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CHECK report for CellNOptR on merida2

This page was generated on 2018-10-17 08:50:06 -0400 (Wed, 17 Oct 2018).

Package 205/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CellNOptR 1.26.0
A.Gabor
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/CellNOptR
Branch: RELEASE_3_7
Last Commit: c38a8b3
Last Changed Date: 2018-04-30 10:35:22 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: CellNOptR
Version: 1.26.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:CellNOptR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CellNOptR_1.26.0.tar.gz
StartedAt: 2018-10-16 20:19:29 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 20:21:56 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 147.3 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: CellNOptR.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:CellNOptR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CellNOptR_1.26.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/CellNOptR.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CellNOptR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CellNOptR’ version ‘1.26.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘RBGL’ ‘graph’ ‘hash’ ‘RCurl’ ‘Rgraphviz’ ‘XML’ ‘ggplot2’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘CellNOptR’ 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 ... OK
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... NOTE
The following files should probably not be installed:
  ‘Fig1.png’, ‘Fig5.png’

Consider the use of a .Rinstignore file: see ‘Writing R Extensions’,
or move the vignette sources from ‘inst/doc’ to ‘vignettes’.
* checking files in ‘vignettes’ ... OK
* checking examples ... WARNING
Found the following significant warnings:
  Warning: working directory was changed to ‘/private/tmp/RtmpYC3Gs6’, resetting
  Warning: working directory was changed to ‘/private/tmp/RtmpYC3Gs6’, resetting
  Warning: working directory was changed to ‘/private/tmp/RtmpYC3Gs6’, resetting
  Warning: working directory was changed to ‘/private/tmp/RtmpYC3Gs6’, resetting
  Warning: working directory was changed to ‘/private/tmp/RtmpYC3Gs6’, resetting
  Warning: working directory was changed to ‘/private/tmp/RtmpYC3Gs6’, resetting
  Warning: working directory was changed to ‘/private/tmp/RtmpYC3Gs6’, resetting
  Warning: working directory was changed to ‘/private/tmp/RtmpYC3Gs6’, resetting
  Warning: working directory was changed to ‘/private/tmp/RtmpYC3Gs6’, resetting
  Warning: working directory was changed to ‘/private/tmp/RtmpYC3Gs6’, resetting
  Warning: working directory was changed to ‘/private/tmp/RtmpYC3Gs6’, resetting
  Warning: working directory was changed to ‘/private/tmp/RtmpYC3Gs6’, resetting
  Warning: working directory was changed to ‘/private/tmp/RtmpYC3Gs6’, resetting
  Warning: working directory was changed to ‘/private/tmp/RtmpYC3Gs6’, resetting
Examples with CPU or elapsed time > 5s
                   user system elapsed
CellNOptR-package 4.957  0.076   5.074
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test_gaBinaryT1.R’
  Running ‘test_gaBinaryT2.R’
  Running ‘test_gaBinaryT3.R’
  Running ‘test_manySteadyStates.R’
  Running ‘test_priorBitString.R’
  Running ‘test_simulateTN.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: 1 WARNING, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.7-bioc/meat/CellNOptR.Rcheck/00check.log’
for details.



Installation output

CellNOptR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL CellNOptR
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘CellNOptR’ ...
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -I./include  -fPIC  -Wall -g -O2  -c getFit.c -o getFit.o
getFit.c:47:6: warning: unused variable 'nReacs' [-Wunused-variable]
        int nReacs = INTEGER(nReacs_in)[0];
            ^
getFit.c:39:6: warning: unused variable 'curr_max' [-Wunused-variable]
        int curr_max = 0;
            ^
getFit.c:41:6: warning: unused variable 'selection' [-Wunused-variable]
        int selection[40];
            ^
getFit.c:40:6: warning: unused variable 'or_max' [-Wunused-variable]
        int or_max = 0;
            ^
getFit.c:42:6: warning: unused variable 'selCounter' [-Wunused-variable]
        int selCounter = 0;
            ^
5 warnings generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -I./include  -fPIC  -Wall -g -O2  -c simulatorT1.c -o simulatorT1.o
simulatorT1.c:288:28: warning: equality comparison with extraneous parentheses [-Wparentheses-equality]
            if((track_cond == nCond)) {
                ˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜
simulatorT1.c:288:28: note: remove extraneous parentheses around the comparison to silence this warning
            if((track_cond == nCond)) {
               ˜           ^       ˜
simulatorT1.c:288:28: note: use '=' to turn this equality comparison into an assignment
            if((track_cond == nCond)) {
                           ^˜
                           =
1 warning generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include  -I./include  -fPIC  -Wall -g -O2  -c simulatorTN.c -o simulatorTN.o
simulatorTN.c:303:24: warning: equality comparison with extraneous parentheses [-Wparentheses-equality]
        if((track_cond == nCond)) {
            ˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜
simulatorTN.c:303:24: note: remove extraneous parentheses around the comparison to silence this warning
        if((track_cond == nCond)) {
           ˜           ^       ˜
simulatorTN.c:303:24: note: use '=' to turn this equality comparison into an assignment
        if((track_cond == nCond)) {
                       ^˜
                       =
simulatorTN.c:501:28: warning: equality comparison with extraneous parentheses [-Wparentheses-equality]
            if((track_cond == nCond)) {
                ˜˜˜˜˜˜˜˜˜˜˜^˜˜˜˜˜˜˜
simulatorTN.c:501:28: note: remove extraneous parentheses around the comparison to silence this warning
            if((track_cond == nCond)) {
               ˜           ^       ˜
simulatorTN.c:501:28: note: use '=' to turn this equality comparison into an assignment
            if((track_cond == nCond)) {
                           ^˜
                           =
2 warnings generated.
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o CellNOptR.so getFit.o simulatorT1.o simulatorTN.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.5/Resources/library/CellNOptR/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘CellNOptR-vignette.Rnw’ 
** testing if installed package can be loaded
* DONE (CellNOptR)

