| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-11-20 12:03 -0500 (Thu, 20 Nov 2025).
| 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" | 4615 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.2 Patched (2025-11-05 r88990) -- "[Not] Part in a Rumble" | 4610 |
| kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble" | 4598 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4668 |
| 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 | TIMEOUT | |||||||||
| merida1 | macOS 12.7.6 Monterey / x86_64 | OK | OK | WARNINGS | OK |  | ||||||||
| kjohnson1 | macOS 13.7.5 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | ERROR | ||||||||||
|
To the developers/maintainers of the decoupleR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to [email protected]: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: 2025-11-18 02:50:22 -0500 (Tue, 18 Nov 2025) |
| EndedAt: 2025-11-18 03:30:22 -0500 (Tue, 18 Nov 2025) |
| EllapsedTime: 2400.8 seconds |
| RetCode: None |
| Status: TIMEOUT |
| 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
[2025-11-18 02:52:05] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-18 02:52:05] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-18 02:52:05] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-11-18 02:52:05] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2025-11-18 02:52:05] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-11-17
[2025-11-18 02:52:05] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.2; ; 2025-11-17 22:04:20 UTC; unix
[2025-11-18 02:52:05] [INFO] [OmnipathR] Package `OmnipathR` version: 3.18.2
[2025-11-18 02:52:05] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-11-18 02:52:06] [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=2025-11-18; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2025-11-18 02:52:06] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.22-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-11-18 02:52:06] [INFO] [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); annotate 1.88.0(2025-11-17); AnnotationDbi 1.72.0(2025-11-17); AUCell 1.32.0(2025-11-17); backports 1.5.0(2024-05-23); beachmat 2.26.0(2025-11-17); Biobase 2.70.0(2025-11-17); BiocGenerics 0.56.0(2025-11-17); BiocParallel 1.44.0(2025-11-17); BiocSingular 1.26.1(2025-11-17); Biostrings 2.78.0(2025-11-17); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.3(2025-08-18); chromote 0.5.1(2025-04-24); cli 3.6.5(2025-04-23); codetools 0.2-20(2024-03-31); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); data.table 1.17.8(2025-07-10); DBI 1.2.3(2024-06-02); decoupleR 2.16.0(2025-11-17); DelayedArray 0.36.0(2025-11-17); DelayedMatrixStats 1.32.0(2025-11-17); digest 0.6.38(2025-11-12); dplyr 1.1.4(2023-11-17); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); GenomicRanges 1.62.0(2025-11-17); glue 1.8.0(2024-09-30); graph 1.88.0(2025-11-17); GSEABase 1.72.0(2025-11-17); GSVA 2.4.1(2025-11-17); h5mread 1.2.0(2025-11-17); HDF5Array 1.38.0(2025-11-17); hms 1.1.4(2025-10-17); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.2.1(2025-10-27); IRanges 2.44.0(2025-11-17); irlba 2.3.5.1(2022-10-03); jsonlite 2.0.0(2025-03-27); KEGGREST 1.50.0(2025-11-17); knitr 1.50(2025-03-16); later 1.4.4(2025-08-27); lattice 0.22-7(2025-04-02); lifecycle 1.0.4(2023-11-07); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); 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(2025-11-17); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); OmnipathR 3.18.2(2025-11-17); otel 0.2.0(2025-08-29); parallelly 1.45.1(2025-07-24); 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 1.2.0(2025-11-04); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.1.0(2025-07-02); readr 2.1.6(2025-11-14); readxl 1.4.5(2025-03-07); rhdf5 2.54.0(2025-11-17); rhdf5filters 1.22.0(2025-11-17); Rhdf5lib 1.32.0(2025-11-17); rjson 0.2.23(2024-09-16); rlang 1.1.6(2025-04-11); rmarkdown 2.30(2025-09-28); RSQLite 2.4.4(2025-11-10); rsvd 1.0.5(2021-04-16); rvest 1.0.5(2025-08-29); S4Arrays 1.10.0(2025-11-17); S4Vectors 0.48.0(2025-11-17); ScaledMatrix 1.18.0(2025-11-17); Seqinfo 1.0.0(2025-11-17); sessioninfo 1.2.3(2025-02-05); SingleCellExperiment 1.32.0(2025-11-17); SparseArray 1.10.2(2025-11-17); sparseMatrixStats 1.22.0(2025-11-17); SpatialExperiment 1.20.0(2025-11-17); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); SummarizedExperiment 1.40.0(2025-11-17); tibble 3.3.0(2025-06-08); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); xfun 0.54(2025-10-30); XML 3.99-0.20(2025-11-08); xml2 1.5.0(2025-11-17); xtable 1.8-4(2019-04-21); XVector 0.50.0(2025-11-17); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2025-11-18 02:52:06] [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
[2025-11-18 02:52:06] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-11-18 02:52:06] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-11-18 02:52:06] [TRACE] [OmnipathR] Contains 9 files.
