BioC 3.5: CHECK report for GRridge on oaxaca

Package: GRridge

Version: 0.99.20

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GRridge_0.99.20.tar.gz

StartedAt: 2017-03-04 04:07:06 -0800 (Sat, 04 Mar 2017)

EndedAt: 2017-03-04 04:15:21 -0800 (Sat, 04 Mar 2017)

EllapsedTime: 494.8 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: GRridge.Rcheck

Warnings: 2

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GRridge_0.99.20.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/GRridge.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GRridge/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GRridge’ version ‘0.99.20’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘penalized’ ‘Iso’ ‘survival’ ‘GSEABase’ ‘BiocGenerics’ ‘Biobase’
  ‘annotate’ ‘graph’
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 ‘GRridge’ can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import ‘stats::xtabs’ by ‘BiocGenerics::xtabs’ when loading ‘GRridge’
  Warning: replacing previous import ‘stats::sd’ by ‘BiocGenerics::sd’ when loading ‘GRridge’
  Warning: replacing previous import ‘stats::mad’ by ‘BiocGenerics::mad’ when loading ‘GRridge’
  Warning: replacing previous import ‘stats::IQR’ by ‘BiocGenerics::IQR’ when loading ‘GRridge’
  Warning: replacing previous import ‘GSEABase::intersect’ by ‘BiocGenerics::intersect’ when loading ‘GRridge’
  Warning: replacing previous import ‘penalized::as.data.frame’ by ‘BiocGenerics::as.data.frame’ when loading ‘GRridge’
  Warning: replacing previous import ‘GSEABase::setdiff’ by ‘BiocGenerics::setdiff’ when loading ‘GRridge’
  Warning: replacing previous import ‘stats::var’ by ‘BiocGenerics::var’ when loading ‘GRridge’
See ‘/Users/biocbuild/bbs-3.5-bioc/meat/GRridge.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
  installed size is  8.9Mb
  sub-directories of 1Mb or more:
    data   8.5Mb
* 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 ... OK
* 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 ... WARNING
  
  Note: significantly better compression could be obtained
        by using R CMD build --resave-data
                    old_size new_size compress
  dataFarkas.rda       3.4Mb    2.5Mb    bzip2
  dataWurdinger.rda    1.9Mb    1.2Mb       xz
* 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
predict.grridge 193.091 10.316 203.455
grridgeCV       100.661  4.340 105.043
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 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: 2 WARNINGs, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/GRridge.Rcheck/00check.log’
for details.

* installing *source* package ‘GRridge’ ...
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import ‘stats::xtabs’ by ‘BiocGenerics::xtabs’ when loading ‘GRridge’
Warning: replacing previous import ‘stats::sd’ by ‘BiocGenerics::sd’ when loading ‘GRridge’
Warning: replacing previous import ‘stats::mad’ by ‘BiocGenerics::mad’ when loading ‘GRridge’
Warning: replacing previous import ‘stats::IQR’ by ‘BiocGenerics::IQR’ when loading ‘GRridge’
Warning: replacing previous import ‘GSEABase::intersect’ by ‘BiocGenerics::intersect’ when loading ‘GRridge’
Warning: replacing previous import ‘penalized::as.data.frame’ by ‘BiocGenerics::as.data.frame’ when loading ‘GRridge’
Warning: replacing previous import ‘GSEABase::setdiff’ by ‘BiocGenerics::setdiff’ when loading ‘GRridge’
Warning: replacing previous import ‘stats::var’ by ‘BiocGenerics::var’ when loading ‘GRridge’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import ‘stats::xtabs’ by ‘BiocGenerics::xtabs’ when loading ‘GRridge’
Warning: replacing previous import ‘stats::sd’ by ‘BiocGenerics::sd’ when loading ‘GRridge’
Warning: replacing previous import ‘stats::mad’ by ‘BiocGenerics::mad’ when loading ‘GRridge’
Warning: replacing previous import ‘stats::IQR’ by ‘BiocGenerics::IQR’ when loading ‘GRridge’
Warning: replacing previous import ‘GSEABase::intersect’ by ‘BiocGenerics::intersect’ when loading ‘GRridge’
Warning: replacing previous import ‘penalized::as.data.frame’ by ‘BiocGenerics::as.data.frame’ when loading ‘GRridge’
Warning: replacing previous import ‘GSEABase::setdiff’ by ‘BiocGenerics::setdiff’ when loading ‘GRridge’
Warning: replacing previous import ‘stats::var’ by ‘BiocGenerics::var’ when loading ‘GRridge’
* DONE (GRridge)

name	user	system	elapsed
CreatePartition	0.100	0.009	0.109
PartitionsSelection	0.003	0.000	0.003
auc	0.414	0.014	0.428
dataFarkas	0.371	0.010	0.381
dataVerlaat	0.036	0.005	0.042
dataWurdinger	3.308	0.120	3.431
grridge	0.099	0.005	0.105
grridgeCV	100.661	4.340	105.043
hello	0.000	0.001	0.000
matchGeneSets	1.946	0.063	2.011
mergeGroups	2.428	0.093	2.522
predict.grridge	193.091	10.316	203.455
roc	2.240	0.020	2.261