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CHECK report for FELLA on merida2

This page was generated on 2019-04-08 12:34:00 -0400 (Mon, 08 Apr 2019).

Package 535/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
FELLA 1.3.1
Sergio Picart-Armada
Snapshot Date: 2019-04-07 17:01:41 -0400 (Sun, 07 Apr 2019)
URL: https://git.bioconductor.org/packages/FELLA
Branch: master
Last Commit: 3fca6aa
Last Changed Date: 2019-02-15 03:55:59 -0400 (Fri, 15 Feb 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  ERROR  skipped 
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK 

Summary

Package: FELLA
Version: 1.3.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:FELLA.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings FELLA_1.3.1.tar.gz
StartedAt: 2019-04-08 00:54:53 -0400 (Mon, 08 Apr 2019)
EndedAt: 2019-04-08 00:58:14 -0400 (Mon, 08 Apr 2019)
EllapsedTime: 201.1 seconds
RetCode: 0
Status:  OK 
CheckDir: FELLA.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:FELLA.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings FELLA_1.3.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/FELLA.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘FELLA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘FELLA’ version ‘1.3.1’
* 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 ‘FELLA’ 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* 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

FELLA.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL FELLA
###
##############################################################################
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘FELLA’ ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (FELLA)

Tests output

FELLA.Rcheck/tests/testthat.Rout


R Under development (unstable) (2018-11-27 r75683) -- "Unsuffered Consequences"
Copyright (C) 2018 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(FELLA)
> 
> test_check("FELLA")

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══ testthat results  ═══════════════════════════════════════════════════════════
OK: 168 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 22.272   3.739  55.408 

Example timings

FELLA.Rcheck/FELLA-Ex.timings

nameusersystemelapsed
FELLA0.4770.0520.549
FELLA.sample0.0210.0010.024
checkArguments0.0030.0000.003
data-funs3.2270.1543.420
enrich-funs3.3660.1253.518
export-funs0.2660.0060.273
getBackground2.1870.0422.240
getCom0.0190.0020.021
getExcluded0.0230.0020.024
getGraph0.0180.0010.020
getInfo0.0190.0020.020
getInput0.0230.0020.025
getMatrix0.0210.0010.022
getName0.0180.0010.020
getPscores0.0600.0080.067
getPvaluesSize0.0300.0020.032
getStatus0.0190.0010.020
getSums0.3550.0080.364
getValid0.0390.0030.043
infere.con2ec0.0040.0010.004
input.sample0.0020.0010.003
is.FELLA.DATA0.0180.0010.018
is.FELLA.USER0.0380.0030.040
largestcc0.0220.0010.023
launchApp000
listApprox000
listCategories0.0000.0000.001
listInternalDatabases0.0010.0000.001
listMethods0.0010.0000.001
mytriangle0.0220.0010.022
plotBipartite0.0840.0030.090
plotLegend0.0360.0020.038
sanitise0.0010.0010.001