| Back to Build/check report for BioC 3.22: simplified long |
|
This page was generated on 2026-02-27 11:57 -0500 (Fri, 27 Feb 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4891 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 541/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| decoupleR 2.16.0 (landing page) Pau Badia-i-Mompel
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| See other builds for decoupleR in R Universe. | ||||||||||||||
|
To the developers/maintainers of the decoupleR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/decoupleR.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: decoupleR |
| Version: 2.16.0 |
| Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:decoupleR.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings decoupleR_2.16.0.tar.gz |
| StartedAt: 2026-02-26 22:43:31 -0500 (Thu, 26 Feb 2026) |
| EndedAt: 2026-02-26 23:06:16 -0500 (Thu, 26 Feb 2026) |
| EllapsedTime: 1365.3 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: decoupleR.Rcheck |
| Warnings: NA |
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###
### Running command:
###
### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:decoupleR.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings decoupleR_2.16.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/decoupleR.Rcheck’
* using R version 4.5.2 (2025-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘decoupleR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘decoupleR’ version ‘2.16.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘decoupleR’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
[2026-02-26 22:44:04] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-26 22:44:04] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 22:44:04] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2026-02-26 22:44:04] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2026-02-26 22:44:04] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2026-02-26
[2026-02-26 22:44:04] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.2; ; 2026-02-26 20:08:22 UTC; unix
[2026-02-26 22:44:04] [INFO] [OmnipathR] Package `OmnipathR` version: 3.18.4
[2026-02-26 22:44:04] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2026-02-26 22:44:04] [INFO] [OmnipathR] Session info: [version=R version 4.5.2 (2025-10-31); os=Ubuntu 24.04.3 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2026-02-26; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2026-02-26 22:44:05] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.22-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2026-02-26 22:44:05] [INFO] [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); annotate 1.88.0(2026-02-26); AnnotationDbi 1.72.0(2026-02-26); AUCell 1.32.0(2026-02-26); backports 1.5.0(2024-05-23); beachmat 2.26.0(2026-02-26); Biobase 2.70.0(2026-02-26); BiocGenerics 0.56.0(2026-02-26); BiocParallel 1.44.0(2026-02-26); BiocSingular 1.26.1(2026-02-26); Biostrings 2.78.0(2026-02-26); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.3.0(2026-01-14); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); chromote 0.5.1(2025-04-24); cli 3.6.5(2025-04-23); codetools 0.2-20(2024-03-31); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); data.table 1.18.2.1(2026-01-27); DBI 1.3.0(2026-02-25); decoupleR 2.16.0(2026-02-26); DelayedArray 0.36.0(2026-02-26); DelayedMatrixStats 1.32.0(2026-02-26); digest 0.6.39(2025-11-19); dplyr 1.2.0(2026-02-03); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); GenomicRanges 1.62.1(2026-02-26); glue 1.8.0(2024-09-30); graph 1.88.1(2026-02-26); GSEABase 1.72.0(2026-02-26); GSVA 2.4.6(2026-02-26); h5mread 1.2.1(2026-02-26); HDF5Array 1.38.0(2026-02-26); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); httr 1.4.8(2026-02-13); httr2 1.2.2(2025-12-08); igraph 2.2.2(2026-02-12); IRanges 2.44.0(2026-02-26); irlba 2.3.7(2026-01-30); jsonlite 2.0.0(2025-03-27); KEGGREST 1.50.0(2026-02-26); knitr 1.51(2025-12-20); later 1.4.7(2026-02-24); lattice 0.22-9(2026-02-09); lifecycle 1.0.5(2026-01-08); logger 0.4.1(2025-09-11); lubridate 1.9.5(2026-02-04); magick 2.9.0(2025-09-08); magrittr 2.0.4(2025-09-12); Matrix 1.7-4(2025-08-28); MatrixGenerics 1.22.0(2026-02-26); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); memuse 4.2-3(2023-01-24); OmnipathR 3.18.4(2026-02-26); otel 0.2.0(2025-08-29); parallelly 1.46.1(2026-01-08); pillar 1.11.1(2025-09-17); 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 1.5.0(2025-11-01); ps 1.9.1(2025-04-12); purrr 1.2.1(2026-01-09); 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 0.3.4(2026-01-17); Rcpp 1.1.1(2026-01-10); readr 2.2.0(2026-02-19); readxl 1.4.5(2025-03-07); rhdf5 2.54.1(2026-02-26); rhdf5filters 1.22.0(2026-02-26); Rhdf5lib 1.32.0(2026-02-26); rjson 0.2.23(2024-09-16); rlang 1.1.7(2026-01-09); rmarkdown 2.30(2025-09-28); RSQLite 2.4.6(2026-02-06); rsvd 1.0.5(2021-04-16); rvest 1.0.5(2025-08-29); S4Arrays 1.10.1(2026-02-26); S4Vectors 0.48.0(2026-02-26); ScaledMatrix 1.18.0(2026-02-26); Seqinfo 1.0.0(2026-02-26); sessioninfo 1.2.3(2025-02-05); SingleCellExperiment 1.32.0(2026-02-26); SparseArray 1.10.8(2026-02-26); sparseMatrixStats 1.22.0(2026-02-26); SpatialExperiment 1.20.0(2026-02-26); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); SummarizedExperiment 1.40.0(2026-02-26); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tzdb 0.5.0(2025-03-15); vctrs 0.7.1(2026-01-23); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.56(2026-01-18); XML 3.99-0.22(2026-02-10); xml2 1.5.2(2026-01-17); xtable 1.8-8(2026-02-22); XVector 0.50.0(2026-02-26); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13)
[2026-02-26 22:44:05] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: GnuTLS/3.8.3; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2026-02-26 22:44:05] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2026-02-26 22:44:05] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2026-02-26 22:44:05] [TRACE] [OmnipathR] Contains 9 files.
[2026-02-26 22:44:05] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2026-02-26 22:44:05] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-26 22:44:05] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 22:44:05] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2026-02-26 22:44:05] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2026-02-26 22:44:05] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2026-02-26 22:44:05] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 22:44:05] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2026-02-26 22:44:05] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 22:44:05] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2026-02-26 22:44:05] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 22:44:05] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2026-02-26 22:44:05] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 22:44:05] [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_dorothea
> ### Title: DoRothEA gene regulatory network.
> ### Aliases: get_dorothea
>
> ### ** Examples
>
> dorothea <- get_dorothea(organism='human', levels=c('A', 'B'))
[2026-02-26 22:45:33] [TRACE] [OmnipathR] Processing args for OmniPath query
[2026-02-26 22:45:33] [TRACE] [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B,C,D],genesymbols=TRUE,organisms=9606,query_type=interactions,datasets=dorothea]
[2026-02-26 22:45:33] [TRACE] [OmnipathR] Organism(s): 9606
[2026-02-26 22:45:33] [TRACE] [OmnipathR] Orthology targets:
[2026-02-26 22:45:33] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-02-26 22:45:33] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-02-26 22:45:33] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-02-26 22:45:33] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-02-26 22:45:33] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-02-26 22:45:33] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-02-26 22:45:33] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-02-26 22:45:33] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2026-02-26 22:45:33] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-26 22:45:33] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-02-26 22:46:33] [TRACE] [OmnipathR] HTTP v1 GET: status 503.
[2026-02-26 22:46:33] [TRACE] [OmnipathR] Downloaded 0 bytes in 1m 0.524481000000002s from omnipathdb.org (0 bytes/s); Redirect: 0s, DNS look up: 0.001843s, Connection: 0.002624s, Pretransfer: 0.202848s, First byte at: 1m 0.524453000000001s
[2026-02-26 22:46:33] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 503 Service Unavailable; Server: nginx; Date: Fri, 27 Feb 2026 03:46:33 GMT; Content-Type: text/plain; charset=utf-8; Content-Length: 82; Connection: keep-alive
[2026-02-26 22:46:33] [WARN] [OmnipathR] HTTP request failed with error: Failed to open 'https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic': The requested URL returned error: 503
[2026-02-26 22:46:33] [WARN] [OmnipathR] Failed to download `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic` (attempt 1/3); error: Failed to open 'https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic': The requested URL returned error: 503
[2026-02-26 22:46:38] [TRACE] [OmnipathR] Attempt 2/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-02-26 22:46:38] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2026-02-26 22:46:38] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-26 22:46:38] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-02-26 22:47:39] [TRACE] [OmnipathR] HTTP v1 GET: status 503.
[2026-02-26 22:47:39] [TRACE] [OmnipathR] Downloaded 0 bytes in 1m 0.963999000000001s from omnipathdb.org (0 bytes/s); Redirect: 0s, DNS look up: 0.001705s, Connection: 0.00255s, Pretransfer: 0.376707s, First byte at: 1m 0.963968999999999s
[2026-02-26 22:47:39] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 503 Service Unavailable; Server: nginx; Date: Fri, 27 Feb 2026 03:47:39 GMT; Content-Type: text/plain; charset=utf-8; Content-Length: 82; Connection: keep-alive
[2026-02-26 22:47:39] [WARN] [OmnipathR] HTTP request failed with error: Failed to open 'https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic': The requested URL returned error: 503
[2026-02-26 22:47:39] [WARN] [OmnipathR] Failed to download `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic` (attempt 2/3); error: Failed to open 'https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic': The requested URL returned error: 503
[2026-02-26 22:47:44] [TRACE] [OmnipathR] Attempt 3/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-02-26 22:47:44] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2026-02-26 22:47:44] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-26 22:47:44] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-02-26 22:48:45] [TRACE] [OmnipathR] HTTP v1 GET: status 503.
[2026-02-26 22:48:45] [TRACE] [OmnipathR] Downloaded 0 bytes in 1m 0.845998000000002s from omnipathdb.org (0 bytes/s); Redirect: 0s, DNS look up: 0.001358s, Connection: 0.00215s, Pretransfer: 0.380078s, First byte at: 1m 0.845936999999999s
[2026-02-26 22:48:45] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 503 Service Unavailable; Server: nginx; Date: Fri, 27 Feb 2026 03:48:45 GMT; Content-Type: text/plain; charset=utf-8; Content-Length: 82; Connection: keep-alive
[2026-02-26 22:48:45] [WARN] [OmnipathR] HTTP request failed with error: Failed to open 'https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic': The requested URL returned error: 503
[2026-02-26 22:48:45] [ERROR] [OmnipathR] Failed to download `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic` (attempt 3/3); error: Failed to open 'https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic': The requested URL returned error: 503
[2026-02-26 22:48:45] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2026-02-26 22:48:45] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2026-02-26
[2026-02-26 22:48:45] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.2; ; 2026-02-26 20:08:22 UTC; unix
[2026-02-26 22:48:45] [INFO] [OmnipathR] Package `OmnipathR` version: 3.18.4
[2026-02-26 22:48:45] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2026-02-26 22:48:46] [INFO] [OmnipathR] Session info: [version=R version 4.5.2 (2025-10-31); os=Ubuntu 24.04.3 LTS; system=x86_64, linux-gnu; ui=X11; language=en; collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2026-02-26; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2026-02-26 22:48:46] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.22-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2026-02-26 22:48:46] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); BiocParallel 1.44.0(2026-02-26); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.3.0(2026-01-14); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); cli 3.6.5(2025-04-23); codetools 0.2-20(2024-03-31); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.3.0(2026-02-25); decoupleR 2.16.0(2026-02-26); digest 0.6.39(2025-11-19); dplyr 1.2.0(2026-02-03); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); httr 1.4.8(2026-02-13); httr2 1.2.2(2025-12-08); igraph 2.2.2(2026-02-12); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.7(2026-02-24); lattice 0.22-9(2026-02-09); lifecycle 1.0.5(2026-01-08); logger 0.4.1(2025-09-11); lubridate 1.9.5(2026-02-04); magrittr 2.0.4(2025-09-12); Matrix 1.7-4(2025-08-28); memoise 2.0.1(2021-11-26); OmnipathR 3.18.4(2026-02-26); otel 0.2.0(2025-08-29); parallelly 1.46.1(2026-01-08); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); purrr 1.2.1(2026-01-09); 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 0.3.4(2026-01-17); Rcpp 1.1.1(2026-01-10); readr 2.2.0(2026-02-19); readxl 1.4.5(2025-03-07); rlang 1.1.7(2026-01-09); rmarkdown 2.30(2025-09-28); RSQLite 2.4.6(2026-02-06); rvest 1.0.5(2025-08-29); selectr 0.5-1(2025-12-17); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tzdb 0.5.0(2025-03-15); utf8 1.2.6(2025-06-08); vctrs 0.7.1(2026-01-23); vroom 1.7.0(2026-01-27); withr 3.0.2(2024-10-28); xfun 0.56(2026-01-18); XML 3.99-0.22(2026-02-10); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13)
[2026-02-26 22:48:46] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: GnuTLS/3.8.3; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2026-02-26 22:48:46] [WARN] [OmnipathR] Failed to download: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`; error: Failed to open 'https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic': The requested URL returned error: 503
[2026-02-26 22:48:46] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2026-02-26 22:48:46] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2026-02-26
[2026-02-26 22:48:46] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.2; ; 2026-02-26 20:08:22 UTC; unix
[2026-02-26 22:48:46] [INFO] [OmnipathR] Package `OmnipathR` version: 3.18.4
[2026-02-26 22:48:46] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2026-02-26 22:48:47] [INFO] [OmnipathR] Session info: [version=R version 4.5.2 (2025-10-31); os=Ubuntu 24.04.3 LTS; system=x86_64, linux-gnu; ui=X11; language=en; collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2026-02-26; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2026-02-26 22:48:47] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.22-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2026-02-26 22:48:47] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); BiocParallel 1.44.0(2026-02-26); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.3.0(2026-01-14); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); cli 3.6.5(2025-04-23); codetools 0.2-20(2024-03-31); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.3.0(2026-02-25); decoupleR 2.16.0(2026-02-26); digest 0.6.39(2025-11-19); dplyr 1.2.0(2026-02-03); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); httr 1.4.8(2026-02-13); httr2 1.2.2(2025-12-08); igraph 2.2.2(2026-02-12); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.7(2026-02-24); lattice 0.22-9(2026-02-09); lifecycle 1.0.5(2026-01-08); logger 0.4.1(2025-09-11); lubridate 1.9.5(2026-02-04); magrittr 2.0.4(2025-09-12); Matrix 1.7-4(2025-08-28); memoise 2.0.1(2021-11-26); OmnipathR 3.18.4(2026-02-26); otel 0.2.0(2025-08-29); parallelly 1.46.1(2026-01-08); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); purrr 1.2.1(2026-01-09); 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 0.3.4(2026-01-17); Rcpp 1.1.1(2026-01-10); readr 2.2.0(2026-02-19); readxl 1.4.5(2025-03-07); rlang 1.1.7(2026-01-09); rmarkdown 2.30(2025-09-28); RSQLite 2.4.6(2026-02-06); rvest 1.0.5(2025-08-29); selectr 0.5-1(2025-12-17); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tzdb 0.5.0(2025-03-15); utf8 1.2.6(2025-06-08); vctrs 0.7.1(2026-01-23); vroom 1.7.0(2026-01-27); withr 3.0.2(2024-10-28); xfun 0.56(2026-01-18); XML 3.99-0.22(2026-02-10); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13)
[2026-02-26 22:48:47] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: GnuTLS/3.8.3; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2026-02-26 22:48:47] [TRACE] [OmnipathR] Attempting `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-02-26 22:48:47] [INFO] [OmnipathR] Retrieving URL: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-02-26 22:48:47] [TRACE] [OmnipathR] Attempt 1/3: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-02-26 22:48:47] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2026-02-26 22:48:47] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-26 22:48:47] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-02-26 22:48:47] [TRACE] [OmnipathR] HTTP v1 GET: status 500.
[2026-02-26 22:48:47] [TRACE] [OmnipathR] Downloaded 0 bytes in 0.33212s from no-tls.omnipathdb.org (0 bytes/s); Redirect: 0s, DNS look up: 0.017369s, Connection: 0.018362s, Pretransfer: 0.018407s, First byte at: 0.332096s
[2026-02-26 22:48:47] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 500 Internal Server Error; Server: nginx; Date: Fri, 27 Feb 2026 03:48:47 GMT; Content-Length: 170; Content-Type: text/html; charset=utf-8; Via: 1.1 phswsa25.partners.org:80 (Cisco-WSA/15.0.1-004); Connection: keep-alive
[2026-02-26 22:48:47] [WARN] [OmnipathR] HTTP request failed with error: Failed to open 'http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic': The requested URL returned error: 500
[2026-02-26 22:48:47] [WARN] [OmnipathR] Failed to download `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic` (attempt 1/3); error: Failed to open 'http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic': The requested URL returned error: 500
[2026-02-26 22:48:52] [TRACE] [OmnipathR] Attempt 2/3: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-02-26 22:48:52] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2026-02-26 22:48:52] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-26 22:48:52] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-02-26 22:48:52] [TRACE] [OmnipathR] HTTP v1 GET: status 500.
