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This page was generated on 2024-04-18 11:32:21 -0400 (Thu, 18 Apr 2024).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson1macOS 13.6.1 Venturaarm644.3.3 (2024-02-29) -- "Angel Food Cake" 4388
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Package 2248/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
wppi 1.10.0  (landing page)
Ana Galhoz
Snapshot Date: 2024-04-16 09:00:03 -0400 (Tue, 16 Apr 2024)
git_url: https://git.bioconductor.org/packages/wppi
git_branch: RELEASE_3_18
git_last_commit: dc6b662
git_last_commit_date: 2023-10-24 11:31:51 -0400 (Tue, 24 Oct 2023)
kjohnson1macOS 13.6.1 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: 1.10.0
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_1.10.0.tar.gz
StartedAt: 2024-04-18 07:42:53 -0400 (Thu, 18 Apr 2024)
EndedAt: 2024-04-18 07:47:57 -0400 (Thu, 18 Apr 2024)
EllapsedTime: 304.6 seconds
RetCode: 0
Status:   OK  
CheckDir: wppi.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### 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_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/wppi.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: aarch64-apple-darwin20 (64-bit)
* 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 13.6.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘wppi/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘wppi’ version ‘1.10.0’
* 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 ... OK
* 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 startup messages can be suppressed ... NOTE
[2024-04-18 07:43:23] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-18 07:43:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-18 07:43:23] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-04-18 07:43:23] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-04-18 07:43:23] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-04-18 07:43:23] [TRACE]   [OmnipathR] Contains 1 files.
[2024-04-18 07:43:23] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-04-18 07:43:23] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-18 07:43:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-18 07:43:23] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-04-18 07:43:23] [TRACE]   [OmnipathR] Pandoc version: `3.1.2`.
[2024-04-18 07:43:23] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-04-18 07:43:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-18 07:43:23] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-04-18 07:43:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-18 07:43:23] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-04-18 07:43:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-18 07:43:23] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-04-18 07:43:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-18 07:43:23] [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
[2024-04-18 07:43:43] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-18 07:43:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-18 07:43:43] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-04-18 07:43:43] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-04-18 07:43:43] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-04-18 07:43:43] [TRACE]   [OmnipathR] Contains 1 files.
[2024-04-18 07:43:43] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-04-18 07:43:43] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-18 07:43:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-18 07:43:43] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-04-18 07:43:43] [TRACE]   [OmnipathR] Pandoc version: `3.1.2`.
[2024-04-18 07:43:43] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-04-18 07:43:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-18 07:43:43] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-04-18 07:43:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-18 07:43:43] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-04-18 07:43:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-18 07:43:43] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-04-18 07:43:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-18 07:43:43] [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                           34.005  0.564  35.062
score_candidate_genes_from_PPI 17.997  0.309  18.656
prioritization_genes           17.566  0.377  18.436
random_walk                    17.123  0.263  17.684
weighted_adj                   13.384  0.217  13.840
count_genes                    10.571  0.485  11.486
wppi_data                       9.450  0.136   9.717
filter_annot_with_network       8.363  0.194   8.909
common_neighbors                6.814  0.285  50.851
functional_annot                2.626  0.149   6.279
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.18-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/4.3-arm64/Resources/library’
* installing *source* package ‘wppi’ ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
[2024-04-16 11:43:23] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-16 11:43:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-16 11:43:23] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-04-16 11:43:23] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-04-16 11:43:23] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-04-16 11:43:23] [TRACE]   [OmnipathR] Contains 1 files.
[2024-04-16 11:43:23] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-04-16 11:43:23] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-16 11:43:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-16 11:43:23] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-04-16 11:43:23] [TRACE]   [OmnipathR] Pandoc version: `3.1.2`.
[2024-04-16 11:43:23] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-04-16 11:43:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-16 11:43:23] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-04-16 11:43:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-16 11:43:23] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-04-16 11:43:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-16 11:43:23] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-04-16 11:43:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-16 11:43:23] [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
[2024-04-16 11:43:27] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-16 11:43:27] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-16 11:43:27] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-04-16 11:43:27] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-04-16 11:43:27] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-04-16 11:43:27] [TRACE]   [OmnipathR] Contains 1 files.
[2024-04-16 11:43:27] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-04-16 11:43:27] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-16 11:43:27] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-16 11:43:27] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-04-16 11:43:27] [TRACE]   [OmnipathR] Pandoc version: `3.1.2`.
[2024-04-16 11:43:27] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-04-16 11:43:27] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-16 11:43:27] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-04-16 11:43:27] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-16 11:43:27] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-04-16 11:43:27] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-16 11:43:27] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-04-16 11:43:27] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-16 11:43:27] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2024-04-16 11:43:31] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-16 11:43:31] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-16 11:43:31] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-04-16 11:43:31] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-04-16 11:43:31] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-04-16 11:43:31] [TRACE]   [OmnipathR] Contains 1 files.
[2024-04-16 11:43:31] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-04-16 11:43:31] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-16 11:43:31] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-16 11:43:31] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-04-16 11:43:31] [TRACE]   [OmnipathR] Pandoc version: `3.1.2`.
[2024-04-16 11:43:31] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-04-16 11:43:31] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-16 11:43:31] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-04-16 11:43:31] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-16 11:43:31] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-04-16 11:43:31] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-16 11:43:31] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-04-16 11:43:31] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-16 11:43:31] [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 6.814 0.28550.851
count_genes10.571 0.48511.486
filter_annot_with_network8.3630.1948.909
functional_annot2.6260.1496.279
graph_from_op3.6350.0403.745
in_omnipath3.9530.0624.070
prioritization_genes17.566 0.37718.436
process_annot1.2650.0261.319
random_walk17.123 0.26317.684
score_candidate_genes_from_PPI17.997 0.30918.656
subgraph_op3.8050.0363.898
weighted_adj13.384 0.21713.840
wppi34.005 0.56435.062
wppi_data9.4500.1369.717
wppi_go_data4.4230.0884.572
wppi_hpo_data1.0230.0171.055
wppi_omnipath_data3.5560.0273.644