Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-06-19 12:04 -0400 (Thu, 19 Jun 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4810 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.0 (2025-04-11 ucrt) -- "How About a Twenty-Six" | 4548 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.0 Patched (2025-04-21 r88169) -- "How About a Twenty-Six" | 4528 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4493 |
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 2287/2309 | 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 | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
taishan | Linux (openEuler 24.03 LTS) / aarch64 | 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: F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:wppi.install-out.txt --library=F:\biocbuild\bbs-3.22-bioc\R\library --no-vignettes --timings wppi_1.17.0.tar.gz |
StartedAt: 2025-06-19 08:03:59 -0400 (Thu, 19 Jun 2025) |
EndedAt: 2025-06-19 08:10:37 -0400 (Thu, 19 Jun 2025) |
EllapsedTime: 398.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: wppi.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:wppi.install-out.txt --library=F:\biocbuild\bbs-3.22-bioc\R\library --no-vignettes --timings wppi_1.17.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.22-bioc/meat/wppi.Rcheck' * using R version 4.5.0 (2025-04-11 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 14.2.0 GNU Fortran (GCC) 14.2.0 * running under: Windows Server 2022 x64 (build 20348) * 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 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 [2025-06-19 08:04:49] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8). [2025-06-19 08:04:49] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-06-19 08:04:49] [INFO] [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2025-06-19 08:04:49] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-06-19 08:04:49] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-06-18 [2025-06-19 08:04:49] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-06-18 19:30:23 UTC; windows [2025-06-19 08:04:49] [INFO] [OmnipathR] Package `OmnipathR` version: 3.17.0 [2025-06-19 08:04:49] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22 [2025-06-19 08:04:49] [INFO] [OmnipathR] Session info: [version=R version 4.5.0 (2025-04-11 ucrt); os=Windows Server 2022 x64 (build 20348); system=x86_64, mingw32; ui=RTerm; language=(EN); collate=C; ctype=English_United States.utf8; tz=America/New_York; date=2025-06-19; pandoc=2.7.3 @ C:/PROGRA~1/Pandoc/ (via rmarkdown); quarto=NA] [2025-06-19 08:04:50] [INFO] [OmnipathR] External libraries: [cairo=1.18.2; cairoFT=; pango=; png=1.6.47; jpeg=9.6; tiff=LIBTIFF, Version 4.7.0; tcl=8.6.16; curl=8.12.1; zlib=1.3.1; bzlib=1.0.8, 13-Jul-2019; xz=5.6.4; deflate=1.23; PCRE=10.45 2025-02-05; ICU=76.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=win_iconv; readline=; BLAS=; lapack=; lapack_version=3.12.1] [2025-06-19 08:04:50] [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 6.3.0(2025-06-06); 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 1.1.2(2025-03-26); 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 3.17.0(2025-06-18); pillar 1.10.2(2025-04-05); 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 1.0.4(2025-02-05); 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 1.0.14(2025-01-12); 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 2.4.1(2025-06-08); 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(2025-06-18); 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) [2025-06-19 08:04:50] [INFO] [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: (OpenSSL/3.5.0) Schannel; libz_version: 1.3; libssh_version: libssh2/1.11.0; libidn_version: NA; host: x86_64-w64-mingw32; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE [2025-06-19 08:04:50] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-06-19 08:04:50] [TRACE] [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2025-06-19 08:04:50] [TRACE] [OmnipathR] Contains 1 files. [2025-06-19 08:04:50] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-06-19 08:04:50] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8). [2025-06-19 08:04:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-06-19 08:04:50] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2025-06-19 08:04:50] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2025-06-19 08:04:50] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.22-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-06-19 08:04:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-06-19 