Pau Badia-i-Mompel
| Snapshot Date: 2025-02-18 13:40 -0500 (Tue, 18 Feb 2025) |
| git_url: https://git.bioconductor.org/packages/decoupleR |
| git_branch: devel |
| git_last_commit: 1d86763 |
| git_last_commit_date: 2024-10-29 11:00:29 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-02-19 11:40 -0500 (Wed, 19 Feb 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" | 4720 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences" | 4482 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2025-01-22 r87618) -- "Unsuffered Consequences" | 4493 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" | 4446 |
| 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 521/2295 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| decoupleR 2.13.0 (landing page) Pau Badia-i-Mompel
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
|
To the developers/maintainers of the decoupleR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/decoupleR.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: decoupleR |
| Version: 2.13.0 |
| Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:decoupleR.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings decoupleR_2.13.0.tar.gz |
| StartedAt: 2025-02-18 21:21:29 -0500 (Tue, 18 Feb 2025) |
| EndedAt: 2025-02-18 21:35:05 -0500 (Tue, 18 Feb 2025) |
| EllapsedTime: 816.1 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: decoupleR.Rcheck |
| Warnings: 1 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:decoupleR.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings decoupleR_2.13.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/decoupleR.Rcheck’
* using R Under development (unstable) (2025-01-20 r87609)
* 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 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘decoupleR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘decoupleR’ version ‘2.13.0’
* 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
[2025-02-18 21:22:01] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 21:22:01] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-18 21:22:01] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-02-18 21:22:01] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2025-02-18 21:22:01] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-02-18
[2025-02-18 21:22:01] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-02-18 20:07:33 UTC; unix
[2025-02-18 21:22:01] [INFO] [OmnipathR] Package `OmnipathR` version: 3.15.9
[2025-02-18 21:22:01] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21
[2025-02-18 21:22:02] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-01-20 r87609); os=Ubuntu 24.04.2 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-02-18; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.5.57 @ /usr/local/bin/quarto]
[2025-02-18 21:22:02] [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-3.21-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-02-18 21:22:02] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2025-02-18 21:22:02] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-02-18 21:22:02] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-02-18 21:22:02] [TRACE] [OmnipathR] Contains 8 files.
[2025-02-18 21:22:02] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-02-18 21:22:02] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 21:22:02] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-18 21:22:02] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-02-18 21:22:02] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2025-02-18 21:22:02] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-02-18 21:22:02] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-18 21:22:02] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-02-18 21:22:02] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-18 21:22:02] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-02-18 21:22:02] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-18 21:22:02] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-02-18 21:22:02] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-18 21:22:02] [TRACE] [OmnipathR] Cache locked: FALSE
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link(s) in Rd file 'run_gsva.Rd':
‘GSVA::gsva’ ‘GeneSetCollection’
Non-topic package-anchored link(s) in Rd file 'pipe.Rd':
‘[magrittr:pipe]{%>%}’
See section 'Cross-references' in the 'Writing R Extensions' manual.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
run_gsva.Rd: GSVA::gsva, GeneSetCollection
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
run_fgsea 27.129 0.640 27.790
get_dorothea 21.325 0.853 24.796
run_aucell 10.147 2.018 12.207
get_collectri 8.281 0.683 15.820
get_progeny 5.943 0.298 13.568
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING, 1 NOTE
See
‘/home/biocbuild/bbs-3.21-bioc/meat/decoupleR.Rcheck/00check.log’
for details.
decoupleR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL decoupleR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’ * installing *source* package ‘decoupleR’ ... ** this is package ‘decoupleR’ version ‘2.13.0’ ** 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 Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(decoupleR)
>
> test_check("decoupleR")
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[2025-02-18 21:25:10] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 21:25:10] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-18 21:25:10] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-02-18 21:25:10] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2025-02-18 21:25:10] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-02-18
[2025-02-18 21:25:10] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-02-18 20:07:33 UTC; unix
[2025-02-18 21:25:10] [INFO] [OmnipathR] Package `OmnipathR` version: 3.15.9
[2025-02-18 21:25:10] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21
[2025-02-18 21:25:11] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-01-20 r87609); os=Ubuntu 24.04.2 LTS; system=x86_64, linux-gnu; ui=X11; language=C; collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-02-18; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.5.57 @ /usr/local/bin/quarto]
[2025-02-18 21:25:11] [INFO] [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.21-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-02-18 21:25:11] [INFO] [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2025-02-18 21:25:11] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-02-18 21:25:11] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-02-18 21:25:11] [TRACE] [OmnipathR] Contains 8 files.
[2025-02-18 21:25:11] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-02-18 21:25:11] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 21:25:11] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-18 21:25:11] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-02-18 21:25:11] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2025-02-18 21:25:11] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-02-18 21:25:11] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-18 21:25:11] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-02-18 21:25:11] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-18 21:25:11] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-02-18 21:25:11] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-18 21:25:11] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-02-18 21:25:11] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-18 21:25:11] [TRACE] [OmnipathR] Cache locked: FALSE
[2025-02-18 21:25:12] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-02-18 21:25:12] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-18 21:25:13] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-02-18 21:25:13] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-18 21:25:13] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2025-02-18 21:25:13] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 21:25:13] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-18 21:25:13] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, no version available.
