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CHECK report for Mergeomics on tokay2

This page was generated on 2018-10-17 08:41:40 -0400 (Wed, 17 Oct 2018).

Package 860/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Mergeomics 1.8.0
Zeyneb Kurt
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/Mergeomics
Branch: RELEASE_3_7
Last Commit: 5ccb53c
Last Changed Date: 2018-04-30 10:35:40 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 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
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: Mergeomics
Version: 1.8.0
Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Mergeomics.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings Mergeomics_1.8.0.tar.gz
StartedAt: 2018-10-17 03:09:42 -0400 (Wed, 17 Oct 2018)
EndedAt: 2018-10-17 03:28:41 -0400 (Wed, 17 Oct 2018)
EllapsedTime: 1139.1 seconds
RetCode: 0
Status:  OK  
CheckDir: Mergeomics.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:Mergeomics.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings Mergeomics_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/Mergeomics.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'Mergeomics/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'Mergeomics' version '1.8.0'
* 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 'Mergeomics' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  8.8Mb
  sub-directories of 1Mb or more:
    extdata   7.5Mb
* 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
kda.analyze: no visible global function definition for 'p.adjust'
kda.analyze.exec: no visible global function definition for 'pnorm'
kda.analyze.simulate: no visible global function definition for 'rnorm'
kda.prepare: no visible global function definition for 'quantile'
kda.prepare: no visible global function definition for 'object.size'
kda.prepare.screen: no visible global function definition for
  'quantile'
kda.prepare.screen: no visible global function definition for 'median'
kda.start: no visible global function definition for 'object.size'
kda2cytoscape: no visible global function definition for 'write.table'
kda2cytoscape.colormap: no visible global function definition for
  'rainbow'
kda2cytoscape.colormap: no visible global function definition for
  'col2rgb'
kda2himmeli: no visible global function definition for 'quantile'
kda2himmeli: no visible global function definition for 'write.table'
kda2himmeli.colormap: no visible global function definition for
  'rainbow'
kda2himmeli.colormap: no visible global function definition for
  'col2rgb'
ssea.analyze: no visible global function definition for 'qnorm'
ssea.analyze: no visible global function definition for 'approx'
ssea.analyze: no visible global function definition for 'pnorm'
ssea.analyze.simulate: no visible global function definition for
  'quantile'
ssea.control: no visible global function definition for 'median'
ssea.control: no visible global function definition for 'object.size'
ssea.meta: no visible global function definition for 'qnorm'
ssea.meta: no visible global function definition for 'quantile'
ssea.meta: no visible global function definition for 'pnorm'
ssea.meta: no visible global function definition for 'median'
ssea.meta: no visible global function definition for 'na.omit'
ssea.prepare: no visible global function definition for 'median'
ssea.prepare: no visible global function definition for 'object.size'
ssea.start: no visible global function definition for 'na.omit'
ssea.start: no visible global function definition for 'object.size'
ssea.start.configure: no visible global function definition for
  'write.table'