Tests output

CellNOptR.Rcheck/tests/test_gaBinaryT1.Rout


R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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.

> #
> #  This file is part of the CNO software
> #
> #  Copyright (c) 2011-2012 - EBI
> #
> #  File author(s): CNO developers (cno-dev@ebi.ac.uk)
> #
> #  Distributed under the GPLv2 License.
> #  See accompanying file LICENSE.txt or copy at
> #      http://www.gnu.org/licenses/gpl-2.0.html
> #
> #  CNO website: http://www.ebi.ac.uk/saezrodriguez/cno
> #
> ##############################################################################
> # $Id$
> 
> # This is a test of the ToyModel and gaBinaryT1
> library(CellNOptR)
Loading required package: RBGL
Loading required package: graph
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Loading required package: hash
hash-2.2.6 provided by Decision Patterns

Loading required package: RCurl
Loading required package: bitops
Loading required package: Rgraphviz
Loading required package: grid
Loading required package: XML

Attaching package: 'XML'

The following object is masked from 'package:graph':

    addNode

Loading required package: ggplot2
> 
> # read data
> pknmodel = readSIF(system.file("ToyModel/ToyPKNMMB.sif", package="CellNOptR"))
> data = readMIDAS(system.file("ToyModel/ToyDataMMB.csv", package="CellNOptR"))
[1] "Your data set comprises  18 conditions (i.e. combinations of time point and treatment)"
[1] "Your data set comprises measurements on  7  different species"
[1] "Your data set comprises  4 stimuli/inhibitors and 1 cell line(s) ( mock )"
[1] "Please be aware that CNO only handles measurements on one cell line at this time."
[1] "Your data file contained 'NaN'. We have assumed that these were missing values and replaced them by NAs."
> cnolist = makeCNOlist(data, subfield=FALSE)
[1] "Please be aware that if you only have some conditions at time zero (e.g.only inhibitor/no inhibitor), the measurements for these conditions will be copied across matching conditions at t=0"
> 
> # preprocessing
> model = preprocessing(cnolist, pknmodel, verbose=FALSE)
> 
> # optimisation
> T1opt<-gaBinaryT1(CNOlist=cnolist,model=model,verbose=FALSE)
> 
> truebs =c(1, 1, 0, 1, 1, 0, 1, 1, 0, 0, 1, 1, 1, 0, 0, 0)
> print(truebs)
 [1] 1 1 0 1 1 0 1 1 0 0 1 1 1 0 0 0
> print(T1opt$bString)
 [1] 1 1 0 1 1 0 1 1 0 0 1 1 1 0 0 0
> 
> # testing valid output
> if (dist(rbind(T1opt$bString, truebs))>2){
+ stop("something wrong going on")
+ }
> 
> # extra call to simulateTN
> SimT1<-simulateTN(CNOlist=cnolist,model=model, bStrings=list(truebs))
> 
> 
> proc.time()
   user  system elapsed 
  3.880   0.213   4.089 

CellNOptR.Rcheck/tests/test_gaBinaryT2.Rout


R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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.

