Multiple platform build/check report for BioC 3.21 - CHECK results for decoupleR on merida1

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"	4833
palomino7	Windows Server 2022 Datacenter	x64	4.5.0 RC (2025-04-04 r88126 ucrt) -- "How About a Twenty-Six"	4574
merida1	macOS 12.7.5 Monterey	x86_64	4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six"	4599
kjohnson1	macOS 13.6.6 Ventura	arm64	4.5.0 RC (2025-04-04 r88129) -- "How About a Twenty-Six"	4553
kunpeng2	Linux (openEuler 24.03 LTS)	aarch64	R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"	4570
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*

CHECK results for decoupleR on merida1

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.

raw results

Summary

Package: decoupleR

Version: 2.14.0

Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:decoupleR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings decoupleR_2.14.0.tar.gz

StartedAt: 2025-05-06 02:12:30 -0400 (Tue, 06 May 2025)

EndedAt: 2025-05-06 02:52:30 -0400 (Tue, 06 May 2025)

EllapsedTime: 2400.1 seconds

RetCode: None

Status: TIMEOUT

CheckDir: decoupleR.Rcheck

Warnings: NA

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:decoupleR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings decoupleR_2.14.0.tar.gz
###
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##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/decoupleR.Rcheck’
* using R version 4.5.0 RC (2025-04-04 r88126)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘decoupleR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘decoupleR’ version ‘2.14.0’
* 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 dependencies in R code ... NOTE
[2025-05-06 02:13:34] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-06 02:13:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-06 02:13:34] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-05-06 02:13:34] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-05-06 02:13:34] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-05-05
[2025-05-06 02:13:34] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-05-05 19:12:55 UTC; unix
[2025-05-06 02:13:34] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.16.0
[2025-05-06 02:13:34] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21
[2025-05-06 02:13:35] [INFO]    [OmnipathR] Session info: [version=R version 4.5.0 RC (2025-04-04 r88126); os=macOS Monterey 12.7.6; system=x86_64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-05-06; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown); quarto=1.4.553 @ /usr/local/bin/quarto]
[2025-05-06 02:13:36] [INFO]    [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=; pango=1.50.14; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.5.0; tcl=8.6.13; curl=8.7.1; zlib=1.2.11; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; PCRE=10.44 2024-06-07; ICU=70.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1]
[2025-05-06 02:13:36] [INFO]    [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); annotate 1.86.0(2025-05-05); AnnotationDbi 1.70.0(2025-05-05); AUCell 1.30.0(2025-05-05); backports 1.5.0(2024-05-23); beachmat 2.24.0(2025-05-05); Biobase 2.68.0(2025-05-05); BiocGenerics 0.54.0(2025-05-05); BiocParallel 1.42.0(2025-05-05); BiocSingular 1.24.0(2025-05-05); Biostrings 2.76.0(2025-05-05); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.2(2024-07-29); chromote 0.5.1(2025-04-24); cli 3.6.5(2025-04-23); codetools 0.2-20(2024-03-31); crayon 1.5.3(2024-06-20); curl 6.2.2(2025-03-24); data.table 1.17.0(2025-02-22); DBI 1.2.3(2024-06-02); decoupleR 2.14.0(2025-05-05); DelayedArray 0.34.1(2025-05-05); DelayedMatrixStats 1.30.0(2025-05-05); 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(2025-05-05); GenomeInfoDbData 1.2.14(2025-04-10); GenomicRanges 1.60.0(2025-05-05); glue 1.8.0(2024-09-30); graph 1.86.0(2025-05-05); GSEABase 1.70.0(2025-05-05); GSVA 2.2.0(2025-05-05); h5mread 1.0.0(2025-05-05); HDF5Array 1.36.0(2025-05-05); 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(2025-05-05); irlba 2.3.5.1(2022-10-03); jsonlite 2.0.0(2025-03-27); KEGGREST 1.48.0(2025-05-05); 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(2025-05-05); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); OmnipathR 3.16.0(2025-05-05); 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 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.0.14(2025-01-12); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rhdf5 2.52.0(2025-05-05); rhdf5filters 1.20.0(2025-05-05); Rhdf5lib 1.30.0(2025-05-05); rjson 0.2.23(2024-09-16); rlang 1.1.6(2025-04-11); rmarkdown 2.29(2024-11-04); RSQLite 2.3.11(2025-05-04); rsvd 1.0.5(2021-04-16); rvest 1.0.4(2024-02-12); S4Arrays 1.8.0(2025-05-05); S4Vectors 0.46.0(2025-05-05); ScaledMatrix 1.16.0(2025-05-05); sessioninfo 1.2.3(2025-02-05); SingleCellExperiment 1.30.1(2025-05-05); SparseArray 1.8.0(2025-05-05); sparseMatrixStats 1.20.0(2025-05-05); SpatialExperiment 1.18.0(2025-05-05); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); SummarizedExperiment 1.38.1(2025-05-05); 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(2025-05-05); 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(2025-05-05); yaml 2.3.10(2024-07-26); zip 2.3.2(2025-02-01)
[2025-05-06 02:13:36] [INFO]    [OmnipathR] CURL: version: 8.11.1; headers: 8.11.1; ssl_version: OpenSSL/3.3.2 (SecureTransport); libz_version: 1.2.11; libssh_version: NA; libidn_version: NA; host: x86_64-apple-darwin22.6.0; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE
[2025-05-06 02:13:36] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-05-06 02:13:36] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-05-06 02:13:36] [TRACE]   [OmnipathR] Contains 4 files.
[2025-05-06 02:13:36] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-05-06 02:13:36] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-06 02:13:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-06 02:13:36] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-05-06 02:13:36] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-05-06 02:13:36] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-05-06 02:13:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-06 02:13:36] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-05-06 02:13:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-06 02:13:37] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-05-06 02:13:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-06 02:13:37] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-05-06 02:13:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-06 02:13:37] [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 ... ERROR
Running examples in ‘decoupleR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: get_collectri
> ### Title: CollecTRI gene regulatory network. Wrapper to access CollecTRI
> ###   gene regulatory network. CollecTRI is a comprehensive resource
> ###   containing a curated collection of transcription factors (TFs) and
> ###   their target genes. It is an expansion of DoRothEA. Each interaction
> ###   is weighted by its mode of regulation (either positive or negative).
> ### Aliases: get_collectri
> 
> ### ** Examples
> 
> collectri <- get_collectri(organism='human', split_complexes=FALSE)
[2025-05-06 02:14:41] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-06 02:14:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-06 02:14:41] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-05-06 02:14:41] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-05-06 02:14:41] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-05-05
[2025-05-06 02:14:41] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-05-05 19:12:55 UTC; unix
[2025-05-06 02:14:41] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.16.0
[2025-05-06 02:14:41] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21
[2025-05-06 02:14:42] [INFO]    [OmnipathR] Session info: [version=R version 4.5.0 RC (2025-04-04 r88126); os=macOS Monterey 12.7.6; system=x86_64, darwin20; ui=X11; language=en; collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-05-06; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown); quarto=1.4.553 @ /usr/local/bin/quarto]
[2025-05-06 02:14:42] [INFO]    [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=; pango=1.50.14; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.5.0; tcl=8.6.13; curl=8.7.1; zlib=1.2.11; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; PCRE=10.44 2024-06-07; ICU=70.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1]
[2025-05-06 02:14:43] [INFO]    [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); BiocParallel 1.42.0(2025-05-05); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.2(2024-07-29); chromote 0.5.1(2025-04-24); cli 3.6.5(2025-04-23); codetools 0.2-20(2024-03-31); crayon 1.5.3(2024-06-20); curl 6.2.2(2025-03-24); DBI 1.2.3(2024-06-02); decoupleR 2.14.0(2025-05-05); 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); glue 1.8.0(2024-09-30); 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); jsonlite 2.0.0(2025-03-27); 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); magrittr 2.0.3(2022-03-30); Matrix 1.7-3(2025-03-11); memoise 2.0.1(2021-11-26); OmnipathR 3.16.0(2025-05-05); parallelly 1.43.0(2025-03-24); pillar 1.10.2(2025-04-05); pkgconfig 2.0.3(2019-09-22); 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 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.0.14(2025-01-12); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.29(2024-11-04); RSQLite 2.3.11(2025-05-04); rvest 1.0.4(2024-02-12); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); 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); utf8 1.2.5(2025-05-01); 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); yaml 2.3.10(2024-07-26); zip 2.3.2(2025-02-01)
[2025-05-06 02:14:43] [INFO]    [OmnipathR] CURL: version: 8.11.1; headers: 8.11.1; ssl_version: OpenSSL/3.3.2 (SecureTransport); libz_version: 1.2.11; libssh_version: NA; libidn_version: NA; host: x86_64-apple-darwin22.6.0; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE
[2025-05-06 02:14:43] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-05-06 02:14:43] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-05-06 02:14:43] [TRACE]   [OmnipathR] Contains 1 files.
[2025-05-06 02:14:43] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-05-06 02:14:43] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-06 02:14:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-06 02:14:43] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-05-06 02:14:43] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-05-06 02:14:43] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-05-06 02:14:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-06 02:14:43] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-05-06 02:14:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-06 02:14:43] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-05-06 02:14:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-06 02:14:43] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-05-06 02:14:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-06 02:14:43] [TRACE]   [OmnipathR] Cache locked: FALSE
[2025-05-06 02:14:43] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2025-05-06 02:14:43] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-06 02:14:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-06 02:14:43] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2025-05-06 02:14:43] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-06 02:14:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-06 02:14:43] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2025-05-06 02:14:43] [TRACE]   [OmnipathR] Cache file path: /Users/biocbuild/Library/Caches/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2025-05-06 02:14:43] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2025-05-06 02:14:43] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2025-05-06 02:14:43] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2025-05-06 02:14:43] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2025-05-06 02:14:43] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-05-06 02:14:43] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-05-06 02:14:43] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-05-06 02:14:43] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-05-06 02:16:14] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: HTTP 504 Gateway Timeout.