ssea2kda: no visible global function definition for 'na.omit'
ssea2kda.import: no visible global function definition for 'na.omit'
tool.aggregate: no visible global function definition for 'na.omit'
tool.cluster: no visible global function definition for 'as.dist'
tool.cluster: no visible global function definition for 'hclust'
tool.fdr.bh: no visible global function definition for 'qnorm'
tool.fdr.bh: no visible global function definition for 'p.adjust'
tool.fdr.bh: no visible global function definition for 'approx'
tool.fdr.empirical: no visible global function definition for 'qnorm'
tool.fdr.empirical: no visible global function definition for 'approx'
tool.metap: no visible global function definition for 'qnorm'
tool.metap: no visible global function definition for 'pnorm'
tool.normalize: no visible global function definition for 'sd'
tool.normalize: no visible global function definition for 'median'
tool.normalize: no visible global function definition for 'optim'
tool.normalize: no visible global function definition for 'ks.test'
tool.normalize.quality: no visible global function definition for 'sd'
tool.normalize.quality: no visible global function definition for
  'ks.test'
tool.overlap: no visible global function definition for 'phyper'
tool.read: no visible global function definition for 'read.delim'
tool.read: no visible global function definition for 'na.omit'
tool.save: no visible global function definition for 'write.table'
tool.unify: no visible global function definition for 'sd'
tool.unify: no visible global function definition for 'quantile'
tool.unify: no visible global function definition for 'approx'
Undefined global functions or variables:
  approx as.dist col2rgb hclust ks.test median na.omit object.size
  optim p.adjust phyper pnorm qnorm quantile rainbow read.delim rnorm
  sd write.table
Consider adding
  importFrom("grDevices", "col2rgb", "rainbow")
  importFrom("stats", "approx", "as.dist", "hclust", "ks.test", "median",
             "na.omit", "optim", "p.adjust", "phyper", "pnorm", "qnorm",
             "quantile", "rnorm", "sd")
  importFrom("utils", "object.size", "read.delim", "write.table")
to your NAMESPACE file.
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
ssea.meta            16.47   0.08   16.55
kda.analyze.test     10.88   0.03   10.92
kda.analyze.simulate 10.86   0.03   10.89
kda.prepare          10.64   0.05   10.68
kda.analyze.exec     10.00   0.07   11.19
ssea2kda              7.37   0.03    7.51
ssea2kda.analyze      6.86   0.00    6.86
ssea.finish.details   5.17   0.01    5.19
ssea.finish           5.07   0.07    5.12
ssea.finish.genes     5.02   0.04    5.07
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
ssea.meta             18.10   0.13   18.24
kda.analyze.test      11.44   0.09   11.53
ssea2kda              10.80   0.07   10.87
ssea2kda.analyze      10.67   0.05   10.78
kda.analyze.simulate  10.47   0.06   10.53
kda.prepare           10.10   0.06   10.16
kda.analyze.exec       9.15   0.10    9.25
ssea.finish.genes      7.44   0.04    7.48
ssea.finish.fdr        7.27   0.07    7.33
ssea.finish            7.23   0.01    7.38
ssea.finish.details    6.31   0.03    6.34
ssea.analyze.simulate  5.88   0.02    5.89
ssea2kda.import        5.86   0.00    5.86
ssea.analyze           5.42   0.05    5.47
ssea.prepare.counts    5.37   0.09    5.64
ssea.control           5.14   0.03    5.17
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  Running 'runTests.R'
 OK
* 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 NOTEs
See
  'C:/Users/biocbuild/bbs-3.7-bioc/meat/Mergeomics.Rcheck/00check.log'
for details.

