] [OmnipathR] Downloaded 700239 annotation records.
[2025-04-23 01:20:07] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-04-23 01:20:07] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-23 01:20:07] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-04-23 01:20:07] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=PROGENy,query_type=annotations]
[2025-04-23 01:20:07] [TRACE] [OmnipathR] Organism(s): 9606
[2025-04-23 01:20:07] [TRACE] [OmnipathR] Orthology targets:
[2025-04-23 01:20:08] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-04-23 01:20:08] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-23 01:20:08] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-04-23 01:20:10] [TRACE] [OmnipathR] Loaded data from RDS `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`.
[2025-04-23 01:20:10] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-04-23 01:20:10] [SUCCESS] [OmnipathR] Loaded 700239 annotation records from cache.
[2025-04-23 01:20:13] [INFO] [OmnipathR] Loading database `Orthologous Matrix (OMA) gene pairs`.
[2025-04-23 01:20:13] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2025-04-23 01:20:13] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2025-04-23 01:20:13] [TRACE] [OmnipathR] Loaded data from RDS `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-04-23 01:20:13] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2025-04-23 01:20:13] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2025-04-23 01:20:13] [TRACE] [OmnipathR] Loaded data from RDS `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-04-23 01:20:13] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2025-04-23 01:20:13] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/api/pairs/HUMAN/MOUSE/?format=tsv&xrefs=UniProtKB%2FSwissProt&per_page=2000000`.
[2025-04-23 01:20:13] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/api/pairs/HUMAN/MOUSE/?format=tsv&xrefs=UniProtKB%2FSwissProt&per_page=2000000`
[2025-04-23 01:20:13] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/api/pairs/HUMAN/MOUSE/?format=tsv&xrefs=UniProtKB%2FSwissProt&per_page=2000000`.
[2025-04-23 01:20:13] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-23 01:20:13] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-23 01:20:13] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-23 01:20:13] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-23 01:20:13] [INFO] [OmnipathR] Cache item `8f45b25c384d814c7de210e7ca40b7e35894e4f1` version 1: status changed from `unknown` to `started`.
[2025-04-23 01:20:13] [TRACE] [OmnipathR] Exporting object to RDS: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/8f45b25c384d814c7de210e7ca40b7e35894e4f1-1.rds`.
[2025-04-23 01:20:13] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/api/pairs/HUMAN/MOUSE/?format=tsv&xrefs=UniProtKB%2FSwissProt&per_page=2000000`
[2025-04-23 01:20:13] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/api/pairs/HUMAN/MOUSE/?format=tsv&xrefs=UniProtKB%2FSwissProt&per_page=2000000`
[2025-04-23 01:20:13] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2025-04-23 01:20:13] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-04-23 01:20:41] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2025-04-23 01:20:41] [TRACE] [OmnipathR] Downloaded 5.2 Kb in 27.56632s from omabrowser.org (194 bytes/s); Redirect: 0s, DNS look up: 0.002227s, Connection: 0.095401s, Pretransfer: 0.202067s, First byte at: 27.566247s
[2025-04-23 01:20:41] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Date: Wed, 23 Apr 2025 05:20:41 GMT; Server: nginx; Strict-Transport-Security: max-age=31536000; includeSubDomains; Content-Type: text/tsv; charset=utf-8; Content-Length: 1187278; X-Total-Count: 22374; Vary: Accept,Origin,Cookie; Allow: GET, HEAD, OPTIONS; content-disposition: attachment; filename=OMA-Pairs_HUMAN-MOUSE_2025-04-23_052039.tsv; X-Frame-Options: SAMEORIGIN; Set-Cookie: __matomo=a46114a30f0524f0; expires=Fri, 23-Apr-2027 05:20:41 UTC; Path=/
[2025-04-23 01:20:43] [TRACE] [OmnipathR] Exported RDS to `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/8f45b25c384d814c7de210e7ca40b7e35894e4f1-1.rds`.
