Multiple platform build/check report for BioC 3.14 - CHECK results for CellNOptR on tokay2

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This page was generated on 2022-04-13 12:06:18 -0400 (Wed, 13 Apr 2022).

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 20.04.4 LTS)	x86_64	4.1.3 (2022-03-10) -- "One Push-Up"	4324
tokay2	Windows Server 2012 R2 Standard	x64	4.1.3 (2022-03-10) -- "One Push-Up"	4077
machv2	macOS 10.14.6 Mojave	x86_64	4.1.3 (2022-03-10) -- "One Push-Up"	4137
Click on any hostname to see more info about the system (e.g. compilers) () as reported by 'uname -p', except on Windows and Mac OS X*

CHECK results for CellNOptR on tokay2

To the developers/maintainers of the CellNOptR package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CellNOptR.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

CellNOptR 1.40.0 (landing page)
A.Gabor

Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)

git_url: https://git.bioconductor.org/packages/CellNOptR

git_branch: RELEASE_3_14

git_last_commit: 5643aae

git_last_commit_date: 2021-10-26 12:01:10 -0400 (Tue, 26 Oct 2021)

nebbiolo2

Linux (Ubuntu 20.04.4 LTS) / x86_64

tokay2

Windows Server 2012 R2 Standard / x64

machv2

macOS 10.14.6 Mojave / x86_64

Summary

Package: CellNOptR

Version: 1.40.0

Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CellNOptR.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings CellNOptR_1.40.0.tar.gz

StartedAt: 2022-04-12 17:02:25 -0400 (Tue, 12 Apr 2022)

EndedAt: 2022-04-12 17:06:34 -0400 (Tue, 12 Apr 2022)

EllapsedTime: 249.0 seconds

RetCode: 0

Status: OK

CheckDir: CellNOptR.Rcheck

Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CellNOptR.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings CellNOptR_1.40.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/CellNOptR.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'CellNOptR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CellNOptR' version '1.40.0'
* 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 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
* 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
build_sif_table_from_rule : rename_gates: no visible binding for global
  variable 'node_in'
build_sif_table_from_rule : rename_gates: no visible binding for global
  variable 'node_out'
build_sif_table_from_rule : simplify_gates: no visible global function
  definition for 'filter'
build_sif_table_from_rule : simplify_gates: no visible binding for
  global variable 'node_in'
build_sif_table_from_rule : simplify_gates: no visible binding for
  global variable 'node_out'
build_sif_table_from_rule : interpret_sif_list: no visible global
  function definition for 'setNames'
build_sif_table_from_rule : interpret_sif_list: no visible binding for
  global variable 'num_or'
build_sif_table_from_rule : interpret_sif_list: no visible binding for
  global variable 'node_out'
build_sif_table_from_rule : interpret_sif_list: no visible binding for
  global variable 'new_node_out'
build_sif_table_from_rule : interpret_sif_list: no visible binding for
  global variable 'node_in'
build_sif_table_from_rule : interpret_sif_list: no visible binding for
  global variable 'new_node_in'
build_sif_table_from_rule : interpret_sif_list: no visible global
  function definition for 'filter'
build_sif_table_from_rule : interpret_sif_list: no visible global
  function definition for 'distinct'
build_sif_table_from_rule : interpret_sif_list: no visible binding for
  global variable 'or_members'
build_sif_table_from_rule : write_sif: no visible binding for global
  variable 'node_in'
build_sif_table_from_rule : write_sif: no visible binding for global
  variable 'node_out'
build_sif_table_from_rule : write_sif: no visible binding for global
  variable 'sign1'
build_sif_table_from_rule : write_sif: no visible binding for global
  variable 'sign2'
crossvalidateBoolean: no visible global function definition for 'error'
readBNET: no visible global function definition for 'mutate'
readBNET: no visible binding for global variable 'factors'
readBNET: no visible binding for global variable 'i_and_gates'
readBNET: no visible binding for global variable '.'
Undefined global functions or variables:
  . distinct error factors filter i_and_gates mutate new_node_in
  new_node_out node_in node_out num_or or_members setNames sign1 sign2
Consider adding
  importFrom("stats", "filter", "setNames")
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 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 use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.14-bioc/R/library/CellNOptR/libs/i386/CellNOptR.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'C:/Users/biocbuild/bbs-3.14-bioc/R/library/CellNOptR/libs/x64/CellNOptR.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                          user system elapsed
crossvalidateBoolean      4.42   0.94    5.36
build_sif_table_from_rule 5.03   0.03    5.06
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                          user system elapsed
crossvalidateBoolean      4.39   0.79    5.21
build_sif_table_from_rule 5.16   0.00    5.16
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'test_gaBinaryT1.R'
  Running 'test_gaBinaryT2.R'
  Running 'test_gaBinaryT3.R'
  Running 'test_import_rules.R'
  Running 'test_manySteadyStates.R'
  Running 'test_priorBitString.R'
  Running 'test_simulateTN.R'
 OK
** running tests for arch 'x64' ...
  Running 'test_gaBinaryT1.R'
  Running 'test_gaBinaryT2.R'
  Running 'test_gaBinaryT3.R'
  Running 'test_import_rules.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: 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/CellNOptR.Rcheck/00check.log'
for details.