[2026-02-26 22:48:52] [TRACE] [OmnipathR] Downloaded 0 bytes in 0.298447s from no-tls.omnipathdb.org (0 bytes/s); Redirect: 0s, DNS look up: 0.00179s, Connection: 0.002687s, Pretransfer: 0.002728s, First byte at: 0.298414s
[2026-02-26 22:48:52] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 500 Internal Server Error; Server: nginx; Date: Fri, 27 Feb 2026 03:48:52 GMT; Content-Length: 170; Content-Type: text/html; charset=utf-8; Via: 1.1 phswsa25.partners.org:80 (Cisco-WSA/15.0.1-004); Connection: keep-alive
[2026-02-26 22:48:52] [WARN] [OmnipathR] HTTP request failed with error: Failed to open 'http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic': The requested URL returned error: 500
[2026-02-26 22:48:52] [WARN] [OmnipathR] Failed to download `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic` (attempt 2/3); error: Failed to open 'http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic': The requested URL returned error: 500
[2026-02-26 22:48:57] [TRACE] [OmnipathR] Attempt 3/3: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-02-26 22:48:57] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2026-02-26 22:48:57] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-26 22:48:57] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-02-26 22:48:58] [TRACE] [OmnipathR] HTTP v1 GET: status 500.
[2026-02-26 22:48:58] [TRACE] [OmnipathR] Downloaded 0 bytes in 0.296216s from no-tls.omnipathdb.org (0 bytes/s); Redirect: 0s, DNS look up: 0.001653s, Connection: 0.002461s, Pretransfer: 0.002508s, First byte at: 0.296151s
[2026-02-26 22:48:58] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 500 Internal Server Error; Server: nginx; Date: Fri, 27 Feb 2026 03:48:58 GMT; Content-Length: 170; Content-Type: text/html; charset=utf-8; Via: 1.1 phswsa25.partners.org:80 (Cisco-WSA/15.0.1-004); Connection: keep-alive
[2026-02-26 22:48:58] [WARN] [OmnipathR] HTTP request failed with error: Failed to open 'http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic': The requested URL returned error: 500
[2026-02-26 22:48:58] [ERROR] [OmnipathR] Failed to download `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic` (attempt 3/3); error: Failed to open 'http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic': The requested URL returned error: 500
[2026-02-26 22:48:58] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2026-02-26 22:48:58] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2026-02-26
[2026-02-26 22:48:58] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.2; ; 2026-02-26 20:08:22 UTC; unix
[2026-02-26 22:48:58] [INFO] [OmnipathR] Package `OmnipathR` version: 3.18.4
[2026-02-26 22:48:58] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2026-02-26 22:48:58] [INFO] [OmnipathR] Session info: [version=R version 4.5.2 (2025-10-31); os=Ubuntu 24.04.3 LTS; system=x86_64, linux-gnu; ui=X11; language=en; collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2026-02-26; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2026-02-26 22:48:58] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.22-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2026-02-26 22:48:59] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); BiocParallel 1.44.0(2026-02-26); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.3.0(2026-01-14); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); cli 3.6.5(2025-04-23); codetools 0.2-20(2024-03-31); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.3.0(2026-02-25); decoupleR 2.16.0(2026-02-26); digest 0.6.39(2025-11-19); dplyr 1.2.0(2026-02-03); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); httr 1.4.8(2026-02-13); httr2 1.2.2(2025-12-08); igraph 2.2.2(2026-02-12); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.7(2026-02-24); lattice 0.22-9(2026-02-09); lifecycle 1.0.5(2026-01-08); logger 0.4.1(2025-09-11); lubridate 1.9.5(2026-02-04); magrittr 2.0.4(2025-09-12); Matrix 1.7-4(2025-08-28); memoise 2.0.1(2021-11-26); OmnipathR 3.18.4(2026-02-26); otel 0.2.0(2025-08-29); parallelly 1.46.1(2026-01-08); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); purrr 1.2.1(2026-01-09); 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 0.3.4(2026-01-17); Rcpp 1.1.1(2026-01-10); readr 2.2.0(2026-02-19); readxl 1.4.5(2025-03-07); rlang 1.1.7(2026-01-09); rmarkdown 2.30(2025-09-28); RSQLite 2.4.6(2026-02-06); rvest 1.0.5(2025-08-29); selectr 0.5-1(2025-12-17); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tzdb 0.5.0(2025-03-15); utf8 1.2.6(2025-06-08); vctrs 0.7.1(2026-01-23); vroom 1.7.0(2026-01-27); withr 3.0.2(2024-10-28); xfun 0.56(2026-01-18); XML 3.99-0.22(2026-02-10); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13)
[2026-02-26 22:48:59] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: GnuTLS/3.8.3; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2026-02-26 22:48:59] [WARN] [OmnipathR] Failed to download: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`; error: Failed to open 'http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic': The requested URL returned error: 500
[2026-02-26 22:48:59] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2026-02-26 22:48:59] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2026-02-26
[2026-02-26 22:48:59] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.2; ; 2026-02-26 20:08:22 UTC; unix
[2026-02-26 22:48:59] [INFO] [OmnipathR] Package `OmnipathR` version: 3.18.4
[2026-02-26 22:48:59] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2026-02-26 22:48:59] [INFO] [OmnipathR] Session info: [version=R version 4.5.2 (2025-10-31); os=Ubuntu 24.04.3 LTS; system=x86_64, linux-gnu; ui=X11; language=en; collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2026-02-26; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2026-02-26 22:48:59] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.22-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2026-02-26 22:49:00] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); BiocParallel 1.44.0(2026-02-26); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.3.0(2026-01-14); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); cli 3.6.5(2025-04-23); codetools 0.2-20(2024-03-31); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.3.0(2026-02-25); decoupleR 2.16.0(2026-02-26); digest 0.6.39(2025-11-19); dplyr 1.2.0(2026-02-03); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); httr 1.4.8(2026-02-13); httr2 1.2.2(2025-12-08); igraph 2.2.2(2026-02-12); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.7(2026-02-24); lattice 0.22-9(2026-02-09); lifecycle 1.0.5(2026-01-08); logger 0.4.1(2025-09-11); lubridate 1.9.5(2026-02-04); magrittr 2.0.4(2025-09-12); Matrix 1.7-4(2025-08-28); memoise 2.0.1(2021-11-26); OmnipathR 3.18.4(2026-02-26); otel 0.2.0(2025-08-29); parallelly 1.46.1(2026-01-08); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); purrr 1.2.1(2026-01-09); 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 0.3.4(2026-01-17); Rcpp 1.1.1(2026-01-10); readr 2.2.0(2026-02-19); readxl 1.4.5(2025-03-07); rlang 1.1.7(2026-01-09); rmarkdown 2.30(2025-09-28); RSQLite 2.4.6(2026-02-06); rvest 1.0.5(2025-08-29); selectr 0.5-1(2025-12-17); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tzdb 0.5.0(2025-03-15); utf8 1.2.6(2025-06-08); vctrs 0.7.1(2026-01-23); vroom 1.7.0(2026-01-27); withr 3.0.2(2024-10-28); xfun 0.56(2026-01-18); XML 3.99-0.22(2026-02-10); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13)
[2026-02-26 22:49:00] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: GnuTLS/3.8.3; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2026-02-26 22:49:00] [SUCCESS] [OmnipathR] Downloaded 0 interactions.
Error in `dplyr::select()`:
! `select()` doesn't handle lists.
Backtrace:
▆
1. ├─decoupleR::get_dorothea(organism = "human", levels = c("A", "B"))
2. │ └─... %>% ...
3. ├─rlang::set_names(., c("source", "confidence", "target", "mor"))
4. ├─dplyr::select(...)
5. ├─dplyr::mutate(...)
6. ├─dplyr::mutate(...)
7. ├─dplyr::mutate(...)
8. ├─dplyr::distinct(...)
9. ├─dplyr::select(...)
10. └─dplyr:::select.list(...)
11. └─rlang::abort("`select()` doesn't handle lists.")
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
get_collectri 30.149 2.534 61.045
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
--- re-building ‘decoupleR.Rmd’ using rmarkdown
--- finished re-building ‘decoupleR.Rmd’
--- re-building ‘pw_bk.Rmd’ using rmarkdown
[2026-02-26 22:56:37] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-26 22:56:37] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 22:56:37] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2026-02-26 22:56:37] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2026-02-26 22:56:37] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2026-02-26
[2026-02-26 22:56:37] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.2; ; 2026-02-26 20:08:22 UTC; unix
[2026-02-26 22:56:37] [INFO] [OmnipathR] Package `OmnipathR` version: 3.18.4
[2026-02-26 22:56:37] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2026-02-26 22:56:38] [INFO] [OmnipathR] Session info: [version=R version 4.5.2 (2025-10-31); os=Ubuntu 24.04.3 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2026-02-26; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2026-02-26 22:56:38] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.22-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2026-02-26 22:56:38] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); BiocManager 1.30.27(2025-11-14); BiocParallel 1.44.0(2026-02-26); BiocStyle 2.38.0(2026-02-26); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.3.0(2026-01-14); bookdown 0.46(2025-12-05); bslib 0.10.0(2026-01-26); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); cli 3.6.5(2025-04-23); codetools 0.2-20(2024-03-31); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.3.0(2026-02-25); decoupleR 2.16.0(2026-02-26); digest 0.6.39(2025-11-19); dplyr 1.2.0(2026-02-03); evaluate 1.0.5(2025-08-27); farver 2.1.2(2024-05-13); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); ggplot2 4.0.2(2026-02-03); ggrepel 0.9.7(2026-02-25); glue 1.8.0(2024-09-30); gtable 0.3.6(2024-10-25); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); httr 1.4.8(2026-02-13); httr2 1.2.2(2025-12-08); igraph 2.2.2(2026-02-12); jquerylib 0.1.4(2021-04-26); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.7(2026-02-24); lattice 0.22-9(2026-02-09); lifecycle 1.0.5(2026-01-08); logger 0.4.1(2025-09-11); lubridate 1.9.5(2026-02-04); magrittr 2.0.4(2025-09-12); Matrix 1.7-4(2025-08-28); memoise 2.0.1(2021-11-26); OmnipathR 3.18.4(2026-02-26); otel 0.2.0(2025-08-29); parallelly 1.46.1(2026-01-08); pheatmap 1.0.13(2025-06-05); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); purrr 1.2.1(2026-01-09); 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 0.3.4(2026-01-17); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.1.1(2026-01-10); readr 2.2.0(2026-02-19); readxl 1.4.5(2025-03-07); rlang 1.1.7(2026-01-09); rmarkdown 2.30(2025-09-28); RSQLite 2.4.6(2026-02-06); rvest 1.0.5(2025-08-29); S7 0.2.1(2025-11-14); sass 0.4.10(2025-04-11); scales 1.4.0(2025-04-24); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tzdb 0.5.0(2025-03-15); utf8 1.2.6(2025-06-08); vctrs 0.7.1(2026-01-23); withr 3.0.2(2024-10-28); xfun 0.56(2026-01-18); XML 3.99-0.22(2026-02-10); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13)
[2026-02-26 22:56:38] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: GnuTLS/3.8.3; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2026-02-26 22:56:38] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2026-02-26 22:56:38] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2026-02-26 22:56:38] [TRACE] [OmnipathR] Contains 14 files.
[2026-02-26 22:56:38] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2026-02-26 22:56:38] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-26 22:56:38] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 22:56:38] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2026-02-26 22:56:38] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2026-02-26 22:56:38] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2026-02-26 22:56:38] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 22:56:38] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2026-02-26 22:56:38] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 22:56:38] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2026-02-26 22:56:38] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 22:56:38] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2026-02-26 22:56:38] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 22:56:38] [TRACE] [OmnipathR] Cache locked: FALSE
[2026-02-26 22:56:38] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-02-26 22:56:39] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 22:56:39] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2026-02-26 22:56:39] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-26 22:56:39] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 22:56:39] [INFO] [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available.
[2026-02-26 22:56:39] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-26 22:56:39] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 22:56:39] [INFO] [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 1.
[2026-02-26 22:56:39] [TRACE] [OmnipathR] Cache file path: /home/biocbuild/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-1.html
[2026-02-26 22:56:39] [INFO] [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html`
[2026-02-26 22:56:39] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`.
[2026-02-26 22:56:39] [TRACE] [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2026-02-26 22:56:39] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2026-02-26 22:56:39] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2026-02-26 22:56:39] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-26 22:56:39] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-02-26 22:56:39] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2026-02-26 22:56:39] [TRACE] [OmnipathR] Sending HTTP request.
[2026-02-26 22:56:40] [TRACE] [OmnipathR] HTTP 200 (OK)
[2026-02-26 22:56:40] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2026-02-26 22:56:40] [TRACE] [OmnipathR] Downloaded 39.9 Kb in 0.819371s from rescued.omnipathdb.org (48.6 Kb/s); Redirect: 0s, DNS look up: 0.167201s, Connection: 0.167977s, Pretransfer: 0.537964s, First byte at: 0.680005s
[2026-02-26 22:56:40] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Fri, 27 Feb 2026 03:56:40 GMT; Content-Type: text/html; charset=utf-8; Last-Modified: Fri, 24 Oct 2025 17:07:34 GMT; Transfer-Encoding: chunked; Connection: keep-alive; ETag: W/"68fbb256-3f5d0"; Expires: Fri, 27 Feb 2026 04:56:40 GMT; Cache-Control: max-age=3600; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2026-02-26 22:56:40] [TRACE] [OmnipathR] Response headers: [Server=nginx,Date=Fri, 27 Feb 2026 03:56:40 GMT,Content-Type=text/html; charset=utf-8,Last-Modified=Fri, 24 Oct 2025 17:07:34 GMT,Transfer-Encoding=chunked,Connection=keep-alive,ETag=W/"68fbb256-3f5d0",Expires=Fri, 27 Feb 2026 04:56:40 GMT,Cache-Control=max-age=3600,Cache-Control=public,X-Frame-Options=DENY,Content-Encoding=gzip]
[2026-02-26 22:56:40] [INFO] [OmnipathR] Download ready [key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, version=1]
[2026-02-26 22:56:40] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-26 22:56:40] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 22:56:40] [INFO] [OmnipathR] Cache item `67b4943ae7fd646a03b760aefa99fe6c41ab2887` version 1: status changed from `unknown` to `ready`.
[2026-02-26 22:56:40] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2026-02-26 22:56:40] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2026-02-26 22:56:40] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2026-02-26 22:56:41] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2026-02-26 22:56:41] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-26 22:56:41] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 22:56:41] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-26 22:56:41] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 22:56:41] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2026-02-26 22:56:41] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2026-02-26 22:56:41] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2026-02-26 22:56:41] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2026-02-26 22:56:41] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2026-02-26 22:56:41] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-26 22:56:41] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-02-26 22:56:41] [TRACE] [OmnipathR] HTTP v2 GET: status 200.
[2026-02-26 22:56:41] [TRACE] [OmnipathR] Downloaded 7.6 Kb in 0.406118s from omabrowser.org (18.6 Kb/s); Redirect: 0s, DNS look up: 0.004359s, Connection: 0.017287s, Pretransfer: 0.080359s, First byte at: 0.40592s
[2026-02-26 22:56:41] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; date: Fri, 27 Feb 2026 03:56:41 GMT; content-type: text/plain; charset=UTF-8; server: cloudflare; strict-transport-security: max-age=31536000; includeSubDomains; last-modified: Wed, 20 Nov 2024 10:20:02 GMT; etag: W/"673db7d2-6517f"; access-control-allow-origin: *; content-encoding: gzip; cf-cache-status: DYNAMIC; vary: accept-encoding; nel: {"report_to":"cf-nel","success_fraction":0.0,"max_age":604800}; report-to: {"group":"cf-nel","max_age":604800,"endpoints":[{"url":"https://a.nel.cloudflare.com/report/v4?s=uvWSXr3bcjyt4dJbHX1aY2iWI6pImPsLA2d%2BsnDfCV%2FlmL2XRbsdc8HliNZHFZscW8vfwc2WDIfBlJqb2aTCzKkLYcCRbTFs0T1sghg1"}]}; cf-ray: 9d44c0f53983a9d6-IAD; alt-svc: h3=":443"; ma=86400
[2026-02-26 22:56:42] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2026-02-26 22:56:42] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1]
[2026-02-26 22:56:42] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-26 22:56:42] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 22:56:42] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.
[2026-02-26 22:56:42] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2026-02-26 22:56:42] [TRACE] [OmnipathR] Looking up in cache: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`.
[2026-02-26 22:56:42] [INFO] [OmnipathR] Cache record does not exist: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2026-02-26 22:56:42] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`.
[2026-02-26 22:56:42] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-26 22:56:42] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 22:56:42] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-26 22:56:42] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 22:56:42] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `unknown` to `started`.