[2025-04-23 01:20:43] [INFO] [OmnipathR] Download ready [key=8f45b25c384d814c7de210e7ca40b7e35894e4f1, version=1]
[2025-04-23 01:20:43] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-23 01:20:43] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-23 01:20:43] [INFO] [OmnipathR] Cache item `8f45b25c384d814c7de210e7ca40b7e35894e4f1` version 1: status changed from `started` to `ready`.
[2025-04-23 01:20:43] [TRACE] [OmnipathR] ID translation table: from `uniprot_entry` to `uniprot`, using `uniprot`.
[2025-04-23 01:20:43] [TRACE] [OmnipathR] Creating ID mapping table from `id` to `accession`, for organism 9606 (only reviewed: TRUE)
[2025-04-23 01:20:43] [TRACE] [OmnipathR] Loading all UniProt records for organism 9606 (only reviewed: TRUE); fields: id,accession
[2025-04-23 01:20:43] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2025-04-23 01:20:43] [TRACE] [OmnipathR] Looking up in cache: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:9606%20AND%20reviewed:true`.
[2025-04-23 01:20:43] [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`
[2025-04-23 01:20:43] [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`.
[2025-04-23 01:20:43] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-23 01:20:43] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-23 01:20:43] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-23 01:20:43] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-23 01:20:43] [INFO] [OmnipathR] Cache item `6558a1824894a625b8e3f80538cd3aa6e8a44379` version 1: status changed from `unknown` to `started`.
[2025-04-23 01:20:43] [TRACE] [OmnipathR] Exporting object to RDS: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/6558a1824894a625b8e3f80538cd3aa6e8a44379-1.rds`.
[2025-04-23 01:20:43] [INFO] [OmnipathR] Retrieving URL: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:9606%20AND%20reviewed:true`
[2025-04-23 01:20:44] [TRACE] [OmnipathR] Attempt 1/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:9606%20AND%20reviewed:true`
[2025-04-23 01:20:44] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2025-04-23 01:20:44] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-04-23 01:20:45] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2025-04-23 01:20:45] [TRACE] [OmnipathR] Downloaded 31 bytes in 0.966079s from rest.uniprot.org (32 bytes/s); Redirect: 0s, DNS look up: 0.186899s, Connection: 0.270251s, Pretransfer: 0.365594s, First byte at: 0.965971s
[2025-04-23 01:20:45] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 ; 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: 05-February-2025; Strict-Transport-Security: max-age=31536000; includeSubDomains; Date: Wed, 23 Apr 2025 05:20:45 GMT; Access-Control-Max-Age: 1728000; X-UniProt-Release: 2025_01; Transfer-Encoding: chunked; Access-Control-Allow-Origin: *; Connection: keep-alive; 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: 05-February-2025
[2025-04-23 01:21:03] [TRACE] [OmnipathR] Exported RDS to `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/6558a1824894a625b8e3f80538cd3aa6e8a44379-1.rds`.
[2025-04-23 01:21:03] [INFO] [OmnipathR] Download ready [key=6558a1824894a625b8e3f80538cd3aa6e8a44379, version=1]
[2025-04-23 01:21:03] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-23 01:21:03] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-23 01:21:03] [INFO] [OmnipathR] Cache item `6558a1824894a625b8e3f80538cd3aa6e8a44379` version 1: status changed from `started` to `ready`.
[2025-04-23 01:21:03] [SUCCESS] [OmnipathR] UniProt (rest.uniprot.org): downloaded 20417 records
[2025-04-23 01:21:03] [TRACE] [OmnipathR] Translating complexes: 0 complexes in data.
[2025-04-23 01:21:03] [TRACE] [OmnipathR] 0 complexes after removing the ones mapping to more than 1 items in target identifier space.
[2025-04-23 01:21:04] [TRACE] [OmnipathR] Translated 0 complexes to 0.
[2025-04-23 01:21:04] [TRACE] [OmnipathR] 13774 rows before translation, 13774 uniprot_entry IDs in column `id_organism_a`.
