Multiple platform build/check report for BioC 3.20 - CHECK results for CellNOptR on kjohnson1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4744
palomino8	Windows Server 2022 Datacenter	x64	4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves"	4487
merida1	macOS 12.7.5 Monterey	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4515
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4467
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 kjohnson1

To the developers/maintainers of the CellNOptR package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results

Summary

Package: CellNOptR

Version: 1.52.0

Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CellNOptR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CellNOptR_1.52.0.tar.gz

StartedAt: 2024-12-20 13:58:31 -0500 (Fri, 20 Dec 2024)

EndedAt: 2024-12-20 14:00:43 -0500 (Fri, 20 Dec 2024)

EllapsedTime: 132.0 seconds

RetCode: 0

Status: OK

CheckDir: CellNOptR.Rcheck

Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CellNOptR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CellNOptR_1.52.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/CellNOptR.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CellNOptR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CellNOptR’ version ‘1.52.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'RBGL', 'graph', 'RCurl', 'Rgraphviz', 'XML', 'ggplot2', 'rmarkdown'
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
* used C compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
* used SDK: ‘MacOSX11.3.sdk’
* 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 code 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 ... NOTE
Package in Depends field not imported from: ‘rmarkdown’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.error.bar: no visible global function definition for ‘arrows’
CNORwrap: no visible global function definition for ‘pdf’
CNORwrap: no visible global function definition for ‘dev.off’
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’
createEdgeAttrs: no visible global function definition for ‘rgb’
crossvalidateBoolean: no visible global function definition for ‘error’
expandGates: no visible global function definition for ‘combn’
gaBinaryT1: no visible global function definition for ‘runif’
gaBinaryTN: no visible global function definition for ‘runif’
graph2sif: no visible global function definition for ‘write.table’
makeCNOlist: no visible binding for global variable ‘var’
mapBack: no visible global function definition for ‘write.table’
plotCNOlist: no visible global function definition for ‘par’
plotCNOlist: no visible global function definition for ‘text’
plotCNOlist: no visible global function definition for ‘axis’
plotCNOlist: no visible global function definition for ‘barplot’
plotCNOlistLarge: no visible global function definition for ‘par’
plotCNOlistLarge: no visible global function definition for ‘dev.new’
plotCNOlistLarge: no visible global function definition for ‘text’
plotCNOlistLarge: no visible global function definition for ‘axis’
plotCNOlistLarge: no visible global function definition for ‘image’
plotCNOlistLargePDF: no visible global function definition for ‘pdf’
plotCNOlistLargePDF: no visible global function definition for
  ‘dev.off’
plotCNOlistPDF: no visible global function definition for ‘pdf’
plotCNOlistPDF: no visible global function definition for ‘dev.off’
plotFit: no visible global function definition for ‘par’
plotFit: no visible global function definition for ‘pdf’
plotFit: no visible global function definition for ‘dev.off’
plotModel: no visible global function definition for ‘pdf’
plotModel: no visible global function definition for ‘png’
plotModel: no visible global function definition for ‘svg’
plotModel: no visible global function definition for ‘read.table’
plotModel: no visible global function definition for
  ‘installed.packages’
plotModel: no visible global function definition for ‘dev.off’
plotOptimResults: no visible global function definition for ‘par’
plotOptimResults: no visible global function definition for ‘text’
plotOptimResults: no visible global function definition for ‘rect’
plotOptimResults: no visible global function definition for ‘points’
plotOptimResults: no visible global function definition for ‘axis’
plotOptimResults: no visible global function definition for ‘image’
plotOptimResultsPDF: no visible global function definition for ‘pdf’
plotOptimResultsPDF: no visible global function definition for
  ‘dev.off’
plotOptimResultsPan: no visible global function definition for ‘par’
plotOptimResultsPan: no visible global function definition for
  ‘split.screen’
plotOptimResultsPan: no visible global function definition for
  ‘heat.colors’
plotOptimResultsPan: no visible global function definition for ‘screen’
plotOptimResultsPan: no visible global function definition for ‘text’
plotOptimResultsPan: no visible global function definition for ‘rect’
plotOptimResultsPan: no visible global function definition for ‘points’
plotOptimResultsPan: no visible global function definition for ‘axis’
plotOptimResultsPan: no visible global function definition for
  ‘barplot’
plotOptimResultsPan: no visible global function definition for ‘image’
plotOptimResultsPan: no visible global function definition for
  ‘plot.new’
plotOptimResultsPan: no visible global function definition for
  ‘segments’
plotOptimResultsPan: no visible global function definition for
  ‘close.screen’
plotOptimResultsPan: no visible global function definition for
  ‘dev.off’
randomizeCNOlist: no visible global function definition for ‘rnorm’
randomizeCNOlist: no visible global function definition for ‘runif’
readBND: no visible global function definition for ‘write.table’
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 ‘.’
readBNET: no visible binding for global variable ‘sif_df’
readBNET: no visible global function definition for ‘write.table’
readMIDAS: no visible global function definition for ‘count.fields’
readMIDAS: no visible global function definition for ‘read.csv’
readMIDAS: no visible global function definition for ‘read.table’
readSBMLQual: no visible global function definition for ‘write.table’
readSIF: no visible global function definition for ‘read.table’
sif2graph: no visible global function definition for ‘read.table’
writeMIDAS: no visible global function definition for ‘write.table’
writeNetworkW: no visible global function definition for ‘write.table’
writeSIF: no visible global function definition for ‘write.table’
writeScaffoldW: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  . arrows axis barplot close.screen combn count.fields dev.new dev.off
  distinct error factors filter heat.colors i_and_gates image
  installed.packages mutate new_node_in new_node_out node_in node_out
  num_or or_members par pdf plot.new png points read.csv read.table
  rect rgb rnorm runif screen segments setNames sif_df sign1 sign2
  split.screen svg text var write.table
Consider adding
  importFrom("grDevices", "dev.new", "dev.off", "heat.colors", "pdf",
             "png", "rgb", "svg")
  importFrom("graphics", "arrows", "axis", "barplot", "close.screen",
             "image", "par", "plot.new", "points", "rect", "screen",
             "segments", "split.screen", "text")
  importFrom("stats", "filter", "rnorm", "runif", "setNames", "var")
  importFrom("utils", "combn", "count.fields", "installed.packages",
             "read.csv", "read.table", "write.table")
to your NAMESPACE file.
* checking Rd files ... NOTE
checkRd: (-1) computeScoreT1.Rd:27: Lost braces
    27 |         a model structure, as created by code{readSIF}, normally pre-processed 
       |                                              ^
checkRd: (-1) computeScoreTN.Rd:26: Lost braces
    26 |         a model structure, as created by code{readSIF}, normally pre-processed 
       |                                              ^
checkRd: (-1) plotModel.Rd:59: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotModel.Rd:60: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotModel.Rd:61: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotModel.Rd:62: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotModel.Rd:63: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotModel.Rd:64: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotModel.Rd:65: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotModel.Rd:66: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotModel.Rd:67: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotModel.Rd:68: Lost braces in \itemize; meant \describe ?
checkRd: (-1) plotModel.Rd:69: Lost braces in \itemize; meant \describe ?
* 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 is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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 ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 5 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/CellNOptR.Rcheck/00check.log’
for details.

