Ana Galhoz
| Snapshot Date: 2026-03-31 13:40 -0400 (Tue, 31 Mar 2026) |
| git_url: https://git.bioconductor.org/packages/wppi |
| git_branch: devel |
| git_last_commit: 40fc535 |
| git_last_commit_date: 2025-10-29 11:08:00 -0400 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-04-01 13:07 -0400 (Wed, 01 Apr 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.6.0 alpha (2026-03-30 r89742) | 4816 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.6.0 alpha (2026-03-28 r89739) | 4539 |
| 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 2353/2374 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| wppi 1.19.0 (landing page) Ana Galhoz
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| See other builds for wppi in R Universe. | ||||||||||||||
|
To the developers/maintainers of the wppi package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/wppi.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: wppi |
| Version: 1.19.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:wppi.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings wppi_1.19.0.tar.gz |
| StartedAt: 2026-03-31 22:11:06 -0400 (Tue, 31 Mar 2026) |
| EndedAt: 2026-03-31 22:15:28 -0400 (Tue, 31 Mar 2026) |
| EllapsedTime: 262.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: wppi.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:wppi.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings wppi_1.19.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/wppi.Rcheck’
* using R version 4.6.0 alpha (2026-03-28 r89739)
* using platform: aarch64-apple-darwin23
* R was compiled by
Apple clang version 17.0.0 (clang-1700.3.19.1)
GNU Fortran (GCC) 14.2.0
* running under: macOS Tahoe 26.3.1
* using session charset: UTF-8
* current time: 2026-04-01 02:11:06 UTC
* using option ‘--no-vignettes’
* checking for file ‘wppi/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘wppi’ version ‘1.19.0’
* 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 ‘wppi’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* 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 whether startup messages can be suppressed ... NOTE
[2026-03-31 22:11:25] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-31 22:11:25] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-03-31 22:11:25] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2026-03-31 22:11:25] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2026-03-31 22:11:25] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2026-03-31
[2026-03-31 22:11:25] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2026-03-31 19:05:24 UTC; unix
[2026-03-31 22:11:25] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.12
[2026-03-31 22:11:25] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23
[2026-03-31 22:11:25] [INFO] [OmnipathR] Session info: [version=R version 4.6.0 alpha (2026-03-28 r89739); os=macOS Tahoe 26.3.1; system=aarch64, darwin23; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2026-03-31; pandoc=3.1.12.3 @ /opt/homebrew/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2026-03-31 22:11:25] [INFO] [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=2.13.2/2.14.2; pango=; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.7.0; tcl=8.6; curl=8.7.1; zlib=1.2.12; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; zstd=1.5.5; PCRE=10.44 2024-06-07; ICU=76.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libRlapack.dylib; lapack_version=3.12.1]
[2026-03-31 22:11:25] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.3.0(2026-01-14); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); chromote 0.5.1(2025-04-24); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.3.0(2026-02-25); digest 0.6.39(2025-11-19); dplyr 1.2.0(2026-02-03); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 2.0.1(2026-03-24); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); httr 1.4.8(2026-02-13); httr2 1.2.2(2025-12-08); igraph 2.2.2(2026-02-12); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.8(2026-03-05); lattice 0.22-9(2026-02-09); lifecycle 1.0.5(2026-01-08); logger 0.4.1(2025-09-11); lubridate 1.9.5(2026-02-04); magrittr 2.0.4(2025-09-12); Matrix 1.7-5(2026-03-21); memoise 2.0.1(2021-11-26); OmnipathR 3.19.12(2026-03-31); otel 0.2.0(2025-08-29); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.5.0(2025-11-01); ps 1.9.2(2026-03-31); purrr 1.2.1(2026-01-09); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.4(2026-01-17); Rcpp 1.1.1(2026-01-10); readr 2.2.0(2026-02-19); readxl 1.4.5(2025-03-07); rlang 1.1.7(2026-01-09); rmarkdown 2.31(2026-03-26); RSQLite 2.4.6(2026-02-06); rvest 1.0.5(2025-08-29); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tzdb 0.5.0(2025-03-15); vctrs 0.7.2(2026-03-21); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); wppi 1.19.0(2026-03-31); xfun 0.57(2026-03-20); XML 3.99-0.23(2026-03-20); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13)
[2026-03-31 22:11:25] [INFO] [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: LibreSSL/3.3.6 (SecureTransport); libz_version: 1.2.12; libssh_version: NA; libidn_version: NA; host: aarch64-apple-darwin23.6.0; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE
[2026-03-31 22:11:25] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2026-03-31 22:11:25] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2026-03-31 22:11:25] [TRACE] [OmnipathR] Contains 1 files.
