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Package 322/553HostnameOS / ArchBUILDCHECKBUILD BIN
manta 1.2.0
David M. Schruth
Snapshot Date: 2012-09-23 17:01:39 -0700 (Sun, 23 Sep 2012)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_10/madman/Rpacks/manta
Last Changed Rev: 64678 / Revision: 69725
Last Changed Date: 2012-03-30 15:05:02 -0700 (Fri, 30 Mar 2012)
lamb2 Linux (openSUSE 11.4) / 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: 1.2.0
Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch manta_1.2.0.tar.gz
StartedAt: 2012-09-24 00:48:58 -0700 (Mon, 24 Sep 2012)
EndedAt: 2012-09-24 00:50:37 -0700 (Mon, 24 Sep 2012)
EllapsedTime: 98.7 seconds
RetCode: 0
Status:  OK 
CheckDir: manta.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.10-bioc/meat/manta.Rcheck'
* using R version 2.15.1 (2012-06-22)
* 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 '1.2.0'
* 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 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 for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 ... OK
* 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-2.10-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
collapseRepliCounts0.1490.0040.153
compbiasPlot0.4100.0110.424
compbiasTest0.4300.0110.440
generateWeights0.6540.0210.676
in2manta32.442 0.47232.924
makeSampleDF0.0210.0030.025
manta0.0830.0100.094
meta2counts0.3740.0080.382
metataxa2subcounts0.0470.0020.050
nf2nr0.0490.0030.052
normfact2absTMM0.0560.0030.059
nr2.5200.0142.536
outliers0.1240.0060.129
plot.manta1.7420.0481.856
pplacer2manta0.8780.0350.914
readSeastar0.0030.0020.006
seastar2counts0.0180.0020.020
summary.manta0.0510.0030.054