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This page was generated on 2021-07-30 15:06:33 -0400 (Fri, 30 Jul 2021).

CHECK results for PFP on machv2

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.

raw results

Package 1375/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PFP 1.0.0  (landing page)
XC Zhang
Snapshot Date: 2021-07-29 04:50:02 -0400 (Thu, 29 Jul 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

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: 2021-07-29 21:54:06 -0400 (Thu, 29 Jul 2021)
EndedAt: 2021-07-29 21:59:15 -0400 (Thu, 29 Jul 2021)
EllapsedTime: 309.6 seconds
RetCode: 0
Status:   OK  
CheckDir: PFP.Rcheck
Warnings: 0

Command output

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### Running 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
###
##############################################################################
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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 22.251  0.185  22.455
* 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
###
##############################################################################
##############################################################################


* 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 
 11.600   0.583  12.179 

Example timings

PFP.Rcheck/PFP-Ex.timings

nameusersystemelapsed
PFP-class0.1940.0640.258
PFPRefnet-class0.9560.1181.075
PFPRefnet_hsa0.5190.0110.531
PFPRefnet_mmu0.5940.0190.613
PFP_score-methods0.0050.0010.006
PFP_test10.0080.0010.009
PFP_test20.0070.0010.009
calc_PFP_score22.251 0.18522.455
data_std0.0140.0020.015
gene_list_hsa0.0020.0010.003
genes_score-methods0.0400.0050.045
get_PFPRefnet0.0000.0010.001
get_asso_net4.0220.0684.119
get_bg_related_kegg2.7470.0452.796
get_exp_cor_edges0.1540.0140.168
get_pathway_info0.1190.0041.866
group-methods0.4740.0050.479
kegg_download0.0010.0010.001
net_info-methods0.4770.0030.480
net_names-methods0.4430.0040.447
network-methods0.4820.0070.489
pathway_info0.0030.0020.004
pathway_info_hsa0.0020.0010.003
pathways_score-methods0.0060.0010.007
plot_PFP-methods0.3260.0080.334
plot_PFPlist0.3140.0060.321
rank_PFP-methods0.2280.0730.301
refnet_info-methods0.0090.0020.011
refnet_names-methods0.0060.0020.007
result_PFP-methods0.0090.0010.010
show_PFP-methods0.0120.0070.018
show_net-methods0.5130.0030.517
stats_test-methods0.0070.0010.008
sub_PFP-methods0.2450.0810.326
subnet-methods0.5530.0030.556
trans_edges_id3.4300.0913.526
trans_graph2PFPRefnet0.8210.0780.900
trans_xml2graph0.0010.0010.001