[2025-02-18 21:25:13] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 21:25:13] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-18 21:25:13] [INFO] [OmnipathR] Created new version for cache record 7332486db7400730697234bad76ca0c8e4d00799: version 1.
[2025-02-18 21:25:13] [TRACE] [OmnipathR] Cache file path: /home/biocbuild/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2025-02-18 21:25:13] [INFO] [OmnipathR] Retrieving URL: `https://www.ensembl.org/info/about/species.html`
[2025-02-18 21:25:13] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`.
[2025-02-18 21:25:13] [TRACE] [OmnipathR] Attempt 1/3: `https://www.ensembl.org/info/about/species.html`
[2025-02-18 21:25:13] [TRACE] [OmnipathR] Preparing httr2 request.
[2025-02-18 21:25:13] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-18 21:25:13] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-18 21:25:13] [TRACE] [OmnipathR] Sending HTTP request.
[2025-02-18 21:25:14] [TRACE] [OmnipathR] HTTP 200
[2025-02-18 21:25:14] [TRACE] [OmnipathR] Downloaded 30.9 Kb in 1.016108s from www.ensembl.org (30.4 Kb/s); Redirect: 0.824497s, DNS look up: 0.00666s, Connection: 0.008221s, Pretransfer: 0.662262s, First byte at: 0.965955s
[2025-02-18 21:25:15] [INFO] [OmnipathR] Download ready [key=7332486db7400730697234bad76ca0c8e4d00799, version=1]
[2025-02-18 21:25:15] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 21:25:15] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-18 21:25:15] [INFO] [OmnipathR] Cache item `7332486db7400730697234bad76ca0c8e4d00799` version 1: status changed from `unknown` to `ready`.
[2025-02-18 21:25:16] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2025-02-18 21:25:16] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2025-02-18 21:25:16] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2025-02-18 21:25:16] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2025-02-18 21:25:16] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 21:25:16] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-18 21:25:16] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 21:25:16] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-18 21:25:16] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2025-02-18 21:25:16] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-02-18 21:25:16] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2025-02-18 21:25:16] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2025-02-18 21:25:16] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-18 21:25:16] [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=TRUE,ssl_verifyhost=TRUE]
[2025-02-18 21:25:17] [TRACE] [OmnipathR] Downloaded 108 Kb in 1.049867s from omabrowser.org (102.9 Kb/s); Redirect: 0s, DNS look up: 0.002339s, Connection: 0.002991s, Pretransfer: 0.335534s, First byte at: 0.419522s
[2025-02-18 21:25:18] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-02-18 21:25:18] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1]
[2025-02-18 21:25:18] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 21:25:18] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-18 21:25:18] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.
[2025-02-18 21:25:18] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`.
[2025-02-18 21:25:18] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-02-18 21:25:18] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=TFcensus,query_type=annotations]
[2025-02-18 21:25:18] [TRACE] [OmnipathR] Organism(s): 9606
[2025-02-18 21:25:18] [TRACE] [OmnipathR] Orthology targets:
[2025-02-18 21:25:19] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-02-18 21:25:19] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-18 21:25:19] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2025-02-18 21:25:19] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2025-02-18 21:25:19] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2025-02-18 21:25:19] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2025-02-18 21:25:19] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2025-02-18 21:25:19] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2025-02-18 21:25:19] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2025-02-18 21:25:19] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-18 21:25:19] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-18 21:25:19] [TRACE] [OmnipathR] Downloaded 29.2 Kb in 0.397431s from omnipathdb.org (73.4 Kb/s); Redirect: 0s, DNS look up: 0.001621s, Connection: 0.0023s, Pretransfer: 0.163675s, First byte at: 0.320665s
[2025-02-18 21:25:21] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=TFcensus&license=academic`
[2025-02-18 21:25:21] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 21:25:21] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-18 21:25:21] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 21:25:21] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-18 21:25:21] [INFO] [OmnipathR] Cache item `6f000d9b5edd9832b1c28754d1c3d9449c1c7490` version 1: status changed from `unknown` to `started`.
[2025-02-18 21:25:21] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/6f000d9b5edd9832b1c28754d1c3d9449c1c7490-1.rds`.
[2025-02-18 21:25:21] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/6f000d9b5edd9832b1c28754d1c3d9449c1c7490-1.rds`.
[2025-02-18 21:25:21] [INFO] [OmnipathR] Download ready [key=6f000d9b5edd9832b1c28754d1c3d9449c1c7490, version=1]
[2025-02-18 21:25:21] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 21:25:21] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-18 21:25:21] [INFO] [OmnipathR] Cache item `6f000d9b5edd9832b1c28754d1c3d9449c1c7490` version 1: status changed from `started` to `ready`.
[2025-02-18 21:25:21] [SUCCESS] [OmnipathR] Downloaded 3099 annotation records.
