Package: ImpulseDE2

Version: 1.10.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ImpulseDE2.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ImpulseDE2_1.10.0.tar.gz

StartedAt: 2020-04-15 03:10:01 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 03:17:28 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 447.6 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 --install=check:ImpulseDE2.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ImpulseDE2_1.10.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/ImpulseDE2.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.10.0’
* 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 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
updateDEAnalysis  44.025  0.309  44.733
plotHeatmap       43.659  0.360  44.414
plotGenes         36.046  0.234  36.576
fitSigmoidModels  25.317  0.433  25.978
runImpulseDE2     24.045  0.145  24.463
get_accessors     22.143  0.173  22.526
writeReportToFile 21.662  0.133  21.969
list_accession    21.223  0.175  21.599
* 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-3.10-bioc/meat/ImpulseDE2.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL ImpulseDE2
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘ImpulseDE2’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (ImpulseDE2)

name	user	system	elapsed
computeNormConst	0.262	0.014	0.276
fitSigmoidModels	25.317	0.433	25.978
get_accessors	22.143	0.173	22.526
list_accession	21.223	0.175	21.599
plotGenes	36.046	0.234	36.576
plotHeatmap	43.659	0.360	44.414
runImpulseDE2	24.045	0.145	24.463
simulateDataSetImpulseDE2	0.03	0.00	0.03
updateDEAnalysis	44.025	0.309	44.733
writeReportToFile	21.662	0.133	21.969