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This page was generated on 2024-04-17 11:37:27 -0400 (Wed, 17 Apr 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4676
palomino4Windows Server 2022 Datacenterx644.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" 4414
merida1macOS 12.7.1 Montereyx86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4437
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 2248/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
wppi 1.10.0  (landing page)
Ana Galhoz
Snapshot Date: 2024-04-15 14:05:01 -0400 (Mon, 15 Apr 2024)
git_url: https://git.bioconductor.org/packages/wppi
git_branch: RELEASE_3_18
git_last_commit: dc6b662
git_last_commit_date: 2023-10-24 11:31:51 -0400 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for wppi on palomino4


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: 1.10.0
Command: F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:wppi.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings wppi_1.10.0.tar.gz
StartedAt: 2024-04-16 06:15:06 -0400 (Tue, 16 Apr 2024)
EndedAt: 2024-04-16 06:19:10 -0400 (Tue, 16 Apr 2024)
EllapsedTime: 244.2 seconds
RetCode: 0
Status:   OK  
CheckDir: wppi.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:wppi.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings wppi_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.18-bioc/meat/wppi.Rcheck'
* using R version 4.3.3 (2024-02-29 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 12.3.0
    GNU Fortran (GCC) 12.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'wppi/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'wppi' version '1.10.0'
* 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 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 startup messages can be suppressed ... NOTE
[2024-04-16 06:15:38] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-16 06:15:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-16 06:15:38] [INFO]    [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-04-16 06:15:38] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-04-16 06:15:38] [TRACE]   [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-04-16 06:15:38] [TRACE]   [OmnipathR] Contains 1 files.
[2024-04-16 06:15:38] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-04-16 06:15:38] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-16 06:15:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-16 06:15:38] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-04-16 06:15:39] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-04-16 06:15:39] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.18-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-04-16 06:15:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-16 06:15:39] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.18-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-04-16 06:15:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-16 06:15:39] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.18-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-04-16 06:15:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-16 06:15:39] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.18-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-04-16 06:15:39] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-16 06:15:39] [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
[2024-04-16 06:15:57] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-16 06:15:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-16 06:15:57] [INFO]    [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-04-16 06:15:57] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-04-16 06:15:57] [TRACE]   [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-04-16 06:15:57] [TRACE]   [OmnipathR] Contains 1 files.
[2024-04-16 06:15:57] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-04-16 06:15:57] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-16 06:15:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-16 06:15:57] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-04-16 06:15:57] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-04-16 06:15:57] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.18-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-04-16 06:15:57] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-16 06:15:58] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.18-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-04-16 06:15:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-16 06:15:58] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.18-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-04-16 06:15:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-16 06:15:58] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.18-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-04-16 06:15:58] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-16 06:15:58] [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                           32.28   0.37   32.65
prioritization_genes           17.64   0.24   17.87
score_candidate_genes_from_PPI 17.43   0.23   17.69
random_walk                    15.93   0.31   16.24
weighted_adj                   12.10   0.19   12.30
count_genes                     9.99   0.47    9.44
wppi_data                       7.33   0.13    7.46
common_neighbors                7.07   0.36    9.82
filter_annot_with_network       7.20   0.11    7.33
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  'F:/biocbuild/bbs-3.18-bioc/meat/wppi.Rcheck/00check.log'
for details.

Installation output

wppi.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD INSTALL wppi
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.18-bioc/R/library'
* installing *source* package 'wppi' ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
[2024-04-15 16:16:20] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-15 16:16:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 16:16:20] [INFO]    [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-04-15 16:16:20] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-04-15 16:16:20] [TRACE]   [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-04-15 16:16:20] [TRACE]   [OmnipathR] Contains 1 files.
[2024-04-15 16:16:20] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-04-15 16:16:20] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-15 16:16:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 16:16:20] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-04-15 16:16:20] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-04-15 16:16:20] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.18-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-04-15 16:16:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 16:16:20] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.18-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-04-15 16:16:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 16:16:20] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.18-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-04-15 16:16:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 16:16:20] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.18-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-04-15 16:16:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 16:16:20] [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
[2024-04-15 16:16:26] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-15 16:16:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 16:16:26] [INFO]    [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-04-15 16:16:26] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-04-15 16:16:26] [TRACE]   [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-04-15 16:16:26] [TRACE]   [OmnipathR] Contains 1 files.
[2024-04-15 16:16:26] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-04-15 16:16:26] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-15 16:16:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 16:16:26] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-04-15 16:16:26] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-04-15 16:16:26] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.18-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-04-15 16:16:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 16:16:26] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.18-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-04-15 16:16:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 16:16:26] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.18-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-04-15 16:16:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 16:16:26] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.18-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-04-15 16:16:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 16:16:26] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2024-04-15 16:16:29] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-15 16:16:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 16:16:29] [INFO]    [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-04-15 16:16:29] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-04-15 16:16:29] [TRACE]   [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-04-15 16:16:29] [TRACE]   [OmnipathR] Contains 1 files.
[2024-04-15 16:16:30] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-04-15 16:16:30] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-04-15 16:16:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 16:16:30] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-04-15 16:16:30] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-04-15 16:16:30] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.18-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-04-15 16:16:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 16:16:30] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.18-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-04-15 16:16:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 16:16:30] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.18-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-04-15 16:16:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 16:16:30] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.18-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-04-15 16:16:30] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-04-15 16:16:30] [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_neighbors7.070.369.82
count_genes9.990.479.44
filter_annot_with_network7.200.117.33
functional_annot2.190.122.59
graph_from_op3.780.023.80
in_omnipath4.440.014.45
prioritization_genes17.64 0.2417.87
process_annot0.890.000.89
random_walk15.93 0.3116.24
score_candidate_genes_from_PPI17.43 0.2317.69
subgraph_op3.080.053.12
weighted_adj12.10 0.1912.30
wppi32.28 0.3732.65
wppi_data7.330.137.46
wppi_go_data3.400.013.42
wppi_hpo_data0.580.050.62
wppi_omnipath_data4.260.004.27