[2025-02-18 21:25:22] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-02-18 21:25:22] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-18 21:25:22] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-02-18 21:25:22] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=PROGENy,query_type=annotations]
[2025-02-18 21:25:22] [TRACE] [OmnipathR] Organism(s): 9606
[2025-02-18 21:25:22] [TRACE] [OmnipathR] Orthology targets:
[2025-02-18 21:25:23] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-02-18 21:25:23] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-18 21:25:23] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-02-18 21:25:23] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-02-18 21:25:23] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-02-18 21:25:23] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-02-18 21:25:23] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-02-18 21:25:23] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-02-18 21:25:23] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-02-18 21:25:23] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-18 21:25:23] [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=TRUE,ssl_verifyhost=TRUE]
[2025-02-18 21:25:31] [TRACE] [OmnipathR] Downloaded 8.9 Mb in 7.343905s from omnipathdb.org (1.2 Mb/s); Redirect: 0s, DNS look up: 0.002119s, Connection: 0.002875s, Pretransfer: 0.170114s, First byte at: 0.334915s
[2025-02-18 21:25:32] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-02-18 21:25:32] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 21:25:32] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-18 21:25:32] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 21:25:32] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-18 21:25:32] [INFO] [OmnipathR] Cache item `3492392585ba05414edfae46801492076437d7e7` version 1: status changed from `unknown` to `started`.
[2025-02-18 21:25:32] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`.
[2025-02-18 21:25:35] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`.
[2025-02-18 21:25:35] [INFO] [OmnipathR] Download ready [key=3492392585ba05414edfae46801492076437d7e7, version=1]
[2025-02-18 21:25:35] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 21:25:35] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-18 21:25:35] [INFO] [OmnipathR] Cache item `3492392585ba05414edfae46801492076437d7e7` version 1: status changed from `started` to `ready`.
[2025-02-18 21:25:35] [SUCCESS] [OmnipathR] Downloaded 700239 annotation records.
[2025-02-18 21:25:37] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-02-18 21:25:37] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-18 21:25:37] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-02-18 21:25:37] [TRACE] [OmnipathR] Arguments for OmniPath query: [wide=TRUE,resources=PROGENy,query_type=annotations]
[2025-02-18 21:25:37] [TRACE] [OmnipathR] Organism(s): 9606
[2025-02-18 21:25:37] [TRACE] [OmnipathR] Orthology targets:
[2025-02-18 21:25:38] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-02-18 21:25:38] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-18 21:25:38] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-02-18 21:25:39] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/3492392585ba05414edfae46801492076437d7e7-1.rds`.
[2025-02-18 21:25:39] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/annotations?resources=PROGENy&license=academic`
[2025-02-18 21:25:39] [SUCCESS] [OmnipathR] Loaded 700239 annotation records from cache.
[2025-02-18 21:25:41] [INFO] [OmnipathR] Loading database `Orthologous Matrix (OMA) gene pairs`.
[2025-02-18 21:25:41] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2025-02-18 21:25:41] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2025-02-18 21:25:42] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-02-18 21:25:42] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2025-02-18 21:25:42] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2025-02-18 21:25:42] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-02-18 21:25:42] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2025-02-18 21:25:42] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/api/pairs/HUMAN/MOUSE/?format=tsv&xrefs=UniProtKB%2FSwissProt&per_page=2000000`.
[2025-02-18 21:25:42] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/api/pairs/HUMAN/MOUSE/?format=tsv&xrefs=UniProtKB%2FSwissProt&per_page=2000000`
[2025-02-18 21:25:42] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/api/pairs/HUMAN/MOUSE/?format=tsv&xrefs=UniProtKB%2FSwissProt&per_page=2000000`.
[2025-02-18 21:25:42] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 21:25:42] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-18 21:25:42] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 21:25:42] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-18 21:25:42] [INFO] [OmnipathR] Cache item `8f45b25c384d814c7de210e7ca40b7e35894e4f1` version 1: status changed from `unknown` to `started`.
[2025-02-18 21:25:42] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/8f45b25c384d814c7de210e7ca40b7e35894e4f1-1.rds`.
[2025-02-18 21:25:42] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/api/pairs/HUMAN/MOUSE/?format=tsv&xrefs=UniProtKB%2FSwissProt&per_page=2000000`
[2025-02-18 21:25:42] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/api/pairs/HUMAN/MOUSE/?format=tsv&xrefs=UniProtKB%2FSwissProt&per_page=2000000`
[2025-02-18 21:25:42] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-18 21:25:42] [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=TRUE,ssl_verifyhost=TRUE]
[2025-02-18 21:26:10] [TRACE] [OmnipathR] Downloaded 1.1 Mb in 28.30214s from omabrowser.org (41 Kb/s); Redirect: 0s, DNS look up: 0.001878s, Connection: 0.002506s, Pretransfer: 0.172105s, First byte at: 26.64148s
[2025-02-18 21:26:11] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/8f45b25c384d814c7de210e7ca40b7e35894e4f1-1.rds`.
[2025-02-18 21:26:11] [INFO] [OmnipathR] Download ready [key=8f45b25c384d814c7de210e7ca40b7e35894e4f1, version=1]
[2025-02-18 21:26:11] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 21:26:11] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-18 21:26:11] [INFO] [OmnipathR] Cache item `8f45b25c384d814c7de210e7ca40b7e35894e4f1` version 1: status changed from `started` to `ready`.
[2025-02-18 21:26:11] [TRACE] [OmnipathR] ID translation table: from `uniprot_entry` to `uniprot`, using `uniprot`.
