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This page was generated on 2025-03-10 12:08 -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
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: 2025-03-06 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 palomino8

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: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:wppi.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings wppi_1.14.0.tar.gz
StartedAt: 2025-03-07 07:18:55 -0500 (Fri, 07 Mar 2025)
EndedAt: 2025-03-07 07:23:44 -0500 (Fri, 07 Mar 2025)
EllapsedTime: 289.5 seconds
RetCode: 0
Status:   OK  
CheckDir: wppi.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:wppi.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings wppi_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/wppi.Rcheck'
* using R version 4.4.3 (2025-02-28 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* 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 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
[2025-03-07 07:19:35] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-07 07:19:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-07 07:19:35] [INFO]    [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-03-07 07:19:35] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-03-07 07:19:35] [TRACE]   [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-03-07 07:19:35] [TRACE]   [OmnipathR] Contains 1 files.
[2025-03-07 07:19:35] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-03-07 07:19:35] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-07 07:19:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-07 07:19:35] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-03-07 07:19:35] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-03-07 07:19:35] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-03-07 07:19:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-07 07:19:35] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-03-07 07:19:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-07 07:19:35] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-03-07 07:19:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-07 07:19:35] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-03-07 07:19:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-07 07:19:35] [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
[2025-03-07 07:19:57] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-07 07:19:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-07 07:19:57] [INFO]    [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-03-07 07:19:57] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-03-07 07:19:57] [TRACE]   [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-03-07 07:19:57] [TRACE]   [OmnipathR] Contains 1 files.
[2025-03-07 07:19:57] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-03-07 07:19:57] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-07 07:19:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-07 07:19:57] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-03-07 07:19:57] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-03-07 07:19:57] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-03-07 07:19:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-07 07:19:57] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-03-07 07:19:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-07 07:19:57] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-03-07 07:19:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-07 07:19:57] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-03-07 07:19:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-07 07:19:57] [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                           39.45   0.82   40.27
score_candidate_genes_from_PPI 21.83   0.42   22.27
prioritization_genes           19.78   0.50   20.28
random_walk                    18.37   0.43   18.80
weighted_adj                   14.11   0.31   14.42
count_genes                    13.31   0.97   13.14
filter_annot_with_network       8.55   0.22    8.82
wppi_data                       7.78   0.17    7.95
common_neighbors                7.57   0.36   10.16
* 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
  'F:/biocbuild/bbs-3.20-bioc/meat/wppi.Rcheck/00check.log'
for details.

Installation output

wppi.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL wppi
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library'
* installing *source* package 'wppi' ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
[2025-03-06 16:47:05] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-06 16:47:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-06 16:47:05] [INFO]    [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-03-06 16:47:05] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-03-06 16:47:05] [TRACE]   [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-03-06 16:47:05] [TRACE]   [OmnipathR] Contains 1 files.
[2025-03-06 16:47:05] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-03-06 16:47:05] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-06 16:47:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-06 16:47:05] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-03-06 16:47:05] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-03-06 16:47:05] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-03-06 16:47:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-06 16:47:05] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-03-06 16:47:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-06 16:47:05] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-03-06 16:47:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-06 16:47:05] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-03-06 16:47:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-06 16:47:05] [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
[2025-03-06 16:47:15] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-06 16:47:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-06 16:47:15] [INFO]    [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-03-06 16:47:15] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-03-06 16:47:15] [TRACE]   [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-03-06 16:47:15] [TRACE]   [OmnipathR] Contains 1 files.
[2025-03-06 16:47:15] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-03-06 16:47:15] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-06 16:47:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-06 16:47:15] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-03-06 16:47:15] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-03-06 16:47:15] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-03-06 16:47:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-06 16:47:15] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-03-06 16:47:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-06 16:47:15] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-03-06 16:47:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-06 16:47:15] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-03-06 16:47:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-06 16:47:15] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2025-03-06 16:47:19] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-06 16:47:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-06 16:47:19] [INFO]    [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-03-06 16:47:19] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-03-06 16:47:19] [TRACE]   [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-03-06 16:47:19] [TRACE]   [OmnipathR] Contains 1 files.
[2025-03-06 16:47:19] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-03-06 16:47:19] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-06 16:47:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-06 16:47:19] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-03-06 16:47:19] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-03-06 16:47:19] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-03-06 16:47:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-06 16:47:19] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-03-06 16:47:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-06 16:47:19] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-03-06 16:47:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-06 16:47:19] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.20-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-03-06 16:47:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-06 16:47:19] [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 7.57 0.3610.16
count_genes13.31 0.9713.14
filter_annot_with_network8.550.228.82
functional_annot2.240.172.70
graph_from_op3.670.063.74
in_omnipath4.590.074.66
prioritization_genes19.78 0.5020.28
process_annot1.130.031.15
random_walk18.37 0.4318.80
score_candidate_genes_from_PPI21.83 0.4222.27
subgraph_op3.630.113.73
weighted_adj14.11 0.3114.42
wppi39.45 0.8240.27
wppi_data7.780.177.95
wppi_go_data4.190.064.25
wppi_hpo_data0.970.020.99
wppi_omnipath_data4.510.014.53