> #
> #  This file is part of the CNO software
> #
> #  Copyright (c) 2011-2012 - EBI
> #
> #  File author(s): CNO developers (cno-dev@ebi.ac.uk)
> #
> #  Distributed under the GPLv2 License.
> #  See accompanying file LICENSE.txt or copy at
> #      http://www.gnu.org/licenses/gpl-2.0.html
> #
> #  CNO website: http://www.ebi.ac.uk/saezrodriguez/cno
> #
> ##############################################################################
> # $Id$
> 
> # This is a test of the ToyModel and gaBinaryT1
> # 
> 
> library(CellNOptR)
Loading required package: RBGL
Loading required package: graph
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Loading required package: hash
hash-2.2.6 provided by Decision Patterns

Loading required package: RCurl
Loading required package: bitops
Loading required package: Rgraphviz
Loading required package: grid
Loading required package: XML

Attaching package: 'XML'

The following object is masked from 'package:graph':

    addNode

Loading required package: ggplot2
> data(CNOlistToy2, package="CellNOptR")
> data(ToyModel2, package="CellNOptR")
> cnolist = CNOlistToy2
> pknmodel = ToyModel2
> 
> model = preprocessing(cnolist, pknmodel, verbose=FALSE)
> T1opt<-gaBinaryT1(CNOlist=cnolist,model=model,verbose=FALSE)
> print(T1opt$bString)
 [1] 1 1 1 1 1 0 1 1 0 0 1 1 1 1 0 0 0 0
> 
> truebs = c(1, 1, 1, 1, 1, 0, 1, 1, 0, 0, 1, 1, 1, 1, 0, 0, 0, 0)
> 
> 
> T2opt<-gaBinaryTN(CNOlist=cnolist,model=model,bStrings=list(truebs),verbose=FALSE)
> truebs2 = c(0, 0, 0, 1, 0, 0, 0)
> 
> print(T2opt$bString)
[1] 0 0 0 1 0 0 0
> 
> proc.time()
   user  system elapsed 
  4.631   0.236   4.851 

CellNOptR.Rcheck/tests/test_gaBinaryT3.Rout


R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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.

> #
> #  This file is part of the CNO software
> #
> #  Copyright (c) 2011-2012 - EBI
> #
> #  File author(s): CNO developers (cno-dev@ebi.ac.uk)
> #
> #  Distributed under the GPLv2 License.
> #  See accompanying file LICENSE.txt or copy at
> #      http://www.gnu.org/licenses/gpl-2.0.html
> #
> #  CNO website: http://www.ebi.ac.uk/saezrodriguez/cno
> #
> ##############################################################################
> # $Id$
> 
> # This is a test of the ToyModel and gaBinaryT1
> # 
> 
> library(CellNOptR)
Loading required package: RBGL
Loading required package: graph
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Loading required package: hash
hash-2.2.6 provided by Decision Patterns

Loading required package: RCurl
Loading required package: bitops
Loading required package: Rgraphviz
Loading required package: grid
Loading required package: XML

Attaching package: 'XML'

The following object is masked from 'package:graph':

    addNode

Loading required package: ggplot2
> 
> pknmodel = readSIF(system.file("ToyModelT3/ToyModelT3.sif", package="CellNOptR"))
> cnolist = CNOlist(system.file("ToyModelT3/ToyDataT3.csv", package="CellNOptR"))
> model = preprocessing(cnolist, pknmodel, verbose=FALSE)
> 
> # expected values
> bestBS = c(1, 1, 1, 0, 1, 1, 1, 1, 0, 1, 1, 1, 0, 0, 0, 0,0)
> bestBS2 <- c(0,0,0,0,0,0,1)
> bestBS3 <- c(0,0,1,0,0,0)
> 
> # just to check that the simulateTN function works 
> SimT1<-simulateTN(CNOlist=cnolist, model=model, bString=list(bestBS))
> SimT2<-simulateTN(CNOlist=cnolist, model=model, bStrings=list(bestBS,bestBS2))
> SimT3<-simulateTN(CNOlist=cnolist, model=model, bStrings=list(bestBS, bestBS2, bestBS3))
> 
> 
> # again, just to check that gaBinary works
> # run T1 first, 
> T1opt<-gaBinaryT1(CNOlist=cnolist,model=model,verbose=FALSE)
> # run T2
> T2opt<-gaBinaryTN(CNOlist=cnolist,model=model,bStrings=list(T1opt$bString),verbose=FALSE)
> # run T3
> T3opt<-gaBinaryTN(CNOlist=cnolist,model=model,bStrings=list(bestBS, bestBS2),verbose=FALSE)
> 
> print( T1opt$bScore)
             
4.545455e-05 
> print( T2opt$bScore)
[1] 5.454545e-05
> print( T3opt$bScore)
[1] 6.363636e-05
> # no using the hardcoded parameters, we can check the output of te scores that
> # must be tiny.
> score1 = computeScoreT1(cnolist, model, bString=bestBS)
> score2 = computeScoreTN(cnolist, model, bStrings=list(bestBS,bestBS2))
> score3 = computeScoreTN(cnolist, model, bStrings=list(bestBS,bestBS2, bestBS3))
> 
> 
> print(score1)
[1] 4.545455e-05
> print(score2)
[1] 5.454545e-05
> print(score3)
[1] 6.363636e-05
> if (score1>0.01 || score2>0.24 || score3>0.1){
+    # ideally, the score should all be close to 0. In practice, it's about 1e-5
+    # However, in the  T3 case, once in while, the score is 0.0953 hence the
+    # score3>0.1
+    stop("errore")
+ }
> cutAndPlot(cnolist, model,bStrings=list(bestBS),plotPDF=TRUE, tag="test1")
$filenames
$filenames[[1]]
[1] "test1_SimResultsT1_1_.pdf"