[2026-02-26 22:56:42] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`.
[2026-02-26 22:56:42] [INFO] [OmnipathR] Retrieving URL: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2026-02-26 22:56:42] [TRACE] [OmnipathR] Attempt 1/3: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2026-02-26 22:57:15] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`.
[2026-02-26 22:57:15] [INFO] [OmnipathR] Download ready [key=56ad6544dc07a2222fa6013d8d83e6e5a35fdf33, version=1]
[2026-02-26 22:57:15] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-26 22:57:15] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 22:57:15] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `started` to `ready`.
[2026-02-26 22:57:15] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`.
[2026-02-26 22:57:15] [TRACE] [OmnipathR] Processing args for OmniPath query
[2026-02-26 22:57:15] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=PROGENy,query_type=annotations]
[2026-02-26 22:57:15] [TRACE] [OmnipathR] Organism(s): 9606
[2026-02-26 22:57:15] [TRACE] [OmnipathR] Orthology targets:
[2026-02-26 22:57:15] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-02-26 22:57:16] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 22:57:16] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2026-02-26 22:57:16] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2026-02-26 22:57:16] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2026-02-26 22:57:16] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2026-02-26 22:57:16] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2026-02-26 22:57:16] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2026-02-26 22:57:16] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2026-02-26 22:57:16] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2026-02-26 22:57:16] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-26 22:57:16] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-02-26 22:58:02] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2026-02-26 22:58:02] [TRACE] [OmnipathR] Downloaded 15.6 Kb in 45.877503s from omnipathdb.org (349 bytes/s); Redirect: 0s, DNS look up: 0.001496s, Connection: 0.002402s, Pretransfer: 0.210928s, First byte at: 45.876984s
[2026-02-26 22:58:02] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Fri, 27 Feb 2026 03:58:02 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Fri, 27 Feb 2026 04:58:02 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; Cache-Control: no-cache, no-store, must-revalidate; Pragma: no-cache; Expires: 0; Content-Encoding: gzip
[2026-02-26 22:59:35] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2026-02-26 22:59:35] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-26 22:59:35] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 22:59:35] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-26 22:59:35] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 22:59:35] [INFO] [OmnipathR] Cache item `3492392585ba05414edfae46801492076437d7e7` version 1: status changed from `unknown` to `started`.
[2026-02-26 22:59:35] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`.
[2026-02-26 22:59:37] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`.
[2026-02-26 22:59:37] [INFO] [OmnipathR] Download ready [key=3492392585ba05414edfae46801492076437d7e7, version=1]
[2026-02-26 22:59:37] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-26 22:59:37] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 22:59:37] [INFO] [OmnipathR] Cache item `3492392585ba05414edfae46801492076437d7e7` version 1: status changed from `started` to `ready`.
[2026-02-26 22:59:37] [SUCCESS] [OmnipathR] Downloaded 699831 annotation records.
Quitting from pw_bk.Rmd:140-145 [sample_mlm]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `mor_mat[[.target, .source]] <- .weight`:
! [[ ]] subscript out of bounds
---
Backtrace:
▆
1. ├─decoupleR::run_mlm(...)
2. │ ├─... %>% ungroup()
3. │ └─decoupleR::.fit_preprocessing(network, mat, center, na.rm, sparse)
4. └─dplyr::ungroup(.)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'pw_bk.Rmd' failed with diagnostics:
[[ ]] subscript out of bounds
--- failed re-building ‘pw_bk.Rmd’
--- re-building ‘pw_sc.Rmd’ using rmarkdown
[2026-02-26 22:59:46] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-26 22:59:46] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 22:59:46] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2026-02-26 22:59:46] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2026-02-26 22:59:46] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2026-02-26
[2026-02-26 22:59:46] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.2; ; 2026-02-26 20:08:22 UTC; unix
[2026-02-26 22:59:46] [INFO] [OmnipathR] Package `OmnipathR` version: 3.18.4
[2026-02-26 22:59:46] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2026-02-26 22:59:47] [INFO] [OmnipathR] Session info: [version=R version 4.5.2 (2025-10-31); os=Ubuntu 24.04.3 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2026-02-26; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2026-02-26 22:59:47] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.22-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2026-02-26 22:59:47] [INFO] [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); backports 1.5.0(2024-05-23); BiocManager 1.30.27(2025-11-14); BiocParallel 1.44.0(2026-02-26); BiocStyle 2.38.0(2026-02-26); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.3.0(2026-01-14); bookdown 0.46(2025-12-05); bslib 0.10.0(2026-01-26); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); cli 3.6.5(2025-04-23); cluster 2.1.8.2(2026-02-05); codetools 0.2-20(2024-03-31); cowplot 1.2.0(2025-07-07); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); data.table 1.18.2.1(2026-01-27); DBI 1.3.0(2026-02-25); decoupleR 2.16.0(2026-02-26); deldir 2.0-4(2024-02-28); digest 0.6.39(2025-11-19); dotCall64 1.2(2024-10-04); dplyr 1.2.0(2026-02-03); evaluate 1.0.5(2025-08-27); farver 2.1.2(2024-05-13); fastDummies 1.7.5(2025-01-20); fastmap 1.2.0(2024-05-15); fitdistrplus 1.2-6(2026-01-24); fs 1.6.6(2025-04-12); future 1.69.0(2026-01-16); future.apply 1.20.2(2026-02-20); generics 0.1.4(2025-05-09); ggplot2 4.0.2(2026-02-03); ggrepel 0.9.7(2026-02-25); ggridges 0.5.7(2025-08-27); globals 0.19.0(2026-02-02); glue 1.8.0(2024-09-30); goftest 1.2-3(2021-10-07); gridExtra 2.3(2017-09-09); gtable 0.3.6(2024-10-25); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); htmlwidgets 1.6.4(2023-12-06); httpuv 1.6.16(2025-04-16); httr 1.4.8(2026-02-13); httr2 1.2.2(2025-12-08); ica 1.0-3(2022-07-08); igraph 2.2.2(2026-02-12); irlba 2.3.7(2026-01-30); jquerylib 0.1.4(2021-04-26); jsonlite 2.0.0(2025-03-27); KernSmooth 2.23-26(2025-01-01); knitr 1.51(2025-12-20); labeling 0.4.3(2023-08-29); later 1.4.7(2026-02-24); lattice 0.22-9(2026-02-09); lazyeval 0.2.2(2019-03-15); lifecycle 1.0.5(2026-01-08); listenv 0.10.0(2025-11-02); lmtest 0.9-40(2022-03-21); logger 0.4.1(2025-09-11); lubridate 1.9.5(2026-02-04); magick 2.9.0(2025-09-08); magrittr 2.0.4(2025-09-12); MASS 7.3-65(2025-02-28); Matrix 1.7-4(2025-08-28); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); mime 0.13(2025-03-17); miniUI 0.1.2(2025-04-17); nlme 3.1-168(2025-03-31); OmnipathR 3.18.4(2026-02-26); otel 0.2.0(2025-08-29); parallelly 1.46.1(2026-01-08); patchwork 1.3.2(2025-08-25); pbapply 1.7-4(2025-07-20); pheatmap 1.0.13(2025-06-05); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); plotly 4.12.0(2026-01-24); plyr 1.8.9(2023-10-02); png 0.1-8(2022-11-29); polyclip 1.10-7(2024-07-23); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); progressr 0.18.0(2025-11-06); promises 1.5.0(2025-11-01); purrr 1.2.1(2026-01-09); 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); RANN 2.6.2(2024-08-25); rappdirs 0.3.4(2026-01-17); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.1.1(2026-01-10); RcppAnnoy 0.0.23(2026-01-12); RcppHNSW 0.6.0(2024-02-04); readr 2.2.0(2026-02-19); readxl 1.4.5(2025-03-07); reshape2 1.4.5(2025-11-12); reticulate 1.45.0(2026-02-13); rlang 1.1.7(2026-01-09); rmarkdown 2.30(2025-09-28); ROCR 1.0-12(2026-01-23); RSpectra 0.16-2(2024-07-18); RSQLite 2.4.6(2026-02-06); Rtsne 0.17(2023-12-07); rvest 1.0.5(2025-08-29); S7 0.2.1(2025-11-14); sass 0.4.10(2025-04-11); scales 1.4.0(2025-04-24); scattermore 1.2(2023-06-12); sctransform 0.4.3(2026-01-10); sessioninfo 1.2.3(2025-02-05); Seurat 5.4.0(2025-12-14); SeuratObject 5.3.0(2025-12-12); shiny 1.13.0(2026-02-20); sp 2.2-1(2026-02-13); spam 2.11-3(2026-01-08); spatstat.data 3.1-9(2025-10-18); spatstat.explore 3.7-0(2026-01-22); spatstat.geom 3.7-0(2026-01-20); spatstat.random 3.4-4(2026-01-21); spatstat.sparse 3.1-0(2024-06-21); spatstat.univar 3.1-6(2026-01-17); spatstat.utils 3.2-1(2026-01-10); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); survival 3.8-6(2026-01-16); tensor 1.5.1(2025-06-17); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tinytex 0.58(2025-11-19); tzdb 0.5.0(2025-03-15); uwot 0.2.4(2025-11-10); vctrs 0.7.1(2026-01-23); viridisLite 0.4.3(2026-02-04); withr 3.0.2(2024-10-28); xfun 0.56(2026-01-18); XML 3.99-0.22(2026-02-10); xml2 1.5.2(2026-01-17); xtable 1.8-8(2026-02-22); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13); zoo 1.8-15(2025-12-15)
[2026-02-26 22:59:47] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: GnuTLS/3.8.3; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2026-02-26 22:59:47] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2026-02-26 22:59:47] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2026-02-26 22:59:47] [TRACE] [OmnipathR] Contains 5 files.
[2026-02-26 22:59:47] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2026-02-26 22:59:47] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-26 22:59:47] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 22:59:47] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2026-02-26 22:59:47] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2026-02-26 22:59:47] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2026-02-26 22:59:47] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 22:59:47] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2026-02-26 22:59:47] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 22:59:47] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2026-02-26 22:59:47] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 22:59:47] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2026-02-26 22:59:47] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 22:59:47] [TRACE] [OmnipathR] Cache locked: FALSE
[2026-02-26 22:59:47] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-02-26 22:59:48] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 22:59:49] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2026-02-26 22:59:49] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-26 22:59:49] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 22:59:49] [INFO] [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available.
[2026-02-26 22:59:49] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-26 22:59:49] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 22:59:49] [INFO] [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 1.
[2026-02-26 22:59:49] [TRACE] [OmnipathR] Cache file path: /home/biocbuild/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-1.html
[2026-02-26 22:59:49] [INFO] [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html`
[2026-02-26 22:59:49] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`.
[2026-02-26 22:59:49] [TRACE] [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2026-02-26 22:59:49] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2026-02-26 22:59:49] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2026-02-26 22:59:49] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-26 22:59:49] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-02-26 22:59:49] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2026-02-26 22:59:49] [TRACE] [OmnipathR] Sending HTTP request.
[2026-02-26 22:59:50] [TRACE] [OmnipathR] HTTP 200 (OK)
[2026-02-26 22:59:50] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2026-02-26 22:59:50] [TRACE] [OmnipathR] Downloaded 39.9 Kb in 0.630345s from rescued.omnipathdb.org (63.2 Kb/s); Redirect: 0s, DNS look up: 0.00185s, Connection: 0.002607s, Pretransfer: 0.346795s, First byte at: 0.492029s
[2026-02-26 22:59:50] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Fri, 27 Feb 2026 03:59:49 GMT; Content-Type: text/html; charset=utf-8; Last-Modified: Fri, 24 Oct 2025 17:07:34 GMT; Transfer-Encoding: chunked; Connection: keep-alive; ETag: W/"68fbb256-3f5d0"; Expires: Fri, 27 Feb 2026 04:59:49 GMT; Cache-Control: max-age=3600; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2026-02-26 22:59:50] [TRACE] [OmnipathR] Response headers: [Server=nginx,Date=Fri, 27 Feb 2026 03:59:49 GMT,Content-Type=text/html; charset=utf-8,Last-Modified=Fri, 24 Oct 2025 17:07:34 GMT,Transfer-Encoding=chunked,Connection=keep-alive,ETag=W/"68fbb256-3f5d0",Expires=Fri, 27 Feb 2026 04:59:49 GMT,Cache-Control=max-age=3600,Cache-Control=public,X-Frame-Options=DENY,Content-Encoding=gzip]
[2026-02-26 22:59:50] [INFO] [OmnipathR] Download ready [key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, version=1]
[2026-02-26 22:59:50] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-26 22:59:50] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 22:59:50] [INFO] [OmnipathR] Cache item `67b4943ae7fd646a03b760aefa99fe6c41ab2887` version 1: status changed from `unknown` to `ready`.
[2026-02-26 22:59:50] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2026-02-26 22:59:50] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2026-02-26 22:59:50] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2026-02-26 22:59:50] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2026-02-26 22:59:50] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-26 22:59:50] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 22:59:51] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-26 22:59:51] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 22:59:51] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2026-02-26 22:59:51] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2026-02-26 22:59:51] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2026-02-26 22:59:51] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2026-02-26 22:59:51] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2026-02-26 22:59:51] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-26 22:59:51] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-02-26 22:59:51] [TRACE] [OmnipathR] HTTP v2 GET: status 200.
[2026-02-26 22:59:51] [TRACE] [OmnipathR] Downloaded 7.6 Kb in 0.424631s from omabrowser.org (17.8 Kb/s); Redirect: 0s, DNS look up: 0.003128s, Connection: 0.016s, Pretransfer: 0.078863s, First byte at: 0.424432s
[2026-02-26 22:59:51] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; date: Fri, 27 Feb 2026 03:59:51 GMT; content-type: text/plain; charset=UTF-8; server: cloudflare; strict-transport-security: max-age=31536000; includeSubDomains; last-modified: Wed, 20 Nov 2024 10:20:02 GMT; etag: W/"673db7d2-6517f"; access-control-allow-origin: *; content-encoding: gzip; cf-cache-status: DYNAMIC; vary: accept-encoding; nel: {"report_to":"cf-nel","success_fraction":0.0,"max_age":604800}; report-to: {"group":"cf-nel","max_age":604800,"endpoints":[{"url":"https://a.nel.cloudflare.com/report/v4?s=YJj6GEciJ9517irCOH9xJF%2BbvTTbaSjoCP%2FdEJuvp7NELyx6mJkvzeeaCGVdSB71NGyKmC%2F52lNDOioj4EUzAwuP3PC6i7jcWvnd6A%3D%3D"}]}; cf-ray: 9d44c598ac4c1779-IAD; alt-svc: h3=":443"; ma=86400
[2026-02-26 22:59:52] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2026-02-26 22:59:52] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1]
[2026-02-26 22:59:52] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-26 22:59:52] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 22:59:52] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.
[2026-02-26 22:59:52] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2026-02-26 22:59:53] [TRACE] [OmnipathR] Looking up in cache: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`.
[2026-02-26 22:59:53] [INFO] [OmnipathR] Cache record does not exist: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2026-02-26 22:59:53] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`.
[2026-02-26 22:59:53] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-26 22:59:53] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 22:59:53] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-26 22:59:53] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 22:59:53] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `unknown` to `started`.
[2026-02-26 22:59:53] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`.
[2026-02-26 22:59:53] [INFO] [OmnipathR] Retrieving URL: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2026-02-26 22:59:53] [TRACE] [OmnipathR] Attempt 1/3: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2026-02-26 23:00:27] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`.
[2026-02-26 23:00:27] [INFO] [OmnipathR] Download ready [key=56ad6544dc07a2222fa6013d8d83e6e5a35fdf33, version=1]
[2026-02-26 23:00:27] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-26 23:00:27] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 23:00:27] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `started` to `ready`.
[2026-02-26 23:00:27] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`.
[2026-02-26 23:00:27] [TRACE] [OmnipathR] Processing args for OmniPath query
[2026-02-26 23:00:27] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=PROGENy,query_type=annotations]
[2026-02-26 23:00:27] [TRACE] [OmnipathR] Organism(s): 9606
[2026-02-26 23:00:27] [TRACE] [OmnipathR] Orthology targets:
[2026-02-26 23:00:27] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-02-26 23:00:31] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 23:00:31] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2026-02-26 23:00:31] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2026-02-26 23:00:31] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2026-02-26 23:00:31] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2026-02-26 23:00:31] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2026-02-26 23:00:31] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2026-02-26 23:00:31] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2026-02-26 23:00:31] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2026-02-26 23:00:31] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-26 23:00:31] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-02-26 23:01:32] [TRACE] [OmnipathR] HTTP v1 GET: status 503.
