Attila Gabor
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/CellNOptR |
| git_branch: master |
| git_last_commit: 35bd6c8 |
| git_last_commit_date: 2022-03-16 05:38:12 -0400 (Wed, 16 Mar 2022) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:07:08 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| 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 | ||||
|
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? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 270/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| CellNOptR 1.41.1 (landing page) Attila Gabor
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | WARNINGS | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: CellNOptR |
| Version: 1.41.1 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:CellNOptR.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings CellNOptR_1.41.1.tar.gz |
| StartedAt: 2022-03-17 18:40:22 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 18:42:35 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 133.7 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: CellNOptR.Rcheck |
| Warnings: 1 |
##############################################################################
##############################################################################
###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:CellNOptR.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings CellNOptR_1.41.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/CellNOptR.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* 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 '1.41.1'
* 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 ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
'methods'
A package should be listed in only one of these fields.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... 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'
gaBinaryT2: 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 ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'plotOptimResultsPan':
plotOptimResultsPan
Code: function(simResults, yInterpol = NULL, xCoords = NULL, CNOlist
= CNOlist, formalism = c("ss1", "ss2", "ssN", "dt",
"ode"), pdf = FALSE, pdfFileName = "", tPt = NULL,
plotParams = list(margin = 0.1, width = 15, height =
12, cmap_scale = 1, cex = 1.6, ymin = NULL, Fac = 1,
rotation = 0))
Docs: function(simResults, yInterpol = NULL, xCoords = NULL, CNOlist
= CNOlist, formalism = c("ss1", "ss2", "ssN", "dt",
"ode"), pdf = FALSE, pdfFileName = "", tPt = NULL,
plotParams = list(margin = 0.1, width = 15, height =
12, cmap_scale = 1, cex = 1.6, ymin = NULL, F = 1,
rotation = 0))
Mismatches in argument default values:
Name: 'plotParams'
Code: list(margin = 0.1, width = 15, height = 12, cmap_scale = 1, cex = 1.6,
ymin = NULL, Fac = 1, rotation = 0)
Docs: list(margin = 0.1, width = 15, height = 12, cmap_scale = 1, cex = 1.6,
ymin = NULL, F = 1, rotation = 0)
* 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 x64 is not available
File 'D:/biocbuild/bbs-3.15-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 ... 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 in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING, 4 NOTEs
See
'D:/biocbuild/bbs-3.15-bioc/meat/CellNOptR.Rcheck/00check.log'
for details.
CellNOptR.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL CellNOptR
###
##############################################################################
##############################################################################
* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'CellNOptR' ...
** using staged installation
** libs
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c simulatorT1.c -o simulatorT1.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I"C:/extsoft/include" -I./include -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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 -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
installing to D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-CellNOptR/00new/CellNOptR/libs/x64
** 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
REDIRECT:topic Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-CellNOptR/00new/CellNOptR/help/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: D:/biocbuild/bbs-3.15-bioc/R/library/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: D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-CellNOptR/00new/CellNOptR/help/readMidas.html
readSBMLQual html
readSIF html
REDIRECT:topic Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.15-bioc/R/library/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: D:/biocbuild/bbs-3.15-bioc/R/library/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
* DONE (CellNOptR)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
DESCRIPTION file of package 'BioMM' is missing or broken
done
CellNOptR.Rcheck/tests/test_gaBinaryT1.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 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-2.2.6.1 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
3.23 0.21 3.42
CellNOptR.Rcheck/tests/test_gaBinaryT2.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 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-2.2.6.1 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
3.68 0.23 3.89
CellNOptR.Rcheck/tests/test_gaBinaryT3.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 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-2.2.6.1 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
4.40 0.28 4.67
CellNOptR.Rcheck/tests/test_import_rules.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 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-2.2.6.1 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("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: 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
2.85 0.25 3.54
CellNOptR.Rcheck/tests/test_manySteadyStates.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 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]]$bString
+
+ simRes[[i]]<-simulateTN(CNOlist,model,bStrings)
+ }
+ }
+ return(list(bStrings=bStrings, Opt=Opt, simRes=simRes))
+ }
>
>
>
> library(CellNOptR)
Loading required package: RBGL
Loading required package: graph
Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Loading required package: hash
hash-2.2.6.1 provided by Decision Patterns
Loading required package: RCurl
Loading required package: Rgraphviz
Loading required package: grid
Loading required package: XML
Attaching package: 'XML'
The following object is masked from 'package:graph':
addNode
Loading required package: ggplot2
>
> # one steady state
> data(CNOlistToy, package="CellNOptR")
> cnolist = CNOlist(CNOlistToy)
> data(ToyModel, package="CellNOptR")
> results = manySteadyStates(cnolist, ToyModel)
> print(results$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
7.73 0.40 8.10
CellNOptR.Rcheck/tests/test_priorBitString.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 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-2.2.6.1 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
1.59 0.25 1.82
CellNOptR.Rcheck/tests/test_simulateTN.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 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.