$mse
     [,1] [,2] [,3] [,4] [,5] [,6]
[1,]    0    0    0    0    0    0
[2,]    0    0    0    0    0    0
[3,]    0    0    0    0    0    0
[4,]    0    0    0    0    0    0
[5,]    0    0    0    0    0    0
[6,]    0    0    0    0    0    0
[7,]    0    0    0    0    0    0

$simResults
$simResults[[1]]
$simResults[[1]]$t0
     [,1] [,2] [,3] [,4] [,5] [,6]
[1,]    0    0    0    0    0    0
[2,]    0    0    0    0    0    0
[3,]    0    0    0    0    0    0
[4,]    0    0    0    0    0    0
[5,]    0    0    0    0    0    0
[6,]    0    0    0    0    0    0
[7,]    0    0    0    0    0    0

$simResults[[1]]$t1
     [,1] [,2] [,3] [,4] [,5] [,6]
[1,]    1    1    1    0    1    0
[2,]    1    1    1    1    1    1
[3,]    0    1    1    0    0    0
[4,]    1    0    0    0    1    0
[5,]    0    0    0    1    0    1
[6,]    1    0    0    1    1    1
[7,]    0    0    0    0    0    0



> cutAndPlot(cnolist, model,bStrings=list(bestBS,bestBS2),plotPDF=TRUE, tag="test2")
$mse
     [,1] [,2] [,3] [,4] [,5] [,6]
[1,]    0    0    0    0    0    0
[2,]    0    0    0    0    0    0
[3,]    0    0    0    0    0    0
[4,]    0    0    0    0    0    0
[5,]    0    0    0    0    0    0
[6,]    0    0    0    0    0    0
[7,]    0    0    0    0    0    0

$filenames
list()

$simResults
$simResults[[1]]
     [,1] [,2] [,3] [,4] [,5] [,6]
[1,]    0    0    0    0    0    0
[2,]    0    0    0    0    0    0
[3,]    0    0    0    0    0    0
[4,]    0    0    0    0    0    0
[5,]    0    0    0    0    0    0
[6,]    0    0    0    0    0    0
[7,]    0    0    0    0    0    0

$simResults[[2]]
     [,1] [,2] [,3] [,4] [,5] [,6]
[1,]    1    1    1    0    1    0
[2,]    1    1    1    1    1    1
[3,]    0    1    1    0    0    0
[4,]    1    0    0    0    1    0
[5,]    0    0    0    1    0    1
[6,]    1    0    0    1    1    1
[7,]    0    0    0    0    0    0

$simResults[[3]]
     [,1] [,2] [,3] [,4] [,5] [,6]
[1,]    1    1    1    0    1    0
[2,]    1    1    1    1    1    0
[3,]    0    1    1    0    0    0
[4,]    1    0    0    0    1    0
[5,]    0    0    0    1    0    0
[6,]    1    0    0    1    1    0
[7,]    0    0    0    0    0    0


> cutAndPlot(cnolist, model, bStrings=list(bestBS,bestBS2,bestBS3),plotPDF=TRUE, tag="test3")
$mse
     [,1] [,2] [,3] [,4] [,5] [,6]
[1,]    0    0    0    0    0    0
[2,]    0    0    0    0    0    0
[3,]    0    0    0    0    0    0
[4,]    0    0    0    0    0    0
[5,]    0    0    0    0    0    0
[6,]    0    0    0    0    0    0
[7,]    0    0    0    0    0    0

$filenames
list()

$simResults
$simResults[[1]]
     [,1] [,2] [,3] [,4] [,5] [,6]
[1,]    0    0    0    0    0    0
[2,]    0    0    0    0    0    0
[3,]    0    0    0    0    0    0
[4,]    0    0    0    0    0    0
[5,]    0    0    0    0    0    0
[6,]    0    0    0    0    0    0
[7,]    0    0    0    0    0    0

$simResults[[2]]
     [,1] [,2] [,3] [,4] [,5] [,6]
[1,]    1    1    1    0    1    0
[2,]    1    1    1    1    1    1
[3,]    0    1    1    0    0    0
[4,]    1    0    0    0    1    0
[5,]    0    0    0    1    0    1
[6,]    1    0    0    1    1    1
[7,]    0    0    0    0    0    0