[2025-04-23 01:21:04] [TRACE] [OmnipathR] 13774 rows after translation; translated 13570 `uniprot_entry` IDs in column `id_organism_a` to 13570 `uniprot` IDs in column `id_organism_a`.
[2025-04-23 01:21:04] [TRACE] [OmnipathR] ID translation table: from `uniprot_entry` to `uniprot`, using `uniprot`.
[2025-04-23 01:21:04] [TRACE] [OmnipathR] Creating ID mapping table from `id` to `accession`, for organism 10090 (only reviewed: TRUE)
[2025-04-23 01:21:04] [TRACE] [OmnipathR] Loading all UniProt records for organism 10090 (only reviewed: TRUE); fields: id,accession
[2025-04-23 01:21:04] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2025-04-23 01:21:04] [TRACE] [OmnipathR] Looking up in cache: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:10090%20AND%20reviewed:true`.
[2025-04-23 01:21:04] [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`
[2025-04-23 01:21:04] [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`.
[2025-04-23 01:21:04] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-23 01:21:04] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-23 01:21:04] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-23 01:21:04] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-23 01:21:04] [INFO] [OmnipathR] Cache item `43ea5f2cdaa9ac7e0e114371af97235cdddd776f` version 1: status changed from `unknown` to `started`.
[2025-04-23 01:21:04] [TRACE] [OmnipathR] Exporting object to RDS: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/43ea5f2cdaa9ac7e0e114371af97235cdddd776f-1.rds`.
[2025-04-23 01:21:04] [INFO] [OmnipathR] Retrieving URL: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:10090%20AND%20reviewed:true`
[2025-04-23 01:21:04] [TRACE] [OmnipathR] Attempt 1/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:10090%20AND%20reviewed:true`
[2025-04-23 01:21:04] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2025-04-23 01:21:04] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-04-23 01:21:05] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2025-04-23 01:21:05] [TRACE] [OmnipathR] Downloaded 31 bytes in 0.661598s from rest.uniprot.org (46 bytes/s); Redirect: 0s, DNS look up: 0.002082s, Connection: 0.084903s, Pretransfer: 0.178789s, First byte at: 0.661472s
[2025-04-23 01:21:05] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 ; 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: 05-February-2025; Strict-Transport-Security: max-age=31536000; includeSubDomains; Date: Wed, 23 Apr 2025 05:21:05 GMT; Access-Control-Max-Age: 1728000; X-UniProt-Release: 2025_01; Transfer-Encoding: chunked; Access-Control-Allow-Origin: *; Connection: keep-alive; 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: 05-February-2025
[2025-04-23 01:21:17] [TRACE] [OmnipathR] Exported RDS to `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/43ea5f2cdaa9ac7e0e114371af97235cdddd776f-1.rds`.
[2025-04-23 01:21:17] [INFO] [OmnipathR] Download ready [key=43ea5f2cdaa9ac7e0e114371af97235cdddd776f, version=1]
[2025-04-23 01:21:17] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-23 01:21:17] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-23 01:21:17] [INFO] [OmnipathR] Cache item `43ea5f2cdaa9ac7e0e114371af97235cdddd776f` version 1: status changed from `started` to `ready`.
[2025-04-23 01:21:17] [SUCCESS] [OmnipathR] UniProt (rest.uniprot.org): downloaded 17228 records
[2025-04-23 01:21:17] [TRACE] [OmnipathR] Translating complexes: 0 complexes in data.
[2025-04-23 01:21:17] [TRACE] [OmnipathR] 0 complexes after removing the ones mapping to more than 1 items in target identifier space.
[2025-04-23 01:21:18] [TRACE] [OmnipathR] Translated 0 complexes to 0.
[2025-04-23 01:21:18] [TRACE] [OmnipathR] 13774 rows before translation, 13773 uniprot_entry IDs in column `id_organism_b`.
[2025-04-23 01:21:18] [TRACE] [OmnipathR] 13774 rows after translation; translated 13273 `uniprot_entry` IDs in column `id_organism_b` to 13273 `uniprot` IDs in column `id_organism_b`.
