Ana Galhoz
| Snapshot Date: 2025-04-22 13:40 -0400 (Tue, 22 Apr 2025) |
| git_url: https://git.bioconductor.org/packages/wppi |
| git_branch: RELEASE_3_21 |
| git_last_commit: c49fef6 |
| git_last_commit_date: 2025-04-15 12:26:01 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-04-24 13:03 -0400 (Thu, 24 Apr 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" | 4831 |
| palomino7 | Windows Server 2022 Datacenter | x64 | 4.5.0 RC (2025-04-04 r88126 ucrt) -- "How About a Twenty-Six" | 4573 |
| 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 2318/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| wppi 1.16.0 (landing page) Ana Galhoz
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | 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: 1.16.0 |
| Command: E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:wppi.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings wppi_1.16.0.tar.gz |
| StartedAt: 2025-04-23 08:00:21 -0400 (Wed, 23 Apr 2025) |
| EndedAt: 2025-04-23 08:07:52 -0400 (Wed, 23 Apr 2025) |
| EllapsedTime: 450.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: wppi.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:wppi.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings wppi_1.16.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/wppi.Rcheck'
* using R version 4.5.0 RC (2025-04-04 r88126 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 '1.16.0'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking 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
[2025-04-23 08:01:15] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-23 08:01:15] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-23 08:01:15] [INFO] [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-04-23 08:01:15] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2025-04-23 08:01:15] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-04-22
[2025-04-23 08:01:15] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-04-22 19:35:47 UTC; windows
[2025-04-23 08:01:15] [INFO] [OmnipathR] Package `OmnipathR` version: 3.16.0
[2025-04-23 08:01:15] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21
[2025-04-23 08:01:23] [INFO] [OmnipathR] Session info: [version=R version 4.5.0 RC (2025-04-04 r88126 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=2025-04-23; pandoc=2.7.3 @ C:/PROGRA~1/Pandoc/ (via rmarkdown); quarto=NA]
[2025-04-23 08:01:26] [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]
[2025-04-23 08:01:26] [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 0.5.0(2025-03-21); cli 3.6.4(2025-02-13); crayon 1.5.3(2024-06-20); curl 6.2.2(2025-03-24); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.3(2025-01-10); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.3(2022-07-05); 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 3.16.0(2025-04-22); 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 1.3.2(2024-11-28); ps 1.9.1(2025-04-12); purrr 1.0.4(2025-02-05); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.0(2024-11-01); 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 2.3.9(2024-12-03); 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 3.2.1(2023-03-20); 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 1.16.0(2025-04-22); 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 2.3.2(2025-02-01)
[2025-04-23 08:01:27] [INFO] [OmnipathR] CURL: version: 8.10.1; headers: 8.10.1; ssl_version: (OpenSSL/3.4.0) 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; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2025-04-23 08:01:29] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-04-23 08:01:29] [TRACE] [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-04-23 08:01:29] [TRACE] [OmnipathR] Contains 1 files.
[2025-04-23 08:01:30] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-04-23 08:01:30] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-23 08:01:32] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-23 08:01:32] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-04-23 08:01:33] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2025-04-23 08:01:33] [TRACE] [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-04-23 08:01:33] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-23 08:01:33] [TRACE] [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-04-23 08:01:33] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-23 08:01:33] [TRACE] [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-04-23 08:01:33] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-23 08:01:33] [TRACE] [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-04-23 08:01:34] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-23 08:01:34] [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
[2025-04-23 08:02:10] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-23 08:02:10] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-23 08:02:10] [INFO] [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-04-23 08:02:11] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2025-04-23 08:02:11] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-04-22
[2025-04-23 08:02:11] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-04-22 19:35:47 UTC; windows
[2025-04-23 08:02:11] [INFO] [OmnipathR] Package `OmnipathR` version: 3.16.0
[2025-04-23 08:02:11] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21
[2025-04-23 08:02:13] [INFO] [OmnipathR] Session info: [version=R version 4.5.0 RC (2025-04-04 r88126 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=2025-04-23; pandoc=2.7.3 @ C:/PROGRA~1/Pandoc/ (via rmarkdown); quarto=NA]
[2025-04-23 08:02:13] [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]
[2025-04-23 08:02:13] [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 0.5.0(2025-03-21); cli 3.6.4(2025-02-13); crayon 1.5.3(2024-06-20); curl 6.2.2(2025-03-24); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.3(2025-01-10); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.3(2022-07-05); 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 3.16.0(2025-04-22); 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 1.3.2(2024-11-28); ps 1.9.1(2025-04-12); purrr 1.0.4(2025-02-05); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.0(2024-11-01); 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 2.3.9(2024-12-03); 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 3.2.1(2023-03-20); 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 1.16.0(2025-04-22); 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 2.3.2(2025-02-01)
[2025-04-23 08:02:14] [INFO] [OmnipathR] CURL: version: 8.10.1; headers: 8.10.1; ssl_version: (OpenSSL/3.4.0) 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; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2025-04-23 08:02:14] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-04-23 08:02:14] [TRACE] [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-04-23 08:02:14] [TRACE] [OmnipathR] Contains 1 files.