[2025-05-06 02:16:19] [TRACE]   [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html`
[2025-05-06 02:16:19] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2025-05-06 02:16:19] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-05-06 02:16:19] [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]
[2025-05-06 02:16:19] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-05-06 02:16:19] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-05-06 02:17:20] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: HTTP 504 Gateway Timeout.
[2025-05-06 02:17:25] [TRACE]   [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html`
[2025-05-06 02:17:25] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2025-05-06 02:17:25] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-05-06 02:17:25] [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]
[2025-05-06 02:17:25] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-05-06 02:17:25] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-05-06 02:18:55] [ERROR]   [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: HTTP 504 Gateway Timeout.
[2025-05-06 02:18:55] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-05-06 02:18:55] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-05-05
[2025-05-06 02:18:55] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-05-05 19:12:55 UTC; unix
[2025-05-06 02:18:55] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.16.0
[2025-05-06 02:18:55] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21
[2025-05-06 02:18:56] [INFO]    [OmnipathR] Session info: [version=R version 4.5.0 RC (2025-04-04 r88126); os=macOS Monterey 12.7.6; system=x86_64, darwin20; ui=X11; language=en; collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-05-06; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown); quarto=1.4.553 @ /usr/local/bin/quarto]
[2025-05-06 02:18:56] [INFO]    [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=; pango=1.50.14; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.5.0; tcl=8.6.13; curl=8.7.1; zlib=1.2.11; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; PCRE=10.44 2024-06-07; ICU=70.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1]
[2025-05-06 02:18:57] [INFO]    [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); BiocParallel 1.42.0(2025-05-05); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.2(2024-07-29); chromote 0.5.1(2025-04-24); cli 3.6.5(2025-04-23); codetools 0.2-20(2024-03-31); crayon 1.5.3(2024-06-20); curl 6.2.2(2025-03-24); DBI 1.2.3(2024-06-02); decoupleR 2.14.0(2025-05-05); 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); glue 1.8.0(2024-09-30); 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); jsonlite 2.0.0(2025-03-27); 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); magrittr 2.0.3(2022-03-30); Matrix 1.7-3(2025-03-11); memoise 2.0.1(2021-11-26); OmnipathR 3.16.0(2025-05-05); parallelly 1.43.0(2025-03-24); pillar 1.10.2(2025-04-05); pkgconfig 2.0.3(2019-09-22); 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 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.0.14(2025-01-12); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.29(2024-11-04); RSQLite 2.3.11(2025-05-04); rvest 1.0.4(2024-02-12); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); 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); utf8 1.2.5(2025-05-01); 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); yaml 2.3.10(2024-07-26); zip 2.3.2(2025-02-01)
[2025-05-06 02:18:57] [INFO]    [OmnipathR] CURL: version: 8.11.1; headers: 8.11.1; ssl_version: OpenSSL/3.3.2 (SecureTransport); libz_version: 1.2.11; libssh_version: NA; libidn_version: NA; host: x86_64-apple-darwin22.6.0; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE
[2025-05-06 02:18:57] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-05-06 02:18:57] [TRACE]   [OmnipathR] Arguments for OmniPath query: [loops=TRUE,organisms=9606,genesymbols=TRUE,query_type=interactions,datasets=collectri]
[2025-05-06 02:18:57] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2025-05-06 02:18:57] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2025-05-06 02:18:57] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-06 02:18:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-06 02:18:57] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 2.
[2025-05-06 02:18:57] [TRACE]   [OmnipathR] Cache file path: /Users/biocbuild/Library/Caches/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-2.html
[2025-05-06 02:18:57] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2025-05-06 02:18:57] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2025-05-06 02:18:57] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2025-05-06 02:18:57] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2025-05-06 02:18:57] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-05-06 02:18:57] [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]
[2025-05-06 02:18:57] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-05-06 02:18:57] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-05-06 02:19:58] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: HTTP 504 Gateway Timeout.
[2025-05-06 02:20:03] [TRACE]   [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html`
[2025-05-06 02:20:03] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2025-05-06 02:20:03] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-05-06 02:20:03] [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]
[2025-05-06 02:20:03] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-05-06 02:20:03] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-05-06 02:21:03] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: HTTP 504 Gateway Timeout.
[2025-05-06 02:21:08] [TRACE]   [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html`
[2025-05-06 02:21:08] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2025-05-06 02:21:08] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-05-06 02:21:08] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-05-06 02:21:08] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-05-06 02:21:08] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-05-06 02:22:09] [ERROR]   [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: HTTP 504 Gateway Timeout.
[2025-05-06 02:22:09] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-05-06 02:22:09] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-05-05
[2025-05-06 02:22:09] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-05-05 19:12:55 UTC; unix
[2025-05-06 02:22:09] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.16.0
[2025-05-06 02:22:09] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21
[2025-05-06 02:22:10] [INFO]    [OmnipathR] Session info: [version=R version 4.5.0 RC (2025-04-04 r88126); os=macOS Monterey 12.7.6; system=x86_64, darwin20; ui=X11; language=en; collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-05-06; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown); quarto=1.4.553 @ /usr/local/bin/quarto]
[2025-05-06 02:22:10] [INFO]    [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=; pango=1.50.14; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.5.0; tcl=8.6.13; curl=8.7.1; zlib=1.2.11; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; PCRE=10.44 2024-06-07; ICU=70.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1]
[2025-05-06 02:22:11] [INFO]    [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); BiocParallel 1.42.0(2025-05-05); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.2(2024-07-29); chromote 0.5.1(2025-04-24); cli 3.6.5(2025-04-23); codetools 0.2-20(2024-03-31); crayon 1.5.3(2024-06-20); curl 6.2.2(2025-03-24); DBI 1.2.3(2024-06-02); decoupleR 2.14.0(2025-05-05); 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); glue 1.8.0(2024-09-30); 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); jsonlite 2.0.0(2025-03-27); 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); magrittr 2.0.3(2022-03-30); Matrix 1.7-3(2025-03-11); memoise 2.0.1(2021-11-26); OmnipathR 3.16.0(2025-05-05); parallelly 1.43.0(2025-03-24); pillar 1.10.2(2025-04-05); pkgconfig 2.0.3(2019-09-22); 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 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.0.14(2025-01-12); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.29(2024-11-04); RSQLite 2.3.11(2025-05-04); rvest 1.0.4(2024-02-12); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); 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); utf8 1.2.5(2025-05-01); 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); yaml 2.3.10(2024-07-26); zip 2.3.2(2025-02-01)
[2025-05-06 02:22:11] [INFO]    [OmnipathR] CURL: version: 8.11.1; headers: 8.11.1; ssl_version: OpenSSL/3.3.2 (SecureTransport); libz_version: 1.2.11; libssh_version: NA; libidn_version: NA; host: x86_64-apple-darwin22.6.0; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE
[2025-05-06 02:22:11] [WARN]    [OmnipathR] Accessing `collectri` as a static table: this is not the recommended way to access OmniPath data; it is only a backup plan for situations when our server or your computer is experiencing issues.
[2025-05-06 02:22:12] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.static.omnipathdb.org/resources/interactions_collectri_9606.tsv.gz`
[2025-05-06 02:22:12] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.static.omnipathdb.org/resources/interactions_collectri_9606.tsv.gz`
[2025-05-06 02:22:12] [TRACE]   [OmnipathR] Attempting `http://no-tls.static.omnipathdb.org/resources/interactions_collectri_9606.tsv.gz`
[2025-05-06 02:22:12] [INFO]    [OmnipathR] Retrieving URL: `http://no-tls.static.omnipathdb.org/resources/interactions_collectri_9606.tsv.gz`
[2025-05-06 02:22:12] [TRACE]   [OmnipathR] Attempt 1/3: `http://no-tls.static.omnipathdb.org/resources/interactions_collectri_9606.tsv.gz`
[2025-05-06 02:22:15] [INFO]    [OmnipathR] Successfully retrieved: `http://no-tls.static.omnipathdb.org/resources/interactions_collectri_9606.tsv.gz`
[2025-05-06 02:22:15] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-06 02:22:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-06 02:22:15] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-06 02:22:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-06 02:22:15] [INFO]    [OmnipathR] Cache item `a2bbed8b281906d09d7cf983d102402e5de5da8c` version 1: status changed from `unknown` to `started`.
[2025-05-06 02:22:15] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/a2bbed8b281906d09d7cf983d102402e5de5da8c-1.rds`.
[2025-05-06 02:22:17] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/a2bbed8b281906d09d7cf983d102402e5de5da8c-1.rds`.
[2025-05-06 02:22:17] [INFO]    [OmnipathR] Download ready [key=a2bbed8b281906d09d7cf983d102402e5de5da8c, version=1]
[2025-05-06 02:22:17] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-06 02:22:17] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-06 02:22:17] [INFO]    [OmnipathR] Cache item `a2bbed8b281906d09d7cf983d102402e5de5da8c` version 1: status changed from `started` to `ready`.
[2025-05-06 02:22:17] [TRACE]   [OmnipathR] Converting JSON column `evidences` to list.
[2025-05-06 02:22:37] [TRACE]   [OmnipathR] Restricting interaction records to datasets: collectri; and resources: any
Error in if (.keep) . else select(., -!!evs_col) : 
  argument is of length zero
Calls: get_collectri ... tidyselect_data_has_predicates -> unnest_evidences -> %>%
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’

