BioC 3.3: CHECK report for MLSeq on zin2

Package: MLSeq

Version: 1.12.2

Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings MLSeq_1.12.2.tar.gz

StartedAt: 2016-10-13 04:24:35 -0700 (Thu, 13 Oct 2016)

EndedAt: 2016-10-13 04:28:12 -0700 (Thu, 13 Oct 2016)

EllapsedTime: 216.2 seconds

RetCode: 0

Status:  OK

CheckDir: MLSeq.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings MLSeq_1.12.2.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/MLSeq.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MLSeq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MLSeq’ version ‘1.12.2’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘caret’ ‘DESeq2’ ‘Biobase’ ‘limma’ ‘randomForest’ ‘edgeR’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘MLSeq’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
classify: no visible global function definition for ‘relevel’
classify: no visible global function definition for ‘model.matrix’
classify: no visible global function definition for
  ‘AnnotatedDataFrame’
classify: no visible global function definition for ‘bagControl’
classify: no visible binding for global variable ‘svmBag’
classify: no visible global function definition for ‘predict’
predictClassify: no visible global function definition for
  ‘model.matrix’
predictClassify: no visible global function definition for
  ‘AnnotatedDataFrame’
predictClassify: no visible global function definition for ‘predict’
Undefined global functions or variables:
  AnnotatedDataFrame bagControl model.matrix predict relevel svmBag
Consider adding
  importFrom("stats", "model.matrix", "predict", "relevel")
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
predictClassify 11.306  0.024  11.324
classify        11.179  0.032  11.224
normalization    7.736  0.008   7.751
deseqTransform   7.678  0.008   7.695
ref              7.518  0.004   7.522
method           7.342  0.008   7.354
trained          7.313  0.012   7.327
confusionMat     7.025  0.016   7.043
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.3-bioc/meat/MLSeq.Rcheck/00check.log’
for details.

* installing *source* package ‘MLSeq’ ...
** 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 (MLSeq)

name	user	system	elapsed
MLSeq-class	0.001	0.000	0.001
cervical	0.005	0.000	0.005
classify	11.179	0.032	11.224
confusionMat	7.025	0.016	7.043
deseqTransform	7.678	0.008	7.695
method	7.342	0.008	7.354
normalization	7.736	0.008	7.751
predictClassify	11.306	0.024	11.324
ref	7.518	0.004	7.522
trained	7.313	0.012	7.327