[2025-11-18 02:52:06] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-11-18 02:52:06] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-18 02:52:06] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-18 02:52:06] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-11-18 02:52:06] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2025-11-18 02:52:06] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-11-18 02:52:06] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-18 02:52:06] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-11-18 02:52:06] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-18 02:52:06] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-11-18 02:52:06] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-18 02:52:06] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-11-18 02:52:06] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-18 02:52:06] [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_resource
> ### Title: Wrapper to access resources inside Omnipath. This wrapper allows
> ### to easily query different prior knowledge resources. To check
> ### available resources run 'decoupleR::show_resources()'. For more
> ### information visit the official website for Omnipath.
> ### Aliases: get_resource
>
> ### ** Examples
>
> df <- decoupleR::get_resource('SIGNOR')
Warning in OmnipathR::get_annotation_resources() :
'OmnipathR::get_annotation_resources' is deprecated.
Use 'annotation_resources' instead.
See help("Deprecated")
[2025-11-18 03:17:04] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
Warning in readLines(con = path, encoding = encoding) :
incomplete final line found on 'https://omnipathdb.org/resources'
[2025-11-18 03:17:06] [TRACE] [OmnipathR] JSON validation successful: TRUE
Warning in OmnipathR::import_omnipath_annotations(resources = name, ..., :
'OmnipathR::import_omnipath_annotations' is deprecated.
Use 'annotations' instead.
See help("Deprecated")
[2025-11-18 03:17:06] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-11-18 03:17:06] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=SIGNOR,query_type=annotations]
[2025-11-18 03:17:06] [TRACE] [OmnipathR] Organism(s): 9606
[2025-11-18 03:17:06] [TRACE] [OmnipathR] Orthology targets:
[2025-11-18 03:17:06] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
Warning in file(con, "r") :
URL 'https://omnipathdb.org/resources': status was 'SSL connect error'
[2025-11-18 03:17:13] [WARN] [OmnipathR] Accessing `SIGNOR` as a static table: this is not the recommended way to access OmniPath data; it is only a backup plan for situations when our server or your computer is experiencing issues.
[2025-11-18 03:17:13] [ERROR] [OmnipathR] [decoupleR] Failed to download annotation resource `SIGNOR` from OmniPath. For more information, see the OmnipathR log.
Error in value[[3L]](cond) :
[decoupleR] Failed to download annotation resource `SIGNOR` from OmniPath. For more information, see the OmnipathR log.
Calls: <Anonymous> ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
get_collectri 30.015 2.527 446.839
get_dorothea 23.948 2.137 699.570
get_progeny 3.403 0.738 326.830
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
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 163
[2025-11-18 03:18:17] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-18 03:18:17] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-18 03:18:17] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-11-18 03:18:17] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2025-11-18 03:18:17] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-11-17
[2025-11-18 03:18:17] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.2; ; 2025-11-17 22:04:20 UTC; unix
[2025-11-18 03:18:17] [INFO] [OmnipathR] Package `OmnipathR` version: 3.18.2
[2025-11-18 03:18:17] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-11-18 03:18:17] [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=2025-11-18; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2025-11-18 03:18:17] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.22-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-11-18 03:18:18] [INFO] [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); annotate 1.88.0(2025-11-17); AnnotationDbi 1.72.0(2025-11-17); AUCell 1.32.0(2025-11-17); backports 1.5.0(2024-05-23); beachmat 2.26.0(2025-11-17); Biobase 2.70.0(2025-11-17); BiocGenerics 0.56.0(2025-11-17); BiocParallel 1.44.0(2025-11-17); BiocSingular 1.26.1(2025-11-17); Biostrings 2.78.0(2025-11-17); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); brio 1.1.5(2024-04-24); broom 1.0.10(2025-09-13); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.3(2025-08-18); class 7.3-23(2025-01-01); cli 3.6.5(2025-04-23); codetools 0.2-20(2024-03-31); cowplot 1.2.0(2025-07-07); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); data.table 1.17.8(2025-07-10); DBI 1.2.3(2024-06-02); decoupleR 2.16.0(2025-11-17); DelayedArray 0.36.0(2025-11-17); DelayedMatrixStats 1.32.0(2025-11-17); desc 1.4.3(2023-12-10); digest 0.6.38(2025-11-12); dplyr 1.1.4(2023-11-17); e1071 1.7-16(2024-09-16); evaluate 1.0.5(2025-08-27); farver 2.1.2(2024-05-13); fastmap 1.2.0(2024-05-15); fastmatch 1.1-6(2024-12-23); fgsea 