[2025-04-23 01:21:18] [INFO] [OmnipathR] Loaded database `Orthologous Matrix (OMA) gene pairs`.
[2025-04-23 01:21:18] [TRACE] [OmnipathR] ID translation table: from `uniprot` to `genesymbol`, using `uniprot`.
[2025-04-23 01:21:18] [TRACE] [OmnipathR] Creating ID mapping table from `accession` to `gene_primary`, for organism 10090 (only reviewed: TRUE)
[2025-04-23 01:21:18] [TRACE] [OmnipathR] Loading all UniProt records for organism 10090 (only reviewed: TRUE); fields: accession,gene_primary
[2025-04-23 01:21:18] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2025-04-23 01:21:18] [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`.
[2025-04-23 01:21:18] [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`
[2025-04-23 01:21:18] [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`.
[2025-04-23 01:21:18] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-23 01:21:18] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-23 01:21:18] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-23 01:21:18] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-23 01:21:18] [INFO] [OmnipathR] Cache item `3ec84ba713c02573704adb50f1a94dab684df34b` version 1: status changed from `unknown` to `started`.
[2025-04-23 01:21:18] [TRACE] [OmnipathR] Exporting object to RDS: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/3ec84ba713c02573704adb50f1a94dab684df34b-1.rds`.
[2025-04-23 01:21:18] [INFO] [OmnipathR] Retrieving URL: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:10090%20AND%20reviewed:true`
[2025-04-23 01:21:18] [TRACE] [OmnipathR] Attempt 1/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:10090%20AND%20reviewed:true`
[2025-04-23 01:21:18] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2025-04-23 01:21:18] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-04-23 01:21:20] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2025-04-23 01:21:20] [TRACE] [OmnipathR] Downloaded 43 bytes in 1.369719s from rest.uniprot.org (31 bytes/s); Redirect: 0s, DNS look up: 0.002518s, Connection: 0.084645s, Pretransfer: 0.177739s, First byte at: 1.369584s
[2025-04-23 01:21:20] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 ; 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: 05-February-2025; Strict-Transport-Security: max-age=31536000; includeSubDomains; Date: Wed, 23 Apr 2025 05:21:20 GMT; Access-Control-Max-Age: 1728000; X-UniProt-Release: 2025_01; Transfer-Encoding: chunked; Access-Control-Allow-Origin: *; Connection: keep-alive; 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: 05-February-2025
[2025-04-23 01:24:28] [WARN] [OmnipathR] Failed to download `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:10090%20AND%20reviewed:true` (attempt 1/3); error: Failure when receiving data from the peer [rest.uniprot.org]
[2025-04-23 01:24:33] [TRACE] [OmnipathR] Attempt 2/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:10090%20AND%20reviewed:true`
[2025-04-23 01:24:33] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2025-04-23 01:24:33] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-04-23 01:24:34] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2025-04-23 01:24:34] [TRACE] [OmnipathR] Downloaded 43 bytes in 0.614524s from rest.uniprot.org (69 bytes/s); Redirect: 0s, DNS look up: 0.002028s, Connection: 0.083732s, Pretransfer: 0.178901s, First byte at: 0.61441s
[2025-04-23 01:24:34] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 ; 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: 05-February-2025; Strict-Transport-Security: max-age=31536000; includeSubDomains; Date: Wed, 23 Apr 2025 05:24:34 GMT; Access-Control-Max-Age: 1728000; X-UniProt-Release: 2025_01; Transfer-Encoding: chunked; Access-Control-Allow-Origin: *; Connection: keep-alive; 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: 05-February-2025
[2025-04-23 01:24:46] [TRACE] [OmnipathR] Exported RDS to `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/3ec84ba713c02573704adb50f1a94dab684df34b-1.rds`.
[2025-04-23 01:24:46] [INFO] [OmnipathR] Download ready [key=3ec84ba713c02573704adb50f1a94dab684df34b, version=1]
[2025-04-23 01:24:46] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-23 01:24:47] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-23 01:24:47] [INFO] [OmnipathR] Cache item `3ec84ba713c02573704adb50f1a94dab684df34b` version 1: status changed from `started` to `ready`.
