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CHECK report for IdMappingAnalysis on tokay2

This page was generated on 2020-04-08 15:15:48 -0400 (Wed, 08 Apr 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE IdMappingAnalysis PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 841/1861HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
IdMappingAnalysis 1.31.1
Alex Lisovich , Roger Day
Snapshot Date: 2020-04-07 16:45:12 -0400 (Tue, 07 Apr 2020)
URL: https://git.bioconductor.org/packages/IdMappingAnalysis
Branch: master
Last Commit: 9aef421
Last Changed Date: 2020-01-06 11:03:19 -0400 (Mon, 06 Jan 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  ERROR 
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ ERROR ] OK 
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  ERROR  OK 

Summary

Package: IdMappingAnalysis
Version: 1.31.1
Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:IdMappingAnalysis.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings IdMappingAnalysis_1.31.1.tar.gz
StartedAt: 2020-04-08 05:15:11 -0400 (Wed, 08 Apr 2020)
EndedAt: 2020-04-08 05:16:37 -0400 (Wed, 08 Apr 2020)
EllapsedTime: 85.5 seconds
RetCode: 1
Status:  ERROR  
CheckDir: IdMappingAnalysis.Rcheck
Warnings: NA

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:IdMappingAnalysis.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings IdMappingAnalysis_1.31.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/IdMappingAnalysis.Rcheck'
* using R version 4.0.0 alpha (2020-03-31 r78116)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'IdMappingAnalysis/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'IdMappingAnalysis' version '1.31.1'
* 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 'IdMappingAnalysis' can be installed ... WARNING
Found the following significant warnings:
  Warning: Package 'IdMappingAnalysis' is deprecated and will be removed from
See 'C:/Users/biocbuild/bbs-3.11-bioc/meat/IdMappingAnalysis.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 ... NOTE
Namespace in Imports field not imported from: 'Biobase'
  All declared Imports should be used.
Packages in Depends field not imported from:
  'R.oo' 'rChoiceDialogs'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... NOTE
Found the following apparent S3 methods exported but not registered:
  boxplot.JointUniquePairs getName.IdMapBase primaryKey.IdMapBase
See section 'Registering S3 methods' in the 'Writing R Extensions'
manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
Bootstrap: no visible global function definition for 'extend'
Bootstrap : FUN: no visible global function definition for 'cor'
Corr: no visible global function definition for 'extend'
Corr: no visible global function definition for 'throw'
Corr: no visible global function definition for 'cor'
CorrData: no visible global function definition for 'extend'
CorrData: no visible global function definition for 'Object'
DataFilter: no visible global function definition for 'extend'
DataFilter: no visible global function definition for 'Object'
Display: no visible global function definition for 'extend'
Display: no visible global function definition for 'Object'
IdMap: no visible global function definition for 'throw'
IdMap: no visible global function definition for 'extend'
IdMapBase: no visible global function definition for 'throw'
IdMapBase: no visible global function definition for 'extend'
IdMapBase: no visible global function definition for 'Object'
IdMapCounts: no visible global function definition for 'throw'
IdMapCounts: no visible global function definition for 'extend'
IdMapDiff: no visible global function definition for 'throw'
IdMapDiff: no visible global function definition for 'extend'
IdMapDiffCounts: no visible global function definition for 'extend'
JointIdMap: no visible global function definition for 'extend'
JointUniquePairs: no visible global function definition for 'extend'
Misc: no visible global function definition for 'extend'
Misc: no visible global function definition for 'Object'
Mixture: no visible global function definition for 'extend'
Mixture: no visible global function definition for 'Object'
Mixture: no visible global function definition for 'density'
Mixture : <anonymous>: no visible global function definition for
  'dnorm'
Subset: no visible global function definition for 'extend'
Subset: no visible global function definition for 'Object'
UniquePairs: no visible global function definition for 'throw'
UniquePairs: no visible global function definition for 'extend'
as.IdMap.UniquePairs: no visible global function definition for
  'getName'
as.MultiSet.CorrData: no visible global function definition for 'new'
as.data.frame.IdMapBase: no visible global function definition for
  'getName'