1.36.0(2025-11-17); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); GenomicRanges 1.62.0(2025-11-17); ggplot2 4.0.1(2025-11-14); glue 1.8.0(2024-09-30); graph 1.88.0(2025-11-17); GSEABase 1.72.0(2025-11-17); GSVA 2.4.1(2025-11-17); gtable 0.3.6(2024-10-25); h5mread 1.2.0(2025-11-17); HDF5Array 1.38.0(2025-11-17); hms 1.1.4(2025-10-17); htmltools 0.5.8.1(2024-04-04); htmlwidgets 1.6.4(2023-12-06); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.2.1(2025-10-27); IRanges 2.44.0(2025-11-17); irlba 2.3.5.1(2022-10-03); jsonlite 2.0.0(2025-03-27); KEGGREST 1.50.0(2025-11-17); kernlab 0.9-33(2024-08-13); KernSmooth 2.23-26(2025-01-01); knitr 1.50(2025-03-16); later 1.4.4(2025-08-27); lattice 0.22-7(2025-04-02); lazyeval 0.2.2(2019-03-15); lifecycle 1.0.4(2023-11-07); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); 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(2025-11-17); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); mixtools 2.0.0.1(2025-03-08); nlme 3.1-168(2025-03-31); OmnipathR 3.18.2(2025-11-17); parallelly 1.45.1(2025-07-24); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); plotly 4.11.0(2025-06-19); png 0.1-8(2022-11-29); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); proxy 0.4-27(2022-06-09); purrr 1.2.0(2025-11-04); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); ranger 0.17.0(2024-11-08); rappdirs 0.3.3(2021-01-31); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.1.0(2025-07-02); readr 2.1.6(2025-11-14); readxl 1.4.5(2025-03-07); rhdf5 2.54.0(2025-11-17); rhdf5filters 1.22.0(2025-11-17); Rhdf5lib 1.32.0(2025-11-17); rjson 0.2.23(2024-09-16); rlang 1.1.6(2025-04-11); rmarkdown 2.30(2025-09-28); rpart 4.1.24(2025-01-07); RSQLite 2.4.4(2025-11-10); rsvd 1.0.5(2021-04-16); rvest 1.0.5(2025-08-29); S4Arrays 1.10.0(2025-11-17); S4Vectors 0.48.0(2025-11-17); S7 0.2.1(2025-11-14); ScaledMatrix 1.18.0(2025-11-17); scales 1.4.0(2025-04-24); segmented 2.1-4(2025-02-28); Seqinfo 1.0.0(2025-11-17); sessioninfo 1.2.3(2025-02-05); SingleCellExperiment 1.32.0(2025-11-17); SparseArray 1.10.2(2025-11-17); sparseMatrixStats 1.22.0(2025-11-17); SpatialExperiment 1.20.0(2025-11-17); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); SummarizedExperiment 1.40.0(2025-11-17); survival 3.8-3(2024-12-17); testthat 3.3.0(2025-11-13); tibble 3.3.0(2025-06-08); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); viper 1.44.0(2025-11-17); viridisLite 0.4.2(2023-05-02); waldo 0.6.2(2025-07-11); withr 3.0.2(2024-10-28); xfun 0.54(2025-10-30); XML 3.99-0.20(2025-11-08); xml2 1.5.0(2025-11-17); xtable 1.8-4(2019-04-21); XVector 0.50.0(2025-11-17); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2025-11-18 03:18:18] [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
[2025-11-18 03:18:18] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-11-18 03:18:18] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-11-18 03:18:18] [TRACE] [OmnipathR] Contains 8 files.
[2025-11-18 03:18:18] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-11-18 03:18:18] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-18 03:18:18] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-18 03:18:18] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-11-18 03:18:18] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2025-11-18 03:18:18] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-11-18 03:18:18] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-18 03:18:18] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-11-18 03:18:18] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-18 03:18:18] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-11-18 03:18:18] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-18 03:18:18] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.22-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-11-18 03:18:18] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-18 03:18:18] [TRACE] [OmnipathR] Cache locked: FALSE
[2025-11-18 03:18:18] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-11-18 03:18:25] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-18 03:18:25] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-11-18 03:18:31] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-18 03:18:31] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2025-11-18 03:18:31] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-18 03:18:31] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-18 03:18:31] [INFO] [OmnipathR] Looking up in cache `https://rescued.omnipathdb.org/ensembl-species.html`: key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, no version available.
[2025-11-18 03:18:31] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-18 03:18:31] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-18 03:18:31] [INFO] [OmnipathR] Created new version for cache record 67b4943ae7fd646a03b760aefa99fe6c41ab2887: version 1.
[2025-11-18 03:18:31] [TRACE] [OmnipathR] Cache file path: /home/biocbuild/.cache/OmnipathR/67b4943ae7fd646a03b760aefa99fe6c41ab2887-1.html
[2025-11-18 03:18:31] [INFO] [OmnipathR] Retrieving URL: `https://rescued.omnipathdb.org/ensembl-species.html`
[2025-11-18 03:18:31] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`.
