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Package 380/658HostnameOS / ArchBUILDCHECKBUILD BIN
manta 1.5.0
Chris Berthiaume , Adrian Marchetti
Snapshot Date: 2013-03-24 17:01:43 -0700 (Sun, 24 Mar 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/manta
Last Changed Rev: 70377 / Revision: 74774
Last Changed Date: 2012-10-10 11:10:16 -0700 (Wed, 10 Oct 2012)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Leopard (10.5.8) / i386  OK [ OK ] OK 

Summary

Package: manta
Version: 1.5.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch manta_1.5.0.tar.gz
StartedAt: 2013-03-25 03:25:16 -0700 (Mon, 25 Mar 2013)
EndedAt: 2013-03-25 03:26:52 -0700 (Mon, 25 Mar 2013)
EllapsedTime: 96.6 seconds
RetCode: 0
Status:  OK 
CheckDir: manta.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/manta.Rcheck'
* using R Under development (unstable) (2013-02-26 r62077)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* 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 ... [5s/5s] 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 DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [40s/40s] OK
Examples with CPU or elapsed time > 5s
           user system elapsed
in2manta 26.092   0.42  26.525
* 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 3 notes.
See
  '/Users/biocbuild/bbs-2.12-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
   'manta.Rnw' using 'UTF-8' 
** testing if installed package can be loaded
* DONE (manta)

manta.Rcheck/manta-Ex.timings:

nameusersystemelapsed
collapseRepliCounts0.0900.0120.103
compbiasPlot0.3400.0150.357
compbiasTest0.2940.0160.311
generateWeights0.4360.0240.460
in2manta26.092 0.42026.525
makeSampleDF0.0380.0130.051
manta0.0600.0200.079
meta2counts0.6250.0180.642
metataxa2subcounts0.0970.0120.107
nf2nr0.0990.0120.111
normfact2absTMM0.0870.0130.101
nr2.5140.0262.542
outliers0.1410.0120.155
plot.manta2.5760.0782.674
pplacer2manta1.2440.0561.303
readSeastar0.0190.0140.033
seastar2counts0.0440.0140.059
summary.manta0.1680.0120.180