08:04:50] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.22-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-06-19 08:04:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-06-19 08:04:50] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.22-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-06-19 08:04:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-06-19 08:04:50] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.22-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-06-19 08:04:50] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-06-19 08:04:50] [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 [2025-06-19 08:05:17] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8). [2025-06-19 08:05:17] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-06-19 08:05:17] [INFO] [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2025-06-19 08:05:18] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-06-19 08:05:18] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-06-18 [2025-06-19 08:05:18] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-06-18 19:30:23 UTC; windows [2025-06-19 08:05:18] [INFO] [OmnipathR] Package `OmnipathR` version: 3.17.0 [2025-06-19 08:05:18] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22 [2025-06-19 08:05:18] [INFO] [OmnipathR] Session info: [version=R version 4.5.0 (2025-04-11 ucrt); os=Windows Server 2022 x64 (build 20348); system=x86_64, mingw32; ui=RTerm; language=(EN); collate=C; ctype=English_United States.utf8; tz=America/New_York; date=2025-06-19; pandoc=2.7.3 @ C:/PROGRA~1/Pandoc/ (via rmarkdown); quarto=NA] [2025-06-19 08:05:18] [INFO] [OmnipathR] External libraries: [cairo=1.18.2; cairoFT=; pango=; png=1.6.47; jpeg=9.6; tiff=LIBTIFF, Version 4.7.0; tcl=8.6.16; curl=8.12.1; zlib=1.3.1; bzlib=1.0.8, 13-Jul-2019; xz=5.6.4; deflate=1.23; PCRE=10.45 2025-02-05; ICU=76.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=win_iconv; readline=; BLAS=; lapack=; lapack_version=3.12.1] [2025-06-19 08:05:19] [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 6.3.0(2025-06-06); 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 1.1.2(2025-03-26); 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 3.17.0(2025-06-18); pillar 1.10.2(2025-04-05); 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 1.0.4(2025-02-05); 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 1.0.14(2025-01-12); 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 2.4.1(2025-06-08); 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(2025-06-18); 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) [2025-06-19 08:05:19] [INFO] [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: (OpenSSL/3.5.0) Schannel; libz_version: 1.3; libssh_version: libssh2/1.11.0; libidn_version: NA; host: x86_64-w64-mingw32; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE [2025-06-19 08:05:19] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-06-19 08:05:19] [TRACE] [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2025-06-19 08:05:19] [TRACE] [OmnipathR] Contains 1 files. [2025-06-19 08:05:19] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-06-19 08:05:19] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8). [2025-06-19 08:05:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-06-19 08:05:19] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2025-06-19 08:05:19] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2025-06-19 08:05:19] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.22-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-06-19 08:05:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-06-19 08:05:19] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.22-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-06-19 08:05:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-06-19 08:05:19] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.22-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-06-19 08:05:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-06-19 08:05:19] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.22-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-06-19 08:05:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-06-19 08:05:19] [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 57.28 1.30 58.69 prioritization_genes 31.58 0.60 32.24 score_candidate_genes_from_PPI 30.28 0.80 31.14 random_walk 30.30 0.68 31.09 weighted_adj 25.39 0.69 26.11 count_genes 16.73 1.37 16.30 common_neighbors 16.67 0.42 18.87 filter_annot_with_network 10.09 0.25 10.39 wppi_data 8.97 0.20 9.17 * 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 'F:/biocbuild/bbs-3.22-bioc/meat/wppi.Rcheck/00check.log' for details.