[2025-11-18 03:18:31] [TRACE] [OmnipathR] Attempt 1/3: `https://rescued.omnipathdb.org/ensembl-species.html`
[2025-11-18 03:18:31] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://rescued.omnipathdb.org/ensembl-species.html`.
[2025-11-18 03:18:31] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-11-18 03:18:31] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-11-18 03:18:31] [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]
[2025-11-18 03:18:31] [TRACE] [OmnipathR] HTTP headers: [User-Agent=Mozilla/5.0 (X11; Linux x86_64; rv:134.0) Gecko/20100101 Firefox/134.0]
[2025-11-18 03:18:31] [TRACE] [OmnipathR] Sending HTTP request.
[2025-11-18 03:18:42] [TRACE] [OmnipathR] HTTP 200 (OK)
[2025-11-18 03:18:42] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2025-11-18 03:18:42] [TRACE] [OmnipathR] Downloaded 39.9 Kb in 11.667057s from rescued.omnipathdb.org (3.4 Kb/s); Redirect: 0s, DNS look up: 0.003873s, Connection: 0.004756s, Pretransfer: 1.59011s, First byte at: 7.64945s
[2025-11-18 03:18:43] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 18 Nov 2025 08:18:32 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: Tue, 18 Nov 2025 09:18:32 GMT; Cache-Control: max-age=3600; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-11-18 03:18:43] [TRACE] [OmnipathR] Response headers: [Server=nginx,Date=Tue, 18 Nov 2025 08:18:32 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=Tue, 18 Nov 2025 09:18:32 GMT,Cache-Control=max-age=3600,Cache-Control=public,X-Frame-Options=DENY,Content-Encoding=gzip]
[2025-11-18 03:18:44] [INFO] [OmnipathR] Download ready [key=67b4943ae7fd646a03b760aefa99fe6c41ab2887, version=1]
[2025-11-18 03:18:44] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-18 03:18:44] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-18 03:18:44] [INFO] [OmnipathR] Cache item `67b4943ae7fd646a03b760aefa99fe6c41ab2887` version 1: status changed from `unknown` to `ready`.
[2025-11-18 03:18:44] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2025-11-18 03:18:44] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2025-11-18 03:18:44] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2025-11-18 03:18:44] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2025-11-18 03:18:44] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-18 03:18:44] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-18 03:18:44] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-18 03:18:44] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-18 03:18:44] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2025-11-18 03:18:44] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-11-18 03:18:44] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2025-11-18 03:18:44] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2025-11-18 03:18:44] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2025-11-18 03:18:44] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-11-18 03:18:44] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-11-18 03:18:45] [TRACE] [OmnipathR] HTTP v2 GET: status 200.
[2025-11-18 03:18:45] [TRACE] [OmnipathR] Downloaded 3.8 Kb in 0.861725s from omabrowser.org (4.4 Kb/s); Redirect: 0s, DNS look up: 0.001648s, Connection: 0.003209s, Pretransfer: 0.573615s, First byte at: 0.861442s
[2025-11-18 03:18:45] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; date: Tue, 18 Nov 2025 08:18:45 GMT; server: nginx; strict-transport-security: max-age=31536000; includeSubDomains; content-type: text/plain; charset=UTF-8; last-modified: Wed, 20 Nov 2024 10:20:02 GMT; etag: W/"673db7d2-6517f"; access-control-allow-origin: *; content-encoding: gzip
[2025-11-18 03:18:57] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-11-18 03:18:57] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1]
[2025-11-18 03:18:57] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-18 03:18:57] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-18 03:18:57] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.
[2025-11-18 03:18:57] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2025-11-18 03:18:57] [TRACE] [OmnipathR] Looking up in cache: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`.
[2025-11-18 03:18:57] [INFO] [OmnipathR] Cache record does not exist: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2025-11-18 03:18:57] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`.
[2025-11-18 03:18:57] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-18 03:18:57] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-18 03:18:57] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-18 03:18:57] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-18 03:18:57] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `unknown` to `started`.
[2025-11-18 03:18:57] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`.
[2025-11-18 03:18:57] [INFO] [OmnipathR] Retrieving URL: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2025-11-18 03:18:57] [TRACE] [OmnipathR] Attempt 1/3: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`
[2025-11-18 03:22:51] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`.
[2025-11-18 03:22:51] [INFO] [OmnipathR] Download ready [key=56ad6544dc07a2222fa6013d8d83e6e5a35fdf33, version=1]
[2025-11-18 03:22:51] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-18 03:22:51] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-18 03:22:52] [INFO] [OmnipathR] Cache item `56ad6544dc07a2222fa6013d8d83e6e5a35fdf33` version 1: status changed from `started` to `ready`.
[2025-11-18 03:22:52] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`.
