Ana Galhoz
| Snapshot Date: 2025-08-08 13:45 -0400 (Fri, 08 Aug 2025) |
| git_url: https://git.bioconductor.org/packages/wppi |
| git_branch: devel |
| git_last_commit: 718f698 |
| git_last_commit_date: 2025-04-15 12:26:01 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-08-09 12:10 -0400 (Sat, 09 Aug 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4818 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4553 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4595 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4537 |
| 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 2295/2317 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| wppi 1.17.0 (landing page) Ana Galhoz
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
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: 1.17.0 |
| 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_1.17.0.tar.gz |
| StartedAt: 2025-08-08 22:13:48 -0400 (Fri, 08 Aug 2025) |
| EndedAt: 2025-08-08 22:16:21 -0400 (Fri, 08 Aug 2025) |
| EllapsedTime: 152.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: wppi.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### 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_1.17.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/wppi.Rcheck’
* using R version 4.5.1 Patched (2025-06-14 r88325)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 16.0.0 (clang-1600.0.26.6)
GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘wppi/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘wppi’ version ‘1.17.0’
* 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
[2025-08-08 22:14:04] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-08 22:14:04] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-08 22:14:04] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-08-08 22:14:04] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2025-08-08 22:14:04] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-08-08
[2025-08-08 22:14:04] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-08-08 19:04:49 UTC; unix
[2025-08-08 22:14:04] [INFO] [OmnipathR] Package `OmnipathR` version: 3.17.4
[2025-08-08 22:14:04] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-08-08 22:14:04] [INFO] [OmnipathR] Session info: [version=R version 4.5.1 Patched (2025-06-14 r88325); os=macOS Ventura 13.7.1; system=aarch64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-08-08; pandoc=3.1.12.3 @ /opt/homebrew/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2025-08-08 22:14:04] [INFO] [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=; pango=1.50.14; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.5.0; tcl=8.6.13; curl=8.7.1; zlib=1.2.11; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; PCRE=10.44 2024-06-07; ICU=70.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1]
[2025-08-08 22:14:04] [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 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.2(2024-07-29); chromote 0.5.1(2025-04-24); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 6.4.0(2025-06-22); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.4(2025-06-18); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.1.4(2025-01-23); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.2(2025-04-08); lattice 0.22-7(2025-04-02); lifecycle 1.0.4(2023-11-07); logger 0.4.0(2024-10-22); lubridate 1.9.4(2024-12-08); magrittr 2.0.3(2022-03-30); Matrix 1.7-3(2025-03-11); memoise 2.0.1(2021-11-26); OmnipathR 3.17.4(2025-08-08); pillar 1.11.0(2025-07-04); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.3.3(2025-05-29); ps 1.9.1(2025-04-12); purrr 1.1.0(2025-07-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.1.0(2025-07-02); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.29(2024-11-04); RSQLite 2.4.2(2025-07-18); rvest 1.0.4(2024-02-12); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); tibble 3.3.0(2025-06-08); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); wppi 1.17.0(2025-08-08); xfun 0.52(2025-04-02); XML 3.99-0.18(2025-01-01); xml2 1.3.8(2025-03-14); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2025-08-08 22:14:04] [INFO] [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: LibreSSL/3.3.6 (SecureTransport); libz_version: 1.2.11; 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
[2025-08-08 22:14:04] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-08-08 22:14:04] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-08-08 22:14:04] [TRACE] [OmnipathR] Contains 1 files.
[2025-08-08 22:14:04] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-08-08 22:14:04] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-08 22:14:04] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-08 22:14:04] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-08-08 22:14:04] [TRACE] [OmnipathR] Pandoc version: `3.1.12.3`.