[2025-04-23 01:24:47] [SUCCESS] [OmnipathR] UniProt (rest.uniprot.org): downloaded 17228 records
[2025-04-23 01:24:47] [TRACE] [OmnipathR] Translating complexes: 0 complexes in data.
[2025-04-23 01:24:47] [TRACE] [OmnipathR] 0 complexes after removing the ones mapping to more than 1 items in target identifier space.
[2025-04-23 01:24:47] [TRACE] [OmnipathR] Translated 0 complexes to 0.
[2025-04-23 01:24:47] [TRACE] [OmnipathR] 164184 rows before translation, 12877 uniprot IDs in column `uniprot`.
[2025-04-23 01:24:48] [TRACE] [OmnipathR] 164184 rows after translation; translated 12877 `uniprot` IDs in column `uniprot` to 12790 `genesymbol` IDs in column `genesymbol`.
[2025-04-23 01:24:48] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-04-23 01:24:48] [TRACE] [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B,C,D],genesymbols=TRUE,organisms=9606,query_type=interactions,datasets=dorothea]
[2025-04-23 01:24:48] [TRACE] [OmnipathR] Organism(s): 9606
[2025-04-23 01:24:48] [TRACE] [OmnipathR] Orthology targets:
[2025-04-23 01:24:48] [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`
[2025-04-23 01:24:48] [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`
[2025-04-23 01:24:48] [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`
[2025-04-23 01:24:48] [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`
[2025-04-23 01:24:48] [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`
[2025-04-23 01:24:48] [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`
[2025-04-23 01:24:48] [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`
[2025-04-23 01:24:48] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2025-04-23 01:24:48] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-04-23 01:24:49] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2025-04-23 01:24:49] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.342962s from omnipathdb.org (45.7 Kb/s); Redirect: 0s, DNS look up: 0.00222s, Connection: 0.084537s, Pretransfer: 0.178219s, First byte at: 0.342389s
[2025-04-23 01:24:49] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 23 Apr 2025 05:24:48 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Wed, 23 Apr 2025 06:24:48 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-04-23 01:24:51] [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`
[2025-04-23 01:24:51] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-23 01:24:51] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-23 01:24:51] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-23 01:24:51] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-23 01:24:51] [INFO] [OmnipathR] Cache item `46d37339bbc3f9a05bb89ccb79278cf1233f5cdf` version 1: status changed from `unknown` to `started`.
[2025-04-23 01:24:51] [TRACE] [OmnipathR] Exporting object to RDS: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/46d37339bbc3f9a05bb89ccb79278cf1233f5cdf-1.rds`.
[2025-04-23 01:24:53] [TRACE] [OmnipathR] Exported RDS to `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/46d37339bbc3f9a05bb89ccb79278cf1233f5cdf-1.rds`.
[2025-04-23 01:24:53] [INFO] [OmnipathR] Download ready [key=46d37339bbc3f9a05bb89ccb79278cf1233f5cdf, version=1]
[2025-04-23 01:24:53] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-23 01:24:53] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-23 01:24:53] [INFO] [OmnipathR] Cache item `46d37339bbc3f9a05bb89ccb79278cf1233f5cdf` version 1: status changed from `started` to `ready`.
[2025-04-23 01:25:02] [SUCCESS] [OmnipathR] Downloaded 278830 interactions.
