BioC 3.4: CHECK report for BioSeqClass on morelia

Package: BioSeqClass

Version: 1.32.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings BioSeqClass_1.32.0.tar.gz

StartedAt: 2017-04-14 23:15:08 -0700 (Fri, 14 Apr 2017)

EndedAt: 2017-04-14 23:18:04 -0700 (Fri, 14 Apr 2017)

EllapsedTime: 176.1 seconds

RetCode: 0

Status:  OK

CheckDir: BioSeqClass.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings BioSeqClass_1.32.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/BioSeqClass.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BioSeqClass/DESCRIPTION’ ... OK
* this is package ‘BioSeqClass’ version ‘1.32.0’
* 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 ‘BioSeqClass’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.6Mb
  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
Malformed Description field: should contain one or more complete sentences.
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
* 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: ‘scatterplot3d’
  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
classifyModelCTREELIBSVM: no visible global function definition for
  ‘plot’
Undefined global functions or variables:
  plot
Consider adding
  importFrom("graphics", "plot")
to your NAMESPACE file.
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
          user system elapsed
classify 7.822  0.349   8.535
* 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-3.4-bioc/meat/BioSeqClass.Rcheck/00check.log’
for details.

* 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
* DONE (BioSeqClass)

name	user	system	elapsed
basic	0.850	0.021	0.871
classify	7.822	0.349	8.535
featureAAindex	0.001	0.000	0.001
featureBDNAVIDEO	0.001	0.000	0.001
featureBinary	0.001	0.000	0.001
featureCKSAAP	0.001	0.000	0.001
featureCTD	0.002	0.000	0.002
featureDIPRODB	0.001	0.000	0.001
featureDOMAIN	0.001	0.000	0.001
featureEvaluate	0.039	0.001	0.040
featureFragmentComposition	0.002	0.000	0.001
featureGapPairComposition	0.001	0.000	0.001
featureHydro	0.002	0.000	0.002
featurePSSM	0.001	0.000	0.001
featurePseudoAAComp	0.002	0.000	0.001
featureSSC	0.005	0.001	0.005
hr	0.006	0.000	0.007
model	1.355	0.019	1.374
performance	1.396	0.020	1.416
selectFFS	0.515	0.014	0.530