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This page was generated on 2023-04-12 11:05:58 -0400 (Wed, 12 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4502
palomino4Windows Server 2022 Datacenterx644.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" 4282
lconwaymacOS 12.5.1 Montereyx86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4310
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 palomino4


To the developers/maintainers of the wppi package:
- Please 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 How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 2165/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
wppi 1.6.0  (landing page)
Ana Galhoz
Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023)
git_url: https://git.bioconductor.org/packages/wppi
git_branch: RELEASE_3_16
git_last_commit: cd4b58e
git_last_commit_date: 2022-11-01 11:24:35 -0400 (Tue, 01 Nov 2022)
nebbiolo2Linux (Ubuntu 20.04.5 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
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: wppi
Version: 1.6.0
Command: F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:wppi.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings wppi_1.6.0.tar.gz
StartedAt: 2023-04-11 07:14:02 -0400 (Tue, 11 Apr 2023)
EndedAt: 2023-04-11 07:17:34 -0400 (Tue, 11 Apr 2023)
EllapsedTime: 211.9 seconds
RetCode: 0
Status:   OK  
CheckDir: wppi.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:wppi.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings wppi_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/wppi.Rcheck'
* using R version 4.2.3 (2023-03-15 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'wppi/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'wppi' version '1.6.0'
* 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 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
[2023-04-11 07:14:42] [INFO]    [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2023-04-11 07:14:42] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2023-04-11 07:14:42] [TRACE]   [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2023-04-11 07:14:42] [TRACE]   [OmnipathR] Contains 1 files.
[2023-04-11 07:14:42] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2023-04-11 07:14:42] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2023-04-11 07:14:42] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2023-04-11 07:14:42] [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                           29.52   0.30   29.83
score_candidate_genes_from_PPI 15.41   0.33   15.75
prioritization_genes           15.13   0.33   15.45
random_walk                    15.21   0.25   15.50
weighted_adj                   11.45   0.21   11.69
count_genes                     7.67   0.69    7.25
filter_annot_with_network       5.78   0.17    5.95
wppi_data                       5.33   0.03    5.35
common_neighbors                5.15   0.20    6.47
* 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: 1 NOTE
See
  'F:/biocbuild/bbs-3.16-bioc/meat/wppi.Rcheck/00check.log'
for details.



Installation output

wppi.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL wppi
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.16-bioc/R/library'
* installing *source* package 'wppi' ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
[2023-04-10 16:05:06] [INFO]    [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2023-04-10 16:05:06] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2023-04-10 16:05:06] [TRACE]   [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2023-04-10 16:05:06] [TRACE]   [OmnipathR] Contains 1 files.
[2023-04-10 16:05:06] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2023-04-10 16:05:06] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2023-04-10 16:05:06] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2023-04-10 16:05:07] [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
[2023-04-10 16:05:12] [INFO]    [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2023-04-10 16:05:12] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2023-04-10 16:05:12] [TRACE]   [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2023-04-10 16:05:12] [TRACE]   [OmnipathR] Contains 1 files.
[2023-04-10 16:05:12] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2023-04-10 16:05:12] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2023-04-10 16:05:12] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2023-04-10 16:05:12] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2023-04-10 16:05:15] [INFO]    [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2023-04-10 16:05:15] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2023-04-10 16:05:15] [TRACE]   [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2023-04-10 16:05:15] [TRACE]   [OmnipathR] Contains 1 files.
[2023-04-10 16:05:15] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2023-04-10 16:05:15] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2023-04-10 16:05:15] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2023-04-10 16:05:15] [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_neighbors5.150.206.47
count_genes7.670.697.25
filter_annot_with_network5.780.175.95
functional_annot1.350.111.70
graph_from_op2.640.052.69
in_omnipath3.120.033.16
prioritization_genes15.13 0.3315.45
process_annot0.550.010.56
random_walk15.21 0.2515.50
score_candidate_genes_from_PPI15.41 0.3315.75
subgraph_op3.110.053.16
weighted_adj11.45 0.2111.69
wppi29.52 0.3029.83
wppi_data5.330.035.35
wppi_go_data2.430.022.46
wppi_hpo_data0.380.030.40
wppi_omnipath_data3.530.003.55