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CHECK report for ELMER on merida2

This page was generated on 2018-10-17 08:54:55 -0400 (Wed, 17 Oct 2018).

Package 441/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ELMER 2.4.4
Tiago Chedraoui Silva
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/ELMER
Branch: RELEASE_3_7
Last Commit: a667145
Last Changed Date: 2018-06-26 15:13:01 -0400 (Tue, 26 Jun 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: ELMER
Version: 2.4.4
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ELMER.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ELMER_2.4.4.tar.gz
StartedAt: 2018-10-16 21:09:40 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 21:28:13 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 1113.6 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: ELMER.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ELMER.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ELMER_2.4.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/ELMER.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ELMER/DESCRIPTION’ ... OK
* this is package ‘ELMER’ version ‘2.4.4’
* 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 ‘ELMER’ 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 ... WARNING
'::' or ':::' import not declared from: 'data.table'
':::' call which should be '::': 'TCGAbiolinks:::TCGAVisualize_volcano'
  See the note in ?`:::` about the use of this operator.
Unexported objects imported by ':::' calls:
  'TCGAbiolinks:::colDataPrepare' 'TCGAbiolinks:::get.GRCh.bioMart'
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
TF.rank.plot: no visible binding for global variable 'pvalue'
TF.rank.plot: no visible binding for global variable 'label'
TF.rank.plot: no visible binding for global variable 'Gene'
addDistNearestTSS: no visible binding for global variable 'Target'
addDistNearestTSS: no visible binding for global variable 'GeneID'
addDistNearestTSS: no visible binding for global variable 'Probe'
addMutCol: no visible binding for global variable 'Hugo_Symbol'
calculateEnrichement : <anonymous>: no visible global function
  definition for 'fisher.test'
findMotifRegion: no visible binding for global variable 'gr'
findMotifRegion: no visible global function definition for
  'write.table'
get.diff.meth: no visible binding for global variable 'x'
get.enriched.motif : <anonymous>: no visible global function definition
  for 'fisher.test'
getRandomPairs: no visible binding for global variable
  'hm450.hg38.manifest'
getTFtargets: no visible binding for global variable 'TF'
heatmapGene: no visible global function definition for 'precede'
heatmapGene: no visible global function definition for
  'subsetByOverlaps'
heatmapGene: no visible binding for global variable 'mae'
motif.enrichment.plot: no visible binding for global variable 'y'
motif.enrichment.plot: no visible binding for global variable 'x'
motif.enrichment.plot: no visible binding for global variable 'z'
motif.enrichment.plot: no visible binding for global variable 'upperOR'
motif.enrichment.plot: no visible binding for global variable 'lowerOR'
motif.enrichment.plot: no visible binding for global variable 'motif'
motif.enrichment.plot: no visible binding for global variable 'OR'
scatter: no visible binding for global variable 'value'
scatter: no visible global function definition for 'cor.test'
scatter: no visible binding for global variable 'mae'
Undefined global functions or variables:
  Gene GeneID Hugo_Symbol OR Probe TF Target cor.test fisher.test gr
  hm450.hg38.manifest label lowerOR mae motif precede pvalue
  subsetByOverlaps upperOR value write.table x y z
Consider adding
  importFrom("stats", "cor.test", "fisher.test")
  importFrom("utils", "write.table")
to your NAMESPACE file.
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                               user system elapsed
get.enriched.motif           26.937  0.816  30.689
createMAE                    20.380  0.583  41.312
getRandomPairs               19.497  0.643  39.371
schematic.plot               15.048  0.184  25.042
get.feature.probe             9.839  0.507  16.678
get.pair                      9.290  0.273  28.407
preAssociationProbeFiltering  8.695  0.289  22.923
GetNearGenes                  8.108  0.311  46.713
scatter.plot                  7.931  0.120   8.121
TF.rank.plot                  4.842  0.255   5.168
getTCGA                       2.998  0.533  10.358
* 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: 1 WARNING, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.7-bioc/meat/ELMER.Rcheck/00check.log’
for details.



Installation output

ELMER.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL ELMER
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘ELMER’ ...
** R
** 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 (ELMER)

Tests output

ELMER.Rcheck/tests/testthat.Rout


R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
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(ELMER)
Loading required package: ELMER.data
> 
> test_check("ELMER")

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══ testthat results  ═══════════════════════════════════════════════════════════
OK: 95 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
121.439   4.995 471.789 

Example timings

ELMER.Rcheck/ELMER-Ex.timings

nameusersystemelapsed
GetNearGenes 8.108 0.31146.713
TCGA.pipe0.0020.0000.003
TF.rank.plot4.8420.2555.168
addDistNearestTSS0.0010.0000.001
addMutCol0.0010.0000.001
calculateEnrichement0.0550.0080.062
createMAE20.380 0.58341.312
createTSVTemplates0.0120.0010.012
findMotifRegion0.0020.0000.002
get.TFs4.5840.1794.813
get.diff.meth1.6690.0651.746
get.enriched.motif26.937 0.81630.689
get.feature.probe 9.839 0.50716.678
get.pair 9.290 0.27328.407
get.permu4.3120.1794.523
getGeneID0.7230.0500.785
getRandomPairs19.497 0.64339.371
getSymbol0.6830.0540.738
getTCGA 2.998 0.53310.358
getTFtargets0.0290.0820.010
getTSS0.0040.0130.001
heatmapGene0.0110.0300.003
heatmapPairs0.0070.0200.002
metBoxPlot0.0060.0180.003
motif.enrichment.plot2.2250.6052.178
preAssociationProbeFiltering 8.695 0.28922.923
promoterMeth0.0010.0000.001
render_report0.0010.0000.002
scatter.plot7.9310.1208.121
schematic.plot15.048 0.18425.042