as.data.frame.IdMapBase: no visible global function definition for
  'throw'
as.data.frame.IdMapBase: no visible global function definition for 'as'
as.list.IdMap: no visible global function definition for 'throw'
boxplot.JointUniquePairs: no visible global function definition for
  'par'
boxplot.JointUniquePairs: no visible global function definition for
  'axis'
boxplot.JointUniquePairs: no visible global function definition for
  'text'
boxplotdataJitter.JointUniquePairs: no visible global function
  definition for 'par'
copy.Display: no visible global function definition for 'dev.cur'
copy.Display: no visible global function definition for 'par'
copy.Display: no visible global function definition for 'png'
copy.Display: no visible global function definition for 'jpeg'
copy.Display: no visible global function definition for 'tiff'
copy.Display: no visible global function definition for 'bmp'
copy.Display: no visible global function definition for 'pdf'
copy.Display: no visible global function definition for 'dev.set'
copy.Display: no visible global function definition for 'dev.copy'
copy.Display: no visible global function definition for 'dev.next'
copy.Display: no visible global function definition for 'dev.off'
corr.boxplot.JointUniquePairs: no visible global function definition
  for 'boxplot'
corr.boxplot.JointUniquePairs: no visible global function definition
  for 'abline'
create.Display: no visible global function definition for 'dev.new'
create.Display: no visible global function definition for 'par'
diffCounts.plot.JointIdMap: no visible global function definition for
  'rselect.list'
diffCounts.plot.JointIdMap: no visible global function definition for
  'par'
ecdf.plot.JointIdMap: no visible global function definition for
  'rselect.list'
ecdf.plot.JointIdMap: no visible global function definition for 'par'
fit2clusters: no visible global function definition for 'rbinom'
fit2clusters: no visible global function definition for 'rgamma'
fit2clusters: no visible global function definition for 'rnorm'
fit2clusters: no visible global function definition for 'dnorm'
fit2clusters: no visible global function definition for 'lines'
fit2clusters: no visible global function definition for 'density'
fit2clusters: no visible global function definition for 'legend'
fit2clusters: no visible global function definition for 'par'
getCorr.JointUniquePairs: no visible global function definition for
  'equals'
getExperimentSet.CorrData: no visible global function definition for
  'throw'
getExperimentSet.CorrData: no visible global function definition for
  'new'
getIdMapList.JointIdMap: no visible global function definition for
  'throw'
interactive.plot.CorrData: no visible global function definition for
  'rselect.list'
interactive.plot.JointUniquePairs: no visible global function
  definition for 'rselect.list'
interactive.plot.JointUniquePairs: no visible global function
  definition for 'par'
line.loess.Display: no visible global function definition for 'loess'
line.loess.Display: no visible global function definition for 'lines'
line.unsorted.Display: no visible global function definition for
  'lines'
merge.IdMap: no visible global function definition for 'getName'
mixture.boxplot.JointUniquePairs: no visible global function definition
  for 'boxplot'
mixture.boxplot.JointUniquePairs: no visible global function definition
  for 'abline'
plot.Bootstrap : BootstrapCorr.plot.internal: no visible global
  function definition for 'par'
plot.Bootstrap : BootstrapCorr.plot.internal: no visible global
  function definition for 'legend'
plot.Corr: no visible global function definition for 'density'
plot.Corr: no visible global function definition for 'plot.new'
plot.Corr: no visible global function definition for 'plot.window'
plot.Corr: no visible global function definition for 'axis'
plot.Corr: no visible global function definition for 'par'
plot.Corr: no visible global function definition for 'box'
plot.Corr: no visible global function definition for 'lines'
plot.Corr: no visible global function definition for 'legend'
plot.Corr: no visible global function definition for 'abline'
plot.CorrData: no visible global function definition for 'cor'
plot.CorrData: no visible global function definition for 'par'
plot.CorrData: no visible global function definition for 'box'
plot.CorrData: no visible global function definition for 'axis'
plot.CorrData: no visible global function definition for 'points'
plot.CorrData: no visible global function definition for 'title'
plot.IdMapCounts: no visible global function definition for 'plot.new'
plot.IdMapCounts: no visible global function definition for
  'plot.window'
plot.IdMapCounts: no visible global function definition for 'title'
plot.IdMapCounts: no visible global function definition for 'axis'