[2025-11-18 03:22:52] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-11-18 03:22:52] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=TFcensus,query_type=annotations]
[2025-11-18 03:22:52] [TRACE] [OmnipathR] Organism(s): 9606
[2025-11-18 03:22:52] [TRACE] [OmnipathR] Orthology targets:
[2025-11-18 03:22:52] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-11-18 03:22:56] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-18 03:22:56] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2025-11-18 03:22:56] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2025-11-18 03:22:56] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2025-11-18 03:22:56] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2025-11-18 03:22:56] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2025-11-18 03:22:56] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2025-11-18 03:22:56] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2025-11-18 03:22:56] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2025-11-18 03:22:56] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-11-18 03:22:56] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-11-18 03:22:59] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2025-11-18 03:22:59] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 2.774963s from omnipathdb.org (5.6 Kb/s); Redirect: 0s, DNS look up: 0.0018s, Connection: 0.002664s, Pretransfer: 1.912372s, First byte at: 2.773952s
[2025-11-18 03:22:59] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 18 Nov 2025 08:22:58 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Tue, 18 Nov 2025 09:22:58 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-11-18 03:23:01] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2025-11-18 03:23:01] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-18 03:23:01] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-18 03:23:01] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-18 03:23:01] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-18 03:23:01] [INFO] [OmnipathR] Cache item `6f000d9b5edd9832b1c28754d1c3d9449c1c7490` version 1: status changed from `unknown` to `started`.
[2025-11-18 03:23:01] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/6f000d9b5edd9832b1c28754d1c3d9449c1c7490-1.rds`.
[2025-11-18 03:23:01] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/6f000d9b5edd9832b1c28754d1c3d9449c1c7490-1.rds`.
[2025-11-18 03:23:01] [INFO] [OmnipathR] Download ready [key=6f000d9b5edd9832b1c28754d1c3d9449c1c7490, version=1]
[2025-11-18 03:23:01] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-11-18 03:23:01] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-18 03:23:01] [INFO] [OmnipathR] Cache item `6f000d9b5edd9832b1c28754d1c3d9449c1c7490` version 1: status changed from `started` to `ready`.
[2025-11-18 03:23:01] [SUCCESS] [OmnipathR] Downloaded 3497 annotation records.
[2025-11-18 03:23:01] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-11-18 03:23:10] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-18 03:23:11] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-11-18 03:23:11] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=PROGENy,query_type=annotations]
[2025-11-18 03:23:11] [TRACE] [OmnipathR] Organism(s): 9606
[2025-11-18 03:23:11] [TRACE] [OmnipathR] Orthology targets:
[2025-11-18 03:23:11] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-11-18 03:23:16] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-11-18 03:23:16] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-11-18 03:23:16] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-11-18 03:23:16] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-11-18 03:23:16] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-11-18 03:23:16] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-11-18 03:23:16] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-11-18 03:23:16] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-11-18 03:23:16] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2025-11-18 03:23:16] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-11-18 03:23:16] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-11-18 03:23:19] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2025-11-18 03:23:19] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 2.401911s from omnipathdb.org (6.5 Kb/s); Redirect: 0s, DNS look up: 0.001554s, Connection: 0.002299s, Pretransfer: 0.782193s, First byte at: 2.401421s
[2025-11-18 03:23:19] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 18 Nov 2025 08:23:17 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Tue, 18 Nov 2025 09:23:17 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-11-18 03:23:34] [WARN] [OmnipathR] Failed to download `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` (attempt 1/3); error: Failure when receiving data from the peer [omnipathdb.org]:
GnuTLS recv error (-9): Error decoding the received TLS packet.
[2025-11-18 03:23:39] [TRACE] [OmnipathR] Attempt 2/3: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-11-18 03:23:39] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2025-11-18 03:23:39] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-11-18 03:23:39] [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]
[2025-11-18 03:23:43] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2025-11-18 03:23:43] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 3.120788s from omnipathdb.org (5 Kb/s); Redirect: 0s, DNS look up: 0.00211s, Connection: 0.003013s, Pretransfer: 0.667989s, First byte at: 3.120326s
[2025-11-18 03:23:43] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 18 Nov 2025 08:23:40 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Tue, 18 Nov 2025 09:23:40 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-11-18 03:24:07] [WARN] [OmnipathR] Failed to download `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` (attempt 2/3); error: Failure when receiving data from the peer [omnipathdb.org]:
GnuTLS recv error (-9): Error decoding the received TLS packet.