Installation output

CellNOptR.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘CellNOptR’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
using SDK: ‘MacOSX11.3.sdk’
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c simulatorT1.c -o simulatorT1.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include   -I./include  -fPIC  -falign-functions=64 -Wall -g -O2  -c simulatorTN.c -o simulatorTN.o
clang -arch arm64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o CellNOptR.so simulatorT1.o simulatorTN.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/00LOCK-CellNOptR/00new/CellNOptR/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (CellNOptR)

Tests output

CellNOptR.Rcheck/tests/test_gaBinaryT1.Rout


R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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, aperm, 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, saveRDS, setdiff, table,
    tapply, union, unique, unsplit, which.max, which.min

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
Loading required package: rmarkdown
> 
> # 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 
  3.197   0.241   3.439

CellNOptR.Rcheck/tests/test_gaBinaryT2.Rout


R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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, aperm, 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, saveRDS, setdiff, table,
    tapply, union, unique, unsplit, which.max, which.min

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
Loading required package: rmarkdown
> 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 
  3.660   0.249   3.919

CellNOptR.Rcheck/tests/test_gaBinaryT3.Rout


R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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, aperm, 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, saveRDS, setdiff, table,
    tapply, union, unique, unsplit, which.max, which.min

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
Loading required package: rmarkdown
> 
> 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 
  4.408   0.272   4.701

CellNOptR.Rcheck/tests/test_import_rules.Rout


R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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, aperm, 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, saveRDS, setdiff, table,
    tapply, union, unique, unsplit, which.max, which.min

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
Loading required package: rmarkdown
> 
> # test readBND ------------------------------------------------------------------
> 
> required_pcks = list("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("./data/example.bnd")
+ 	#model = readBND("https://maboss.curie.fr/pub/example1.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: tidyr
Loading required namespace: readr
Loading required package: dplyr

