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CHECK report for manta on merida2

This page was generated on 2019-04-09 13:26:49 -0400 (Tue, 09 Apr 2019).

Package 896/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
manta 1.29.1
Chris Berthiaume , Adrian Marchetti
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/manta
Branch: master
Last Commit: d1a8eae
Last Changed Date: 2019-01-04 13:37:21 -0400 (Fri, 04 Jan 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
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK 

Summary

Package: manta
Version: 1.29.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:manta.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings manta_1.29.1.tar.gz
StartedAt: 2019-04-09 01:56:21 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 01:58:07 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 106.4 seconds
RetCode: 0
Status:  OK 
CheckDir: manta.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:manta.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings manta_1.29.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/manta.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 ‘manta/DESCRIPTION’ ... OK
* this is package ‘manta’ version ‘1.29.1’
* 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 ‘manta’ 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 ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* 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 ... NOTE
'library' or 'require' calls in package code:
  ‘RSQLite’ ‘plotrix’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘.meta2metasum’
* checking S3 generic/method consistency ... NOTE
Found the following apparent S3 methods exported but not registered:
  plot.manta summary.manta
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.MTDheatplot: no visible global function definition for ‘gray’
.MTDheatplot: no visible global function definition for
  ‘colorRampPalette’
.MTDheatplot: no visible global function definition for ‘abline’
.MTDheatplot: no visible global function definition for ‘segments’
.MTDheatplot: no visible global function definition for ‘par’
.MTDheatplot: no visible global function definition for ‘plot’
.aggBinCounts: no visible global function definition for ‘hist’
.aggDESigCumDist: no visible global function definition for ‘hist’
.as.DGEList: no visible global function definition for ‘new’
.as.manta: no visible global function definition for ‘new’
.as.manta: no visible binding for global variable ‘samples’
.as.manta: no visible binding for global variable ‘counts’
.calcTMMvar: no visible binding for global variable ‘x’
.checkMetaLev: no visible binding for global variable ‘meta.sum’
.meta2metasum: no visible global function definition for ‘aggregate’
.normalize: no visible global function definition for ‘var’
.normalize: no visible global function definition for ‘calcNormFactors’
.wtd.var: no visible global function definition for ‘var’
compbiasPlot: no visible global function definition for ‘rainbow’
compbiasPlot: no visible binding for global variable ‘RAy’
compbiasPlot: no visible global function definition for ‘plot’
compbiasPlot : <anonymous>: no visible global function definition for
  ‘hist’
compbiasPlot: no visible binding for global variable ‘legend’
compbiasPlot: no visible global function definition for ‘legend’
compbiasPlot: no visible global function definition for ‘boxplot’
compbiasPlot: no visible global function definition for ‘violins’
compbiasTest: no visible global function definition for ‘anova’
compbiasTest: no visible global function definition for ‘lm’
counts2manta: no visible binding for global variable ‘agg’
manta: no visible global function definition for ‘new’
manta: no visible global function definition for ‘calcNormFactors’
manta: no visible global function definition for ‘estimateCommonDisp’
manta.ra: no visible global function definition for ‘par’
manta.ra: no visible global function definition for ‘legend’
manta.ra: no visible global function definition for ‘gray’
nf2nr: no visible global function definition for ‘calcNormFactors’
nr: no visible binding for global variable ‘x’
nr: no visible global function definition for ‘calcNormFactors’
outGenes: no visible global function definition for ‘p.adjust’
outGenes: no visible binding for global variable ‘PValue’
outGenes: no visible binding for global variable ‘R’
plot.manta: no visible global function definition for ‘par’
plot.manta: no visible global function definition for ‘legend’
plot.manta: no visible global function definition for ‘gray’
pplacer2manta: no visible global function definition for ‘dbDriver’
pplacer2manta: no visible global function definition for ‘dbConnect’
pplacer2manta: no visible global function definition for ‘dbReadTable’
pplacer2manta: no visible global function definition for ‘dbDisconnect’
pplacer2manta: no visible global function definition for ‘dbGetQuery’
readSeastar: no visible global function definition for ‘read.delim’
Undefined global functions or variables:
  PValue R RAy abline agg aggregate anova boxplot calcNormFactors
  colorRampPalette counts dbConnect dbDisconnect dbDriver dbGetQuery
  dbReadTable estimateCommonDisp gray hist legend lm meta.sum new
  p.adjust par plot rainbow read.delim samples segments var violins x
Consider adding
  importFrom("grDevices", "colorRampPalette", "gray", "rainbow")
  importFrom("graphics", "abline", "boxplot", "hist", "legend", "par",
             "plot", "segments")
  importFrom("methods", "new")
  importFrom("stats", "aggregate", "anova", "lm", "p.adjust", "var")
  importFrom("utils", "read.delim")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 ... NOTE
S3 methods shown with full name in documentation object 'summary.manta':
  ‘summary.manta’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
           user system elapsed
in2manta 17.481  0.047  17.682
* 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: 5 NOTEs
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/manta.Rcheck/00check.log’
for details.



Installation output

manta.Rcheck/00install.out

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL manta
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘manta’ ...
** 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 (manta)

Tests output


Example timings

manta.Rcheck/manta-Ex.timings

nameusersystemelapsed
cmdArgsToVariables0.0010.0000.000
collapseRepliCounts0.0280.0010.029
compbiasPlot0.1520.0050.162
compbiasTest0.1340.0030.136
generateWeights0.2550.0130.269
in2manta17.481 0.04717.682
makeSampleDF0.0140.0010.015
manta0.0200.0020.022
meta2counts0.4710.0020.480
metataxa2subcounts0.0340.0000.037
nf2nr0.0530.0010.054
normfact2absTMM0.0430.0010.044
nr1.5890.0121.620
outliers0.1410.0020.148
plot.manta1.7070.0871.812
pplacer2manta0.8990.0230.941
readSeastar0.0030.0000.007
seastar2counts0.0150.0000.016
summary.manta0.0370.0000.038