Package: manta

Version: 1.5.0

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings manta_1.5.0.tar.gz

StartedAt: 2013-03-25 02:51:31 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 02:53:22 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 110.6 seconds

RetCode: 0

Status:  OK

CheckDir: manta.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/manta.Rcheck’
* using R version 3.0.0 beta (2013-03-19 r62328)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘manta/DESCRIPTION’ ... OK
* this is package ‘manta’ version ‘1.5.0’
* 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  5.6Mb
  sub-directories of 1Mb or more:
    doc       1.4Mb
    extdata   4.0Mb
* checking package 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 for unstated dependencies in R code ... OK
* 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 installed files from ‘inst/doc’ ... OK
* checking examples ... [48s/48s] OK
Examples with CPU or elapsed time > 5s
           user system elapsed
in2manta 33.486  0.048  34.053
* 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 4 notes.
See
  ‘/home/biocbuild/bbs-2.12-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
   ‘manta.Rnw’ using ‘UTF-8’ 
** testing if installed package can be loaded
* DONE (manta)

name	user	system	elapsed
collapseRepliCounts	0.144	0.004	0.149
compbiasPlot	0.416	0.012	0.427
compbiasTest	0.436	0.008	0.445
generateWeights	0.900	0.012	0.921
in2manta	33.486	0.048	34.053
makeSampleDF	0.052	0.008	0.057
manta	0.096	0.004	0.100
meta2counts	0.632	0.008	0.642
metataxa2subcounts	0.268	0.000	0.267
nf2nr	0.064	0.000	0.067
normfact2absTMM	0.076	0.004	0.081
nr	2.980	0.020	3.078
outliers	0.180	0.004	0.206
plot.manta	3.168	0.048	3.234
pplacer2manta	1.188	0.020	1.209
readSeastar	0.020	0.004	0.020
seastar2counts	0.036	0.000	0.037
summary.manta	0.056	0.004	0.059