[2025-04-23 08:02:14] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-04-23 08:02:14] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-04-23 08:02:14] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-23 08:02:14] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-04-23 08:02:14] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2025-04-23 08:02:14] [TRACE] [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-04-23 08:02:14] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-23 08:02:14] [TRACE] [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-04-23 08:02:14] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-23 08:02:14] [TRACE] [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-04-23 08:02:14] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-23 08:02:14] [TRACE] [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-04-23 08:02:14] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-04-23 08:02:14] [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 56.97 1.45 59.20
score_candidate_genes_from_PPI 31.20 0.81 32.49
random_walk 30.38 0.64 31.47
prioritization_genes 29.97 0.72 31.19
weighted_adj 26.48 0.61 27.45
count_genes 16.25 1.14 16.35
common_neighbors 16.75 0.28 21.31
wppi_data 10.70 0.19 11.28
filter_annot_with_network 10.49 0.27 11.03
wppi_omnipath_data 4.87 0.03 5.23
* 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
'E:/biocbuild/bbs-3.21-bioc/meat/wppi.Rcheck/00check.log'
for details.
wppi.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL wppi ### ############################################################################## ############################################################################## * installing to library 'E:/biocbuild/bbs-3.21-bioc/R/library' * installing *source* package 'wppi' ... ** this is package 'wppi' version '1.16.0' ** using staged installation ** R ** byte-compile and prepare package for lazy loading [2025-04-22 15:38:42] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8). [2025-04-22 15:38:42] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-22 15:38:42] [INFO] [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2025-04-22 15:38:42] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-04-22 15:38:42] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-04-22 [2025-04-22 15:38:42] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-04-22 19:35:47 UTC; windows [2025-04-22 15:38:42] [INFO] [OmnipathR] Package `OmnipathR` version: 3.16.0 [2025-04-22 15:38:42] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21 [2025-04-22 15:38:44] [INFO] [OmnipathR] Session info: [version=R version 4.5.0 RC (2025-04-04 r88126 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=2025-04-22; pandoc=2.7.3 @ C:/PROGRA~1/Pandoc/ (via rmarkdown); quarto=NA] [2025-04-22 15:38:44] [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] [2025-04-22 15:38:44] [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 0.5.0(2025-03-21); cli 3.6.4(2025-02-13); crayon 1.5.3(2024-06-20); curl 6.2.2(2025-03-24); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.3(2025-01-10); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.3(2022-07-05); 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 3.16.0(2025-04-22); 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 1.3.2(2024-11-28); ps 1.9.1(2025-04-12); purrr 1.0.4(2025-02-05); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.0(2024-11-01); 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 2.3.9(2024-12-03); 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 3.2.1(2023-03-20); 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 1.16.0(2025-04-22); 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 2.3.2(2025-02-01) [2025-04-22 15:38:44] [INFO] [OmnipathR] CURL: version: 8.10.1; headers: 8.10.1; ssl_version: (OpenSSL/3.4.0) 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; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE [2025-04-22 15:38:44] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-04-22 15:38:44] [TRACE] [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2025-04-22 15:38:44] [TRACE] [OmnipathR] Contains 1 files. [2025-04-22 15:38:44] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-04-22 15:38:44] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8). [2025-04-22 15:38:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-22 15:38:45] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2025-04-22 15:38:45] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2025-04-22 15:38:45] [TRACE] [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-04-22 15:38:45] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-22 15:38:45] [TRACE] [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-04-22 15:38:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-22 15:38:46] [TRACE] [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-04-22 15:38:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-22 15:38:46] [TRACE] [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-04-22 15:38:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-22 15:38:46] [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 [2025-04-22 15:38:55] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8). [2025-04-22 15:38:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-22 15:38:55] [INFO] [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2025-04-22 15:38:55] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-04-22 15:38:55] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-04-22 [2025-04-22 15:38:55] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-04-22 19:35:47 UTC; windows [2025-04-22 15:38:55] [INFO] [OmnipathR] Package `OmnipathR` version: 3.16.0 [2025-04-22 15:38:55] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21 [2025-04-22 15:38:56] [INFO] [OmnipathR] Session info: [version=R version 4.5.0 RC (2025-04-04 r88126 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=2025-04-22; pandoc=2.7.3 @ C:/PROGRA~1/Pandoc/ (via rmarkdown); quarto=NA] [2025-04-22 15:38:57] [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] [2025-04-22 15:38:57] [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 0.5.0(2025-03-21); cli 