A.Gabor
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/CellNOptR |
| Branch: RELEASE_3_11 |
| Last Commit: bc86474 |
| Last Changed Date: 2020-04-27 14:27:42 -0400 (Mon, 27 Apr 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:54:32 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE CellNOptR PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 253/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| CellNOptR 1.34.0 A.Gabor
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | [ WARNINGS ] | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | |
| Package: CellNOptR |
| Version: 1.34.0 |
| Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:CellNOptR.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings CellNOptR_1.34.0.tar.gz |
| StartedAt: 2020-10-16 23:39:51 -0400 (Fri, 16 Oct 2020) |
| EndedAt: 2020-10-16 23:42:23 -0400 (Fri, 16 Oct 2020) |
| EllapsedTime: 151.4 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: CellNOptR.Rcheck |
| Warnings: 5 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:CellNOptR.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings CellNOptR_1.34.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/CellNOptR.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CellNOptR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CellNOptR’ version ‘1.34.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
'RBGL', 'graph', 'hash', 'RCurl', 'Rgraphviz', 'XML', 'ggplot2'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘CellNOptR’ can be installed ... WARNING
Found the following significant warnings:
simulatorT1.c:502:20: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
See ‘/home/biocbuild/bbs-3.11-bioc/meat/CellNOptR.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... WARNING
'::' or ':::' imports not declared from:
‘foreach’ ‘plyr’
'loadNamespace' or 'requireNamespace' call not declared from: ‘plyr’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
build_sif_table_from_rule : rename_gates: no visible global function
definition for ‘mutate_if’
build_sif_table_from_rule : rename_gates: no visible global function
definition for ‘mutate’
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 global function
definition for ‘mutate’
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 global
function definition for ‘mutate_if’
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 ‘mutate’
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 global
function definition for ‘unnest’
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 ‘distinct’
build_sif_table_from_rule : interpret_sif_list: no visible global
function definition for ‘group_by’
build_sif_table_from_rule : interpret_sif_list: no visible global
function definition for ‘summarise’
build_sif_table_from_rule : interpret_sif_list: no visible global
function definition for ‘select’
build_sif_table_from_rule : interpret_sif_list: no visible binding for
global variable ‘or_members’
build_sif_table_from_rule : interpret_sif_list: no visible global
function definition for ‘ungroup’
build_sif_table_from_rule : write_sif: no visible global function
definition for ‘mutate’
build_sif_table_from_rule : write_sif: no visible binding for global
variable ‘node_in’
build_sif_table_from_rule : write_sif: no visible binding for global
variable ‘node_out’
build_sif_table_from_rule : write_sif: no visible binding for global
variable ‘sign1’
build_sif_table_from_rule : write_sif: no visible binding for global
variable ‘sign2’
crossvalidateBoolean: no visible global function definition for ‘error’
crossvalidateBoolean: no visible global function definition for
‘%dopar%’
readBND: no visible global function definition for ‘read_file’
readBNET: no visible global function definition for ‘rowwise’
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 global function definition for ‘do’
readBNET: no visible binding for global variable ‘.’
readBNET: no visible global function definition for ‘unnest’
readBNET: no visible global function definition for ‘ungroup’
Undefined global functions or variables:
%dopar% . distinct do error factors filter group_by i_and_gates
mutate mutate_if new_node_in new_node_out node_in node_out num_or
or_members read_file rowwise select setNames sign1 sign2 summarise
ungroup unnest
Consider adding
importFrom("stats", "filter", "setNames")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented data sets:
‘cnodata’ ‘pknmodel’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'normaliseCNOlist':
normaliseCNOlist
Code: function(CNOlist, EC50Data = 0.5, HillCoef = 2, EC50Noise = 0,
detection = 0, saturation = Inf, changeTh = 0,
norm2TorCtrl = NULL, mode = "time", options =
list(rescale_negative = TRUE), verbose = FALSE)
Docs: function(CNOlist, EC50Data = 0.5, HillCoef = 2, EC50Noise = 0,
detection = 0, saturation = Inf, changeTh = 0,
norm2TorCtrl = NULL, mode = "time", options =
list(rescale_negative = T), verbose = FALSE)
Mismatches in argument default values:
Name: 'options' Code: list(rescale_negative = TRUE) Docs: list(rescale_negative = T)
* checking Rd \usage sections ... WARNING
Bad \usage lines found in documentation object 'createAndRunILP':
createAndRunILP <- function(model = model,
midas = midas,
cnolist = cnolist,
accountForModelSize = accountForModelSize,
sizeFac = sizeFac,
source_path = source_path,
mipGap = mipGap,
relGap = relGap,
timelimit = timelimit,
cplexPath = cplexPath,
method = method,
numSolutions = numSolutions,
limitPop = limitPop,
poolIntensity = poolIntensity,
poolReplace = poolReplace)
Bad \usage lines found in documentation object 'createILPBitstringAll':
createILPBitstringAll<- function(cplexSolutionFileName,
y_vector,
binary_variables)
Bad \usage lines found in documentation object 'create_binaries':
create_binaries <- function(model,
midas,
numberOfExperiments,
y_vector)
Bad \usage lines found in documentation object 'crossvalidateBoolean':
crossvalidateBoolean = function(CNOlist,model,nfolds=10,foldid=NULL,
type=c('datapoint','experiment','observable'),timeIndex = 2,parallel=FALSE, ...)
