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BioC 3.5: CHECK report for manta on veracruz2

This page was generated on 2017-08-16 13:30:06 -0400 (Wed, 16 Aug 2017).

Package 747/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
manta 1.22.0
Chris Berthiaume , Adrian Marchetti
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/manta
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: manta
Version: 1.22.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings manta_1.22.0.tar.gz
StartedAt: 2017-08-16 04:49:04 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 04:50:38 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 93.8 seconds
RetCode: 0
Status:  OK 
CheckDir: manta.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings manta_1.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/manta.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 ‘1.22.0’
* 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 ... NOTE
  installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc       1.4Mb
    extdata   4.0Mb
* 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 loading without being on the library search path ... 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
          user system elapsed
in2manta 14.67  0.046  15.133
* 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-3.5-bioc/meat/manta.Rcheck/00check.log’
for details.


manta.Rcheck/00install.out:

* installing *source* package ‘manta’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (manta)

manta.Rcheck/manta-Ex.timings:

nameusersystemelapsed
cmdArgsToVariables0.0010.0000.001
collapseRepliCounts0.2580.0020.264
compbiasPlot0.1450.0020.147
compbiasTest0.3140.0040.319
generateWeights0.5120.0070.542
in2manta14.670 0.04615.133
makeSampleDF0.0160.0000.016
manta0.0290.0020.032
meta2counts0.3440.0010.368
metataxa2subcounts0.0350.0010.037
nf2nr0.040.000.04
normfact2absTMM0.0270.0000.027
nr1.1480.0041.169
outliers0.1820.0020.185
plot.manta1.4530.0621.577
pplacer2manta0.6880.0140.725
readSeastar0.0020.0000.002
seastar2counts0.0130.0000.013
summary.manta0.0750.0010.076