Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:05:37 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the CellNOptR package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CellNOptR.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 266/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
CellNOptR 1.38.0 (landing page) A.Gabor
| nebbiolo1 | Linux (Ubuntu 20.04.2 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: 1.38.0 |
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:CellNOptR.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings CellNOptR_1.38.0.tar.gz |
StartedAt: 2021-10-14 09:11:54 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 09:13:44 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 110.4 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: CellNOptR.Rcheck |
Warnings: 5 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:CellNOptR.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings CellNOptR_1.38.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/CellNOptR.Rcheck’ * using R version 4.1.1 (2021-08-10) * 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 ‘1.38.0’ * 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-3.13-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 * 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-3.13-bioc/meat/CellNOptR.Rcheck/00check.log’ for details.
CellNOptR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL CellNOptR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’ * installing *source* package ‘CellNOptR’ ... ** using staged installation ** libs gcc -I"/home/biocbuild/bbs-3.13-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] 47 | int nReacs = INTEGER(nReacs_in)[0]; | ^~~~~~ getFit.c:42:6: warning: unused variable ‘selCounter’ [-Wunused-variable] 42 | int selCounter = 0; | ^~~~~~~~~~ getFit.c:41:6: warning: unused variable ‘selection’ [-Wunused-variable] 41 | int selection[40]; | ^~~~~~~~~ getFit.c:40:6: warning: unused variable ‘or_max’ [-Wunused-variable] 40 | int or_max = 0; | ^~~~~~ getFit.c:39:6: warning: unused variable ‘curr_max’ [-Wunused-variable] 39 | int curr_max = 0; | ^~~~~~~~ gcc -I"/home/biocbuild/bbs-3.13-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] 502 | 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-3.13-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-3.13-bioc/R/lib -L/usr/local/lib -o CellNOptR.so getFit.o simulatorT1.o simulatorTN.o -L/home/biocbuild/bbs-3.13-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.13-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 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 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.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 2.900 0.152 3.042
CellNOptR.Rcheck/tests/test_gaBinaryT2.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 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.max, which.min Loading required package: hash hash-2.2.6.1 provided by Decision Patterns Loading required package: RCurl Loading required package: Rgraphviz Loading required package: grid Loading required package: XML Attaching package: 'XML' The following object is masked from 'package:graph': addNode Loading required package: ggplot2 > data(CNOlistToy2, package="CellNOptR") > data(ToyModel2, package="CellNOptR") > cnolist = CNOlistToy2 > pknmodel = ToyModel2 > > model = preprocessing(cnolist, pknmodel, verbose=FALSE) > T1opt<-gaBinaryT1(CNOlist=cnolist,model=model,verbose=FALSE) > print(T1opt$bString) [1] 1 1 1 1 1 0 1 1 0 0 1 1 1 1 0 0 0 0 > > truebs = c(1, 1, 1, 1, 1, 0, 1, 1, 0, 0, 1, 1, 1, 1, 0, 0, 0, 0) > > > T2opt<-gaBinaryTN(CNOlist=cnolist,model=model,bStrings=list(truebs),verbose=FALSE) > truebs2 = c(0, 0, 0, 1, 0, 0, 0) > > print(T2opt$bString) [1] 0 0 0 1 0 0 0 > > proc.time() user system elapsed 3.761 0.143 3.894