[2026-03-31 22:11:25] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2026-03-31 22:11:25] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-31 22:11:25] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-03-31 22:11:25] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2026-03-31 22:11:25] [TRACE] [OmnipathR] Pandoc version: `3.1.12.3`.
[2026-03-31 22:11:25] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2026-03-31 22:11:25] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-03-31 22:11:25] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2026-03-31 22:11:25] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-03-31 22:11:25] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2026-03-31 22:11:25] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-03-31 22:11:25] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2026-03-31 22:11:25] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-03-31 22:11:25] [TRACE] [OmnipathR] Cache locked: FALSE
It looks like this package (or a package it requires) has a startup
message which cannot be suppressed: see ?packageStartupMessage.
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
[2026-03-31 22:11:34] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-31 22:11:34] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-03-31 22:11:34] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2026-03-31 22:11:34] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2026-03-31 22:11:34] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2026-03-31
[2026-03-31 22:11:34] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2026-03-31 19:05:24 UTC; unix
[2026-03-31 22:11:34] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.12
[2026-03-31 22:11:34] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23
[2026-03-31 22:11:34] [INFO] [OmnipathR] Session info: [version=R version 4.6.0 alpha (2026-03-28 r89739); os=macOS Tahoe 26.3.1; system=aarch64, darwin23; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2026-03-31; pandoc=3.1.12.3 @ /opt/homebrew/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2026-03-31 22:11:34] [INFO] [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=2.13.2/2.14.2; pango=; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.7.0; tcl=8.6; curl=8.7.1; zlib=1.2.12; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; zstd=1.5.5; PCRE=10.44 2024-06-07; ICU=76.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libRlapack.dylib; lapack_version=3.12.1]
[2026-03-31 22:11:34] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.3.0(2026-01-14); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); chromote 0.5.1(2025-04-24); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.3.0(2026-02-25); digest 0.6.39(2025-11-19); dplyr 1.2.0(2026-02-03); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 2.0.1(2026-03-24); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); httr 1.4.8(2026-02-13); httr2 1.2.2(2025-12-08); igraph 2.2.2(2026-02-12); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.8(2026-03-05); lattice 0.22-9(2026-02-09); lifecycle 1.0.5(2026-01-08); logger 0.4.1(2025-09-11); lubridate 1.9.5(2026-02-04); magrittr 2.0.4(2025-09-12); Matrix 1.7-5(2026-03-21); memoise 2.0.1(2021-11-26); OmnipathR 3.19.12(2026-03-31); otel 0.2.0(2025-08-29); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.5.0(2025-11-01); ps 1.9.2(2026-03-31); purrr 1.2.1(2026-01-09); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.4(2026-01-17); Rcpp 1.1.1(2026-01-10); readr 2.2.0(2026-02-19); readxl 1.4.5(2025-03-07); rlang 1.1.7(2026-01-09); rmarkdown 2.31(2026-03-26); RSQLite 2.4.6(2026-02-06); rvest 1.0.5(2025-08-29); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tzdb 0.5.0(2025-03-15); vctrs 0.7.2(2026-03-21); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); wppi 1.19.0(2026-03-31); xfun 0.57(2026-03-20); XML 3.99-0.23(2026-03-20); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13)
[2026-03-31 22:11:34] [INFO] [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: LibreSSL/3.3.6 (SecureTransport); libz_version: 1.2.12; libssh_version: NA; libidn_version: NA; host: aarch64-apple-darwin23.6.0; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE
[2026-03-31 22:11:34] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2026-03-31 22:11:34] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2026-03-31 22:11:34] [TRACE] [OmnipathR] Contains 1 files.
[2026-03-31 22:11:34] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2026-03-31 22:11:34] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2026-03-31 22:11:34] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-03-31 22:11:34] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2026-03-31 22:11:34] [TRACE] [OmnipathR] Pandoc version: `3.1.12.3`.