Installation output

decoupleR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL decoupleR
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘decoupleR’ ...
** this is package ‘decoupleR’ version ‘2.14.0’
** 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)

Tests output

decoupleR.Rcheck/tests/testthat.Rout


R version 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(decoupleR)
> 
> test_check("decoupleR")

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[2025-05-06 02:24:39] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-06 02:24:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-06 02:24:39] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-05-06 02:24:39] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-05-06 02:24:39] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-05-05
[2025-05-06 02:24:39] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-05-05 19:12:55 UTC; unix
[2025-05-06 02:24:39] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.16.0
[2025-05-06 02:24:39] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21
[2025-05-06 02:24:41] [INFO]    [OmnipathR] Session info: [version=R version 4.5.0 RC (2025-04-04 r88126); os=macOS Monterey 12.7.6; system=x86_64, darwin20; ui=X11; language=C; collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-05-06; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown); quarto=1.4.553 @ /usr/local/bin/quarto]
[2025-05-06 02:24:41] [INFO]    [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=; pango=1.50.14; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.5.0; tcl=8.6.13; curl=8.7.1; zlib=1.2.11; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; PCRE=10.44 2024-06-07; ICU=70.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1]
[2025-05-06 02:24:42] [INFO]    [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); annotate 1.86.0(2025-05-05); AnnotationDbi 1.70.0(2025-05-05); AUCell 1.30.0(2025-05-05); backports 1.5.0(2024-05-23); beachmat 2.24.0(2025-05-05); Biobase 2.68.0(2025-05-05); BiocGenerics 0.54.0(2025-05-05); BiocParallel 1.42.0(2025-05-05); BiocSingular 1.24.0(2025-05-05); Biostrings 2.76.0(2025-05-05); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); brio 1.1.5(2024-04-24); broom 1.0.8(2025-03-28); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.2(2024-07-29); chromote 0.5.1(2025-04-24); class 7.3-23(2025-01-01); cli 3.6.5(2025-04-23); codetools 0.2-20(2024-03-31); cowplot 1.1.3(2024-01-22); crayon 1.5.3(2024-06-20); curl 6.2.2(2025-03-24); data.table 1.17.0(2025-02-22); DBI 1.2.3(2024-06-02); decoupleR 2.14.0(2025-05-05); DelayedArray 0.34.1(2025-05-05); DelayedMatrixStats 1.30.0(2025-05-05); desc 1.4.3(2023-12-10); dichromat 2.0-0.1(2022-05-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); e1071 1.7-16(2024-09-16); evaluate 1.0.3(2025-01-10); farver 2.1.2(2024-05-13); fastmap 1.2.0(2024-05-15); fastmatch 1.1-6(2024-12-23); fgsea 1.34.0(2025-05-05); fs 1.6.6(2025-04-12); generics 0.1.3(2022-07-05); GenomeInfoDb 1.44.0(2025-05-05); GenomeInfoDbData 1.2.14(2025-04-10); GenomicRanges 1.60.0(2025-05-05); ggplot2 3.5.2(2025-04-09); glue 1.8.0(2024-09-30); graph 1.86.0(2025-05-05); GSEABase 1.70.0(2025-05-05); GSVA 2.2.0(2025-05-05); gtable 0.3.6(2024-10-25); h5mread 1.0.0(2025-05-05); HDF5Array 1.36.0(2025-05-05); 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(2025-05-05); irlba 2.3.5.1(2022-10-03); jsonlite 2.0.0(2025-03-27); KEGGREST 1.48.0(2025-05-05); 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(2025-05-05); 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 3.16.0(2025-05-05); 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 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); ranger 0.17.0(2024-11-08); rappdirs 0.3.3(2021-01-31); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.0.14(2025-01-12); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rhdf5 2.52.0(2025-05-05); rhdf5filters 1.20.0(2025-05-05); Rhdf5lib 1.30.0(2025-05-05); 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 2.3.11(2025-05-04); rsvd 1.0.5(2021-04-16); rvest 1.0.4(2024-02-12); S4Arrays 1.8.0(2025-05-05); S4Vectors 0.46.0(2025-05-05); ScaledMatrix 1.16.0(2025-05-05); 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(2025-05-05); SparseArray 1.8.0(2025-05-05); sparseMatrixStats 1.20.0(2025-05-05); SpatialExperiment 1.18.0(2025-05-05); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); SummarizedExperiment 1.38.1(2025-05-05); 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(2025-05-05); vctrs 0.6.5(2023-12-01); viper 1.42.0(2025-05-05); 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(2025-05-05); yaml 2.3.10(2024-07-26); zip 2.3.2(2025-02-01)
[2025-05-06 02:24:42] [INFO]    [OmnipathR] CURL: version: 8.11.1; headers: 8.11.1; ssl_version: OpenSSL/3.3.2 (SecureTransport); libz_version: 1.2.11; libssh_version: NA; libidn_version: NA; host: x86_64-apple-darwin22.6.0; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE
[2025-05-06 02:24:42] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-05-06 02:24:42] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-05-06 02:24:42] [TRACE]   [OmnipathR] Contains 4 files.
[2025-05-06 02:24:42] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-05-06 02:24:42] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-06 02:24:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-06 02:24:42] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-05-06 02:24:42] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-05-06 02:24:42] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-05-06 02:24:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-06 02:24:42] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-05-06 02:24:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-06 02:24:42] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-05-06 02:24:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-06 02:24:42] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-05-06 02:24:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-06 02:24:42] [TRACE]   [OmnipathR] Cache locked: FALSE
[2025-05-06 02:24:49] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-05-06 02:24:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-06 02:24:50] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-05-06 02:24:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-06 02:24:50] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2025-05-06 02:24:50] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-06 02:24:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-06 02:24:50] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2025-05-06 02:24:50] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-06 02:24:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-06 02:24:50] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2025-05-06 02:24:50] [TRACE]   [OmnipathR] Cache file path: /Users/biocbuild/Library/Caches/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2025-05-06 02:24:50] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2025-05-06 02:24:50] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2025-05-06 02:24:50] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2025-05-06 02:24:50] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2025-05-06 02:24:50] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-05-06 02:24:50] [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]
[2025-05-06 02:24:50] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-05-06 02:24:50] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-05-06 02:27:27] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: HTTP 504 Gateway Timeout.
[2025-05-06 02:27:32] [TRACE]   [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html`
[2025-05-06 02:27:32] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2025-05-06 02:27:32] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-05-06 02:27:32] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-05-06 02:27:32] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-05-06 02:27:32] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-05-06 02:28:32] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: HTTP 504 Gateway Timeout.
[2025-05-06 02:28:38] [TRACE]   [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html`
[2025-05-06 02:28:38] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2025-05-06 02:28:38] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-05-06 02:28:38] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-05-06 02:28:38] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-05-06 02:28:38] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-05-06 02:29:38] [ERROR]   [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: HTTP 504 Gateway Timeout.