Bad \usage lines found in documentation object 'ilpBinaryT1':
ilpBinaryT1 <- function(cnolist,
model,
sizeFac = 0.0001,
mipGap = 0,
relGap = 0,
timelimit = 3600,
cplexPath,
method = "quadratic",
numSolutions = 100,
limitPop = 500,
poolIntensity = 4,
poolReplace = 2)
Bad \usage lines found in documentation object 'ilpBinaryT2':
ilpBinaryT2 <- function(cnolist,
model,
sizeFac = 0.0001,
mipGap = 0,
relGap = 0,
timelimit = 3600,
cplexPath,
method = "quadratic",
numSolutions = 100,
limitPop = 500,
poolIntensity = 4,
poolReplace = 2)
Bad \usage lines found in documentation object 'ilpBinaryTN':
ilpBinaryTN <- function(cnolist,
model,
sizeFac = 0.0001,
mipGap = 0,
relGap = 0,
timelimit = 3600,
cplexPath,
method = "quadratic",
numSolutions = 100,
limitPop = 500,
poolIntensity = 0,
poolReplace = 2,
timeIndices = c(1, 2))
Bad \usage lines found in documentation object 'invokeCPLEX':
invokeCPLEX <- function(inputFileName,
outputFileName,
mipGap=mipGap,
relGap = relGap,
timelimit=timelimit,
cplexPath = cplexPath,
numSolutions = numSolutions,
limitPop = limitPop,
poolIntensity = poolIntensity,
poolReplace = poolReplace)
Bad \usage lines found in documentation object 'writeFile':
writeFile <- function(objectiveFunction,
constraints,
bounds,
binaries,
cplexPath)
Bad \usage lines found in documentation object 'writeObjectiveFunction':
writeObjectiveFunction <- function(model,
midasExperimentPart,
y_vector=y_vector,
accountForModelSize = TRUE,
sizeFac = .000001,
meansOfMeasurements_at_t0,
method = "quadratic" )
Bad \usage lines found in documentation object 'write_bounds':
write_bounds <- function(model,
midasTreatmentPart,
y_vector,
binary_variables)
Bad \usage lines found in documentation object 'write_constraints':
write_constraints <- function(model,
midasExperimentPart,
midasTreatmentPart,
reaction_sets,
y_vector,
midas,
binary_variables)
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
crossvalidateBoolean 5.425 0.148 5.582
* 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: 5 WARNINGs, 3 NOTEs
See
‘/home/biocbuild/bbs-3.11-bioc/meat/CellNOptR.Rcheck/00check.log’
for details.
CellNOptR.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL CellNOptR
###
##############################################################################
##############################################################################
* installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’
* installing *source* package ‘CellNOptR’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -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;
^~~~~~~~
gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -c simulatorT1.c -o simulatorT1.o
simulatorT1.c: In function ‘simulatorT1’:
simulatorT1.c:502:20: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
if (MA[i][j]<0.95 & MA[i][j]>0.05) // actually we could check if they are exatly 0 or 1
~~~~~~~~^~~~~
gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -c simulatorTN.c -o simulatorTN.o
gcc -shared -L/home/biocbuild/bbs-3.11-bioc/R/lib -L/usr/local/lib -o CellNOptR.so getFit.o simulatorT1.o simulatorTN.o -L/home/biocbuild/bbs-3.11-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.11-bioc/R/library/00LOCK-CellNOptR/00new/CellNOptR/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (CellNOptR)
CellNOptR.Rcheck/tests/test_gaBinaryT1.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> #
> # This file is part of the CNO software
> #
> # Copyright (c) 2011-2012 - EBI
> #
> # File author(s): CNO developers (cno-dev@ebi.ac.uk)
> #
> # Distributed under the GPLv2 License.
