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This page was generated on 2023-03-16 11:02:07 -0400 (Thu, 16 Mar 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson2macOS 12.6.1 Montereyarm64R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences" 4115
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CHECK results for PFP on kjohnson2


To the developers/maintainers of the PFP package:
Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1475/2189HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PFP 1.7.0  (landing page)
XC Zhang
Snapshot Date: 2023-03-13 13:00:01 -0400 (Mon, 13 Mar 2023)
git_url: https://git.bioconductor.org/packages/PFP
git_branch: master
git_last_commit: c11fb9c
git_last_commit_date: 2022-11-01 11:23:44 -0400 (Tue, 01 Nov 2022)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: PFP
Version: 1.7.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:PFP.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings PFP_1.7.0.tar.gz
StartedAt: 2023-03-14 09:35:35 -0400 (Tue, 14 Mar 2023)
EndedAt: 2023-03-14 09:37:13 -0400 (Tue, 14 Mar 2023)
EllapsedTime: 97.8 seconds
RetCode: 0
Status:   OK  
CheckDir: PFP.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:PFP.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings PFP_1.7.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/PFP.Rcheck’
* using R Under development (unstable) (2023-01-10 r83596)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 13.0.0 (clang-1300.0.29.3)
    GNU Fortran (GCC) 12.0.1 20220312 (experimental)
* running under: macOS Monterey 12.6.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PFP/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PFP’ version ‘1.7.0’
* 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 ‘PFP’ 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 ... OK
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* 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: OK


Installation output

PFP.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL PFP
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’
* installing *source* package ‘PFP’ ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (PFP)

Tests output

PFP.Rcheck/tests/testthat.Rout


R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(PFP)

> test_check('PFP')
[ FAIL 0 | WARN 6 | SKIP 0 | PASS 31 ]

[ FAIL 0 | WARN 6 | SKIP 0 | PASS 31 ]
> 
> proc.time()
   user  system elapsed 
  3.794   0.152   3.941 

Example timings

PFP.Rcheck/PFP-Ex.timings

nameusersystemelapsed
PFP-class0.0390.0140.053
PFPRefnet-class0.2560.0180.274
PFPRefnet_hsa0.1720.0030.175
PFPRefnet_mmu0.2650.0020.267
PFP_score-methods0.0030.0010.003
PFP_test10.0020.0000.003
PFP_test20.0020.0010.002
calc_PFP_score4.1240.0524.177
data_std0.0050.0000.007
gene_list_hsa0.0010.0010.001
genes_score-methods0.0020.0000.003
get_PFPRefnet000
get_asso_net1.0930.0231.117
get_bg_related_kegg0.5920.0190.610
get_exp_cor_edges0.0680.0040.072
get_pathway_info0.0440.0021.434
group-methods0.1940.0000.195
kegg_download000
net_info-methods0.1770.0000.178
net_names-methods0.1740.0010.175
network-methods0.1740.0020.176
pathway_info0.0010.0000.002
pathway_info_hsa0.0010.0000.001
pathways_score-methods0.0020.0000.002
plot_PFP-methods0.1130.0030.115
plot_PFPlist0.0730.0010.074
rank_PFP-methods0.0390.0130.053
refnet_info-methods0.0030.0010.003
refnet_names-methods0.0020.0000.003
result_PFP-methods0.0020.0000.003
show_PFP-methods0.0030.0020.004
show_net-methods0.1810.0010.182
stats_test-methods0.0020.0000.003
sub_PFP-methods0.0370.0130.051
subnet-methods0.1800.0000.181
trans_edges_id0.6700.0090.679
trans_graph2PFPRefnet0.2500.0170.267
trans_xml2graph0.0010.0000.000