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This page was generated on 2024-04-17 11:36:30 -0400 (Wed, 17 Apr 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4676
palomino4Windows Server 2022 Datacenterx644.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" 4414
merida1macOS 12.7.1 Montereyx86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4437
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 2248/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
wppi 1.10.0  (landing page)
Ana Galhoz
Snapshot Date: 2024-04-15 14:05:01 -0400 (Mon, 15 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)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows 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
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for wppi on nebbiolo2


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: 1.10.0
Command: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:wppi.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings wppi_1.10.0.tar.gz
StartedAt: 2024-04-16 05:14:12 -0400 (Tue, 16 Apr 2024)
EndedAt: 2024-04-16 05:20:31 -0400 (Tue, 16 Apr 2024)
EllapsedTime: 378.6 seconds
RetCode: 0
Status:   OK  
CheckDir: wppi.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:wppi.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings wppi_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/wppi.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* 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 loading without being on the library search path ... OK
* checking startup messages can be suppressed ... NOTE
[2024-04-16 05:14:40] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-16 05:14:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-16 05:14:40] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-04-16 05:14:40] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-04-16 05:14:40] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-04-16 05:14:40] [TRACE]   [OmnipathR] Contains 1 files.
[2024-04-16 05:14:40] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-04-16 05:14:40] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-16 05:14:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-16 05:14:40] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-04-16 05:14:40] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-04-16 05:14:40] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.18-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-04-16 05:14:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-16 05:14:40] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.18-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-04-16 05:14:40] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-16 05:14:41] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.18-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-04-16 05:14:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-16 05:14:41] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.18-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-04-16 05:14:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-16 05:14:41] [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
[2024-04-16 05:14:53] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-16 05:14:53] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-16 05:14:53] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-04-16 05:14:53] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-04-16 05:14:53] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-04-16 05:14:53] [TRACE]   [OmnipathR] Contains 1 files.
[2024-04-16 05:14:53] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-04-16 05:14:53] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-16 05:14:53] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-16 05:14:53] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-04-16 05:14:53] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-04-16 05:14:53] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.18-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-04-16 05:14:53] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-16 05:14:53] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.18-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-04-16 05:14:53] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-16 05:14:54] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.18-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-04-16 05:14:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-16 05:14:54] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.18-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-04-16 05:14:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-16 05:14:54] [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                           28.637  0.200  28.837
prioritization_genes           14.827  0.128  14.956
random_walk                    14.279  0.172  14.452
score_candidate_genes_from_PPI 14.251  0.123  14.374
weighted_adj                   10.172  0.048  10.219
count_genes                     8.669  0.589   8.973
common_neighbors                6.812  0.330  49.891
wppi_data                       6.659  0.060   6.719
filter_annot_with_network       6.239  0.112   6.351
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘wppi_workflow.Rmd’ using ‘UTF-8’... OK
 OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/wppi.Rcheck/00check.log’
for details.

Installation output

wppi.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL wppi
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.18-bioc/R/site-library’
* installing *source* package ‘wppi’ ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
[2024-04-15 15:31:54] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-15 15:31:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 15:31:54] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-04-15 15:31:54] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-04-15 15:31:54] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-04-15 15:31:54] [TRACE]   [OmnipathR] Contains 1 files.
[2024-04-15 15:31:54] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-04-15 15:31:54] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-15 15:31:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 15:31:54] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-04-15 15:31:54] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-04-15 15:31:54] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.18-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-04-15 15:31:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 15:31:54] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.18-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-04-15 15:31:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 15:31:54] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.18-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-04-15 15:31:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 15:31:54] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.18-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-04-15 15:31:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 15:31:54] [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
[2024-04-15 15:31:57] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-15 15:31:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 15:31:57] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-04-15 15:31:57] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-04-15 15:31:57] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-04-15 15:31:57] [TRACE]   [OmnipathR] Contains 1 files.
[2024-04-15 15:31:57] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-04-15 15:31:57] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-15 15:31:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 15:31:57] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-04-15 15:31:57] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-04-15 15:31:57] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.18-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-04-15 15:31:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 15:31:58] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.18-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-04-15 15:31:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 15:31:58] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.18-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-04-15 15:31:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 15:31:58] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.18-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-04-15 15:31:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 15:31:58] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2024-04-15 15:32:00] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-15 15:32:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 15:32:00] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-04-15 15:32:00] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-04-15 15:32:00] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-04-15 15:32:00] [TRACE]   [OmnipathR] Contains 1 files.
[2024-04-15 15:32:00] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-04-15 15:32:00] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-15 15:32:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 15:32:00] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-04-15 15:32:00] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-04-15 15:32:00] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.18-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-04-15 15:32:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 15:32:00] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.18-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-04-15 15:32:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 15:32:00] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.18-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-04-15 15:32:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 15:32:00] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.18-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-04-15 15:32:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 15:32:00] [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 6.812 0.33049.891
count_genes8.6690.5898.973
filter_annot_with_network6.2390.1126.351
functional_annot1.9540.2053.394
graph_from_op3.1500.0443.195
in_omnipath3.3690.0283.396
prioritization_genes14.827 0.12814.956
process_annot0.8410.0240.865
random_walk14.279 0.17214.452
score_candidate_genes_from_PPI14.251 0.12314.374
subgraph_op3.3150.0603.374
weighted_adj10.172 0.04810.219
wppi28.637 0.20028.837
wppi_data6.6590.0606.719
wppi_go_data2.2230.0202.243
wppi_hpo_data0.7720.0120.784
wppi_omnipath_data3.1910.0043.194