T.Cokelaer
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/CellNOptR |
| Branch: RELEASE_3_6 |
| Last Commit: a29bc89 |
| Last Changed Date: 2017-11-07 02:30:12 -0400 (Tue, 07 Nov 2017) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:21:22 -0400 (Thu, 12 Apr 2018).
| Package 196/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| CellNOptR 1.24.1 T.Cokelaer
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: CellNOptR |
| Version: 1.24.1 |
| Command: rm -rf CellNOptR.buildbin-libdir CellNOptR.Rcheck && mkdir CellNOptR.buildbin-libdir CellNOptR.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CellNOptR.buildbin-libdir CellNOptR_1.24.1.tar.gz >CellNOptR.Rcheck\00install.out 2>&1 && cp CellNOptR.Rcheck\00install.out CellNOptR-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=CellNOptR.buildbin-libdir --install="check:CellNOptR-install.out" --force-multiarch --no-vignettes --timings CellNOptR_1.24.1.tar.gz |
| StartedAt: 2018-04-11 22:46:09 -0400 (Wed, 11 Apr 2018) |
| EndedAt: 2018-04-11 22:49:37 -0400 (Wed, 11 Apr 2018) |
| EllapsedTime: 208.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: CellNOptR.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### rm -rf CellNOptR.buildbin-libdir CellNOptR.Rcheck && mkdir CellNOptR.buildbin-libdir CellNOptR.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CellNOptR.buildbin-libdir CellNOptR_1.24.1.tar.gz >CellNOptR.Rcheck\00install.out 2>&1 && cp CellNOptR.Rcheck\00install.out CellNOptR-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=CellNOptR.buildbin-libdir --install="check:CellNOptR-install.out" --force-multiarch --no-vignettes --timings CellNOptR_1.24.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/CellNOptR.Rcheck'
* using R version 3.4.4 (2018-03-15)
* 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 '1.24.1'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
'RBGL' 'graph' 'hash' 'ggplot2' 'RCurl' 'Rgraphviz' 'XML'
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
Malformed Title field: should not end in a period.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' calls to packages already attached by Depends:
'RBGL' 'RCurl' 'Rgraphviz' 'XML' 'hash'
Please remove these calls from your code.
'library' or 'require' call to 'igraph' in package code.
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
'RCurl' 'Rgraphviz' 'XML' 'ggplot2' 'hash' 'methods'
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'
CNOdata: no visible global function definition for 'getURL'
CNOlist: no visible global function definition for 'new'
createEdgeAttrs: no visible global function definition for 'rgb'
expandGates: no visible global function definition for 'combn'
findNONC : modeltoGraphNEL: no visible global function definition for
'new'
gaBinaryT1: no visible global function definition for 'runif'
gaBinaryT1: no visible global function definition for 'hash'
gaBinaryT1 : getObj: no visible global function definition for
'has.key'
gaBinaryT2: no visible global function definition for 'runif'
gaBinaryT2: no visible global function definition for 'hash'
gaBinaryT2 : getObj: no visible global function definition for
'has.key'
gaBinaryTN: no visible global function definition for 'runif'
gaBinaryTN: no visible global function definition for 'hash'
gaBinaryTN : getObj: no visible global function definition for
'has.key'
graph2sif: no visible global function definition for 'write.table'
makeCNOlist: no visible binding for global variable 'var'
mapBack : SearchPath: no visible binding for global variable 'tail'
mapBack: no visible global function definition for 'write.table'
model2igraph: no visible global function definition for
'igraph.from.graphNEL'
plotCNOlist: no visible global function definition for 'par'
plotCNOlist: no visible global function definition for 'text'
plotCNOlist: no visible global function definition for 'lines'
plotCNOlist: no visible global function definition for 'axis'