[2026-02-26 23:01:32] [TRACE] [OmnipathR] Downloaded 0 bytes in 1m 0.534455000000001s from omnipathdb.org (0 bytes/s); Redirect: 0s, DNS look up: 0.001668s, Connection: 0.002575s, Pretransfer: 0.344825s, First byte at: 1m 0.534422999999997s
[2026-02-26 23:01:32] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 503 Service Unavailable; Server: nginx; Date: Fri, 27 Feb 2026 04:01:32 GMT; Content-Type: text/plain; charset=utf-8; Content-Length: 82; Connection: keep-alive
[2026-02-26 23:01:32] [WARN] [OmnipathR] HTTP request failed with error: Failed to open 'https://omnipathdb.org/annotations?resources=PROGENy&license=academic': The requested URL returned error: 503
[2026-02-26 23:01:32] [WARN] [OmnipathR] Failed to download `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` (attempt 1/3); error: Failed to open 'https://omnipathdb.org/annotations?resources=PROGENy&license=academic': The requested URL returned error: 503
[2026-02-26 23:01:37] [TRACE] [OmnipathR] Attempt 2/3: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2026-02-26 23:01:37] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2026-02-26 23:01:37] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-26 23:01:37] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-02-26 23:02:13] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2026-02-26 23:02:13] [TRACE] [OmnipathR] Downloaded 15.6 Kb in 36.319247s from omnipathdb.org (440 bytes/s); Redirect: 0s, DNS look up: 0.001831s, Connection: 0.002799s, Pretransfer: 0.229288s, First byte at: 36.318413s
[2026-02-26 23:02:13] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Fri, 27 Feb 2026 04:02:13 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Fri, 27 Feb 2026 05:02:13 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; Cache-Control: no-cache, no-store, must-revalidate; Pragma: no-cache; Expires: 0; Content-Encoding: gzip
[2026-02-26 23:02:51] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2026-02-26 23:02:51] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-26 23:02:51] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 23:02:51] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-26 23:02:51] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 23:02:51] [INFO] [OmnipathR] Cache item `3492392585ba05414edfae46801492076437d7e7` version 1: status changed from `unknown` to `started`.
[2026-02-26 23:02:51] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`.
[2026-02-26 23:02:53] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`.
[2026-02-26 23:02:53] [INFO] [OmnipathR] Download ready [key=3492392585ba05414edfae46801492076437d7e7, version=1]
[2026-02-26 23:02:53] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-26 23:02:53] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 23:02:53] [INFO] [OmnipathR] Cache item `3492392585ba05414edfae46801492076437d7e7` version 1: status changed from `started` to `ready`.
[2026-02-26 23:02:53] [SUCCESS] [OmnipathR] Downloaded 699831 annotation records.
Quitting from pw_sc.Rmd:108-116 [mlm]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `mor_mat[[.target, .source]] <- .weight`:
! [[ ]] subscript out of bounds
---
Backtrace:
▆
1. ├─decoupleR::run_mlm(...)
2. │ ├─... %>% ungroup()
3. │ └─decoupleR::.fit_preprocessing(network, mat, center, na.rm, sparse)
4. └─dplyr::ungroup(.)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'pw_sc.Rmd' failed with diagnostics:
[[ ]] subscript out of bounds
--- failed re-building ‘pw_sc.Rmd’
--- re-building ‘tf_bk.Rmd’ using rmarkdown
[2026-02-26 23:02:58] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-26 23:02:58] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 23:02:58] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2026-02-26 23:02:58] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2026-02-26 23:02:58] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2026-02-26
[2026-02-26 23:02:58] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.2; ; 2026-02-26 20:08:22 UTC; unix
[2026-02-26 23:02:58] [INFO] [OmnipathR] Package `OmnipathR` version: 3.18.4
[2026-02-26 23:02:58] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2026-02-26 23:02:59] [INFO] [OmnipathR] Session info: [version=R version 4.5.2 (2025-10-31); os=Ubuntu 24.04.3 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2026-02-26; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2026-02-26 23:02:59] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.22-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2026-02-26 23:02:59] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); BiocManager 1.30.27(2025-11-14); BiocParallel 1.44.0(2026-02-26); BiocStyle 2.38.0(2026-02-26); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.3.0(2026-01-14); bookdown 0.46(2025-12-05); bslib 0.10.0(2026-01-26); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); cli 3.6.5(2025-04-23); codetools 0.2-20(2024-03-31); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.3.0(2026-02-25); decoupleR 2.16.0(2026-02-26); digest 0.6.39(2025-11-19); dplyr 1.2.0(2026-02-03); evaluate 1.0.5(2025-08-27); farver 2.1.2(2024-05-13); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); ggplot2 4.0.2(2026-02-03); ggrepel 0.9.7(2026-02-25); glue 1.8.0(2024-09-30); gtable 0.3.6(2024-10-25); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); httr 1.4.8(2026-02-13); httr2 1.2.2(2025-12-08); igraph 2.2.2(2026-02-12); jquerylib 0.1.4(2021-04-26); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.7(2026-02-24); lattice 0.22-9(2026-02-09); lifecycle 1.0.5(2026-01-08); logger 0.4.1(2025-09-11); lubridate 1.9.5(2026-02-04); magrittr 2.0.4(2025-09-12); Matrix 1.7-4(2025-08-28); memoise 2.0.1(2021-11-26); OmnipathR 3.18.4(2026-02-26); otel 0.2.0(2025-08-29); parallelly 1.46.1(2026-01-08); pheatmap 1.0.13(2025-06-05); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); purrr 1.2.1(2026-01-09); 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 0.3.4(2026-01-17); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.1.1(2026-01-10); readr 2.2.0(2026-02-19); readxl 1.4.5(2025-03-07); rlang 1.1.7(2026-01-09); rmarkdown 2.30(2025-09-28); RSQLite 2.4.6(2026-02-06); rvest 1.0.5(2025-08-29); S7 0.2.1(2025-11-14); sass 0.4.10(2025-04-11); scales 1.4.0(2025-04-24); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tzdb 0.5.0(2025-03-15); utf8 1.2.6(2025-06-08); vctrs 0.7.1(2026-01-23); withr 3.0.2(2024-10-28); xfun 0.56(2026-01-18); XML 3.99-0.22(2026-02-10); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13)
[2026-02-26 23:02:59] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: GnuTLS/3.8.3; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2026-02-26 23:02:59] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2026-02-26 23:02:59] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2026-02-26 23:02:59] [TRACE] [OmnipathR] Contains 5 files.
[2026-02-26 23:02:59] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2026-02-26 23:02:59] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-26 23:02:59] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 23:02:59] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2026-02-26 23:02:59] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2026-02-26 23:02:59] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2026-02-26 23:02:59] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 23:02:59] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2026-02-26 23:02:59] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 23:02:59] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2026-02-26 23:02:59] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 23:02:59] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2026-02-26 23:02:59] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 23:02:59] [TRACE] [OmnipathR] Cache locked: FALSE
[2026-02-26 23:02:59] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2026-02-26 23:02:59] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-26 23:02:59] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 23:02:59] [INFO] [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available.
[2026-02-26 23:02:59] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-26 23:02:59] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 23:02:59] [INFO] [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 1.
[2026-02-26 23:02:59] [TRACE] [OmnipathR] Cache file path: /home/biocbuild/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-1.html
[2026-02-26 23:02:59] [INFO] [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html`
[2026-02-26 23:02:59] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`.
[2026-02-26 23:02:59] [TRACE] [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2026-02-26 23:02:59] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2026-02-26 23:02:59] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2026-02-26 23:02:59] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-26 23:02:59] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-02-26 23:02:59] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2026-02-26 23:02:59] [TRACE] [OmnipathR] Sending HTTP request.
[2026-02-26 23:03:00] [TRACE] [OmnipathR] HTTP 200 (OK)
[2026-02-26 23:03:00] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2026-02-26 23:03:00] [TRACE] [OmnipathR] Downloaded 39.9 Kb in 0.645934s from rescued.omnipathdb.org (61.7 Kb/s); Redirect: 0s, DNS look up: 0.002255s, Connection: 0.003088s, Pretransfer: 0.347352s, First byte at: 0.498094s
[2026-02-26 23:03:00] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Fri, 27 Feb 2026 04:02:59 GMT; Content-Type: text/html; charset=utf-8; Last-Modified: Fri, 24 Oct 2025 17:07:34 GMT; Transfer-Encoding: chunked; Connection: keep-alive; ETag: W/"68fbb256-3f5d0"; Expires: Fri, 27 Feb 2026 05:02:59 GMT; Cache-Control: max-age=3600; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2026-02-26 23:03:00] [TRACE] [OmnipathR] Response headers: [Server=nginx,Date=Fri, 27 Feb 2026 04:02:59 GMT,Content-Type=text/html; charset=utf-8,Last-Modified=Fri, 24 Oct 2025 17:07:34 GMT,Transfer-Encoding=chunked,Connection=keep-alive,ETag=W/"68fbb256-3f5d0",Expires=Fri, 27 Feb 2026 05:02:59 GMT,Cache-Control=max-age=3600,Cache-Control=public,X-Frame-Options=DENY,Content-Encoding=gzip]
[2026-02-26 23:03:00] [INFO] [OmnipathR] Download ready [key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, version=1]
[2026-02-26 23:03:00] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-26 23:03:00] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 23:03:00] [INFO] [OmnipathR] Cache item `67b4943ae7fd646a03b760aefa99fe6c41ab2887` version 1: status changed from `unknown` to `ready`.
[2026-02-26 23:03:01] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2026-02-26 23:03:01] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2026-02-26 23:03:01] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2026-02-26 23:03:01] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2026-02-26 23:03:01] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-26 23:03:01] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 23:03:01] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-26 23:03:01] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 23:03:01] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2026-02-26 23:03:01] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2026-02-26 23:03:01] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2026-02-26 23:03:01] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2026-02-26 23:03:01] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2026-02-26 23:03:01] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-26 23:03:01] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-02-26 23:03:01] [TRACE] [OmnipathR] HTTP v2 GET: status 200.
[2026-02-26 23:03:01] [TRACE] [OmnipathR] Downloaded 6.7 Kb in 0.439878s from omabrowser.org (15.2 Kb/s); Redirect: 0s, DNS look up: 0.004723s, Connection: 0.017803s, Pretransfer: 0.090747s, First byte at: 0.439643s
[2026-02-26 23:03:01] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; date: Fri, 27 Feb 2026 04:03:01 GMT; content-type: text/plain; charset=UTF-8; server: cloudflare; strict-transport-security: max-age=31536000; includeSubDomains; last-modified: Wed, 20 Nov 2024 10:20:02 GMT; etag: W/"673db7d2-6517f"; access-control-allow-origin: *; content-encoding: gzip; cf-cache-status: DYNAMIC; vary: accept-encoding; nel: {"report_to":"cf-nel","success_fraction":0.0,"max_age":604800}; report-to: {"group":"cf-nel","max_age":604800,"endpoints":[{"url":"https://a.nel.cloudflare.com/report/v4?s=VrPa8DAu5%2F9YHrniPeAuRm3LbJWhZAq6oeiNpqmugYTVXNjHoF%2BOLYvTysO1kdLEMumILJlcExBpTXdeqCx4mNbQEJNFjp8kRj6yi9M9"}]}; cf-ray: 9d44ca3d6e9415cd-IAD; alt-svc: h3=":443"; ma=86400
[2026-02-26 23:03:02] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2026-02-26 23:03:02] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1]
[2026-02-26 23:03:02] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-26 23:03:02] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 23:03:02] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.
[2026-02-26 23:03:02] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2026-02-26 23:03:02] [TRACE] [OmnipathR] Looking up in cache: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`.
[2026-02-26 23:03:02] [INFO] [OmnipathR] Cache record does not exist: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2026-02-26 23:03:02] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`.
[2026-02-26 23:03:02] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-26 23:03:02] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 23:03:02] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-26 23:03:02] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 23:03:02] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `unknown` to `started`.
[2026-02-26 23:03:02] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`.
[2026-02-26 23:03:02] [INFO] [OmnipathR] Retrieving URL: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2026-02-26 23:03:02] [TRACE] [OmnipathR] Attempt 1/3: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2026-02-26 23:03:34] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`.
[2026-02-26 23:03:34] [INFO] [OmnipathR] Download ready [key=56ad6544dc07a2222fa6013d8d83e6e5a35fdf33, version=1]
[2026-02-26 23:03:34] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-26 23:03:34] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 23:03:34] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `started` to `ready`.
[2026-02-26 23:03:34] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`.
[2026-02-26 23:03:35] [TRACE] [OmnipathR] Processing args for OmniPath query
[2026-02-26 23:03:35] [TRACE] [OmnipathR] Arguments for OmniPath query: [loops=TRUE,organisms=9606,genesymbols=TRUE,query_type=interactions,datasets=collectri]
[2026-02-26 23:03:35] [TRACE] [OmnipathR] Organism(s): 9606
[2026-02-26 23:03:35] [TRACE] [OmnipathR] Orthology targets:
[2026-02-26 23:03:35] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2026-02-26 23:03:35] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2026-02-26 23:03:35] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2026-02-26 23:03:35] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2026-02-26 23:03:35] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2026-02-26 23:03:35] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2026-02-26 23:03:35] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2026-02-26 23:03:35] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2026-02-26 23:03:35] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-26 23:03:35] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-02-26 23:03:58] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2026-02-26 23:03:58] [TRACE] [OmnipathR] Downloaded 15.6 Kb in 22.971576s from omnipathdb.org (697 bytes/s); Redirect: 0s, DNS look up: 0.001566s, Connection: 0.002179s, Pretransfer: 0.203117s, First byte at: 22.971133s
[2026-02-26 23:03:58] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Fri, 27 Feb 2026 04:03:57 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Fri, 27 Feb 2026 05:03:57 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; Cache-Control: no-cache, no-store, must-revalidate; Pragma: no-cache; Expires: 0; Content-Encoding: gzip
[2026-02-26 23:04:00] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2026-02-26 23:04:00] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-26 23:04:00] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 23:04:00] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-26 23:04:00] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 23:04:00] [INFO] [OmnipathR] Cache item `b10176737ba43d460b13709623189f3911123779` version 1: status changed from `unknown` to `started`.
[2026-02-26 23:04:00] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/b10176737ba43d460b13709623189f3911123779-1.rds`.
[2026-02-26 23:04:00] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/b10176737ba43d460b13709623189f3911123779-1.rds`.
[2026-02-26 23:04:00] [INFO] [OmnipathR] Download ready [key=b10176737ba43d460b13709623189f3911123779, version=1]
[2026-02-26 23:04:00] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-26 23:04:00] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 23:04:00] [INFO] [OmnipathR] Cache item `b10176737ba43d460b13709623189f3911123779` version 1: status changed from `started` to `ready`.
[2026-02-26 23:04:03] [SUCCESS] [OmnipathR] Downloaded 64979 interactions.
[2026-02-26 23:04:03] [TRACE] [OmnipathR] Processing args for OmniPath query
[2026-02-26 23:04:03] [TRACE] [OmnipathR] Arguments for OmniPath query: [genesymbols=TRUE,resources=CollecTRI,strict_evidences=TRUE,query_type=interactions,datasets=tf_mirna]
[2026-02-26 23:04:03] [TRACE] [OmnipathR] Organism(s): 9606
[2026-02-26 23:04:03] [TRACE] [OmnipathR] Orthology targets:
[2026-02-26 23:04:03] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-02-26 23:04:04] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 23:04:04] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2026-02-26 23:04:04] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2026-02-26 23:04:04] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2026-02-26 23:04:04] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2026-02-26 23:04:04] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2026-02-26 23:04:04] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2026-02-26 23:04:04] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2026-02-26 23:04:04] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2026-02-26 23:04:04] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-26 23:04:04] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-02-26 23:04:07] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2026-02-26 23:04:07] [TRACE] [OmnipathR] Downloaded 9.1 Kb in 2.737137s from omnipathdb.org (3.3 Kb/s); Redirect: 0s, DNS look up: 0.001871s, Connection: 0.002645s, Pretransfer: 0.28081s, First byte at: 2.736561s
[2026-02-26 23:04:07] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Fri, 27 Feb 2026 04:04:07 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Fri, 27 Feb 2026 05:04:07 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; Cache-Control: no-cache, no-store, must-revalidate; Pragma: no-cache; Expires: 0; Content-Encoding: gzip
[2026-02-26 23:04:07] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2026-02-26 23:04:07] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-26 23:04:07] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 23:04:07] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-26 23:04:07] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 23:04:07] [INFO] [OmnipathR] Cache item `f7d34500401ba98803b7d2b26c48f64cee1eea1b` version 1: status changed from `unknown` to `started`.
[2026-02-26 23:04:07] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/f7d34500401ba98803b7d2b26c48f64cee1eea1b-1.rds`.
[2026-02-26 23:04:07] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/f7d34500401ba98803b7d2b26c48f64cee1eea1b-1.rds`.
[2026-02-26 23:04:07] [INFO] [OmnipathR] Download ready [key=f7d34500401ba98803b7d2b26c48f64cee1eea1b, version=1]
[2026-02-26 23:04:07] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-26 23:04:07] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 23:04:07] [INFO] [OmnipathR] Cache item `f7d34500401ba98803b7d2b26c48f64cee1eea1b` version 1: status changed from `started` to `ready`.
