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BioC 2.13: CHECK report for OCplus on moscato1

This page was generated on 2014-04-05 09:49:20 -0700 (Sat, 05 Apr 2014).

Package 490/750HostnameOS / ArchBUILDCHECKBUILD BIN
OCplus 1.36.0
Alexander Ploner
Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/OCplus
Last Changed Rev: 81642 / Revision: 88450
Last Changed Date: 2013-10-14 14:29:21 -0700 (Mon, 14 Oct 2013)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK [ OK ] OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 

Summary

Package: OCplus
Version: 1.36.0
Command: rm -rf OCplus.buildbin-libdir && mkdir OCplus.buildbin-libdir && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=OCplus.buildbin-libdir OCplus_1.36.0.tar.gz >OCplus-install.out 2>&1 && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD check --library=OCplus.buildbin-libdir --install="check:OCplus-install.out" --force-multiarch --no-vignettes --timings OCplus_1.36.0.tar.gz && mv OCplus.buildbin-libdir/* OCplus.Rcheck/ && rmdir OCplus.buildbin-libdir
StartedAt: 2014-04-05 05:32:18 -0700 (Sat, 05 Apr 2014)
EndedAt: 2014-04-05 05:34:31 -0700 (Sat, 05 Apr 2014)
EllapsedTime: 133.1 seconds
RetCode: 0
Status:  OK  
CheckDir: OCplus.Rcheck
Warnings: 0

Command output

* using log directory 'D:/biocbld/bbs-2.13-bioc/meat/OCplus.Rcheck'
* using R version 3.0.3 (2014-03-06)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'OCplus/DESCRIPTION' ... OK
* this is package 'OCplus' version '1.36.0'
* 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 'OCplus' can be installed ... 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
* 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
* 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 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.
See the information on DESCRIPTION files in the chapter 'Creating R
packages' of the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 the 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 for old-style vignette sources ... NOTE
Vignette sources only in 'inst/doc':
  'OCplus.Rnw'
A 'vignettes' directory will be required as from R 3.1.0
* checking examples ...
** running examples for arch 'i386' ... [29s] OK
Examples with CPU or elapsed time > 5s
           user system elapsed
samplesize 9.44   0.06    9.51
tMixture   5.51   0.06    5.71
** running examples for arch 'x64' ... [36s] OK
Examples with CPU or elapsed time > 5s
            user system elapsed
samplesize 10.97   0.06   12.07
tMixture    6.32   0.08    6.42
* 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

NOTE: There were 4 notes.
See
  'D:/biocbld/bbs-2.13-bioc/meat/OCplus.Rcheck/00check.log'
for details.

OCplus.Rcheck/00install.out:


install for i386

* 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

install for x64

* installing *source* package 'OCplus' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'OCplus' as OCplus_1.36.0.zip
* DONE (OCplus)

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

nameusersystemelapsed
EOC1.170.051.28
FDR000
MAsim.smyth0.30.00.3
OCshow2.050.022.30
TOC0.730.010.75
average.fdr2.250.002.24
fdr1d0.680.000.69
fdr2d0.850.000.84
plot.FDR.result0.230.020.25
plot.fdr1d.result0.860.000.86
plot.fdr2d.result1.400.021.42
samplesize9.440.069.51
smooth1d0.060.000.06
summary.fdr.result0.610.000.92
tMixture5.510.065.71

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

nameusersystemelapsed
EOC1.810.003.09
FDR000
MAsim.smyth0.510.000.55
OCshow2.840.002.84
TOC0.700.050.75
average.fdr1.590.001.77
fdr1d0.640.000.64
fdr2d0.90.00.9
plot.FDR.result0.280.000.29
plot.fdr1d.result0.580.000.57
plot.fdr2d.result1.040.001.55
samplesize10.97 0.0612.07
smooth1d0.080.000.08
summary.fdr.result0.800.020.81
tMixture6.320.086.42