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BioC 3.2: CHECK report for manta on linux1.bioconductor.org

This page was generated on 2015-10-27 17:25:20 -0400 (Tue, 27 Oct 2015).

Package 588/1104HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
manta 1.16.0
Chris Berthiaume , Adrian Marchetti
Snapshot Date: 2015-10-26 19:24:07 -0400 (Mon, 26 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/manta
Last Changed Rev: 109589 / Revision: 109947
Last Changed Date: 2015-10-13 15:36:05 -0400 (Tue, 13 Oct 2015)
linux1.bioconductor.org Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
windows1.bioconductor.org Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: manta
Version: 1.16.0
Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings manta_1.16.0.tar.gz
StartedAt: 2015-10-27 05:14:59 -0400 (Tue, 27 Oct 2015)
EndedAt: 2015-10-27 05:15:49 -0400 (Tue, 27 Oct 2015)
EllapsedTime: 50.3 seconds
RetCode: 0
Status:  OK 
CheckDir: manta.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings manta_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/manta.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘manta/DESCRIPTION’ ... OK
* this is package ‘manta’ version ‘1.16.0’
* 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 ... [2s/2s] 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [21s/21s] OK
Examples with CPU or elapsed time > 5s
           user system elapsed
in2manta 15.127  0.008  15.136
* 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

Status: 5 NOTEs
See
  ‘/home/biocbuild/bbs-3.2-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
cmdArgsToVariables000
collapseRepliCounts0.0320.0010.032
compbiasPlot0.1660.0000.166
compbiasTest0.1730.0030.177
generateWeights0.4450.0000.446
in2manta15.127 0.00815.136
makeSampleDF0.0090.0000.008
manta0.0140.0000.014
meta2counts0.1330.0000.132
metataxa2subcounts0.0240.0000.024
nf2nr0.0260.0000.025
normfact2absTMM0.0260.0000.025
nr0.8810.0000.882
outliers0.0740.0000.073
plot.manta1.6700.0401.709
pplacer2manta0.4220.0080.430
readSeastar0.0020.0000.002
seastar2counts0.010.000.01
summary.manta0.0250.0000.025