plotCNOlist: no visible global function definition for 'image'
plotCNOlist2: no visible global function definition for 'ggplot'
plotCNOlist2: no visible global function definition for 'aes'
plotCNOlist2: no visible binding for global variable 'values'
plotCNOlist2: no visible global function definition for 'geom_point'
plotCNOlist2: no visible global function definition for 'geom_line'
plotCNOlist2: no visible global function definition for 'xlab'
plotCNOlist2: no visible global function definition for 'ylab'
plotCNOlist2: no visible global function definition for 'facet_grid'
plotCNOlist2: no visible global function definition for 'theme_bw'
plotCNOlist2: no visible global function definition for 'theme'
plotCNOlist2: no visible global function definition for 'element_text'
plotCNOlist2: no visible global function definition for 'element_rect'
plotCNOlist2: no visible global function definition for 'ylim'
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 'lines'
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 'new'
plotModel: no visible global function definition for
'installed.packages'
plotModel: no visible global function definition for 'layoutGraph'
plotModel: no visible global function definition for 'renderGraph'
plotModel: no visible global function definition for 'toDot'
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 'lines'
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 'lines'
plotOptimResultsPan: no visible global function definition for 'points'
plotOptimResultsPan: no visible global function definition for 'axis'
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'
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 'xmlTreeParse'
readSBMLQual: no visible global function definition for 'xmlRoot'
readSBMLQual: no visible global function definition for 'xmlChildren'
readSBMLQual: no visible global function definition for 'xmlApply'
readSBMLQual : <anonymous>: no visible global function definition for
'xmlGetAttr'
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'
sif2graph: no visible global function definition for 'new'
writeDot : modeltoGraphNEL: no visible global function definition for
'new'
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:
aes arrows axis close.screen combn count.fields dev.new dev.off
element_rect element_text facet_grid geom_line geom_point getURL
ggplot has.key hash heat.colors igraph.from.graphNEL image
installed.packages layoutGraph lines new par pdf plot.new png points
read.csv read.table rect renderGraph rgb rnorm runif screen segments
split.screen svg tail text theme theme_bw toDot values var
write.table xlab xmlApply xmlChildren xmlGetAttr xmlRoot xmlTreeParse
ylab ylim
Consider adding
importFrom("grDevices", "dev.new", "dev.off", "heat.colors", "pdf",
"png", "rgb", "svg")
importFrom("graphics", "arrows", "axis", "close.screen", "image",
"lines", "par", "plot.new", "points", "rect", "screen",
"segments", "split.screen", "text")
importFrom("methods", "new")
importFrom("stats", "rnorm", "runif", "var")
importFrom("utils", "combn", "count.fields", "installed.packages",
"read.csv", "read.table", "tail", "write.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.6-bioc/meat/CellNOptR.buildbin-libdir/CellNOptR/libs/i386/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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'test_gaBinaryT1.R'
Running 'test_gaBinaryT2.R'
Running 'test_gaBinaryT3.R'
Running 'test_manySteadyStates.R'
Running 'test_priorBitString.R'
Running 'test_simulateTN.R'
OK
** running tests for arch 'x64' ...
Running 'test_gaBinaryT1.R'
Running 'test_gaBinaryT2.R'
Running 'test_gaBinaryT3.R'
Running 'test_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: 5 NOTEs
See
'C:/Users/biocbuild/bbs-3.6-bioc/meat/CellNOptR.Rcheck/00check.log'
for details.
CellNOptR.Rcheck/00install.out
install for i386
* installing *source* package 'CellNOptR' ...