[2026-02-26 23:04:07] [TRACE] [OmnipathR] Converting JSON column `evidences` to list.
[2026-02-26 23:04:07] [TRACE] [OmnipathR] Restricting interaction records to datasets: tf_mirna; and resources: CollecTRI
[2026-02-26 23:04:07] [TRACE] [OmnipathR] Filtering evidence columns: positive, negative, directed, undirected; to datasets: tf_mirna; and resources: CollecTRI; excluding resources: none
[2026-02-26 23:04:08] [SUCCESS] [OmnipathR] Downloaded 207 interactions.
--- finished re-building ‘tf_bk.Rmd’
--- re-building ‘tf_sc.Rmd’ using rmarkdown
[2026-02-26 23:04:42] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-26 23:04:42] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 23:04:42] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2026-02-26 23:04:42] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2026-02-26 23:04:42] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2026-02-26
[2026-02-26 23:04:42] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.2; ; 2026-02-26 20:08:22 UTC; unix
[2026-02-26 23:04:42] [INFO] [OmnipathR] Package `OmnipathR` version: 3.18.4
[2026-02-26 23:04:42] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2026-02-26 23:04:42] [INFO] [OmnipathR] Session info: [version=R version 4.5.2 (2025-10-31); os=Ubuntu 24.04.3 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2026-02-26; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2026-02-26 23:04:42] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.22-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2026-02-26 23:04:42] [INFO] [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); backports 1.5.0(2024-05-23); BiocManager 1.30.27(2025-11-14); BiocParallel 1.44.0(2026-02-26); BiocStyle 2.38.0(2026-02-26); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.3.0(2026-01-14); bookdown 0.46(2025-12-05); bslib 0.10.0(2026-01-26); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); cli 3.6.5(2025-04-23); cluster 2.1.8.2(2026-02-05); codetools 0.2-20(2024-03-31); cowplot 1.2.0(2025-07-07); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); data.table 1.18.2.1(2026-01-27); DBI 1.3.0(2026-02-25); decoupleR 2.16.0(2026-02-26); deldir 2.0-4(2024-02-28); digest 0.6.39(2025-11-19); dotCall64 1.2(2024-10-04); dplyr 1.2.0(2026-02-03); evaluate 1.0.5(2025-08-27); farver 2.1.2(2024-05-13); fastDummies 1.7.5(2025-01-20); fastmap 1.2.0(2024-05-15); fitdistrplus 1.2-6(2026-01-24); fs 1.6.6(2025-04-12); future 1.69.0(2026-01-16); future.apply 1.20.2(2026-02-20); generics 0.1.4(2025-05-09); ggplot2 4.0.2(2026-02-03); ggrepel 0.9.7(2026-02-25); ggridges 0.5.7(2025-08-27); globals 0.19.0(2026-02-02); glue 1.8.0(2024-09-30); goftest 1.2-3(2021-10-07); gridExtra 2.3(2017-09-09); gtable 0.3.6(2024-10-25); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); htmlwidgets 1.6.4(2023-12-06); httpuv 1.6.16(2025-04-16); httr 1.4.8(2026-02-13); httr2 1.2.2(2025-12-08); ica 1.0-3(2022-07-08); igraph 2.2.2(2026-02-12); irlba 2.3.7(2026-01-30); jquerylib 0.1.4(2021-04-26); jsonlite 2.0.0(2025-03-27); KernSmooth 2.23-26(2025-01-01); knitr 1.51(2025-12-20); labeling 0.4.3(2023-08-29); later 1.4.7(2026-02-24); lattice 0.22-9(2026-02-09); lazyeval 0.2.2(2019-03-15); lifecycle 1.0.5(2026-01-08); listenv 0.10.0(2025-11-02); lmtest 0.9-40(2022-03-21); logger 0.4.1(2025-09-11); lubridate 1.9.5(2026-02-04); magick 2.9.0(2025-09-08); magrittr 2.0.4(2025-09-12); MASS 7.3-65(2025-02-28); Matrix 1.7-4(2025-08-28); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); mime 0.13(2025-03-17); miniUI 0.1.2(2025-04-17); nlme 3.1-168(2025-03-31); OmnipathR 3.18.4(2026-02-26); otel 0.2.0(2025-08-29); parallelly 1.46.1(2026-01-08); patchwork 1.3.2(2025-08-25); pbapply 1.7-4(2025-07-20); pheatmap 1.0.13(2025-06-05); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); plotly 4.12.0(2026-01-24); plyr 1.8.9(2023-10-02); png 0.1-8(2022-11-29); polyclip 1.10-7(2024-07-23); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); progressr 0.18.0(2025-11-06); promises 1.5.0(2025-11-01); purrr 1.2.1(2026-01-09); 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); RANN 2.6.2(2024-08-25); rappdirs 0.3.4(2026-01-17); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.1.1(2026-01-10); RcppAnnoy 0.0.23(2026-01-12); RcppHNSW 0.6.0(2024-02-04); readr 2.2.0(2026-02-19); readxl 1.4.5(2025-03-07); reshape2 1.4.5(2025-11-12); reticulate 1.45.0(2026-02-13); rlang 1.1.7(2026-01-09); rmarkdown 2.30(2025-09-28); ROCR 1.0-12(2026-01-23); RSpectra 0.16-2(2024-07-18); RSQLite 2.4.6(2026-02-06); Rtsne 0.17(2023-12-07); rvest 1.0.5(2025-08-29); S7 0.2.1(2025-11-14); sass 0.4.10(2025-04-11); scales 1.4.0(2025-04-24); scattermore 1.2(2023-06-12); sctransform 0.4.3(2026-01-10); sessioninfo 1.2.3(2025-02-05); Seurat 5.4.0(2025-12-14); SeuratObject 5.3.0(2025-12-12); shiny 1.13.0(2026-02-20); sp 2.2-1(2026-02-13); spam 2.11-3(2026-01-08); spatstat.data 3.1-9(2025-10-18); spatstat.explore 3.7-0(2026-01-22); spatstat.geom 3.7-0(2026-01-20); spatstat.random 3.4-4(2026-01-21); spatstat.sparse 3.1-0(2024-06-21); spatstat.univar 3.1-6(2026-01-17); spatstat.utils 3.2-1(2026-01-10); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); survival 3.8-6(2026-01-16); tensor 1.5.1(2025-06-17); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tinytex 0.58(2025-11-19); tzdb 0.5.0(2025-03-15); uwot 0.2.4(2025-11-10); vctrs 0.7.1(2026-01-23); viridisLite 0.4.3(2026-02-04); withr 3.0.2(2024-10-28); xfun 0.56(2026-01-18); XML 3.99-0.22(2026-02-10); xml2 1.5.2(2026-01-17); xtable 1.8-8(2026-02-22); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13); zoo 1.8-15(2025-12-15)
[2026-02-26 23:04:42] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: GnuTLS/3.8.3; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2026-02-26 23:04:42] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2026-02-26 23:04:43] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2026-02-26 23:04:43] [TRACE] [OmnipathR] Contains 6 files.
[2026-02-26 23:04:43] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2026-02-26 23:04:43] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-26 23:04:43] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 23:04:43] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2026-02-26 23:04:43] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2026-02-26 23:04:43] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2026-02-26 23:04:43] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 23:04:43] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2026-02-26 23:04:43] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 23:04:43] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2026-02-26 23:04:43] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 23:04:43] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2026-02-26 23:04:43] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 23:04:43] [TRACE] [OmnipathR] Cache locked: FALSE
[2026-02-26 23:04:43] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2026-02-26 23:04:43] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-26 23:04:43] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 23:04:43] [INFO] [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available.
[2026-02-26 23:04:43] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-26 23:04:43] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 23:04:43] [INFO] [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 1.
[2026-02-26 23:04:43] [TRACE] [OmnipathR] Cache file path: /home/biocbuild/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-1.html
[2026-02-26 23:04:43] [INFO] [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html`
[2026-02-26 23:04:43] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`.
[2026-02-26 23:04:43] [TRACE] [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2026-02-26 23:04:43] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2026-02-26 23:04:43] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2026-02-26 23:04:43] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-26 23:04:43] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-02-26 23:04:43] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2026-02-26 23:04:43] [TRACE] [OmnipathR] Sending HTTP request.
[2026-02-26 23:04:44] [TRACE] [OmnipathR] HTTP 200 (OK)
[2026-02-26 23:04:44] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2026-02-26 23:04:44] [TRACE] [OmnipathR] Downloaded 39.9 Kb in 0.639569s from rescued.omnipathdb.org (62.3 Kb/s); Redirect: 0s, DNS look up: 0.001712s, Connection: 0.00233s, Pretransfer: 0.341129s, First byte at: 0.491459s
[2026-02-26 23:04:44] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Fri, 27 Feb 2026 04:04:44 GMT; Content-Type: text/html; charset=utf-8; Last-Modified: Fri, 24 Oct 2025 17:07:34 GMT; Transfer-Encoding: chunked; Connection: keep-alive; ETag: W/"68fbb256-3f5d0"; Expires: Fri, 27 Feb 2026 05:04:44 GMT; Cache-Control: max-age=3600; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2026-02-26 23:04:44] [TRACE] [OmnipathR] Response headers: [Server=nginx,Date=Fri, 27 Feb 2026 04:04:44 GMT,Content-Type=text/html; charset=utf-8,Last-Modified=Fri, 24 Oct 2025 17:07:34 GMT,Transfer-Encoding=chunked,Connection=keep-alive,ETag=W/"68fbb256-3f5d0",Expires=Fri, 27 Feb 2026 05:04:44 GMT,Cache-Control=max-age=3600,Cache-Control=public,X-Frame-Options=DENY,Content-Encoding=gzip]
[2026-02-26 23:04:44] [INFO] [OmnipathR] Download ready [key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, version=1]
[2026-02-26 23:04:44] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-26 23:04:44] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 23:04:44] [INFO] [OmnipathR] Cache item `67b4943ae7fd646a03b760aefa99fe6c41ab2887` version 1: status changed from `unknown` to `ready`.
[2026-02-26 23:04:45] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2026-02-26 23:04:45] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2026-02-26 23:04:45] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2026-02-26 23:04:45] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2026-02-26 23:04:45] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-26 23:04:45] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 23:04:45] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-26 23:04:45] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 23:04:45] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2026-02-26 23:04:45] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2026-02-26 23:04:45] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2026-02-26 23:04:45] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2026-02-26 23:04:45] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2026-02-26 23:04:45] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-26 23:04:45] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-02-26 23:04:45] [TRACE] [OmnipathR] HTTP v2 GET: status 200.
[2026-02-26 23:04:45] [TRACE] [OmnipathR] Downloaded 6.7 Kb in 0.20169s from omabrowser.org (33.1 Kb/s); Redirect: 0s, DNS look up: 0.003356s, Connection: 0.017707s, Pretransfer: 0.081068s, First byte at: 0.201423s
[2026-02-26 23:04:45] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; date: Fri, 27 Feb 2026 04:04:45 GMT; content-type: text/plain; charset=UTF-8; server: cloudflare; strict-transport-security: max-age=31536000; includeSubDomains; last-modified: Wed, 20 Nov 2024 10:20:02 GMT; etag: W/"673db7d2-6517f"; access-control-allow-origin: *; content-encoding: gzip; cf-cache-status: DYNAMIC; vary: accept-encoding; nel: {"report_to":"cf-nel","success_fraction":0.0,"max_age":604800}; report-to: {"group":"cf-nel","max_age":604800,"endpoints":[{"url":"https://a.nel.cloudflare.com/report/v4?s=8e7PRZSen7K%2FaEfcQ%2F9J%2BAiz40VaKqxG%2FXrOoXgoaRIZuW6xRw2dnP61Vf09ELTM0DuHBNa1na5d44FhHY5r%2BEJxoXDiKZ1n%2Fe1FPXMW"}]}; cf-ray: 9d44ccc75ba7e625-IAD; alt-svc: h3=":443"; ma=86400
[2026-02-26 23:04:46] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2026-02-26 23:04:46] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1]
[2026-02-26 23:04:46] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-26 23:04:46] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 23:04:47] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.
[2026-02-26 23:04:47] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2026-02-26 23:04:47] [TRACE] [OmnipathR] Looking up in cache: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`.
[2026-02-26 23:04:47] [INFO] [OmnipathR] Cache record does not exist: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2026-02-26 23:04:47] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`.
[2026-02-26 23:04:47] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-26 23:04:47] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 23:04:47] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-26 23:04:47] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 23:04:47] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `unknown` to `started`.
[2026-02-26 23:04:47] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`.
[2026-02-26 23:04:47] [INFO] [OmnipathR] Retrieving URL: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2026-02-26 23:04:47] [TRACE] [OmnipathR] Attempt 1/3: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2026-02-26 23:05:24] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`.
[2026-02-26 23:05:24] [INFO] [OmnipathR] Download ready [key=56ad6544dc07a2222fa6013d8d83e6e5a35fdf33, version=1]
[2026-02-26 23:05:24] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-26 23:05:24] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 23:05:24] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `started` to `ready`.
[2026-02-26 23:05:24] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`.
[2026-02-26 23:05:24] [TRACE] [OmnipathR] Processing args for OmniPath query
[2026-02-26 23:05:24] [TRACE] [OmnipathR] Arguments for OmniPath query: [loops=TRUE,organisms=9606,genesymbols=TRUE,query_type=interactions,datasets=collectri]
[2026-02-26 23:05:24] [TRACE] [OmnipathR] Organism(s): 9606
[2026-02-26 23:05:24] [TRACE] [OmnipathR] Orthology targets:
[2026-02-26 23:05:24] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2026-02-26 23:05:24] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2026-02-26 23:05:24] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2026-02-26 23:05:24] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2026-02-26 23:05:24] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2026-02-26 23:05:24] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2026-02-26 23:05:24] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2026-02-26 23:05:24] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2026-02-26 23:05:24] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-26 23:05:24] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-02-26 23:05:47] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2026-02-26 23:05:47] [TRACE] [OmnipathR] Downloaded 15.6 Kb in 22.369948s from omnipathdb.org (715 bytes/s); Redirect: 0s, DNS look up: 0.003763s, Connection: 0.004506s, Pretransfer: 0.384425s, First byte at: 22.369389s
[2026-02-26 23:05:47] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Fri, 27 Feb 2026 04:05:47 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Fri, 27 Feb 2026 05:05:47 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; Cache-Control: no-cache, no-store, must-revalidate; Pragma: no-cache; Expires: 0; Content-Encoding: gzip
[2026-02-26 23:05:49] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2026-02-26 23:05:49] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-26 23:05:49] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 23:05:49] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-26 23:05:49] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 23:05:49] [INFO] [OmnipathR] Cache item `b10176737ba43d460b13709623189f3911123779` version 1: status changed from `unknown` to `started`.
[2026-02-26 23:05:49] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/b10176737ba43d460b13709623189f3911123779-1.rds`.
[2026-02-26 23:05:50] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/b10176737ba43d460b13709623189f3911123779-1.rds`.
[2026-02-26 23:05:50] [INFO] [OmnipathR] Download ready [key=b10176737ba43d460b13709623189f3911123779, version=1]
[2026-02-26 23:05:50] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-26 23:05:50] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 23:05:50] [INFO] [OmnipathR] Cache item `b10176737ba43d460b13709623189f3911123779` version 1: status changed from `started` to `ready`.
[2026-02-26 23:05:52] [SUCCESS] [OmnipathR] Downloaded 64979 interactions.
[2026-02-26 23:05:52] [TRACE] [OmnipathR] Processing args for OmniPath query
[2026-02-26 23:05:52] [TRACE] [OmnipathR] Arguments for OmniPath query: [genesymbols=TRUE,resources=CollecTRI,strict_evidences=TRUE,query_type=interactions,datasets=tf_mirna]
[2026-02-26 23:05:52] [TRACE] [OmnipathR] Organism(s): 9606
[2026-02-26 23:05:52] [TRACE] [OmnipathR] Orthology targets:
[2026-02-26 23:05:52] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-02-26 23:05:54] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 23:05:54] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2026-02-26 23:05:54] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2026-02-26 23:05:54] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2026-02-26 23:05:54] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2026-02-26 23:05:54] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2026-02-26 23:05:54] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2026-02-26 23:05:54] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2026-02-26 23:05:54] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2026-02-26 23:05:54] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-26 23:05:54] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-02-26 23:05:58] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2026-02-26 23:05:58] [TRACE] [OmnipathR] Downloaded 9.1 Kb in 4.415123s from omnipathdb.org (2.1 Kb/s); Redirect: 0s, DNS look up: 0.00225s, Connection: 0.003038s, Pretransfer: 0.36292s, First byte at: 4.414004s
[2026-02-26 23:05:58] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Fri, 27 Feb 2026 04:05:58 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Fri, 27 Feb 2026 05:05:58 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; Cache-Control: no-cache, no-store, must-revalidate; Pragma: no-cache; Expires: 0; Content-Encoding: gzip
[2026-02-26 23:05:59] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2026-02-26 23:05:59] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-26 23:05:59] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 23:05:59] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-26 23:05:59] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 23:05:59] [INFO] [OmnipathR] Cache item `f7d34500401ba98803b7d2b26c48f64cee1eea1b` version 1: status changed from `unknown` to `started`.
