BioC 3.5: CHECK report for BioSeqClass on malbec2

Package: BioSeqClass

Version: 1.34.0

Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings BioSeqClass_1.34.0.tar.gz

StartedAt: 2017-08-15 21:32:17 -0400 (Tue, 15 Aug 2017)

EndedAt: 2017-08-15 21:34:45 -0400 (Tue, 15 Aug 2017)

EllapsedTime: 147.5 seconds

RetCode: 0

Status:  OK

CheckDir: BioSeqClass.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings BioSeqClass_1.34.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/BioSeqClass.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BioSeqClass/DESCRIPTION’ ... OK
* this is package ‘BioSeqClass’ version ‘1.34.0’
* 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  6.7Mb
  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 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 6.44  0.144   5.353
* 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
  ‘/home/biocbuild/bbs-3.5-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	0.636	0.008	0.642
classify	6.440	0.144	5.353
featureAAindex	0.000	0.000	0.001
featureBDNAVIDEO	0	0	0
featureBinary	0.004	0.000	0.000
featureCKSAAP	0	0	0
featureCTD	0.000	0.000	0.001
featureDIPRODB	0.004	0.000	0.000
featureDOMAIN	0	0	0
featureEvaluate	0.016	0.000	0.015
featureFragmentComposition	0	0	0
featureGapPairComposition	0.004	0.000	0.000
featureHydro	0.000	0.000	0.001
featurePSSM	0	0	0
featurePseudoAAComp	0.000	0.000	0.001
featureSSC	0.000	0.000	0.002
hr	0.000	0.000	0.004
model	0.756	0.020	0.777
performance	1.052	0.028	1.081
selectFFS	0.260	0.008	0.266