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This page was generated on 2025-02-01 11:44 -0500 (Sat, 01 Feb 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" 4704
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences" 4467
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2025-01-22 r87618) -- "Unsuffered Consequences" 4478
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" 4431
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 2268/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
wppi 1.15.0  (landing page)
Ana Galhoz
Snapshot Date: 2025-01-31 13:40 -0500 (Fri, 31 Jan 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)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for wppi on lconway

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: 1.15.0
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: 2025-01-31 23:49:15 -0500 (Fri, 31 Jan 2025)
EndedAt: 2025-01-31 23:54:04 -0500 (Fri, 31 Jan 2025)
EllapsedTime: 289.4 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_1.15.0.tar.gz
###
##############################################################################
##############################################################################


* 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
[2025-01-31 23:49:49] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-31 23:49:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-31 23:49:49] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-01-31 23:49:49] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-01-31 23:49:49] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-01-31 23:49:49] [TRACE]   [OmnipathR] Contains 1 files.
[2025-01-31 23:49:49] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-01-31 23:49:49] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-31 23:49:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-31 23:49:49] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-01-31 23:49:49] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-01-31 23:49:49] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-01-31 23:49:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-31 23:49:49] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-01-31 23:49:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-31 23:49:49] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-01-31 23:49:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-31 23:49:49] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-01-31 23:49:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-31 23:49:49] [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
[2025-01-31 23:50:08] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-31 23:50:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-31 23:50:08] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-01-31 23:50:08] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-01-31 23:50:08] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-01-31 23:50:08] [TRACE]   [OmnipathR] Contains 1 files.
[2025-01-31 23:50:08] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-01-31 23:50:08] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-31 23:50:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-31 23:50:08] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-01-31 23:50:09] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-01-31 23:50:09] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-01-31 23:50:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-31 23:50:09] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-01-31 23:50:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-31 23:50:09] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-01-31 23:50:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-31 23:50:09] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-01-31 23:50:09] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-31 23:50:09] [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                           40.421  0.708  41.259
score_candidate_genes_from_PPI 23.076  0.375  23.536
random_walk                    22.258  0.340  22.654
prioritization_genes           21.507  0.371  21.922
weighted_adj                   17.152  0.332  17.544
common_neighbors               13.284  0.338  18.629
count_genes                    10.623  0.862  17.059
filter_annot_with_network       7.281  0.207   7.507
wppi_data                       5.814  0.144   5.970
* 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.

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/4.5-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
[2025-01-31 15:26:28] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-31 15:26:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-31 15:26:28] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-01-31 15:26:28] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-01-31 15:26:28] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-01-31 15:26:28] [TRACE]   [OmnipathR] Contains 1 files.
[2025-01-31 15:26:28] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-01-31 15:26:28] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-31 15:26:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-31 15:26:28] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-01-31 15:26:28] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-01-31 15:26:28] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-01-31 15:26:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-31 15:26:28] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-01-31 15:26:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-31 15:26:28] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-01-31 15:26:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-31 15:26:28] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-01-31 15:26:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-31 15:26:28] [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
[2025-01-31 15:26:33] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-31 15:26:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-31 15:26:33] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-01-31 15:26:33] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-01-31 15:26:33] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-01-31 15:26:33] [TRACE]   [OmnipathR] Contains 1 files.
[2025-01-31 15:26:33] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-01-31 15:26:33] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-31 15:26:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-31 15:26:34] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-01-31 15:26:34] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-01-31 15:26:34] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-01-31 15:26:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-31 15:26:34] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-01-31 15:26:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-31 15:26:34] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-01-31 15:26:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-31 15:26:34] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-01-31 15:26:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-31 15:26:34] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2025-01-31 15:26:38] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-31 15:26:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-31 15:26:38] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-01-31 15:26:38] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-01-31 15:26:38] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-01-31 15:26:38] [TRACE]   [OmnipathR] Contains 1 files.
[2025-01-31 15:26:38] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-01-31 15:26:38] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-31 15:26:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-31 15:26:38] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2025-01-31 15:26:38] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-01-31 15:26:38] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-01-31 15:26:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-31 15:26:38] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-01-31 15:26:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-31 15:26:38] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-01-31 15:26:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-31 15:26:39] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-01-31 15:26:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-31 15:26:39] [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_neighbors13.284 0.33818.629
count_genes10.623 0.86217.059
filter_annot_with_network7.2810.2077.507
functional_annot1.9070.4082.483
graph_from_op3.3240.0283.356
in_omnipath3.2680.0413.320
prioritization_genes21.507 0.37121.922
process_annot0.9280.0080.937
random_walk22.258 0.34022.654
score_candidate_genes_from_PPI23.076 0.37523.536
subgraph_op3.6630.0303.709
weighted_adj17.152 0.33217.544
wppi40.421 0.70841.259
wppi_data5.8140.1445.970
wppi_go_data2.9220.0682.993
wppi_hpo_data0.5520.0030.555
wppi_omnipath_data2.7430.0392.797