Installation output

Mergeomics.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/Mergeomics_1.8.0.tar.gz && rm -rf Mergeomics.buildbin-libdir && mkdir Mergeomics.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=Mergeomics.buildbin-libdir Mergeomics_1.8.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL Mergeomics_1.8.0.zip && rm Mergeomics_1.8.0.tar.gz Mergeomics_1.8.0.zip
###
##############################################################################
##############################################################################


  % 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 2971k  100 2971k    0     0  32.4M      0 --:--:-- --:--:-- --:--:-- 34.9M

install for i386

* installing *source* package 'Mergeomics' ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'Mergeomics'
    finding HTML links ... done
    MSEA.KDA.onestep                        html  
    Mergeomics-package                      html  
    job.kda                                 html  
    kda.analyze                             html  
    kda.analyze.exec                        html  
    kda.analyze.simulate                    html  
    kda.analyze.test                        html  
    kda.configure                           html  
    kda.finish                              html  
    kda.finish.estimate                     html  
    kda.finish.save                         html  
    kda.finish.summarize                    html  
    kda.finish.trim                         html  
    kda.prepare                             html  
    kda.prepare.overlap                     html  
    kda.prepare.screen                      html  
    kda.start                               html  
    kda.start.edges                         html  
    kda.start.identify                      html  
    kda.start.modules                       html  
    kda2cytoscape                           html  
    kda2cytoscape.colorize                  html  
    kda2cytoscape.colormap                  html  
    kda2cytoscape.drivers                   html  
    kda2cytoscape.edges                     html  
    kda2cytoscape.exec                      html  
    kda2cytoscape.identify                  html  
    kda2himmeli                             html  
    kda2himmeli.colorize                    html  
    kda2himmeli.colormap                    html  
    kda2himmeli.drivers                     html  
    kda2himmeli.edges                       html  
    kda2himmeli.exec                        html  
    kda2himmeli.identify                    html  
    ssea.analyze                            html  
    ssea.analyze.observe                    html  
    ssea.analyze.randgenes                  html  
    ssea.analyze.randloci                   html  
    ssea.analyze.simulate                   html  
    ssea.analyze.statistic                  html  
    ssea.control                            html  
    ssea.finish                             html  
    ssea.finish.details                     html  
    ssea.finish.fdr                         html  
    ssea.finish.genes                       html  
    ssea.meta                               html  
    ssea.prepare                            html  
    ssea.prepare.counts                     html  
    ssea.prepare.structure                  html  
    ssea.start                              html  
    ssea.start.configure                    html  
    ssea.start.identify                     html  
    ssea.start.relabel                      html  
    ssea2kda                                html  
    ssea2kda.analyze                        html  
    ssea2kda.import                         html  
    tool.aggregate                          html  
    tool.cluster                            html  
    tool.cluster.static                     html  
    tool.coalesce                           html  
    tool.coalesce.exec                      html  
    tool.coalesce.find                      html  
    tool.coalesce.merge                     html  
    tool.fdr                                html  
    tool.fdr.bh                             html  
    tool.fdr.empirical                      html  
    tool.graph                              html  
    tool.graph.degree                       html  
    tool.graph.list                         html  
    tool.metap                              html  
    tool.normalize                          html  
    tool.normalize.quality                  html  
    tool.overlap                            html  
    tool.read                               html  
    tool.save                               html  
    tool.subgraph                           html  
    tool.subgraph.find                      html  
    tool.subgraph.search                    html  
    tool.subgraph.stats                     html  
    tool.translate                          html  
    tool.unify                              html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'Mergeomics' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'Mergeomics' as Mergeomics_1.8.0.zip
* DONE (Mergeomics)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'Mergeomics' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

Mergeomics.Rcheck/tests_i386/runTests.Rout


R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> BiocGenerics:::testPackage("Mergeomics")

KDA Version:12.7.2015

Parameters:
  Search depth: 1
  Search direction: 1
  Maximum overlap: 0.33
  Minimum module size: 20
  Minimum degree: automatic
  Maximum degree: automatic
  Edge factor: 0
  Random seed: 1

Importing edges...
     TAIL               HEAD               WEIGHT 
 Length:140663      Length:140663      Min.   :1  
 Class :character   Class :character   1st Qu.:1  
 Mode  :character   Mode  :character   Median :1  
                                       Mean   :1  
                                       3rd Qu.:1  
                                       Max.   :1  

Importing modules...
    MODULE              NODE          
 Length:1643        Length:1643       
 Class :character   Class :character  
 Mode  :character   Mode  :character  
Graph: 6.586784 Mb

Minimum degree set to 20 

Maximum degree set to 278 

Collecting hubs...
4876 hubs (25.21%)
Graph: 10.54147 Mb

Analyzing network...
6675: Dhcr7, n=114, p=1.09e-15
6648: Brap, n=20, p=5.50e-01
6643: Usp38, n=23, p=4.72e-07
5582: Yes1, n=319, p=3.53e-03
4746: Tcf7l2, n=73, p=1.57e-02
4708: Tpte, n=86, p=9.49e-02
4511: Plg, n=160, p=1.45e-01
4464: Tsc22d3, n=487, p=7.03e-13
4407: Dntt, n=93, p=9.53e-21
4360: Slc10a6, n=132, p=3.28e-08
4588,..: Lrg1, n=86, p=1.17e-09

