BioC 3.1: CHECK report for MLInterfaces on zin2

Package: MLInterfaces

Version: 1.48.0

Command: /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings MLInterfaces_1.48.0.tar.gz

StartedAt: 2015-10-09 03:35:58 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 03:37:49 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 111.0 seconds

RetCode: 0

Status:  OK

CheckDir: MLInterfaces.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings MLInterfaces_1.48.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.1-bioc/meat/MLInterfaces.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MLInterfaces/DESCRIPTION’ ... OK
* this is package ‘MLInterfaces’ version ‘1.48.0’
* 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 ‘MLInterfaces’ can be installed ... [8s/8s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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
'library' or 'require' calls in package code:
  ‘RColorBrewer’ ‘gbm’ ‘kernlab’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Unexported objects imported by ':::' calls:
  ‘rpart:::predict.rpart’ ‘stats:::plot.hclust’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
gbm2: no visible global function definition for ‘gbm’
predict.gbm2: no visible global function definition for ‘predict.gbm’
planarPlot,classifierOutput-ExpressionSet-character: no visible global
  function definition for ‘brewer.pal’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [29s/27s] OK
Examples with CPU or elapsed time > 5s
             user system elapsed
MLearn-new 14.107  0.612  14.352
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [4s/4s]
 [4s/4s] OK
* 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.1-bioc/meat/MLInterfaces.Rcheck/00check.log’
for details.

* installing *source* package ‘MLInterfaces’ ...
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (MLInterfaces)

name	user	system	elapsed
MLearn-new	14.107	0.612	14.352
RAB	0.139	0.004	0.143
balKfold.xvspec	0.026	0.004	0.030
classifierOutput-class	1.620	0.120	2.585
clusteringOutput-class	0.002	0.000	0.001
confuMat-methods	0.248	0.004	0.253
confuTab	0.006	0.000	0.006
fs.absT	0.030	0.008	0.039
fsHistory	2.465	0.087	0.081
learnerSchema-class	0.000	0.000	0.001
performance-analytics	0.003	0.000	0.005
planarPlot-methods	2.355	0.144	2.501
predict.classifierOutput	2.223	0.000	2.225
raboostCont-class	0.001	0.000	0.001
varImpStruct-class	0.656	0.008	0.664
xvalLoop	0.002	0.000	0.001
xvalSpec	0.147	0.054	0.148