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This page was generated on 2025-02-01 11:41 -0500 (Sat, 01 Feb 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" 4704
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences" 4467
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2025-01-22 r87618) -- "Unsuffered Consequences" 4478
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" 4431
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 2268/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
wppi 1.15.0  (landing page)
Ana Galhoz
Snapshot Date: 2025-01-31 13:40 -0500 (Fri, 31 Jan 2025)
git_url: https://git.bioconductor.org/packages/wppi
git_branch: devel
git_last_commit: 321e17d
git_last_commit_date: 2024-10-29 10:58:10 -0500 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

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: 2025-02-01 03:40:26 -0500 (Sat, 01 Feb 2025)
EndedAt: 2025-02-01 03:46:08 -0500 (Sat, 01 Feb 2025)
EllapsedTime: 342.2 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) (2025-01-20 r87609)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* 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
[2025-02-01 03:40:58] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-01 03:40:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-01 03:40:58] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-02-01 03:40:58] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-02-01 03:40:58] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-02-01 03:40:58] [TRACE]   [OmnipathR] Contains 1 files.
[2025-02-01 03:40:58] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-02-01 03:40:58] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-01 03:40:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-01 03:40:58] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-02-01 03:40:58] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-02-01 03:40:58] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-02-01 03:40:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-01 03:40:58] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-02-01 03:40:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-01 03:40:58] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-02-01 03:40:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-01 03:40:58] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-02-01 03:40:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-01 03:40:58] [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
[2025-02-01 03:41:15] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-01 03:41:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-01 03:41:15] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-02-01 03:41:15] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-02-01 03:41:15] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-02-01 03:41:15] [TRACE]   [OmnipathR] Contains 1 files.
[2025-02-01 03:41:15] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-02-01 03:41:15] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-01 03:41:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-01 03:41:15] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-02-01 03:41:15] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-02-01 03:41:15] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-02-01 03:41:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-01 03:41:15] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-02-01 03:41:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-01 03:41:15] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-02-01 03:41:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-01 03:41:15] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-02-01 03:41:15] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-01 03:41:16] [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                           43.102  0.257  43.360
prioritization_genes           22.611  0.470  23.081
score_candidate_genes_from_PPI 22.506  0.224  22.779
random_walk                    21.740  0.330  22.072
weighted_adj                   18.867  0.166  19.034
common_neighbors               12.129  0.406  17.468
count_genes                    10.073  0.668  11.139
wppi_data                       7.523  0.101   7.624
filter_annot_with_network       7.047  0.175   7.223
* 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

##############################################################################
##############################################################################
###
### 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’ ...
** this is package ‘wppi’ version ‘1.15.0’
** using staged installation
** R
** byte-compile and prepare package for lazy loading
[2025-01-31 15:39:14] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-31 15:39:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-31 15:39:14] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-01-31 15:39:14] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-01-31 15:39:14] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-01-31 15:39:14] [TRACE]   [OmnipathR] Contains 1 files.
[2025-01-31 15:39:14] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-01-31 15:39:14] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-31 15:39:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-31 15:39:14] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-01-31 15:39:14] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-01-31 15:39:14] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-01-31 15:39:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-31 15:39:14] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-01-31 15:39:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-31 15:39:14] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-01-31 15:39:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-31 15:39:14] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-01-31 15:39:14] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-31 15:39:14] [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
[2025-01-31 15:39:18] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-31 15:39:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-31 15:39:18] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-01-31 15:39:18] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-01-31 15:39:18] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-01-31 15:39:18] [TRACE]   [OmnipathR] Contains 1 files.
[2025-01-31 15:39:18] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-01-31 15:39:18] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-31 15:39:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-31 15:39:18] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-01-31 15:39:18] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-01-31 15:39:18] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-01-31 15:39:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-31 15:39:18] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-01-31 15:39:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-31 15:39:18] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-01-31 15:39:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-31 15:39:18] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-01-31 15:39:18] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-31 15:39:18] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2025-01-31 15:39:21] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-31 15:39:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-31 15:39:21] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-01-31 15:39:21] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-01-31 15:39:21] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-01-31 15:39:22] [TRACE]   [OmnipathR] Contains 1 files.
[2025-01-31 15:39:22] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-01-31 15:39:22] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-01-31 15:39:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-31 15:39:22] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-01-31 15:39:22] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-01-31 15:39:22] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-01-31 15:39:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-31 15:39:22] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-01-31 15:39:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-31 15:39:22] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-01-31 15:39:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-31 15:39:22] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-01-31 15:39:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-01-31 15:39:22] [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_neighbors12.129 0.40617.468
count_genes10.073 0.66811.139
filter_annot_with_network7.0470.1757.223
functional_annot2.0540.1242.757
graph_from_op3.0910.0993.189
in_omnipath3.3080.1423.450
prioritization_genes22.611 0.47023.081
process_annot0.9330.0190.952
random_walk21.740 0.33022.072
score_candidate_genes_from_PPI22.506 0.22422.779
subgraph_op3.0660.0283.094
weighted_adj18.867 0.16619.034
wppi43.102 0.25743.360
wppi_data7.5230.1017.624
wppi_go_data3.5650.0583.622
wppi_hpo_data0.6910.0060.698
wppi_omnipath_data3.0450.0383.084