[2026-03-31 22:11:34] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2026-03-31 22:11:35] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-03-31 22:11:35] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2026-03-31 22:11:35] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-03-31 22:11:35] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2026-03-31 22:11:35] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-03-31 22:11:35] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2026-03-31 22:11:35] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2026-03-31 22:11:35] [TRACE] [OmnipathR] Cache locked: FALSE
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* 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
common_neighbors 24.174 4.314 40.416
wppi 22.402 5.054 28.157
prioritization_genes 21.430 5.791 32.006
random_walk 20.737 6.111 32.233
score_candidate_genes_from_PPI 20.249 5.708 30.771
weighted_adj 9.325 1.253 10.962
count_genes 6.989 0.712 8.230
filter_annot_with_network 5.331 0.440 6.381
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 3 NOTEs
See
‘/Users/biocbuild/bbs-3.23-bioc/meat/wppi.Rcheck/00check.log’
for details.
wppi.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL wppi ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.6/Resources/library’ * installing *source* package ‘wppi’ ... ** this is package ‘wppi’ version ‘1.19.0’ ** using staged installation ** R ** byte-compile and prepare package for lazy loading [2026-03-31 15:05:35] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-31 15:05:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-31 15:05:35] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2026-03-31 15:05:35] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2026-03-31 15:05:35] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2026-03-31 [2026-03-31 15:05:35] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2026-03-31 19:05:24 UTC; unix [2026-03-31 15:05:35] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.12 [2026-03-31 15:05:35] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23 [2026-03-31 15:05:35] [INFO] [OmnipathR] Session info: [version=R version 4.6.0 alpha (2026-03-28 r89739); os=macOS Tahoe 26.3.1; system=aarch64, darwin23; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2026-03-31; pandoc=3.1.12.3 @ /opt/homebrew/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto] [2026-03-31 15:05:35] [INFO] [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=2.13.2/2.14.2; pango=; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.7.0; tcl=8.6; curl=8.7.1; zlib=1.2.12; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; zstd=1.5.5; PCRE=10.44 2024-06-07; ICU=76.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libRlapack.dylib; lapack_version=3.12.1] [2026-03-31 15:05:35] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.3.0(2026-01-14); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); chromote 0.5.1(2025-04-24); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.3.0(2026-02-25); digest 0.6.39(2025-11-19); dplyr 1.2.0(2026-02-03); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 2.0.1(2026-03-24); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); httr 1.4.8(2026-02-13); httr2 1.2.2(2025-12-08); igraph 2.2.2(2026-02-12); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.8(2026-03-05); lattice 0.22-9(2026-02-09); lifecycle 1.0.5(2026-01-08); logger 0.4.1(2025-09-11); lubridate 1.9.5(2026-02-04); magrittr 2.0.4(2025-09-12); Matrix 1.7-5(2026-03-21); memoise 2.0.1(2021-11-26); OmnipathR 3.19.12(2026-03-31); otel 0.2.0(2025-08-29); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.5.0(2025-11-01); ps 1.9.2(2026-03-31); purrr 1.2.1(2026-01-09); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.4(2026-01-17); Rcpp 1.1.1(2026-01-10); readr 2.2.0(2026-02-19); readxl 1.4.5(2025-03-07); rlang 1.1.7(2026-01-09); rmarkdown 2.31(2026-03-26); RSQLite 2.4.6(2026-02-06); rvest 1.0.5(2025-08-29); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tzdb 0.5.0(2025-03-15); vctrs 0.7.2(2026-03-21); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); wppi 1.19.0(2026-03-31); xfun 0.57(2026-03-20); XML 3.99-0.23(2026-03-20); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13) [2026-03-31 15:05:35] [INFO] [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: LibreSSL/3.3.6 (SecureTransport); libz_version: 1.2.12; libssh_version: NA; libidn_version: NA; host: aarch64-apple-darwin23.6.0; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE [2026-03-31 15:05:35] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2026-03-31 15:05:35] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2026-03-31 15:05:35] [TRACE] [OmnipathR] Contains 1 files. [2026-03-31 15:05:35] [TRACE] [OmnipathR] Cache is locked: FALSE. [2026-03-31 15:05:35] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-31 15:05:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-31 15:05:35] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2026-03-31 15:05:35] [TRACE] [OmnipathR] Pandoc version: `3.1.12.3`. [2026-03-31 15:05:35] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2026-03-31 