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This page was generated on 2023-04-12 10:55:33 -0400 (Wed, 12 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.1 LTS)x86_644.3.0 alpha (2023-04-03 r84154) 4547
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_64R Under development (unstable) (2023-02-14 r83833) -- "Unsuffered Consequences" 4333
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

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.

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 2189/2207HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
wppi 1.7.0  (landing page)
Ana Galhoz
Snapshot Date: 2023-04-11 14:00:16 -0400 (Tue, 11 Apr 2023)
git_url: https://git.bioconductor.org/packages/wppi
git_branch: devel
git_last_commit: c0740ca
git_last_commit_date: 2022-11-01 11:24:35 -0400 (Tue, 01 Nov 2022)
nebbiolo1Linux (Ubuntu 22.04.1 LTS) / x86_64  OK    OK    OK  
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  

Summary

Package: wppi
Version: 1.7.0
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_1.7.0.tar.gz
StartedAt: 2023-04-12 00:26:03 -0400 (Wed, 12 Apr 2023)
EndedAt: 2023-04-12 00:30:17 -0400 (Wed, 12 Apr 2023)
EllapsedTime: 253.3 seconds
RetCode: 0
Status:   OK  
CheckDir: wppi.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### 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_1.7.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/wppi.Rcheck’
* using R version 4.3.0 alpha (2023-04-03 r84154)
* using platform: x86_64-pc-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 ‘1.7.0’
* 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
[2023-04-12 00:26:28] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-12 00:26:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-04-12 00:26:28] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2023-04-12 00:26:28] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2023-04-12 00:26:28] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2023-04-12 00:26:28] [TRACE]   [OmnipathR] Contains 1 files.
[2023-04-12 00:26:28] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2023-04-12 00:26:28] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-12 00:26:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-04-12 00:26:28] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2023-04-12 00:26:28] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2023-04-12 00:26:29] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2023-04-12 00:26:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-04-12 00:26:29] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2023-04-12 00:26:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-04-12 00:26:29] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2023-04-12 00:26:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-04-12 00:26:29] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2023-04-12 00:26:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-04-12 00:26:29] [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
[2023-04-12 00:26:42] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-12 00:26:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-04-12 00:26:42] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2023-04-12 00:26:42] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2023-04-12 00:26:42] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2023-04-12 00:26:42] [TRACE]   [OmnipathR] Contains 1 files.
[2023-04-12 00:26:42] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2023-04-12 00:26:42] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-12 00:26:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-04-12 00:26:42] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2023-04-12 00:26:42] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2023-04-12 00:26:42] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2023-04-12 00:26:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-04-12 00:26:42] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2023-04-12 00:26:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-04-12 00:26:42] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2023-04-12 00:26:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-04-12 00:26:42] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2023-04-12 00:26:42] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-04-12 00:26:42] [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                           30.132  0.212  30.345
score_candidate_genes_from_PPI 15.995  0.181  16.176
random_walk                    15.531  0.152  15.684
prioritization_genes           15.203  0.185  15.389
weighted_adj                   11.496  0.052  11.549
count_genes                     8.036  0.547   8.174
wppi_data                       6.589  0.048   6.637
common_neighbors                5.603  0.359   8.536
filter_annot_with_network       5.844  0.116   5.962
* 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/site-library’
* installing *source* package ‘wppi’ ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
[2023-04-11 15:24:46] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-11 15:24:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-04-11 15:24:46] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2023-04-11 15:24:46] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2023-04-11 15:24:46] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2023-04-11 15:24:46] [TRACE]   [OmnipathR] Contains 1 files.
[2023-04-11 15:24:46] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2023-04-11 15:24:46] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-11 15:24:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-04-11 15:24:46] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2023-04-11 15:24:46] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2023-04-11 15:24:46] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2023-04-11 15:24:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-04-11 15:24:46] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2023-04-11 15:24:46] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-04-11 15:24:47] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2023-04-11 15:24:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-04-11 15:24:47] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2023-04-11 15:24:47] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-04-11 15:24:47] [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
[2023-04-11 15:24:49] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-11 15:24:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-04-11 15:24:49] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2023-04-11 15:24:49] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2023-04-11 15:24:49] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2023-04-11 15:24:49] [TRACE]   [OmnipathR] Contains 1 files.
[2023-04-11 15:24:49] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2023-04-11 15:24:49] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-11 15:24:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-04-11 15:24:49] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2023-04-11 15:24:49] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2023-04-11 15:24:49] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2023-04-11 15:24:49] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-04-11 15:24:50] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2023-04-11 15:24:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-04-11 15:24:50] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2023-04-11 15:24:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-04-11 15:24:50] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2023-04-11 15:24:50] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-04-11 15:24:50] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2023-04-11 15:24:52] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-11 15:24:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-04-11 15:24:52] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2023-04-11 15:24:52] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2023-04-11 15:24:52] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2023-04-11 15:24:52] [TRACE]   [OmnipathR] Contains 1 files.
[2023-04-11 15:24:52] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2023-04-11 15:24:52] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-11 15:24:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-04-11 15:24:52] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2023-04-11 15:24:52] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2023-04-11 15:24:52] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2023-04-11 15:24:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-04-11 15:24:52] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2023-04-11 15:24:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-04-11 15:24:52] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2023-04-11 15:24:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-04-11 15:24:52] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2023-04-11 15:24:52] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2023-04-11 15:24:52] [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_neighbors5.6030.3598.536
count_genes8.0360.5478.174
filter_annot_with_network5.8440.1165.962
functional_annot1.3330.1102.488
graph_from_op3.2840.0843.368
in_omnipath3.2310.0133.243
prioritization_genes15.203 0.18515.389
process_annot0.5560.0000.556
random_walk15.531 0.15215.684
score_candidate_genes_from_PPI15.995 0.18116.176
subgraph_op3.0500.0043.055
weighted_adj11.496 0.05211.549
wppi30.132 0.21230.345
wppi_data6.5890.0486.637
wppi_go_data2.2130.0242.238
wppi_hpo_data0.4090.0080.417
wppi_omnipath_data3.3520.0563.410