> # See accompanying file LICENSE.txt or copy at
> # http://www.gnu.org/licenses/gpl-2.0.html
> #
> # CNO website: http://www.ebi.ac.uk/saezrodriguez/cno
> #
> ##############################################################################
> # $Id$
>
> # This is a test of the ToyModel and gaBinaryT1
> library(CellNOptR)
Loading required package: RBGL
Loading required package: graph
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, 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, 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
4.586 0.129 4.699
CellNOptR.Rcheck/tests/test_gaBinaryT2.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> #
> # This file is part of the CNO software
> #
> # Copyright (c) 2011-2012 - EBI
> #
> # File author(s): CNO developers (cno-dev@ebi.ac.uk)
> #
> # Distributed under the GPLv2 License.
> # See accompanying file LICENSE.txt or copy at
> # http://www.gnu.org/licenses/gpl-2.0.html
> #
> # CNO website: http://www.ebi.ac.uk/saezrodriguez/cno
> #
> ##############################################################################
> # $Id$
>
> # This is a test of the ToyModel and gaBinaryT1
> #
>
> library(CellNOptR)
Loading required package: RBGL
Loading required package: graph
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, 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, 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
7.333 0.161 7.530
CellNOptR.Rcheck/tests/test_gaBinaryT3.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> #
> # This file is part of the CNO software
> #
> # Copyright (c) 2011-2012 - EBI
> #
> # File author(s): CNO developers (cno-dev@ebi.ac.uk)
> #
> # Distributed under the GPLv2 License.
> # See accompanying file LICENSE.txt or copy at
> # http://www.gnu.org/licenses/gpl-2.0.html
> #
> # CNO website: http://www.ebi.ac.uk/saezrodriguez/cno
> #
> ##############################################################################
> # $Id$
>
> # This is a test of the ToyModel and gaBinaryT1
> #
>
> library(CellNOptR)
Loading required package: RBGL
Loading required package: graph
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, 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, 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
8.154 0.133 8.569
CellNOptR.Rcheck/tests/test_import_rules.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, 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, 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("plyr","dplyr","tidyr","readr")
>
> if(!all(unlist(lapply(required_pcks,requireNamespace)))){
+ print("the following packages need to be installed to use readBND:")
+ print(unlist(required_pcks))
+ print("Please, install the packages manually for this feature.")
+
+ }else{
+ #download.file("https://maboss.curie.fr/pub/example.bnd",destfile = "./tests/example.bnd")
+ #model = readBND("./tests/example.bnd")
+ model = readBND("https://maboss.curie.fr/pub/example.bnd")
+
+ # basic checks for being a CellNoptR model:
+ stopifnot(is.list(model))
+ stopifnot(length(model)==4)
+ stopifnot(all(names(model) %in% c("reacID","namesSpecies","interMat","notMat")))
+ stopifnot(length(model$reacID)==ncol(model$interMat))
+ stopifnot(length(model$reacID)==ncol(model$notMat))
+ stopifnot(length(model$namesSpecies)==nrow(model$interMat))
+ stopifnot(length(model$namesSpecies)==nrow(model$notMat))
+
+ #plotModel(model)
+
+
+
+ }
Loading required namespace: plyr
Loading required namespace: tidyr
Loading required namespace: readr
Loading required package: plyr
Attaching package: 'plyr'
The following object is masked from 'package:graph':
join
Loading required package: dplyr
Attaching package: 'dplyr'
The following objects are masked from 'package:plyr':
arrange, count, desc, failwith, id, mutate, rename, summarise,
summarize
The following object is masked from 'package:graph':
union
The following objects are masked from 'package:BiocGenerics':
combine, intersect, setdiff, union
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
Loading required package: tidyr
Attaching package: 'tidyr'
The following object is masked from 'package:RCurl':
complete
Loading required package: readr
Warning messages:
1: In readBND("https://maboss.curie.fr/pub/example.bnd") :
experimental BND reader. Use with care (July 2018).
2: In readBNET(fh) :
experimental BNET reader. Use with care (February 2018).
3: `cols` is now required when using unnest().
Please use `cols = c(sif_df)`
>
>
>
> proc.time()
user system elapsed
3.806 0.150 4.562
CellNOptR.Rcheck/tests/test_manySteadyStates.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> #
> # This file is part of the CNO software
> #
> # Copyright (c) 2011-2012 - EBI
> #
> # File author(s): CNO developers (cno-dev@ebi.ac.uk)
> #
> # Distributed under the GPLv2 License.