15:05:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-31 15:05:35] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2026-03-31 15:05:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-31 15:05:35] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-03-31 15:05:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-31 15:05:35] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2026-03-31 15:05:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-31 15:05:35] [TRACE] [OmnipathR] Cache locked: FALSE Note: wrong number of arguments to '/' ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location [2026-03-31 15:05:37] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-31 15:05:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-31 15:05:37] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2026-03-31 15:05:37] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2026-03-31 15:05:37] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2026-03-31 [2026-03-31 15:05:37] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2026-03-31 19:05:24 UTC; unix [2026-03-31 15:05:37] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.12 [2026-03-31 15:05:37] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23 [2026-03-31 15:05:37] [INFO] [OmnipathR] Session info: [version=R version 4.6.0 alpha (2026-03-28 r89739); os=macOS Tahoe 26.3.1; system=aarch64, darwin23; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2026-03-31; pandoc=3.1.12.3 @ /opt/homebrew/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto] [2026-03-31 15:05:37] [INFO] [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=2.13.2/2.14.2; pango=; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.7.0; tcl=8.6; curl=8.7.1; zlib=1.2.12; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; zstd=1.5.5; PCRE=10.44 2024-06-07; ICU=76.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libRlapack.dylib; lapack_version=3.12.1] [2026-03-31 15:05:38] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.3.0(2026-01-14); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); chromote 0.5.1(2025-04-24); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.3.0(2026-02-25); digest 0.6.39(2025-11-19); dplyr 1.2.0(2026-02-03); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 2.0.1(2026-03-24); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); httr 1.4.8(2026-02-13); httr2 1.2.2(2025-12-08); igraph 2.2.2(2026-02-12); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.8(2026-03-05); lattice 0.22-9(2026-02-09); lifecycle 1.0.5(2026-01-08); logger 0.4.1(2025-09-11); lubridate 1.9.5(2026-02-04); magrittr 2.0.4(2025-09-12); Matrix 1.7-5(2026-03-21); memoise 2.0.1(2021-11-26); OmnipathR 3.19.12(2026-03-31); otel 0.2.0(2025-08-29); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.5.0(2025-11-01); ps 1.9.2(2026-03-31); purrr 1.2.1(2026-01-09); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.4(2026-01-17); Rcpp 1.1.1(2026-01-10); readr 2.2.0(2026-02-19); readxl 1.4.5(2025-03-07); rlang 1.1.7(2026-01-09); rmarkdown 2.31(2026-03-26); RSQLite 2.4.6(2026-02-06); rvest 1.0.5(2025-08-29); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tzdb 0.5.0(2025-03-15); vctrs 0.7.2(2026-03-21); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); wppi 1.19.0(2026-03-31); xfun 0.57(2026-03-20); XML 3.99-0.23(2026-03-20); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13) [2026-03-31 15:05:38] [INFO] [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: LibreSSL/3.3.6 (SecureTransport); libz_version: 1.2.12; libssh_version: NA; libidn_version: NA; host: aarch64-apple-darwin23.6.0; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE [2026-03-31 15:05:38] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2026-03-31 15:05:38] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2026-03-31 15:05:38] [TRACE] [OmnipathR] Contains 1 files. [2026-03-31 15:05:38] [TRACE] [OmnipathR] Cache is locked: FALSE. [2026-03-31 15:05:38] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-31 15:05:38] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-31 15:05:38] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2026-03-31 15:05:38] [TRACE] [OmnipathR] Pandoc version: `3.1.12.3`. [2026-03-31 15:05:38] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2026-03-31 15:05:38] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-31 15:05:38] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2026-03-31 15:05:38] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-31 15:05:38] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-03-31 15:05:38] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-31 15:05:38] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2026-03-31 15:05:38] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-31 15:05:38] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2026-03-31 15:05:39] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-31 15:05:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-31 15:05:39] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2026-03-31 15:05:39] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2026-03-31 15:05:39] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2026-03-31 [2026-03-31 