[2026-02-26 23:05:59] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/f7d34500401ba98803b7d2b26c48f64cee1eea1b-1.rds`.
[2026-02-26 23:05:59] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/f7d34500401ba98803b7d2b26c48f64cee1eea1b-1.rds`.
[2026-02-26 23:05:59] [INFO] [OmnipathR] Download ready [key=f7d34500401ba98803b7d2b26c48f64cee1eea1b, version=1]
[2026-02-26 23:05:59] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-26 23:05:59] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 23:05:59] [INFO] [OmnipathR] Cache item `f7d34500401ba98803b7d2b26c48f64cee1eea1b` version 1: status changed from `started` to `ready`.
[2026-02-26 23:05:59] [TRACE] [OmnipathR] Converting JSON column `evidences` to list.
[2026-02-26 23:05:59] [TRACE] [OmnipathR] Restricting interaction records to datasets: tf_mirna; and resources: CollecTRI
[2026-02-26 23:05:59] [TRACE] [OmnipathR] Filtering evidence columns: positive, negative, directed, undirected; to datasets: tf_mirna; and resources: CollecTRI; excluding resources: none
[2026-02-26 23:06:00] [SUCCESS] [OmnipathR] Downloaded 207 interactions.
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--- finished re-building ‘tf_sc.Rmd’
SUMMARY: processing the following files failed:
‘pw_bk.Rmd’ ‘pw_sc.Rmd’
Error: Vignette re-building failed.
Execution halted
* checking PDF version of manual ... OK
* DONE
Status: 2 ERRORs, 1 WARNING, 1 NOTE
See
‘/home/biocbuild/bbs-3.22-bioc/meat/decoupleR.Rcheck/00check.log’
for details.
decoupleR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL decoupleR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’ * installing *source* package ‘decoupleR’ ... ** this is package ‘decoupleR’ version ‘2.16.0’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (decoupleR)
decoupleR.Rcheck/tests/testthat.Rout
R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(decoupleR)
>
> test_check("decoupleR")
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Warning: stack imbalance in '.Call', 162 then 164
[2026-02-26 22:50:00] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-26 22:50:00] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 22:50:00] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2026-02-26 22:50:00] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2026-02-26 22:50:00] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2026-02-26
[2026-02-26 22:50:00] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.2; ; 2026-02-26 20:08:22 UTC; unix
[2026-02-26 22:50:00] [INFO] [OmnipathR] Package `OmnipathR` version: 3.18.4
[2026-02-26 22:50:00] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2026-02-26 22:50:00] [INFO] [OmnipathR] Session info: [version=R version 4.5.2 (2025-10-31); os=Ubuntu 24.04.3 LTS; system=x86_64, linux-gnu; ui=X11; language=C; collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2026-02-26; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2026-02-26 22:50:00] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.22-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2026-02-26 22:50:01] [INFO] [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); annotate 1.88.0(2026-02-26); AnnotationDbi 1.72.0(2026-02-26); AUCell 1.32.0(2026-02-26); backports 1.5.0(2024-05-23); beachmat 2.26.0(2026-02-26); Biobase 2.70.0(2026-02-26); BiocGenerics 0.56.0(2026-02-26); BiocParallel 1.44.0(2026-02-26); BiocSingular 1.26.1(2026-02-26); Biostrings 2.78.0(2026-02-26); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.3.0(2026-01-14); brio 1.1.5(2024-04-24); broom 1.0.12(2026-01-27); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); class 7.3-23(2025-01-01); cli 3.6.5(2025-04-23); codetools 0.2-20(2024-03-31); cowplot 1.2.0(2025-07-07); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); data.table 1.18.2.1(2026-01-27); DBI 1.3.0(2026-02-25); decoupleR 2.16.0(2026-02-26); DelayedArray 0.36.0(2026-02-26); DelayedMatrixStats 1.32.0(2026-02-26); desc 1.4.3(2023-12-10); digest 0.6.39(2025-11-19); dplyr 1.2.0(2026-02-03); e1071 1.7-17(2025-12-18); evaluate 1.0.5(2025-08-27); farver 2.1.2(2024-05-13); fastmap 1.2.0(2024-05-15); fastmatch 1.1-8(2026-01-17); fgsea 1.36.2(2026-02-26); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); GenomicRanges 1.62.1(2026-02-26); ggplot2 4.0.2(2026-02-03); glue 1.8.0(2024-09-30); graph 1.88.1(2026-02-26); GSEABase 1.72.0(2026-02-26); GSVA 2.4.6(2026-02-26); gtable 0.3.6(2024-10-25); h5mread 1.2.1(2026-02-26); HDF5Array 1.38.0(2026-02-26); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); htmlwidgets 1.6.4(2023-12-06); httr 1.4.8(2026-02-13); httr2 1.2.2(2025-12-08); igraph 2.2.2(2026-02-12); IRanges 2.44.0(2026-02-26); irlba 2.3.7(2026-01-30); jsonlite 2.0.0(2025-03-27); KEGGREST 1.50.0(2026-02-26); kernlab 0.9-33(2024-08-13); KernSmooth 2.23-26(2025-01-01); knitr 1.51(2025-12-20); later 1.4.7(2026-02-24); lattice 0.22-9(2026-02-09); lazyeval 0.2.2(2019-03-15); lifecycle 1.0.5(2026-01-08); logger 0.4.1(2025-09-11); lubridate 1.9.5(2026-02-04); magick 2.9.0(2025-09-08); magrittr 2.0.4(2025-09-12); MASS 7.3-65(2025-02-28); Matrix 1.7-4(2025-08-28); MatrixGenerics 1.22.0(2026-02-26); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); memuse 4.2-3(2023-01-24); mixtools 2.0.0.1(2025-03-08); nlme 3.1-168(2025-03-31); OmnipathR 3.18.4(2026-02-26); otel 0.2.0(2025-08-29); parallelly 1.46.1(2026-01-08); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); plotly 4.12.0(2026-01-24); png 0.1-8(2022-11-29); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); proxy 0.4-29(2025-12-29); purrr 1.2.1(2026-01-09); 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 0.18.0(2026-01-16); rappdirs 0.3.4(2026-01-17); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.1.1(2026-01-10); readr 2.2.0(2026-02-19); readxl 1.4.5(2025-03-07); rhdf5 2.54.1(2026-02-26); rhdf5filters 1.22.0(2026-02-26); Rhdf5lib 1.32.0(2026-02-26); rjson 0.2.23(2024-09-16); rlang 1.1.7(2026-01-09); rmarkdown 2.30(2025-09-28); rpart 4.1.24(2025-01-07); RSQLite 2.4.6(2026-02-06); rsvd 1.0.5(2021-04-16); rvest 1.0.5(2025-08-29); S4Arrays 1.10.1(2026-02-26); S4Vectors 0.48.0(2026-02-26); S7 0.2.1(2025-11-14); ScaledMatrix 1.18.0(2026-02-26); scales 1.4.0(2025-04-24); segmented 2.2-1(2026-01-29); Seqinfo 1.0.0(2026-02-26); sessioninfo 1.2.3(2025-02-05); SingleCellExperiment 1.32.0(2026-02-26); SparseArray 1.10.8(2026-02-26); sparseMatrixStats 1.22.0(2026-02-26); SpatialExperiment 1.20.0(2026-02-26); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); SummarizedExperiment 1.40.0(2026-02-26); survival 3.8-6(2026-01-16); testthat 3.3.2(2026-01-11); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tzdb 0.5.0(2025-03-15); vctrs 0.7.1(2026-01-23); viper 1.44.0(2026-02-26); viridisLite 0.4.3(2026-02-04); waldo 0.6.2(2025-07-11); withr 3.0.2(2024-10-28); xfun 0.56(2026-01-18); XML 3.99-0.22(2026-02-10); xml2 1.5.2(2026-01-17); xtable 1.8-8(2026-02-22); XVector 0.50.0(2026-02-26); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13)
[2026-02-26 22:50:01] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: GnuTLS/3.8.3; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2026-02-26 22:50:01] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2026-02-26 22:50:01] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2026-02-26 22:50:01] [TRACE] [OmnipathR] Contains 6 files.
[2026-02-26 22:50:01] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2026-02-26 22:50:01] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-26 22:50:01] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 22:50:01] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2026-02-26 22:50:01] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2026-02-26 22:50:01] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2026-02-26 22:50:01] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 22:50:01] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2026-02-26 22:50:01] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 22:50:01] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2026-02-26 22:50:01] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 22:50:01] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2026-02-26 22:50:01] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 22:50:01] [TRACE] [OmnipathR] Cache locked: FALSE
[2026-02-26 22:50:01] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-02-26 22:50:02] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 22:50:02] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-02-26 22:50:03] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 22:50:03] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2026-02-26 22:50:03] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-26 22:50:03] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 22:50:03] [INFO] [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available.
[2026-02-26 22:50:03] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-26 22:50:03] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 22:50:03] [INFO] [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 1.
[2026-02-26 22:50:03] [TRACE] [OmnipathR] Cache file path: /home/biocbuild/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-1.html
[2026-02-26 22:50:03] [INFO] [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html`
[2026-02-26 22:50:03] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`.
[2026-02-26 22:50:03] [TRACE] [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2026-02-26 22:50:03] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2026-02-26 22:50:03] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2026-02-26 22:50:03] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-26 22:50:03] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-02-26 22:50:03] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2026-02-26 22:50:03] [TRACE] [OmnipathR] Sending HTTP request.
[2026-02-26 22:50:04] [TRACE] [OmnipathR] HTTP 200 (OK)
[2026-02-26 22:50:04] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2026-02-26 22:50:04] [TRACE] [OmnipathR] Downloaded 39.9 Kb in 0.623419s from rescued.omnipathdb.org (63.9 Kb/s); Redirect: 0s, DNS look up: 0.001523s, Connection: 0.002237s, Pretransfer: 0.339008s, First byte at: 0.484126s
[2026-02-26 22:50:04] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Fri, 27 Feb 2026 03:50:03 GMT; Content-Type: text/html; charset=utf-8; Last-Modified: Fri, 24 Oct 2025 17:07:34 GMT; Transfer-Encoding: chunked; Connection: keep-alive; ETag: W/"68fbb256-3f5d0"; Expires: Fri, 27 Feb 2026 04:50:03 GMT; Cache-Control: max-age=3600; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2026-02-26 22:50:04] [TRACE] [OmnipathR] Response headers: [Server=nginx,Date=Fri, 27 Feb 2026 03:50:03 GMT,Content-Type=text/html; charset=utf-8,Last-Modified=Fri, 24 Oct 2025 17:07:34 GMT,Transfer-Encoding=chunked,Connection=keep-alive,ETag=W/"68fbb256-3f5d0",Expires=Fri, 27 Feb 2026 04:50:03 GMT,Cache-Control=max-age=3600,Cache-Control=public,X-Frame-Options=DENY,Content-Encoding=gzip]
[2026-02-26 22:50:05] [INFO] [OmnipathR] Download ready [key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, version=1]
[2026-02-26 22:50:05] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-26 22:50:05] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 22:50:05] [INFO] [OmnipathR] Cache item `67b4943ae7fd646a03b760aefa99fe6c41ab2887` version 1: status changed from `unknown` to `ready`.
[2026-02-26 22:50:05] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2026-02-26 22:50:05] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2026-02-26 22:50:05] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2026-02-26 22:50:05] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2026-02-26 22:50:05] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-26 22:50:05] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 22:50:05] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-26 22:50:05] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 22:50:06] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2026-02-26 22:50:06] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2026-02-26 22:50:06] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2026-02-26 22:50:06] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2026-02-26 22:50:06] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2026-02-26 22:50:06] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-26 22:50:06] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-02-26 22:50:06] [TRACE] [OmnipathR] HTTP v2 GET: status 200.
[2026-02-26 22:50:06] [TRACE] [OmnipathR] Downloaded 7.6 Kb in 0.431702s from omabrowser.org (17.5 Kb/s); Redirect: 0s, DNS look up: 0.022606s, Connection: 0.035507s, Pretransfer: 0.102879s, First byte at: 0.431485s
[2026-02-26 22:50:06] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; date: Fri, 27 Feb 2026 03:50:06 GMT; content-type: text/plain; charset=UTF-8; server: cloudflare; strict-transport-security: max-age=31536000; includeSubDomains; last-modified: Wed, 20 Nov 2024 10:20:02 GMT; etag: W/"673db7d2-6517f"; access-control-allow-origin: *; content-encoding: gzip; cf-cache-status: DYNAMIC; vary: accept-encoding; nel: {"report_to":"cf-nel","success_fraction":0.0,"max_age":604800}; report-to: {"group":"cf-nel","max_age":604800,"endpoints":[{"url":"https://a.nel.cloudflare.com/report/v4?s=5Zo0yO4Yu5tPLwh2WKaGWQWS%2Fgi%2BBut3R4n2CKY%2B5pzbHbH%2FyLsRVeTfOuPRLmCl1%2FqJbBdsAD2OdAodFXlc9xgy%2F7FCWM31mkeSRUSL"}]}; cf-ray: 9d44b7506911f508-IAD; alt-svc: h3=":443"; ma=86400
[2026-02-26 22:50:08] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2026-02-26 22:50:08] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1]
[2026-02-26 22:50:08] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-26 22:50:08] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 22:50:08] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.
[2026-02-26 22:50:08] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2026-02-26 22:50:08] [TRACE] [OmnipathR] Looking up in cache: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`.
[2026-02-26 22:50:08] [INFO] [OmnipathR] Cache record does not exist: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2026-02-26 22:50:08] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`.
[2026-02-26 22:50:08] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-26 22:50:08] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 22:50:08] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-26 22:50:08] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 22:50:08] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `unknown` to `started`.
[2026-02-26 22:50:08] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`.
[2026-02-26 22:50:08] [INFO] [OmnipathR] Retrieving URL: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2026-02-26 22:50:08] [TRACE] [OmnipathR] Attempt 1/3: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2026-02-26 22:50:40] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`.
[2026-02-26 22:50:40] [INFO] [OmnipathR] Download ready [key=56ad6544dc07a2222fa6013d8d83e6e5a35fdf33, version=1]
[2026-02-26 22:50:40] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-26 22:50:40] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 22:50:40] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `started` to `ready`.
[2026-02-26 22:50:40] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`.
[2026-02-26 22:50:40] [TRACE] [OmnipathR] Processing args for OmniPath query
[2026-02-26 22:50:40] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=TFcensus,query_type=annotations]
[2026-02-26 22:50:40] [TRACE] [OmnipathR] Organism(s): 9606
[2026-02-26 22:50:40] [TRACE] [OmnipathR] Orthology targets:
[2026-02-26 22:50:40] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-02-26 22:50:41] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 22:50:41] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2026-02-26 22:50:41] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2026-02-26 22:50:41] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2026-02-26 22:50:41] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2026-02-26 22:50:41] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2026-02-26 22:50:41] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2026-02-26 22:50:41] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2026-02-26 22:50:41] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2026-02-26 22:50:41] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-26 22:50:41] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-02-26 22:50:49] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2026-02-26 22:50:49] [TRACE] [OmnipathR] Downloaded 15.6 Kb in 8.290544s from omnipathdb.org (1.9 Kb/s); Redirect: 0s, DNS look up: 0.001587s, Connection: 0.002548s, Pretransfer: 0.199939s, First byte at: 8.289555s
[2026-02-26 22:50:50] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Fri, 27 Feb 2026 03:50:49 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Fri, 27 Feb 2026 04:50:49 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; Cache-Control: no-cache, no-store, must-revalidate; Pragma: no-cache; Expires: 0; Content-Encoding: gzip
[2026-02-26 22:50:51] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2026-02-26 22:50:51] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-26 22:50:51] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 22:50:51] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-26 22:50:51] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 22:50:51] [INFO] [OmnipathR] Cache item `6f000d9b5edd9832b1c28754d1c3d9449c1c7490` version 1: status changed from `unknown` to `started`.
[2026-02-26 22:50:51] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/6f000d9b5edd9832b1c28754d1c3d9449c1c7490-1.rds`.
[2026-02-26 22:50:51] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/6f000d9b5edd9832b1c28754d1c3d9449c1c7490-1.rds`.
[2026-02-26 22:50:51] [INFO] [OmnipathR] Download ready [key=6f000d9b5edd9832b1c28754d1c3d9449c1c7490, version=1]
[2026-02-26 22:50:51] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-26 22:50:51] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 22:50:51] [INFO] [OmnipathR] Cache item `6f000d9b5edd9832b1c28754d1c3d9449c1c7490` version 1: status changed from `started` to `ready`.
