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BioC 3.0: CHECK report for manta on oaxaca

This page was generated on 2015-04-10 10:05:45 -0700 (Fri, 10 Apr 2015).

Package 505/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
manta 1.12.0
Chris Berthiaume , Adrian Marchetti
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/manta
Last Changed Rev: 95439 / Revision: 102249
Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK 

Summary

Package: manta
Version: 1.12.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch manta_1.12.0.tar.gz
StartedAt: 2015-04-10 00:55:55 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 00:57:33 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 97.7 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 --no-multiarch manta_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/manta.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘manta/DESCRIPTION’ ... OK
* this is package ‘manta’ version ‘1.12.0’
* 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 ‘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
.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’
.normalize: no visible global function definition for ‘calcNormFactors’
compbiasPlot: no visible binding for global variable ‘RAy’
compbiasPlot: no visible global function definition for ‘violins’
counts2manta: no visible binding for global variable ‘agg’
manta: no visible global function definition for ‘calcNormFactors’
manta: no visible global function definition for ‘estimateCommonDisp’
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 binding for global variable ‘PValue’
outGenes: no visible binding for global variable ‘R’
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’
* 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 ... [32s/33s] OK
Examples with CPU or elapsed time > 5s
           user system elapsed
in2manta 21.421  0.059  22.033
* 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

NOTE: There were 5 notes.
See
  ‘/Users/biocbuild/bbs-3.0-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
cmdArgsToVariables0.0000.0000.001
collapseRepliCounts0.0390.0000.082
compbiasPlot0.2640.0050.270
compbiasTest0.2790.0050.285
generateWeights0.9280.0120.951
in2manta21.421 0.05922.033
makeSampleDF0.0350.0010.036
manta0.0490.0010.052
meta2counts0.3140.0030.319
metataxa2subcounts0.0500.0010.051
nf2nr0.0460.0010.046
normfact2absTMM0.0480.0010.049
nr2.0550.0152.090
outliers0.1220.0020.128
plot.manta2.2610.0722.467
pplacer2manta0.9810.0181.004
readSeastar0.0050.0010.006
seastar2counts0.0290.0010.030
summary.manta0.0480.0010.049