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This page was generated on 2025-03-20 12:11 -0400 (Thu, 20 Mar 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.3 (2025-02-28) -- "Trophy Case" 4756
palomino8Windows Server 2022 Datacenterx644.4.3 (2025-02-28 ucrt) -- "Trophy Case" 4487
merida1macOS 12.7.5 Montereyx86_644.4.3 (2025-02-28) -- "Trophy Case" 4514
kjohnson1macOS 13.6.6 Venturaarm644.4.3 (2025-02-28) -- "Trophy Case" 4441
taishanLinux (openEuler 24.03 LTS)aarch644.4.3 (2025-02-28) -- "Trophy Case" 4406
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Package 2269/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
wppi 1.14.0  (landing page)
Ana Galhoz
Snapshot Date: 2025-03-17 13:00 -0400 (Mon, 17 Mar 2025)
git_url: https://git.bioconductor.org/packages/wppi
git_branch: RELEASE_3_20
git_last_commit: 240f65a
git_last_commit_date: 2024-10-29 10:58:10 -0400 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  

CHECK results for wppi on kjohnson1

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.

raw results


Summary

Package: wppi
Version: 1.14.0
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_1.14.0.tar.gz
StartedAt: 2025-03-19 13:15:04 -0400 (Wed, 19 Mar 2025)
EndedAt: 2025-03-19 13:19:33 -0400 (Wed, 19 Mar 2025)
EllapsedTime: 269.3 seconds
RetCode: 0
Status:   OK  
CheckDir: wppi.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/wppi.Rcheck’
* using R version 4.4.3 (2025-02-28)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘wppi/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘wppi’ version ‘1.14.0’
* 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
[2025-03-19 13:15:37] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-19 13:15:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-19 13:15:37] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-03-19 13:15:37] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-03-19 13:15:37] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-03-19 13:15:37] [TRACE]   [OmnipathR] Contains 1 files.
[2025-03-19 13:15:37] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-03-19 13:15:37] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-19 13:15:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-19 13:15:37] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-03-19 13:15:37] [TRACE]   [OmnipathR] Pandoc version: `3.1.2`.
[2025-03-19 13:15:37] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-03-19 13:15:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-19 13:15:37] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-03-19 13:15:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-19 13:15:37] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-03-19 13:15:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-19 13:15:37] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-03-19 13:15:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-19 13:15:37] [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
[2025-03-19 13:15:57] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-19 13:15:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-19 13:15:57] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-03-19 13:15:57] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-03-19 13:15:57] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-03-19 13:15:57] [TRACE]   [OmnipathR] Contains 1 files.
[2025-03-19 13:15:57] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-03-19 13:15:57] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-19 13:15:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-19 13:15:57] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-03-19 13:15:57] [TRACE]   [OmnipathR] Pandoc version: `3.1.2`.
[2025-03-19 13:15:57] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-03-19 13:15:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-19 13:15:57] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-03-19 13:15:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-19 13:15:57] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-03-19 13:15:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-19 13:15:57] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-03-19 13:15:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-19 13:15:57] [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                           35.438  0.560  36.423
score_candidate_genes_from_PPI 18.715  0.337  19.343
prioritization_genes           17.951  0.383  18.988
random_walk                    16.988  0.295  17.563
weighted_adj                   13.375  0.222  13.859
count_genes                    12.046  0.581  13.267
wppi_data                       9.388  0.134   9.622
filter_annot_with_network       8.829  0.207   9.413
common_neighbors                6.803  0.284   8.736
* 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-3.20-bioc/meat/wppi.Rcheck/00check.log’
for details.

Installation output

wppi.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL wppi
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘wppi’ ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
[2025-03-17 17:44:05] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 17:44:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-17 17:44:05] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-03-17 17:44:05] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-03-17 17:44:05] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-03-17 17:44:05] [TRACE]   [OmnipathR] Contains 1 files.
[2025-03-17 17:44:05] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-03-17 17:44:05] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 17:44:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-17 17:44:05] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-03-17 17:44:05] [TRACE]   [OmnipathR] Pandoc version: `3.1.2`.
[2025-03-17 17:44:05] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-03-17 17:44:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-17 17:44:05] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-03-17 17:44:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-17 17:44:05] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-03-17 17:44:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-17 17:44:05] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-03-17 17:44:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-17 17:44:05] [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
[2025-03-17 17:44:09] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 17:44:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-17 17:44:09] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-03-17 17:44:09] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-03-17 17:44:09] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-03-17 17:44:09] [TRACE]   [OmnipathR] Contains 1 files.
[2025-03-17 17:44:09] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-03-17 17:44:09] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 17:44:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-17 17:44:09] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-03-17 17:44:09] [TRACE]   [OmnipathR] Pandoc version: `3.1.2`.
[2025-03-17 17:44:09] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-03-17 17:44:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-17 17:44:09] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-03-17 17:44:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-17 17:44:09] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-03-17 17:44:10] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-17 17:44:10] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-03-17 17:44:10] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-17 17:44:10] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2025-03-17 17:44:13] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 17:44:13] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-17 17:44:13] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-03-17 17:44:13] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-03-17 17:44:13] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-03-17 17:44:13] [TRACE]   [OmnipathR] Contains 1 files.
[2025-03-17 17:44:13] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-03-17 17:44:13] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 17:44:13] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-17 17:44:13] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-03-17 17:44:13] [TRACE]   [OmnipathR] Pandoc version: `3.1.2`.
[2025-03-17 17:44:13] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-03-17 17:44:13] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-17 17:44:13] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-03-17 17:44:13] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-17 17:44:13] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-03-17 17:44:13] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-17 17:44:13] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-03-17 17:44:13] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-17 17:44:13] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package keeps a record of temporary installation path
* DONE (wppi)

Tests output


Example timings

wppi.Rcheck/wppi-Ex.timings

nameusersystemelapsed
common_neighbors6.8030.2848.736
count_genes12.046 0.58113.267
filter_annot_with_network8.8290.2079.413
functional_annot2.1060.1633.953
graph_from_op3.7160.0513.989
in_omnipath3.6900.0503.848
prioritization_genes17.951 0.38318.988
process_annot1.0800.0211.136
random_walk16.988 0.29517.563
score_candidate_genes_from_PPI18.715 0.33719.343
subgraph_op3.1380.0593.226
weighted_adj13.375 0.22213.859
wppi35.438 0.56036.423
wppi_data9.3880.1349.622
wppi_go_data4.7700.1134.924
wppi_hpo_data0.9030.0180.969
wppi_omnipath_data3.6400.0313.710