** libs
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -I./include -O3 -Wall -std=gnu99 -mtune=generic -c getFit.c -o getFit.o
getFit.c: In function 'getFit':
getFit.c:47:6: warning: unused variable 'nReacs' [-Wunused-variable]
int nReacs = INTEGER(nReacs_in)[0];
^
getFit.c:42:6: warning: unused variable 'selCounter' [-Wunused-variable]
int selCounter = 0;
^
getFit.c:41:6: warning: unused variable 'selection' [-Wunused-variable]
int selection[40];
^
getFit.c:40:6: warning: unused variable 'or_max' [-Wunused-variable]
int or_max = 0;
^
getFit.c:39:6: warning: unused variable 'curr_max' [-Wunused-variable]
int curr_max = 0;
^
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -I./include -O3 -Wall -std=gnu99 -mtune=generic -c simulatorT1.c -o simulatorT1.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -I./include -O3 -Wall -std=gnu99 -mtune=generic -c simulatorTN.c -o simulatorTN.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o CellNOptR.dll tmp.def getFit.o simulatorT1.o simulatorTN.o -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/CellNOptR.buildbin-libdir/CellNOptR/libs/i386
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
converting help for package 'CellNOptR'
finding HTML links ... done
CNORbool html
CNORwrap html
CNOdata html
CNOlist-class html
CNOlist-methods html
CNOlistDREAM html
CNOlistToy html
CNOlistToy2 html
CNOlistToyMMB html
CellNOptR-package html
DreamModel html
ToyModel html
ToyModel2 html
buildBitString html
cSimulator html
checkSignals html
compressModel html
computeScoreT1 html
computeScoreTN 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
indexFinder html
internals html
makeCNOlist html
mapBack html
model2igraph html
model2sif html
normaliseCNOlist 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
preprocessing html
randomizeCNOlist html
readMIDAS html
readSBMLQual html
readSIF html
residualError html
sif2graph html
simulateT1 html
simulateTN html
simulatorT0 html
simulatorT1 html
simulatorT2 html
simulatorTN html
writeDot html
writeMIDAS html
writeNetwork html
writeReport html
writeSIF html
writeScaffold html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'CellNOptR' ...
** libs
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -I./include -O2 -Wall -std=gnu99 -mtune=generic -c getFit.c -o getFit.o
getFit.c: In function 'getFit':
getFit.c:47:6: warning: unused variable 'nReacs' [-Wunused-variable]
int nReacs = INTEGER(nReacs_in)[0];
^
getFit.c:42:6: warning: unused variable 'selCounter' [-Wunused-variable]
int selCounter = 0;
^
getFit.c:41:6: warning: unused variable 'selection' [-Wunused-variable]
int selection[40];
^
getFit.c:40:6: warning: unused variable 'or_max' [-Wunused-variable]
int or_max = 0;
^
getFit.c:39:6: warning: unused variable 'curr_max' [-Wunused-variable]
int curr_max = 0;
^
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -I./include -O2 -Wall -std=gnu99 -mtune=generic -c simulatorT1.c -o simulatorT1.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -I./include -O2 -Wall -std=gnu99 -mtune=generic -c simulatorTN.c -o simulatorTN.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o CellNOptR.dll tmp.def getFit.o simulatorT1.o simulatorTN.o -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/CellNOptR.buildbin-libdir/CellNOptR/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CellNOptR' as CellNOptR_1.24.1.zip
* DONE (CellNOptR)
In R CMD INSTALL
In R CMD INSTALL
|
CellNOptR.Rcheck/tests_i386/test_gaBinaryT1.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> #
> # This file is part of the CNO software
> #
> # Copyright (c) 2011-2012 - EBI
> #
> # File author(s): CNO developers (cno-dev@ebi.ac.uk)
> #
> # Distributed under the GPLv2 License.
> # See accompanying file LICENSE.txt or copy at
> # http://www.gnu.org/licenses/gpl-2.0.html
> #
> # CNO website: http://www.ebi.ac.uk/saezrodriguez/cno
> #
> ##############################################################################
> # $Id$
>
> # This is a test of the ToyModel and gaBinaryT1
> library(CellNOptR)
Loading required package: RBGL
Loading required package: graph
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colMeans, colSums, colnames, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unsplit, which,
which.max, which.min
Loading required package: hash
hash-2.2.6 provided by Decision Patterns
Loading required package: ggplot2
Loading required package: RCurl
Loading required package: bitops
Loading required package: Rgraphviz
Loading required package: grid
Loading required package: XML
Attaching package: 'XML'
The following object is masked from 'package:graph':
addNode
>
> # 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
3.20 0.03 3.21
|
CellNOptR.Rcheck/tests_x64/test_gaBinaryT1.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> #
> # This file is part of the CNO software
> #
> # Copyright (c) 2011-2012 - EBI
> #
> # File author(s): CNO developers (cno-dev@ebi.ac.uk)
> #
> # Distributed under the GPLv2 License.
