BioC 3.5: CHECK report for ImpulseDE2 on veracruz2

Package: ImpulseDE2

Version: 1.0.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ImpulseDE2_1.0.0.tar.gz

StartedAt: 2017-08-16 04:15:42 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 04:21:34 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 352.2 seconds

RetCode: 0

Status:  OK

CheckDir: ImpulseDE2.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 ImpulseDE2_1.0.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/ImpulseDE2.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ImpulseDE2/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ImpulseDE2’ version ‘1.0.0’
* package encoding: UTF-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 ‘ImpulseDE2’ can be installed ... 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
plotGenes: no visible global function definition for ‘error’
plotGenes: no visible binding for global variable ‘normCounts’
plotGenes: no visible binding for global variable ‘Condition’
plotGenes: no visible binding for global variable ‘Batch’
plotGenes: no visible binding for global variable ‘value’
plotGenes: no visible binding for global variable ‘BatchFit’
Undefined global functions or variables:
  Batch BatchFit Condition error normCounts value
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
plotHeatmap       30.382  0.181  31.561
updateDEAnalysis  28.368  0.165  29.332
plotGenes         25.245  0.132  26.229
fitSigmoidModels  16.544  0.144  17.196
get_accessors     15.211  0.085  15.742
list_accession    15.075  0.075  15.583
runImpulseDE2     14.994  0.087  15.544
writeReportToFile 14.199  0.071  14.611
* 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-3.5-bioc/meat/ImpulseDE2.Rcheck/00check.log’
for details.

* installing *source* package ‘ImpulseDE2’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (ImpulseDE2)

name	user	system	elapsed
computeNormConst	0.155	0.012	0.167
fitSigmoidModels	16.544	0.144	17.196
get_accessors	15.211	0.085	15.742
list_accession	15.075	0.075	15.583
plotGenes	25.245	0.132	26.229
plotHeatmap	30.382	0.181	31.561
runImpulseDE2	14.994	0.087	15.544
simulateDataSetImpulseDE2	0.015	0.001	0.015
updateDEAnalysis	28.368	0.165	29.332
writeReportToFile	14.199	0.071	14.611