BioC 3.2: CHECK report for MLSeq on oaxaca

Package: MLSeq

Version: 1.8.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings MLSeq_1.8.0.tar.gz

StartedAt: 2015-10-27 05:44:18 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 05:49:09 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 291.0 seconds

RetCode: 0

Status:  OK

CheckDir: MLSeq.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings MLSeq_1.8.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/MLSeq.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.8.0’
* 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 ... [22s/22s] 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
  ‘AnnotatedDataFrame’
classify: no visible global function definition for ‘bagControl’
classify: no visible binding for global variable ‘svmBag’
predictClassify: no visible global function definition for
  ‘AnnotatedDataFrame’
* 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 ... [71s/71s] OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
classify        14.268  0.167  14.442
predictClassify 13.552  0.093  13.653
normalization    5.867  0.031   5.903
method           5.417  0.025   5.446
confusionMat     5.326  0.033   5.364
trained          5.186  0.029   5.220
deseqTransform   4.996  0.034   5.034
* 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
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/MLSeq.Rcheck/00check.log’
for details.

* installing *source* package ‘MLSeq’ ...
** R
** data
** inst
** preparing package for lazy loading
Note: the specification for S3 class “family” in package ‘MatrixModels’ seems equivalent to one from package ‘lme4’: not turning on duplicate class definitions for this class.
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Note: the specification for S3 class “family” in package ‘MatrixModels’ seems equivalent to one from package ‘lme4’: not turning on duplicate class definitions for this class.
* DONE (MLSeq)

name	user	system	elapsed
MLSeq-class	0.000	0.000	0.001
cervical	0.005	0.001	0.006
classify	14.268	0.167	14.442
confusionMat	5.326	0.033	5.364
deseqTransform	4.996	0.034	5.034
method	5.417	0.025	5.446
normalization	5.867	0.031	5.903
predictClassify	13.552	0.093	13.653
ref	4.855	0.031	4.887
trained	5.186	0.029	5.220