[2025-11-18 03:24:12] [TRACE] [OmnipathR] Attempt 3/3: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-11-18 03:24:12] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2025-11-18 03:24:12] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-11-18 03:24:12] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-11-18 03:24:14] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2025-11-18 03:24:14] [TRACE] [OmnipathR] Downloaded 15.7 Kb in 2.176608s from omnipathdb.org (7.2 Kb/s); Redirect: 0s, DNS look up: 0.001811s, Connection: 0.002634s, Pretransfer: 1.413209s, First byte at: 2.175765s
[2025-11-18 03:24:14] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 18 Nov 2025 08:24:13 GMT; Content-Type: text/plain; charset=utf-8; Transfer-Encoding: chunked; Connection: keep-alive; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Tue, 18 Nov 2025 09:24:13 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip
[2025-11-18 03:28:01] [ERROR] [OmnipathR] Failed to download `https://omnipathdb.org/annotations?resources=PROGENy&license=academic` (attempt 3/3); error: Failure when receiving data from the peer [omnipathdb.org]:
GnuTLS recv error (-9): Error decoding the received TLS packet.
[2025-11-18 03:28:01] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2025-11-18 03:28:01] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-11-17
[2025-11-18 03:28:01] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.2; ; 2025-11-17 22:04:20 UTC; unix
[2025-11-18 03:28:01] [INFO] [OmnipathR] Package `OmnipathR` version: 3.18.2
[2025-11-18 03:28:01] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-11-18 03:28:02] [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=2025-11-18; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2025-11-18 03:28:02] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.22-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-11-18 03:28:02] [INFO] [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); annotate 1.88.0(2025-11-17); AnnotationDbi 1.72.0(2025-11-17); AUCell 1.32.0(2025-11-17); backports 1.5.0(2024-05-23); beachmat 2.26.0(2025-11-17); Biobase 2.70.0(2025-11-17); BiocGenerics 0.56.0(2025-11-17); BiocParallel 1.44.0(2025-11-17); BiocSingular 1.26.1(2025-11-17); Biostrings 2.78.0(2025-11-17); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); brio 1.1.5(2024-04-24); broom 1.0.10(2025-09-13); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.3(2025-08-18); class 7.3-23(2025-01-01); cli 3.6.5(2025-04-23); codetools 0.2-20(2024-03-31); cowplot 1.2.0(2025-07-07); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); data.table 1.17.8(2025-07-10); DBI 1.2.3(2024-06-02); decoupleR 2.16.0(2025-11-17); DelayedArray 0.36.0(2025-11-17); DelayedMatrixStats 1.32.0(2025-11-17); desc 1.4.3(2023-12-10); digest 0.6.38(2025-11-12); dplyr 1.1.4(2023-11-17); e1071 1.7-16(2024-09-16); evaluate 1.0.5(2025-08-27); farver 2.1.2(2024-05-13); fastmap 1.2.0(2024-05-15); fastmatch 1.1-6(2024-12-23); fgsea 1.36.0(2025-11-17); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); GenomicRanges 1.62.0(2025-11-17); ggplot2 4.0.1(2025-11-14); glue 1.8.0(2024-09-30); graph 1.88.0(2025-11-17); GSEABase 1.72.0(2025-11-17); GSVA 2.4.1(2025-11-17); gtable 0.3.6(2024-10-25); h5mread 1.2.0(2025-11-17); HDF5Array 1.38.0(2025-11-17); hms 1.1.4(2025-10-17); htmltools 0.5.8.1(2024-04-04); htmlwidgets 1.6.4(2023-12-06); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.2.1(2025-10-27); IRanges 2.44.0(2025-11-17); irlba 2.3.5.1(2022-10-03); jsonlite 2.0.0(2025-03-27); KEGGREST 1.50.0(2025-11-17); kernlab 0.9-33(2024-08-13); KernSmooth 2.23-26(2025-01-01); knitr 1.50(2025-03-16); later 1.4.4(2025-08-27); lattice 0.22-7(2025-04-02); lazyeval 0.2.2(2019-03-15); lifecycle 1.0.4(2023-11-07); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); 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(2025-11-17); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); mixtools 2.0.0.1(2025-03-08); nlme 3.1-168(2025-03-31); OmnipathR 3.18.2(2025-11-17); parallelly 1.45.1(2025-07-24); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); plotly 4.11.0(2025-06-19); png 