BioC 2.14: CHECK report for manta on petty

Package: manta

Version: 1.10.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch manta_1.10.0.tar.gz

StartedAt: 2014-10-07 22:46:08 -0700 (Tue, 07 Oct 2014)

EndedAt: 2014-10-07 22:48:21 -0700 (Tue, 07 Oct 2014)

EllapsedTime: 132.7 seconds

RetCode: 0

Status:  OK

CheckDir: manta.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch manta_1.10.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/manta.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘manta/DESCRIPTION’ ... OK
* this is package ‘manta’ version ‘1.10.0’
* 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 ... [6s/6s] 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
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’
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.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’
compbiasPlot: no visible binding for global variable ‘RAy’
compbiasPlot: no visible global function definition for ‘violins’
counts2manta: no visible binding for global variable ‘agg’
nr: no visible binding for global variable ‘x’
outGenes: no visible binding for global variable ‘PValue’
outGenes: no visible binding for global variable ‘R’
* 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 the 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 ... [51s/52s] OK
Examples with CPU or elapsed time > 5s
           user system elapsed
in2manta 35.611  0.104  36.093
* 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

NOTE: There were 5 notes.
See
  ‘/Users/biocbuild/bbs-2.14-bioc/meat/manta.Rcheck/00check.log’
for details.

* 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)

name	user	system	elapsed
cmdArgsToVariables	0.001	0.001	0.001
collapseRepliCounts	0.071	0.003	0.075
compbiasPlot	0.499	0.015	0.515
compbiasTest	0.346	0.005	0.351
generateWeights	0.641	0.011	0.653
in2manta	35.611	0.104	36.093
makeSampleDF	0.023	0.001	0.024
manta	0.035	0.004	0.039
meta2counts	0.651	0.005	0.659
metataxa2subcounts	0.062	0.002	0.065
nf2nr	0.070	0.002	0.072
normfact2absTMM	0.066	0.002	0.071
nr	3.268	0.017	3.336
outliers	0.189	0.004	0.196
plot.manta	3.365	0.103	3.521
pplacer2manta	1.560	0.030	1.599
readSeastar	0.008	0.001	0.009
seastar2counts	0.058	0.001	0.063
summary.manta	0.074	0.002	0.077