$simResults[[3]]
     [,1] [,2] [,3] [,4] [,5] [,6]
[1,]    1    1    1    0    1    0
[2,]    1    1    1    1    1    0
[3,]    0    1    1    0    0    0
[4,]    1    0    0    0    1    0
[5,]    0    0    0    1    0    0
[6,]    1    0    0    1    1    0
[7,]    0    0    0    0    0    0

$simResults[[4]]
     [,1] [,2] [,3] [,4] [,5] [,6]
[1,]    0    1    1    0    0    0
[2,]    0    0    0    1    0    1
[3,]    0    1    1    0    0    0
[4,]    0    0    0    0    0    0
[5,]    0    0    0    1    0    1
[6,]    0    0    0    1    0    1
[7,]    0    0    0    0    0    0


> 
> 
> 
> warnings()
> 
> proc.time()
   user  system elapsed 
  5.365   0.213   5.577 

CellNOptR.Rcheck/tests/test_manySteadyStates.Rout


R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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.

> #
> #  This file is part of the CNO software
> #
> #  Copyright (c) 2011-2012 - EBI
> #
> #  File author(s): CNO developers (cno-dev@ebi.ac.uk)
> #
> #  Distributed under the GPLv2 License.
> #  See accompanying file LICENSE.txt or copy at
> #      http://www.gnu.org/licenses/gpl-2.0.html
> #
> #  CNO website: http://www.ebi.ac.uk/saezrodriguez/software.html
> #
> ##############################################################################
> # $Id$
> 
> # This test runs optimisation using Boolean logic at different time points
> # Author: S.Schrier, T.Cokelaer
> 
> 
> 
> manySteadyStates <-function(
+   CNOlist,
+   model,
+   sizeFac=0.0001,
+   NAFac=1,
+   popSize=50,
+   pMutation=0.5,
+   maxTime=60,
+   maxGens=500,
+   stallGenMax=100,
+   selPress=1.2,
+   elitism=5,
+   relTol=0.1,
+   verbose=FALSE,
+   priorBitString=NULL){
+ 
+ 
+     #initialize Opt array
+     Opt<-list()    
+     #initialze a bString array  
+     bStrings<-list()
+     simRes<-list()
+ 
+ 
+     T1opt<-gaBinaryT1(CNOlist=CNOlist,
+                   model=model,
+                   stallGenMax=stallGenMax,
+                   sizeFac=sizeFac,
+                   NAFac=NAFac,
+                   popSize=popSize,
+                   pMutation=pMutation,
+                   maxTime=maxTime,
+                   maxGens=maxGens,
+                   selPress=selPress,
+                   elitism=elitism,
+                   relTol=relTol,
+                   verbose=verbose,
+                   priorBitString=priorBitString)
+ 
+     Opt[[1]]<-T1opt
+     simT1<-simulateTN(CNOlist=CNOlist, model=model, bStrings=list(T1opt$bString))
+     simRes[[1]]<-simT1
+     bStrings[[1]] = T1opt$bString
+ 
+     if (length(CNOlist@signals)>2){
+         for(i in 3:length(CNOlist@signals)){
+             Opt[[i-1]]<-gaBinaryTN(CNOlist=CNOlist,
+                         model=model,
+                         bStrings=bStrings,
+                         stallGenMax=stallGenMax,
+                         maxTime=maxTime,
+                         sizeFac=sizeFac,
+                         NAFac=NAFac,
+                         popSize=popSize,
+                         pMutation=pMutation,
+                         maxGens=maxGens,
+                         selPress=selPress,
+                         elitism=elitism,
+                         relTol=relTol,
+                         verbose=verbose,
+                         priorBitString=priorBitString)
+ 
+             bStrings[[i-1]] = Opt[[i-1]]$bString
+ 
+             simRes[[i]]<-simulateTN(CNOlist,model,bStrings)
+         }
+     }   
+     return(list(bStrings=bStrings, Opt=Opt, simRes=simRes))
+ }
> 
> 
> 
> library(CellNOptR)
Loading required package: RBGL
Loading required package: graph
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Loading required package: hash
hash-2.2.6 provided by Decision Patterns

Loading required package: RCurl
Loading required package: bitops
Loading required package: Rgraphviz
Loading required package: grid
Loading required package: XML

Attaching package: 'XML'

The following object is masked from 'package:graph':

    addNode

Loading required package: ggplot2
> 
> # one steady state
> data(CNOlistToy, package="CellNOptR")
> cnolist = CNOlist(CNOlistToy)
> data(ToyModel, package="CellNOptR")
> results = manySteadyStates(cnolist, ToyModel)
> print(results$bStrings)
[[1]]
 [1] 1 1 1 1 1 0 1 0 1 1 1 1 0 1 1 0