0.1-8(2022-11-29); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); proxy 0.4-27(2022-06-09); purrr 1.2.0(2025-11-04); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); ranger 0.17.0(2024-11-08); rappdirs 0.3.3(2021-01-31); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.1.0(2025-07-02); readr 2.1.6(2025-11-14); readxl 1.4.5(2025-03-07); rhdf5 2.54.0(2025-11-17); rhdf5filters 1.22.0(2025-11-17); Rhdf5lib 1.32.0(2025-11-17); rjson 0.2.23(2024-09-16); rlang 1.1.6(2025-04-11); rmarkdown 2.30(2025-09-28); rpart 4.1.24(2025-01-07); RSQLite 2.4.4(2025-11-10); rsvd 1.0.5(2021-04-16); rvest 1.0.5(2025-08-29); S4Arrays 1.10.0(2025-11-17); S4Vectors 0.48.0(2025-11-17); S7 0.2.1(2025-11-14); ScaledMatrix 1.18.0(2025-11-17); scales 1.4.0(2025-04-24); segmented 2.1-4(2025-02-28); selectr 0.4-2(2019-11-20); Seqinfo 1.0.0(2025-11-17); sessioninfo 1.2.3(2025-02-05); SingleCellExperiment 1.32.0(2025-11-17); SparseArray 1.10.2(2025-11-17); sparseMatrixStats 1.22.0(2025-11-17); SpatialExperiment 1.20.0(2025-11-17); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); SummarizedExperiment 1.40.0(2025-11-17); survival 3.8-3(2024-12-17); testthat 3.3.0(2025-11-13); tibble 3.3.0(2025-06-08); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); viper 1.44.0(2025-11-17); viridisLite 0.4.2(2023-05-02); vroom 1.6.6(2025-09-19); waldo 0.6.2(2025-07-11); withr 3.0.2(2024-10-28); xfun 0.54(2025-10-30); XML 3.99-0.20(2025-11-08); xml2 1.5.0(2025-11-17); xtable 1.8-4(2019-04-21); XVector 0.50.0(2025-11-17); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2025-11-18 03:28:02] [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
[2025-11-18 03:28:03] [WARN] [OmnipathR] Failed to download: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`; error: Failure when receiving data from the peer [omnipathdb.org]:
GnuTLS recv error (-9): Error decoding the received TLS packet.
[2025-11-18 03:28:03] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2025-11-18 03:28:03] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-11-17
[2025-11-18 03:28:03] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.2; ; 2025-11-17 22:04:20 UTC; unix
[2025-11-18 03:28:03] [INFO] [OmnipathR] Package `OmnipathR` version: 3.18.2
[2025-11-18 03:28:03] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-11-18 03:28:04] [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=C; collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-11-18; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2025-11-18 03:28:04] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.22-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-11-18 03:28:04] [INFO] [OmnipathR] Loaded packages: abind 1.4-8(2024-09-12); annotate 1.88.0(2025-11-17); AnnotationDbi 1.72.0(2025-11-17); AUCell 1.32.0(2025-11-17); backports 1.5.0(2024-05-23); beachmat 2.26.0(2025-11-17); Biobase 2.70.0(2025-11-17); BiocGenerics 0.56.0(2025-11-17); BiocParallel 1.44.0(2025-11-17); BiocSingular 1.26.1(2025-11-17); Biostrings 2.78.0(2025-11-17); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.2.4(2023-03-17); brio 1.1.5(2024-04-24); broom 1.0.10(2025-09-13); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.3(2025-08-18); class 7.3-23(2025-01-01); cli 3.6.5(2025-04-23); codetools 0.2-20(2024-03-31); cowplot 1.2.0(2025-07-07); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); data.table 1.17.8(2025-07-10); DBI 1.2.3(2024-06-02); decoupleR 2.16.0(2025-11-17); DelayedArray 0.36.0(2025-11-17); DelayedMatrixStats 1.32.0(2025-11-17); desc 1.4.3(2023-12-10); digest 0.6.38(2025-11-12); dplyr 1.1.4(2023-11-17); e1071 1.7-16(2024-09-16); evaluate 1.0.5(2025-08-27); farver 2.1.2(2024-05-13); fastmap 1.2.0(2024-05-15); fastmatch 1.1-6(2024-12-23); fgsea 1.36.0(2025-11-17); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); GenomicRanges 1.62.0(2025-11-17); ggplot2 4.0.1(2025-11-14); glue 1.8.0(2024-09-30); graph 1.88.0(2025-11-17); GSEABase 1.72.0(2025-11-17); GSVA 2.4.1(2025-11-17); gtable 0.3.6(2024-10-25); h5mread 1.2.0(2025-11-17); HDF5Array 1.38.0(2025-11-17); hms 1.1.4(2025-10-17); htmltools 0.5.8.1(2024-04-04); htmlwidgets 1.6.4(2023-12-06); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.2.1(2025-10-27); IRanges 