BioC 3.6: CHECK report for ImpulseDE2 on veracruz1

Package: ImpulseDE2

Version: 1.1.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ImpulseDE2_1.1.0.tar.gz

StartedAt: 2017-08-16 04:30:50 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 04:36:40 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 350.9 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_1.1.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-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 ‘1.1.0’
* 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       30.540  0.175  31.705
updateDEAnalysis  28.283  0.172  29.284
plotGenes         25.129  0.120  25.945
fitSigmoidModels  16.580  0.142  17.265
get_accessors     15.021  0.084  15.455
writeReportToFile 14.625  0.072  15.076
runImpulseDE2     14.492  0.071  15.042
list_accession    14.433  0.073  14.933
* 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-3.6-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	0.182	0.015	0.197
fitSigmoidModels	16.580	0.142	17.265
get_accessors	15.021	0.084	15.455
list_accession	14.433	0.073	14.933
plotGenes	25.129	0.120	25.945
plotHeatmap	30.540	0.175	31.705
runImpulseDE2	14.492	0.071	15.042
simulateDataSetImpulseDE2	0.019	0.000	0.019
updateDEAnalysis	28.283	0.172	29.284
writeReportToFile	14.625	0.072	15.076