Installation output

CellNOptR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/CellNOptR_1.40.0.tar.gz && rm -rf CellNOptR.buildbin-libdir && mkdir CellNOptR.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CellNOptR.buildbin-libdir CellNOptR_1.40.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL CellNOptR_1.40.0.zip && rm CellNOptR_1.40.0.tar.gz CellNOptR_1.40.0.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
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 83 1416k   83 1181k    0     0  1133k      0  0:00:01  0:00:01 --:--:-- 1133k
100 1416k  100 1416k    0     0  1226k      0  0:00:01  0:00:01 --:--:-- 1226k

install for i386

* installing *source* package 'CellNOptR' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -I./include    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c simulatorT1.c -o simulatorT1.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -I./include    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c simulatorTN.c -o simulatorTN.o
C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o CellNOptR.dll tmp.def simulatorT1.o simulatorTN.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/CellNOptR.buildbin-libdir/00LOCK-CellNOptR/00new/CellNOptR/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'CellNOptR'
    finding HTML links ... done
    CNORbool                                html  
    CNORwrap                                html  
    CNOdata                                 html  
    CNOlist-class                           html  
    CNOlist-methods                         html  
    CNOlistDREAM                            html  
    CNOlistToy                              html  
    CNOlistToy2                             html  
    CNOlistToyMMB                           html  
    CellNOptR-package                       html  
    DreamModel                              html  
    ToyModel                                html  
    ToyModel2                               html  
    buildBitString                          html  
    build_sif_table_from_rule               html  
    cSimulator                              html  
    checkSignals                            html  
    compressModel                           html  
    computeScoreT1                          html  
    computeScoreTN                          html  
    createAndRunILP                         html  
    createILPBitstringAll                   html  
    create_binaries                         html  
    crossInhibitedData                      html  
    crossvalidateBoolean                    html  
    cutAndPlot                              html  
    cutAndPlotResultsT1                     html  
    cutAndPlotResultsTN                     html  
    cutCNOlist                              html  
    cutModel                                html  
    cutNONC                                 html  
    cutSimList                              html  
    defaultParameters                       html  
    exhaustive                              html  
    expandGates                             html  
    findNONC                                html  
    gaBinaryT1                              html  
    gaBinaryT2                              html  
    gaBinaryTN                              html  
    getFit                                  html  
    graph2sif                               html  
    ilpBinaryT1                             html  
    ilpBinaryT2                             html  
    ilpBinaryTN                             html  
    indexFinder                             html  
    internals                               html  
    invokeCPLEX                             html  
    makeCNOlist                             html  
    mapBack                                 html  
    model2igraph                            html  
    model2sif                               html  
    normaliseCNOlist                        html  
    pknmodel                                html  
    plot-methods                            html  
    plotCNOlist                             html  
    plotCNOlist2                            html  
    plotCNOlistLarge                        html  
    plotCNOlistLargePDF                     html  
    plotCNOlistPDF                          html  
    plotFit                                 html  
    plotModel                               html  
    plotOptimResults                        html  
    plotOptimResultsPDF                     html  
    plotOptimResultsPan                     html  
    prep4sim                                html  
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.14-bioc/meat/CellNOptR.buildbin-libdir/00LOCK-CellNOptR/00new/CellNOptR/help/prep4Sim.html
    preprocessing                           html  
    randomizeCNOlist                        html  
    readBND                                 html  
    readBNET                                html  
    readMIDAS                               html  
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.14-bioc/meat/CellNOptR.buildbin-libdir/00LOCK-CellNOptR/00new/CellNOptR/help/readMidas.html
    readSBMLQual                            html  
    readSIF                                 html  
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.14-bioc/meat/CellNOptR.buildbin-libdir/00LOCK-CellNOptR/00new/CellNOptR/help/readSIF.html
    residualError                           html  
    sif2graph                               html  
    simulateT1                              html  
    simulateTN                              html  
    simulatorT0                             html  
    simulatorT1                             html  
    simulatorT2                             html  
    simulatorTN                             html  
    toSBML                                  html  
    writeDot                                html  
    writeFile                               html  
    writeMIDAS                              html  
    writeNetwork                            html  
    writeObjectiveFunction                  html  
    writeReport                             html  
    writeSIF                                html  
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.14-bioc/meat/CellNOptR.buildbin-libdir/00LOCK-CellNOptR/00new/CellNOptR/help/writeSif.html
    writeScaffold                           html  
    write_bounds                            html  
    write_constraints                       html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'CellNOptR' ...
** libs
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -I./include    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c simulatorT1.c -o simulatorT1.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG     -I"C:/extsoft/include"  -I./include    -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c simulatorTN.c -o simulatorTN.o
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o CellNOptR.dll tmp.def simulatorT1.o simulatorTN.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/CellNOptR.buildbin-libdir/CellNOptR/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CellNOptR' as CellNOptR_1.40.0.zip
* DONE (CellNOptR)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'CellNOptR' successfully unpacked and MD5 sums checked