> # See accompanying file LICENSE.txt or copy at
> # http://www.gnu.org/licenses/gpl-2.0.html
> #
> # CNO website: http://www.ebi.ac.uk/saezrodriguez/software.html
> #
> ##############################################################################
> # $Id$
>
> # This test runs optimisation using Boolean logic at different time points
> # Author: S.Schrier, T.Cokelaer
>
>
>
> manySteadyStates <-function(
+ CNOlist,
+ model,
+ sizeFac=0.0001,
+ NAFac=1,
+ popSize=50,
+ pMutation=0.5,
+ maxTime=60,
+ maxGens=500,
+ stallGenMax=100,
+ selPress=1.2,
+ elitism=5,
+ relTol=0.1,
+ verbose=FALSE,
+ priorBitString=NULL){
+
+
+ #initialize Opt array
+ Opt<-list()
+ #initialze a bString array
+ bStrings<-list()
+ simRes<-list()
+
+
+ T1opt<-gaBinaryT1(CNOlist=CNOlist,
+ model=model,
+ stallGenMax=stallGenMax,
+ sizeFac=sizeFac,
+ NAFac=NAFac,
+ popSize=popSize,
+ pMutation=pMutation,
+ maxTime=maxTime,
+ maxGens=maxGens,
+ selPress=selPress,
+ elitism=elitism,
+ relTol=relTol,
+ verbose=verbose,
+ priorBitString=priorBitString)
+
+ Opt[[1]]<-T1opt
+ simT1<-simulateTN(CNOlist=CNOlist, model=model, bStrings=list(T1opt$bString))
+ simRes[[1]]<-simT1
+ bStrings[[1]] = T1opt$bString
+
+ if (length(CNOlist@signals)>2){
+ for(i in 3:length(CNOlist@signals)){
+ Opt[[i-1]]<-gaBinaryTN(CNOlist=CNOlist,
+ model=model,
+ bStrings=bStrings,
+ stallGenMax=stallGenMax,
+ maxTime=maxTime,
+ sizeFac=sizeFac,
+ NAFac=NAFac,
+ popSize=popSize,
+ pMutation=pMutation,
+ maxGens=maxGens,
+ selPress=selPress,
+ elitism=elitism,
+ relTol=relTol,
+ verbose=verbose,
+ priorBitString=priorBitString)
+
+ bStrings[[i-1]] = Opt[[i-1]]$bString
+
+ simRes[[i]]<-simulateTN(CNOlist,model,bStrings)
+ }
+ }
+ return(list(bStrings=bStrings, Opt=Opt, simRes=simRes))
+ }
>
>
>
> library(CellNOptR)
Loading required package: RBGL
Loading required package: graph
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which, which.max, which.min
Loading required package: hash
hash-2.2.6.1 provided by Decision Patterns
Loading required package: RCurl
Loading required package: Rgraphviz
Loading required package: grid
Loading required package: XML
Attaching package: 'XML'
The following object is masked from 'package:graph':
addNode
Loading required package: ggplot2
>
> # one steady state
> data(CNOlistToy, package="CellNOptR")
> cnolist = CNOlist(CNOlistToy)
> data(ToyModel, package="CellNOptR")
> results = manySteadyStates(cnolist, ToyModel)
> print(results$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
11.763 0.143 11.950
CellNOptR.Rcheck/tests/test_priorBitString.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> #
> # This file is part of the CNO software
> #
> # Copyright (c) 2011-2012 - EBI
> #
> # File author(s): CNO developers (cno-dev@ebi.ac.uk)
> #
> # Distributed under the GPLv2 License.
> # See accompanying file LICENSE.txt or copy at
> # http://www.gnu.org/licenses/gpl-2.0.html
> #
> # CNO website: http://www.ebi.ac.uk/saezrodriguez/software.html
> #
> ##############################################################################
> # $Id$
> # test if the priorBitString is used correctly in gaBinaryT1DO NOT MODIFY please (TC, June 2012)
>
> library(CellNOptR)
Loading required package: RBGL
Loading required package: graph
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, 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, 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
1.860 0.092 2.000
CellNOptR.Rcheck/tests/test_simulateTN.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> #
> # This file is part of the CNO software
> #
> # Copyright (c) 2011-2012 - EBI
> #
> # File author(s): CNO developers (cno-dev@ebi.ac.uk)
> #
> # Distributed under the GPLv2 License.
> # See accompanying file LICENSE.txt or copy at
> # http://www.gnu.org/licenses/gpl-2.0.html
> #
> # CNO website: http://www.ebi.ac.uk/saezrodriguez/software.html
> #
> ##############################################################################
> # $Id$
> # This test runs T3 data set to compute the scores (must be zero), and run
> # cutAndPlot plot on each time points.
