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This page was generated on 2025-03-10 12:12 -0400 (Mon, 10 Mar 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.3 (2025-02-28) -- "Trophy Case" 4670
palomino8Windows Server 2022 Datacenterx644.4.3 (2025-02-28 ucrt) -- "Trophy Case" 4355
merida1macOS 12.7.5 Montereyx86_644.4.3 (2025-02-28) -- "Trophy Case" 4446
kjohnson1macOS 13.6.6 Venturaarm644.4.3 (2025-02-28) -- "Trophy Case" 4439
taishanLinux (openEuler 24.03 LTS)aarch644.4.3 (2025-02-28) -- "Trophy Case" 4306
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Package 2269/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
wppi 1.14.0  (landing page)
Ana Galhoz
Snapshot Date: 2025-03-06 13:00 -0500 (Thu, 06 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 -0500 (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: 2025-03-08 13:31:28 -0500 (Sat, 08 Mar 2025)
EndedAt: 2025-03-08 13:35:55 -0500 (Sat, 08 Mar 2025)
EllapsedTime: 267.1 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
[2025-03-08 13:32:00] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-08 13:32:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-08 13:32:00] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-03-08 13:32:00] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-03-08 13:32:00] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-03-08 13:32:00] [TRACE]   [OmnipathR] Contains 1 files.
[2025-03-08 13:32:00] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-03-08 13:32:00] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-08 13:32:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-08 13:32:00] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-03-08 13:32:00] [TRACE]   [OmnipathR] Pandoc version: `3.1.2`.
[2025-03-08 13:32:00] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-03-08 13:32:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-08 13:32:00] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-03-08 13:32:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-08 13:32:00] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-03-08 13:32:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-08 13:32:00] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-03-08 13:32:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-08 13:32:00] [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
[2025-03-08 13:32:20] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-08 13:32:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-08 13:32:20] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-03-08 13:32:20] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-03-08 13:32:20] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-03-08 13:32:20] [TRACE]   [OmnipathR] Contains 1 files.
[2025-03-08 13:32:20] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-03-08 13:32:20] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-08 13:32:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-08 13:32:20] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-03-08 13:32:20] [TRACE]   [OmnipathR] Pandoc version: `3.1.2`.
[2025-03-08 13:32:20] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-03-08 13:32:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-08 13:32:20] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-03-08 13:32:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-08 13:32:21] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-03-08 13:32:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-08 13:32:21] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-03-08 13:32:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-08 13:32:21] [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                           32.347  0.492  33.389
score_candidate_genes_from_PPI 18.718  0.318  19.221
prioritization_genes           17.946  0.348  18.658
random_walk                    16.622  0.311  17.194
weighted_adj                   13.818  0.273  14.213
count_genes                    12.874  0.549  13.374
wppi_data                       9.336  0.151   9.617
filter_annot_with_network       8.816  0.215   9.397
common_neighbors                6.409  0.296  11.434
* 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
[2025-03-06 17:32:55] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-06 17:32:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-06 17:32:55] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-03-06 17:32:55] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-03-06 17:32:55] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-03-06 17:32:55] [TRACE]   [OmnipathR] Contains 1 files.
[2025-03-06 17:32:55] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-03-06 17:32:55] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-06 17:32:55] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-06 17:32:55] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-03-06 17:32:56] [TRACE]   [OmnipathR] Pandoc version: `3.1.2`.
[2025-03-06 17:32:56] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-03-06 17:32:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-06 17:32:56] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-03-06 17:32:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-06 17:32:56] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-03-06 17:32:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-06 17:32:56] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-03-06 17:32:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-06 17:32:56] [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
[2025-03-06 17:33:00] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-06 17:33:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-06 17:33:00] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-03-06 17:33:00] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-03-06 17:33:00] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-03-06 17:33:00] [TRACE]   [OmnipathR] Contains 1 files.
[2025-03-06 17:33:00] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-03-06 17:33:00] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-06 17:33:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-06 17:33:00] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-03-06 17:33:00] [TRACE]   [OmnipathR] Pandoc version: `3.1.2`.
[2025-03-06 17:33:00] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-03-06 17:33:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-06 17:33:00] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-03-06 17:33:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-06 17:33:00] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-03-06 17:33:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-06 17:33:00] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-03-06 17:33:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-06 17:33:00] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2025-03-06 17:33:04] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-06 17:33:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-06 17:33:04] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-03-06 17:33:04] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-03-06 17:33:04] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-03-06 17:33:04] [TRACE]   [OmnipathR] Contains 1 files.
[2025-03-06 17:33:04] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-03-06 17:33:04] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-06 17:33:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-06 17:33:04] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-03-06 17:33:04] [TRACE]   [OmnipathR] Pandoc version: `3.1.2`.
[2025-03-06 17:33:04] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-03-06 17:33:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-06 17:33:04] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-03-06 17:33:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-06 17:33:04] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-03-06 17:33:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-06 17:33:04] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-03-06 17:33:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-06 17:33:05] [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_neighbors 6.409 0.29611.434
count_genes12.874 0.54913.374
filter_annot_with_network8.8160.2159.397
functional_annot1.8200.1563.232
graph_from_op3.6770.0573.778
in_omnipath3.6940.0613.777
prioritization_genes17.946 0.34818.658
process_annot1.0770.0241.112
random_walk16.622 0.31117.194
score_candidate_genes_from_PPI18.718 0.31819.221
subgraph_op3.7230.0383.778
weighted_adj13.818 0.27314.213
wppi32.347 0.49233.389
wppi_data9.3360.1519.617
wppi_go_data4.7300.1124.890
wppi_hpo_data0.9040.0300.938
wppi_omnipath_data3.6500.0303.716