plot.IdMapCounts: no visible global function definition for 'par'
plot.IdMapCounts: no visible global function definition for 'box'
plot.IdMapCounts: no visible global function definition for 'ecdf'
plot.IdMapCounts: no visible global function definition for 'lines'
plot.IdMapCounts: no visible global function definition for 'legend'
plot.IdMapDiffCounts : plotValGroup: no visible global function
  definition for 'rect'
plot.IdMapDiffCounts: no visible global function definition for
  'plot.new'
plot.IdMapDiffCounts: no visible global function definition for 'par'
plot.IdMapDiffCounts: no visible global function definition for
  'plot.window'
plot.IdMapDiffCounts: no visible global function definition for 'title'
plot.IdMapDiffCounts: no visible global function definition for 'axis'
plot.IdMapDiffCounts: no visible global function definition for 'mtext'
plot.IdMapDiffCounts: no visible global function definition for 'lines'
plot.IdMapDiffCounts: no visible global function definition for 'text'
plot.IdMapDiffCounts: no visible global function definition for
  'abline'
plot.Mixture: no visible global function definition for 'plot.new'
plot.Mixture: no visible global function definition for 'plot.window'
plot.Mixture: no visible global function definition for 'axis'
plot.Mixture: no visible global function definition for 'par'
plot.Mixture: no visible global function definition for 'box'
plot.Mixture: no visible global function definition for 'lines'
plot.Mixture: no visible global function definition for 'density'
plot.Mixture: no visible global function definition for 'rug'
plot.Mixture: no visible global function definition for 'dnorm'
plot.Mixture : <anonymous>: no visible global function definition for
  'dnorm'
plot.Mixture: no visible global function definition for 'legend'
plot.Mixture: no visible global function definition for 'abline'
progressMsg.Display: no visible global function definition for
  'flush.console'
textBoundingBox.Display: no visible global function definition for
  'strwidth'
textBoundingBox.Display: no visible global function definition for
  'strheight'
textBoundingBox.Display: no visible global function definition for
  'par'
to.index.expr.Misc: no visible global function definition for 'tail'
unique.UniquePairs: no visible global function definition for 'getName'
zoom.pars.Display: no visible global function definition for 'par'
Undefined global functions or variables:
  Object abline as axis bmp box boxplot cor density dev.copy dev.cur
  dev.new dev.next dev.off dev.set dnorm ecdf equals extend
  flush.console getName jpeg legend lines loess mtext new par pdf
  plot.new plot.window png points rbinom rect rgamma rnorm rselect.list
  rug strheight strwidth tail text throw tiff title
Consider adding
  importFrom("grDevices", "bmp", "dev.copy", "dev.cur", "dev.new",
             "dev.next", "dev.off", "dev.set", "jpeg", "pdf", "png",
             "tiff")
  importFrom("graphics", "abline", "axis", "box", "boxplot", "legend",
             "lines", "mtext", "par", "plot.new", "plot.window",
             "points", "rect", "rug", "strheight", "strwidth", "text",
             "title")
  importFrom("methods", "as", "new")
  importFrom("stats", "cor", "density", "dnorm", "ecdf", "loess",
             "rbinom", "rgamma", "rnorm")
  importFrom("utils", "flush.console", "tail")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... NOTE
prepare_Rd: DataFilter.Rd:41-42: Dropping empty section \arguments
prepare_Rd: Display.Rd:41-42: Dropping empty section \arguments
prepare_Rd: Misc.Rd:41-42: Dropping empty section \arguments
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... ERROR
Running examples in 'IdMappingAnalysis-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: IdMap
> ### Title: The ID Map class
> ### Aliases: IdMap
> ### Keywords: classes
> 
> ### ** Examples
> 
>  obj<-IdMap(examples$identDfList[[2]]);
>  obj$primaryKey();
Error in UseMethod("primaryKey") : 
  no applicable method for 'primaryKey' applied to an object of class "c('IdMap', 'IdMapBase', 'Object')"
Calls: <Anonymous> -> primaryKey
Execution halted
** running examples for arch 'x64' ... ERROR
Running examples in 'IdMappingAnalysis-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: IdMap
> ### Title: The ID Map class
> ### Aliases: IdMap
> ### Keywords: classes
> 
> ### ** Examples
> 
>  obj<-IdMap(examples$identDfList[[2]]);
>  obj$primaryKey();
Error in UseMethod("primaryKey") : 
  no applicable method for 'primaryKey' applied to an object of class "c('IdMap', 'IdMapBase', 'Object')"
Calls: <Anonymous> -> primaryKey
Execution halted
* 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: 2 ERRORs, 1 WARNING, 5 NOTEs
See
  'C:/Users/biocbuild/bbs-3.11-bioc/meat/IdMappingAnalysis.Rcheck/00check.log'
for details.

