BioC 2.13: CHECK report for BioSeqClass on moscato1

Package: BioSeqClass

Version: 1.20.0

Command: rm -rf BioSeqClass.buildbin-libdir && mkdir BioSeqClass.buildbin-libdir && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=BioSeqClass.buildbin-libdir BioSeqClass_1.20.0.tar.gz >BioSeqClass-install.out 2>&1 && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD check --library=BioSeqClass.buildbin-libdir --install="check:BioSeqClass-install.out" --force-multiarch --no-vignettes --timings BioSeqClass_1.20.0.tar.gz && mv BioSeqClass.buildbin-libdir/* BioSeqClass.Rcheck/ && rmdir BioSeqClass.buildbin-libdir

StartedAt: 2014-04-05 02:34:33 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 02:39:46 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 313.3 seconds

RetCode: 0

Status:  OK

CheckDir: BioSeqClass.Rcheck

Warnings: 0

* using log directory 'D:/biocbld/bbs-2.13-bioc/meat/BioSeqClass.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 'BioSeqClass/DESCRIPTION' ... OK
* this is package 'BioSeqClass' version '1.20.0'
* 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 'BioSeqClass' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data      2.9Mb
    scripts   3.0Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  'scatterplot3d'
A package should be listed in only one of these fields.
* 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: 'scatterplot3d'
  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 ... 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 ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from 'inst/doc' ... OK
* checking for old-style vignette sources ... NOTE
Vignette sources only in 'inst/doc':
  'BioSeqClass.Rnw'
A 'vignettes' directory will be required as from R 3.1.0
* checking examples ...
** running examples for arch 'i386' ... [31s] OK
Examples with CPU or elapsed time > 5s
         user system elapsed
classify 8.35   0.03   10.36
** running examples for arch 'x64' ... [26s] OK
Examples with CPU or elapsed time > 5s
         user system elapsed
classify 7.02      0    9.81
* 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/BioSeqClass.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'BioSeqClass' ...
** R
** data
** 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 'BioSeqClass' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BioSeqClass' as BioSeqClass_1.20.0.zip
* DONE (BioSeqClass)

name	user	system	elapsed
basic	1.99	0.05	2.05
classify	8.35	0.03	10.36
featureAAindex	0.01	0.00	0.02
featureBDNAVIDEO	0	0	0
featureBinary	0.00	0.01	0.01
featureCKSAAP	0	0	0
featureCTD	0	0	0
featureDIPRODB	0.00	0.02	0.02
featureDOMAIN	0	0	0
featureEvaluate	0.03	0.00	0.03
featureFragmentComposition	0	0	0
featureGapPairComposition	0.02	0.00	0.02
featureHydro	0.01	0.00	0.01
featurePSSM	0	0	0
featurePseudoAAComp	0	0	0
featureSSC	0	0	0
hr	0.02	0.00	0.01
model	2.05	0.00	2.04
performance	2.58	0.00	2.59
selectFFS	1.86	0.00	1.86

name	user	system	elapsed
basic	1.71	0.03	1.73
classify	7.02	0.00	9.81
featureAAindex	0	0	0
featureBDNAVIDEO	0.01	0.00	0.02
featureBinary	0	0	0
featureCKSAAP	0	0	0
featureCTD	0	0	0
featureDIPRODB	0	0	0
featureDOMAIN	0	0	0
featureEvaluate	0.05	0.00	0.04
featureFragmentComposition	0	0	0
featureGapPairComposition	0.01	0.00	0.02
featureHydro	0	0	0
featurePSSM	0	0	0
featurePseudoAAComp	0	0	0
featureSSC	0.02	0.00	0.02
hr	0.01	0.00	0.02
model	1.70	0.01	1.71
performance	2.09	0.00	2.11
selectFFS	1.02	0.02	1.03