[2025-04-23 01:25:14] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-04-23 01:25:14] [TRACE] [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B,C,D],genesymbols=TRUE,organisms=10090,query_type=interactions,datasets=dorothea]
[2025-04-23 01:25:14] [TRACE] [OmnipathR] Organism(s): 10090
[2025-04-23 01:25:14] [TRACE] [OmnipathR] Orthology targets:
[2025-04-23 01:25:14] [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`
[2025-04-23 01:25:14] [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`
[2025-04-23 01:25:14] [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`
[2025-04-23 01:25:14] [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`
[2025-04-23 01:25:14] [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`
[2025-04-23 01:25:14] [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`
[2025-04-23 01:25:14] [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`
[2025-04-23 01:25:14] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2025-04-23 01:25:14] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-04-23 01:25:15] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2025-04-23 01:25:15] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.346351s from omnipathdb.org (45.2 Kb/s); Redirect: 0s, DNS look up: 0.007591s, Connection: 0.092934s, Pretransfer: 0.182939s, First byte at: 0.345716s
[2025-04-23 01:25:15] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 23 Apr 2025 05:25:15 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Wed, 23 Apr 2025 06:25:15 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-04-23 01:25:17] [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`
[2025-04-23 01:25:17] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-23 01:25:17] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-23 01:25:17] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-23 01:25:17] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-23 01:25:17] [INFO] [OmnipathR] Cache item `ff347dedf78ef5e38c9c6d8eed291fa901aa3791` version 1: status changed from `unknown` to `started`.
[2025-04-23 01:25:18] [TRACE] [OmnipathR] Exporting object to RDS: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/ff347dedf78ef5e38c9c6d8eed291fa901aa3791-1.rds`.
[2025-04-23 01:25:19] [TRACE] [OmnipathR] Exported RDS to `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/ff347dedf78ef5e38c9c6d8eed291fa901aa3791-1.rds`.
[2025-04-23 01:25:19] [INFO] [OmnipathR] Download ready [key=ff347dedf78ef5e38c9c6d8eed291fa901aa3791, version=1]
[2025-04-23 01:25:19] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-23 01:25:19] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-23 01:25:19] [INFO] [OmnipathR] Cache item `ff347dedf78ef5e38c9c6d8eed291fa901aa3791` version 1: status changed from `started` to `ready`.
[2025-04-23 01:25:27] [SUCCESS] [OmnipathR] Downloaded 234298 interactions.
[2025-04-23 01:25:37] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-04-23 01:25:37] [TRACE] [OmnipathR] Arguments for OmniPath query: [loops=TRUE,organisms=9606,genesymbols=TRUE,query_type=interactions,datasets=collectri]
[2025-04-23 01:25:37] [TRACE] [OmnipathR] Organism(s): 9606
[2025-04-23 01:25:37] [TRACE] [OmnipathR] Orthology targets:
[2025-04-23 01:25:37] [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`
[2025-04-23 01:25:37] [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`
[2025-04-23 01:25:37] [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`
[2025-04-23 01:25:37] [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`
[2025-04-23 01:25:37] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2025-04-23 01:25:37] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2025-04-23 01:25:37] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2025-04-23 01:25:37] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2025-04-23 01:25:37] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-04-23 01:25:38] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2025-04-23 01:25:38] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 0.518866s from omnipathdb.org (30.2 Kb/s); Redirect: 0s, DNS look up: 0.179992s, Connection: 0.262871s, Pretransfer: 0.354923s, First byte at: 0.517926s
[2025-04-23 01:25:38] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 23 Apr 2025 05:25:37 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Wed, 23 Apr 2025 06:25:37 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-04-23 01:25:40] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2025-04-23 01:25:40] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-23 01:25:40] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-23 01:25:40] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-23 01:25:40] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-23 01:25:40] [INFO] [OmnipathR] Cache item `b10176737ba43d460b13709623189f3911123779` version 1: status changed from `unknown` to `started`.
[2025-04-23 01:25:40] [TRACE] [OmnipathR] Exporting object to RDS: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/b10176737ba43d460b13709623189f3911123779-1.rds`.
[2025-04-23 01:25:40] [TRACE] [OmnipathR] Exported RDS to `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/b10176737ba43d460b13709623189f3911123779-1.rds`.
[2025-04-23 01:25:40] [INFO] [OmnipathR] Download ready [key=b10176737ba43d460b13709623189f3911123779, version=1]
[2025-04-23 01:25:40] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-23 01:25:40] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-23 01:25:40] [INFO] [OmnipathR] Cache item `b10176737ba43d460b13709623189f3911123779` version 1: status changed from `started` to `ready`.
