Back to Multiple platform build/check report for BioC 3.19:   simplified   long
ABCDEFGHIJKLMNOPQRSTUV[W]XYZ

This page was generated on 2024-03-04 11:40:09 -0500 (Mon, 04 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4676
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences" 4414
merida1macOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4441
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-01-16 r85812) -- "Unsuffered Consequences" 4417
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 2233/2251HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
wppi 1.11.0  (landing page)
Ana Galhoz
Snapshot Date: 2024-03-01 14:00:22 -0500 (Fri, 01 Mar 2024)
git_url: https://git.bioconductor.org/packages/wppi
git_branch: devel
git_last_commit: 3625a02
git_last_commit_date: 2023-10-24 11:31:51 -0500 (Tue, 24 Oct 2023)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / 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: 1.11.0
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_1.11.0.tar.gz
StartedAt: 2024-03-02 12:26:14 -0500 (Sat, 02 Mar 2024)
EndedAt: 2024-03-02 12:35:08 -0500 (Sat, 02 Mar 2024)
EllapsedTime: 534.2 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_1.11.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/wppi.Rcheck’
* using R Under development (unstable) (2024-01-16 r85808)
* 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 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘wppi/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘wppi’ version ‘1.11.0’
* 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 R 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
[2024-03-02 12:27:10] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-02 12:27:10] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-02 12:27:10] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-03-02 12:27:10] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-03-02 12:27:10] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-03-02 12:27:10] [TRACE]   [OmnipathR] Contains 1 files.
[2024-03-02 12:27:10] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-03-02 12:27:10] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-02 12:27:10] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-02 12:27:10] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-03-02 12:27:11] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-03-02 12:27:11] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-03-02 12:27:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-02 12:27:11] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-03-02 12:27:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-02 12:27:11] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-03-02 12:27:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-02 12:27:11] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-03-02 12:27:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-02 12:27:11] [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
[2024-03-02 12:27:46] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-02 12:27:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-02 12:27:46] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-03-02 12:27:46] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-03-02 12:27:46] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-03-02 12:27:46] [TRACE]   [OmnipathR] Contains 1 files.
[2024-03-02 12:27:46] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-03-02 12:27:46] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-02 12:27:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-02 12:27:46] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-03-02 12:27:46] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-03-02 12:27:46] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-03-02 12:27:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-02 12:27:46] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-03-02 12:27:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-02 12:27:46] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-03-02 12:27:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-02 12:27:46] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-03-02 12:27:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-02 12:27:47] [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                           66.562  1.035  79.742
score_candidate_genes_from_PPI 34.730  0.578  41.709
prioritization_genes           34.120  0.590  41.337
random_walk                    33.543  0.510  40.714
weighted_adj                   25.636  0.380  31.473
common_neighbors               14.842  0.644  20.635
wppi_data                      15.211  0.235  17.442
count_genes                    13.759  1.620  16.211
filter_annot_with_network      14.181  0.274  16.758
subgraph_op                     9.224  0.104  11.330
in_omnipath                     9.115  0.116  11.412
graph_from_op                   9.065  0.109  10.600
wppi_omnipath_data              9.009  0.102  10.109
functional_annot                3.574  0.416  11.858
* 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-3.19-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
[2024-03-01 16:04:20] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-01 16:04:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-01 16:04:20] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-03-01 16:04:20] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-03-01 16:04:20] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-03-01 16:04:20] [TRACE]   [OmnipathR] Contains 1 files.
[2024-03-01 16:04:20] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-03-01 16:04:20] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-01 16:04:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-01 16:04:20] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-03-01 16:04:20] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-03-01 16:04:20] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-03-01 16:04:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-01 16:04:20] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-03-01 16:04:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-01 16:04:20] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-03-01 16:04:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-01 16:04:20] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-03-01 16:04:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-01 16:04:20] [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
[2024-03-01 16:04:28] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-01 16:04:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-01 16:04:28] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-03-01 16:04:28] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-03-01 16:04:28] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-03-01 16:04:28] [TRACE]   [OmnipathR] Contains 1 files.
[2024-03-01 16:04:28] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-03-01 16:04:28] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-01 16:04:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-01 16:04:28] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-03-01 16:04:29] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-03-01 16:04:29] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-03-01 16:04:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-01 16:04:29] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-03-01 16:04:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-01 16:04:29] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-03-01 16:04:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-01 16:04:29] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-03-01 16:04:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-01 16:04:29] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2024-03-01 16:04:35] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-01 16:04:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-01 16:04:35] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-03-01 16:04:35] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-03-01 16:04:35] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-03-01 16:04:35] [TRACE]   [OmnipathR] Contains 1 files.
[2024-03-01 16:04:35] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-03-01 16:04:35] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-03-01 16:04:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-01 16:04:35] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-03-01 16:04:35] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-03-01 16:04:35] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-03-01 16:04:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-01 16:04:35] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-03-01 16:04:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-01 16:04:36] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-03-01 16:04:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-01 16:04:36] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-03-01 16:04:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-03-01 16:04:36] [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_neighbors14.842 0.64420.635
count_genes13.759 1.62016.211
filter_annot_with_network14.181 0.27416.758
functional_annot 3.574 0.41611.858
graph_from_op 9.065 0.10910.600
in_omnipath 9.115 0.11611.412
prioritization_genes34.120 0.59041.337
process_annot1.7240.0362.111
random_walk33.543 0.51040.714
score_candidate_genes_from_PPI34.730 0.57841.709
subgraph_op 9.224 0.10411.330
weighted_adj25.636 0.38031.473
wppi66.562 1.03579.742
wppi_data15.211 0.23517.442
wppi_go_data4.3440.0414.901
wppi_hpo_data1.4730.0491.711
wppi_omnipath_data 9.009 0.10210.109