Package: ImpulseDE2

Version: 1.4.0

Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:ImpulseDE2.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings ImpulseDE2_1.4.0.tar.gz

StartedAt: 2018-10-16 01:16:56 -0400 (Tue, 16 Oct 2018)

EndedAt: 2018-10-16 01:21:24 -0400 (Tue, 16 Oct 2018)

EllapsedTime: 268.6 seconds

RetCode: 0

Status:  OK

CheckDir: ImpulseDE2.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:ImpulseDE2.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings ImpulseDE2_1.4.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/ImpulseDE2.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-pc-linux-gnu (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 ‘1.4.0’
* 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
plotHeatmap       25.596  0.084  25.703
updateDEAnalysis  24.336  0.072  24.421
plotGenes         21.356  0.028  21.405
fitSigmoidModels  14.028  0.184  14.249
runImpulseDE2     13.508  0.064  13.578
list_accession    13.140  0.016  13.165
get_accessors     12.876  0.032  12.912
writeReportToFile 12.876  0.020  12.906
* 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
  ‘/home/biocbuild/bbs-3.7-bioc/meat/ImpulseDE2.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL ImpulseDE2
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* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’
* installing *source* package ‘ImpulseDE2’ ...
** 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
* DONE (ImpulseDE2)

name	user	system	elapsed
computeNormConst	0.668	0.000	0.667
fitSigmoidModels	14.028	0.184	14.249
get_accessors	12.876	0.032	12.912
list_accession	13.140	0.016	13.165
plotGenes	21.356	0.028	21.405
plotHeatmap	25.596	0.084	25.703
runImpulseDE2	13.508	0.064	13.578
simulateDataSetImpulseDE2	0.016	0.000	0.013
updateDEAnalysis	24.336	0.072	24.421
writeReportToFile	12.876	0.020	12.906