[2025-08-08 22:14:04] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-08-08 22:14:04] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-08 22:14:04] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-08-08 22:14:04] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-08 22:14:04] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-08-08 22:14:04] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-08 22:14:04] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-08-08 22:14:04] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-08 22:14:04] [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
[2025-08-08 22:14:12] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-08 22:14:12] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-08 22:14:12] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-08-08 22:14:12] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2025-08-08 22:14:12] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-08-08
[2025-08-08 22:14:12] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-08-08 19:04:49 UTC; unix
[2025-08-08 22:14:12] [INFO] [OmnipathR] Package `OmnipathR` version: 3.17.4
[2025-08-08 22:14:12] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22
[2025-08-08 22:14:13] [INFO] [OmnipathR] Session info: [version=R version 4.5.1 Patched (2025-06-14 r88325); os=macOS Ventura 13.7.1; system=aarch64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-08-08; pandoc=3.1.12.3 @ /opt/homebrew/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto]
[2025-08-08 22:14:13] [INFO] [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=; pango=1.50.14; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.5.0; tcl=8.6.13; curl=8.7.1; zlib=1.2.11; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; PCRE=10.44 2024-06-07; ICU=70.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1]
[2025-08-08 22:14:13] [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 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.2(2024-07-29); chromote 0.5.1(2025-04-24); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 6.4.0(2025-06-22); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.4(2025-06-18); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.1.4(2025-01-23); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.2(2025-04-08); lattice 0.22-7(2025-04-02); lifecycle 1.0.4(2023-11-07); logger 0.4.0(2024-10-22); lubridate 1.9.4(2024-12-08); magrittr 2.0.3(2022-03-30); Matrix 1.7-3(2025-03-11); memoise 2.0.1(2021-11-26); OmnipathR 3.17.4(2025-08-08); pillar 1.11.0(2025-07-04); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.3.3(2025-05-29); ps 1.9.1(2025-04-12); purrr 1.1.0(2025-07-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.1.0(2025-07-02); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.29(2024-11-04); RSQLite 2.4.2(2025-07-18); rvest 1.0.4(2024-02-12); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); tibble 3.3.0(2025-06-08); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); wppi 1.17.0(2025-08-08); xfun 0.52(2025-04-02); XML 3.99-0.18(2025-01-01); xml2 1.3.8(2025-03-14); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13)
[2025-08-08 22:14:13] [INFO] [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: LibreSSL/3.3.6 (SecureTransport); libz_version: 1.2.11; 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
[2025-08-08 22:14:13] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-08-08 22:14:13] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-08-08 22:14:13] [TRACE] [OmnipathR] Contains 1 files.
[2025-08-08 22:14:13] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-08-08 22:14:13] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-08-08 22:14:13] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-08 22:14:13] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-08-08 22:14:13] [TRACE] [OmnipathR] Pandoc version: `3.1.12.3`.
[2025-08-08 22:14:13] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-08-08 22:14:13] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-08 22:14:13] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-08-08 22:14:13] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-08 22:14:13] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-08-08 22:14:13] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-08 22:14:13] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-08-08 22:14:13] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-08-08 22:14:13] [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
wppi 17.486 2.641 20.985
common_neighbors 13.179 1.818 24.177
prioritization_genes 9.226 1.496 11.484
score_candidate_genes_from_PPI 9.170 1.359 11.208
random_walk 8.630 1.421 10.541
weighted_adj 7.406 0.866 8.406
count_genes 6.143 0.406 7.129
* 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-3.22-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/4.5-arm64/Resources/library’ * installing *source* package ‘wppi’ ... ** this is package ‘wppi’ version ‘1.17.0’ ** using staged installation ** R ** byte-compile and prepare package for lazy loading [2025-08-08 15:04:59] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-08 15:04:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-08 15:04:59] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-08-08 15:04:59] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-08-08 15:04:59] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-08-08 [2025-08-08 15:04:59] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-08-08 19:04:49 UTC; unix [2025-08-08 15:04:59] [INFO] [OmnipathR] Package `OmnipathR` version: 3.17.4 [2025-08-08 15:04:59] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22 [2025-08-08 15:04:59] [INFO] [OmnipathR] Session info: [version=R version 4.5.1 Patched (2025-06-14 r88325); os=macOS Ventura 13.7.1; system=aarch64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-08-08; pandoc=3.1.12.3 @ /opt/homebrew/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto] [2025-08-08 15:04:59] [INFO] [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=; pango=1.50.14; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.5.0; tcl=8.6.13; curl=8.7.1; zlib=1.2.11; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; PCRE=10.44 2024-06-07; ICU=70.