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BioC 3.0: CHECK report for manta on moscato1

This page was generated on 2015-04-10 09:47:41 -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: rm -rf manta.buildbin-libdir manta.Rcheck && mkdir manta.buildbin-libdir manta.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=manta.buildbin-libdir manta_1.12.0.tar.gz >manta.Rcheck\00install.out 2>&1 && cp manta.Rcheck\00install.out manta-install.out && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=manta.buildbin-libdir --install="check:manta-install.out" --force-multiarch --no-vignettes --timings manta_1.12.0.tar.gz
StartedAt: 2015-04-10 02:43:08 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 02:45:34 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 145.8 seconds
RetCode: 0
Status:  OK  
CheckDir: manta.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf manta.buildbin-libdir manta.Rcheck && mkdir manta.buildbin-libdir manta.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=manta.buildbin-libdir manta_1.12.0.tar.gz >manta.Rcheck\00install.out 2>&1 && cp manta.Rcheck\00install.out manta-install.out  && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=manta.buildbin-libdir --install="check:manta-install.out" --force-multiarch --no-vignettes --timings manta_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.0-bioc/meat/manta.Rcheck'
* using R version 3.1.3 (2015-03-09)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* 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 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 '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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [26s] OK
Examples with CPU or elapsed time > 5s
          user system elapsed
in2manta 16.91   0.02   16.93
** running examples for arch 'x64' ... [33s] OK
Examples with CPU or elapsed time > 5s
          user system elapsed
in2manta 20.86      0   20.86
* 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
  'D:/biocbld/bbs-3.0-bioc/meat/manta.Rcheck/00check.log'
for details.

manta.Rcheck/00install.out:


install for i386

* 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

install for x64

* installing *source* package 'manta' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'manta' as manta_1.12.0.zip
* DONE (manta)

manta.Rcheck/examples_i386/manta-Ex.timings:

nameusersystemelapsed
cmdArgsToVariables000
collapseRepliCounts0.030.000.03
compbiasPlot0.210.000.21
compbiasTest0.240.010.25
generateWeights0.610.000.61
in2manta16.91 0.0216.93
makeSampleDF0.010.000.01
manta0.030.000.03
meta2counts0.310.000.31
metataxa2subcounts0.050.000.05
nf2nr0.030.000.03
normfact2absTMM0.050.000.05
nr1.540.001.54
outliers0.090.000.10
plot.manta2.280.012.29
pplacer2manta0.700.020.71
readSeastar000
seastar2counts0.030.000.04
summary.manta0.030.000.03

manta.Rcheck/examples_x64/manta-Ex.timings:

nameusersystemelapsed
cmdArgsToVariables000
collapseRepliCounts0.040.000.03
compbiasPlot0.240.000.25
compbiasTest0.270.000.26
generateWeights0.640.000.64
in2manta20.86 0.0020.86
makeSampleDF0.030.000.03
manta0.030.010.05
meta2counts0.50.00.5
metataxa2subcounts0.060.000.06
nf2nr0.060.000.06
normfact2absTMM0.070.000.07
nr3.320.003.32
outliers0.190.000.19
plot.manta2.660.022.68
pplacer2manta1.030.051.28
readSeastar0.020.000.01
seastar2counts0.030.000.04
summary.manta0.060.000.06