Multiple platform build/check report for BioC 3.11 - CHECK report for CeTF on celaya2

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:CeTF.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CeTF_0.99.12.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/CeTF.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CeTF/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CeTF’ version ‘0.99.12’
* 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 ‘CeTF’ 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
histPlot            11.181  0.027  11.272
clustCoef           10.920  0.260  11.561
PCIT                10.866  0.144  11.099
clustCoefPercentage  9.921  0.031  10.215
netConditionsPlot    9.212  0.142   9.356
runAnalysis          8.724  0.152   8.922
* 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

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL CeTF
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘CeTF’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (CeTF)

Tests output


R Under development (unstable) (2019-12-14 r77572) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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("CeTF")

> test_check("CeTF")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 32 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 20.714   1.869  22.603

Example timings

name	user	system	elapsed
CeTFdemo	0.004	0.002	0.006
InputData-methods	0.028	0.008	0.036
NetworkData-methods	0.087	0.014	0.101
OutputData-methods	0.095	0.037	0.133
PCIT	10.866	0.144	11.099
RIF	1.013	0.057	1.070
RIF_input	0.002	0.002	0.004
SmearPlot	1.934	0.093	2.045
TFs	0.002	0.002	0.005
bivar.awk	0.014	0.002	0.019
clustCoef	10.920	0.260	11.561
clustCoefPercentage	9.921	0.031	10.215
densityPlot	3.088	0.022	3.239
expDiff	0.648	0.015	0.662
getDE-methods	0.031	0.004	0.035
getData-methods	0.026	0.003	0.031
getGroupGO	0.000	0.000	0.001
histPlot	11.181	0.027	11.272
netConditionsPlot	9.212	0.142	9.356
netGOTFPlot	0.001	0.001	0.002
normExp	0.142	0.050	0.192
runAnalysis	8.724	0.152	8.922
simCounts	0.002	0.002	0.003
simNorm	0.003	0.002	0.005
tolerance	0.002	0.000	0.002

CHECK report for CeTF on celaya2

Summary

Command output

Installation output

Tests output

Example timings