> # See accompanying file LICENSE.txt or copy at
> # http://www.gnu.org/licenses/gpl-2.0.html
> #
> # CNO website: http://www.ebi.ac.uk/saezrodriguez/cno
> #
> ##############################################################################
> # $Id$
>
> # This is a test of the ToyModel and gaBinaryT1
> library(CellNOptR)
Loading required package: RBGL
Loading required package: graph
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colMeans, colSums, colnames, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unsplit, which,
which.max, which.min
Loading required package: hash
hash-2.2.6 provided by Decision Patterns
Loading required package: ggplot2
Loading required package: RCurl
Loading required package: bitops
Loading required package: Rgraphviz
Loading required package: grid
Loading required package: XML
Attaching package: 'XML'
The following object is masked from 'package:graph':
addNode
>
> # 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
3.92 0.10 4.01
|
|
CellNOptR.Rcheck/tests_i386/test_gaBinaryT2.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> #
> # This file is part of the CNO software
> #
> # Copyright (c) 2011-2012 - EBI
> #
> # File author(s): CNO developers (cno-dev@ebi.ac.uk)
> #
> # Distributed under the GPLv2 License.
> # See accompanying file LICENSE.txt or copy at
> # http://www.gnu.org/licenses/gpl-2.0.html
> #
> # CNO website: http://www.ebi.ac.uk/saezrodriguez/cno
> #
> ##############################################################################
> # $Id$
>
> # This is a test of the ToyModel and gaBinaryT1
> #
>
> library(CellNOptR)
Loading required package: RBGL
Loading required package: graph
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colMeans, colSums, colnames, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unsplit, which,
which.max, which.min
Loading required package: hash
hash-2.2.6 provided by Decision Patterns
Loading required package: ggplot2
Loading required package: RCurl
Loading required package: bitops
Loading required package: Rgraphviz
Loading required package: grid
Loading required package: XML
Attaching package: 'XML'
The following object is masked from 'package:graph':
addNode
> data(CNOlistToy2, package="CellNOptR")
> data(ToyModel2, package="CellNOptR")
> cnolist = CNOlistToy2
> pknmodel = ToyModel2
>
> model = preprocessing(cnolist, pknmodel, verbose=FALSE)
> T1opt<-gaBinaryT1(CNOlist=cnolist,model=model,verbose=FALSE)
> print(T1opt$bString)
[1] 1 1 1 1 1 0 1 1 0 0 1 1 1 1 0 0 0 0
>
> truebs = c(1, 1, 1, 1, 1, 0, 1, 1, 0, 0, 1, 1, 1, 1, 0, 0, 0, 0)
>
>
> T2opt<-gaBinaryTN(CNOlist=cnolist,model=model,bStrings=list(truebs),verbose=FALSE)
> truebs2 = c(0, 0, 0, 1, 0, 0, 0)
>
> print(T2opt$bString)
[1] 0 0 0 1 0 0 0
>
> proc.time()
user system elapsed
4.15 0.09 4.23
|
CellNOptR.Rcheck/tests_x64/test_gaBinaryT2.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> #
> # This file is part of the CNO software
> #
> # Copyright (c) 2011-2012 - EBI
> #
> # File author(s): CNO developers (cno-dev@ebi.ac.uk)
> #
> # Distributed under the GPLv2 License.
