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CHECK results for PFP on machv2

This page was generated on 2021-06-11 14:06:43 -0400 (Fri, 11 Jun 2021).

Package 1375/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PFP 1.0.0  (landing page)
XC Zhang
Snapshot Date: 2021-06-10 06:50:12 -0400 (Thu, 10 Jun 2021)
URL: https://git.bioconductor.org/packages/PFP
Branch: RELEASE_3_13
Last Commit: 80a0d85
Last Changed Date: 2021-05-19 12:58:46 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
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? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

Summary

Package: PFP
Version: 1.0.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:PFP.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings PFP_1.0.0.tar.gz
StartedAt: 2021-06-10 22:02:53 -0400 (Thu, 10 Jun 2021)
EndedAt: 2021-06-10 22:08:06 -0400 (Thu, 10 Jun 2021)
EllapsedTime: 312.8 seconds
RetCode: 0
Status:   OK  
CheckDir: PFP.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:PFP.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings PFP_1.0.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/PFP.Rcheck’
* using R version 4.1.0 (2021-05-18)
* 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 ‘1.0.0’
* 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 22.53  0.178  22.732
* 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

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL PFP
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/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 4.1.0 (2021-05-18) -- "Camp Pontanezen"
Copyright (C) 2021 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 ]
> 
> proc.time()
   user  system elapsed 
 12.242   0.598  12.848 

Example timings

PFP.Rcheck/PFP-Ex.timings

nameusersystemelapsed
PFP-class0.2100.0650.274
PFPRefnet-class0.8680.1030.971
PFPRefnet_hsa0.4730.0080.482
PFPRefnet_mmu0.5220.0150.538
PFP_score-methods0.0090.0020.010
PFP_test10.0050.0010.006
PFP_test20.0040.0000.006
calc_PFP_score22.530 0.17822.732
data_std0.0120.0030.015
gene_list_hsa0.0010.0010.003
genes_score-methods0.0090.0020.011
get_PFPRefnet0.0000.0010.001
get_asso_net4.1920.0854.285
get_bg_related_kegg3.1850.0593.247
get_exp_cor_edges0.1660.0140.180
get_pathway_info0.1400.0041.910
group-methods0.5380.0030.542
kegg_download0.0000.0010.001
net_info-methods0.5100.0040.516
net_names-methods0.5900.0050.597
network-methods0.5090.0050.514
pathway_info0.0030.0020.005
pathway_info_hsa0.0020.0020.004
pathways_score-methods0.0060.0020.008
plot_PFP-methods0.3670.0050.373
plot_PFPlist0.2490.0040.253
rank_PFP-methods0.2050.0670.273
refnet_info-methods0.0050.0010.006
refnet_names-methods0.0050.0010.006
result_PFP-methods0.0110.0010.013
show_PFP-methods0.0070.0060.014
show_net-methods0.4730.0040.476
stats_test-methods0.0090.0020.010
sub_PFP-methods0.2490.0730.323
subnet-methods0.5060.0030.510
trans_edges_id3.5880.0893.688
trans_graph2PFPRefnet0.7840.0850.871
trans_xml2graph0.0010.0000.001