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This page was generated on 2025-03-20 12:09 -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
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 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 merida1

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: 2025-03-18 11:41:50 -0400 (Tue, 18 Mar 2025)
EndedAt: 2025-03-18 11:50:30 -0400 (Tue, 18 Mar 2025)
EllapsedTime: 520.6 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: x86_64-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 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 ‘1.14.0’
* 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
[2025-03-18 11:42:49] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 11:42:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 11:42:49] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-03-18 11:42:49] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-03-18 11:42:49] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-03-18 11:42:49] [TRACE]   [OmnipathR] Contains 1 files.
[2025-03-18 11:42:49] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-03-18 11:42:49] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 11:42:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 11:42:49] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-03-18 11:42:49] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-03-18 11:42:49] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-03-18 11:42:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 11:42:49] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-03-18 11:42:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 11:42:49] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-03-18 11:42:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 11:42:50] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-03-18 11:42:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 11:42:50] [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
[2025-03-18 11:43:26] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 11:43:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 11:43:26] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-03-18 11:43:26] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-03-18 11:43:26] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-03-18 11:43:26] [TRACE]   [OmnipathR] Contains 1 files.
[2025-03-18 11:43:26] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-03-18 11:43:26] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-18 11:43:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 11:43:26] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-03-18 11:43:26] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-03-18 11:43:26] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-03-18 11:43:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 11:43:26] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-03-18 11:43:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 11:43:26] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-03-18 11:43:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 11:43:26] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-03-18 11:43:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-18 11:43:26] [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                           62.476  0.596  63.251
score_candidate_genes_from_PPI 36.833  0.422  38.704
prioritization_genes           35.690  0.431  37.370
random_walk                    35.328  0.382  37.801
weighted_adj                   26.280  0.272  26.603
count_genes                    17.079  1.805  17.120
filter_annot_with_network      15.569  0.246  15.920
common_neighbors               15.082  0.623  49.711
wppi_data                      13.614  0.134  13.764
in_omnipath                     9.171  0.048   9.326
graph_from_op                   9.149  0.063   9.256
subgraph_op                     8.927  0.033   9.075
wppi_omnipath_data              7.236  0.045   7.290
wppi_go_data                    4.984  0.095   5.085
functional_annot                3.619  0.354  10.221
* 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-x86_64/Resources/library’
* installing *source* package ‘wppi’ ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
[2025-03-17 16:54:52] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 16:54:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-17 16:54:52] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-03-17 16:54:52] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-03-17 16:54:52] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-03-17 16:54:52] [TRACE]   [OmnipathR] Contains 1 files.
[2025-03-17 16:54:52] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-03-17 16:54:52] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 16:54:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-17 16:54:52] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-03-17 16:54:52] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-03-17 16:54:52] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-03-17 16:54:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-17 16:54:52] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-03-17 16:54:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-17 16:54:53] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-03-17 16:54:53] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-17 16:54:53] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-03-17 16:54:53] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-17 16:54:53] [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 16:55:01] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 16:55:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-17 16:55:01] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-03-17 16:55:01] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-03-17 16:55:01] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-03-17 16:55:01] [TRACE]   [OmnipathR] Contains 1 files.
[2025-03-17 16:55:01] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-03-17 16:55:01] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 16:55:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-17 16:55:01] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-03-17 16:55:02] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-03-17 16:55:02] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-03-17 16:55:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-17 16:55:02] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-03-17 16:55:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-17 16:55:02] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-03-17 16:55:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-17 16:55:02] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-03-17 16:55:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-17 16:55:02] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2025-03-17 16:55:09] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 16:55:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-17 16:55:09] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-03-17 16:55:09] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-03-17 16:55:09] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-03-17 16:55:09] [TRACE]   [OmnipathR] Contains 1 files.
[2025-03-17 16:55:09] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-03-17 16:55:09] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-17 16:55:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-17 16:55:09] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-03-17 16:55:09] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-03-17 16:55:09] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-03-17 16:55:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-17 16:55:09] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-03-17 16:55:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-17 16:55:09] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-03-17 16:55:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-17 16:55:09] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-03-17 16:55:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-17 16:55:10] [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_neighbors15.082 0.62349.711
count_genes17.079 1.80517.120
filter_annot_with_network15.569 0.24615.920
functional_annot 3.619 0.35410.221
graph_from_op9.1490.0639.256
in_omnipath9.1710.0489.326
prioritization_genes35.690 0.43137.370
process_annot1.7410.0141.858
random_walk35.328 0.38237.801
score_candidate_genes_from_PPI36.833 0.42238.704
subgraph_op8.9270.0339.075
weighted_adj26.280 0.27226.603
wppi62.476 0.59663.251
wppi_data13.614 0.13413.764
wppi_go_data4.9840.0955.085
wppi_hpo_data1.1830.0071.232
wppi_omnipath_data7.2360.0457.290