> # See accompanying file LICENSE.txt or copy at
> # http://www.gnu.org/licenses/gpl-2.0.html
> #
> # CNO website: http://www.ebi.ac.uk/saezrodriguez/cno
> #
> ##############################################################################
> # $Id$
>
> # This is a test of the ToyModel and gaBinaryT1
> #
>
> library(CellNOptR)
Loading required package: RBGL
Loading required package: graph
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colMeans, colSums, colnames, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unsplit, which,
which.max, which.min
Loading required package: hash
hash-2.2.6 provided by Decision Patterns
Loading required package: ggplot2
Loading required package: RCurl
Loading required package: bitops
Loading required package: Rgraphviz
Loading required package: grid
Loading required package: XML
Attaching package: 'XML'
The following object is masked from 'package:graph':
addNode
> data(CNOlistToy2, package="CellNOptR")
> data(ToyModel2, package="CellNOptR")
> cnolist = CNOlistToy2
> pknmodel = ToyModel2
>
> model = preprocessing(cnolist, pknmodel, verbose=FALSE)
> T1opt<-gaBinaryT1(CNOlist=cnolist,model=model,verbose=FALSE)
> print(T1opt$bString)
[1] 1 1 1 1 1 0 1 1 0 0 1 1 1 1 0 0 0 0
>
> truebs = c(1, 1, 1, 1, 1, 0, 1, 1, 0, 0, 1, 1, 1, 1, 0, 0, 0, 0)
>
>
> T2opt<-gaBinaryTN(CNOlist=cnolist,model=model,bStrings=list(truebs),verbose=FALSE)
> truebs2 = c(0, 0, 0, 1, 0, 0, 0)
>
> print(T2opt$bString)
[1] 0 0 0 1 0 0 0
>
> proc.time()
user system elapsed
5.17 0.12 5.28
|
|
CellNOptR.Rcheck/tests_i386/test_gaBinaryT3.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> #
> # This file is part of the CNO software
> #
> # Copyright (c) 2011-2012 - EBI
> #
> # File author(s): CNO developers (cno-dev@ebi.ac.uk)
> #
> # Distributed under the GPLv2 License.
> # See accompanying file LICENSE.txt or copy at
> # http://www.gnu.org/licenses/gpl-2.0.html
> #
> # CNO website: http://www.ebi.ac.uk/saezrodriguez/cno
> #
> ##############################################################################
> # $Id$
>
> # This is a test of the ToyModel and gaBinaryT1
> #
>
> library(CellNOptR)
Loading required package: RBGL
Loading required package: graph
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colMeans, colSums, colnames, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unsplit, which,
which.max, which.min
Loading required package: hash
hash-2.2.6 provided by Decision Patterns
Loading required package: ggplot2
Loading required package: RCurl
Loading required package: bitops
Loading required package: Rgraphviz
Loading required package: grid
Loading required package: XML
Attaching package: 'XML'
The following object is masked from 'package:graph':
addNode
>
> 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()
NULL
>
> proc.time()
user system elapsed
6.48 0.10 6.57
|
CellNOptR.Rcheck/tests_x64/test_gaBinaryT3.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> #
> # This file is part of the CNO software
> #
> # Copyright (c) 2011-2012 - EBI
> #
> # File author(s): CNO developers (cno-dev@ebi.ac.uk)
> #
> # Distributed under the GPLv2 License.
> # See accompanying file LICENSE.txt or copy at
> # http://www.gnu.org/licenses/gpl-2.0.html
> #
> # CNO website: http://www.ebi.ac.uk/saezrodriguez/cno
> #
> ##############################################################################
> # $Id$
>
> # This is a test of the ToyModel and gaBinaryT1
> #
>
> library(CellNOptR)
Loading required package: RBGL
Loading required package: graph
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colMeans, colSums, colnames, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unsplit, which,
which.max, which.min
Loading required package: hash
hash-2.2.6 provided by Decision Patterns
Loading required package: ggplot2
Loading required package: RCurl
Loading required package: bitops
Loading required package: Rgraphviz
Loading required package: grid
Loading required package: XML
Attaching package: 'XML'
The following object is masked from 'package:graph':
addNode
>
> 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()
NULL
>
> proc.time()
user system elapsed
8.29 0.07 8.36
|
|
CellNOptR.Rcheck/tests_i386/test_manySteadyStates.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> #
> # This file is part of the CNO software
> #
> # Copyright (c) 2011-2012 - EBI
> #
> # File author(s): CNO developers (cno-dev@ebi.ac.uk)
> #
> # Distributed under the GPLv2 License.
