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CHECK report for manta on merida2

This page was generated on 2018-10-17 08:50:14 -0400 (Wed, 17 Oct 2018).

Package 824/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
manta 1.26.0
Chris Berthiaume , Adrian Marchetti
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/manta
Branch: RELEASE_3_7
Last Commit: ff327c8
Last Changed Date: 2018-04-30 10:35:23 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 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
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: manta
Version: 1.26.0
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_1.26.0.tar.gz
StartedAt: 2018-10-16 22:21:32 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 22:23:06 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 94.0 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_1.26.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/manta.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 ‘manta/DESCRIPTION’ ... OK
* this is package ‘manta’ version ‘1.26.0’
* 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 ... OK
* 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 15.818   0.05   15.98
* 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: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.7-bioc/meat/manta.Rcheck/00check.log’
for details.



Installation output

manta.Rcheck/00install.out

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL manta
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/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
cmdArgsToVariables0.0010.0000.001
collapseRepliCounts0.0370.0010.038
compbiasPlot0.1590.0040.165
compbiasTest0.1460.0030.149
generateWeights0.2270.0070.233
in2manta15.818 0.05015.980
makeSampleDF0.0140.0000.015
manta0.0240.0020.027
meta2counts0.3810.0030.384
metataxa2subcounts0.0400.0010.041
nf2nr0.0340.0000.034
normfact2absTMM0.0450.0000.046
nr1.2000.0121.216
outliers0.1530.0020.156
plot.manta1.4350.0791.531
pplacer2manta0.7810.0190.809
readSeastar0.0050.0000.006
seastar2counts0.0140.0010.015
summary.manta0.0430.0010.043