Installation output

IdMappingAnalysis.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/IdMappingAnalysis_1.31.1.tar.gz && rm -rf IdMappingAnalysis.buildbin-libdir && mkdir IdMappingAnalysis.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=IdMappingAnalysis.buildbin-libdir IdMappingAnalysis_1.31.1.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL IdMappingAnalysis_1.31.1.zip && rm IdMappingAnalysis_1.31.1.tar.gz IdMappingAnalysis_1.31.1.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 1660k  100 1660k    0     0  21.4M      0 --:--:-- --:--:-- --:--:-- 23.8M

install for i386

* installing *source* package 'IdMappingAnalysis' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** demo
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'IdMappingAnalysis'
    finding HTML links ... done
    000-LB-.IdMapBase                       html  
    Bootstrap                               html  
    Corr                                    html  
    CorrData                                html  
    CsvList.merge.Misc                      html  
    DataFilter                              html  
    Display                                 html  
    Generic.Roo                             html  
    IdMap                                   html  
    IdMapBase                               html  
    IdMapCounts                             html  
    IdMapDiff                               html  
    IdMapDiffCounts                         html  
    JointIdMap                              html  
    JointUniquePairs                        html  
    Misc                                    html  
    Mixture                                 html  
    Subset                                  html  
    UniquePairs                             html  
    aligned.IdMapBase                       html  
    as.IdMap.UniquePairs                    html  
    as.MultiSet.CorrData                    html  
    as.UniquePairs.IdMap                    html  
    as.data.frame.IdMapBase                 html  
    as.data.frame.JointIdMap                html  
    as.list.IdMap                           html  
    boxplot.JointUniquePairs                html  
    boxplotdataJitter.JointUniquePairs      html  
    byColNames.Subset                       html  
    byColumn.Subset                         html  
    byRow.Subset                            html  
    byRowNames.Subset                       html  
    clust.Mixture                           html  
    copy.Display                            html  
    corr.boxplot.JointUniquePairs           html  
    corr.plot.JointUniquePairs              html  
    create.Display                          html  
    create.UniquePairs                      html  
    diffCounts.plot.JointIdMap              html  
    dim.IdMapBase                           html  
    dimnames.IdMapBase                      html  
    do.apply.DataFilter                     html  
    do.glm.JointUniquePairs                 html  
    ecdf.plot.JointIdMap                    html  
    equals.UniquePairs                      html  
    examples                                html  
    expectedUtility                         html  
    fisherTransform.DataFilter              html  
    fisherTransformInverse.DataFilter       html  
    fisherTransformJacobean.DataFilter      html  
    fit2clusters                            html  
    getBootstrap.JointUniquePairs           html  
    getCompoundEvents.IdMapDiffCounts       html  
    getCompoundGroups.IdMapDiffCounts       html  
    getCorr.JointUniquePairs                html  
    getCorrData.JointUniquePairs            html  
    getCorrDataFrame.JointUniquePairs       html  
    getCounts.IdMap                         html  
    getCounts.JointIdMap                    html  
    getData.Corr                            html  
    getData.Mixture                         html  
    getDiff.JointIdMap                      html  
    getExperimentSet.CorrData               html  
    getIdMapList.JointIdMap                 html  
    getMapNames.JointIdMap                  html  
    getMapNames.JointUniquePairs            html  
    getMatch.UniquePairs                    html  
    getMatchInfo.JointIdMap                 html  
