Ana Galhoz
| Snapshot Date: 2025-02-12 13:40 -0500 (Wed, 12 Feb 2025) |
| git_url: https://git.bioconductor.org/packages/wppi |
| git_branch: devel |
| git_last_commit: 321e17d |
| git_last_commit_date: 2024-10-29 10:58:10 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-02-13 11:43 -0500 (Thu, 13 Feb 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" | 4719 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences" | 4481 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2025-01-22 r87618) -- "Unsuffered Consequences" | 4492 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" | 4445 |
| 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 2274/2295 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| wppi 1.15.0 (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 | | ||||||||
| 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: 1.15.0 |
| 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_1.15.0.tar.gz |
| StartedAt: 2025-02-13 00:07:21 -0500 (Thu, 13 Feb 2025) |
| EndedAt: 2025-02-13 00:13:56 -0500 (Thu, 13 Feb 2025) |
| EllapsedTime: 395.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: wppi.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:wppi.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings wppi_1.15.0.tar.gz
###
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##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/wppi.Rcheck’
* using R Under development (unstable) (2025-01-22 r87618)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘wppi/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘wppi’ version ‘1.15.0’
* 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
[2025-02-13 00:08:00] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-13 00:08:00] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-13 00:08:00] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-02-13 00:08:01] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2025-02-13 00:08:01] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-02-12
[2025-02-13 00:08:01] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-02-12 20:27:07 UTC; unix
[2025-02-13 00:08:01] [INFO] [OmnipathR] Package `OmnipathR` version: 3.15.8
[2025-02-13 00:08:01] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21
[2025-02-13 00:08:01] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-01-22 r87618); os=macOS Monterey 12.7.6; system=x86_64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-02-13; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown); quarto=NA]
[2025-02-13 00:08:01] [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=10.42 2022-12-11; ICU=70.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRlapack.dylib; lapack_version=3.12.0]
[2025-02-13 00:08:01] [INFO] [OmnipathR] CURL: version: 8.11.1; headers: 8.11.1; ssl_version: OpenSSL/3.3.2 (SecureTransport); libz_version: 1.2.11; libssh_version: NA; libidn_version: NA; host: x86_64-apple-darwin22.6.0; 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
[2025-02-13 00:08:01] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-02-13 00:08:01] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-02-13 00:08:01] [TRACE] [OmnipathR] Contains 1 files.
[2025-02-13 00:08:01] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-02-13 00:08:01] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-13 00:08:01] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-13 00:08:01] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-02-13 00:08:01] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2025-02-13 00:08:01] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-02-13 00:08:01] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-13 00:08:01] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-02-13 00:08:01] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-13 00:08:01] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-02-13 00:08:01] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-13 00:08:01] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-02-13 00:08:01] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-13 00:08:01] [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
[2025-02-13 00:08:24] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-13 00:08:24] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-13 00:08:24] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-02-13 00:08:24] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA
[2025-02-13 00:08:24] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-02-12
[2025-02-13 00:08:24] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-02-12 20:27:07 UTC; unix
[2025-02-13 00:08:24] [INFO] [OmnipathR] Package `OmnipathR` version: 3.15.8
[2025-02-13 00:08:24] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21
[2025-02-13 00:08:25] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-01-22 r87618); os=macOS Monterey 12.7.6; system=x86_64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-02-13; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown); quarto=NA]
[2025-02-13 00:08:25] [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=10.42 2022-12-11; ICU=70.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRlapack.dylib; lapack_version=3.12.0]
[2025-02-13 00:08:25] [INFO] [OmnipathR] CURL: version: 8.11.1; headers: 8.11.1; ssl_version: OpenSSL/3.3.2 (SecureTransport); libz_version: 1.2.11; libssh_version: NA; libidn_version: NA; host: x86_64-apple-darwin22.6.0; 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
[2025-02-13 00:08:25] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2025-02-13 00:08:25] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-02-13 00:08:25] [TRACE] [OmnipathR] Contains 1 files.