[2025-05-06 02:29:38] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-05-06 02:29:38] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-05-05
[2025-05-06 02:29:38] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-05-05 19:12:55 UTC; unix
[2025-05-06 02:29:38] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.16.0
[2025-05-06 02:29:38] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21
[2025-05-06 02:29:40] [INFO]    [OmnipathR] Session info: [version=R version 4.5.0 RC (2025-04-04 r88126); os=macOS Monterey 12.7.6; system=x86_64, darwin20; ui=X11; language=C; collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-05-06; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown); quarto=1.4.553 @ /usr/local/bin/quarto]
[2025-05-06 02:29:40] [INFO]    [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=; pango=1.50.14; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.5.0; tcl=8.6.13; curl=8.7.1; zlib=1.2.11; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; PCRE=10.44 2024-06-07; ICU=70.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1]
[2025-05-06 02:29:40] [INFO]    [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); annotate 1.86.0(2025-05-05); AnnotationDbi 1.70.0(2025-05-05); AUCell 1.30.0(2025-05-05); backports 1.5.0(2024-05-23); beachmat 2.24.0(2025-05-05); Biobase 2.68.0(2025-05-05); BiocGenerics 0.54.0(2025-05-05); BiocParallel 1.42.0(2025-05-05); BiocSingular 1.24.0(2025-05-05); Biostrings 2.76.0(2025-05-05); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); brio 1.1.5(2024-04-24); broom 1.0.8(2025-03-28); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.2(2024-07-29); chromote 0.5.1(2025-04-24); class 7.3-23(2025-01-01); cli 3.6.5(2025-04-23); codetools 0.2-20(2024-03-31); cowplot 1.1.3(2024-01-22); crayon 1.5.3(2024-06-20); curl 6.2.2(2025-03-24); data.table 1.17.0(2025-02-22); DBI 1.2.3(2024-06-02); decoupleR 2.14.0(2025-05-05); DelayedArray 0.34.1(2025-05-05); DelayedMatrixStats 1.30.0(2025-05-05); desc 1.4.3(2023-12-10); dichromat 2.0-0.1(2022-05-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); e1071 1.7-16(2024-09-16); evaluate 1.0.3(2025-01-10); farver 2.1.2(2024-05-13); fastmap 1.2.0(2024-05-15); fastmatch 1.1-6(2024-12-23); fgsea 1.34.0(2025-05-05); fs 1.6.6(2025-04-12); generics 0.1.3(2022-07-05); GenomeInfoDb 1.44.0(2025-05-05); GenomeInfoDbData 1.2.14(2025-04-10); GenomicRanges 1.60.0(2025-05-05); ggplot2 3.5.2(2025-04-09); glue 1.8.0(2024-09-30); graph 1.86.0(2025-05-05); GSEABase 1.70.0(2025-05-05); GSVA 2.2.0(2025-05-05); gtable 0.3.6(2024-10-25); h5mread 1.0.0(2025-05-05); HDF5Array 1.36.0(2025-05-05); 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(2025-05-05); irlba 2.3.5.1(2022-10-03); jsonlite 2.0.0(2025-03-27); KEGGREST 1.48.0(2025-05-05); 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(2025-05-05); 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 3.16.0(2025-05-05); 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 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); ranger 0.17.0(2024-11-08); rappdirs 0.3.3(2021-01-31); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.0.14(2025-01-12); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rhdf5 2.52.0(2025-05-05); rhdf5filters 1.20.0(2025-05-05); Rhdf5lib 1.30.0(2025-05-05); 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 2.3.11(2025-05-04); rsvd 1.0.5(2021-04-16); rvest 1.0.4(2024-02-12); S4Arrays 1.8.0(2025-05-05); S4Vectors 0.46.0(2025-05-05); ScaledMatrix 1.16.0(2025-05-05); 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(2025-05-05); SparseArray 1.8.0(2025-05-05); sparseMatrixStats 1.20.0(2025-05-05); SpatialExperiment 1.18.0(2025-05-05); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); SummarizedExperiment 1.38.1(2025-05-05); 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(2025-05-05); vctrs 0.6.5(2023-12-01); viper 1.42.0(2025-05-05); 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(2025-05-05); yaml 2.3.10(2024-07-26); zip 2.3.2(2025-02-01)
[2025-05-06 02:29:40] [INFO]    [OmnipathR] CURL: version: 8.11.1; headers: 8.11.1; ssl_version: OpenSSL/3.3.2 (SecureTransport); libz_version: 1.2.11; libssh_version: NA; libidn_version: NA; host: x86_64-apple-darwin22.6.0; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE
[2025-05-06 02:29:42] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-05-06 02:29:42] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=TFcensus,query_type=annotations]
[2025-05-06 02:29:42] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2025-05-06 02:29:42] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2025-05-06 02:29:42] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-06 02:29:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-06 02:29:42] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 2.
[2025-05-06 02:29:42] [TRACE]   [OmnipathR] Cache file path: /Users/biocbuild/Library/Caches/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-2.html
[2025-05-06 02:29:42] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2025-05-06 02:29:42] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2025-05-06 02:29:42] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2025-05-06 02:29:42] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2025-05-06 02:29:42] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-05-06 02:29:42] [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]
[2025-05-06 02:29:42] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-05-06 02:29:42] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-05-06 02:31:13] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: HTTP 504 Gateway Timeout.
[2025-05-06 02:31:18] [TRACE]   [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html`
[2025-05-06 02:31:18] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2025-05-06 02:31:18] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-05-06 02:31:18] [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]
[2025-05-06 02:31:18] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-05-06 02:31:18] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-05-06 02:32:49] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: HTTP 504 Gateway Timeout.
[2025-05-06 02:32:54] [TRACE]   [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html`
[2025-05-06 02:32:54] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2025-05-06 02:32:54] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-05-06 02:32:54] [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]
[2025-05-06 02:32:54] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-05-06 02:32:54] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-05-06 02:33:54] [ERROR]   [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: HTTP 504 Gateway Timeout.
[2025-05-06 02:33:54] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-05-06 02:33:54] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-05-05
[2025-05-06 02:33:54] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-05-05 19:12:55 UTC; unix
[2025-05-06 02:33:54] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.16.0
[2025-05-06 02:33:54] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21
[2025-05-06 02:33:55] [INFO]    [OmnipathR] Session info: [version=R version 4.5.0 RC (2025-04-04 r88126); os=macOS Monterey 12.7.6; system=x86_64, darwin20; ui=X11; language=C; collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-05-06; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown); quarto=1.4.553 @ /usr/local/bin/quarto]
[2025-05-06 02:33:55] [INFO]    [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=; pango=1.50.14; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.5.0; tcl=8.6.13; curl=8.7.1; zlib=1.2.11; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; PCRE=10.44 2024-06-07; ICU=70.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1]