Tests output

CellNOptR.Rcheck/tests_i386/test_gaBinaryT1.Rout R version 4.1.3 (2022-03-10) -- "One Push-Up" Copyright (C) 2022 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. > # > # 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 Attaching package: 'BiocGenerics' 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, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: hash hash-2.2.6.2 provided by Decision Patterns Loading required package: RCurl 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 3.64 0.14 3.76	CellNOptR.Rcheck/tests_x64/test_gaBinaryT1.Rout R version 4.1.3 (2022-03-10) -- "One Push-Up" Copyright (C) 2022 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. > # > # 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 Attaching package: 'BiocGenerics' 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, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: hash hash-2.2.6.2 provided by Decision Patterns Loading required package: RCurl 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 4.17 0.20 4.35
CellNOptR.Rcheck/tests_i386/test_gaBinaryT2.Rout R version 4.1.3 (2022-03-10) -- "One Push-Up" Copyright (C) 2022 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. > # > # 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 Attaching package: 'BiocGenerics' 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, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: hash hash-2.2.6.2 provided by Decision Patterns Loading required package: RCurl 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 5.20 0.20 5.37	CellNOptR.Rcheck/tests_x64/test_gaBinaryT2.Rout R version 4.1.3 (2022-03-10) -- "One Push-Up" Copyright (C) 2022 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. > # > # 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 Attaching package: 'BiocGenerics' 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, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: hash hash-2.2.6.2 provided by Decision Patterns Loading required package: RCurl 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 4.81 0.12 4.92
CellNOptR.Rcheck/tests_i386/test_gaBinaryT3.Rout R version 4.1.3 (2022-03-10) -- "One Push-Up" Copyright (C) 2022 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. > # > # 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 Attaching package: 'BiocGenerics' 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, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: hash hash-2.2.6.2 provided by Decision Patterns Loading required package: RCurl 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 5.34 0.17 5.48	CellNOptR.Rcheck/tests_x64/test_gaBinaryT3.Rout R version 4.1.3 (2022-03-10) -- "One Push-Up" Copyright (C) 2022 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. > # > # 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 Attaching package: 'BiocGenerics' 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, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: hash hash-2.2.6.2 provided by Decision Patterns Loading required package: RCurl 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) initBstring 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 5.60 0.09 5.68
CellNOptR.Rcheck/tests_i386/test_import_rules.Rout R version 4.1.3 (2022-03-10) -- "One Push-Up" Copyright (C) 2022 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. > library(CellNOptR) Loading required package: RBGL Loading required package: graph Loading required package: BiocGenerics Attaching package: 'BiocGenerics' 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, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: hash hash-2.2.6.2 provided by Decision Patterns Loading required package: RCurl 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 > > # test readBND ------------------------------------------------------------------ > > required_pcks = list("plyr","dplyr","tidyr","readr") > > if(!all(unlist(lapply(required_pcks,requireNamespace)))){ + print("the following packages need to be installed to use readBND:") + print(unlist(required_pcks)) + print("Please, install the packages manually for this feature.") + + }else{ + #download.file("https://maboss.curie.fr/pub/example.bnd",destfile = "./tests/example.bnd") + #model = readBND("./tests/example.bnd") + model = readBND("https://maboss.curie.fr/pub/example.bnd") + + # basic checks for