[2025-04-23 01:25:43] [SUCCESS] [OmnipathR] Downloaded 64958 interactions.
[2025-04-23 01:25:43] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-04-23 01:25:43] [TRACE] [OmnipathR] Arguments for OmniPath query: [genesymbols=TRUE,resources=CollecTRI,strict_evidences=TRUE,query_type=interactions,datasets=tf_mirna]
[2025-04-23 01:25:43] [TRACE] [OmnipathR] Organism(s): 9606
[2025-04-23 01:25:43] [TRACE] [OmnipathR] Orthology targets:
[2025-04-23 01:25:44] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-04-23 01:25:44] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-23 01:25:44] [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`
[2025-04-23 01:25:44] [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`
[2025-04-23 01:25:44] [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`
[2025-04-23 01:25:44] [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`
[2025-04-23 01:25:44] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2025-04-23 01:25:44] [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`
[2025-04-23 01:25:44] [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`
[2025-04-23 01:25:44] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2025-04-23 01:25:44] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-04-23 01:25:44] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2025-04-23 01:25:44] [TRACE] [OmnipathR] Downloaded 9.5 Kb in 0.256392s from omnipathdb.org (37 Kb/s); Redirect: 0s, DNS look up: 0.001973s, Connection: 0.083085s, Pretransfer: 0.174147s, First byte at: 0.255819s
[2025-04-23 01:25:44] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Wed, 23 Apr 2025 05:25:44 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Wed, 23 Apr 2025 06:25:44 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-04-23 01:25:45] [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`
[2025-04-23 01:25:46] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-23 01:25:46] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-23 01:25:46] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-23 01:25:46] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-23 01:25:46] [INFO] [OmnipathR] Cache item `f7d34500401ba98803b7d2b26c48f64cee1eea1b` version 1: status changed from `unknown` to `started`.
[2025-04-23 01:25:46] [TRACE] [OmnipathR] Exporting object to RDS: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/f7d34500401ba98803b7d2b26c48f64cee1eea1b-1.rds`.
[2025-04-23 01:25:46] [TRACE] [OmnipathR] Exported RDS to `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/f7d34500401ba98803b7d2b26c48f64cee1eea1b-1.rds`.
[2025-04-23 01:25:46] [INFO] [OmnipathR] Download ready [key=f7d34500401ba98803b7d2b26c48f64cee1eea1b, version=1]
[2025-04-23 01:25:46] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-23 01:25:46] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-23 01:25:46] [INFO] [OmnipathR] Cache item `f7d34500401ba98803b7d2b26c48f64cee1eea1b` version 1: status changed from `started` to `ready`.
[2025-04-23 01:25:46] [TRACE] [OmnipathR] Converting JSON column `evidences` to list.
[2025-04-23 01:25:46] [TRACE] [OmnipathR] Restricting interaction records to datasets: tf_mirna; and resources: CollecTRI
[2025-04-23 01:25:46] [TRACE] [OmnipathR] Filtering evidence columns: positive, negative, directed, undirected; to datasets: tf_mirna; and resources: CollecTRI; excluding resources: none
[2025-04-23 01:25:47] [SUCCESS] [OmnipathR] Downloaded 232 interactions.
[2025-04-23 01:25:47] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-04-23 01:25:47] [TRACE] [OmnipathR] Arguments for OmniPath query: [loops=TRUE,organisms=9606,genesymbols=TRUE,query_type=interactions,datasets=collectri]
[2025-04-23 01:25:47] [TRACE] [OmnipathR] Organism(s): 9606
[2025-04-23 01:25:47] [TRACE] [OmnipathR] Orthology targets:
[2025-04-23 01:25:47] [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`
[2025-04-23 01:25:47] [TRACE] [OmnipathR] Loaded data from RDS `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/b10176737ba43d460b13709623189f3911123779-1.rds`.
