Back to Multiple platform build/check report for BioC 3.16
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This page was generated on 2022-06-24 11:08:21 -0400 (Fri, 24 Jun 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 Patched (2022-06-02 r82447) -- "Vigorous Calisthenics" 4331
palomino4Windows Server 2022 Datacenterx644.2.0 Patched (2022-06-02 r82447 ucrt) -- "Vigorous Calisthenics" 4136
lconwaymacOS 12.2.1 Montereyx86_644.2.0 Patched (2022-05-29 r82424) -- "Vigorous Calisthenics" 4147
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 PFP on lconway


To the developers/maintainers of the PFP package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/PFP.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 1425/2118HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PFP 1.5.0  (landing page)
XC Zhang
Snapshot Date: 2022-06-23 14:00:04 -0400 (Thu, 23 Jun 2022)
git_url: https://git.bioconductor.org/packages/PFP
git_branch: master
git_last_commit: ff627a7
git_last_commit_date: 2022-04-26 12:11:55 -0400 (Tue, 26 Apr 2022)
nebbiolo2Linux (Ubuntu 20.04.4 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 12.2.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: PFP
Version: 1.5.0
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_1.5.0.tar.gz
StartedAt: 2022-06-23 21:48:37 -0400 (Thu, 23 Jun 2022)
EndedAt: 2022-06-23 21:52:15 -0400 (Thu, 23 Jun 2022)
EllapsedTime: 217.6 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_1.5.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/PFP.Rcheck’
* using R version 4.2.0 Patched (2022-05-29 r82424)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PFP/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PFP’ version ‘1.5.0’
* 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
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
calc_PFP_score 11.09   0.14  11.245
* 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/4.2/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 version 4.2.0 Patched (2022-05-29 r82424) -- "Vigorous Calisthenics"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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 
  8.673   0.488   9.165 

Example timings

PFP.Rcheck/PFP-Ex.timings

nameusersystemelapsed
PFP-class0.1490.0450.194
PFPRefnet-class0.4910.0530.545
PFPRefnet_hsa0.3330.0070.340
PFPRefnet_mmu0.4120.0060.418
PFP_score-methods0.0050.0010.007
PFP_test10.0060.0010.008
PFP_test20.0040.0010.005
calc_PFP_score11.090 0.14011.245
data_std0.0070.0010.009
gene_list_hsa0.0010.0010.002
genes_score-methods0.0040.0000.004
get_PFPRefnet000
get_asso_net2.2790.0632.347
get_bg_related_kegg1.4710.0651.554
get_exp_cor_edges0.1500.0160.167
get_pathway_info0.0830.0042.186
group-methods0.3360.0030.340
kegg_download0.0010.0000.001
net_info-methods0.2900.0020.292
net_names-methods0.3130.0030.317
network-methods0.3520.0050.358
pathway_info0.0030.0010.004
pathway_info_hsa0.0020.0010.003
pathways_score-methods0.0050.0010.007
plot_PFP-methods0.2270.0040.231
plot_PFPlist0.1500.0020.152
rank_PFP-methods0.0950.0310.125
refnet_info-methods0.0030.0010.004
refnet_names-methods0.0050.0010.006
result_PFP-methods0.0070.0010.009
show_PFP-methods0.0060.0050.012
show_net-methods0.3310.0030.334
stats_test-methods0.0040.0010.004
sub_PFP-methods0.1250.0390.163
subnet-methods0.3850.0030.389
trans_edges_id1.6400.0681.713
trans_graph2PFPRefnet0.4870.0500.537
trans_xml2graph000