BioC 3.6: CHECK report for BiocSklearn on malbec1

Package: BiocSklearn

Version: 0.0.8

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings BiocSklearn_0.0.8.tar.gz

StartedAt: 2017-08-15 21:33:59 -0400 (Tue, 15 Aug 2017)

EndedAt: 2017-08-15 21:34:29 -0400 (Tue, 15 Aug 2017)

EllapsedTime: 30.2 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: BiocSklearn.Rcheck

Warnings: 1

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### Running command:
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###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings BiocSklearn_0.0.8.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/BiocSklearn.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BiocSklearn/DESCRIPTION’ ... OK
* this is package ‘BiocSklearn’ version ‘0.0.8’
* 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 ‘BiocSklearn’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 29.5Mb
  sub-directories of 1Mb or more:
    ban_6_17  29.1Mb
* 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 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 ... WARNING
Undocumented arguments in documentation object 'H5matref'
  ‘filename’
Documented arguments not in \usage in documentation object 'H5matref':
  ‘file’

Duplicated \argument entries in documentation object 'SkDecomp-class':
  ‘x’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... 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
H5matref 4.464   0.38   8.207
* 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: 1 WARNING, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.6-bioc/meat/BiocSklearn.Rcheck/00check.log’
for details.

* installing *source* package ‘BiocSklearn’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (BiocSklearn)

name	user	system	elapsed
H5matref	4.464	0.380	8.207
h5mat	0.004	0.000	0.003
skIncrPCA	0.012	0.000	0.029
skPCA	0.008	0.000	0.006
skPartialPCA_step	0.012	0.000	0.015