> # See accompanying file LICENSE.txt or copy at
> # http://www.gnu.org/licenses/gpl-2.0.html
> #
> # CNO website: http://www.ebi.ac.uk/saezrodriguez/software.html
> #
> ##############################################################################
> # $Id$
>
> # This test runs optimisation using Boolean logic at different time points
> # Author: S.Schrier, T.Cokelaer
>
>
>
> manySteadyStates <-function(
+ CNOlist,
+ model,
+ sizeFac=0.0001,
+ NAFac=1,
+ popSize=50,
+ pMutation=0.5,
+ maxTime=60,
+ maxGens=500,
+ stallGenMax=100,
+ selPress=1.2,
+ elitism=5,
+ relTol=0.1,
+ verbose=FALSE,
+ priorBitString=NULL){
+
+
+ #initialize Opt array
+ Opt<-list()
+ #initialze a bString array
+ bStrings<-list()
+ simRes<-list()
+
+
+ T1opt<-gaBinaryT1(CNOlist=CNOlist,
+ model=model,
+ stallGenMax=stallGenMax,
+ sizeFac=sizeFac,
+ NAFac=NAFac,
+ popSize=popSize,
+ pMutation=pMutation,
+ maxTime=maxTime,
+ maxGens=maxGens,
+ selPress=selPress,
+ elitism=elitism,
+ relTol=relTol,
+ verbose=verbose,
+ priorBitString=priorBitString)
+
+ Opt[[1]]<-T1opt
+ simT1<-simulateTN(CNOlist=CNOlist, model=model, bStrings=list(T1opt$bString))
+ simRes[[1]]<-simT1
+ bStrings[[1]] = T1opt$bString
+
+ if (length(CNOlist@signals)>2){
+ for(i in 3:length(CNOlist@signals)){
+ Opt[[i-1]]<-gaBinaryTN(CNOlist=CNOlist,
+ model=model,
+ bStrings=bStrings,
+ stallGenMax=stallGenMax,
+ maxTime=maxTime,
+ sizeFac=sizeFac,
+ NAFac=NAFac,
+ popSize=popSize,
+ pMutation=pMutation,
+ maxGens=maxGens,
+ selPress=selPress,
+ elitism=elitism,
+ relTol=relTol,
+ verbose=verbose,
+ priorBitString=priorBitString)
+
+ bStrings[[i-1]] = Opt[[i-1]]$bString
+
+ simRes[[i]]<-simulateTN(CNOlist,model,bStrings)
+ }
+ }
+ return(list(bStrings=bStrings, Opt=Opt, simRes=simRes))
+ }
>
>
>
> library(CellNOptR)
Loading required package: RBGL
Loading required package: graph
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colMeans, colSums, colnames, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unsplit, which,
which.max, which.min
Loading required package: hash
hash-2.2.6 provided by Decision Patterns
Loading required package: ggplot2
Loading required package: RCurl
Loading required package: bitops
Loading required package: Rgraphviz
Loading required package: grid
Loading required package: XML
Attaching package: 'XML'
The following object is masked from 'package:graph':
addNode
>
> # one steady state
> data(CNOlistToy, package="CellNOptR")
> cnolist = CNOlist(CNOlistToy)
> data(ToyModel, package="CellNOptR")
> results = manySteadyStates(cnolist, ToyModel)
> print(results$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
7.51 0.06 7.57
|
CellNOptR.Rcheck/tests_x64/test_manySteadyStates.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> #
> # This file is part of the CNO software
> #
> # Copyright (c) 2011-2012 - EBI
> #
> # File author(s): CNO developers (cno-dev@ebi.ac.uk)
> #
> # Distributed under the GPLv2 License.
