BioC 3.1: CHECK report for RUVnormalize on petty

Package: RUVnormalize

Version: 1.2.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings RUVnormalize_1.2.0.tar.gz

StartedAt: 2015-10-09 01:50:48 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 01:52:01 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 72.8 seconds

RetCode: 0

Status:  OK

CheckDir: RUVnormalize.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 RUVnormalize_1.2.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/RUVnormalize.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RUVnormalize/DESCRIPTION’ ... OK
* this is package ‘RUVnormalize’ version ‘1.2.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: ‘spams’
* 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 ‘RUVnormalize’ can be installed ... [3s/3s] 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 ... NOTE
'library' or 'require' call to ‘spams’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [31s/31s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
clScore           8.224  0.308   8.597
svdPlot           6.660  0.451   7.114
naiveRandRUV      6.728  0.299   7.032
naiveReplicateRUV 5.441  0.402   5.850
* 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-3.1-bioc/meat/RUVnormalize.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
clScore	8.224	0.308	8.597
iterativeRUV	0.420	0.006	0.426
naiveRandRUV	6.728	0.299	7.032
naiveReplicateRUV	5.441	0.402	5.850
svdPlot	6.660	0.451	7.114