being a CellNoptR model: + stopifnot(is.list(model)) + stopifnot(length(model)==4) + stopifnot(all(names(model) %in% c("reacID","namesSpecies","interMat","notMat"))) + stopifnot(length(model$reacID)==ncol(model$interMat)) + stopifnot(length(model$reacID)==ncol(model$notMat)) + stopifnot(length(model$namesSpecies)==nrow(model$interMat)) + stopifnot(length(model$namesSpecies)==nrow(model$notMat)) + + #plotModel(model) + + + + } Loading required namespace: plyr Loading required namespace: tidyr Loading required namespace: readr Loading required package: plyr Attaching package: 'plyr' The following object is masked from 'package:graph': join Loading required package: dplyr Attaching package: 'dplyr' The following objects are masked from 'package:plyr': arrange, count, desc, failwith, id, mutate, rename, summarise, summarize The following object is masked from 'package:graph': union The following objects are masked from 'package:BiocGenerics': combine, intersect, setdiff, union The following objects are masked from 'package:stats': filter, lag The following objects are masked from 'package:base': intersect, setdiff, setequal, union Loading required package: tidyr Attaching package: 'tidyr' The following object is masked from 'package:RCurl': complete Loading required package: readr Warning messages: 1: In readBND("https://maboss.curie.fr/pub/example.bnd") : experimental BND reader. Use with care (July 2018). 2: In readBNET(fh) : experimental BNET reader. Use with care (February 2018). 3: `cols` is now required when using unnest(). Please use `cols = c(sif_df)` > > > > proc.time() user system elapsed 3.31 0.20 3.92	CellNOptR.Rcheck/tests_x64/test_import_rules.Rout R version 4.1.3 (2022-03-10) -- "One Push-Up" Copyright (C) 2022 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. > library(CellNOptR) Loading required package: RBGL Loading required package: graph Loading required package: BiocGenerics Attaching package: 'BiocGenerics' 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, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: hash hash-2.2.6.2 provided by Decision Patterns Loading required package: RCurl 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 > > # test readBND ------------------------------------------------------------------ > > required_pcks = list("plyr","dplyr","tidyr","readr") > > if(!all(unlist(lapply(required_pcks,requireNamespace)))){ + print("the following packages need to be installed to use readBND:") + print(unlist(required_pcks)) + print("Please, install the packages manually for this feature.") + + }else{ + #download.file("https://maboss.curie.fr/pub/example.bnd",destfile = "./tests/example.bnd") + #model = readBND("./tests/example.bnd") + model = readBND("https://maboss.curie.fr/pub/example.bnd") + + # basic checks for being a CellNoptR model: + stopifnot(is.list(model)) + stopifnot(length(model)==4) + stopifnot(all(names(model) %in% c("reacID","namesSpecies","interMat","notMat"))) + stopifnot(length(model$reacID)==ncol(model$interMat)) + stopifnot(length(model$reacID)==ncol(model$notMat)) + stopifnot(length(model$namesSpecies)==nrow(model$interMat)) + stopifnot(length(model$namesSpecies)==nrow(model$notMat)) + + #plotModel(model) + + + + } Loading required namespace: plyr Loading required namespace: tidyr Loading required namespace: readr Loading required package: plyr Attaching package: 'plyr' The following object is masked from 'package:graph': join Loading required package: dplyr Attaching package: 'dplyr' The following objects are masked from 'package:plyr': arrange, count, desc, failwith, id, mutate, rename, summarise, summarize The following object is masked from 'package:graph': union The following objects are masked from 'package:BiocGenerics': combine, intersect, setdiff, union The following objects are masked from 'package:stats': filter, lag The following objects are masked from 'package:base': intersect, setdiff, setequal, union Loading required package: tidyr Attaching package: 'tidyr' The following object is masked from 'package:RCurl': complete Loading required package: readr Warning messages: 1: In readBND("https://maboss.curie.fr/pub/example.bnd") : experimental BND reader. Use with care (July 2018). 2: In readBNET(fh) : experimental BNET reader. Use with care (February 2018). 3: `cols` is now required when using unnest(). Please use `cols = c(sif_df)` > > > > proc.time() user system elapsed 3.26 0.17 3.84