[2025-02-18 21:26:11] [TRACE] [OmnipathR] Creating ID mapping table from `id` to `accession`, for organism 9606 (only reviewed: TRUE)
[2025-02-18 21:26:11] [TRACE] [OmnipathR] Loading all UniProt records for organism 9606 (only reviewed: TRUE); fields: id,accession
[2025-02-18 21:26:11] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2025-02-18 21:26:11] [TRACE] [OmnipathR] Looking up in cache: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:9606%20AND%20reviewed:true`.
[2025-02-18 21:26:11] [INFO] [OmnipathR] Cache record does not exist: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:9606%20AND%20reviewed:true`
[2025-02-18 21:26:11] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:9606%20AND%20reviewed:true`.
[2025-02-18 21:26:11] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 21:26:11] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-18 21:26:12] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 21:26:12] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-18 21:26:12] [INFO] [OmnipathR] Cache item `6558a1824894a625b8e3f80538cd3aa6e8a44379` version 1: status changed from `unknown` to `started`.
[2025-02-18 21:26:12] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/6558a1824894a625b8e3f80538cd3aa6e8a44379-1.rds`.
[2025-02-18 21:26:12] [INFO] [OmnipathR] Retrieving URL: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:9606%20AND%20reviewed:true`
[2025-02-18 21:26:12] [TRACE] [OmnipathR] Attempt 1/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:9606%20AND%20reviewed:true`
[2025-02-18 21:26:12] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-18 21:26:12] [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=TRUE,ssl_verifyhost=TRUE]
[2025-02-18 21:28:35] [TRACE] [OmnipathR] Downloaded 128.7 Kb in 2m 22.968952s from rest.uniprot.org (921 bytes/s); Redirect: 0s, DNS look up: 0.00396s, Connection: 0.004637s, Pretransfer: 0.576058s, First byte at: 1.954293s
[2025-02-18 21:28:36] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/6558a1824894a625b8e3f80538cd3aa6e8a44379-1.rds`.
[2025-02-18 21:28:36] [INFO] [OmnipathR] Download ready [key=6558a1824894a625b8e3f80538cd3aa6e8a44379, version=1]
[2025-02-18 21:28:36] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 21:28:36] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-18 21:28:36] [INFO] [OmnipathR] Cache item `6558a1824894a625b8e3f80538cd3aa6e8a44379` version 1: status changed from `started` to `ready`.
[2025-02-18 21:28:36] [SUCCESS] [OmnipathR] UniProt (rest.uniprot.org): downloaded 20417 records
[2025-02-18 21:28:36] [TRACE] [OmnipathR] Translating complexes: 0 complexes in data.
[2025-02-18 21:28:36] [TRACE] [OmnipathR] 0 complexes after removing the ones mapping to more than 1 items in target identifier space.
[2025-02-18 21:28:36] [TRACE] [OmnipathR] Translated 0 complexes to 0.
[2025-02-18 21:28:36] [TRACE] [OmnipathR] 13774 rows before translation, 13774 uniprot_entry IDs in column `id_organism_a`.
[2025-02-18 21:28:36] [TRACE] [OmnipathR] 13774 rows after translation; translated 13570 `uniprot_entry` IDs in column `id_organism_a` to 13570 `uniprot` IDs in column `id_organism_a`.
[2025-02-18 21:28:36] [TRACE] [OmnipathR] ID translation table: from `uniprot_entry` to `uniprot`, using `uniprot`.
[2025-02-18 21:28:36] [TRACE] [OmnipathR] Creating ID mapping table from `id` to `accession`, for organism 10090 (only reviewed: TRUE)
[2025-02-18 21:28:36] [TRACE] [OmnipathR] Loading all UniProt records for organism 10090 (only reviewed: TRUE); fields: id,accession
[2025-02-18 21:28:36] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2025-02-18 21:28:36] [TRACE] [OmnipathR] Looking up in cache: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:10090%20AND%20reviewed:true`.
[2025-02-18 21:28:36] [INFO] [OmnipathR] Cache record does not exist: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:10090%20AND%20reviewed:true`
[2025-02-18 21:28:36] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:10090%20AND%20reviewed:true`.
[2025-02-18 21:28:36] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 21:28:36] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-18 21:28:36] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 21:28:36] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-18 21:28:36] [INFO] [OmnipathR] Cache item `43ea5f2cdaa9ac7e0e114371af97235cdddd776f` version 1: status changed from `unknown` to `started`.
[2025-02-18 21:28:36] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/43ea5f2cdaa9ac7e0e114371af97235cdddd776f-1.rds`.
[2025-02-18 21:28:36] [INFO] [OmnipathR] Retrieving URL: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:10090%20AND%20reviewed:true`
[2025-02-18 21:28:36] [TRACE] [OmnipathR] Attempt 1/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=id,accession&query=organism_id:10090%20AND%20reviewed:true`
[2025-02-18 21:28:36] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-18 21:28:36] [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=TRUE,ssl_verifyhost=TRUE]
[2025-02-18 21:28:48] [TRACE] [OmnipathR] Downloaded 110.4 Kb in 11.803589s from rest.uniprot.org (9.4 Kb/s); Redirect: 0s, DNS look up: 0.003783s, Connection: 0.004556s, Pretransfer: 0.492399s, First byte at: 0.981505s
[2025-02-18 21:28:50] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/43ea5f2cdaa9ac7e0e114371af97235cdddd776f-1.rds`.