> 
> # two steady state
> data(CNOlistToy2, package="CellNOptR")
> cnolist = CNOlist(CNOlistToy2)
> data(ToyModel2, package="CellNOptR")
> results = manySteadyStates(cnolist, ToyModel2)
> print(results$bStrings)
[[1]]
 [1] 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 0 0

[[2]]
[1] 0 0 1

> 
> # 3 steady state
> ToyModel3 = readSIF(system.file("ToyModelT3/ToyModelT3.sif", package="CellNOptR"))
> cnolist = CNOlist(system.file("ToyModelT3/ToyDataT3.csv", package="CellNOptR"))
> results = manySteadyStates(cnolist, ToyModel3)
> print(results$bStrings)
[[1]]
 [1] 1 1 1 1 1 1 1 1 1 1 0 0 1 1 1 1 1 1 0

[[2]]
[1] 0 0 0

[[3]]
[1] 0 0 0

> 
> 
> 
> proc.time()
   user  system elapsed 
  8.647   0.263   8.890 

CellNOptR.Rcheck/tests/test_priorBitString.Rout


R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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.

> #
> #  This file is part of the CNO software
> #
> #  Copyright (c) 2011-2012 - EBI
> #
> #  File author(s): CNO developers (cno-dev@ebi.ac.uk)
> #
> #  Distributed under the GPLv2 License.
> #  See accompanying file LICENSE.txt or copy at
> #      http://www.gnu.org/licenses/gpl-2.0.html
> #
> #  CNO website: http://www.ebi.ac.uk/saezrodriguez/software.html
> #
> ##############################################################################
> # $Id$
> # test if the priorBitString is used correctly in gaBinaryT1DO NOT MODIFY please (TC, June 2012)
> 
> library(CellNOptR)
Loading required package: RBGL
Loading required package: graph
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Loading required package: hash
hash-2.2.6 provided by Decision Patterns

Loading required package: RCurl
Loading required package: bitops
Loading required package: Rgraphviz
Loading required package: grid
Loading required package: XML

Attaching package: 'XML'

The following object is masked from 'package:graph':

    addNode

Loading required package: ggplot2
> 
> 
> # Load T1 and T2 data. Only T1 is used here below.
> data(ToyModel, package="CellNOptR")
> data(CNOlistToy, package="CellNOptR")
> cnolist = CNOlistToy
> pknmodel = ToyModel
> 
> # preprocessing
> model = preprocessing(cnolist, pknmodel)
[1] "The following species are measured: Akt, Hsp27, NFkB, Erk, p90RSK, Jnk, cJun"
[1] "The following species are stimulated: EGF, TNFa"
[1] "The following species are inhibited: Raf, PI3K"
[1] "The following species are not observable and/or not controllable: "
> 
> # computeScoreT1 with init string made of ones
> initBstring<-rep(1,length(model$reacID))
> 
> 
> 
> priorBitString = rep(NA, length(model$reacID))
> priorBitString[1] = 0
> priorBitString[2] = 0
> priorBitString[3] = 0
> priorBitString[4] = 0
> 
> # Second, you call the gaBinaryT1 function by providing the priorBitString
> # argument:
> ToyT1opt<-gaBinaryT1(CNOlist=CNOlistToy, model=model,
+     initBstring=initBstring, maxGens=10, popSize=5,
+     verbose=FALSE, priorBitString=priorBitString)
> 
> 
> for (x in ToyT1opt$results[,7]){
+      x = strsplit(x ,",")[[1]]
+      if (as.numeric(x[[1]]) != 0 ){ stop("first element must be 0")}
+      if (as.numeric(x[[2]]) != 0 ){ stop("second element must be 0")}
+      if (as.numeric(x[[3]]) != 0 ){ stop("tirdh element must be 0")}
+      if (as.numeric(x[[4]]) != 0 ){ stop("fourth element must be 0")}
+ }
> 
> 
> 
> proc.time()
   user  system elapsed 
  1.603   0.119   1.701 

CellNOptR.Rcheck/tests/test_simulateTN.Rout


R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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.

> #
> #  This file is part of the CNO software
> #
> #  Copyright (c) 2011-2012 - EBI
> #
> #  File author(s): CNO developers (cno-dev@ebi.ac.uk)
> #
> #  Distributed under the GPLv2 License.
> #  See accompanying file LICENSE.txt or copy at
> #      http://www.gnu.org/licenses/gpl-2.0.html
> #
> #  CNO website: http://www.ebi.ac.uk/saezrodriguez/software.html
> #
> ##############################################################################
> # $Id$
> # This test runs T3 data set to compute the scores (must be zero), and run
> # cutAndPlot plot on each time points.
> 
> # DO NOT MODIFY please (TC, June 2012)
> 
> library(CellNOptR)
Loading required package: RBGL
Loading required package: graph
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Loading required package: hash
hash-2.2.6 provided by Decision Patterns