CellNOptR.Rcheck/tests_i386/test_manySteadyStates.Rout R version 4.1.3 (2022-03-10) -- "One Push-Up" Copyright (C) 2022 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. > # > # 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]]$bString + + simRes[[i]]<-simulateTN(CNOlist,model,bStrings) + } + } + return(list(bStrings=bStrings, Opt=Opt, simRes=simRes)) + } > > > > library(CellNOptR) Loading required package: RBGL Loading required package: graph Loading required package: BiocGenerics Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: hash hash-2.2.6.2 provided by Decision Patterns Loading required package: RCurl Loading required package: Rgraphviz Loading required package: grid Loading required package: XML Attaching package: 'XML' The following object is masked from 'package:graph': addNode Loading required package: ggplot2 > > # one steady state > data(CNOlistToy, package="CellNOptR") > cnolist = CNOlist(CNOlistToy) > data(ToyModel, package="CellNOptR") > results = manySteadyStates(cnolist, ToyModel) > print(results$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 8.82 0.21 9.04	CellNOptR.Rcheck/tests_x64/test_manySteadyStates.Rout R version 4.1.3 (2022-03-10) -- "One Push-Up" Copyright (C) 2022 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. > # > # 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]]$bString + + simRes[[i]]<-simulateTN(CNOlist,model,bStrings) + } + } + return(list(bStrings=bStrings, Opt=Opt, simRes=simRes)) + } > > > > library(CellNOptR) Loading required package: RBGL Loading required package: graph Loading required package: BiocGenerics Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: hash hash-2.2.6.2 provided by Decision Patterns Loading required package: RCurl Loading required package: Rgraphviz Loading required package: grid Loading required package: XML Attaching package: 'XML' The following object is masked from 'package:graph': addNode Loading required package: ggplot2 > > # one steady state > data(CNOlistToy, package="CellNOptR") > cnolist = CNOlist(CNOlistToy) > data(ToyModel, package="CellNOptR") > results = manySteadyStates(cnolist, ToyModel) > print(results$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 11.39 0.23 11.60
CellNOptR.Rcheck/tests_i386/test_priorBitString.Rout R version 4.1.3 (2022-03-10) -- "One Push-Up" Copyright (C) 2022 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. > # > # 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 Attaching package: 'BiocGenerics' 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, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: hash hash-2.2.6.2 provided by Decision Patterns Loading required package: RCurl 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 2.12 0.26 2.37	CellNOptR.Rcheck/tests_x64/test_priorBitString.Rout R version 4.1.3 (2022-03-10) -- "One Push-Up" Copyright (C) 2022 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. > # > # 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 Attaching package: 'BiocGenerics' 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, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: hash hash-2.2.6.2 provided by Decision Patterns Loading required package: RCurl 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 2.28 0.12 2.39
CellNOptR.Rcheck/tests_i386/test_simulateTN.Rout R version 4.1.3 (2022-03-10) -- "One Push-Up" Copyright (C) 2022 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. > # > # 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 Attaching package: 'BiocGenerics' 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, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: hash hash-2.2.6.2 provided by Decision Patterns Loading required package: RCurl 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 3.06 0.21 3.26	CellNOptR.Rcheck/tests_x64/test_simulateTN.Rout R version 4.1.3 (2022-03-10) -- "One Push-Up" Copyright (C) 2022 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. > # > # 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 Attaching package: 'BiocGenerics' 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, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: hash hash-2.2.6.2 provided by Decision Patterns Loading required package: RCurl 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 2.96 0.17 3.12

