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BioC 3.5: CHECK report for ImpulseDE2 on tokay2

This page was generated on 2017-08-16 13:26:54 -0400 (Wed, 16 Aug 2017).

Package 669/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ImpulseDE2 1.0.0
David S Fischer
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/ImpulseDE2
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: ImpulseDE2
Version: 1.0.0
Command: rm -rf ImpulseDE2.buildbin-libdir ImpulseDE2.Rcheck && mkdir ImpulseDE2.buildbin-libdir ImpulseDE2.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ImpulseDE2.buildbin-libdir ImpulseDE2_1.0.0.tar.gz >ImpulseDE2.Rcheck\00install.out 2>&1 && cp ImpulseDE2.Rcheck\00install.out ImpulseDE2-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=ImpulseDE2.buildbin-libdir --install="check:ImpulseDE2-install.out" --force-multiarch --no-vignettes --timings ImpulseDE2_1.0.0.tar.gz
StartedAt: 2017-08-16 00:38:06 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 00:48:43 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 636.9 seconds
RetCode: 0
Status:  OK  
CheckDir: ImpulseDE2.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf ImpulseDE2.buildbin-libdir ImpulseDE2.Rcheck && mkdir ImpulseDE2.buildbin-libdir ImpulseDE2.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ImpulseDE2.buildbin-libdir ImpulseDE2_1.0.0.tar.gz >ImpulseDE2.Rcheck\00install.out 2>&1 && cp ImpulseDE2.Rcheck\00install.out ImpulseDE2-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=ImpulseDE2.buildbin-libdir --install="check:ImpulseDE2-install.out" --force-multiarch --no-vignettes --timings ImpulseDE2_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/ImpulseDE2.Rcheck'
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
plotHeatmap       29.62   0.00   29.62
plotGenes         24.55   0.00   24.55
updateDEAnalysis  23.99   0.01   24.00
runImpulseDE2     16.41   0.02   16.44
list_accession    15.94   0.02   15.95
fitSigmoidModels  15.02   0.12   15.14
get_accessors     14.45   0.00   14.46
writeReportToFile 13.20   0.02   13.22
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
updateDEAnalysis  33.69   0.02   33.70
plotHeatmap       28.47   0.00   28.47
plotGenes         25.69   0.00   25.70
writeReportToFile 20.75   0.03   20.78
runImpulseDE2     18.52   0.00   18.51
fitSigmoidModels  16.33   0.04   16.38
get_accessors     15.49   0.00   15.48
list_accession    15.15   0.00   15.16
* 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
  'C:/Users/biocbuild/bbs-3.5-bioc/meat/ImpulseDE2.Rcheck/00check.log'
for details.


ImpulseDE2.Rcheck/00install.out:


install for i386

* 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

install for x64

* installing *source* package 'ImpulseDE2' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ImpulseDE2' as ImpulseDE2_1.0.0.zip
* DONE (ImpulseDE2)

ImpulseDE2.Rcheck/examples_i386/ImpulseDE2-Ex.timings:

nameusersystemelapsed
computeNormConst0.180.020.20
fitSigmoidModels15.02 0.1215.14
get_accessors14.45 0.0014.46
list_accession15.94 0.0215.95
plotGenes24.55 0.0024.55
plotHeatmap29.62 0.0029.62
runImpulseDE216.41 0.0216.44
simulateDataSetImpulseDE20.010.000.01
updateDEAnalysis23.99 0.0124.00
writeReportToFile13.20 0.0213.22

ImpulseDE2.Rcheck/examples_x64/ImpulseDE2-Ex.timings:

nameusersystemelapsed
computeNormConst0.150.000.16
fitSigmoidModels16.33 0.0416.38
get_accessors15.49 0.0015.48
list_accession15.15 0.0015.16
plotGenes25.69 0.0025.70
plotHeatmap28.47 0.0028.47
runImpulseDE218.52 0.0018.51
simulateDataSetImpulseDE20.010.000.02
updateDEAnalysis33.69 0.0233.70
writeReportToFile20.75 0.0320.78