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This page was generated on 2024-05-13 11:32:16 -0400 (Mon, 13 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson1macOS 13.6.6 Venturaarm644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4378
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Package 2212/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
wppi 1.13.0  (landing page)
Ana Galhoz
Snapshot Date: 2024-05-11 09:00:03 -0400 (Sat, 11 May 2024)
git_url: https://git.bioconductor.org/packages/wppi
git_branch: devel
git_last_commit: 65eba9a
git_last_commit_date: 2024-04-30 11:33:03 -0400 (Tue, 30 Apr 2024)
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    NA  

CHECK results for wppi on kjohnson1


To the developers/maintainers of the wppi package:
- 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: 1.13.0
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_1.13.0.tar.gz
StartedAt: 2024-05-13 06:45:13 -0400 (Mon, 13 May 2024)
EndedAt: 2024-05-13 06:49:09 -0400 (Mon, 13 May 2024)
EllapsedTime: 236.1 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_1.13.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc-mac-arm64/meat/wppi.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* 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 13.6.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘wppi/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘wppi’ version ‘1.13.0’
* 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
[2024-05-13 06:45:40] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-13 06:45:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-13 06:45:40] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-05-13 06:45:40] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-05-13 06:45:40] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-05-13 06:45:40] [TRACE]   [OmnipathR] Contains 1 files.
[2024-05-13 06:45:40] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-05-13 06:45:40] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-13 06:45:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-13 06:45:40] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-05-13 06:45:40] [TRACE]   [OmnipathR] Pandoc version: `3.1.2`.
[2024-05-13 06:45:40] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-05-13 06:45:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-13 06:45:40] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-05-13 06:45:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-13 06:45:40] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-05-13 06:45:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-13 06:45:40] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-05-13 06:45:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-13 06:45:40] [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
[2024-05-13 06:45:58] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-13 06:45:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-13 06:45:58] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-05-13 06:45:58] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-05-13 06:45:58] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-05-13 06:45:58] [TRACE]   [OmnipathR] Contains 1 files.
[2024-05-13 06:45:58] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-05-13 06:45:58] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-13 06:45:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-13 06:45:58] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-05-13 06:45:58] [TRACE]   [OmnipathR] Pandoc version: `3.1.2`.
[2024-05-13 06:45:58] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-05-13 06:45:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-13 06:45:58] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-05-13 06:45:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-13 06:45:58] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-05-13 06:45:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-13 06:45:58] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-05-13 06:45:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-13 06:45:58] [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                           31.404  0.530  32.434
prioritization_genes           16.301  0.308  17.026
score_candidate_genes_from_PPI 16.047  0.284  16.737
random_walk                    15.799  0.310  16.259
weighted_adj                   12.789  0.261  13.161
count_genes                     9.472  0.417  10.032
wppi_data                       7.808  0.119   7.967
filter_annot_with_network       7.173  0.180   7.466
common_neighbors                6.514  0.268   8.325
* 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-mac-arm64/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
[2024-05-11 11:39:38] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-11 11:39:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-11 11:39:38] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-05-11 11:39:38] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-05-11 11:39:38] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-05-11 11:39:38] [TRACE]   [OmnipathR] Contains 1 files.
[2024-05-11 11:39:38] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-05-11 11:39:38] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-11 11:39:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-11 11:39:38] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-05-11 11:39:38] [TRACE]   [OmnipathR] Pandoc version: `3.1.2`.
[2024-05-11 11:39:38] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-05-11 11:39:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-11 11:39:38] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-05-11 11:39:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-11 11:39:38] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-05-11 11:39:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-11 11:39:38] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-05-11 11:39:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-11 11:39:38] [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
[2024-05-11 11:39:42] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-11 11:39:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-11 11:39:42] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-05-11 11:39:42] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-05-11 11:39:42] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-05-11 11:39:42] [TRACE]   [OmnipathR] Contains 1 files.
[2024-05-11 11:39:42] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-05-11 11:39:42] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-11 11:39:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-11 11:39:42] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-05-11 11:39:42] [TRACE]   [OmnipathR] Pandoc version: `3.1.2`.
[2024-05-11 11:39:42] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-05-11 11:39:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-11 11:39:42] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-05-11 11:39:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-11 11:39:42] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-05-11 11:39:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-11 11:39:42] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-05-11 11:39:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-11 11:39:42] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2024-05-11 11:39:45] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-11 11:39:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-11 11:39:45] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-05-11 11:39:45] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-05-11 11:39:45] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-05-11 11:39:45] [TRACE]   [OmnipathR] Contains 1 files.
[2024-05-11 11:39:45] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-05-11 11:39:45] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-11 11:39:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-11 11:39:45] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-05-11 11:39:45] [TRACE]   [OmnipathR] Pandoc version: `3.1.2`.
[2024-05-11 11:39:45] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-05-11 11:39:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-11 11:39:45] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-05-11 11:39:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-11 11:39:45] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-05-11 11:39:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-11 11:39:45] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-05-11 11:39:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-11 11:39:45] [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_neighbors6.5140.2688.325
count_genes 9.472 0.41710.032
filter_annot_with_network7.1730.1807.466
functional_annot1.8980.1233.273
graph_from_op3.6330.0583.774
in_omnipath4.1390.0524.238
prioritization_genes16.301 0.30817.026
process_annot1.1210.0281.197
random_walk15.799 0.31016.259
score_candidate_genes_from_PPI16.047 0.28416.737
subgraph_op3.8490.0333.895
weighted_adj12.789 0.26113.161
wppi31.404 0.53032.434
wppi_data7.8080.1197.967
wppi_go_data4.1500.0774.237
wppi_hpo_data0.8890.0250.916
wppi_omnipath_data3.6890.0283.731