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This page was generated on 2024-05-30 11:35:23 -0400 (Thu, 30 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4753
lconwaymacOS 12.7.1 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4518
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 2282/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
wppi 1.12.0  (landing page)
Ana Galhoz
Snapshot Date: 2024-05-29 14:00:10 -0400 (Wed, 29 May 2024)
git_url: https://git.bioconductor.org/packages/wppi
git_branch: RELEASE_3_19
git_last_commit: 1ad2e46
git_last_commit_date: 2024-04-30 11:33:03 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64see weekly results here

CHECK results for wppi on nebbiolo1


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: 1.12.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:wppi.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings wppi_1.12.0.tar.gz
StartedAt: 2024-05-30 03:52:50 -0400 (Thu, 30 May 2024)
EndedAt: 2024-05-30 03:57:12 -0400 (Thu, 30 May 2024)
EllapsedTime: 261.3 seconds
RetCode: 0
Status:   OK  
CheckDir: wppi.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:wppi.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings wppi_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/wppi.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-pc-linux-gnu
* 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 ‘1.12.0’
* 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 loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... NOTE
[2024-05-30 03:53:18] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-30 03:53:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-30 03:53:18] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-05-30 03:53:18] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-05-30 03:53:18] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-05-30 03:53:18] [TRACE]   [OmnipathR] Contains 1 files.
[2024-05-30 03:53:18] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-05-30 03:53:18] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-30 03:53:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-30 03:53:18] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-05-30 03:53:18] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-05-30 03:53:18] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-05-30 03:53:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-30 03:53:18] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-05-30 03:53:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-30 03:53:18] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-05-30 03:53:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-30 03:53:18] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-05-30 03:53:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-30 03:53:18] [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
[2024-05-30 03:53:32] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-30 03:53:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-30 03:53:32] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-05-30 03:53:32] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-05-30 03:53:32] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-05-30 03:53:32] [TRACE]   [OmnipathR] Contains 1 files.
[2024-05-30 03:53:32] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-05-30 03:53:32] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-30 03:53:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-30 03:53:32] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-05-30 03:53:32] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-05-30 03:53:32] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-05-30 03:53:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-30 03:53:32] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-05-30 03:53:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-30 03:53:32] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-05-30 03:53:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-30 03:53:32] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-05-30 03:53:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-30 03:53:32] [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                           28.379  0.203  28.584
score_candidate_genes_from_PPI 14.223  0.148  14.371
prioritization_genes           13.786  0.279  14.065
random_walk                    13.481  0.163  13.644
weighted_adj                   10.460  0.100  10.560
count_genes                     8.835  0.584   8.895
common_neighbors                6.716  0.636  15.343
wppi_data                       6.522  0.076   6.598
filter_annot_with_network       6.192  0.099   6.292
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/wppi.Rcheck/00check.log’
for details.

Installation output

wppi.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL wppi
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’
* installing *source* package ‘wppi’ ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
[2024-05-29 15:27:42] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-29 15:27:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-29 15:27:42] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-05-29 15:27:42] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-05-29 15:27:42] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-05-29 15:27:42] [TRACE]   [OmnipathR] Contains 1 files.
[2024-05-29 15:27:42] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-05-29 15:27:42] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-29 15:27:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-29 15:27:42] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-05-29 15:27:42] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-05-29 15:27:42] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-05-29 15:27:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-29 15:27:42] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-05-29 15:27:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-29 15:27:42] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-05-29 15:27:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-29 15:27:42] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-05-29 15:27:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-29 15:27:42] [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
[2024-05-29 15:27:45] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-29 15:27:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-29 15:27:45] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-05-29 15:27:45] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-05-29 15:27:45] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-05-29 15:27:45] [TRACE]   [OmnipathR] Contains 1 files.
[2024-05-29 15:27:45] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-05-29 15:27:45] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-29 15:27:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-29 15:27:45] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-05-29 15:27:45] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-05-29 15:27:45] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-05-29 15:27:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-29 15:27:45] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-05-29 15:27:45] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-29 15:27:45] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-05-29 15:27:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-29 15:27:46] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-05-29 15:27:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-29 15:27:46] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2024-05-29 15:27:48] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-29 15:27:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-29 15:27:48] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2024-05-29 15:27:48] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-05-29 15:27:48] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2024-05-29 15:27:48] [TRACE]   [OmnipathR] Contains 1 files.
[2024-05-29 15:27:48] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-05-29 15:27:48] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-29 15:27:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-29 15:27:48] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2024-05-29 15:27:48] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-05-29 15:27:48] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-05-29 15:27:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-29 15:27:48] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-05-29 15:27:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-29 15:27:48] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-05-29 15:27:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-29 15:27:48] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-05-29 15:27:48] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-29 15:27:48] [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 6.716 0.63615.343
count_genes8.8350.5848.895
filter_annot_with_network6.1920.0996.292
functional_annot2.0190.2243.469
graph_from_op3.1480.1003.247
in_omnipath3.4360.0993.536
prioritization_genes13.786 0.27914.065
process_annot0.8010.0200.821
random_walk13.481 0.16313.644
score_candidate_genes_from_PPI14.223 0.14814.371
subgraph_op3.5920.0563.648
weighted_adj10.46 0.1010.56
wppi28.379 0.20328.584
wppi_data6.5220.0766.598
wppi_go_data2.6130.0242.637
wppi_hpo_data1.0770.0121.090
wppi_omnipath_data3.0140.0003.014