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This page was generated on 2025-03-31 12:13 -0400 (Mon, 31 Mar 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.3 (2025-02-28) -- "Trophy Case" 4764
palomino8Windows Server 2022 Datacenterx644.4.3 (2025-02-28 ucrt) -- "Trophy Case" 4495
merida1macOS 12.7.5 Montereyx86_644.4.3 (2025-02-28) -- "Trophy Case" 4522
kjohnson1macOS 13.6.6 Venturaarm644.4.3 (2025-02-28) -- "Trophy Case" 4449
taishanLinux (openEuler 24.03 LTS)aarch644.4.3 (2025-02-28) -- "Trophy Case" 4426
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: 2025-03-27 13:00 -0400 (Thu, 27 Mar 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 -0400 (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    OK    OK  

CHECK results for wppi on taishan

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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: wppi
Version: 1.14.0
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:wppi.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings wppi_1.14.0.tar.gz
StartedAt: 2025-03-28 11:47:23 -0000 (Fri, 28 Mar 2025)
EndedAt: 2025-03-28 11:52:40 -0000 (Fri, 28 Mar 2025)
EllapsedTime: 317.2 seconds
RetCode: 0
Status:   OK  
CheckDir: wppi.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:wppi.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings wppi_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/wppi.Rcheck’
* using R version 4.4.3 (2025-02-28)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* 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
[2025-03-28 11:48:01] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-28 11:48:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-28 11:48:01] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-03-28 11:48:01] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-03-28 11:48:01] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-03-28 11:48:01] [TRACE]   [OmnipathR] Contains 1 files.
[2025-03-28 11:48:01] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-03-28 11:48:01] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-28 11:48:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-28 11:48:01] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-03-28 11:48:01] [TRACE]   [OmnipathR] Pandoc version: `2.12`.
[2025-03-28 11:48:01] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.3/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-03-28 11:48:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-28 11:48:01] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.3/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-03-28 11:48:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-28 11:48:02] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.3/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-03-28 11:48:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-28 11:48:02] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.3/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-03-28 11:48:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-28 11:48:02] [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
[2025-03-28 11:48:22] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-28 11:48:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-28 11:48:22] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-03-28 11:48:22] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-03-28 11:48:22] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-03-28 11:48:22] [TRACE]   [OmnipathR] Contains 1 files.
[2025-03-28 11:48:22] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-03-28 11:48:22] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-28 11:48:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-28 11:48:22] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-03-28 11:48:22] [TRACE]   [OmnipathR] Pandoc version: `2.12`.
[2025-03-28 11:48:22] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.3/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-03-28 11:48:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-28 11:48:22] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.3/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-03-28 11:48:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-28 11:48:22] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.3/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-03-28 11:48:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-28 11:48:22] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.3/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-03-28 11:48:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-28 11:48:22] [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                           42.152  0.131  42.396
score_candidate_genes_from_PPI 21.337  0.072  21.462
prioritization_genes           21.154  0.108  21.338
random_walk                    20.910  0.105  21.063
weighted_adj                   16.557  0.070  16.667
count_genes                    13.045  0.603  23.270
wppi_data                       8.903  0.040   8.958
common_neighbors                8.036  0.407  16.608
filter_annot_with_network       8.302  0.106   8.417
functional_annot                2.159  0.166  19.866
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* 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/R/R/bin/R CMD INSTALL wppi
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.4.3/site-library’
* installing *source* package ‘wppi’ ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
[2025-03-27 21:07:14] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-27 21:07:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-27 21:07:14] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-03-27 21:07:14] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-03-27 21:07:14] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-03-27 21:07:14] [TRACE]   [OmnipathR] Contains 1 files.
[2025-03-27 21:07:14] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-03-27 21:07:14] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-27 21:07:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-27 21:07:14] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-03-27 21:07:14] [TRACE]   [OmnipathR] Pandoc version: `2.12`.
[2025-03-27 21:07:14] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.3/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-03-27 21:07:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-27 21:07:14] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.3/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-03-27 21:07:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-27 21:07:14] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.3/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-03-27 21:07:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-27 21:07:14] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.3/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-03-27 21:07:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-27 21:07:14] [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
[2025-03-27 21:07:19] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-27 21:07:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-27 21:07:19] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-03-27 21:07:19] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-03-27 21:07:19] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-03-27 21:07:19] [TRACE]   [OmnipathR] Contains 1 files.
[2025-03-27 21:07:19] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-03-27 21:07:19] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-27 21:07:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-27 21:07:19] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-03-27 21:07:19] [TRACE]   [OmnipathR] Pandoc version: `2.12`.
[2025-03-27 21:07:19] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.3/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-03-27 21:07:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-27 21:07:19] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.3/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-03-27 21:07:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-27 21:07:19] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.3/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-03-27 21:07:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-27 21:07:19] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.3/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-03-27 21:07:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-27 21:07:19] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2025-03-27 21:07:23] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-27 21:07:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-27 21:07:23] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-03-27 21:07:23] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-03-27 21:07:23] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-03-27 21:07:23] [TRACE]   [OmnipathR] Contains 1 files.
[2025-03-27 21:07:23] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-03-27 21:07:24] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-03-27 21:07:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-27 21:07:24] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-03-27 21:07:24] [TRACE]   [OmnipathR] Pandoc version: `2.12`.
[2025-03-27 21:07:24] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.3/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-03-27 21:07:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-27 21:07:24] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.3/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-03-27 21:07:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-27 21:07:24] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.3/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-03-27 21:07:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-27 21:07:24] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.4.3/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-03-27 21:07:24] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-03-27 21:07:24] [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 8.036 0.40716.608
count_genes13.045 0.60323.270
filter_annot_with_network8.3020.1068.417
functional_annot 2.159 0.16619.866
graph_from_op4.2340.0134.258
in_omnipath4.3100.0434.368
prioritization_genes21.154 0.10821.338
process_annot0.9960.0010.999
random_walk20.910 0.10521.063
score_candidate_genes_from_PPI21.337 0.07221.462
subgraph_op4.4060.0254.440
weighted_adj16.557 0.07016.667
wppi42.152 0.13142.396
wppi_data8.9030.0408.958
wppi_go_data3.3480.0243.377
wppi_hpo_data0.8370.0040.843
wppi_omnipath_data4.3170.0214.345