Example timings

CellNOptR.Rcheck/examples_i386/CellNOptR-Ex.timings

name	user	system	elapsed
CNORbool	1.85	0.03	1.88
CNORwrap	0.76	0.05	0.98
CNOdata	0	0	0
CNOlist-class	0.19	0.00	0.19
CNOlist-methods	0.09	0.00	0.09
CellNOptR-package	3.90	0.03	3.92
buildBitString	0	0	0
build_sif_table_from_rule	5.03	0.03	5.06
checkSignals	0	0	0
compressModel	0.01	0.00	0.02
computeScoreT1	0.02	0.00	0.01
computeScoreTN	0.03	0.00	0.03
crossInhibitedData	0	0	0
crossvalidateBoolean	4.42	0.94	5.36
cutAndPlot	0.16	0.02	0.17
cutAndPlotResultsT1	0.23	0.00	0.24
cutAndPlotResultsTN	0.31	0.00	0.31
cutNONC	0.00	0.01	0.02
defaultParameters	0	0	0
exhaustive	0.41	0.02	0.42
expandGates	0	0	0
findNONC	0.02	0.00	0.01
gaBinaryT1	0.23	0.00	0.24
gaBinaryT2	0.11	0.00	0.11
gaBinaryTN	0.11	0.00	0.11
getFit	0.01	0.00	0.01
ilpBinaryT1	0.19	0.00	0.19
ilpBinaryT2	0.17	0.00	0.17
ilpBinaryTN	0.16	0.01	0.17
indexFinder	0.02	0.00	0.02
makeCNOlist	0.01	0.00	0.02
normaliseCNOlist	0	0	0
plot-methods	0.08	0.00	0.07
plotCNOlist	0.06	0.00	0.07
plotCNOlist2	1.63	0.00	1.62
plotCNOlistLarge	0.15	0.00	0.16
plotCNOlistLargePDF	0.16	0.02	0.17
plotCNOlistPDF	0.06	0.00	0.06
plotFit	0.05	0.00	0.05
plotModel	0.37	0.00	0.37
plotOptimResults	0.10	0.01	0.11
plotOptimResultsPDF	0.09	0.00	0.10
plotOptimResultsPan	0.16	0.02	0.17
prep4sim	0	0	0
preprocessing	0.01	0.00	0.01
randomizeCNOlist	0	0	0
readMIDAS	0.02	0.00	0.02
readSBMLQual	0	0	0
readSIF	0	0	0
residualError	0	0	0
simulateT1	0	0	0
simulateTN	0.00	0.02	0.01
simulatorT0	0	0	0
simulatorT1	0.00	0.01	0.02
simulatorT2	0	0	0
simulatorTN	0.02	0.00	0.01
writeDot	0.03	0.02	0.05
writeMIDAS	0.02	0.00	0.02
writeNetwork	0.04	0.00	0.04
writeReport	0.04	0.03	0.06
writeSIF	0	0	0
writeScaffold	0.07	0.01	0.10