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> #
> # 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-2.2.6.1 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
2.79 0.17 2.95
CellNOptR.Rcheck/CellNOptR-Ex.timings
| name | user | system | elapsed | |
| CNORbool | 1.74 | 0.02 | 1.75 | |
| CNORwrap | 0.78 | 0.06 | 0.85 | |
| CNOdata | 0 | 0 | 0 | |
| CNOlist-class | 0.07 | 0.00 | 0.07 | |
| CNOlist-methods | 0.09 | 0.00 | 0.09 | |
| CellNOptR-package | 3.19 | 0.03 | 3.25 | |
| buildBitString | 0 | 0 | 0 | |
| build_sif_table_from_rule | 4.04 | 0.02 | 4.06 | |
| checkSignals | 0 | 0 | 0 | |
| compressModel | 0.02 | 0.00 | 0.01 | |
| computeScoreT1 | 0.01 | 0.00 | 0.02 | |
| computeScoreTN | 0.02 | 0.00 | 0.02 | |
| crossInhibitedData | 0.00 | 0.01 | 0.01 | |
| crossvalidateBoolean | 3.45 | 0.94 | 4.52 | |
| cutAndPlot | 0.12 | 0.03 | 0.15 | |
| cutAndPlotResultsT1 | 0.18 | 0.00 | 0.17 | |
| cutAndPlotResultsTN | 0.23 | 0.00 | 0.24 | |
| cutNONC | 0 | 0 | 0 | |
| defaultParameters | 0.02 | 0.00 | 0.01 | |
| exhaustive | 0.29 | 0.00 | 0.30 | |
| expandGates | 0.02 | 0.00 | 0.02 | |
| findNONC | 0 | 0 | 0 | |
| gaBinaryT1 | 0.17 | 0.00 | 0.17 | |
| gaBinaryT2 | 0.09 | 0.00 | 0.09 | |
| gaBinaryTN | 0.1 | 0.0 | 0.1 | |
| getFit | 0.01 | 0.00 | 0.01 | |
| ilpBinaryT1 | 0.16 | 0.00 | 0.16 | |
| ilpBinaryT2 | 0.2 | 0.0 | 0.2 | |
| ilpBinaryTN | 0.18 | 0.02 | 0.20 | |
| indexFinder | 0 | 0 | 0 | |
| makeCNOlist | 0.03 | 0.00 | 0.04 | |
| normaliseCNOlist | 0 | 0 | 0 | |
| plot-methods | 0.06 | 0.01 | 0.07 | |
| plotCNOlist | 0.07 | 0.00 | 0.06 | |
| plotCNOlist2 | 1.99 | 0.00 | 1.98 | |
| plotCNOlistLarge | 0.17 | 0.00 | 0.30 | |
| plotCNOlistLargePDF | 0.16 | 0.00 | 1.00 | |
| plotCNOlistPDF | 0.04 | 0.00 | 0.31 | |
| plotFit | 0.06 | 0.00 | 0.06 | |
| plotModel | 0.46 | 0.00 | 0.46 | |
| plotOptimResults | 0.08 | 0.00 | 0.08 | |
| plotOptimResultsPDF | 0.06 | 0.02 | 0.07 | |
| plotOptimResultsPan | 0.19 | 0.00 | 0.19 | |
| prep4sim | 0 | 0 | 0 | |
| preprocessing | 0.01 | 0.00 | 0.02 | |
| randomizeCNOlist | 0 | 0 | 0 | |
| readMIDAS | 0.00 | 0.00 | 0.01 | |
| readSBMLQual | 0 | 0 | 0 | |
| readSIF | 0.02 | 0.00 | 0.02 | |
| residualError | 0 | 0 | 0 | |
| simulateT1 | 0.01 | 0.00 | 0.01 | |
| simulateTN | 0 | 0 | 0 | |
| simulatorT0 | 0.02 | 0.00 | 0.02 | |
| simulatorT1 | 0 | 0 | 0 | |
| simulatorT2 | 0 | 0 | 0 | |
| simulatorTN | 0 | 0 | 0 | |
| writeDot | 0.04 | 0.00 | 0.04 | |
| writeMIDAS | 0.00 | 0.00 | 0.01 | |
| writeNetwork | 0.03 | 0.02 | 0.05 | |
| writeReport | 0.01 | 0.00 | 0.01 | |
| writeSIF | 0.02 | 0.00 | 0.02 | |
| writeScaffold | 0.01 | 0.01 | 0.03 | |