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BioC 3.0: CHECK report for OCplus on perceval

This page was generated on 2015-04-10 09:52:57 -0700 (Fri, 10 Apr 2015).

Package 616/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
OCplus 1.40.0
Alexander Ploner
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/OCplus
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: OCplus
Version: 1.40.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch OCplus_1.40.0.tar.gz
StartedAt: 2015-04-10 04:26:54 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 04:28:16 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 82.4 seconds
RetCode: 0
Status:  OK 
CheckDir: OCplus.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch OCplus_1.40.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/OCplus.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘OCplus/DESCRIPTION’ ... OK
* this is package ‘OCplus’ version ‘1.40.0’
* 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 ‘OCplus’ can be installed ... [4s/5s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Package in Depends field not imported from: ‘akima’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
plot.fdr2d.result: no visible global function definition for ‘interp’
Tornadoplot: no visible global function definition for ‘interp’
Volcanoplot: no visible global function definition for ‘interp’
* checking Rd files ... NOTE
prepare_Rd: tstatistics.Rd:38-39: Dropping empty section \examples
* 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 'plot.FDR.result':
  ‘plot.FDR.result’

S3 methods shown with full name in documentation object 'plot.fdr1d.result':
  ‘plot.fdr1d.result’

S3 methods shown with full name in documentation object 'plot.fdr2d.result':
  ‘plot.fdr2d.result’

S3 methods shown with full name in documentation object 'summary.fdr.result':
  ‘summary.fdr.result’

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 ... [27s/28s] OK
Examples with CPU or elapsed time > 5s
            user system elapsed
samplesize 8.332  0.205   9.058
* 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 4 notes.
See
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/OCplus.Rcheck/00check.log’
for details.

OCplus.Rcheck/00install.out:

* installing *source* package ‘OCplus’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (OCplus)

OCplus.Rcheck/OCplus-Ex.timings:

nameusersystemelapsed
EOC1.4380.0471.546
FDR0.0030.0010.005
MAsim.smyth0.4520.0160.480
OCshow2.0310.1092.150
TOC0.4710.0420.540
average.fdr1.7890.1441.998
fdr1d0.7680.0950.869
fdr2d1.0700.0811.164
plot.FDR.result0.3270.0360.373
plot.fdr1d.result0.6280.0980.746
plot.fdr2d.result0.9770.1071.104
samplesize8.3320.2059.058
smooth1d0.0540.0110.065
summary.fdr.result0.6830.0920.780
tMixture4.6520.1794.839