[2025-05-06 02:33:56] [INFO]    [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); annotate 1.86.0(2025-05-05); AnnotationDbi 1.70.0(2025-05-05); AUCell 1.30.0(2025-05-05); backports 1.5.0(2024-05-23); beachmat 2.24.0(2025-05-05); Biobase 2.68.0(2025-05-05); BiocGenerics 0.54.0(2025-05-05); BiocParallel 1.42.0(2025-05-05); BiocSingular 1.24.0(2025-05-05); Biostrings 2.76.0(2025-05-05); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); brio 1.1.5(2024-04-24); broom 1.0.8(2025-03-28); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.2(2024-07-29); chromote 0.5.1(2025-04-24); class 7.3-23(2025-01-01); cli 3.6.5(2025-04-23); codetools 0.2-20(2024-03-31); cowplot 1.1.3(2024-01-22); crayon 1.5.3(2024-06-20); curl 6.2.2(2025-03-24); data.table 1.17.0(2025-02-22); DBI 1.2.3(2024-06-02); decoupleR 2.14.0(2025-05-05); DelayedArray 0.34.1(2025-05-05); DelayedMatrixStats 1.30.0(2025-05-05); desc 1.4.3(2023-12-10); dichromat 2.0-0.1(2022-05-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); e1071 1.7-16(2024-09-16); evaluate 1.0.3(2025-01-10); farver 2.1.2(2024-05-13); fastmap 1.2.0(2024-05-15); fastmatch 1.1-6(2024-12-23); fgsea 1.34.0(2025-05-05); fs 1.6.6(2025-04-12); generics 0.1.3(2022-07-05); GenomeInfoDb 1.44.0(2025-05-05); GenomeInfoDbData 1.2.14(2025-04-10); GenomicRanges 1.60.0(2025-05-05); ggplot2 3.5.2(2025-04-09); glue 1.8.0(2024-09-30); graph 1.86.0(2025-05-05); GSEABase 1.70.0(2025-05-05); GSVA 2.2.0(2025-05-05); gtable 0.3.6(2024-10-25); h5mread 1.0.0(2025-05-05); HDF5Array 1.36.0(2025-05-05); 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(2025-05-05); irlba 2.3.5.1(2022-10-03); jsonlite 2.0.0(2025-03-27); KEGGREST 1.48.0(2025-05-05); 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(2025-05-05); 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 3.16.0(2025-05-05); 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 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); ranger 0.17.0(2024-11-08); rappdirs 0.3.3(2021-01-31); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.0.14(2025-01-12); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rhdf5 2.52.0(2025-05-05); rhdf5filters 1.20.0(2025-05-05); Rhdf5lib 1.30.0(2025-05-05); 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 2.3.11(2025-05-04); rsvd 1.0.5(2021-04-16); rvest 1.0.4(2024-02-12); S4Arrays 1.8.0(2025-05-05); S4Vectors 0.46.0(2025-05-05); ScaledMatrix 1.16.0(2025-05-05); 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(2025-05-05); SparseArray 1.8.0(2025-05-05); sparseMatrixStats 1.20.0(2025-05-05); SpatialExperiment 1.18.0(2025-05-05); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); SummarizedExperiment 1.38.1(2025-05-05); 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(2025-05-05); vctrs 0.6.5(2023-12-01); viper 1.42.0(2025-05-05); 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(2025-05-05); yaml 2.3.10(2024-07-26); zip 2.3.2(2025-02-01)
[2025-05-06 02:33:56] [INFO]    [OmnipathR] CURL: version: 8.11.1; headers: 8.11.1; ssl_version: OpenSSL/3.3.2 (SecureTransport); libz_version: 1.2.11; libssh_version: NA; libidn_version: NA; host: x86_64-apple-darwin22.6.0; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE
[2025-05-06 02:33:57] [WARN]    [OmnipathR] Accessing `TFcensus` as a static table: this is not the recommended way to access OmniPath data; it is only a backup plan for situations when our server or your computer is experiencing issues.
[2025-05-06 02:33:58] [ERROR]   [OmnipathR] [decoupleR] Failed to download annotation resource `TFcensus` from OmniPath. For more information, see the OmnipathR log.
[2025-05-06 02:33:59] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-05-06 02:33:59] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-06 02:33:59] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2025-05-06 02:33:59] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2025-05-06 02:33:59] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-06 02:33:59] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-06 02:33:59] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 3.
[2025-05-06 02:33:59] [TRACE]   [OmnipathR] Cache file path: /Users/biocbuild/Library/Caches/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-3.html
[2025-05-06 02:33:59] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2025-05-06 02:33:59] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2025-05-06 02:33:59] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2025-05-06 02:33:59] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2025-05-06 02:33:59] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-05-06 02:33:59] [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]
[2025-05-06 02:33:59] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-05-06 02:33:59] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-05-06 02:34:59] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: HTTP 504 Gateway Timeout.
[2025-05-06 02:35:04] [TRACE]   [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html`
[2025-05-06 02:35:04] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2025-05-06 02:35:04] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-05-06 02:35:04] [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]
[2025-05-06 02:35:04] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-05-06 02:35:04] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-05-06 02:36:05] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: HTTP 504 Gateway Timeout.
[2025-05-06 02:36:10] [TRACE]   [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html`
[2025-05-06 02:36:10] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2025-05-06 02:36:10] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-05-06 02:36:10] [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]
[2025-05-06 02:36:10] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-05-06 02:36:10] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-05-06 02:37:10] [ERROR]   [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: HTTP 504 Gateway Timeout.
[2025-05-06 02:37:11] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-05-06 02:37:11] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-05-05
[2025-05-06 02:37:11] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-05-05 19:12:55 UTC; unix
[2025-05-06 02:37:11] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.16.0
[2025-05-06 02:37:11] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21
[2025-05-06 02:37:12] [INFO]    [OmnipathR] Session info: [version=R version 4.5.0 RC (2025-04-04 r88126); os=macOS Monterey 12.7.6; system=x86_64, darwin20; ui=X11; language=C; collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-05-06; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown); quarto=1.4.553 @ /usr/local/bin/quarto]
[2025-05-06 02:37:12] [INFO]    [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=; pango=1.50.14; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.5.0; tcl=8.6.13; curl=8.7.1; zlib=1.2.11; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; PCRE=10.44 2024-06-07; ICU=70.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1]
[2025-05-06 02:37:12] [INFO]    [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); annotate 1.86.0(2025-05-05); AnnotationDbi 1.70.0(2025-05-05); AUCell 1.30.0(2025-05-05); backports 1.5.0(2024-05-23); beachmat 2.24.0(2025-05-05); Biobase 2.68.0(2025-05-05); BiocGenerics 0.54.0(2025-05-05); BiocParallel 1.42.0(2025-05-05); BiocSingular 1.24.0(2025-05-05); Biostrings 2.76.0(2025-05-05); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); brio 1.1.5(2024-04-24); broom 1.0.8(2025-03-28); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.2(2024-07-29); chromote 0.5.1(2025-04-24); class 7.3-23(2025-01-01); cli 3.6.5(2025-04-23); codetools 0.2-20(2024-03-31); cowplot 1.1.3(2024-01-22); crayon 1.5.3(2024-06-20); curl 6.2.2(2025-03-24); data.table 1.17.0(2025-02-22); DBI 1.2.3(2024-06-02); decoupleR 2.14.0(2025-05-05); DelayedArray 0.34.1(2025-05-05); DelayedMatrixStats 1.30.0(2025-05-05); desc 1.4.3(2023-12-10); dichromat 2.0-0.1(2022-05-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); e1071 1.7-16(2024-09-16); evaluate 1.0.3(2025-01-10); farver 2.1.2(2024-05-13); fastmap 1.2.0(2024-05-15); fastmatch 1.1-6(2024-12-23); fgsea 1.34.0(2025-05-05); fs 1.6.6(2025-04-12); generics 0.1.3(2022-07-05); GenomeInfoDb 1.44.0(2025-05-05); GenomeInfoDbData 1.2.14(2025-04-10); GenomicRanges 1.60.0(2025-05-05); ggplot2 3.5.2(2025-04-09); glue 1.8.0(2024-09-30); graph 1.86.0(2025-05-05); GSEABase 1.70.0(2025-05-05); GSVA 2.2.0(2025-05-05); gtable 0.3.6(2024-10-25); h5mread 1.0.0(2025-05-05); HDF5Array 1.36.0(2025-05-05); 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(2025-05-05); irlba 2.3.5.1(2022-10-03); jsonlite 2.0.0(2025-03-27); KEGGREST 1.48.0(2025-05-05); 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(2025-05-05); 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 3.16.0(2025-05-05); 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 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); ranger 0.17.0(2024-11-08); rappdirs 0.3.3(2021-01-31); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.0.14(2025-01-12); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rhdf5 2.52.0(2025-05-05); rhdf5filters 1.20.0(2025-05-05); Rhdf5lib 1.30.0(2025-05-05); 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 2.3.11(2025-05-04); rsvd 1.0.5(2021-04-16); rvest 1.0.4(2024-02-12); S4Arrays 1.8.0(2025-05-05); S4Vectors 0.46.0(2025-05-05); ScaledMatrix 1.16.0(2025-05-05); 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(2025-05-05); SparseArray 1.8.0(2025-05-05); sparseMatrixStats 1.20.0(2025-05-05); SpatialExperiment 1.18.0(2025-05-05); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); SummarizedExperiment 1.38.1(2025-05-05); 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(2025-05-05); vctrs 0.6.5(2023-12-01); viper 1.42.0(2025-05-05); 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(2025-05-05); yaml 2.3.10(2024-07-26); zip 2.3.2(2025-02-01)