[2025-02-13 00:08:25] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2025-02-13 00:08:25] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-13 00:08:25] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-13 00:08:25] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-02-13 00:08:25] [TRACE] [OmnipathR] Pandoc version: `2.7.3`.
[2025-02-13 00:08:25] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-02-13 00:08:25] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-13 00:08:25] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-02-13 00:08:25] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-13 00:08:25] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-02-13 00:08:25] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-13 00:08:25] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-02-13 00:08:25] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-02-13 00:08:25] [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 48.420 9.975 57.762
random_walk 33.009 7.507 40.928
prioritization_genes 32.900 7.046 40.248
score_candidate_genes_from_PPI 29.154 6.617 36.050
weighted_adj 19.416 2.687 21.966
common_neighbors 15.912 1.741 34.037
count_genes 10.876 1.389 17.702
filter_annot_with_network 7.607 0.390 8.053
wppi_data 5.916 0.194 6.099
* 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-3.21-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-x86_64/Resources/library’ * installing *source* package ‘wppi’ ... ** this is package ‘wppi’ version ‘1.15.0’ ** using staged installation ** R ** byte-compile and prepare package for lazy loading [2025-02-12 15:27:39] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-12 15:27:39] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-12 15:27:39] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-02-12 15:27:39] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-02-12 15:27:39] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-02-12 [2025-02-12 15:27:39] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-02-12 20:27:07 UTC; unix [2025-02-12 15:27:39] [INFO] [OmnipathR] Package `OmnipathR` version: 3.15.8 [2025-02-12 15:27:39] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21 [2025-02-12 15:27:40] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-01-22 r87618); os=macOS Monterey 12.7.6; system=x86_64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-02-12; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown); quarto=NA] [2025-02-12 15:27:40] [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=10.42 2022-12-11; ICU=70.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRlapack.dylib; lapack_version=3.12.0] [2025-02-12 15:27:40] [INFO] [OmnipathR] CURL: version: 8.11.1; headers: 8.11.1; ssl_version: OpenSSL/3.3.2 (SecureTransport); libz_version: 1.2.11; libssh_version: NA; libidn_version: NA; host: x86_64-apple-darwin22.6.0; 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 [2025-02-12 15:27:40] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-02-12 15:27:40] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-02-12 15:27:40] [TRACE] [OmnipathR] Contains 1 files. [2025-02-12 15:27:40] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-02-12 15:27:40] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-12 15:27:40] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-12 15:27:40] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-02-12 15:27:40] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2025-02-12 15:27:40] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-02-12 15:27:40] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-12 15:27:40] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-02-12 15:27:40] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-12 15:27:40] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-02-12 15:27:40] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-12 15:27:40] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-02-12 15:27:40] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-12 15:27:40] [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 [2025-02-12 15:27:46] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-12 15:27:46] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-12 15:27:46] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-02-12 15:27:46] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-02-12 15:27:46] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-02-12 [2025-02-12 15:27:46] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-02-12 20:27:07 UTC; unix [2025-02-12 15:27:46] [INFO] [OmnipathR] Package `OmnipathR` version: 3.15.8 [2025-02-12 15:27:46] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21 [2025-02-12 15:27:47] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-01-22 r87618); os=macOS Monterey 12.7.6; system=x86_64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-02-12; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown); quarto=NA] [2025-02-12 15:27:47] [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=10.42 2022-12-11; ICU=70.