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1] [2025-08-08 15:04:59] [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 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.2(2024-07-29); chromote 0.5.1(2025-04-24); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 6.4.0(2025-06-22); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.4(2025-06-18); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.1.4(2025-01-23); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.2(2025-04-08); lattice 0.22-7(2025-04-02); lifecycle 1.0.4(2023-11-07); logger 0.4.0(2024-10-22); lubridate 1.9.4(2024-12-08); magrittr 2.0.3(2022-03-30); Matrix 1.7-3(2025-03-11); memoise 2.0.1(2021-11-26); OmnipathR 3.17.4(2025-08-08); pillar 1.11.0(2025-07-04); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.3.3(2025-05-29); ps 1.9.1(2025-04-12); purrr 1.1.0(2025-07-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.1.0(2025-07-02); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.29(2024-11-04); RSQLite 2.4.2(2025-07-18); rvest 1.0.4(2024-02-12); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); tibble 3.3.0(2025-06-08); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); wppi 1.17.0(2025-08-08); xfun 0.52(2025-04-02); XML 3.99-0.18(2025-01-01); xml2 1.3.8(2025-03-14); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13) [2025-08-08 15:04:59] [INFO] [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: LibreSSL/3.3.6 (SecureTransport); libz_version: 1.2.11; 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 [2025-08-08 15:04:59] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-08-08 15:04:59] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-08-08 15:04:59] [TRACE] [OmnipathR] Contains 1 files. [2025-08-08 15:04:59] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-08-08 15:04:59] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-08 15:04:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-08 15:04:59] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-08-08 15:04:59] [TRACE] [OmnipathR] Pandoc version: `3.1.12.3`. [2025-08-08 15:04:59] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-08-08 15:04:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-08 15:04:59] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-08-08 15:04:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-08 15:04:59] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-08-08 15:04:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-08 15:04:59] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-08-08 15:04:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-08 15:04:59] [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 [2025-08-08 15:05:01] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-08 15:05:01] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-08 15:05:01] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-08-08 15:05:01] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-08-08 15:05:01] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-08-08 [2025-08-08 15:05:01] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-08-08 19:04:49 UTC; unix [2025-08-08 15:05:01] [INFO] [OmnipathR] Package `OmnipathR` version: 3.17.4 [2025-08-08 15:05:01] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22 [2025-08-08 15:05:01] [INFO] [OmnipathR] Session info: [version=R version 4.5.1 Patched (2025-06-14 r88325); os=macOS Ventura 13.7.1; system=aarch64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-08-08; pandoc=3.1.12.3 @ /opt/homebrew/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto] [2025-08-08 15:05:01] [INFO] [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=; pango=1.50.14; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.5.0; tcl=8.6.13; curl=8.7.1; zlib=1.2.11; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; PCRE=10.44 2024-06-07; ICU=70.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1] [2025-08-08 15:05:01] [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 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.2(2024-07-29); chromote 0.5.1(2025-04-24); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 6.4.0(2025-06-22); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.4(2025-06-18); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.1.4(2025-01-23); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.2(2025-04-08); lattice 0.22-7(2025-04-02); lifecycle 1.0.4(2023-11-07); logger 0.4.0(2024-10-22); lubridate 1.9.4(2024-12-08); magrittr 2.0.3(2022-03-30); Matrix 1.7-3(2025-03-11); memoise 2.0.1(2021-11-26); OmnipathR 3.17.4(2025-08-08); pillar 1.11.0(2025-07-04); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.3.3(2025-05-29); ps 1.9.1(2025-04-12); purrr 1.1.0(2025-07-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.1.0(2025-07-02); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.29(2024-11-04); RSQLite 2.4.2(2025-07-18); rvest 1.0.4(2024-02-12); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); tibble 3.3.0(2025-06-08); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); wppi 1.17.0(2025-08-08); xfun 0.52(2025-04-02); XML 3.99-0.18(2025-01-01); xml2 1.3.8(2025-03-14); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13) [2025-08-08 15:05:01] [INFO] [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: LibreSSL/3.3.6 (SecureTransport); libz_version: 1.2.11; 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 [2025-08-08 15:05:01] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-08-08 15:05:01] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-08-08 15:05:01] [TRACE] [OmnipathR] Contains 1 files. [2025-08-08 15:05:01] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-08-08 15:05:01] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-08 