MSEA Version:01.04.2016

Parameters:
  Permutation type: gene
  Permutations: 100
  Random seed: 1
  Minimum gene count: 10
  Maximum gene count: 500
  Maximum overlap between genes: 0.33

Importing modules...
    MODULE             DESCR          
 Length:20          Length:20         
 Class :character   Class :character  
 Mode  :character   Mode  :character  
    MODULE              GENE          
 Length:2906        Length:2906       
 Class :character   Class :character  
 Mode  :character   Mode  :character  

Importing marker values...
    MARKER              VALUE         
 Length:76866       Min.   :  0.8094  
 Class :character   1st Qu.:  0.9450  
 Mode  :character   Median :  1.1374  
                    Mean   :  1.3944  
                    3rd Qu.:  1.4688  
                    Max.   :323.0100  

Importing mapping data...
     GENE              MARKER         
 Length:132705      Length:132705     
 Class :character   Class :character  
 Mode  :character   Mode  :character  

Merging genes containing shared markers...
WARNING! Limited overlap analysis due to large number of groups.

197165/1673535 
400352/1673535 
595780/1673535 
796416/1673535 
989253/1673535 
1185917/1673535 
1390405/1673535 
1594681/1673535 
1673535 comparisons

21115 comparisons

13861 comparisons

12880 comparisons
Job: 8.950638 Mb

Preparing data structures...
Job: 13.98173 Mb

Adding positive controls...
Job: 14.23988 Mb

Estimating enrichment...
100/100 cycles

Normalizing scores...


RUNIT TEST PROTOCOL -- Wed Oct 17 03:21:24 2018 
*********************************************** 
Number of test functions: 2 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
Mergeomics RUnit Tests - 2 test functions, 0 errors, 0 failures
Number of test functions: 2 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
 332.54    0.76  333.32

Mergeomics.Rcheck/tests_x64/runTests.Rout


R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> BiocGenerics:::testPackage("Mergeomics")

KDA Version:12.7.2015

Parameters:
  Search depth: 1
  Search direction: 1
  Maximum overlap: 0.33
  Minimum module size: 20
  Minimum degree: automatic
  Maximum degree: automatic
  Edge factor: 0
  Random seed: 1

Importing edges...
     TAIL               HEAD               WEIGHT 
 Length:140663      Length:140663      Min.   :1  
 Class :character   Class :character   1st Qu.:1  
 Mode  :character   Mode  :character   Median :1  
                                       Mean   :1  
                                       3rd Qu.:1  
                                       Max.   :1  

Importing modules...
    MODULE              NODE          
 Length:1643        Length:1643       
 Class :character   Class :character  
 Mode  :character   Mode  :character  
Graph: 7.694687 Mb

Minimum degree set to 20 

Maximum degree set to 278 

Collecting hubs...
4876 hubs (25.21%)
Graph: 13.28496 Mb

Analyzing network...
6675: Dhcr7, n=114, p=1.09e-15
6648: Brap, n=20, p=5.50e-01
6643: Usp38, n=23, p=4.72e-07
5582: Yes1, n=319, p=3.53e-03
4746: Tcf7l2, n=73, p=1.57e-02
4708: Tpte, n=86, p=9.49e-02
4511: Plg, n=160, p=1.45e-01
4464: Tsc22d3, n=487, p=7.03e-13
4407: Dntt, n=93, p=9.53e-21
4360: Slc10a6, n=132, p=3.28e-08
4588,..: Lrg1, n=86, p=1.17e-09

MSEA Version:01.04.2016

Parameters:
  Permutation type: gene
  Permutations: 100
  Random seed: 1
  Minimum gene count: 10
  Maximum gene count: 500
  Maximum overlap between genes: 0.33