> # See accompanying file LICENSE.txt or copy at
> # http://www.gnu.org/licenses/gpl-2.0.html
> #
> # CNO website: http://www.ebi.ac.uk/saezrodriguez/software.html
> #
> ##############################################################################
> # $Id$
>
> # This test runs optimisation using Boolean logic at different time points
> # Author: S.Schrier, T.Cokelaer
>
>
>
> manySteadyStates <-function(
+ CNOlist,
+ model,
+ sizeFac=0.0001,
+ NAFac=1,
+ popSize=50,
+ pMutation=0.5,
+ maxTime=60,
+ maxGens=500,
+ stallGenMax=100,
+ selPress=1.2,
+ elitism=5,
+ relTol=0.1,
+ verbose=FALSE,
+ priorBitString=NULL){
+
+
+ #initialize Opt array
+ Opt<-list()
+ #initialze a bString array
+ bStrings<-list()
+ simRes<-list()
+
+
+ T1opt<-gaBinaryT1(CNOlist=CNOlist,
+ model=model,
+ stallGenMax=stallGenMax,
+ sizeFac=sizeFac,
+ NAFac=NAFac,
+ popSize=popSize,
+ pMutation=pMutation,
+ maxTime=maxTime,
+ maxGens=maxGens,
+ selPress=selPress,
+ elitism=elitism,
+ relTol=relTol,
+ verbose=verbose,
+ priorBitString=priorBitString)
+
+ Opt[[1]]<-T1opt
+ simT1<-simulateTN(CNOlist=CNOlist, model=model, bStrings=list(T1opt$bString))
+ simRes[[1]]<-simT1
+ bStrings[[1]] = T1opt$bString
+
+ if (length(CNOlist@signals)>2){
+ for(i in 3:length(CNOlist@signals)){
+ Opt[[i-1]]<-gaBinaryTN(CNOlist=CNOlist,
+ model=model,
+ bStrings=bStrings,
+ stallGenMax=stallGenMax,
+ maxTime=maxTime,
+ sizeFac=sizeFac,
+ NAFac=NAFac,
+ popSize=popSize,
+ pMutation=pMutation,
+ maxGens=maxGens,
+ selPress=selPress,
+ elitism=elitism,
+ relTol=relTol,
+ verbose=verbose,
+ priorBitString=priorBitString)
+
+ bStrings[[i-1]] = Opt[[i-1]]$bString
+
+ simRes[[i]]<-simulateTN(CNOlist,model,bStrings)
+ }
+ }
+ return(list(bStrings=bStrings, Opt=Opt, simRes=simRes))
+ }
>
>
>
> library(CellNOptR)
Loading required package: RBGL
Loading required package: graph
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colMeans, colSums, colnames, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unsplit, which,
which.max, which.min
Loading required package: hash
hash-2.2.6 provided by Decision Patterns
Loading required package: ggplot2
Loading required package: RCurl
Loading required package: bitops
Loading required package: Rgraphviz
Loading required package: grid
Loading required package: XML
Attaching package: 'XML'
The following object is masked from 'package:graph':
addNode
>
> # one steady state
> data(CNOlistToy, package="CellNOptR")
> cnolist = CNOlist(CNOlistToy)
> data(ToyModel, package="CellNOptR")
> results = manySteadyStates(cnolist, ToyModel)
> print(results$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
10.64 0.14 10.76
|
|
CellNOptR.Rcheck/tests_i386/test_priorBitString.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> #
> # This file is part of the CNO software
> #
> # Copyright (c) 2011-2012 - EBI
> #
> # File author(s): CNO developers (cno-dev@ebi.ac.uk)
> #
> # Distributed under the GPLv2 License.
> # See accompanying file LICENSE.txt or copy at
> # http://www.gnu.org/licenses/gpl-2.0.html
> #
> # CNO website: http://www.ebi.ac.uk/saezrodriguez/software.html
> #
> ##############################################################################
> # $Id$
> # test if the priorBitString is used correctly in gaBinaryT1DO NOT MODIFY please (TC, June 2012)
>
> library(CellNOptR)
Loading required package: RBGL
Loading required package: graph
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colMeans, colSums, colnames, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unsplit, which,
which.max, which.min
Loading required package: hash
hash-2.2.6 provided by Decision Patterns
Loading required package: ggplot2
Loading required package: RCurl
Loading required package: bitops
Loading required package: Rgraphviz
Loading required package: grid
Loading required package: XML
Attaching package: 'XML'
The following object is masked from 'package:graph':
addNode
>
>
> # 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
1.60 0.04 1.64
|
CellNOptR.Rcheck/tests_x64/test_priorBitString.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> #
> # This file is part of the CNO software
> #
> # Copyright (c) 2011-2012 - EBI
> #
> # File author(s): CNO developers (cno-dev@ebi.ac.uk)
> #
> # Distributed under the GPLv2 License.