[2025-02-18 21:28:50] [INFO] [OmnipathR] Download ready [key=43ea5f2cdaa9ac7e0e114371af97235cdddd776f, version=1]
[2025-02-18 21:28:50] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 21:28:50] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-18 21:28:50] [INFO] [OmnipathR] Cache item `43ea5f2cdaa9ac7e0e114371af97235cdddd776f` version 1: status changed from `started` to `ready`.
[2025-02-18 21:28:50] [SUCCESS] [OmnipathR] UniProt (rest.uniprot.org): downloaded 17228 records
[2025-02-18 21:28:50] [TRACE] [OmnipathR] Translating complexes: 0 complexes in data.
[2025-02-18 21:28:50] [TRACE] [OmnipathR] 0 complexes after removing the ones mapping to more than 1 items in target identifier space.
[2025-02-18 21:28:50] [TRACE] [OmnipathR] Translated 0 complexes to 0.
[2025-02-18 21:28:50] [TRACE] [OmnipathR] 13774 rows before translation, 13773 uniprot_entry IDs in column `id_organism_b`.
[2025-02-18 21:28:50] [TRACE] [OmnipathR] 13774 rows after translation; translated 13273 `uniprot_entry` IDs in column `id_organism_b` to 13273 `uniprot` IDs in column `id_organism_b`.
[2025-02-18 21:28:50] [INFO] [OmnipathR] Loaded database `Orthologous Matrix (OMA) gene pairs`.
[2025-02-18 21:28:50] [TRACE] [OmnipathR] ID translation table: from `uniprot` to `genesymbol`, using `uniprot`.
[2025-02-18 21:28:50] [TRACE] [OmnipathR] Creating ID mapping table from `accession` to `gene_primary`, for organism 10090 (only reviewed: TRUE)
[2025-02-18 21:28:50] [TRACE] [OmnipathR] Loading all UniProt records for organism 10090 (only reviewed: TRUE); fields: accession,gene_primary
[2025-02-18 21:28:50] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2025-02-18 21:28:50] [TRACE] [OmnipathR] Looking up in cache: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:10090%20AND%20reviewed:true`.
[2025-02-18 21:28:50] [INFO] [OmnipathR] Cache record does not exist: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:10090%20AND%20reviewed:true`
[2025-02-18 21:28:50] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:10090%20AND%20reviewed:true`.
[2025-02-18 21:28:50] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 21:28:50] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-18 21:28:50] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 21:28:50] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-18 21:28:50] [INFO] [OmnipathR] Cache item `3ec84ba713c02573704adb50f1a94dab684df34b` version 1: status changed from `unknown` to `started`.
[2025-02-18 21:28:50] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/3ec84ba713c02573704adb50f1a94dab684df34b-1.rds`.
[2025-02-18 21:28:50] [INFO] [OmnipathR] Retrieving URL: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:10090%20AND%20reviewed:true`
[2025-02-18 21:28:50] [TRACE] [OmnipathR] Attempt 1/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:10090%20AND%20reviewed:true`
[2025-02-18 21:28:50] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-18 21:28:50] [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=TRUE,ssl_verifyhost=TRUE]
[2025-02-18 21:30:38] [WARN] [OmnipathR] Failed to download `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:10090%20AND%20reviewed:true` (attempt 1/3); error: Stream error in the HTTP/2 framing layer [rest.uniprot.org]: HTTP/2 stream 1 was not closed cleanly: INTERNAL_ERROR (err 2)
[2025-02-18 21:30:43] [TRACE] [OmnipathR] Attempt 2/3: `https://rest.uniprot.org/uniprotkb/stream?format=tsv&fields=accession,gene_primary&query=organism_id:10090%20AND%20reviewed:true`
[2025-02-18 21:30:43] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-18 21:30:43] [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=TRUE,ssl_verifyhost=TRUE]
[2025-02-18 21:30:55] [TRACE] [OmnipathR] Downloaded 110.4 Kb in 12.129257s from rest.uniprot.org (9.1 Kb/s); Redirect: 0s, DNS look up: 0.002045s, Connection: 0.00293s, Pretransfer: 0.4921s, First byte at: 1.218412s
[2025-02-18 21:30:58] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/3ec84ba713c02573704adb50f1a94dab684df34b-1.rds`.
[2025-02-18 21:30:58] [INFO] [OmnipathR] Download ready [key=3ec84ba713c02573704adb50f1a94dab684df34b, version=1]
[2025-02-18 21:30:58] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 21:30:58] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-18 21:30:58] [INFO] [OmnipathR] Cache item `3ec84ba713c02573704adb50f1a94dab684df34b` version 1: status changed from `started` to `ready`.
[2025-02-18 21:30:58] [SUCCESS] [OmnipathR] UniProt (rest.uniprot.org): downloaded 17228 records
[2025-02-18 21:30:59] [TRACE] [OmnipathR] Translating complexes: 0 complexes in data.