Attaching package: 'dplyr'

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
> 
> 
> 
> proc.time()
   user  system elapsed 
  2.797   0.242   3.049

CellNOptR.Rcheck/tests/test_manySteadyStates.Rout


R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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, aperm, 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, saveRDS, setdiff, table,
    tapply, union, unique, unsplit, which.max, which.min

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
Loading required package: rmarkdown
> 
> # 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 
  4.931   0.222   5.326

CellNOptR.Rcheck/tests/test_priorBitString.Rout


R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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, aperm, 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, saveRDS, setdiff, table,
    tapply, union, unique, unsplit, which.max, which.min

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
Loading required package: rmarkdown
> 
> 
> # 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 
  2.369   0.206   2.571

CellNOptR.Rcheck/tests/test_simulateTN.Rout


R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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, aperm, 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, saveRDS, setdiff, table,
    tapply, union, unique, unsplit, which.max, which.min

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
Loading required package: rmarkdown
> 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 
  2.989   0.243   3.234

Example timings

CellNOptR.Rcheck/CellNOptR-Ex.timings

name	user	system	elapsed
CNORbool	0.842	0.042	0.886
CNORwrap	0.549	0.055	0.611
CNOdata	0.000	0.000	0.001
CNOlist-class	0.069	0.007	0.076
CNOlist-methods	0.051	0.004	0.054
CellNOptR-package	2.125	0.082	2.253
buildBitString	0.000	0.001	0.000
build_sif_table_from_rule	1.513	0.019	1.537
checkSignals	0.004	0.002	0.005
compressModel	0.005	0.002	0.007
computeScoreT1	0.012	0.001	0.013
computeScoreTN	0.022	0.002	0.024
crossInhibitedData	0.004	0.001	0.005
crossvalidateBoolean	2.955	0.593	3.576
cutAndPlot	0.167	0.008	0.175
cutAndPlotResultsT1	0.197	0.008	0.204
cutAndPlotResultsTN	0.285	0.008	0.295
cutCNOlist	0.005	0.002	0.007
cutModel	0.002	0.001	0.003
cutNONC	0.006	0.001	0.008
defaultParameters	0.003	0.001	0.004
exhaustive	0.460	0.009	0.472
expandGates	0.027	0.001	0.029
findNONC	0.008	0.002	0.010
gaBinaryT1	0.173	0.003	0.176
gaBinaryTN	0.120	0.002	0.124
getFit	0.007	0.001	0.008
graph2sif	0.018	0.002	0.021
ilpBinaryT1	0.238	0.008	0.247
ilpBinaryT2	0.205	0.007	0.214
ilpBinaryTN	0.222	0.007	0.232
indexFinder	0.006	0.002	0.010
makeCNOlist	0.013	0.002	0.015
model2igraph	0.079	0.004	0.084
model2sif	0.002	0.002	0.004
normaliseCNOlist	0.024	0.001	0.025
plot-methods	0.069	0.004	0.074
plotCNOlist	0.054	0.004	0.057
plotCNOlist2	2.470	0.018	2.496
plotCNOlistLarge	0.165	0.007	0.176
plotCNOlistLargePDF	0.149	0.007	0.160
plotCNOlistPDF	0.056	0.004	0.062
plotFit	0.056	0.003	0.059
plotModel	0.282	0.007	0.291
plotOptimResults	0.095	0.005	0.100
plotOptimResultsPDF	0.415	0.008	0.425
plotOptimResultsPan	0.146	0.011	0.158
prep4sim	0.003	0.001	0.004
preprocessing	0.008	0.002	0.011
randomizeCNOlist	0.002	0.001	0.003
readBND	0	0	0
readMIDAS	0.014	0.003	0.017
readSBMLQual	0	0	0
readSIF	0.005	0.002	0.006
residualError	0.003	0.000	0.004
sif2graph	0.012	0.002	0.014
simulateT1	0.008	0.002	0.011
simulateTN	0.005	0.001	0.007
simulatorT0	0.006	0.002	0.007
simulatorT1	0.007	0.004	0.022
simulatorT2	0.003	0.001	0.004
simulatorTN	0.006	0.002	0.008
toSBML	0.008	0.006	0.014
writeDot	0.037	0.016	0.053
writeMIDAS	0.011	0.006	0.017
writeNetwork	0.036	0.015	0.052
writeReport	0.033	0.010	0.042
writeSIF	0.004	0.002	0.007
writeScaffold	0.029	0.013	0.043