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This page was generated on 2025-01-23 12:06 -0500 (Thu, 23 Jan 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4746
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4493
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4517
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4469
taishanLinux (openEuler 24.03 LTS)aarch644.4.2 (2024-10-31) -- "Pile of Leaves" 4394
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 2269/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
wppi 1.14.0  (landing page)
Ana Galhoz
Snapshot Date: 2025-01-20 13:00 -0500 (Mon, 20 Jan 2025)
git_url: https://git.bioconductor.org/packages/wppi
git_branch: RELEASE_3_20
git_last_commit: 240f65a
git_last_commit_date: 2024-10-29 10:58:10 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    ERROR  skipped

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: 1.14.0
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:wppi.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings wppi_1.14.0.tar.gz
StartedAt: 2025-01-21 03:15:26 -0500 (Tue, 21 Jan 2025)
EndedAt: 2025-01-21 03:19:58 -0500 (Tue, 21 Jan 2025)
EllapsedTime: 272.2 seconds
RetCode: 0
Status:   OK  
CheckDir: wppi.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:wppi.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings wppi_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/wppi.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘wppi/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘wppi’ version ‘1.14.0’
* 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
[2025-01-21 03:15:56] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-21 03:15:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-21 03:15:56] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-01-21 03:15:56] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-01-21 03:15:56] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-01-21 03:15:56] [TRACE]   [OmnipathR] Contains 1 files.
[2025-01-21 03:15:56] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-01-21 03:15:56] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-21 03:15:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-21 03:15:56] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-01-21 03:15:56] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-01-21 03:15:56] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-01-21 03:15:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-21 03:15:56] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-01-21 03:15:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-21 03:15:56] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-01-21 03:15:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-21 03:15:56] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-01-21 03:15:56] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-21 03:15:56] [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
[2025-01-21 03:16:11] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-21 03:16:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-21 03:16:11] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-01-21 03:16:11] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-01-21 03:16:11] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-01-21 03:16:11] [TRACE]   [OmnipathR] Contains 1 files.
[2025-01-21 03:16:11] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-01-21 03:16:11] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-21 03:16:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-21 03:16:11] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-01-21 03:16:11] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-01-21 03:16:11] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-01-21 03:16:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-21 03:16:11] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-01-21 03:16:11] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-21 03:16:12] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-01-21 03:16:12] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-21 03:16:12] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-01-21 03:16:12] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-21 03:16:12] [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                           29.933  0.098  30.032
score_candidate_genes_from_PPI 15.970  0.136  16.108
prioritization_genes           14.984  0.231  15.215
random_walk                    14.740  0.157  14.897
weighted_adj                   12.308  0.136  12.444
count_genes                     9.886  0.687  10.588
filter_annot_with_network       6.867  0.130   6.999
wppi_data                       6.690  0.027   6.717
common_neighbors                6.039  0.375  11.654
* 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-3.20-bioc/meat/wppi.Rcheck/00check.log’
for details.

Installation output

wppi.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL wppi
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘wppi’ ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
[2025-01-20 15:32:29] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-20 15:32:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-20 15:32:29] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-01-20 15:32:29] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-01-20 15:32:29] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-01-20 15:32:30] [TRACE]   [OmnipathR] Contains 1 files.
[2025-01-20 15:32:30] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-01-20 15:32:30] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-20 15:32:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-20 15:32:30] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-01-20 15:32:30] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-01-20 15:32:30] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-01-20 15:32:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-20 15:32:30] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-01-20 15:32:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-20 15:32:30] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-01-20 15:32:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-20 15:32:30] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-01-20 15:32:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-20 15:32:30] [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
[2025-01-20 15:32:34] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-20 15:32:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-20 15:32:34] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-01-20 15:32:34] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-01-20 15:32:34] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-01-20 15:32:34] [TRACE]   [OmnipathR] Contains 1 files.
[2025-01-20 15:32:34] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-01-20 15:32:34] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-20 15:32:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-20 15:32:34] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-01-20 15:32:34] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-01-20 15:32:34] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-01-20 15:32:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-20 15:32:34] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-01-20 15:32:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-20 15:32:34] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-01-20 15:32:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-20 15:32:34] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-01-20 15:32:34] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-20 15:32:34] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2025-01-20 15:32:38] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-20 15:32:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-20 15:32:38] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-01-20 15:32:38] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-01-20 15:32:38] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-01-20 15:32:38] [TRACE]   [OmnipathR] Contains 1 files.
[2025-01-20 15:32:38] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-01-20 15:32:38] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-20 15:32:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-20 15:32:38] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-01-20 15:32:38] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-01-20 15:32:38] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-01-20 15:32:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-20 15:32:38] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-01-20 15:32:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-20 15:32:38] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-01-20 15:32:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-20 15:32:38] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.20-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-01-20 15:32:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-20 15:32:38] [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 6.039 0.37511.654
count_genes 9.886 0.68710.588
filter_annot_with_network6.8670.1306.999
functional_annot1.9180.1502.614
graph_from_op3.1820.0833.266
in_omnipath3.1550.0433.200
prioritization_genes14.984 0.23115.215
process_annot0.8080.0130.820
random_walk14.740 0.15714.897
score_candidate_genes_from_PPI15.970 0.13616.108
subgraph_op3.2550.0023.257
weighted_adj12.308 0.13612.444
wppi29.933 0.09830.032
wppi_data6.6900.0276.717
wppi_go_data3.0260.0043.031
wppi_hpo_data1.1020.0091.110
wppi_omnipath_data2.8270.0042.833