[2025-02-18 21:30:59] [TRACE] [OmnipathR] 0 complexes after removing the ones mapping to more than 1 items in target identifier space.
[2025-02-18 21:30:59] [TRACE] [OmnipathR] Translated 0 complexes to 0.
[2025-02-18 21:30:59] [TRACE] [OmnipathR] 164184 rows before translation, 12877 uniprot IDs in column `uniprot`.
[2025-02-18 21:30:59] [TRACE] [OmnipathR] 164184 rows after translation; translated 12877 `uniprot` IDs in column `uniprot` to 12790 `genesymbol` IDs in column `genesymbol`.
[2025-02-18 21:30:59] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-02-18 21:30:59] [TRACE] [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B,C,D],genesymbols=TRUE,organisms=9606,query_type=interactions,datasets=dorothea]
[2025-02-18 21:30:59] [TRACE] [OmnipathR] Organism(s): 9606
[2025-02-18 21:30:59] [TRACE] [OmnipathR] Orthology targets:
[2025-02-18 21:30:59] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2025-02-18 21:30:59] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2025-02-18 21:30:59] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2025-02-18 21:30:59] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2025-02-18 21:30:59] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2025-02-18 21:30:59] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2025-02-18 21:30:59] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2025-02-18 21:30:59] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-18 21:30:59] [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=TRUE,ssl_verifyhost=TRUE]
[2025-02-18 21:31:03] [TRACE] [OmnipathR] Downloaded 3.3 Mb in 3.566823s from omnipathdb.org (954.7 Kb/s); Redirect: 0s, DNS look up: 0.004207s, Connection: 0.00502s, Pretransfer: 0.329662s, First byte at: 0.487852s
[2025-02-18 21:31:05] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=9606&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2025-02-18 21:31:05] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 21:31:05] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-18 21:31:05] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 21:31:05] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-18 21:31:05] [INFO] [OmnipathR] Cache item `46d37339bbc3f9a05bb89ccb79278cf1233f5cdf` version 1: status changed from `unknown` to `started`.
[2025-02-18 21:31:05] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/46d37339bbc3f9a05bb89ccb79278cf1233f5cdf-1.rds`.
[2025-02-18 21:31:06] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/46d37339bbc3f9a05bb89ccb79278cf1233f5cdf-1.rds`.
[2025-02-18 21:31:06] [INFO] [OmnipathR] Download ready [key=46d37339bbc3f9a05bb89ccb79278cf1233f5cdf, version=1]
[2025-02-18 21:31:06] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 21:31:06] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-18 21:31:06] [INFO] [OmnipathR] Cache item `46d37339bbc3f9a05bb89ccb79278cf1233f5cdf` version 1: status changed from `started` to `ready`.
[2025-02-18 21:31:15] [SUCCESS] [OmnipathR] Downloaded 278830 interactions.
[2025-02-18 21:31:24] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-02-18 21:31:24] [TRACE] [OmnipathR] Arguments for OmniPath query: [dorothea_levels=[A,B,C,D],genesymbols=TRUE,organisms=10090,query_type=interactions,datasets=dorothea]
[2025-02-18 21:31:24] [TRACE] [OmnipathR] Organism(s): 10090
[2025-02-18 21:31:24] [TRACE] [OmnipathR] Orthology targets:
[2025-02-18 21:31:24] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=10090&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2025-02-18 21:31:24] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=10090&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2025-02-18 21:31:24] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=10090&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2025-02-18 21:31:24] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=10090&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2025-02-18 21:31:24] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=10090&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2025-02-18 21:31:24] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=10090&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2025-02-18 21:31:24] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=10090&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2025-02-18 21:31:24] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-18 21:31:24] [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=TRUE,ssl_verifyhost=TRUE]
[2025-02-18 21:31:28] [TRACE] [OmnipathR] Downloaded 2.9 Mb in 3.016583s from omnipathdb.org (972.1 Kb/s); Redirect: 0s, DNS look up: 0.001778s, Connection: 0.002392s, Pretransfer: 0.321618s, First byte at: 0.478148s
[2025-02-18 21:31:29] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=dorothea&organisms=10090&dorothea_levels=A,B,C,D&fields=sources,references,curation_effort,dorothea_level&license=academic`
[2025-02-18 21:31:29] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 21:31:29] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-18 21:31:29] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 21:31:29] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-18 21:31:29] [INFO] [OmnipathR] Cache item `ff347dedf78ef5e38c9c6d8eed291fa901aa3791` version 1: status changed from `unknown` to `started`.
[2025-02-18 21:31:29] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/ff347dedf78ef5e38c9c6d8eed291fa901aa3791-1.rds`.
[2025-02-18 21:31:30] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/ff347dedf78ef5e38c9c6d8eed291fa901aa3791-1.rds`.
[2025-02-18 21:31:30] [INFO] [OmnipathR] Download ready [key=ff347dedf78ef5e38c9c6d8eed291fa901aa3791, version=1]
[2025-02-18 21:31:30] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 21:31:30] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-18 21:31:30] [INFO] [OmnipathR] Cache item `ff347dedf78ef5e38c9c6d8eed291fa901aa3791` version 1: status changed from `started` to `ready`.
