Multiple platform build/check report for BioC 3.21 - CHECK results for wppi on nebbiolo1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.1 LTS)	x86_64	R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences"	4760
palomino7	Windows Server 2022 Datacenter	x64	R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences"	4479
lconway	macOS 12.7.1 Monterey	x86_64	R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"	4443
kjohnson3	macOS 13.7.1 Ventura	arm64	R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"	4398
kunpeng2	Linux (openEuler 22.03 LTS-SP1)	aarch64	R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences"	4391
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.
- 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: 1.15.0

Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:wppi.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings wppi_1.15.0.tar.gz

StartedAt: 2025-01-11 03:26:10 -0500 (Sat, 11 Jan 2025)

EndedAt: 2025-01-11 03:31:49 -0500 (Sat, 11 Jan 2025)

EllapsedTime: 338.9 seconds

RetCode: 0

Status: OK

CheckDir: wppi.Rcheck

Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:wppi.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings wppi_1.15.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/wppi.Rcheck’
* using R Under development (unstable) (2024-10-21 r87258)
* 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 ‘1.15.0’
* 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
[2025-01-11 03:26:41] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-11 03:26:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-11 03:26:41] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-01-11 03:26:41] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-01-11 03:26:41] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-01-11 03:26:41] [TRACE]   [OmnipathR] Contains 1 files.
[2025-01-11 03:26:41] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-01-11 03:26:41] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-11 03:26:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-11 03:26:41] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-01-11 03:26:41] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2025-01-11 03:26:41] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-01-11 03:26:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-11 03:26:41] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-01-11 03:26:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-11 03:26:41] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-01-11 03:26:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-11 03:26:41] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-01-11 03:26:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-11 03:26:41] [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
[2025-01-11 03:26:57] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-11 03:26:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-11 03:26:57] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-01-11 03:26:57] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-01-11 03:26:57] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-01-11 03:26:57] [TRACE]   [OmnipathR] Contains 1 files.
[2025-01-11 03:26:57] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-01-11 03:26:57] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-11 03:26:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-11 03:26:57] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-01-11 03:26:57] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2025-01-11 03:26:57] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-01-11 03:26:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-11 03:26:57] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-01-11 03:26:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-11 03:26:57] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-01-11 03:26:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-11 03:26:57] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-01-11 03:26:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-11 03:26:57] [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                           42.647  0.187  42.835
score_candidate_genes_from_PPI 22.252  0.233  22.486
prioritization_genes           21.174  0.279  21.553
random_walk                    20.505  0.195  20.701
weighted_adj                   17.625  0.125  17.752
common_neighbors               12.364  0.973  18.589
count_genes                    10.292  0.848  12.255
filter_annot_with_network       6.892  0.152   7.043
wppi_data                       6.975  0.015   6.990
* 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-3.21-bioc/meat/wppi.Rcheck/00check.log’
for details.

Installation output

wppi.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL wppi
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘wppi’ ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
[2025-01-10 15:32:19] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-10 15:32:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-10 15:32:19] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-01-10 15:32:19] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-01-10 15:32:19] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-01-10 15:32:19] [TRACE]   [OmnipathR] Contains 1 files.
[2025-01-10 15:32:19] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-01-10 15:32:19] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-10 15:32:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-10 15:32:19] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-01-10 15:32:19] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2025-01-10 15:32:19] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-01-10 15:32:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-10 15:32:19] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-01-10 15:32:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-10 15:32:19] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-01-10 15:32:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-10 15:32:19] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-01-10 15:32:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-10 15:32:19] [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
[2025-01-10 15:32:23] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-10 15:32:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-10 15:32:23] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-01-10 15:32:23] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-01-10 15:32:23] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-01-10 15:32:23] [TRACE]   [OmnipathR] Contains 1 files.
[2025-01-10 15:32:23] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-01-10 15:32:23] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-10 15:32:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-10 15:32:23] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-01-10 15:32:23] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2025-01-10 15:32:23] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-01-10 15:32:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-10 15:32:23] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-01-10 15:32:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-10 15:32:23] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-01-10 15:32:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-10 15:32:23] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-01-10 15:32:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-10 15:32:23] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2025-01-10 15:32:26] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-10 15:32:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-10 15:32:26] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-01-10 15:32:26] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-01-10 15:32:26] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-01-10 15:32:26] [TRACE]   [OmnipathR] Contains 1 files.
[2025-01-10 15:32:26] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-01-10 15:32:26] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-10 15:32:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-10 15:32:26] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-01-10 15:32:26] [TRACE]   [OmnipathR] Pandoc version: `3.1.3`.
[2025-01-10 15:32:26] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-01-10 15:32:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-10 15:32:26] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-01-10 15:32:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-10 15:32:26] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-01-10 15:32:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-10 15:32:26] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-01-10 15:32:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-10 15:32:26] [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

name	user	system	elapsed
common_neighbors	12.364	0.973	18.589
count_genes	10.292	0.848	12.255
filter_annot_with_network	6.892	0.152	7.043
functional_annot	1.959	0.172	4.670
graph_from_op	3.250	0.069	3.319
in_omnipath	3.283	0.016	3.299
prioritization_genes	21.174	0.279	21.553
process_annot	0.872	0.032	0.903
random_walk	20.505	0.195	20.701
score_candidate_genes_from_PPI	22.252	0.233	22.486
subgraph_op	3.182	0.036	3.217
weighted_adj	17.625	0.125	17.752
wppi	42.647	0.187	42.835
wppi_data	6.975	0.015	6.990
wppi_go_data	3.425	0.004	3.429
wppi_hpo_data	0.660	0.005	0.666
wppi_omnipath_data	3.087	0.003	3.090