[2026-02-26 22:50:51] [SUCCESS] [OmnipathR] Downloaded 3497 annotation records.
[2026-02-26 22:50:51] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-02-26 22:50:52] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 22:50:52] [TRACE] [OmnipathR] Processing args for OmniPath query
[2026-02-26 22:50:52] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=PROGENy,query_type=annotations]
[2026-02-26 22:50:53] [TRACE] [OmnipathR] Organism(s): 9606
[2026-02-26 22:50:53] [TRACE] [OmnipathR] Orthology targets:
[2026-02-26 22:50:53] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-02-26 22:50:54] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 22:50:54] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2026-02-26 22:50:54] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2026-02-26 22:50:54] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2026-02-26 22:50:54] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2026-02-26 22:50:54] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2026-02-26 22:50:54] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2026-02-26 22:50:54] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2026-02-26 22:50:54] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2026-02-26 22:50:54] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-26 22:50:54] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-02-26 22:51:29] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2026-02-26 22:51:29] [TRACE] [OmnipathR] Downloaded 15.6 Kb in 35.759854s from omnipathdb.org (447 bytes/s); Redirect: 0s, DNS look up: 0.002258s, Connection: 0.002924s, Pretransfer: 0.212807s, First byte at: 35.758965s
[2026-02-26 22:51:29] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Fri, 27 Feb 2026 03:51:29 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Fri, 27 Feb 2026 04:51:29 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; Cache-Control: no-cache, no-store, must-revalidate; Pragma: no-cache; Expires: 0; Content-Encoding: gzip
[2026-02-26 22:52:23] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2026-02-26 22:52:23] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-26 22:52:23] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 22:52:23] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-26 22:52:23] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 22:52:23] [INFO] [OmnipathR] Cache item `3492392585ba05414edfae46801492076437d7e7` version 1: status changed from `unknown` to `started`.
[2026-02-26 22:52:23] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`.
[2026-02-26 22:52:26] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`.
[2026-02-26 22:52:26] [INFO] [OmnipathR] Download ready [key=3492392585ba05414edfae46801492076437d7e7, version=1]
[2026-02-26 22:52:26] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-26 22:52:26] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 22:52:26] [INFO] [OmnipathR] Cache item `3492392585ba05414edfae46801492076437d7e7` version 1: status changed from `started` to `ready`.
[2026-02-26 22:52:26] [SUCCESS] [OmnipathR] Downloaded 699831 annotation records.
[2026-02-26 22:52:27] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-02-26 22:52:28] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 22:52:28] [TRACE] [OmnipathR] Processing args for OmniPath query
[2026-02-26 22:52:28] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=PROGENy,query_type=annotations]
[2026-02-26 22:52:28] [TRACE] [OmnipathR] Organism(s): 9606
[2026-02-26 22:52:28] [TRACE] [OmnipathR] Orthology targets:
[2026-02-26 22:52:28] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-02-26 22:52:30] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 22:52:30] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2026-02-26 22:52:31] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`.
[2026-02-26 22:52:31] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2026-02-26 22:52:31] [SUCCESS] [OmnipathR] Loaded 699831 annotation records from cache.
[2026-02-26 22:52:32] [INFO] [OmnipathR] Loading database `Orthologous Matrix (OMA) gene pairs`.
[2026-02-26 22:52:32] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2026-02-26 22:52:32] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2026-02-26 22:52:32] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2026-02-26 22:52:32] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2026-02-26 22:52:32] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2026-02-26 22:52:33] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2026-02-26 22:52:33] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2026-02-26 22:52:33] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/api/pairs/HUMAN/MOUSE/?format=tsv&xrefs=UniProtKB%2FSwissProt&per_page=2000000`.
[2026-02-26 22:52:33] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/api/pairs/HUMAN/MOUSE/?format=tsv&xrefs=UniProtKB%2FSwissProt&per_page=2000000`
[2026-02-26 22:52:33] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/api/pairs/HUMAN/MOUSE/?format=tsv&xrefs=UniProtKB%2FSwissProt&per_page=2000000`.
[2026-02-26 22:52:33] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-26 22:52:33] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 22:52:33] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-26 22:52:33] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 22:52:33] [INFO] [OmnipathR] Cache item `8f45b25c384d814c7de210e7ca40b7e35894e4f1` version 1: status changed from `unknown` to `started`.
[2026-02-26 22:52:33] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/8f45b25c384d814c7de210e7ca40b7e35894e4f1-1.rds`.
[2026-02-26 22:52:33] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/api/pairs/HUMAN/MOUSE/?format=tsv&xrefs=UniProtKB%2FSwissProt&per_page=2000000`
[2026-02-26 22:52:33] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/api/pairs/HUMAN/MOUSE/?format=tsv&xrefs=UniProtKB%2FSwissProt&per_page=2000000`
[2026-02-26 22:52:33] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2026-02-26 22:52:33] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-26 22:52:33] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-02-26 22:52:44] [TRACE] [OmnipathR] HTTP v2 GET: status 200.
[2026-02-26 22:52:44] [TRACE] [OmnipathR] Downloaded 4 Kb in 11.682259s from omabrowser.org (350 bytes/s); Redirect: 0s, DNS look up: 0.000802s, Connection: 0.013709s, Pretransfer: 0.105965s, First byte at: 11.681513s
[2026-02-26 22:52:44] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; date: Fri, 27 Feb 2026 03:52:44 GMT; content-type: text/tsv; charset=utf-8; content-length: 1187278; server: cloudflare; strict-transport-security: max-age=31536000; includeSubDomains; x-total-count: 22374; vary: Accept,origin,Cookie; allow: GET, HEAD, OPTIONS; content-disposition: attachment; filename=OMA-Pairs_HUMAN-MOUSE_2026-02-27_035244.tsv; x-frame-options: DENY; x-content-type-options: nosniff; referrer-policy: same-origin; cross-origin-opener-policy: same-origin; set-cookie: __matomo=8244793c6b91d491; expires=Sun, 27-Feb-2028 03:52:44 UTC; Path=/; cf-cache-status: DYNAMIC; nel: {"report_to":"cf-nel","success_fraction":0.0,"max_age":604800}; report-to: {"group":"cf-nel","max_age":604800,"endpoints":[{"url":"https://a.nel.cloudflare.com/report/v4?s=AxUvvBFkMcxzftxQMEt4DgstE1sU3ozo4oWKp7NNEusXUYt%2BUMSRYisMGxjWYGRW633%2B0VpU7A%2FILrGnDk78Wv36jUg8RTQVlmHPrUbC"}]}; cf-ray: 9d44bae81daa2902-IAD; alt-svc: h3=":443"; ma=86400
[2026-02-26 22:52:47] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/8f45b25c384d814c7de210e7ca40b7e35894e4f1-1.rds`.
[2026-02-26 22:52:47] [INFO] [OmnipathR] Download ready [key=8f45b25c384d814c7de210e7ca40b7e35894e4f1, version=1]
[2026-02-26 22:52:47] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-26 22:52:47] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 22:52:47] [INFO] [OmnipathR] Cache item `8f45b25c384d814c7de210e7ca40b7e35894e4f1` version 1: status changed from `started` to `ready`.
[2026-02-26 22:52:47] [TRACE] [OmnipathR] ID translation table: from `uniprot_entry` to `uniprot`, using `uniprot`.
[2026-02-26 22:52:47] [TRACE] [OmnipathR] Creating ID mapping table from `id` to `accession`, for organism 9606 (only reviewed: TRUE)
[2026-02-26 22:52:47] [TRACE] [OmnipathR] Loading all UniProt records for organism 9606 (only reviewed: TRUE); fields: id,accession
[2026-02-26 22:52:47] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2026-02-26 22:52:47] [TRACE] [OmnipathR] Looking up in cache: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:9606%20AND%20reviewed:true`.
[2026-02-26 22:52:47] [INFO] [OmnipathR] Cache record does not exist: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:9606%20AND%20reviewed:true`
[2026-02-26 22:52:47] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:9606%20AND%20reviewed:true`.
[2026-02-26 22:52:47] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-26 22:52:47] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 22:52:47] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-26 22:52:47] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 22:52:47] [INFO] [OmnipathR] Cache item `6558a1824894a625b8e3f80538cd3aa6e8a44379` version 1: status changed from `unknown` to `started`.
[2026-02-26 22:52:47] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/6558a1824894a625b8e3f80538cd3aa6e8a44379-1.rds`.
[2026-02-26 22:52:47] [INFO] [OmnipathR] Retrieving URL: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:9606%20AND%20reviewed:true`
[2026-02-26 22:52:47] [TRACE] [OmnipathR] Attempt 1/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:9606%20AND%20reviewed:true`
[2026-02-26 22:52:47] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2026-02-26 22:52:47] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-26 22:52:47] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-02-26 22:52:48] [TRACE] [OmnipathR] HTTP v2 GET: status 200.
[2026-02-26 22:52:48] [TRACE] [OmnipathR] Downloaded 31 bytes in 0.782968s from rest.uniprot.org (39 bytes/s); Redirect: 0s, DNS look up: 0.005417s, Connection: 0.006275s, Pretransfer: 0.471185s, First byte at: 0.782896s
[2026-02-26 22:52:48] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; vary: accept,accept-encoding,x-uniprot-release,x-api-deployment-date, User-Agent, Accept-Encoding; cache-control: public, max-age=43200; content-type: text/plain;format=tsv; content-encoding: gzip; access-control-allow-credentials: true; access-control-expose-headers: Link, X-Total-Results, X-UniProt-Release, X-UniProt-Release-Date, X-API-Deployment-Date; x-api-deployment-date: 09-February-2026; strict-transport-security: max-age=31536000; includeSubDomains; date: Fri, 27 Feb 2026 03:52:48 GMT; access-control-max-age: 1728000; x-uniprot-release: 2026_01; access-control-allow-origin: *; accept-ranges: bytes; access-control-allow-methods: GET, PUT, POST, DELETE, PATCH, OPTIONS; access-control-allow-headers: DNT,Keep-Alive,User-Agent,X-Requested-With,If-Modified-Since,Cache-Control,Content-Type,Range,Authorization; x-uniprot-release-date: 28-January-2026
[2026-02-26 22:52:58] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/6558a1824894a625b8e3f80538cd3aa6e8a44379-1.rds`.
[2026-02-26 22:52:58] [INFO] [OmnipathR] Download ready [key=6558a1824894a625b8e3f80538cd3aa6e8a44379, version=1]
[2026-02-26 22:52:58] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-26 22:52:58] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 22:52:58] [INFO] [OmnipathR] Cache item `6558a1824894a625b8e3f80538cd3aa6e8a44379` version 1: status changed from `started` to `ready`.
[2026-02-26 22:52:58] [SUCCESS] [OmnipathR] UniProt (rest.uniprot.org): downloaded 20431 records
[2026-02-26 22:52:58] [TRACE] [OmnipathR] Translating complexes: 0 complexes in data.
[2026-02-26 22:52:58] [TRACE] [OmnipathR] 0 complexes after removing the ones mapping to more than 1 items in target identifier space.
[2026-02-26 22:52:58] [TRACE] [OmnipathR] Translated 0 complexes to 0.
[2026-02-26 22:52:58] [TRACE] [OmnipathR] 13774 rows before translation, 13774 uniprot_entry IDs in column `id_organism_a`.
[2026-02-26 22:52:58] [TRACE] [OmnipathR] 13774 rows after translation; translated 13523 `uniprot_entry` IDs in column `id_organism_a` to 13523 `uniprot` IDs in column `id_organism_a`.
[2026-02-26 22:52:58] [TRACE] [OmnipathR] ID translation table: from `uniprot_entry` to `uniprot`, using `uniprot`.
[2026-02-26 22:52:58] [TRACE] [OmnipathR] Creating ID mapping table from `id` to `accession`, for organism 10090 (only reviewed: TRUE)
[2026-02-26 22:52:58] [TRACE] [OmnipathR] Loading all UniProt records for organism 10090 (only reviewed: TRUE); fields: id,accession
[2026-02-26 22:52:58] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2026-02-26 22:52:58] [TRACE] [OmnipathR] Looking up in cache: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:10090%20AND%20reviewed:true`.
[2026-02-26 22:52:58] [INFO] [OmnipathR] Cache record does not exist: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:10090%20AND%20reviewed:true`
[2026-02-26 22:52:58] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:10090%20AND%20reviewed:true`.
[2026-02-26 22:52:58] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-26 22:52:58] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 22:52:58] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-26 22:52:58] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 22:52:58] [INFO] [OmnipathR] Cache item `43ea5f2cdaa9ac7e0e114371af97235cdddd776f` version 1: status changed from `unknown` to `started`.
[2026-02-26 22:52:58] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/43ea5f2cdaa9ac7e0e114371af97235cdddd776f-1.rds`.
[2026-02-26 22:52:58] [INFO] [OmnipathR] Retrieving URL: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:10090%20AND%20reviewed:true`
[2026-02-26 22:52:58] [TRACE] [OmnipathR] Attempt 1/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:10090%20AND%20reviewed:true`
[2026-02-26 22:52:58] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2026-02-26 22:52:58] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-26 22:52:58] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-02-26 22:52:59] [TRACE] [OmnipathR] HTTP v2 GET: status 200.
[2026-02-26 22:52:59] [TRACE] [OmnipathR] Downloaded 31 bytes in 0.50951s from rest.uniprot.org (60 bytes/s); Redirect: 0s, DNS look up: 0.001744s, Connection: 0.002513s, Pretransfer: 0.229035s, First byte at: 0.509435s
[2026-02-26 22:52:59] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; vary: accept,accept-encoding,x-uniprot-release,x-api-deployment-date, User-Agent, Accept-Encoding; cache-control: public, max-age=43200; content-type: text/plain;format=tsv; content-encoding: gzip; access-control-allow-credentials: true; access-control-expose-headers: Link, X-Total-Results, X-UniProt-Release, X-UniProt-Release-Date, X-API-Deployment-Date; x-api-deployment-date: 09-February-2026; strict-transport-security: max-age=31536000; includeSubDomains; date: Fri, 27 Feb 2026 03:52:59 GMT; access-control-max-age: 1728000; x-uniprot-release: 2026_01; access-control-allow-origin: *; accept-ranges: bytes; access-control-allow-methods: GET, PUT, POST, DELETE, PATCH, OPTIONS; access-control-allow-headers: DNT,Keep-Alive,User-Agent,X-Requested-With,If-Modified-Since,Cache-Control,Content-Type,Range,Authorization; x-uniprot-release-date: 28-January-2026
[2026-02-26 22:53:05] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/43ea5f2cdaa9ac7e0e114371af97235cdddd776f-1.rds`.
[2026-02-26 22:53:05] [INFO] [OmnipathR] Download ready [key=43ea5f2cdaa9ac7e0e114371af97235cdddd776f, version=1]
[2026-02-26 22:53:05] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-26 22:53:05] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 22:53:05] [INFO] [OmnipathR] Cache item `43ea5f2cdaa9ac7e0e114371af97235cdddd776f` version 1: status changed from `started` to `ready`.
[2026-02-26 22:53:05] [SUCCESS] [OmnipathR] UniProt (rest.uniprot.org): downloaded 17252 records
[2026-02-26 22:53:06] [TRACE] [OmnipathR] Translating complexes: 0 complexes in data.
[2026-02-26 22:53:06] [TRACE] [OmnipathR] 0 complexes after removing the ones mapping to more than 1 items in target identifier space.
[2026-02-26 22:53:06] [TRACE] [OmnipathR] Translated 0 complexes to 0.
[2026-02-26 22:53:06] [TRACE] [OmnipathR] 13774 rows before translation, 13773 uniprot_entry IDs in column `id_organism_b`.
[2026-02-26 22:53:06] [TRACE] [OmnipathR] 13774 rows after translation; translated 13226 `uniprot_entry` IDs in column `id_organism_b` to 13226 `uniprot` IDs in column `id_organism_b`.
[2026-02-26 22:53:06] [INFO] [OmnipathR] Loaded database `Orthologous Matrix (OMA) gene pairs`.
[2026-02-26 22:53:06] [TRACE] [OmnipathR] ID translation table: from `uniprot` to `genesymbol`, using `uniprot`.
[2026-02-26 22:53:06] [TRACE] [OmnipathR] Creating ID mapping table from `accession` to `gene_primary`, for organism 10090 (only reviewed: TRUE)
[2026-02-26 22:53:06] [TRACE] [OmnipathR] Loading all UniProt records for organism 10090 (only reviewed: TRUE); fields: accession,gene_primary
[2026-02-26 22:53:06] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2026-02-26 22:53:06] [TRACE] [OmnipathR] Looking up in cache: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:10090%20AND%20reviewed:true`.
[2026-02-26 22:53:06] [INFO] [OmnipathR] Cache record does not exist: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:10090%20AND%20reviewed:true`
[2026-02-26 22:53:06] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:10090%20AND%20reviewed:true`.