[2025-02-18 21:31:38] [SUCCESS] [OmnipathR] Downloaded 234298 interactions.
[2025-02-18 21:31:46] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-02-18 21:31:46] [TRACE] [OmnipathR] Arguments for OmniPath query: [loops=TRUE,organisms=9606,genesymbols=TRUE,query_type=interactions,datasets=collectri]
[2025-02-18 21:31:46] [TRACE] [OmnipathR] Organism(s): 9606
[2025-02-18 21:31:46] [TRACE] [OmnipathR] Orthology targets:
[2025-02-18 21:31:46] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2025-02-18 21:31:46] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2025-02-18 21:31:46] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2025-02-18 21:31:46] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2025-02-18 21:31:46] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2025-02-18 21:31:46] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2025-02-18 21:31:46] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2025-02-18 21:31:46] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-18 21:31:46] [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=TRUE,ssl_verifyhost=TRUE]
[2025-02-18 21:31:48] [TRACE] [OmnipathR] Downloaded 1.5 Mb in 1.965489s from omnipathdb.org (758.3 Kb/s); Redirect: 0s, DNS look up: 0.00222s, Connection: 0.002858s, Pretransfer: 0.161612s, First byte at: 0.315921s
[2025-02-18 21:31:49] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2025-02-18 21:31:49] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 21:31:49] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-18 21:31:49] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 21:31:49] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-18 21:31:49] [INFO] [OmnipathR] Cache item `b10176737ba43d460b13709623189f3911123779` version 1: status changed from `unknown` to `started`.
[2025-02-18 21:31:49] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/b10176737ba43d460b13709623189f3911123779-1.rds`.
[2025-02-18 21:31:50] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/b10176737ba43d460b13709623189f3911123779-1.rds`.
[2025-02-18 21:31:50] [INFO] [OmnipathR] Download ready [key=b10176737ba43d460b13709623189f3911123779, version=1]
[2025-02-18 21:31:50] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 21:31:50] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-18 21:31:50] [INFO] [OmnipathR] Cache item `b10176737ba43d460b13709623189f3911123779` version 1: status changed from `started` to `ready`.
[2025-02-18 21:31:52] [SUCCESS] [OmnipathR] Downloaded 64958 interactions.
[2025-02-18 21:31:52] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-02-18 21:31:52] [TRACE] [OmnipathR] Arguments for OmniPath query: [genesymbols=TRUE,resources=CollecTRI,strict_evidences=TRUE,query_type=interactions,datasets=tf_mirna]
[2025-02-18 21:31:52] [TRACE] [OmnipathR] Organism(s): 9606
[2025-02-18 21:31:52] [TRACE] [OmnipathR] Orthology targets:
[2025-02-18 21:31:52] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-02-18 21:31:52] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-18 21:31:53] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2025-02-18 21:31:53] [INFO] [OmnipathR] Cache record does not exist: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2025-02-18 21:31:53] [TRACE] [OmnipathR] Looking up in cache: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2025-02-18 21:31:53] [INFO] [OmnipathR] Cache record does not exist: `http://no-tls.omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2025-02-18 21:31:53] [TRACE] [OmnipathR] Attempting `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2025-02-18 21:31:53] [INFO] [OmnipathR] Retrieving URL: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2025-02-18 21:31:53] [TRACE] [OmnipathR] Attempt 1/3: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2025-02-18 21:31:53] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-18 21:31:53] [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=TRUE,ssl_verifyhost=TRUE]
[2025-02-18 21:31:53] [TRACE] [OmnipathR] Downloaded 9.5 Kb in 0.237493s from omnipathdb.org (40 Kb/s); Redirect: 0s, DNS look up: 0.00192s, Connection: 0.00277s, Pretransfer: 0.159161s, First byte at: 0.236992s
[2025-02-18 21:31:54] [INFO] [OmnipathR] Successfully retrieved: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2025-02-18 21:31:54] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 21:31:54] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-18 21:31:54] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 21:31:54] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-18 21:31:54] [INFO] [OmnipathR] Cache item `f7d34500401ba98803b7d2b26c48f64cee1eea1b` version 1: status changed from `unknown` to `started`.
[2025-02-18 21:31:54] [TRACE] [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/f7d34500401ba98803b7d2b26c48f64cee1eea1b-1.rds`.
[2025-02-18 21:31:54] [TRACE] [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/f7d34500401ba98803b7d2b26c48f64cee1eea1b-1.rds`.
[2025-02-18 21:31:54] [INFO] [OmnipathR] Download ready [key=f7d34500401ba98803b7d2b26c48f64cee1eea1b, version=1]
[2025-02-18 21:31:54] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-18 21:31:54] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-18 21:31:54] [INFO] [OmnipathR] Cache item `f7d34500401ba98803b7d2b26c48f64cee1eea1b` version 1: status changed from `started` to `ready`.
[2025-02-18 21:31:54] [TRACE] [OmnipathR] Converting JSON column `evidences` to list.
[2025-02-18 21:31:54] [TRACE] [OmnipathR] Restricting interaction records to datasets: tf_mirna; and resources: CollecTRI
[2025-02-18 21:31:54] [TRACE] [OmnipathR] Filtering evidence columns: positive, negative, directed, undirected; to datasets: tf_mirna; and resources: CollecTRI; excluding resources: none
[2025-02-18 21:31:55] [SUCCESS] [OmnipathR] Downloaded 232 interactions.