Loading required package: RCurl
Loading required package: bitops
Loading required package: Rgraphviz
Loading required package: grid
Loading required package: XML

Attaching package: 'XML'

The following object is masked from 'package:graph':

    addNode

Loading required package: ggplot2
> pknmodel = readSIF(system.file("ToyModelT3/ToyModelT3.sif", package="CellNOptR"))
> cnolist = CNOlist(system.file("ToyModelT3/ToyDataT3.csv",  package="CellNOptR"))
> 
> model = preprocessing(cnolist, pknmodel)
[1] "The following species are measured: AKT, MEK, ERK, P38, JNK, NFKB"
[1] "The following species are stimulated: TGFa, TNFa"
[1] "The following species are inhibited: PI3K, MEK"
[1] "The following species are not observable and/or not controllable: "
> 
> # computeScoreT1 with init string made of ones
> verbose = FALSE
> initBstring<-rep(1,length(model$reacID))
> score = computeScoreT1(cnolist, model,bString=rep(1,length(model$reacID)))
> bestBS = c(1, 1, 1, 0, 1, 1, 1, 1, 0, 1, 1, 1, 0, 0, 0, 0,0)
> bestBS2 <- c(0,0,0,0,0,0,1) # given by running gaBinaryTN
> bestBS3 <- c(0,0,1,0,0,0) # given by running gaBinaryTN
> 
> 
> SimT1<-simulateTN(CNOlist=cnolist, model=model, bString=list(bestBS))
> SimT2<-simulateTN(CNOlist=cnolist, model=model, bStrings=list(bestBS, bestBS2))
> SimT3<-simulateTN(CNOlist=cnolist, model=model, bStrings=list(bestBS, bestBS2, bestBS3))
> 
> score1 = computeScoreT1(cnolist, model, bString=bestBS)
> score2 = computeScoreTN(cnolist, model, bStrings=list(bestBS,bestBS2))
> score3 = computeScoreTN(cnolist, model, bStrings=list(bestBS,bestBS2, bestBS3))
> 
> print(score1)
[1] 4.545455e-05
> print(score2)
[1] 5.454545e-05
> print(score3)
[1] 6.363636e-05
> if (score1>0.01 || score2>0.024){
+    stop("errore")
+ }
> cutAndPlot(cnolist, model,bStrings=list(bestBS),plotPDF=TRUE, tag="test1")
$filenames
$filenames[[1]]
[1] "test1_SimResultsT1_1_.pdf"


$mse
     [,1] [,2] [,3] [,4] [,5] [,6]
[1,]    0    0    0    0    0    0
[2,]    0    0    0    0    0    0
[3,]    0    0    0    0    0    0
[4,]    0    0    0    0    0    0
[5,]    0    0    0    0    0    0
[6,]    0    0    0    0    0    0
[7,]    0    0    0    0    0    0

$simResults
$simResults[[1]]
$simResults[[1]]$t0
     [,1] [,2] [,3] [,4] [,5] [,6]
[1,]    0    0    0    0    0    0
[2,]    0    0    0    0    0    0
[3,]    0    0    0    0    0    0
[4,]    0    0    0    0    0    0
[5,]    0    0    0    0    0    0
[6,]    0    0    0    0    0    0
[7,]    0    0    0    0    0    0

$simResults[[1]]$t1
     [,1] [,2] [,3] [,4] [,5] [,6]
[1,]    1    1    1    0    1    0
[2,]    1    1    1    1    1    1
[3,]    0    1    1    0    0    0
[4,]    1    0    0    0    1    0
[5,]    0    0    0    1    0    1
[6,]    1    0    0    1    1    1
[7,]    0    0    0    0    0    0



> cutAndPlot(cnolist, model,bStrings=list(bestBS,bestBS2),plotPDF=TRUE, tag="test2")
$mse
     [,1] [,2] [,3] [,4] [,5] [,6]
[1,]    0    0    0    0    0    0
[2,]    0    0    0    0    0    0
[3,]    0    0    0    0    0    0
[4,]    0    0    0    0    0    0
[5,]    0    0    0    0    0    0
[6,]    0    0    0    0    0    0
[7,]    0    0    0    0    0    0

$filenames
list()

$simResults
$simResults[[1]]
     [,1] [,2] [,3] [,4] [,5] [,6]
[1,]    0    0    0    0    0    0
[2,]    0    0    0    0    0    0
[3,]    0    0    0    0    0    0
[4,]    0    0    0    0    0    0
[5,]    0    0    0    0    0    0
[6,]    0    0    0    0    0    0
[7,]    0    0    0    0    0    0