[2026-02-26 22:53:06] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-26 22:53:06] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 22:53:06] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-26 22:53:06] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 22:53:06] [INFO] [OmnipathR] Cache item `3ec84ba713c02573704adb50f1a94dab684df34b` version 1: status changed from `unknown` to `started`.
[2026-02-26 22:53:06] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/3ec84ba713c02573704adb50f1a94dab684df34b-1.rds`.
[2026-02-26 22:53:06] [INFO] [OmnipathR] Retrieving URL: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:10090%20AND%20reviewed:true`
[2026-02-26 22:53:06] [TRACE] [OmnipathR] Attempt 1/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:10090%20AND%20reviewed:true`
[2026-02-26 22:53:06] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2026-02-26 22:53:06] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-26 22:53:06] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-02-26 22:53:07] [TRACE] [OmnipathR] HTTP v2 GET: status 200.
[2026-02-26 22:53:07] [TRACE] [OmnipathR] Downloaded 43 bytes in 0.732842s from rest.uniprot.org (58 bytes/s); Redirect: 0s, DNS look up: 0.003771s, Connection: 0.00468s, Pretransfer: 0.456259s, First byte at: 0.732779s
[2026-02-26 22:53:07] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; vary: accept,accept-encoding,x-uniprot-release,x-api-deployment-date, User-Agent, Accept-Encoding; cache-control: public, max-age=43200; content-type: text/plain;format=tsv; content-encoding: gzip; access-control-allow-credentials: true; access-control-expose-headers: Link, X-Total-Results, X-UniProt-Release, X-UniProt-Release-Date, X-API-Deployment-Date; x-api-deployment-date: 09-February-2026; strict-transport-security: max-age=31536000; includeSubDomains; date: Fri, 27 Feb 2026 03:53:07 GMT; access-control-max-age: 1728000; x-uniprot-release: 2026_01; access-control-allow-origin: *; accept-ranges: bytes; access-control-allow-methods: GET, PUT, POST, DELETE, PATCH, OPTIONS; access-control-allow-headers: DNT,Keep-Alive,User-Agent,X-Requested-With,If-Modified-Since,Cache-Control,Content-Type,Range,Authorization; x-uniprot-release-date: 28-January-2026
[2026-02-26 22:53:13] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/3ec84ba713c02573704adb50f1a94dab684df34b-1.rds`.
[2026-02-26 22:53:13] [INFO] [OmnipathR] Download ready [key=3ec84ba713c02573704adb50f1a94dab684df34b, version=1]
[2026-02-26 22:53:13] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-26 22:53:13] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 22:53:13] [INFO] [OmnipathR] Cache item `3ec84ba713c02573704adb50f1a94dab684df34b` version 1: status changed from `started` to `ready`.
[2026-02-26 22:53:13] [SUCCESS] [OmnipathR] UniProt (rest.uniprot.org): downloaded 17252 records
[2026-02-26 22:53:13] [TRACE] [OmnipathR] Translating complexes: 0 complexes in data.
[2026-02-26 22:53:13] [TRACE] [OmnipathR] 0 complexes after removing the ones mapping to more than 1 items in target identifier space.
[2026-02-26 22:53:13] [TRACE] [OmnipathR] Translated 0 complexes to 0.
[2026-02-26 22:53:13] [TRACE] [OmnipathR] 163601 rows before translation, 12830 uniprot IDs in column `uniprot`.
[2026-02-26 22:53:13] [TRACE] [OmnipathR] 163601 rows after translation; translated 12830 `uniprot` IDs in column `uniprot` to 12748 `genesymbol` IDs in column `genesymbol`.
[2026-02-26 22:53:13] [TRACE] [OmnipathR] Processing args for OmniPath query
[2026-02-26 22:53:13] [TRACE] [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B,C,D],genesymbols=TRUE,organisms=9606,query_type=interactions,datasets=dorothea]
[2026-02-26 22:53:13] [TRACE] [OmnipathR] Organism(s): 9606
[2026-02-26 22:53:13] [TRACE] [OmnipathR] Orthology targets:
[2026-02-26 22:53:13] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-02-26 22:53:14] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-02-26 22:53:14] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-02-26 22:53:14] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-02-26 22:53:14] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-02-26 22:53:14] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-02-26 22:53:14] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-02-26 22:53:14] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2026-02-26 22:53:14] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-26 22:53:14] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-02-26 22:53:35] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2026-02-26 22:53:35] [TRACE] [OmnipathR] Downloaded 15.6 Kb in 21.838907s from omnipathdb.org (733 bytes/s); Redirect: 0s, DNS look up: 0.001423s, Connection: 0.002341s, Pretransfer: 0.213458s, First byte at: 21.838471s
[2026-02-26 22:53:35] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Fri, 27 Feb 2026 03:53:35 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Fri, 27 Feb 2026 04:53:35 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; Cache-Control: no-cache, no-store, must-revalidate; Pragma: no-cache; Expires: 0; Content-Encoding: gzip
[2026-02-26 22:53:40] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-02-26 22:53:40] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-26 22:53:40] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 22:53:40] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-26 22:53:40] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 22:53:40] [INFO] [OmnipathR] Cache item `46d37339bbc3f9a05bb89ccb79278cf1233f5cdf` version 1: status changed from `unknown` to `started`.
[2026-02-26 22:53:40] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/46d37339bbc3f9a05bb89ccb79278cf1233f5cdf-1.rds`.
[2026-02-26 22:53:42] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/46d37339bbc3f9a05bb89ccb79278cf1233f5cdf-1.rds`.
[2026-02-26 22:53:42] [INFO] [OmnipathR] Download ready [key=46d37339bbc3f9a05bb89ccb79278cf1233f5cdf, version=1]
[2026-02-26 22:53:42] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-26 22:53:42] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 22:53:42] [INFO] [OmnipathR] Cache item `46d37339bbc3f9a05bb89ccb79278cf1233f5cdf` version 1: status changed from `started` to `ready`.
[2026-02-26 22:53:54] [SUCCESS] [OmnipathR] Downloaded 278677 interactions.
[2026-02-26 22:54:05] [TRACE] [OmnipathR] Processing args for OmniPath query
[2026-02-26 22:54:05] [TRACE] [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B,C,D],genesymbols=TRUE,organisms=10090,query_type=interactions,datasets=dorothea]
[2026-02-26 22:54:05] [TRACE] [OmnipathR] Organism(s): 10090
[2026-02-26 22:54:05] [TRACE] [OmnipathR] Orthology targets:
[2026-02-26 22:54:05] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=10090&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-02-26 22:54:05] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=10090&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-02-26 22:54:05] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=10090&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-02-26 22:54:05] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=10090&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-02-26 22:54:05] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=10090&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-02-26 22:54:05] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=10090&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-02-26 22:54:05] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=10090&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-02-26 22:54:05] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2026-02-26 22:54:05] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-26 22:54:05] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-02-26 22:54:54] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2026-02-26 22:54:54] [TRACE] [OmnipathR] Downloaded 15.6 Kb in 48.358342s from omnipathdb.org (331 bytes/s); Redirect: 0s, DNS look up: 0.001485s, Connection: 0.002263s, Pretransfer: 0.210026s, First byte at: 48.357216s
[2026-02-26 22:54:54] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Fri, 27 Feb 2026 03:54:53 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Fri, 27 Feb 2026 04:54:53 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; Cache-Control: no-cache, no-store, must-revalidate; Pragma: no-cache; Expires: 0; Content-Encoding: gzip
[2026-02-26 22:54:58] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=10090&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2026-02-26 22:54:58] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-26 22:54:58] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 22:54:58] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-26 22:54:58] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 22:54:58] [INFO] [OmnipathR] Cache item `ff347dedf78ef5e38c9c6d8eed291fa901aa3791` version 1: status changed from `unknown` to `started`.
[2026-02-26 22:54:58] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/ff347dedf78ef5e38c9c6d8eed291fa901aa3791-1.rds`.
[2026-02-26 22:54:59] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/ff347dedf78ef5e38c9c6d8eed291fa901aa3791-1.rds`.
[2026-02-26 22:54:59] [INFO] [OmnipathR] Download ready [key=ff347dedf78ef5e38c9c6d8eed291fa901aa3791, version=1]
[2026-02-26 22:54:59] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-26 22:54:59] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 22:54:59] [INFO] [OmnipathR] Cache item `ff347dedf78ef5e38c9c6d8eed291fa901aa3791` version 1: status changed from `started` to `ready`.
[2026-02-26 22:55:07] [SUCCESS] [OmnipathR] Downloaded 249440 interactions.
[2026-02-26 22:55:17] [TRACE] [OmnipathR] Processing args for OmniPath query
[2026-02-26 22:55:17] [TRACE] [OmnipathR] Arguments for OmniPath query: [loops=TRUE,organisms=9606,genesymbols=TRUE,query_type=interactions,datasets=collectri]
[2026-02-26 22:55:17] [TRACE] [OmnipathR] Organism(s): 9606
[2026-02-26 22:55:17] [TRACE] [OmnipathR] Orthology targets:
[2026-02-26 22:55:17] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2026-02-26 22:55:17] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2026-02-26 22:55:17] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2026-02-26 22:55:17] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2026-02-26 22:55:17] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2026-02-26 22:55:17] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2026-02-26 22:55:17] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2026-02-26 22:55:17] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2026-02-26 22:55:17] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-26 22:55:17] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-02-26 22:55:23] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2026-02-26 22:55:23] [TRACE] [OmnipathR] Downloaded 15.6 Kb in 6.341478s from omnipathdb.org (2.5 Kb/s); Redirect: 0s, DNS look up: 0.020516s, Connection: 0.021264s, Pretransfer: 0.381337s, First byte at: 6.340919s
[2026-02-26 22:55:23] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Fri, 27 Feb 2026 03:55:23 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Fri, 27 Feb 2026 04:55:23 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; Cache-Control: no-cache, no-store, must-revalidate; Pragma: no-cache; Expires: 0; Content-Encoding: gzip
[2026-02-26 22:55:27] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2026-02-26 22:55:27] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-26 22:55:27] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 22:55:27] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-26 22:55:27] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 22:55:27] [INFO] [OmnipathR] Cache item `b10176737ba43d460b13709623189f3911123779` version 1: status changed from `unknown` to `started`.
[2026-02-26 22:55:27] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/b10176737ba43d460b13709623189f3911123779-1.rds`.
[2026-02-26 22:55:28] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/b10176737ba43d460b13709623189f3911123779-1.rds`.
[2026-02-26 22:55:28] [INFO] [OmnipathR] Download ready [key=b10176737ba43d460b13709623189f3911123779, version=1]
[2026-02-26 22:55:28] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-26 22:55:28] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 22:55:28] [INFO] [OmnipathR] Cache item `b10176737ba43d460b13709623189f3911123779` version 1: status changed from `started` to `ready`.
[2026-02-26 22:55:30] [SUCCESS] [OmnipathR] Downloaded 64979 interactions.
[2026-02-26 22:55:30] [TRACE] [OmnipathR] Processing args for OmniPath query
[2026-02-26 22:55:30] [TRACE] [OmnipathR] Arguments for OmniPath query: [genesymbols=TRUE,resources=CollecTRI,strict_evidences=TRUE,query_type=interactions,datasets=tf_mirna]
[2026-02-26 22:55:30] [TRACE] [OmnipathR] Organism(s): 9606
[2026-02-26 22:55:30] [TRACE] [OmnipathR] Orthology targets:
[2026-02-26 22:55:30] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-02-26 22:55:31] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 22:55:31] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2026-02-26 22:55:31] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2026-02-26 22:55:31] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2026-02-26 22:55:31] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2026-02-26 22:55:31] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2026-02-26 22:55:31] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2026-02-26 22:55:31] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2026-02-26 22:55:31] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2026-02-26 22:55:31] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2026-02-26 22:55:31] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2026-02-26 22:55:32] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2026-02-26 22:55:33] [TRACE] [OmnipathR] Downloaded 9.1 Kb in 1.258136s from omnipathdb.org (7.3 Kb/s); Redirect: 0s, DNS look up: 0.002005s, Connection: 0.003117s, Pretransfer: 0.360198s, First byte at: 1.257768s
[2026-02-26 22:55:33] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Fri, 27 Feb 2026 03:55:32 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Expires: Fri, 27 Feb 2026 04:55:32 GMT; Cache-Control: max-age=3600; X-Frame-Options: DENY; Cache-Control: no-cache, no-store, must-revalidate; Pragma: no-cache; Expires: 0; Content-Encoding: gzip
[2026-02-26 22:55:34] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2026-02-26 22:55:34] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-26 22:55:34] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 22:55:34] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-26 22:55:34] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 22:55:34] [INFO] [OmnipathR] Cache item `f7d34500401ba98803b7d2b26c48f64cee1eea1b` version 1: status changed from `unknown` to `started`.
[2026-02-26 22:55:34] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/f7d34500401ba98803b7d2b26c48f64cee1eea1b-1.rds`.
[2026-02-26 22:55:34] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/f7d34500401ba98803b7d2b26c48f64cee1eea1b-1.rds`.
[2026-02-26 22:55:34] [INFO] [OmnipathR] Download ready [key=f7d34500401ba98803b7d2b26c48f64cee1eea1b, version=1]
[2026-02-26 22:55:34] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2026-02-26 22:55:34] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 22:55:34] [INFO] [OmnipathR] Cache item `f7d34500401ba98803b7d2b26c48f64cee1eea1b` version 1: status changed from `started` to `ready`.
[2026-02-26 22:55:34] [TRACE] [OmnipathR] Converting JSON column `evidences` to list.
[2026-02-26 22:55:34] [TRACE] [OmnipathR] Restricting interaction records to datasets: tf_mirna; and resources: CollecTRI
[2026-02-26 22:55:34] [TRACE] [OmnipathR] Filtering evidence columns: positive, negative, directed, undirected; to datasets: tf_mirna; and resources: CollecTRI; excluding resources: none
[2026-02-26 22:55:35] [SUCCESS] [OmnipathR] Downloaded 207 interactions.
[2026-02-26 22:55:35] [TRACE] [OmnipathR] Processing args for OmniPath query
[2026-02-26 22:55:35] [TRACE] [OmnipathR] Arguments for OmniPath query: [loops=TRUE,organisms=9606,genesymbols=TRUE,query_type=interactions,datasets=collectri]
[2026-02-26 22:55:35] [TRACE] [OmnipathR] Organism(s): 9606
[2026-02-26 22:55:35] [TRACE] [OmnipathR] Orthology targets:
[2026-02-26 22:55:35] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2026-02-26 22:55:35] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/b10176737ba43d460b13709623189f3911123779-1.rds`.
[2026-02-26 22:55:35] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2026-02-26 22:55:37] [SUCCESS] [OmnipathR] Loaded 64979 interactions from cache.
[2026-02-26 22:55:37] [TRACE] [OmnipathR] Processing args for OmniPath query
[2026-02-26 22:55:37] [TRACE] [OmnipathR] Arguments for OmniPath query: [genesymbols=TRUE,resources=CollecTRI,strict_evidences=TRUE,query_type=interactions,datasets=tf_mirna]
[2026-02-26 22:55:37] [TRACE] [OmnipathR] Organism(s): 9606
[2026-02-26 22:55:37] [TRACE] [OmnipathR] Orthology targets:
[2026-02-26 22:55:37] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2026-02-26 22:55:38] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-02-26 22:55:39] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2026-02-26 22:55:39] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/f7d34500401ba98803b7d2b26c48f64cee1eea1b-1.rds`.
[2026-02-26 22:55:39] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2026-02-26 22:55:39] [TRACE] [OmnipathR] Converting JSON column `evidences` to list.
[2026-02-26 22:55:39] [TRACE] [OmnipathR] Restricting interaction records to datasets: tf_mirna; and resources: CollecTRI
[2026-02-26 22:55:39] [TRACE] [OmnipathR] Filtering evidence columns: positive, negative, directed, undirected; to datasets: tf_mirna; and resources: CollecTRI; excluding resources: none
[2026-02-26 22:55:39] [SUCCESS] [OmnipathR] Loaded 207 interactions from cache.
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Attaching package: 'dplyr'
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
[ FAIL 0 | WARN 9 | SKIP 0 | PASS 35 ]
[ FAIL 0 | WARN 9 | SKIP 0 | PASS 35 ]
>
> proc.time()
user system elapsed
188.447 25.581 434.497
decoupleR.Rcheck/decoupleR-Ex.timings
| name | user | system | elapsed | |
| check_corr | 0.075 | 0.026 | 0.102 | |
| convert_f_defaults | 0.056 | 0.013 | 0.070 | |
| decouple | 0 | 0 | 0 | |
| dot-fit_preprocessing | 0.024 | 0.000 | 0.024 | |
| extract_sets | 0.022 | 0.001 | 0.023 | |
| filt_minsize | 0.039 | 0.004 | 0.042 | |
| get_collectri | 30.149 | 2.534 | 61.045 | |