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This page was generated on 2021-08-03 12:06:55 -0400 (Tue, 03 Aug 2021).

CHECK results for PFP on merida1

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 1357/2015HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PFP 1.1.0  (landing page)
XC Zhang
Snapshot Date: 2021-08-02 14:50:09 -0400 (Mon, 02 Aug 2021)
URL: https://git.bioconductor.org/packages/PFP
Branch: master
Last Commit: a3e8d80
Last Changed Date: 2021-05-19 12:58:46 -0400 (Wed, 19 May 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  NO, package depends on 'KEGGgraph' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: PFP
Version: 1.1.0
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_1.1.0.tar.gz
StartedAt: 2021-08-03 05:25:39 -0400 (Tue, 03 Aug 2021)
EndedAt: 2021-08-03 05:31:05 -0400 (Tue, 03 Aug 2021)
EllapsedTime: 326.6 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_1.1.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/PFP.Rcheck’
* using R version 4.1.0 RC (2021-05-16 r80304)
* 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 ‘1.1.0’
* 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 22.998  0.113  23.146
* 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/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 RC (2021-05-16 r80304) -- "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 
 12.183   0.587  12.775 

Example timings

PFP.Rcheck/PFP-Ex.timings

nameusersystemelapsed
PFP-class0.2280.0800.309
PFPRefnet-class0.7640.0790.844
PFPRefnet_hsa0.4410.0120.453
PFPRefnet_mmu0.5360.0200.557
PFP_score-methods0.0070.0010.008
PFP_test10.0070.0010.008
PFP_test20.0080.0020.009
calc_PFP_score22.998 0.11323.146
data_std0.0130.0010.014
gene_list_hsa0.0010.0020.003
genes_score-methods0.0090.0020.011
get_PFPRefnet0.0010.0000.001
get_asso_net3.4710.0603.545
get_bg_related_kegg3.6170.0743.695
get_exp_cor_edges0.1590.0170.176
get_pathway_info0.1250.0031.807
group-methods0.4840.0030.488
kegg_download0.0010.0000.001
net_info-methods0.5310.0070.538
net_names-methods0.5360.0030.540
network-methods0.4840.0050.489
pathway_info0.0030.0020.005
pathway_info_hsa0.0030.0010.004
pathways_score-methods0.0070.0020.008
plot_PFP-methods0.3390.0080.347
plot_PFPlist0.2960.0050.301
rank_PFP-methods0.2530.0770.330
refnet_info-methods0.0090.0020.009
refnet_names-methods0.0070.0020.009
result_PFP-methods0.0100.0020.012
show_PFP-methods0.0120.0080.020
show_net-methods0.5190.0110.531
stats_test-methods0.0080.0010.010
sub_PFP-methods0.2800.0660.345
subnet-methods0.5100.0030.514
trans_edges_id2.8960.0292.927
trans_graph2PFPRefnet0.8510.0770.929
trans_xml2graph0.0010.0000.000