[2025-04-23 01:25:47] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2025-04-23 01:25:50] [SUCCESS] [OmnipathR] Loaded 64958 interactions from cache.
[2025-04-23 01:25:50] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-04-23 01:25:50] [TRACE] [OmnipathR] Arguments for OmniPath query: [genesymbols=TRUE,resources=CollecTRI,strict_evidences=TRUE,query_type=interactions,datasets=tf_mirna]
[2025-04-23 01:25:50] [TRACE] [OmnipathR] Organism(s): 9606
[2025-04-23 01:25:50] [TRACE] [OmnipathR] Orthology targets:
[2025-04-23 01:25:50] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-04-23 01:25:50] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-23 01:25:50] [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`
[2025-04-23 01:25:50] [TRACE] [OmnipathR] Loaded data from RDS `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/f7d34500401ba98803b7d2b26c48f64cee1eea1b-1.rds`.
[2025-04-23 01:25:50] [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`
[2025-04-23 01:25:50] [TRACE] [OmnipathR] Converting JSON column `evidences` to list.
[2025-04-23 01:25:50] [TRACE] [OmnipathR] Restricting interaction records to datasets: tf_mirna; and resources: CollecTRI
[2025-04-23 01:25:50] [TRACE] [OmnipathR] Filtering evidence columns: positive, negative, directed, undirected; to datasets: tf_mirna; and resources: CollecTRI; excluding resources: none
[2025-04-23 01:25:51] [SUCCESS] [OmnipathR] Loaded 232 interactions from cache.
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Attaching package: 'dplyr'
The following object is masked from 'package:testthat':
matches
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
[ FAIL 0 | WARN 19 | SKIP 0 | PASS 35 ]
[ FAIL 0 | WARN 19 | SKIP 0 | PASS 35 ]
>
> proc.time()
user system elapsed
195.65 6.98 573.76
decoupleR.Rcheck/decoupleR-Ex.timings
| name | user | system | elapsed | |
| check_corr | 0.08 | 0.01 | 0.32 | |
| convert_f_defaults | 0.07 | 0.00 | 0.07 | |
| decouple | 0 | 0 | 0 | |
| dot-fit_preprocessing | 0.03 | 0.00 | 0.06 | |
| extract_sets | 0.03 | 0.00 | 0.03 | |
| filt_minsize | 0.03 | 0.02 | 0.04 | |
| get_collectri | 9.22 | 0.79 | 16.58 | |
| get_dorothea | 24.78 | 0.53 | 26.21 | |
| get_profile_of | 0 | 0 | 0 | |
| get_progeny | 6.38 | 0.49 | 8.85 | |
| get_resource | 0.91 | 0.11 | 2.90 | |
| get_toy_data | 0 | 0 | 0 | |
| intersect_regulons | 0.03 | 0.00 | 0.03 | |
| pipe | 0 | 0 | 0 | |
| pivot_wider_profile | 0 | 0 | 0 | |
| randomize_matrix | 0 | 0 | 0 | |
| rename_net | 0.04 | 0.00 | 0.04 | |
| run_aucell | 8.70 | 0.70 | 9.49 | |
| run_consensus | 2.34 | 0.16 | 2.50 | |
| run_fgsea | 23.02 | 0.04 | 23.08 | |
| run_gsva | 1.94 | 0.47 | 1.92 | |
| run_mdt | 0.39 | 0.17 | 0.31 | |
| run_mlm | 0.14 | 0.02 | 0.12 | |
| run_ora | 0.50 | 0.01 | 0.52 | |
| run_udt | 0.39 | 0.02 | 0.40 | |
| run_ulm | 0.11 | 0.00 | 0.11 | |
| run_viper | 0.87 | 0.15 | 1.03 | |
| run_wmean | 0.83 | 0.00 | 0.83 | |
| run_wsum | 1.02 | 0.02 | 1.03 | |
| show_methods | 0.04 | 0.01 | 0.06 | |
| show_resources | 0.01 | 0.00 | 0.50 | |
| tidyeval | 0 | 0 | 0 | |