CellNOptR.Rcheck/examples_x64/CellNOptR-Ex.timings

name	user	system	elapsed
CNORbool	1.81	0.00	1.81
CNORwrap	0.78	0.05	0.85
CNOdata	0	0	0
CNOlist-class	0.11	0.00	0.11
CNOlist-methods	0.06	0.00	0.06
CellNOptR-package	3.55	0.08	3.62
buildBitString	0	0	0
build_sif_table_from_rule	5.16	0.00	5.16
checkSignals	0.01	0.00	0.02
compressModel	0	0	0
computeScoreT1	0.02	0.00	0.01
computeScoreTN	0.03	0.00	0.03
crossInhibitedData	0	0	0
crossvalidateBoolean	4.39	0.79	5.21
cutAndPlot	0.19	0.00	0.18
cutAndPlotResultsT1	0.20	0.04	0.24
cutAndPlotResultsTN	0.33	0.00	0.33
cutNONC	0.02	0.00	0.01
defaultParameters	0	0	0
exhaustive	0.37	0.03	0.41
expandGates	0.02	0.00	0.01
findNONC	0	0	0
gaBinaryT1	0.37	0.01	0.39
gaBinaryT2	0.22	0.00	0.22
gaBinaryTN	0.20	0.00	0.21
getFit	0.02	0.00	0.01
ilpBinaryT1	0.23	0.00	0.24
ilpBinaryT2	0.22	0.00	0.21
ilpBinaryTN	0.19	0.02	0.21
indexFinder	0	0	0
makeCNOlist	0.01	0.00	0.01
normaliseCNOlist	0.02	0.00	0.02
plot-methods	0.08	0.00	0.08
plotCNOlist	0.09	0.00	0.09
plotCNOlist2	2.17	0.01	2.19
plotCNOlistLarge	0.18	0.00	0.17
plotCNOlistLargePDF	0.17	0.00	0.17
plotCNOlistPDF	0.14	0.00	0.14
plotFit	0.08	0.00	0.08
plotModel	0.48	0.02	0.50
plotOptimResults	0.13	0.00	0.13
plotOptimResultsPDF	0.11	0.00	0.10
plotOptimResultsPan	0.20	0.00	0.21
prep4sim	0	0	0
preprocessing	0.01	0.00	0.01
randomizeCNOlist	0	0	0
readMIDAS	0.02	0.00	0.02
readSBMLQual	0	0	0
readSIF	0.02	0.00	0.01
residualError	0	0	0
simulateT1	0	0	0
simulateTN	0	0	0
simulatorT0	0.02	0.00	0.02
simulatorT1	0	0	0
simulatorT2	0	0	0
simulatorTN	0.01	0.00	0.01
writeDot	0.06	0.00	0.06
writeMIDAS	0.02	0.00	0.02
writeNetwork	0.03	0.01	0.05
writeReport	0.02	0.02	0.03
writeSIF	0.01	0.00	0.01
writeScaffold	0.03	0.02	0.05