Package: BioSeqClass

Version: 1.42.0

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:BioSeqClass.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings BioSeqClass_1.42.0.tar.gz

StartedAt: 2019-10-16 00:08:15 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 00:10:41 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 146.0 seconds

RetCode: 0

Status:  OK

CheckDir: BioSeqClass.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:BioSeqClass.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings BioSeqClass_1.42.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/BioSeqClass.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.42.0’
* 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  6.5Mb
  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 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
          user system elapsed
classify 6.452  0.309   7.074
* 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-3.9-bioc/meat/BioSeqClass.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL BioSeqClass
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘BioSeqClass’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (BioSeqClass)

name	user	system	elapsed
basic	0.659	0.012	0.670
classify	6.452	0.309	7.074
featureAAindex	0	0	0
featureBDNAVIDEO	0	0	0
featureBinary	0.000	0.000	0.001
featureCKSAAP	0.001	0.000	0.000
featureCTD	0.001	0.000	0.000
featureDIPRODB	0	0	0
featureDOMAIN	0	0	0
featureEvaluate	0.012	0.000	0.012
featureFragmentComposition	0	0	0
featureGapPairComposition	0	0	0
featureHydro	0.000	0.000	0.001
featurePSSM	0.000	0.000	0.001
featurePseudoAAComp	0	0	0
featureSSC	0.002	0.000	0.001
hr	0.002	0.000	0.002
model	0.761	0.016	0.778
performance	0.773	0.003	0.778
selectFFS	0.553	0.000	0.553