[2025-05-06 02:37:12] [INFO]    [OmnipathR] CURL: version: 8.11.1; headers: 8.11.1; ssl_version: OpenSSL/3.3.2 (SecureTransport); libz_version: 1.2.11; libssh_version: NA; libidn_version: NA; host: x86_64-apple-darwin22.6.0; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE
[2025-05-06 02:37:13] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-05-06 02:37:13] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=PROGENy,query_type=annotations]
[2025-05-06 02:37:13] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2025-05-06 02:37:13] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2025-05-06 02:37:13] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-06 02:37:13] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-06 02:37:13] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 4.
[2025-05-06 02:37:14] [TRACE]   [OmnipathR] Cache file path: /Users/biocbuild/Library/Caches/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-4.html
[2025-05-06 02:37:14] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2025-05-06 02:37:14] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2025-05-06 02:37:14] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2025-05-06 02:37:14] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2025-05-06 02:37:14] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-05-06 02:37:14] [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]
[2025-05-06 02:37:14] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-05-06 02:37:14] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-05-06 02:38:14] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: HTTP 504 Gateway Timeout.
[2025-05-06 02:38:19] [TRACE]   [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html`
[2025-05-06 02:38:19] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2025-05-06 02:38:19] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-05-06 02:38:19] [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]
[2025-05-06 02:38:19] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-05-06 02:38:19] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-05-06 02:39:50] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: HTTP 504 Gateway Timeout.
[2025-05-06 02:39:55] [TRACE]   [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html`
[2025-05-06 02:39:55] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2025-05-06 02:39:55] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-05-06 02:39:55] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,tcp_keepcnt=13,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-05-06 02:39:55] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-05-06 02:39:55] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-05-06 02:41:25] [ERROR]   [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: HTTP 504 Gateway Timeout.
[2025-05-06 02:41:25] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-05-06 02:41:25] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-05-05
[2025-05-06 02:41:25] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-05-05 19:12:55 UTC; unix
[2025-05-06 02:41:25] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.16.0
[2025-05-06 02:41:25] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21
[2025-05-06 02:41:26] [INFO]    [OmnipathR] Session info: [version=R version 4.5.0 RC (2025-04-04 r88126); os=macOS Monterey 12.7.6; system=x86_64, darwin20; ui=X11; language=C; collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-05-06; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown); quarto=1.4.553 @ /usr/local/bin/quarto]
[2025-05-06 02:41:26] [INFO]    [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=; pango=1.50.14; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.5.0; tcl=8.6.13; curl=8.7.1; zlib=1.2.11; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; PCRE=10.44 2024-06-07; ICU=70.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1]
[2025-05-06 02:41:27] [INFO]    [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); annotate 1.86.0(2025-05-05); AnnotationDbi 1.70.0(2025-05-05); AUCell 1.30.0(2025-05-05); backports 1.5.0(2024-05-23); beachmat 2.24.0(2025-05-05); Biobase 2.68.0(2025-05-05); BiocGenerics 0.54.0(2025-05-05); BiocParallel 1.42.0(2025-05-05); BiocSingular 1.24.0(2025-05-05); Biostrings 2.76.0(2025-05-05); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); brio 1.1.5(2024-04-24); broom 1.0.8(2025-03-28); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.2(2024-07-29); chromote 0.5.1(2025-04-24); class 7.3-23(2025-01-01); cli 3.6.5(2025-04-23); codetools 0.2-20(2024-03-31); cowplot 1.1.3(2024-01-22); crayon 1.5.3(2024-06-20); curl 6.2.2(2025-03-24); data.table 1.17.0(2025-02-22); DBI 1.2.3(2024-06-02); decoupleR 2.14.0(2025-05-05); DelayedArray 0.34.1(2025-05-05); DelayedMatrixStats 1.30.0(2025-05-05); desc 1.4.3(2023-12-10); dichromat 2.0-0.1(2022-05-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); e1071 1.7-16(2024-09-16); evaluate 1.0.3(2025-01-10); farver 2.1.2(2024-05-13); fastmap 1.2.0(2024-05-15); fastmatch 1.1-6(2024-12-23); fgsea 1.34.0(2025-05-05); fs 1.6.6(2025-04-12); generics 0.1.3(2022-07-05); GenomeInfoDb 1.44.0(2025-05-05); GenomeInfoDbData 1.2.14(2025-04-10); GenomicRanges 1.60.0(2025-05-05); ggplot2 3.5.2(2025-04-09); glue 1.8.0(2024-09-30); graph 1.86.0(2025-05-05); GSEABase 1.70.0(2025-05-05); GSVA 2.2.0(2025-05-05); gtable 0.3.6(2024-10-25); h5mread 1.0.0(2025-05-05); HDF5Array 1.36.0(2025-05-05); 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(2025-05-05); irlba 2.3.5.1(2022-10-03); jsonlite 2.0.0(2025-03-27); KEGGREST 1.48.0(2025-05-05); 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(2025-05-05); 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 3.16.0(2025-05-05); 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 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); ranger 0.17.0(2024-11-08); rappdirs 0.3.3(2021-01-31); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.0.14(2025-01-12); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rhdf5 2.52.0(2025-05-05); rhdf5filters 1.20.0(2025-05-05); Rhdf5lib 1.30.0(2025-05-05); 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 2.3.11(2025-05-04); rsvd 1.0.5(2021-04-16); rvest 1.0.4(2024-02-12); S4Arrays 1.8.0(2025-05-05); S4Vectors 0.46.0(2025-05-05); ScaledMatrix 1.16.0(2025-05-05); 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(2025-05-05); SparseArray 1.8.0(2025-05-05); sparseMatrixStats 1.20.0(2025-05-05); SpatialExperiment 1.18.0(2025-05-05); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); SummarizedExperiment 1.38.1(2025-05-05); 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(2025-05-05); vctrs 0.6.5(2023-12-01); viper 1.42.0(2025-05-05); 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(2025-05-05); yaml 2.3.10(2024-07-26); zip 2.3.2(2025-02-01)
[2025-05-06 02:41:27] [INFO]    [OmnipathR] CURL: version: 8.11.1; headers: 8.11.1; ssl_version: OpenSSL/3.3.2 (SecureTransport); libz_version: 1.2.11; libssh_version: NA; libidn_version: NA; host: x86_64-apple-darwin22.6.0; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE
[2025-05-06 02:41:28] [WARN]    [OmnipathR] Accessing `PROGENy` as a static table: this is not the recommended way to access OmniPath data; it is only a backup plan for situations when our server or your computer is experiencing issues.
[2025-05-06 02:41:35] [TRACE]   [OmnipathR] Looking up in cache: `http://no-tls.static.omnipathdb.org/resources/annotations_PROGENy_9606.tsv.gz`
[2025-05-06 02:41:35] [INFO]    [OmnipathR] Cache record does not exist: `http://no-tls.static.omnipathdb.org/resources/annotations_PROGENy_9606.tsv.gz`
[2025-05-06 02:41:35] [TRACE]   [OmnipathR] Attempting `http://no-tls.static.omnipathdb.org/resources/annotations_PROGENy_9606.tsv.gz`