Importing modules...
    MODULE             DESCR          
 Length:20          Length:20         
 Class :character   Class :character  
 Mode  :character   Mode  :character  
    MODULE              GENE          
 Length:2906        Length:2906       
 Class :character   Class :character  
 Mode  :character   Mode  :character  

Importing marker values...
    MARKER              VALUE         
 Length:76866       Min.   :  0.8094  
 Class :character   1st Qu.:  0.9450  
 Mode  :character   Median :  1.1374  
                    Mean   :  1.3944  
                    3rd Qu.:  1.4688  
                    Max.   :323.0100  

Importing mapping data...
     GENE              MARKER         
 Length:132705      Length:132705     
 Class :character   Class :character  
 Mode  :character   Mode  :character  

Merging genes containing shared markers...
WARNING! Limited overlap analysis due to large number of groups.

107390/1673535 
242492/1673535 
341954/1673535 
474421/1673535 
609758/1673535 
749964/1673535 
905467/1673535 
1041399/1673535 
1198839/1673535 
1350808/1673535 
1502474/1673535 
1643369/1673535 
1673535 comparisons

21115 comparisons

13861 comparisons

12880 comparisons
Job: 11.66891 Mb

Preparing data structures...
Job: 17.11776 Mb

Adding positive controls...
Job: 17.42039 Mb

Estimating enrichment...
100/100 cycles

Normalizing scores...


RUNIT TEST PROTOCOL -- Wed Oct 17 03:28:31 2018 
*********************************************** 
Number of test functions: 2 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
Mergeomics RUnit Tests - 2 test functions, 0 errors, 0 failures
Number of test functions: 2 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
 425.98    0.76  427.03

Example timings

Mergeomics.Rcheck/examples_i386/Mergeomics-Ex.timings

nameusersystemelapsed
MSEA.KDA.onestep0.020.000.01
job.kda0.030.000.03
kda.analyze0.010.000.86
kda.analyze.exec10.00 0.0711.19
kda.analyze.simulate10.86 0.0310.89
kda.analyze.test10.88 0.0310.92
kda.configure000
kda.finish0.150.000.15
kda.finish.estimate0.080.030.11
kda.finish.save0.140.000.14
kda.finish.summarize0.160.000.16
kda.finish.trim0.150.000.16
kda.prepare10.64 0.0510.68
kda.prepare.overlap000
kda.prepare.screen000
kda.start1.160.041.21
kda.start.edges0.000.020.01
kda.start.identify000
kda.start.modules000
kda2cytoscape0.610.030.74
kda2cytoscape.colorize000
kda2cytoscape.colormap000
kda2cytoscape.drivers0.280.020.29
kda2cytoscape.edges0.240.020.25
kda2cytoscape.exec0.280.010.29
kda2cytoscape.identify0.020.000.02
kda2himmeli0.500.050.80
kda2himmeli.colorize000
kda2himmeli.colormap000
kda2himmeli.drivers0.200.000.21
kda2himmeli.edges0.190.020.21
kda2himmeli.exec0.230.000.23
kda2himmeli.identify000
ssea.analyze4.630.064.97
ssea.analyze.observe3.400.003.41
ssea.analyze.randgenes4.220.014.23
ssea.analyze.randloci3.860.023.88
ssea.analyze.simulate4.690.054.73
ssea.analyze.statistic000
ssea.control3.060.043.11
ssea.finish5.070.075.12
ssea.finish.details5.170.015.19
ssea.finish.fdr4.640.024.65
ssea.finish.genes5.020.045.07
ssea.meta16.47 0.0816.55
ssea.prepare4.520.004.51
ssea.prepare.counts3.860.003.86
ssea.prepare.structure4.100.004.09
ssea.start3.500.023.52
ssea.start.configure0.390.000.39
ssea.start.identify000
ssea.start.relabel4.060.034.09
ssea2kda7.370.037.51
ssea2kda.analyze6.860.006.86
ssea2kda.import4.650.054.70
tool.aggregate000
tool.cluster0.050.000.05
tool.cluster.static000
tool.coalesce0.030.000.03
tool.coalesce.exec0.090.000.09
tool.coalesce.find0.090.000.09
tool.coalesce.merge0.080.000.08
tool.fdr0.020.000.02
tool.fdr.bh000
tool.fdr.empirical000
tool.graph1.200.031.23
tool.graph.degree1.110.041.16
tool.graph.list0.970.051.01
tool.metap000
tool.normalize0.030.000.04
tool.normalize.quality0.020.000.01
tool.overlap000
tool.read0.20.00.2
tool.save0.020.000.02
tool.subgraph0.160.000.15
tool.subgraph.find0.140.000.14
tool.subgraph.search0.140.000.14
tool.subgraph.stats0.140.000.14
tool.translate0.040.000.03
tool.unify000