$simResults[[2]]
     [,1] [,2] [,3] [,4] [,5] [,6]
[1,]    1    1    1    0    1    0
[2,]    1    1    1    1    1    1
[3,]    0    1    1    0    0    0
[4,]    1    0    0    0    1    0
[5,]    0    0    0    1    0    1
[6,]    1    0    0    1    1    1
[7,]    0    0    0    0    0    0

$simResults[[3]]
     [,1] [,2] [,3] [,4] [,5] [,6]
[1,]    1    1    1    0    1    0
[2,]    1    1    1    1    1    0
[3,]    0    1    1    0    0    0
[4,]    1    0    0    0    1    0
[5,]    0    0    0    1    0    0
[6,]    1    0    0    1    1    0
[7,]    0    0    0    0    0    0


> cutAndPlot(cnolist, model, bStrings=list(bestBS,bestBS2,bestBS3),plotPDF=TRUE, tag="test3")
$mse
     [,1] [,2] [,3] [,4] [,5] [,6]
[1,]    0    0    0    0    0    0
[2,]    0    0    0    0    0    0
[3,]    0    0    0    0    0    0
[4,]    0    0    0    0    0    0
[5,]    0    0    0    0    0    0
[6,]    0    0    0    0    0    0
[7,]    0    0    0    0    0    0

$filenames
list()

$simResults
$simResults[[1]]
     [,1] [,2] [,3] [,4] [,5] [,6]
[1,]    0    0    0    0    0    0
[2,]    0    0    0    0    0    0
[3,]    0    0    0    0    0    0
[4,]    0    0    0    0    0    0
[5,]    0    0    0    0    0    0
[6,]    0    0    0    0    0    0
[7,]    0    0    0    0    0    0

$simResults[[2]]
     [,1] [,2] [,3] [,4] [,5] [,6]
[1,]    1    1    1    0    1    0
[2,]    1    1    1    1    1    1
[3,]    0    1    1    0    0    0
[4,]    1    0    0    0    1    0
[5,]    0    0    0    1    0    1
[6,]    1    0    0    1    1    1
[7,]    0    0    0    0    0    0

$simResults[[3]]
     [,1] [,2] [,3] [,4] [,5] [,6]
[1,]    1    1    1    0    1    0
[2,]    1    1    1    1    1    0
[3,]    0    1    1    0    0    0
[4,]    1    0    0    0    1    0
[5,]    0    0    0    1    0    0
[6,]    1    0    0    1    1    0
[7,]    0    0    0    0    0    0

$simResults[[4]]
     [,1] [,2] [,3] [,4] [,5] [,6]
[1,]    0    1    1    0    0    0
[2,]    0    0    0    1    0    1
[3,]    0    1    1    0    0    0
[4,]    0    0    0    0    0    0
[5,]    0    0    0    1    0    1
[6,]    0    0    0    1    0    1
[7,]    0    0    0    0    0    0


> 
> 
> proc.time()
   user  system elapsed 
  2.260   0.151   2.391 

Example timings

CellNOptR.Rcheck/CellNOptR-Ex.timings

nameusersystemelapsed
CNORbool2.1780.0812.268
CNOdata0.0010.0000.002
CNOlist-class0.1060.0030.109
CNOlist-methods0.0830.0020.085
CellNOptR-package4.9570.0765.074
buildBitString0.0030.0000.003
checkSignals0.0050.0000.006
compressModel0.0080.0010.009
computeScoreT10.0180.0010.019
computeScoreTN0.0370.0010.039
crossInhibitedData0.0060.0000.007
cutAndPlot0.2450.0040.254
cutAndPlotResultsT10.3190.0050.330
cutAndPlotResultsTN0.4360.0050.445
cutNONC0.0110.0010.012
defaultParameters0.0050.0010.005
exhaustive0.6200.0170.643
expandGates0.0150.0010.017
findNONC0.0070.0010.008
gaBinaryT10.3480.0030.356
gaBinaryT20.1990.0010.201
gaBinaryTN0.1610.0010.163
getFit0.0080.0010.009
indexFinder0.0040.0010.005
normaliseCNOlist0.0110.0010.012
plot-methods0.1090.0030.112
plotCNOlist0.0700.0020.073
plotCNOlist22.6400.0242.672
plotCNOlistLarge0.2310.0030.235
plotFit0.0670.0020.072
plotModel1.8090.1772.002
plotOptimResultsPan0.2130.0030.217
prep4sim0.0040.0010.004
preprocessing0.0100.0010.011
randomizeCNOlist0.0020.0010.003
readSBMLQual0.0010.0000.002
residualError0.0050.0010.005
simulateT10.0120.0010.013
simulateTN0.0060.0010.007
simulatorT00.0070.0010.007
simulatorT10.0080.0000.008
simulatorT20.0060.0010.007
simulatorTN0.0090.0010.009