3.6.4(2025-02-13); crayon 1.5.3(2024-06-20); curl 6.2.2(2025-03-24); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.3(2025-01-10); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.3(2022-07-05); 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 3.16.0(2025-04-22); 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 1.3.2(2024-11-28); ps 1.9.1(2025-04-12); purrr 1.0.4(2025-02-05); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.0(2024-11-01); 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 2.3.9(2024-12-03); 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 3.2.1(2023-03-20); 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 1.16.0(2025-04-22); 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 2.3.2(2025-02-01) [2025-04-22 15:38:57] [INFO] [OmnipathR] CURL: version: 8.10.1; headers: 8.10.1; ssl_version: (OpenSSL/3.4.0) 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; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE [2025-04-22 15:38:57] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-04-22 15:38:57] [TRACE] [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2025-04-22 15:38:57] [TRACE] [OmnipathR] Contains 1 files. [2025-04-22 15:38:57] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-04-22 15:38:58] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8). [2025-04-22 15:38:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-22 15:38:58] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2025-04-22 15:38:58] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2025-04-22 15:38:58] [TRACE] [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-04-22 15:38:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-22 15:38:58] [TRACE] [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-04-22 15:38:58] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-22 15:38:59] [TRACE] [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-04-22 15:38:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-22 15:38:59] [TRACE] [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-04-22 15:38:59] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-22 15:38:59] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2025-04-22 15:39:02] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8). [2025-04-22 15:39:02] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-22 15:39:02] [INFO] [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2025-04-22 15:39:02] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-04-22 15:39:02] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-04-22 [2025-04-22 15:39:02] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-04-22 19:35:47 UTC; windows [2025-04-22 15:39:02] [INFO] [OmnipathR] Package `OmnipathR` version: 3.16.0 [2025-04-22 15:39:02] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21 [2025-04-22 15:39:03] [INFO] [OmnipathR] Session info: [version=R version 4.5.0 RC (2025-04-04 r88126 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=2025-04-22; pandoc=2.7.3 @ C:/PROGRA~1/Pandoc/ (via rmarkdown); quarto=NA] [2025-04-22 15:39:03] [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] [2025-04-22 15:39:04] [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 0.5.0(2025-03-21); cli 3.6.4(2025-02-13); crayon 1.5.3(2024-06-20); curl 6.2.2(2025-03-24); DBI 1.2.3(2024-06-02); digest 0.6.37(2024-08-19); dplyr 1.1.4(2023-11-17); evaluate 1.0.3(2025-01-10); fastmap 1.2.0(2024-05-15); fs 1.6.6(2025-04-12); generics 0.1.3(2022-07-05); 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 3.16.0(2025-04-22); 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 1.3.2(2024-11-28); ps 1.9.1(2025-04-12); purrr 1.0.4(2025-02-05); R.methodsS3 1.8.2(2022-06-13); R.oo 1.27.0(2024-11-01); 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 2.3.9(2024-12-03); 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 3.2.1(2023-03-20); 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 1.16.0(2025-04-22); 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 2.3.2(2025-02-01) [2025-04-22 15:39:04] [INFO] [OmnipathR] CURL: version: 8.10.1; headers: 8.10.1; ssl_version: (OpenSSL/3.4.0) 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; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE [2025-04-22 15:39:04] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-04-22 15:39:04] [TRACE] [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2025-04-22 15:39:04] [TRACE] [OmnipathR] Contains 1 files. [2025-04-22 15:39:04] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-04-22 15:39:04] [TRACE] [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8). [2025-04-22 15:39:04] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-22 15:39:04] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2025-04-22 15:39:05] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2025-04-22 15:39:05] [TRACE] [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-04-22 15:39:05] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-22 15:39:05] [TRACE] [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-04-22 15:39:05] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-22 15:39:05] [TRACE] [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-04-22 15:39:05] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-22 15:39:05] [TRACE] [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-04-22 15:39:05] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-04-22 15:39:05] [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 | 16.75 | 0.28 | 21.31 | |
| count_genes | 16.25 | 1.14 | 16.35 | |
| filter_annot_with_network | 10.49 | 0.27 | 11.03 | |
| functional_annot | 2.43 | 0.15 | 3.46 | |
| graph_from_op | 4.36 | 0.08 | 4.66 | |
| in_omnipath | 4.64 | 0.06 | 4.89 | |
| prioritization_genes | 29.97 | 0.72 | 31.19 | |
| process_annot | 1.08 | 0.02 | 1.19 | |
| random_walk | 30.38 | 0.64 | 31.47 | |
| score_candidate_genes_from_PPI | 31.20 | 0.81 | 32.49 | |
| subgraph_op | 4.30 | 0.05 | 4.50 | |
| weighted_adj | 26.48 | 0.61 | 27.45 | |
| wppi | 56.97 | 1.45 | 59.20 | |
| wppi_data | 10.70 | 0.19 | 11.28 | |
| wppi_go_data | 3.78 | 0.11 | 4.07 | |
| wppi_hpo_data | 0.77 | 0.04 | 0.91 | |
| wppi_omnipath_data | 4.87 | 0.03 | 5.23 | |