> # See accompanying file LICENSE.txt or copy at
> # http://www.gnu.org/licenses/gpl-2.0.html
> #
> # CNO website: http://www.ebi.ac.uk/saezrodriguez/software.html
> #
> ##############################################################################
> # $Id$
> # test if the priorBitString is used correctly in gaBinaryT1DO NOT MODIFY please (TC, June 2012)
>
> library(CellNOptR)
Loading required package: RBGL
Loading required package: graph
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colMeans, colSums, colnames, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unsplit, which,
which.max, which.min
Loading required package: hash
hash-2.2.6 provided by Decision Patterns
Loading required package: ggplot2
Loading required package: RCurl
Loading required package: bitops
Loading required package: Rgraphviz
Loading required package: grid
Loading required package: XML
Attaching package: 'XML'
The following object is masked from 'package:graph':
addNode
>
>
> # 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
2.34 0.03 2.37
|
|
CellNOptR.Rcheck/tests_i386/test_simulateTN.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> #
> # This file is part of the CNO software
> #
> # Copyright (c) 2011-2012 - EBI
> #
> # File author(s): CNO developers (cno-dev@ebi.ac.uk)
> #
> # Distributed under the GPLv2 License.
> # See accompanying file LICENSE.txt or copy at
> # http://www.gnu.org/licenses/gpl-2.0.html
> #
> # CNO website: http://www.ebi.ac.uk/saezrodriguez/software.html
> #
> ##############################################################################
> # $Id$
> # This test runs T3 data set to compute the scores (must be zero), and run
> # cutAndPlot plot on each time points.
>
> # DO NOT MODIFY please (TC, June 2012)
>
> library(CellNOptR)
Loading required package: RBGL
Loading required package: graph
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colMeans, colSums, colnames, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unsplit, which,
which.max, which.min
Loading required package: hash
hash-2.2.6 provided by Decision Patterns
Loading required package: ggplot2
Loading required package: RCurl
Loading required package: bitops
Loading required package: Rgraphviz
Loading required package: grid
Loading required package: XML
Attaching package: 'XML'
The following object is masked from 'package:graph':
addNode
> 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
2.50 0.20 2.68
|
CellNOptR.Rcheck/tests_x64/test_simulateTN.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> #
> # This file is part of the CNO software
> #
> # Copyright (c) 2011-2012 - EBI
> #
> # File author(s): CNO developers (cno-dev@ebi.ac.uk)
> #
> # Distributed under the GPLv2 License.
> # See accompanying file LICENSE.txt or copy at
> # http://www.gnu.org/licenses/gpl-2.0.html
> #
> # CNO website: http://www.ebi.ac.uk/saezrodriguez/software.html
> #
> ##############################################################################
> # $Id$
> # This test runs T3 data set to compute the scores (must be zero), and run
> # cutAndPlot plot on each time points.
>
> # DO NOT MODIFY please (TC, June 2012)
>
> library(CellNOptR)
Loading required package: RBGL
Loading required package: graph
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colMeans, colSums, colnames, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unsplit, which,
which.max, which.min
Loading required package: hash
hash-2.2.6 provided by Decision Patterns
Loading required package: ggplot2
Loading required package: RCurl
Loading required package: bitops
Loading required package: Rgraphviz
Loading required package: grid
Loading required package: XML
Attaching package: 'XML'
The following object is masked from 'package:graph':
addNode
> 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
2.90 0.07 2.98
|
|
CellNOptR.Rcheck/examples_i386/CellNOptR-Ex.timings
|
CellNOptR.Rcheck/examples_x64/CellNOptR-Ex.timings
|