[2025-05-06 02:41:35] [INFO]    [OmnipathR] Retrieving URL: `http://no-tls.static.omnipathdb.org/resources/annotations_PROGENy_9606.tsv.gz`
[2025-05-06 02:41:35] [TRACE]   [OmnipathR] Attempt 1/3: `http://no-tls.static.omnipathdb.org/resources/annotations_PROGENy_9606.tsv.gz`
[2025-05-06 02:41:39] [INFO]    [OmnipathR] Successfully retrieved: `http://no-tls.static.omnipathdb.org/resources/annotations_PROGENy_9606.tsv.gz`
[2025-05-06 02:41:39] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-06 02:41:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-06 02:41:39] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-06 02:41:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-06 02:41:39] [INFO]    [OmnipathR] Cache item `103f85125e0134e3d65e4e63d22c339270d103e8` version 1: status changed from `unknown` to `started`.
[2025-05-06 02:41:39] [TRACE]   [OmnipathR] Exporting object to RDS: `/Users/biocbuild/Library/Caches/OmnipathR/103f85125e0134e3d65e4e63d22c339270d103e8-1.rds`.
[2025-05-06 02:41:44] [TRACE]   [OmnipathR] Exported RDS to `/Users/biocbuild/Library/Caches/OmnipathR/103f85125e0134e3d65e4e63d22c339270d103e8-1.rds`.
[2025-05-06 02:41:44] [INFO]    [OmnipathR] Download ready [key=103f85125e0134e3d65e4e63d22c339270d103e8, version=1]
[2025-05-06 02:41:44] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-06 02:41:44] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-06 02:41:44] [INFO]    [OmnipathR] Cache item `103f85125e0134e3d65e4e63d22c339270d103e8` version 1: status changed from `started` to `ready`.
[2025-05-06 02:41:44] [SUCCESS] [OmnipathR] Downloaded 700239 annotation records.
[2025-05-06 02:41:48] [TRACE]   [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-05-06 02:41:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-06 02:41:48] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2025-05-06 02:41:48] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2025-05-06 02:41:48] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-06 02:41:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-06 02:41:48] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 5.
[2025-05-06 02:41:48] [TRACE]   [OmnipathR] Cache file path: /Users/biocbuild/Library/Caches/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-5.html
[2025-05-06 02:41:48] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2025-05-06 02:41:48] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2025-05-06 02:41:48] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2025-05-06 02:41:48] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2025-05-06 02:41:48] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-05-06 02:41:48] [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]
[2025-05-06 02:41:48] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-05-06 02:41:48] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-05-06 02:42:48] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: HTTP 504 Gateway Timeout.
[2025-05-06 02:42:53] [TRACE]   [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html`
[2025-05-06 02:42:53] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2025-05-06 02:42:53] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-05-06 02:42:53] [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]
[2025-05-06 02:42:53] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-05-06 02:42:53] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-05-06 02:44:24] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: HTTP 404 Not Found.
[2025-05-06 02:44:29] [TRACE]   [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html`
[2025-05-06 02:44:29] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2025-05-06 02:44:29] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-05-06 02:44:29] [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]
[2025-05-06 02:44:29] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-05-06 02:44:29] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-05-06 02:45:30] [ERROR]   [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: HTTP 504 Gateway Timeout.
[2025-05-06 02:45:30] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-05-06 02:45:30] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-05-05
[2025-05-06 02:45:30] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-05-05 19:12:55 UTC; unix
[2025-05-06 02:45:30] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.16.0
[2025-05-06 02:45:30] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21
[2025-05-06 02:45:31] [INFO]    [OmnipathR] Session info: [version=R version 4.5.0 RC (2025-04-04 r88126); os=macOS Monterey 12.7.6; system=x86_64, darwin20; ui=X11; language=C; collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-05-06; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown); quarto=1.4.553 @ /usr/local/bin/quarto]
[2025-05-06 02:45:31] [INFO]    [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=; pango=1.50.14; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.5.0; tcl=8.6.13; curl=8.7.1; zlib=1.2.11; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; PCRE=10.44 2024-06-07; ICU=70.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1]
[2025-05-06 02:45:32] [INFO]    [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); annotate 1.86.0(2025-05-05); AnnotationDbi 1.70.0(2025-05-05); AUCell 1.30.0(2025-05-05); backports 1.5.0(2024-05-23); beachmat 2.24.0(2025-05-05); Biobase 2.68.0(2025-05-05); BiocGenerics 0.54.0(2025-05-05); BiocParallel 1.42.0(2025-05-05); BiocSingular 1.24.0(2025-05-05); Biostrings 2.76.0(2025-05-05); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); brio 1.1.5(2024-04-24); broom 1.0.8(2025-03-28); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.2(2024-07-29); chromote 0.5.1(2025-04-24); class 7.3-23(2025-01-01); cli 3.6.5(2025-04-23); codetools 0.2-20(2024-03-31); cowplot 1.1.3(2024-01-22); crayon 1.5.3(2024-06-20); curl 6.2.2(2025-03-24); data.table 1.17.0(2025-02-22); DBI 1.2.3(2024-06-02); decoupleR 2.14.0(2025-05-05); DelayedArray 0.34.1(2025-05-05); DelayedMatrixStats 1.30.0(2025-05-05); desc 1.4.3(2023-12-10); dichromat 2.0-0.1(2022-05-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); e1071 1.7-16(2024-09-16); evaluate 1.0.3(2025-01-10); farver 2.1.2(2024-05-13); fastmap 1.2.0(2024-05-15); fastmatch 1.1-6(2024-12-23); fgsea 1.34.0(2025-05-05); fs 1.6.6(2025-04-12); generics 0.1.3(2022-07-05); GenomeInfoDb 1.44.0(2025-05-05); GenomeInfoDbData 1.2.14(2025-04-10); GenomicRanges 1.60.0(2025-05-05); ggplot2 3.5.2(2025-04-09); glue 1.8.0(2024-09-30); graph 1.86.0(2025-05-05); GSEABase 1.70.0(2025-05-05); GSVA 2.2.0(2025-05-05); gtable 0.3.6(2024-10-25); h5mread 1.0.0(2025-05-05); HDF5Array 1.36.0(2025-05-05); 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(2025-05-05); irlba 2.3.5.1(2022-10-03); jsonlite 2.0.0(2025-03-27); KEGGREST 1.48.0(2025-05-05); 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(2025-05-05); 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 3.16.0(2025-05-05); 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 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); ranger 0.17.0(2024-11-08); rappdirs 0.3.3(2021-01-31); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.0.14(2025-01-12); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rhdf5 2.52.0(2025-05-05); rhdf5filters 1.20.0(2025-05-05); Rhdf5lib 1.30.0(2025-05-05); 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 2.3.11(2025-05-04); rsvd 1.0.5(2021-04-16); rvest 1.0.4(2024-02-12); S4Arrays 1.8.0(2025-05-05); S4Vectors 0.46.0(2025-05-05); ScaledMatrix 1.16.0(2025-05-05); 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(2025-05-05); SparseArray 1.8.0(2025-05-05); sparseMatrixStats 1.20.0(2025-05-05); SpatialExperiment 1.18.0(2025-05-05); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); SummarizedExperiment 1.38.1(2025-05-05); 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(2025-05-05); vctrs 0.6.5(2023-12-01); viper 1.42.0(2025-05-05); viridisLite 0.4.2(2023-05-02); vroom 1.6.5(2023-12-05); 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(2025-05-05); yaml 2.3.10(2024-07-26); zip 2.3.2(2025-02-01)
[2025-05-06 02:45:32] [INFO]    [OmnipathR] CURL: version: 8.11.1; headers: 8.11.1; ssl_version: OpenSSL/3.3.2 (SecureTransport); libz_version: 1.2.11; libssh_version: NA; libidn_version: NA; host: x86_64-apple-darwin22.6.0; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE
[2025-05-06 02:45:33] [TRACE]   [OmnipathR] Processing args for OmniPath query
[2025-05-06 02:45:33] [TRACE]   [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=PROGENy,query_type=annotations]
