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BioC 3.2: CHECK report for OCplus on oaxaca

This page was generated on 2015-10-27 17:38:15 -0400 (Tue, 27 Oct 2015).

Package 719/1104HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
OCplus 1.44.0
Alexander Ploner
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/OCplus
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: OCplus
Version: 1.44.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings OCplus_1.44.0.tar.gz
StartedAt: 2015-10-27 06:13:24 -0400 (Tue, 27 Oct 2015)
EndedAt: 2015-10-27 06:14:28 -0400 (Tue, 27 Oct 2015)
EllapsedTime: 64.0 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 OCplus_1.44.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/OCplus.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘OCplus/DESCRIPTION’ ... OK
* this is package ‘OCplus’ version ‘1.44.0’
* 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 ... [3s/3s] 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
Tornadoplot: no visible global function definition for ‘interp’
Volcanoplot: no visible global function definition for ‘interp’
plot.fdr2d.result: 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 ... [21s/21s] OK
Examples with CPU or elapsed time > 5s
            user system elapsed
samplesize 6.839  0.284   7.139
* 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: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-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
EOC0.5990.0350.637
FDR0.0020.0000.002
MAsim.smyth0.2820.0140.296
OCshow1.4740.0701.550
TOC0.3860.0330.421
average.fdr1.3850.0821.505
fdr1d0.4910.0420.533
fdr2d0.7290.0630.792
plot.FDR.result0.1910.0150.206
plot.fdr1d.result0.4810.0530.535
plot.fdr2d.result0.7630.0480.812
samplesize6.8390.2847.139
smooth1d0.0390.0070.046
summary.fdr.result0.5410.0500.592
tMixture4.0450.2684.315