15:05:39] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.6.0; ; 2026-03-31 19:05:24 UTC; unix [2026-03-31 15:05:39] [INFO] [OmnipathR] Package `OmnipathR` version: 3.19.12 [2026-03-31 15:05:39] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.23 [2026-03-31 15:05:39] [INFO] [OmnipathR] Session info: [version=R version 4.6.0 alpha (2026-03-28 r89739); os=macOS Tahoe 26.3.1; system=aarch64, darwin23; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2026-03-31; pandoc=3.1.12.3 @ /opt/homebrew/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto] [2026-03-31 15:05:39] [INFO] [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=2.13.2/2.14.2; pango=; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.7.0; tcl=8.6; curl=8.7.1; zlib=1.2.12; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; zstd=1.5.5; PCRE=10.44 2024-06-07; ICU=76.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libRlapack.dylib; lapack_version=3.12.1] [2026-03-31 15:05:39] [INFO] [OmnipathR] Loaded packages: backports 1.5.0(2024-05-23); bit 4.6.0(2025-03-06); bit64 4.6.0-1(2025-01-16); blob 1.3.0(2026-01-14); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.4(2026-02-03); chromote 0.5.1(2025-04-24); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 7.0.0(2025-08-19); DBI 1.3.0(2026-02-25); digest 0.6.39(2025-11-19); dplyr 1.2.0(2026-02-03); evaluate 1.0.5(2025-08-27); fastmap 1.2.0(2024-05-15); fs 2.0.1(2026-03-24); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.4(2025-10-17); htmltools 0.5.9(2025-12-04); httr 1.4.8(2026-02-13); httr2 1.2.2(2025-12-08); igraph 2.2.2(2026-02-12); jsonlite 2.0.0(2025-03-27); knitr 1.51(2025-12-20); later 1.4.8(2026-03-05); lattice 0.22-9(2026-02-09); lifecycle 1.0.5(2026-01-08); logger 0.4.1(2025-09-11); lubridate 1.9.5(2026-02-04); magrittr 2.0.4(2025-09-12); Matrix 1.7-5(2026-03-21); memoise 2.0.1(2021-11-26); OmnipathR 3.19.12(2026-03-31); otel 0.2.0(2025-08-29); pillar 1.11.1(2025-09-17); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.5.0(2025-11-01); ps 1.9.2(2026-03-31); purrr 1.2.1(2026-01-09); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.4(2026-01-17); Rcpp 1.1.1(2026-01-10); readr 2.2.0(2026-02-19); readxl 1.4.5(2025-03-07); rlang 1.1.7(2026-01-09); rmarkdown 2.31(2026-03-26); RSQLite 2.4.6(2026-02-06); rvest 1.0.5(2025-08-29); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.6.0(2025-11-04); tibble 3.3.1(2026-01-11); tidyr 1.3.2(2025-12-19); tidyselect 1.2.1(2024-03-11); timechange 0.4.0(2026-01-29); tzdb 0.5.0(2025-03-15); vctrs 0.7.2(2026-03-21); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); wppi 1.19.0(2026-03-31); xfun 0.57(2026-03-20); XML 3.99-0.23(2026-03-20); xml2 1.5.2(2026-01-17); yaml 2.3.12(2025-12-10); zip 2.3.3(2025-05-13) [2026-03-31 15:05:39] [INFO] [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: LibreSSL/3.3.6 (SecureTransport); libz_version: 1.2.12; libssh_version: NA; libidn_version: NA; host: aarch64-apple-darwin23.6.0; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: FALSE; url_parser: TRUE [2026-03-31 15:05:39] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2026-03-31 15:05:39] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2026-03-31 15:05:39] [TRACE] [OmnipathR] Contains 1 files. [2026-03-31 15:05:39] [TRACE] [OmnipathR] Cache is locked: FALSE. [2026-03-31 15:05:39] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2026-03-31 15:05:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-31 15:05:39] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2026-03-31 15:05:39] [TRACE] [OmnipathR] Pandoc version: `3.1.12.3`. [2026-03-31 15:05:39] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2026-03-31 15:05:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-31 15:05:39] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2026-03-31 15:05:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-31 15:05:39] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2026-03-31 15:05:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-31 15:05:39] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.6/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2026-03-31 15:05:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2026-03-31 15:05:39] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package keeps a record of temporary installation path * DONE (wppi)
wppi.Rcheck/wppi-Ex.timings
| name | user | system | elapsed | |
| common_neighbors | 24.174 | 4.314 | 40.416 | |
| count_genes | 6.989 | 0.712 | 8.230 | |
| filter_annot_with_network | 5.331 | 0.440 | 6.381 | |
| functional_annot | 1.580 | 0.261 | 2.384 | |
| graph_from_op | 3.373 | 0.432 | 4.292 | |
| in_omnipath | 2.995 | 0.281 | 3.713 | |
| prioritization_genes | 21.430 | 5.791 | 32.006 | |
| process_annot | 0.572 | 0.049 | 0.681 | |
| random_walk | 20.737 | 6.111 | 32.233 | |
| score_candidate_genes_from_PPI | 20.249 | 5.708 | 30.771 | |
| subgraph_op | 2.737 | 0.459 | 3.415 | |
| weighted_adj | 9.325 | 1.253 | 10.962 | |
| wppi | 22.402 | 5.054 | 28.157 | |
| wppi_data | 4.192 | 0.120 | 4.339 | |
| wppi_go_data | 1.869 | 0.017 | 1.894 | |
| wppi_hpo_data | 0.340 | 0.007 | 0.349 | |
| wppi_omnipath_data | 1.838 | 0.102 | 1.938 | |