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CHECK report for ImpulseDE2 on tokay2

This page was generated on 2019-04-09 12:30:56 -0400 (Tue, 09 Apr 2019).

Package 797/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ImpulseDE2 1.7.1
David S Fischer
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/ImpulseDE2
Branch: master
Last Commit: 933737f
Last Changed Date: 2019-01-04 13:15:10 -0400 (Fri, 04 Jan 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK 

Summary

Package: ImpulseDE2
Version: 1.7.1
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ImpulseDE2.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings ImpulseDE2_1.7.1.tar.gz
StartedAt: 2019-04-09 03:37:54 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 03:47:55 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 601.1 seconds
RetCode: 0
Status:  OK  
CheckDir: ImpulseDE2.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ImpulseDE2.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings ImpulseDE2_1.7.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/ImpulseDE2.Rcheck'
* using R Under development (unstable) (2019-03-09 r76216)
* 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 '1.7.1'
* 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
* 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 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
updateDEAnalysis  30.54   0.08   53.54
plotHeatmap       28.64   0.11   28.75
plotGenes         20.67   0.02   20.69
runImpulseDE2     16.71   0.01   16.72
get_accessors     14.27   0.00   14.26
fitSigmoidModels  13.84   0.31   14.15
writeReportToFile 13.77   0.00   13.77
list_accession    13.61   0.00   13.61
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
updateDEAnalysis  30.00   0.00   30.00
plotHeatmap       28.85   0.01   28.86
plotGenes         24.31   0.02   24.32
runImpulseDE2     18.47   0.00   18.47
list_accession    18.09   0.01   18.11
fitSigmoidModels  16.55   0.11   19.75
get_accessors     14.80   0.00   14.80
writeReportToFile 14.56   0.02   14.58
* 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-3.9-bioc/meat/ImpulseDE2.Rcheck/00check.log'
for details.



Installation output

ImpulseDE2.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/ImpulseDE2_1.7.1.tar.gz && rm -rf ImpulseDE2.buildbin-libdir && mkdir ImpulseDE2.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ImpulseDE2.buildbin-libdir ImpulseDE2_1.7.1.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL ImpulseDE2_1.7.1.zip && rm ImpulseDE2_1.7.1.tar.gz ImpulseDE2_1.7.1.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 58625  100 58625    0     0  1009k      0 --:--:-- --:--:-- --:--:-- 1145k

install for i386

* installing *source* package 'ImpulseDE2' ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'ImpulseDE2'
    finding HTML links ... done
    ImpulseDE2Object-class                  html  
    append_strReport                        html  
    computeNormConst                        html  
    computeSizeFactors                      html  
    estimateImpulseParam                    html  
    estimateSigmoidParam                    html  
    evalImpulse                             html  
    evalImpulse_comp                        html  
    evalLogLikImpulse                       html  
    evalLogLikImpulse_comp                  html  
    evalLogLikMu                            html  
    evalLogLikMu_comp                       html  
    evalLogLikSigmoid                       html  
    evalLogLikSigmoid_comp                  html  
    evalSigmoid                             html  
    evalSigmoid_comp                        html  
    fitConstImpulse                         html  
    fitConstImpulseGene                     html  
    fitConstModel                           html  
    fitImpulseModel                         html  
    fitModels                               html  
    fitSigmoidGene                          html  
    fitSigmoidModel                         html  
    fitSigmoidModels                        html  
    get_accessors                           html  
    list_accession                          html  
    plotGenes                               html  
    plotHeatmap                             html  
    processData                             html  
    runDEAnalysis                           html  
    runDESeq2                               html  
    runImpulseDE2                           html  
    set_accessors                           html  
    simulateDataSetImpulseDE2               html  
    updateDEAnalysis                        html  
    writeReportToFile                       html  
** 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

install for x64

* installing *source* package 'ImpulseDE2' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ImpulseDE2' as ImpulseDE2_1.7.1.zip
* DONE (ImpulseDE2)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'ImpulseDE2' successfully unpacked and MD5 sums checked

Tests output


Example timings

ImpulseDE2.Rcheck/examples_i386/ImpulseDE2-Ex.timings

nameusersystemelapsed
computeNormConst0.160.020.18
fitSigmoidModels13.84 0.3114.15
get_accessors14.27 0.0014.26
list_accession13.61 0.0013.61
plotGenes20.67 0.0220.69
plotHeatmap28.64 0.1128.75
runImpulseDE216.71 0.0116.72
simulateDataSetImpulseDE20.030.000.03
updateDEAnalysis30.54 0.0853.54
writeReportToFile13.77 0.0013.77

ImpulseDE2.Rcheck/examples_x64/ImpulseDE2-Ex.timings

nameusersystemelapsed
computeNormConst0.160.000.15
fitSigmoidModels16.55 0.1119.75
get_accessors14.8 0.014.8
list_accession18.09 0.0118.11
plotGenes24.31 0.0224.32
plotHeatmap28.85 0.0128.86
runImpulseDE218.47 0.0018.47
simulateDataSetImpulseDE20.010.000.02
updateDEAnalysis30 030
writeReportToFile14.56 0.0214.58