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This page was generated on 2023-05-10 10:04:43 -0000 (Wed, 10 May 2023).

HostnameOSArch (*)R versionInstalled pkgs
kunpeng1Linux (Ubuntu 22.04.1 LTS)aarch64R Under development (unstable) (2023-03-12 r83975) -- "Unsuffered Consequences" 6211
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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 2176/2194HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
wppi 1.9.0  (landing page)
Ana Galhoz
Snapshot Date: 2023-05-08 19:11:19 -0000 (Mon, 08 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/bbs-3.17-bioc/R/bin/R CMD check --install=check:wppi.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings wppi_1.9.0.tar.gz
StartedAt: 2023-05-10 08:16:52 -0000 (Wed, 10 May 2023)
EndedAt: 2023-05-10 08:22:46 -0000 (Wed, 10 May 2023)
EllapsedTime: 353.5 seconds
RetCode: 0
Status:   OK  
CheckDir: wppi.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:wppi.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings wppi_1.9.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/wppi.Rcheck’
* using R Under development (unstable) (2023-03-12 r83975)
* 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 startup messages can be suppressed ... NOTE
[2023-05-10 08:17:16] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-10 08:17:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-05-10 08:17:16] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2023-05-10 08:17:16] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2023-05-10 08:17:16] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2023-05-10 08:17:16] [TRACE]   [OmnipathR] Contains 1 files.
[2023-05-10 08:17:16] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2023-05-10 08:17:16] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-10 08:17:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-05-10 08:17:16] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2023-05-10 08:17:16] [TRACE]   [OmnipathR] Pandoc version: `2.9.2.1`.
[2023-05-10 08:17:16] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2023-05-10 08:17:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-05-10 08:17:16] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2023-05-10 08:17:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-05-10 08:17:16] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2023-05-10 08:17:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-05-10 08:17:16] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2023-05-10 08:17:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-05-10 08:17:16] [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
[2023-05-10 08:17:32] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-10 08:17:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-05-10 08:17:32] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2023-05-10 08:17:32] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2023-05-10 08:17:32] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2023-05-10 08:17:32] [TRACE]   [OmnipathR] Contains 1 files.
[2023-05-10 08:17:32] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2023-05-10 08:17:32] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-10 08:17:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-05-10 08:17:32] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2023-05-10 08:17:32] [TRACE]   [OmnipathR] Pandoc version: `2.9.2.1`.
[2023-05-10 08:17:32] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2023-05-10 08:17:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-05-10 08:17:32] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2023-05-10 08:17:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-05-10 08:17:32] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2023-05-10 08:17:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-05-10 08:17:32] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2023-05-10 08:17:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-05-10 08:17:32] [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                           39.900  0.239  40.142
prioritization_genes           20.511  0.270  20.781
score_candidate_genes_from_PPI 20.375  0.167  20.542
random_walk                    20.026  0.183  20.209
weighted_adj                   15.373  0.124  15.498
count_genes                    11.166  1.017  17.622
wppi_data                       8.097  0.064   8.160
filter_annot_with_network       7.861  0.142   8.004
common_neighbors                7.318  0.302  12.449
functional_annot                1.834  0.172  12.153
* 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-3.17-bioc/meat/wppi.Rcheck/00check.log’
for details.

Installation output

wppi.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL wppi
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library’
* installing *source* package ‘wppi’ ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
[2023-05-08 21:57:00] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-08 21:57:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-05-08 21:57:00] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2023-05-08 21:57:00] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2023-05-08 21:57:00] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2023-05-08 21:57:00] [TRACE]   [OmnipathR] Contains 1 files.
[2023-05-08 21:57:00] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2023-05-08 21:57:00] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-08 21:57:00] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-05-08 21:57:00] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2023-05-08 21:57:01] [TRACE]   [OmnipathR] Pandoc version: `2.9.2.1`.
[2023-05-08 21:57:01] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2023-05-08 21:57:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-05-08 21:57:01] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2023-05-08 21:57:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-05-08 21:57:01] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2023-05-08 21:57:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-05-08 21:57:01] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2023-05-08 21:57:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-05-08 21:57:01] [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
[2023-05-08 21:57:05] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-08 21:57:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-05-08 21:57:05] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2023-05-08 21:57:05] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2023-05-08 21:57:05] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2023-05-08 21:57:05] [TRACE]   [OmnipathR] Contains 1 files.
[2023-05-08 21:57:05] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2023-05-08 21:57:05] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-08 21:57:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-05-08 21:57:05] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2023-05-08 21:57:05] [TRACE]   [OmnipathR] Pandoc version: `2.9.2.1`.
[2023-05-08 21:57:05] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2023-05-08 21:57:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-05-08 21:57:05] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2023-05-08 21:57:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-05-08 21:57:05] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2023-05-08 21:57:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-05-08 21:57:05] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2023-05-08 21:57:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-05-08 21:57:05] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2023-05-08 21:57:08] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-08 21:57:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-05-08 21:57:08] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2023-05-08 21:57:08] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2023-05-08 21:57:08] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2023-05-08 21:57:08] [TRACE]   [OmnipathR] Contains 1 files.
[2023-05-08 21:57:08] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2023-05-08 21:57:08] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-05-08 21:57:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-05-08 21:57:08] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2023-05-08 21:57:08] [TRACE]   [OmnipathR] Pandoc version: `2.9.2.1`.
[2023-05-08 21:57:08] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2023-05-08 21:57:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-05-08 21:57:08] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2023-05-08 21:57:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-05-08 21:57:08] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2023-05-08 21:57:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-05-08 21:57:08] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2023-05-08 21:57:08] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-05-08 21:57:08] [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 7.318 0.30212.449
count_genes11.166 1.01717.622
filter_annot_with_network7.8610.1428.004
functional_annot 1.834 0.17212.153
graph_from_op4.2270.1074.334
in_omnipath4.2240.1004.325
prioritization_genes20.511 0.27020.781
process_annot0.7170.0080.726
random_walk20.026 0.18320.209
score_candidate_genes_from_PPI20.375 0.16720.542
subgraph_op4.2650.0164.281
weighted_adj15.373 0.12415.498
wppi39.900 0.23940.142
wppi_data8.0970.0648.160
wppi_go_data3.5300.0523.582
wppi_hpo_data0.4610.0160.477
wppi_omnipath_data4.0760.0004.075