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This page was generated on 2021-10-22 12:04:08 -0400 (Fri, 22 Oct 2021).

CHECK results for PFP on nebbiolo2

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 1396/2075HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PFP 1.1.0  (landing page)
XC Zhang
Snapshot Date: 2021-10-21 14:50:08 -0400 (Thu, 21 Oct 2021)
git_url: https://git.bioconductor.org/packages/PFP
git_branch: master
git_last_commit: a3e8d80
git_last_commit_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  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    NA  

Summary

Package: PFP
Version: 1.1.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:PFP.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings PFP_1.1.0.tar.gz
StartedAt: 2021-10-21 21:19:32 -0400 (Thu, 21 Oct 2021)
EndedAt: 2021-10-21 21:22:52 -0400 (Thu, 21 Oct 2021)
EllapsedTime: 199.8 seconds
RetCode: 0
Status:   OK  
CheckDir: PFP.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:PFP.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings PFP_1.1.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/PFP.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-pc-linux-gnu (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 11.705  0.031  11.737
* 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:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL PFP
###
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* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/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 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 
  7.802   0.355   8.142 

Example timings

PFP.Rcheck/PFP-Ex.timings

nameusersystemelapsed
PFP-class0.1140.0200.134
PFPRefnet-class0.5290.0160.545
PFPRefnet_hsa0.3020.0000.302
PFPRefnet_mmu0.3680.0200.388
PFP_score-methods0.0060.0000.005
PFP_test10.0040.0000.005
PFP_test20.0040.0000.004
calc_PFP_score11.705 0.03111.737
data_std0.0060.0040.010
gene_list_hsa0.0010.0000.001
genes_score-methods0.0040.0000.004
get_PFPRefnet0.0000.0000.001
get_asso_net1.7940.0081.801
get_bg_related_kegg1.7420.0001.742
get_exp_cor_edges0.0980.0280.126
get_pathway_info0.0980.0322.214
group-methods0.2950.0000.296
kegg_download0.0010.0000.001
net_info-methods0.3220.0150.339
net_names-methods0.2830.0120.295
network-methods0.2830.0000.283
pathway_info0.0030.0000.002
pathway_info_hsa0.0020.0000.001
pathways_score-methods0.0040.0000.004
plot_PFP-methods0.3030.0040.307
plot_PFPlist0.1700.0040.175
rank_PFP-methods0.1540.0010.154
refnet_info-methods0.0040.0000.004
refnet_names-methods0.0040.0000.004
result_PFP-methods0.0050.0000.005
show_PFP-methods0.0050.0000.006
show_net-methods0.2880.0030.292
stats_test-methods0.0040.0000.004
sub_PFP-methods0.1040.0160.120
subnet-methods0.2940.0110.306
trans_edges_id2.4770.0992.577
trans_graph2PFPRefnet0.5010.0320.533
trans_xml2graph0.0000.0000.001