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This page was generated on 2024-05-04 11:38:47 -0400 (Sat, 04 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4753
palomino3Windows Server 2022 Datacenterx644.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" 4486
lconwaymacOS 12.7.1 Montereyx86_644.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" 4519
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4479
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 2282/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
wppi 1.12.0  (landing page)
Ana Galhoz
Snapshot Date: 2024-05-03 14:00:19 -0400 (Fri, 03 May 2024)
git_url: https://git.bioconductor.org/packages/wppi
git_branch: RELEASE_3_19
git_last_commit: 1ad2e46
git_last_commit_date: 2024-04-30 11:33:03 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows 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
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  
kjohnson3macOS 13.6.5 Ventura / arm64see weekly results here

CHECK results for wppi on palomino3


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: 1.12.0
Command: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:wppi.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings wppi_1.12.0.tar.gz
StartedAt: 2024-05-04 09:22:26 -0400 (Sat, 04 May 2024)
EndedAt: 2024-05-04 09:26:59 -0400 (Sat, 04 May 2024)
EllapsedTime: 272.8 seconds
RetCode: 0
Status:   OK  
CheckDir: wppi.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:wppi.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings wppi_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/wppi.Rcheck'
* using R version 4.4.0 beta (2024-04-15 r86425 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* 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 '1.12.0'
* 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 ... 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 whether startup messages can be suppressed ... NOTE
[2024-05-04 09:23:01] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-04 09:23:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-04 09:23:01] [INFO]    [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-05-04 09:23:01] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-05-04 09:23:01] [TRACE]   [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-05-04 09:23:01] [TRACE]   [OmnipathR] Contains 1 files.
[2024-05-04 09:23:01] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-05-04 09:23:01] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-04 09:23:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-04 09:23:01] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-05-04 09:23:01] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-05-04 09:23:01] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.19-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-05-04 09:23:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-04 09:23:01] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.19-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-05-04 09:23:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-04 09:23:01] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.19-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-05-04 09:23:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-04 09:23:02] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.19-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-05-04 09:23:02] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-04 09:23:02] [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
[2024-05-04 09:23:19] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-04 09:23:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-04 09:23:19] [INFO]    [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-05-04 09:23:19] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-05-04 09:23:19] [TRACE]   [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-05-04 09:23:19] [TRACE]   [OmnipathR] Contains 1 files.
[2024-05-04 09:23:19] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-05-04 09:23:19] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-04 09:23:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-04 09:23:19] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-05-04 09:23:19] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-05-04 09:23:19] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.19-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-05-04 09:23:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-04 09:23:19] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.19-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-05-04 09:23:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-04 09:23:19] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.19-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-05-04 09:23:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-04 09:23:19] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.19-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-05-04 09:23:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-04 09:23:19] [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                           33.47   0.86   34.34
score_candidate_genes_from_PPI 17.46   0.41   17.88
prioritization_genes           17.00   0.46   17.45
random_walk                    16.24   0.41   16.64
weighted_adj                   12.03   0.36   12.39
count_genes                    10.36   0.77    9.84
common_neighbors                7.24   0.38   33.22
filter_annot_with_network       6.98   0.21    7.22
wppi_data                       6.79   0.14    6.94
* 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
  'F:/biocbuild/bbs-3.19-bioc/meat/wppi.Rcheck/00check.log'
for details.


Installation output

wppi.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL wppi
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.19-bioc/R/library'
* installing *source* package 'wppi' ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
[2024-05-03 17:19:21] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-03 17:19:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-03 17:19:21] [INFO]    [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-05-03 17:19:21] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-05-03 17:19:21] [TRACE]   [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-05-03 17:19:21] [TRACE]   [OmnipathR] Contains 1 files.
[2024-05-03 17:19:21] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-05-03 17:19:21] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-03 17:19:21] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-03 17:19:21] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-05-03 17:19:22] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-05-03 17:19:22] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.19-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-05-03 17:19:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-03 17:19:22] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.19-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-05-03 17:19:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-03 17:19:22] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.19-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-05-03 17:19:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-03 17:19:22] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.19-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-05-03 17:19:22] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-03 17:19:22] [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
[2024-05-03 17:19:28] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-03 17:19:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-03 17:19:28] [INFO]    [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-05-03 17:19:28] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-05-03 17:19:28] [TRACE]   [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-05-03 17:19:28] [TRACE]   [OmnipathR] Contains 1 files.
[2024-05-03 17:19:28] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-05-03 17:19:28] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-03 17:19:28] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-03 17:19:28] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-05-03 17:19:29] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-05-03 17:19:29] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.19-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-05-03 17:19:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-03 17:19:29] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.19-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-05-03 17:19:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-03 17:19:29] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.19-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-05-03 17:19:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-03 17:19:29] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.19-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-05-03 17:19:29] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-03 17:19:29] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2024-05-03 17:19:32] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-03 17:19:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-03 17:19:32] [INFO]    [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-05-03 17:19:32] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-05-03 17:19:32] [TRACE]   [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-05-03 17:19:32] [TRACE]   [OmnipathR] Contains 1 files.
[2024-05-03 17:19:32] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-05-03 17:19:32] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-05-03 17:19:32] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-03 17:19:32] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-05-03 17:19:33] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-05-03 17:19:33] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.19-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-05-03 17:19:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-03 17:19:33] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.19-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-05-03 17:19:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-03 17:19:33] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.19-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-05-03 17:19:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-03 17:19:33] [TRACE]   [OmnipathR] Reading JSON from `F:/biocbuild/bbs-3.19-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-05-03 17:19:33] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-05-03 17:19:33] [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 7.24 0.3833.22
count_genes10.36 0.77 9.84
filter_annot_with_network6.980.217.22
functional_annot2.550.252.97
graph_from_op4.080.084.16
in_omnipath4.800.064.86
prioritization_genes17.00 0.4617.45
process_annot1.000.041.05
random_walk16.24 0.4116.64
score_candidate_genes_from_PPI17.46 0.4117.88
subgraph_op4.790.044.83
weighted_adj12.03 0.3612.39
wppi33.47 0.8634.34
wppi_data6.790.146.94
wppi_go_data3.310.073.38
wppi_hpo_data0.720.010.73
wppi_omnipath_data3.840.053.89