2.44.0(2025-11-17); irlba 2.3.5.1(2022-10-03); jsonlite 2.0.0(2025-03-27); KEGGREST 1.50.0(2025-11-17); kernlab 0.9-33(2024-08-13); KernSmooth 2.23-26(2025-01-01); knitr 1.50(2025-03-16); later 1.4.4(2025-08-27); lattice 0.22-7(2025-04-02); lazyeval 0.2.2(2019-03-15); lifecycle 1.0.4(2023-11-07); logger 0.4.1(2025-09-11); lubridate 1.9.4(2024-12-08); 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(2025-11-17); matrixStats 1.5.0(2025-01-07); memoise 2.0.1(2021-11-26); mixtools 2.0.0.1(2025-03-08); nlme 3.1-168(2025-03-31); OmnipathR 3.18.2(2025-11-17); parallelly 1.45.1(2025-07-24); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); plotly 4.11.0(2025-06-19); png 0.1-8(2022-11-29); prettyunits 1.2.0(2023-09-24); progress 1.2.3(2023-12-06); proxy 0.4-27(2022-06-09); purrr 1.2.0(2025-11-04); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); ranger 0.17.0(2024-11-08); rappdirs 0.3.3(2021-01-31); RColorBrewer 1.1-3(2022-04-03); Rcpp 1.1.0(2025-07-02); readr 2.1.6(2025-11-14); readxl 1.4.5(2025-03-07); rhdf5 2.54.0(2025-11-17); rhdf5filters 1.22.0(2025-11-17); Rhdf5lib 1.32.0(2025-11-17); rjson 0.2.23(2024-09-16); rlang 1.1.6(2025-04-11); rmarkdown 2.30(2025-09-28); rpart 4.1.24(2025-01-07); RSQLite 2.4.4(2025-11-10); rsvd 1.0.5(2021-04-16); rvest 1.0.5(2025-08-29); S4Arrays 1.10.0(2025-11-17); S4Vectors 0.48.0(2025-11-17); S7 0.2.1(2025-11-14); ScaledMatrix 1.18.0(2025-11-17); scales 1.4.0(2025-04-24); segmented 2.1-4(2025-02-28); selectr 0.4-2(2019-11-20); Seqinfo 1.0.0(2025-11-17); sessioninfo 1.2.3(2025-02-05); SingleCellExperiment 1.32.0(2025-11-17); SparseArray 1.10.2(2025-11-17); sparseMatrixStats 1.22.0(2025-11-17); SpatialExperiment 1.20.0(2025-11-17); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); SummarizedExperiment 1.40.0(2025-11-17); survival 3.8-3(2024-12-17); testthat 3.3.0(2025-11-13); tibble 3.3.0(2025-06-08); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); viper 1.44.0(2025-11-17); viridisLite 0.4.2(2023-05-02); vroom 1.6.6(2025-09-19); waldo 0.6.2(2025-07-11); withr 3.0.2(2024-10-28); xfun 0.54(2025-10-30); XML 3.99-0.20(2025-11-08); xml2 1.5.0(2025-11-17); xtable 1.8-4(2019-04-21); XVector 0.50.0(2025-11-17); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2025-11-18 03:28:04] [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
[2025-11-18 03:28:04] [TRACE] [OmnipathR] Attempting `http://no-tls.omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-11-18 03:28:04] [INFO] [OmnipathR] Retrieving URL: `http://no-tls.omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-11-18 03:28:04] [TRACE] [OmnipathR] Attempt 1/3: `http://no-tls.omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-11-18 03:28:04] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2025-11-18 03:28:04] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-11-18 03:28:04] [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]
[2025-11-18 03:28:12] [TRACE] [OmnipathR] HTTP v1 GET: status 200.
[2025-11-18 03:28:12] [TRACE] [OmnipathR] Downloaded 1.4 Kb in 8.510991s from no-tls.omnipathdb.org (162 bytes/s); Redirect: 0s, DNS look up: 0.020956s, Connection: 0.021832s, Pretransfer: 0.021868s, First byte at: 8.510905s
[2025-11-18 03:28:12] [TRACE] [OmnipathR] HTTP headers: HTTP/1.1 200 OK; Server: nginx; Date: Tue, 18 Nov 2025 08:28:04 GMT; Cache-Control: max-age=3600; Access-Control-Allow-Origin: *; Expires: Tue, 18 Nov 2025 09:28:04 GMT; Cache-Control: public; X-Frame-Options: DENY; Content-Encoding: gzip; Transfer-Encoding: chunked; Content-Type: text/plain; charset=utf-8; Via: 1.1 phswsa6.partners.org:80 (Cisco-WSA/15.2.0-164); Connection: keep-alive
decoupleR.Rcheck/decoupleR-Ex.timings
| name | user | system | elapsed | |
| check_corr | 0.071 | 0.013 | 0.085 | |
| convert_f_defaults | 0.045 | 0.001 | 0.045 | |
| decouple | 0.001 | 0.000 | 0.001 | |
| dot-fit_preprocessing | 0.020 | 0.014 | 0.035 | |
| extract_sets | 0.022 | 0.001 | 0.023 | |
| filt_minsize | 0.039 | 0.005 | 0.043 | |
| get_collectri | 30.015 | 2.527 | 446.839 | |
| get_dorothea | 23.948 | 2.137 | 699.570 | |
| get_profile_of | 0 | 0 | 0 | |
| get_progeny | 3.403 | 0.738 | 326.830 | |