BioC 3.2: CHECK report for biobroom on perceval

Package: biobroom

Version: 1.1.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings biobroom_1.1.1.tar.gz

StartedAt: 2015-10-27 05:47:09 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 05:48:25 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 75.0 seconds

RetCode: 0

Status:  OK

CheckDir: biobroom.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 biobroom_1.1.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/biobroom.Rcheck’
* using R version 3.2.2 Patched (2015-10-08 r69496)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘biobroom/DESCRIPTION’ ... OK
* this is package ‘biobroom’ version ‘1.1.1’
* 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 ‘biobroom’ can be installed ... [4s/4s] 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
tidy_matrix: no visible binding for global variable ‘value’
tidy_matrix: no visible binding for global variable ‘gene’
tidy.DESeqDataSet: no visible binding for global variable ‘term’
tidy.DESeqDataSet: no visible binding for global variable ‘.’
tidy.DESeqDataSet: no visible global function definition for ‘counts’
tidy.DESeqDataSet: no visible binding for global variable ‘gene’
tidy.ExpressionSet: no visible binding for global variable ‘sample.id’
tidy.ExpressionSet: no visible binding for global variable ‘value’
tidy.ExpressionSet: no visible binding for global variable ‘gene’
tidy.ExpressionSet: no visible global function definition for ‘pData’
tidy.MArrayLM: no visible binding for global variable ‘term’
tidy.MArrayLM: no visible binding for global variable ‘estimate’
tidy.MArrayLM: no visible binding for global variable ‘gene’
tidy.MSnSet: no visible binding for global variable ‘sample.id’
tidy.MSnSet: no visible binding for global variable ‘value’
tidy.MSnSet: no visible binding for global variable ‘protein’
tidy.MSnSet: no visible global function definition for ‘pData’
tidy.qvalue: no visible binding for global variable ‘smoothed’
tidy.qvalue: no visible binding for global variable ‘pi0’
tidy.qvalue: no visible binding for global variable ‘lambda’
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [24s/25s] OK
Examples with CPU or elapsed time > 5s
                user system elapsed
DESeq2_tidiers 9.719  0.201   9.998
edgeR_tidiers  6.074  0.258   6.332
* 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 NOTE
See
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/biobroom.Rcheck/00check.log’
for details.

* installing *source* package ‘biobroom’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (biobroom)

name	user	system	elapsed
DESeq2_tidiers	9.719	0.201	9.998
ExpressionSet_tidiers	2.375	0.035	2.410
MSnSet_tidiers	2.699	0.094	3.047
edgeR_tidiers	6.074	0.258	6.332
limma_tidiers	0.334	0.002	0.337
qvalue_tidiers	0.900	0.004	0.915