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This page was generated on 2023-05-31 05:44:46 -0000 (Wed, 31 May 2023).

HostnameOSArch (*)R versionInstalled pkgs
kunpeng1Linux (Ubuntu 22.04.1 LTS)aarch644.3.0 (2023-04-21) -- "Already Tomorrow" 4219
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CHECK results for wppi on kunpeng1


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.

Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details.

raw results

Package 2179/2197HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
wppi 1.9.0  (landing page)
Ana Galhoz
Snapshot Date: 2023-05-29 10:19:22 -0000 (Mon, 29 May 2023)
git_url: https://git.bioconductor.org/packages/wppi
git_branch: devel
git_last_commit: 64a68df
git_last_commit_date: 2023-04-25 15:28:27 -0000 (Tue, 25 Apr 2023)
kunpeng1Linux (Ubuntu 22.04.1 LTS) / aarch64  OK    OK    OK  

Summary

Package: wppi
Version: 1.9.0
Command: /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:wppi.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings wppi_1.9.0.tar.gz
StartedAt: 2023-05-30 22:31:29 -0000 (Tue, 30 May 2023)
EndedAt: 2023-05-30 22:45:28 -0000 (Tue, 30 May 2023)
EllapsedTime: 839.1 seconds
RetCode: 0
Status:   OK  
CheckDir: wppi.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:wppi.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings wppi_1.9.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/wppi.Rcheck’
* using R version 4.3.0 (2023-04-21)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘wppi/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘wppi’ version ‘1.9.0’
* 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
[2023-05-30 22:31:58] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-30 22:31:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-05-30 22:31:58] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2023-05-30 22:31:58] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2023-05-30 22:31:58] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2023-05-30 22:31:58] [TRACE]   [OmnipathR] Contains 1 files.
[2023-05-30 22:31:58] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2023-05-30 22:31:58] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-30 22:31:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-05-30 22:31:58] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2023-05-30 22:31:58] [TRACE]   [OmnipathR] Pandoc version: `2.9.2.1`.
[2023-05-30 22:31:58] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.3.0/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2023-05-30 22:31:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-05-30 22:31:58] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.3.0/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2023-05-30 22:31:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-05-30 22:31:58] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.3.0/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2023-05-30 22:31:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-05-30 22:31:58] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.3.0/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2023-05-30 22:31:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-05-30 22:31:58] [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
[2023-05-30 22:32:15] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-30 22:32:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-05-30 22:32:15] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2023-05-30 22:32:15] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2023-05-30 22:32:15] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2023-05-30 22:32:15] [TRACE]   [OmnipathR] Contains 1 files.
[2023-05-30 22:32:15] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2023-05-30 22:32:15] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-30 22:32:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-05-30 22:32:15] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2023-05-30 22:32:15] [TRACE]   [OmnipathR] Pandoc version: `2.9.2.1`.
[2023-05-30 22:32:15] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.3.0/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2023-05-30 22:32:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-05-30 22:32:15] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.3.0/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2023-05-30 22:32:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-05-30 22:32:15] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.3.0/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2023-05-30 22:32:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-05-30 22:32:15] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.3.0/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2023-05-30 22:32:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-05-30 22:32:15] [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                           41.986  0.132  42.118
prioritization_genes           21.497  0.086  21.584
score_candidate_genes_from_PPI 20.971  0.071  21.043
random_walk                    20.801  0.131  20.932
weighted_adj                   15.905  0.039  15.945
count_genes                    11.204  0.817  19.297
common_neighbors                7.950  0.828 131.015
wppi_data                       8.432  0.028   8.461
filter_annot_with_network       7.991  0.111   8.102
functional_annot                1.845  0.139  10.266
* 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
 NONE
* 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/R/R-4.3.0/bin/R CMD INSTALL wppi
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.3.0/site-library’
* installing *source* package ‘wppi’ ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
[2023-05-29 13:18:35] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-29 13:18:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-05-29 13:18:35] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2023-05-29 13:18:35] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2023-05-29 13:18:35] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2023-05-29 13:18:35] [TRACE]   [OmnipathR] Contains 1 files.
[2023-05-29 13:18:35] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2023-05-29 13:18:35] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-29 13:18:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-05-29 13:18:35] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2023-05-29 13:18:35] [TRACE]   [OmnipathR] Pandoc version: `2.9.2.1`.
[2023-05-29 13:18:35] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.3.0/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2023-05-29 13:18:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-05-29 13:18:35] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.3.0/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2023-05-29 13:18:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-05-29 13:18:35] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.3.0/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2023-05-29 13:18:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-05-29 13:18:35] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.3.0/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2023-05-29 13:18:35] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-05-29 13:18:35] [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
[2023-05-29 13:18:39] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-29 13:18:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-05-29 13:18:39] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2023-05-29 13:18:39] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2023-05-29 13:18:39] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2023-05-29 13:18:39] [TRACE]   [OmnipathR] Contains 1 files.
[2023-05-29 13:18:39] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2023-05-29 13:18:39] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-29 13:18:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-05-29 13:18:39] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2023-05-29 13:18:39] [TRACE]   [OmnipathR] Pandoc version: `2.9.2.1`.
[2023-05-29 13:18:39] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.3.0/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2023-05-29 13:18:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-05-29 13:18:39] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.3.0/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2023-05-29 13:18:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-05-29 13:18:39] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.3.0/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2023-05-29 13:18:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-05-29 13:18:39] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.3.0/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2023-05-29 13:18:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-05-29 13:18:39] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2023-05-29 13:18:43] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-29 13:18:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-05-29 13:18:43] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2023-05-29 13:18:43] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2023-05-29 13:18:43] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2023-05-29 13:18:43] [TRACE]   [OmnipathR] Contains 1 files.
[2023-05-29 13:18:43] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2023-05-29 13:18:43] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-29 13:18:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-05-29 13:18:43] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2023-05-29 13:18:43] [TRACE]   [OmnipathR] Pandoc version: `2.9.2.1`.
[2023-05-29 13:18:43] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.3.0/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2023-05-29 13:18:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-05-29 13:18:43] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.3.0/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2023-05-29 13:18:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-05-29 13:18:43] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.3.0/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2023-05-29 13:18:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-05-29 13:18:43] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.3.0/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2023-05-29 13:18:43] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-05-29 13:18:43] [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 7.950 0.828131.015
count_genes11.204 0.81719.297
filter_annot_with_network7.9910.1118.102
functional_annot 1.845 0.13910.266
graph_from_op4.4820.0554.538
in_omnipath4.4920.0074.500
prioritization_genes21.497 0.08621.584
process_annot0.7540.0080.762
random_walk20.801 0.13120.932
score_candidate_genes_from_PPI20.971 0.07121.043
subgraph_op4.4060.0004.407
weighted_adj15.905 0.03915.945
wppi41.986 0.13242.118
wppi_data8.4320.0288.461
wppi_go_data3.5220.0163.538
wppi_hpo_data0.4790.0040.484
wppi_omnipath_data4.2620.0044.266