[2025-02-18 21:31:55] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-02-18 21:31:55] [TRACE] [OmnipathR] Arguments for OmniPath query: [loops=TRUE,organisms=9606,genesymbols=TRUE,query_type=interactions,datasets=collectri]
[2025-02-18 21:31:55] [TRACE] [OmnipathR] Organism(s): 9606
[2025-02-18 21:31:55] [TRACE] [OmnipathR] Orthology targets:
[2025-02-18 21:31:55] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2025-02-18 21:31:55] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/b10176737ba43d460b13709623189f3911123779-1.rds`.
[2025-02-18 21:31:55] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=collectri&organisms=9606&fields=sources,references,curation_effort&loops=yes&license=academic`
[2025-02-18 21:31:57] [SUCCESS] [OmnipathR] Loaded 64958 interactions from cache.
[2025-02-18 21:31:57] [TRACE] [OmnipathR] Processing args for OmniPath query
[2025-02-18 21:31:57] [TRACE] [OmnipathR] Arguments for OmniPath query: [genesymbols=TRUE,resources=CollecTRI,strict_evidences=TRUE,query_type=interactions,datasets=tf_mirna]
[2025-02-18 21:31:57] [TRACE] [OmnipathR] Organism(s): 9606
[2025-02-18 21:31:57] [TRACE] [OmnipathR] Orthology targets:
[2025-02-18 21:31:58] [TRACE] [OmnipathR] Reading JSON from `https://omnipathdb.org/resources` (encoding: UTF-8).
[2025-02-18 21:31:58] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-18 21:31:58] [TRACE] [OmnipathR] Looking up in cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2025-02-18 21:31:58] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/f7d34500401ba98803b7d2b26c48f64cee1eea1b-1.rds`.
[2025-02-18 21:31:58] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&resources=CollecTRI&datasets=tf_mirna&organisms=9606&fields=evidences,sources,references,curation_effort&license=academic`
[2025-02-18 21:31:58] [TRACE] [OmnipathR] Converting JSON column `evidences` to list.
[2025-02-18 21:31:58] [TRACE] [OmnipathR] Restricting interaction records to datasets: tf_mirna; and resources: CollecTRI
[2025-02-18 21:31:58] [TRACE] [OmnipathR] Filtering evidence columns: positive, negative, directed, undirected; to datasets: tf_mirna; and resources: CollecTRI; excluding resources: none
[2025-02-18 21:31:58] [SUCCESS] [OmnipathR] Loaded 232 interactions from cache.
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Attaching package: 'dplyr'
The following object is masked from 'package:testthat':
matches
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
[ FAIL 0 | WARN 9 | SKIP 0 | PASS 35 ]
[ FAIL 0 | WARN 9 | SKIP 0 | PASS 35 ]
>
> proc.time()
user system elapsed
146.003 19.138 493.195
decoupleR.Rcheck/decoupleR-Ex.timings
| name | user | system | elapsed | |
| check_corr | 0.085 | 0.009 | 0.095 | |
| convert_f_defaults | 0.051 | 0.015 | 0.066 | |
| decouple | 0.001 | 0.000 | 0.000 | |
| dot-fit_preprocessing | 0.022 | 0.005 | 0.026 | |
| extract_sets | 0.022 | 0.002 | 0.023 | |
| filt_minsize | 0.045 | 0.000 | 0.045 | |
| get_collectri | 8.281 | 0.683 | 15.820 | |
| get_dorothea | 21.325 | 0.853 | 24.796 | |
| get_profile_of | 0.000 | 0.001 | 0.000 | |
| get_progeny | 5.943 | 0.298 | 13.568 | |
| get_resource | 1.105 | 0.024 | 2.816 | |
| get_toy_data | 0.002 | 0.001 | 0.003 | |
| intersect_regulons | 0.030 | 0.004 | 0.034 | |
| pipe | 0 | 0 | 0 | |
| pivot_wider_profile | 0 | 0 | 0 | |
| randomize_matrix | 0 | 0 | 0 | |
| rename_net | 0.039 | 0.007 | 0.045 | |
| run_aucell | 10.147 | 2.018 | 12.207 | |
| run_consensus | 2.051 | 0.387 | 2.444 | |
| run_fgsea | 27.129 | 0.640 | 27.790 | |
| run_gsva | 1.811 | 0.467 | 2.291 | |
| run_mdt | 0.213 | 0.030 | 0.242 | |
| run_mlm | 0.092 | 0.004 | 0.096 | |
| run_ora | 0.447 | 0.047 | 0.495 | |
| run_udt | 0.273 | 0.031 | 0.305 | |
| run_ulm | 0.072 | 0.012 | 0.084 | |
| run_viper | 0.756 | 0.265 | 1.025 | |
| run_wmean | 0.705 | 0.051 | 0.757 | |
| run_wsum | 0.712 | 0.045 | 0.757 | |
| show_methods | 0.049 | 0.002 | 0.051 | |
| show_resources | 0.180 | 0.010 | 0.863 | |
| tidyeval | 0 | 0 | 0 | |