Mergeomics.Rcheck/examples_x64/Mergeomics-Ex.timings

nameusersystemelapsed
MSEA.KDA.onestep000
job.kda0.020.000.01
kda.analyze0.020.000.01
kda.analyze.exec9.150.109.25
kda.analyze.simulate10.47 0.0610.53
kda.analyze.test11.44 0.0911.53
kda.configure0.020.000.02
kda.finish0.120.020.14
kda.finish.estimate0.080.000.08
kda.finish.save0.080.010.09
kda.finish.summarize0.080.000.08
kda.finish.trim0.070.020.09
kda.prepare10.10 0.0610.16
kda.prepare.overlap000
kda.prepare.screen0.010.000.02
kda.start1.280.081.36
kda.start.edges000
kda.start.identify000
kda.start.modules0.020.000.01
kda2cytoscape0.360.020.38
kda2cytoscape.colorize000
kda2cytoscape.colormap000
kda2cytoscape.drivers0.140.000.14
kda2cytoscape.edges0.140.010.15
kda2cytoscape.exec0.170.000.17
kda2cytoscape.identify000
kda2himmeli0.360.050.41
kda2himmeli.colorize000
kda2himmeli.colormap000
kda2himmeli.drivers0.140.000.14
kda2himmeli.edges0.200.030.29
kda2himmeli.exec0.350.001.22
kda2himmeli.identify000
ssea.analyze5.420.055.47
ssea.analyze.observe4.010.044.06
ssea.analyze.randgenes3.890.003.89
ssea.analyze.randloci4.140.054.19
ssea.analyze.simulate5.880.025.89
ssea.analyze.statistic000
ssea.control5.140.035.17
ssea.finish7.230.017.38
ssea.finish.details6.310.036.34
ssea.finish.fdr7.270.077.33
ssea.finish.genes7.440.047.48
ssea.meta18.10 0.1318.24
ssea.prepare3.800.033.82
ssea.prepare.counts5.370.095.64
ssea.prepare.structure4.670.044.72
ssea.start3.300.033.33
ssea.start.configure0.550.000.54
ssea.start.identify0.010.000.02
ssea.start.relabel4.330.004.33
ssea2kda10.80 0.0710.87
ssea2kda.analyze10.67 0.0510.78
ssea2kda.import5.860.005.86
tool.aggregate000
tool.cluster0.050.000.05
tool.cluster.static000
tool.coalesce0.040.000.05
tool.coalesce.exec0.160.000.15
tool.coalesce.find0.200.000.21
tool.coalesce.merge0.210.000.20
tool.fdr000
tool.fdr.bh000
tool.fdr.empirical0.010.000.02
tool.graph1.810.031.84
tool.graph.degree1.790.051.83
tool.graph.list2.030.062.09
tool.metap0.010.000.02
tool.normalize0.050.000.04
tool.normalize.quality0.030.000.03
tool.overlap0.020.000.02
tool.read0.340.020.36
tool.save0.020.000.02
tool.subgraph0.140.000.14
tool.subgraph.find0.120.010.14
tool.subgraph.search0.120.020.14
tool.subgraph.stats0.200.000.21
tool.translate0.050.000.04
tool.unify000