BioC 3.5: CHECK report for ImpulseDE2 on toluca2

Package: ImpulseDE2

Version: 0.99.8

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ImpulseDE2_0.99.8.tar.gz

StartedAt: 2017-04-23 05:28:19 -0400 (Sun, 23 Apr 2017)

EndedAt: 2017-04-23 05:35:35 -0400 (Sun, 23 Apr 2017)

EllapsedTime: 435.2 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_0.99.8.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/ImpulseDE2.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘0.99.8’
* 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       41.401  0.234  41.684
updateDEAnalysis  38.780  0.215  39.034
plotGenes         34.236  0.167  34.449
fitSigmoidModels  22.132  0.185  22.345
get_accessors     20.581  0.113  20.716
list_accession    19.816  0.091  19.938
writeReportToFile 19.747  0.088  19.861
runImpulseDE2     19.590  0.090  19.705
* 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	0.235	0.012	0.249
fitSigmoidModels	22.132	0.185	22.345
get_accessors	20.581	0.113	20.716
list_accession	19.816	0.091	19.938
plotGenes	34.236	0.167	34.449
plotHeatmap	41.401	0.234	41.684
runImpulseDE2	19.590	0.090	19.705
simulateDataSetImpulseDE2	0.026	0.000	0.025
updateDEAnalysis	38.780	0.215	39.034
writeReportToFile	19.747	0.088	19.861