wppi.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.22-bioc\R\bin\R.exe CMD INSTALL wppi ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.22-bioc/R/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 [2025-06-18 15:33:59] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8). [2025-06-18 15:33:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-06-18 15:33:59] [INFO] [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2025-06-18 15:33:59] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-06-18 15:33:59] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-06-18 [2025-06-18 15:33:59] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-06-18 19:30:23 UTC; windows [2025-06-18 15:33:59] [INFO] [OmnipathR] Package `OmnipathR` version: 3.17.0 [2025-06-18 15:33:59] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22 [2025-06-18 15:33:59] [INFO] [OmnipathR] Session info: [version=R version 4.5.0 (2025-04-11 ucrt); os=Windows Server 2022 x64 (build 20348); system=x86_64, mingw32; ui=RTerm; language=(EN); collate=C; ctype=English_United States.utf8; tz=America/New_York; date=2025-06-18; pandoc=2.7.3 @ C:/PROGRA~1/Pandoc/ (via rmarkdown); quarto=NA] [2025-06-18 15:34:00] [INFO] [OmnipathR] External libraries: [cairo=1.18.2; cairoFT=; pango=; png=1.6.47; jpeg=9.6; tiff=LIBTIFF, Version 4.7.0; tcl=8.6.16; curl=8.12.1; zlib=1.3.1; bzlib=1.0.8, 13-Jul-2019; xz=5.6.4; deflate=1.23; PCRE=10.45 2025-02-05; ICU=76.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=win_iconv; readline=; BLAS=; lapack=; lapack_version=3.12.1] [2025-06-18 15:34:00] [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 6.3.0(2025-06-06); 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 1.1.2(2025-03-26); 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 3.17.0(2025-06-18); pillar 1.10.2(2025-04-05); 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 1.0.4(2025-02-05); 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 1.0.14(2025-01-12); 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 2.4.1(2025-06-08); 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(2025-06-18); 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) [2025-06-18 15:34:00] [INFO] [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: (OpenSSL/3.5.0) Schannel; libz_version: 1.3; libssh_version: libssh2/1.11.0; libidn_version: NA; host: x86_64-w64-mingw32; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE [2025-06-18 15:34:00] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-06-18 15:34:00] [TRACE] [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2025-06-18 15:34:00] [TRACE] [OmnipathR] Contains 1 files. [2025-06-18 15:34:00] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-06-18 15:34:00] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8). [2025-06-18 15:34:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-06-18 15:34:00] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2025-06-18 15:34:00] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2025-06-18 15:34:00] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.22-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-06-18 15:34:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-06-18 15:34:00] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.22-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-06-18 15:34:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-06-18 15:34:00] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.22-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-06-18 15:34:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-06-18 15:34:00] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.22-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-06-18 15:34:00] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-06-18 15:34:00] [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 [2025-06-18 15:34:09] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8). [2025-06-18 15:34:09] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-06-18 15:34:09] [INFO] [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2025-06-18 15:34:09] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-06-18 15:34:09] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-06-18 [2025-06-18 15:34:09] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-06-18 19:30:23 UTC; windows [2025-06-18 15:34:09] [INFO] [OmnipathR] Package `OmnipathR` version: 3.17.0 [2025-06-18 15:34:09] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22 [2025-06-18 15:34:10] [INFO] [OmnipathR] Session info: [version=R version 4.5.0 (2025-04-11 ucrt); os=Windows Server 2022 x64 (build 20348); system=x86_64, mingw32; ui=RTerm; language=(EN); collate=C; ctype=English_United States.utf8; tz=America/New_York; date=2025-06-18; pandoc=2.7.3 @ C:/PROGRA~1/Pandoc/ (via rmarkdown); quarto=NA] [2025-06-18 15:34:10] [INFO] [OmnipathR] External libraries: [cairo=1.18.2; cairoFT=; pango=; png=1.6.47; jpeg=9.6; tiff=LIBTIFF, Version 4.7.0; tcl=8.6.16; curl=8.12.1; zlib=1.3.1; bzlib=1.0.8, 13-Jul-2019; xz=5.6.4; deflate=1.23; PCRE=10.45 2025-02-05; ICU=76.