    getMatchInfo.JointUniquePairs           html  
    getMixture.JointUniquePairs             html  
    getName.IdMapBase                       html  
    getSampleNames.CorrData                 html  
    getStats.IdMapCounts                    html  
    getStats.Mixture                        html  
    getUnionIdMap.JointIdMap                html  
    getUniquePairs.Corr                     html  
    getUniquePairs.CorrData                 html  
    getUniquePairs.JointUniquePairs         html  
    interactive.corr.boxplot.JointUniquePairs
                                            html  
    interactive.corr.plot.JointUniquePairs
                                            html  
    interactive.mixture.boxplot.JointUniquePairs
                                            html  
    interactive.mixture.plot.JointUniquePairs
                                            html  
    interactive.plot.CorrData               html  
    interactive.plot.JointUniquePairs       html  
    interleave.Misc                         html  
    line.loess.Display                      html  
    line.unsorted.Display                   html  
    logTen.DataFilter                       html  
    merge.IdMap                             html  
    minAvgCountConstraint.DataFilter        html  
    minCountConstraint.DataFilter           html  
    minCountGroupConstraint.DataFilter      html  
    mixture.boxplot.JointUniquePairs        html  
    mixture.plot.JointUniquePairs           html  
    pack.experiments.CorrData               html  
    plot.Bootstrap                          html  
    plot.Corr                               html  
    plot.CorrData                           html  
    plot.IdMapCounts                        html  
    plot.IdMapDiffCounts                    html  
    plot.Mixture                            html  
    primaryIDs.IdMapBase                    html  
    primaryKey.CorrData                     html  
    primaryKey.IdMapBase                    html  
    primaryKey.Mixture                      html  
    progressMsg.Display                     html  
    removeNASeries.DataFilter               html  
    secondaryKey.CorrData                   html  
    secondaryKey.IdMapBase                  html  
    secondaryKey.Mixture                    html  
    subsetCorr.JointUniquePairs             html  
    subsetData.JointUniquePairs             html  
    subsetGroups.JointUniquePairs           html  
    summary.IdMapDiffCounts                 html  
    swapKeys.IdMap                          html  
    swapKeys.UniquePairs                    html  
    textBoundingBox.Display                 html  
    to.base.Misc                            html  
    to.binary.logical.Misc                  html  
    to.index.expr.Misc                      html  
    unique.UniquePairs                      html  
    words.Misc                              html  
    zoom.pars.Display                       html  
** building package indices
** installing vignettes
   'IdMappingAnalysis.Rnw' using 'latin-9' 
** testing if installed package can be loaded from temporary location
Warning: Package 'IdMappingAnalysis' is deprecated and will be removed from
  Bioconductor version 3.12
** testing if installed package can be loaded from final location
Warning: Package 'IdMappingAnalysis' is deprecated and will be removed from
  Bioconductor version 3.12
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'IdMappingAnalysis' ...
** testing if installed package can be loaded
Warning: Package 'IdMappingAnalysis' is deprecated and will be removed from
  Bioconductor version 3.12
* MD5 sums
packaged installation of 'IdMappingAnalysis' as IdMappingAnalysis_1.31.1.zip
* DONE (IdMappingAnalysis)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'IdMappingAnalysis' successfully unpacked and MD5 sums checked

Tests output

Example timings

IdMappingAnalysis.Rcheck/examples_i386/IdMappingAnalysis-Ex.timings

nameusersystemelapsed
000-LB-.IdMapBase0.140.010.16
Bootstrap3.880.023.89
Corr0.240.000.24
CorrData0.010.000.01
CsvList.merge.Misc000

IdMappingAnalysis.Rcheck/examples_x64/IdMappingAnalysis-Ex.timings

nameusersystemelapsed
000-LB-.IdMapBase0.110.020.12
Bootstrap4.530.014.55
Corr0.330.020.34
CorrData0.030.000.03
CsvList.merge.Misc000