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRlapack.dylib; lapack_version=3.12.0] [2025-02-12 15:27:47] [INFO] [OmnipathR] CURL: version: 8.11.1; headers: 8.11.1; ssl_version: OpenSSL/3.3.2 (SecureTransport); libz_version: 1.2.11; libssh_version: NA; libidn_version: NA; host: x86_64-apple-darwin22.6.0; 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 [2025-02-12 15:27:47] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-02-12 15:27:47] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-02-12 15:27:47] [TRACE] [OmnipathR] Contains 1 files. [2025-02-12 15:27:47] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-02-12 15:27:47] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-12 15:27:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-12 15:27:47] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-02-12 15:27:47] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2025-02-12 15:27:47] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-02-12 15:27:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-12 15:27:47] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-02-12 15:27:47] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-12 15:27:48] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-02-12 15:27:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-12 15:27:48] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-02-12 15:27:48] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-12 15:27:48] [TRACE] [OmnipathR] Cache locked: FALSE ** testing if installed package can be loaded from final location [2025-02-12 15:27:52] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-12 15:27:52] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-12 15:27:52] [INFO] [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-02-12 15:27:52] [INFO] [OmnipathR] Package `OmnipathR` packaged: NA [2025-02-12 15:27:52] [INFO] [OmnipathR] Package `OmnipathR` date/publication: 2025-02-12 [2025-02-12 15:27:52] [INFO] [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-02-12 20:27:07 UTC; unix [2025-02-12 15:27:52] [INFO] [OmnipathR] Package `OmnipathR` version: 3.15.8 [2025-02-12 15:27:52] [INFO] [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21 [2025-02-12 15:27:53] [INFO] [OmnipathR] Session info: [version=R Under development (unstable) (2025-01-22 r87618); os=macOS Monterey 12.7.6; system=x86_64, darwin20; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-02-12; pandoc=2.7.3 @ /usr/local/bin/ (via rmarkdown); quarto=NA] [2025-02-12 15:27:53] [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=10.42 2022-12-11; ICU=70.1; TRE=TRE 0.8.0 R_fixes (BSD); iconv=Apple or GNU libiconv 1.11 /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libR.dylib; readline=5.2; BLAS=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRblas.0.dylib; lapack=/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRlapack.dylib; lapack_version=3.12.0] [2025-02-12 15:27:53] [INFO] [OmnipathR] CURL: version: 8.11.1; headers: 8.11.1; ssl_version: OpenSSL/3.3.2 (SecureTransport); libz_version: 1.2.11; libssh_version: NA; libidn_version: NA; host: x86_64-apple-darwin22.6.0; 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 [2025-02-12 15:27:53] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2025-02-12 15:27:53] [TRACE] [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-02-12 15:27:53] [TRACE] [OmnipathR] Contains 1 files. [2025-02-12 15:27:53] [TRACE] [OmnipathR] Cache is locked: FALSE. [2025-02-12 15:27:53] [TRACE] [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8). [2025-02-12 15:27:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-12 15:27:53] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`. [2025-02-12 15:27:53] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2025-02-12 15:27:53] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2025-02-12 15:27:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-12 15:27:53] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2025-02-12 15:27:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-12 15:27:53] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2025-02-12 15:27:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-12 15:27:53] [TRACE] [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2025-02-12 15:27:53] [TRACE] [OmnipathR] JSON validation successful: TRUE [2025-02-12 15:27:53] [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 | 15.912 | 1.741 | 34.037 | |
| count_genes | 10.876 | 1.389 | 17.702 | |
| filter_annot_with_network | 7.607 | 0.390 | 8.053 | |
| functional_annot | 2.501 | 0.384 | 3.072 | |
| graph_from_op | 3.905 | 0.243 | 4.181 | |
| in_omnipath | 3.872 | 0.246 | 4.162 | |
| prioritization_genes | 32.900 | 7.046 | 40.248 | |
| process_annot | 0.976 | 0.046 | 1.030 | |
| random_walk | 33.009 | 7.507 | 40.928 | |
| score_candidate_genes_from_PPI | 29.154 | 6.617 | 36.050 | |
| subgraph_op | 3.624 | 0.534 | 4.202 | |
| weighted_adj | 19.416 | 2.687 | 21.966 | |
| wppi | 48.420 | 9.975 | 57.762 | |
| wppi_data | 5.916 | 0.194 | 6.099 | |
| wppi_go_data | 2.563 | 0.071 | 2.634 | |
| wppi_hpo_data | 0.528 | 0.006 | 0.533 | |
| wppi_omnipath_data | 2.800 | 0.155 | 2.945 | |