15:05:01] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-08 15:05:01] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-08-08 15:05:01] [TRACE] [OmnipathR] Pandoc version: `3.1.12.3`. [2025-08-08 15:05:01] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-08-08 15:05:01] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-08 15:05:01] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-08-08 15:05:01] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-08 15:05:01] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-08-08 15:05:01] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-08 15:05:01] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-08-08 15:05:01] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-08 15:05:01] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2025-08-08 15:05:03] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-08 15:05:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-08 15:05:03] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-08-08 15:05:03] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-08-08 15:05:03] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-08-08 [2025-08-08 15:05:03] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.1; ; 2025-08-08 19:04:49 UTC; unix [2025-08-08 15:05:03] [INFO] [OmnipathR] Package `OmnipathR` version: 3.17.4 [2025-08-08 15:05:03] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22 [2025-08-08 15:05:03] [INFO] [OmnipathR] Session info: [version=R version 4.5.1 Patched (2025-06-14 r88325); os=macOS Ventura 13.7.1; system=aarch64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-08-08; pandoc=3.1.12.3 @ /opt/homebrew/bin/ (via rmarkdown); quarto=1.7.32 @ /usr/local/bin/quarto] [2025-08-08 15:05:03] [INFO] [OmnipathR] External libraries: [cairo=1.17.6; cairoFT=; pango=1.50.14; png=1.6.44; jpeg=9.5; tiff=LIBTIFF, Version 4.5.0; tcl=8.6.13; curl=8.7.1; zlib=1.2.11; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.23; PCRE=10.44 2024-06-07; ICU=70.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRlapack.dylib; lapack_version=3.12.1] [2025-08-08 15:05:03] [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 1.2.4(2023-03-17); cachem 1.1.0(2024-05-16); cellranger 1.1.0(2016-07-27); checkmate 2.3.2(2024-07-29); chromote 0.5.1(2025-04-24); cli 3.6.5(2025-04-23); crayon 1.5.3(2024-06-20); curl 6.4.0(2025-06-22); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.4(2025-06-18); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.4(2025-05-09); glue 1.8.0(2024-09-30); hms 1.1.3(2023-03-21); htmltools 0.5.8.1(2024-04-04); httr 1.4.7(2023-08-15); httr2 1.2.1(2025-07-22); igraph 2.1.4(2025-01-23); jsonlite 2.0.0(2025-03-27); knitr 1.50(2025-03-16); later 1.4.2(2025-04-08); lattice 0.22-7(2025-04-02); lifecycle 1.0.4(2023-11-07); logger 0.4.0(2024-10-22); lubridate 1.9.4(2024-12-08); magrittr 2.0.3(2022-03-30); Matrix 1.7-3(2025-03-11); memoise 2.0.1(2021-11-26); OmnipathR 3.17.4(2025-08-08); pillar 1.11.0(2025-07-04); pkgconfig 2.0.3(2019-09-22); prettyunits 1.2.0(2023-09-24); processx 3.8.6(2025-02-21); progress 1.2.3(2023-12-06); promises 1.3.3(2025-05-29); ps 1.9.1(2025-04-12); purrr 1.1.0(2025-07-10); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.1(2025-05-02); R.utils 2.13.0(2025-02-24); R6 2.6.1(2025-02-15); rappdirs 0.3.3(2021-01-31); Rcpp 1.1.0(2025-07-02); readr 2.1.5(2024-01-10); readxl 1.4.5(2025-03-07); rlang 1.1.6(2025-04-11); rmarkdown 2.29(2024-11-04); RSQLite 2.4.2(2025-07-18); rvest 1.0.4(2024-02-12); sessioninfo 1.2.3(2025-02-05); stringi 1.8.7(2025-03-27); stringr 1.5.1(2023-11-14); tibble 3.3.0(2025-06-08); tidyr 1.3.1(2024-01-24); tidyselect 1.2.1(2024-03-11); timechange 0.3.0(2024-01-18); tzdb 0.5.0(2025-03-15); vctrs 0.6.5(2023-12-01); websocket 1.4.4(2025-04-10); withr 3.0.2(2024-10-28); wppi 1.17.0(2025-08-08); xfun 0.52(2025-04-02); XML 3.99-0.18(2025-01-01); xml2 1.3.8(2025-03-14); yaml 2.3.10(2024-07-26); zip 2.3.3(2025-05-13) [2025-08-08 15:05:03] [INFO] [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: LibreSSL/3.3.6 (SecureTransport); libz_version: 1.2.11; 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 [2025-08-08 15:05:03] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-08-08 15:05:03] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-08-08 15:05:03] [TRACE] [OmnipathR] Contains 1 files. [2025-08-08 15:05:03] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-08-08 15:05:03] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-08-08 15:05:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-08 15:05:03] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-08-08 15:05:03] [TRACE] [OmnipathR] Pandoc version: `3.1.12.3`. [2025-08-08 15:05:03] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-08-08 15:05:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-08 15:05:03] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-08-08 15:05:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-08 15:05:03] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-08-08 15:05:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-08 15:05:03] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-08-08 15:05:03] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-08-08 15:05:03] [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 | 13.179 | 1.818 | 24.177 | |
| count_genes | 6.143 | 0.406 | 7.129 | |
| filter_annot_with_network | 3.307 | 0.097 | 3.450 | |
| functional_annot | 1.080 | 0.100 | 1.586 | |
| graph_from_op | 1.272 | 0.079 | 1.430 | |
| in_omnipath | 1.334 | 0.058 | 1.398 | |
| prioritization_genes | 9.226 | 1.496 | 11.484 | |
| process_annot | 0.365 | 0.021 | 0.400 | |
| random_walk | 8.630 | 1.421 | 10.541 | |
| score_candidate_genes_from_PPI | 9.170 | 1.359 | 11.208 | |
| subgraph_op | 1.373 | 0.126 | 1.597 | |
| weighted_adj | 7.406 | 0.866 | 8.406 | |
| wppi | 17.486 | 2.641 | 20.985 | |
| wppi_data | 3.670 | 0.099 | 3.772 | |
| wppi_go_data | 1.542 | 0.030 | 1.580 | |
| wppi_hpo_data | 0.467 | 0.017 | 0.486 | |
| wppi_omnipath_data | 1.432 | 0.051 | 1.497 | |