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CHECK report for FELLA on celaya2

This page was generated on 2019-09-17 13:21:41 -0400 (Tue, 17 Sep 2019).

Package 544/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
FELLA 1.4.1
Sergio Picart-Armada
Snapshot Date: 2019-09-16 17:00:49 -0400 (Mon, 16 Sep 2019)
URL: https://git.bioconductor.org/packages/FELLA
Branch: RELEASE_3_9
Last Commit: 36e66c6
Last Changed Date: 2019-07-14 04:16:52 -0400 (Sun, 14 Jul 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
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

Summary

Package: FELLA
Version: 1.4.1
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_1.4.1.tar.gz
StartedAt: 2019-09-17 02:34:09 -0400 (Tue, 17 Sep 2019)
EndedAt: 2019-09-17 02:38:09 -0400 (Tue, 17 Sep 2019)
EllapsedTime: 240.5 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_1.4.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/FELLA.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.4.1’
* 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
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘FELLA’ ...
** using staged installation
** 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 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 (FELLA)

Tests output

FELLA.Rcheck/tests/testthat.Rout


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
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(FELLA)
> 
> test_check("FELLA")

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══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 168 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 27.778   8.716  66.486 

Example timings

FELLA.Rcheck/FELLA-Ex.timings

nameusersystemelapsed
FELLA0.5760.1020.713
FELLA.sample0.0200.0020.023
checkArguments0.0030.0000.004
data-funs3.8310.3434.246
enrich-funs4.5270.3674.982
export-funs0.3670.0130.381
getBackground2.4420.0642.582
getCom0.0230.0030.025
getExcluded0.0240.0040.028
getGraph0.0200.0020.023
getInfo0.0210.0020.024
getInput0.0250.0050.029
getMatrix0.0370.0040.041
getName0.0190.0040.022
getPscores0.0520.0050.057
getPvaluesSize0.0650.0070.072
getStatus0.0210.0020.023
getSums0.4440.0060.450
getValid0.0390.0040.044
infere.con2ec0.0050.0010.005
input.sample0.0010.0010.003
is.FELLA.DATA0.0140.0010.015
is.FELLA.USER0.0420.0040.047
largestcc0.0280.0010.029
launchApp0.0000.0000.001
listApprox000
listCategories0.0010.0000.001
listInternalDatabases0.0020.0010.002
listMethods0.0000.0010.001
mytriangle0.0310.0020.034
plotBipartite0.1140.0070.122
plotLegend0.0460.0030.049
sanitise000