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BioC 3.6: CHECK report for BioSeqClass on veracruz1

This page was generated on 2017-08-16 13:40:48 -0400 (Wed, 16 Aug 2017).

Package 134/1410HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BioSeqClass 1.35.0
Li Hong
Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/BioSeqClass
Last Changed Rev: 129129 / Revision: 131943
Last Changed Date: 2017-04-24 15:50:57 -0400 (Mon, 24 Apr 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: BioSeqClass
Version: 1.35.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings BioSeqClass_1.35.0.tar.gz
StartedAt: 2017-08-16 00:28:53 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 00:31:32 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 159.3 seconds
RetCode: 0
Status:  OK 
CheckDir: BioSeqClass.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings BioSeqClass_1.35.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/BioSeqClass.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BioSeqClass/DESCRIPTION’ ... OK
* this is package ‘BioSeqClass’ version ‘1.35.0’
* 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 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 6.484    0.3   5.801
* 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-3.6-bioc/meat/BioSeqClass.Rcheck/00check.log’
for details.


BioSeqClass.Rcheck/00install.out:

* 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)

BioSeqClass.Rcheck/BioSeqClass-Ex.timings:

nameusersystemelapsed
basic0.6750.0220.715
classify6.4840.3005.801
featureAAindex0.0030.0010.002
featureBDNAVIDEO0.0010.0000.001
featureBinary0.0010.0000.002
featureCKSAAP0.0010.0000.001
featureCTD0.0010.0000.001
featureDIPRODB0.0010.0000.001
featureDOMAIN0.0010.0000.000
featureEvaluate0.0340.0000.034
featureFragmentComposition0.0010.0010.001
featureGapPairComposition0.0020.0000.002
featureHydro0.0020.0000.002
featurePSSM0.0010.0000.002
featurePseudoAAComp0.0010.0000.001
featureSSC0.0040.0000.005
hr0.0060.0000.007
model0.7920.0220.839
performance0.7680.0130.814
selectFFS0.5350.0090.559