>
> # DO NOT MODIFY please (TC, June 2012)
>
> library(CellNOptR)
Loading required package: RBGL
Loading required package: graph
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, 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, 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
2.568 0.126 2.703
CellNOptR.Rcheck/CellNOptR-Ex.timings
| name | user | system | elapsed | |
| CNORbool | 2.258 | 0.004 | 2.274 | |
| CNORwrap | 1.118 | 0.020 | 1.153 | |
| CNOdata | 0 | 0 | 0 | |
| CNOlist-class | 0.142 | 0.001 | 0.142 | |
| CNOlist-methods | 0.106 | 0.000 | 0.106 | |
| CellNOptR-package | 4.728 | 0.007 | 4.736 | |
| buildBitString | 0.001 | 0.000 | 0.000 | |
| build_sif_table_from_rule | 2.426 | 0.008 | 2.434 | |
| checkSignals | 0.006 | 0.000 | 0.006 | |
| compressModel | 0.007 | 0.000 | 0.008 | |
| computeScoreT1 | 0.017 | 0.003 | 0.021 | |
| computeScoreTN | 0.038 | 0.000 | 0.038 | |
| crossInhibitedData | 0.006 | 0.000 | 0.005 | |
| crossvalidateBoolean | 5.425 | 0.148 | 5.582 | |
| cutAndPlot | 0.334 | 0.008 | 0.342 | |
| cutAndPlotResultsT1 | 0.413 | 0.004 | 0.417 | |
| cutAndPlotResultsTN | 0.598 | 0.004 | 0.602 | |
| cutNONC | 0.01 | 0.00 | 0.01 | |
| defaultParameters | 0.005 | 0.000 | 0.005 | |
| exhaustive | 0.502 | 0.008 | 0.510 | |
| expandGates | 0.011 | 0.000 | 0.011 | |
| findNONC | 0.006 | 0.000 | 0.006 | |
| gaBinaryT1 | 0.285 | 0.000 | 0.285 | |
| gaBinaryT2 | 0.141 | 0.000 | 0.141 | |
| gaBinaryTN | 0.155 | 0.000 | 0.155 | |
| getFit | 0.007 | 0.000 | 0.007 | |
| ilpBinaryT1 | 0.214 | 0.000 | 0.214 | |
| ilpBinaryT2 | 0.208 | 0.000 | 0.208 | |
| ilpBinaryTN | 0.172 | 0.000 | 0.172 | |
| indexFinder | 0.003 | 0.000 | 0.003 | |
| makeCNOlist | 0.022 | 0.000 | 0.023 | |
| normaliseCNOlist | 0.005 | 0.000 | 0.005 | |
| plot-methods | 0.070 | 0.008 | 0.079 | |
| plotCNOlist | 0.079 | 0.000 | 0.080 | |
| plotCNOlist2 | 2.067 | 0.020 | 2.088 | |
| plotCNOlistLarge | 0.165 | 0.000 | 0.165 | |
| plotCNOlistLargePDF | 0.172 | 0.000 | 0.172 | |
| plotCNOlistPDF | 0.069 | 0.000 | 0.068 | |
| plotFit | 0.059 | 0.000 | 0.058 | |
| plotModel | 0.541 | 0.000 | 0.542 | |
| plotOptimResults | 0.153 | 0.000 | 0.153 | |
| plotOptimResultsPDF | 0.135 | 0.000 | 0.136 | |
| plotOptimResultsPan | 0.310 | 0.000 | 0.309 | |
| prep4sim | 0.003 | 0.000 | 0.004 | |
| preprocessing | 0.011 | 0.000 | 0.010 | |
| randomizeCNOlist | 0.002 | 0.000 | 0.002 | |
| readMIDAS | 0.018 | 0.004 | 0.022 | |
| readSBMLQual | 0.001 | 0.000 | 0.000 | |
| readSIF | 0.005 | 0.000 | 0.006 | |
| residualError | 0.004 | 0.000 | 0.003 | |
| simulateT1 | 0.012 | 0.000 | 0.011 | |
| simulateTN | 0.009 | 0.000 | 0.009 | |
| simulatorT0 | 0.005 | 0.004 | 0.009 | |
| simulatorT1 | 0.009 | 0.000 | 0.009 | |
| simulatorT2 | 0.014 | 0.000 | 0.013 | |
| simulatorTN | 0.007 | 0.000 | 0.008 | |
| writeDot | 0.053 | 0.008 | 0.061 | |
| writeMIDAS | 0.019 | 0.000 | 0.018 | |
| writeNetwork | 0.059 | 0.004 | 0.063 | |
| writeReport | 0.030 | 0.004 | 0.035 | |
| writeSIF | 0.007 | 0.000 | 0.007 | |
| writeScaffold | 0.057 | 0.000 | 0.056 | |