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=win_iconv; readline=; BLAS=; lapack=; lapack_version=3.12.1] [2025-06-18 15:34:11] [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 6.3.0(2025-06-06); 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 1.1.2(2025-03-26); 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 3.17.0(2025-06-18); pillar 1.10.2(2025-04-05); 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 1.0.4(2025-02-05); 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 1.0.14(2025-01-12); 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 2.4.1(2025-06-08); 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(2025-06-18); 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) [2025-06-18 15:34:11] [INFO] [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: (OpenSSL/3.5.0) Schannel; libz_version: 1.3; libssh_version: libssh2/1.11.0; libidn_version: NA; host: x86_64-w64-mingw32; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE [2025-06-18 15:34:11] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-06-18 15:34:11] [TRACE] [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2025-06-18 15:34:11] [TRACE] [OmnipathR] Contains 1 files. [2025-06-18 15:34:11] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-06-18 15:34:11] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8). [2025-06-18 15:34:11] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-06-18 15:34:11] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2025-06-18 15:34:11] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2025-06-18 15:34:11] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.22-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-06-18 15:34:11] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-06-18 15:34:11] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.22-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-06-18 15:34:11] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-06-18 15:34:11] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.22-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-06-18 15:34:11] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-06-18 15:34:11] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.22-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-06-18 15:34:11] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-06-18 15:34:11] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2025-06-18 15:34:14] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8). [2025-06-18 15:34:14] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-06-18 15:34:14] [INFO] [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2025-06-18 15:34:14] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-06-18 15:34:14] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-06-18 [2025-06-18 15:34:14] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-06-18 19:30:23 UTC; windows [2025-06-18 15:34:14] [INFO] [OmnipathR] Package `OmnipathR` version: 3.17.0 [2025-06-18 15:34:14] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.22 [2025-06-18 15:34:15] [INFO] [OmnipathR] Session info: [version=R version 4.5.0 (2025-04-11 ucrt); os=Windows Server 2022 x64 (build 20348); system=x86_64, mingw32; ui=RTerm; language=(EN); collate=C; ctype=English_United States.utf8; tz=America/New_York; date=2025-06-18; pandoc=2.7.3 @ C:/PROGRA~1/Pandoc/ (via rmarkdown); quarto=NA] [2025-06-18 15:34:15] [INFO] [OmnipathR] External libraries: [cairo=1.18.2; cairoFT=; pango=; png=1.6.47; jpeg=9.6; tiff=LIBTIFF, Version 4.7.0; tcl=8.6.16; curl=8.12.1; zlib=1.3.1; bzlib=1.0.8, 13-Jul-2019; xz=5.6.4; deflate=1.23; PCRE=10.45 2025-02-05; ICU=76.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=win_iconv; readline=; BLAS=; lapack=; lapack_version=3.12.1] [2025-06-18 15:34:15] [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 6.3.0(2025-06-06); 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 1.1.2(2025-03-26); 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 3.17.0(2025-06-18); pillar 1.10.2(2025-04-05); 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 1.0.4(2025-02-05); 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 1.0.14(2025-01-12); 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 2.4.1(2025-06-08); 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(2025-06-18); 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) [2025-06-18 15:34:15] [INFO] [OmnipathR] CURL: version: 8.14.1; headers: 8.14.1; ssl_version: (OpenSSL/3.5.0) Schannel; libz_version: 1.3; libssh_version: libssh2/1.11.0; libidn_version: NA; host: x86_64-w64-mingw32; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp, ws, wss; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE [2025-06-18 15:34:15] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-06-18 15:34:15] [TRACE] [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2025-06-18 15:34:15] [TRACE] [OmnipathR] Contains 1 files. [2025-06-18 15:34:15] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-06-18 15:34:15] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8). [2025-06-18 15:34:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-06-18 15:34:15] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2025-06-18 15:34:15] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2025-06-18 15:34:15] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.22-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-06-18 15:34:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-06-18 15:34:16] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.22-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-06-18 15:34:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-06-18 15:34:16] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.22-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-06-18 15:34:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-06-18 15:34:16] [TRACE] [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.22-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-06-18 15:34:16] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-06-18 15:34:16] [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 | 16.67 | 0.42 | 18.87 | |
count_genes | 16.73 | 1.37 | 16.30 | |
filter_annot_with_network | 10.09 | 0.25 | 10.39 | |
functional_annot | 3.03 | 0.25 | 3.41 | |
graph_from_op | 4.22 | 0.10 | 4.31 | |
in_omnipath | 4.08 | 0.12 | 4.20 | |
prioritization_genes | 31.58 | 0.60 | 32.24 | |
process_annot | 1.12 | 0.03 | 1.16 | |
random_walk | 30.30 | 0.68 | 31.09 | |
score_candidate_genes_from_PPI | 30.28 | 0.80 | 31.14 | |
subgraph_op | 4.58 | 0.03 | 4.62 | |
weighted_adj | 25.39 | 0.69 | 26.11 | |
wppi | 57.28 | 1.30 | 58.69 | |
wppi_data | 8.97 | 0.20 | 9.17 | |
wppi_go_data | 4.86 | 0.11 | 4.97 | |
wppi_hpo_data | 0.92 | 0.05 | 0.97 | |
wppi_omnipath_data | 4.06 | 0.06 | 4.13 | |