[2025-05-06 02:45:33] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2025-05-06 02:45:33] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2025-05-06 02:45:33] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-06 02:45:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-06 02:45:33] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 6.
[2025-05-06 02:45:33] [TRACE]   [OmnipathR] Cache file path: /Users/biocbuild/Library/Caches/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-6.html
[2025-05-06 02:45:33] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2025-05-06 02:45:33] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2025-05-06 02:45:33] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2025-05-06 02:45:33] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2025-05-06 02:45:33] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-05-06 02:45:33] [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]
[2025-05-06 02:45:33] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-05-06 02:45:33] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-05-06 02:47:36] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 1/3); error: HTTP 504 Gateway Timeout.
[2025-05-06 02:47:41] [TRACE]   [OmnipathR] Attempt 2/3: `https://www.ensembl.org/info/about/species.html`
[2025-05-06 02:47:41] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2025-05-06 02:47:41] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-05-06 02:47:41] [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]
[2025-05-06 02:47:41] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-05-06 02:47:41] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-05-06 02:49:11] [WARN]    [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 2/3); error: HTTP 504 Gateway Timeout.
[2025-05-06 02:49:16] [TRACE]   [OmnipathR] Attempt 3/3: `https://www.ensembl.org/info/about/species.html`
[2025-05-06 02:49:16] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2025-05-06 02:49:16] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-05-06 02:49:16] [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]
[2025-05-06 02:49:16] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-05-06 02:49:16] [TRACE]   [OmnipathR] Sending HTTP request.
[2025-05-06 02:50:47] [ERROR]   [OmnipathR] Failed to download `https://www.ensembl.org/info/about/species.html` (attempt 3/3); error: HTTP 504 Gateway Timeout.
[2025-05-06 02:50:47] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-05-06 02:50:47] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-05-05
[2025-05-06 02:50:47] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-05-05 19:12:55 UTC; unix
[2025-05-06 02:50:47] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.16.0
[2025-05-06 02:50:47] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21
[2025-05-06 02:50:48] [INFO]    [OmnipathR] Session info: [version=R version 4.5.0 RC (2025-04-04 r88126); os=macOS Monterey 12.7.6; system=x86_64, darwin20; ui=X11; language=C; collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-05-06; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown); quarto=1.4.553 @ /usr/local/bin/quarto]
[2025-05-06 02:50:48] [INFO]    [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=; pango=1.50.14; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.5.0; tcl=8.6.13; curl=8.7.1; zlib=1.2.11; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; PCRE=10.44 2024-06-07; ICU=70.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1]
[2025-05-06 02:50:49] [INFO]    [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); annotate 1.86.0(2025-05-05); AnnotationDbi 1.70.0(2025-05-05); AUCell 1.30.0(2025-05-05); backports 1.5.0(2024-05-23); beachmat 2.24.0(2025-05-05); Biobase 2.68.0(2025-05-05); BiocGenerics 0.54.0(2025-05-05); BiocParallel 1.42.0(2025-05-05); BiocSingular 1.24.0(2025-05-05); Biostrings 2.76.0(2025-05-05); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); brio 1.1.5(2024-04-24); broom 1.0.8(2025-03-28); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.2(2024-07-29); chromote 0.5.1(2025-04-24); class 7.3-23(2025-01-01); cli 3.6.5(2025-04-23); codetools 0.2-20(2024-03-31); cowplot 1.1.3(2024-01-22); crayon 1.5.3(2024-06-20); curl 6.2.2(2025-03-24); data.table 1.17.0(2025-02-22); DBI 1.2.3(2024-06-02); decoupleR 2.14.0(2025-05-05); DelayedArray 0.34.1(2025-05-05); DelayedMatrixStats 1.30.0(2025-05-05); desc 1.4.3(2023-12-10); dichromat 2.0-0.1(2022-05-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); e1071 1.7-16(2024-09-16); evaluate 1.0.3(2025-01-10); farver 2.1.2(2024-05-13); fastmap 1.2.0(2024-05-15); fastmatch 1.1-6(2024-12-23); fgsea 1.34.0(2025-05-05); fs 1.6.6(2025-04-12); generics 0.1.3(2022-07-05); GenomeInfoDb 1.44.0(2025-05-05); GenomeInfoDbData 1.2.14(2025-04-10); GenomicRanges 1.60.0(2025-05-05); ggplot2 3.5.2(2025-04-09); glue 1.8.0(2024-09-30); graph 1.86.0(2025-05-05); GSEABase 1.70.0(2025-05-05); GSVA 2.2.0(2025-05-05); gtable 0.3.6(2024-10-25); h5mread 1.0.0(2025-05-05); HDF5Array 1.36.0(2025-05-05); 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(2025-05-05); irlba 2.3.5.1(2022-10-03); jsonlite 2.0.0(2025-03-27); KEGGREST 1.48.0(2025-05-05); 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(2025-05-05); 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 3.16.0(2025-05-05); 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 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); ranger 0.17.0(2024-11-08); rappdirs 0.3.3(2021-01-31); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.0.14(2025-01-12); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rhdf5 2.52.0(2025-05-05); rhdf5filters 1.20.0(2025-05-05); Rhdf5lib 1.30.0(2025-05-05); 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 2.3.11(2025-05-04); rsvd 1.0.5(2021-04-16); rvest 1.0.4(2024-02-12); S4Arrays 1.8.0(2025-05-05); S4Vectors 0.46.0(2025-05-05); ScaledMatrix 1.16.0(2025-05-05); 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(2025-05-05); SparseArray 1.8.0(2025-05-05); sparseMatrixStats 1.20.0(2025-05-05); SpatialExperiment 1.18.0(2025-05-05); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); SummarizedExperiment 1.38.1(2025-05-05); 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(2025-05-05); vctrs 0.6.5(2023-12-01); viper 1.42.0(2025-05-05); viridisLite 0.4.2(2023-05-02); vroom 1.6.5(2023-12-05); 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(2025-05-05); yaml 2.3.10(2024-07-26); zip 2.3.2(2025-02-01)
[2025-05-06 02:50:49] [INFO]    [OmnipathR] CURL: version: 8.11.1; headers: 8.11.1; ssl_version: OpenSSL/3.3.2 (SecureTransport); libz_version: 1.2.11; libssh_version: NA; libidn_version: NA; host: x86_64-apple-darwin22.6.0; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE
[2025-05-06 02:50:50] [WARN]    [OmnipathR] Accessing `PROGENy` as a static table: this is not the recommended way to access OmniPath data; it is only a backup plan for situations when our server or your computer is experiencing issues.
[2025-05-06 02:50:51] [ERROR]   [OmnipathR] [decoupleR] Failed to download annotation resource `PROGENy` from OmniPath. For more information, see the OmnipathR log.
[2025-05-06 02:50:51] [INFO]    [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2025-05-06 02:50:51] [INFO]    [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2025-05-06 02:50:51] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-05-06 02:50:51] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-05-06 02:50:51] [INFO]    [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 7.
[2025-05-06 02:50:51] [TRACE]   [OmnipathR] Cache file path: /Users/biocbuild/Library/Caches/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-7.html
[2025-05-06 02:50:51] [INFO]    [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2025-05-06 02:50:51] [TRACE]   [OmnipathR] Downloading by `httr2` in `download_base`.
[2025-05-06 02:50:51] [TRACE]   [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2025-05-06 02:50:51] [TRACE]   [OmnipathR] Preparing httr2 request to URL `https://www.ensembl.org/info/about/species.html`.
[2025-05-06 02:50:51] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-05-06 02:50:51] [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]
[2025-05-06 02:50:51] [TRACE]   [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-05-06 02:50:51] [TRACE]   [OmnipathR] Sending HTTP request.

Example timings

decoupleR.Rcheck/decoupleR-Ex.timings

name	user	system	elapsed
check_corr	0.162	0.026	0.209
convert_f_defaults	0.088	0.009	0.102
decouple	0.002	0.001	0.003
dot-fit_preprocessing	0.044	0.007	0.053
extract_sets	0.043	0.002	0.047
filt_minsize	0.085	0.002	0.092