CellNOptR.Rcheck/tests/test_gaBinaryT3.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 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.max, which.min Loading required package: hash hash-2.2.6.1 provided by Decision Patterns Loading required package: RCurl Loading required package: Rgraphviz Loading required package: grid Loading required package: XML Attaching package: 'XML' The following object is masked from 'package:graph': addNode Loading required package: ggplot2 > > pknmodel = readSIF(system.file("ToyModelT3/ToyModelT3.sif", package="CellNOptR")) > cnolist = CNOlist(system.file("ToyModelT3/ToyDataT3.csv", package="CellNOptR")) > model = preprocessing(cnolist, pknmodel, verbose=FALSE) > > # expected values > bestBS = c(1, 1, 1, 0, 1, 1, 1, 1, 0, 1, 1, 1, 0, 0, 0, 0,0) > bestBS2 <- c(0,0,0,0,0,0,1) > bestBS3 <- c(0,0,1,0,0,0) > > # just to check that the simulateTN function works > SimT1<-simulateTN(CNOlist=cnolist, model=model, bString=list(bestBS)) > SimT2<-simulateTN(CNOlist=cnolist, model=model, bStrings=list(bestBS,bestBS2)) > SimT3<-simulateTN(CNOlist=cnolist, model=model, bStrings=list(bestBS, bestBS2, bestBS3)) > > > # again, just to check that gaBinary works > # run T1 first, > T1opt<-gaBinaryT1(CNOlist=cnolist,model=model,verbose=FALSE) > # run T2 > T2opt<-gaBinaryTN(CNOlist=cnolist,model=model,bStrings=list(T1opt$bString),verbose=FALSE) > # run T3 > T3opt<-gaBinaryTN(CNOlist=cnolist,model=model,bStrings=list(bestBS, bestBS2),verbose=FALSE) > > print( T1opt$bScore) 4.545455e-05 > print( T2opt$bScore) [1] 5.454545e-05 > print( T3opt$bScore) [1] 6.363636e-05 > # no using the hardcoded parameters, we can check the output of te scores that > # must be tiny. > score1 = computeScoreT1(cnolist, model, bString=bestBS) > score2 = computeScoreTN(cnolist, model, bStrings=list(bestBS,bestBS2)) > score3 = computeScoreTN(cnolist, model, bStrings=list(bestBS,bestBS2, bestBS3)) > > > print(score1) [1] 4.545455e-05 > print(score2) [1] 5.454545e-05 > print(score3) [1] 6.363636e-05 > if (score1>0.01 || score2>0.24 || score3>0.1){ + # ideally, the score should all be close to 0. In practice, it's about 1e-5 + # However, in the T3 case, once in while, the score is 0.0953 hence the + # score3>0.1 + stop("errore") + } > cutAndPlot(cnolist, model,bStrings=list(bestBS),plotPDF=TRUE, tag="test1") $filenames $filenames[[1]] [1] "test1_SimResultsT1_1_.pdf" $mse [,1] [,2] [,3] [,4] [,5] [,6] [1,] 0 0 0 0 0 0 [2,] 0 0 0 0 0 0 [3,] 0 0 0 0 0 0 [4,] 0 0 0 0 0 0 [5,] 0 0 0 0 0 0 [6,] 0 0 0 0 0 0 [7,] 0 0 0 0 0 0 $simResults $simResults[[1]] $simResults[[1]]$t0 [,1] [,2] [,3] [,4] [,5] [,6] [1,] 0 0 0 0 0 0 [2,] 0 0 0 0 0 0 [3,] 0 0 0 0 0 0 [4,] 0 0 0 0 0 0 [5,] 0 0 0 0 0 0 [6,] 0 0 0 0 0 0 [7,] 0 0 0 0 0 0 $simResults[[1]]$t1 [,1] [,2] [,3] [,4] [,5] [,6] [1,] 1 1 1 0 1 0 [2,] 1 1 1 1 1 1 [3,] 0 1 1 0 0 0 [4,] 1 0 0 0 1 0 [5,] 0 0 0 1 0 1 [6,] 1 0 0 1 1 1 [7,] 0 0 0 0 0 0 > cutAndPlot(cnolist, model,bStrings=list(bestBS,bestBS2),plotPDF=TRUE, tag="test2") $mse [,1] [,2] [,3] [,4] [,5] [,6] [1,] 0 0 0 0 0 0 [2,] 0 0 0 0 0 0 [3,] 0 0 0 0 0 0 [4,] 0 0 0 0 0 0 [5,] 0 0 0 0 0 0 [6,] 0 0 0 0 0 0 [7,] 0 0 0 0 0 0 $filenames list() $simResults $simResults[[1]] [,1] [,2] [,3] [,4] [,5] [,6] [1,] 0 0 0 0 0 0 [2,] 0 0 0 0 0 0 [3,] 0 0 0 0 0 0 [4,] 0 0 0 0 0 0 [5,] 0 0 0 0 0 0 [6,] 0 0 0 0 0 0 [7,] 0 0 0 0 0 0 $simResults[[2]] [,1] [,2] [,3] [,4] [,5] [,6] [1,] 1 1 1 0 1 0 [2,] 1 1 1 1 1 1 [3,] 0 1 1 0 0 0 [4,] 1 0 0 0 1 0 [5,] 0 0 0 1 0 1 [6,] 1 0 0 1 1 1 [7,] 0 0 0 0 0 0 $simResults[[3]] [,1] [,2] [,3] [,4] [,5] [,6] [1,] 1 1 1 0 1 0 [2,] 1 1 1 1 1 0 [3,] 0 1 1 0 0 0 [4,] 1 0 0 0 1 0 [5,] 0 0 0 1 0 0 [6,] 1 0 0 1 1 0 [7,] 0 0 0 0 0 0 > cutAndPlot(cnolist, model, bStrings=list(bestBS,bestBS2,bestBS3),plotPDF=TRUE, tag="test3") $mse [,1] [,2] [,3] [,4] [,5] [,6] [1,] 0 0 0 0 0 0 [2,] 0 0 0 0 0 0 [3,] 0 0 0 0 0 0 [4,] 0 0 0 0 0 0 [5,] 0 0 0 0 0 0 [6,] 0 0 0 0 0 0 [7,] 0 0 0 0 0 0 $filenames list() $simResults $simResults[[1]] [,1] [,2] [,3] [,4] [,5] [,6] [1,] 0 0 0 0 0 0 [2,] 0 0 0 0 0 0 [3,] 0 0 0 0 0 0 [4,] 0 0 0 0 0 0 [5,] 0 0 0 0 0 0 [6,] 0 0 0 0 0 0 [7,] 0 0 0 0 0 0 $simResults[[2]] [,1] [,2] [,3] [,4] [,5] [,6] [1,] 1 1 1 0 1 0 [2,] 1 1 1 1 1 1 [3,] 0 1 1 0 0 0 [4,] 1 0 0 0 1 0 [5,] 0 0 0 1 0 1 [6,] 1 0 0 1 1 1 [7,] 0 0 0 0 0 0 $simResults[[3]] [,1] [,2] [,3] [,4] [,5] [,6] [1,] 1 1 1 0 1 0 [2,] 1 1 1 1 1 0 [3,] 0 1 1 0 0 0 [4,] 1 0 0 0 1 0 [5,] 0 0 0 1 0 0 [6,] 1 0 0 1 1 0 [7,] 0 0 0 0 0 0 $simResults[[4]] [,1] [,2] [,3] [,4] [,5] [,6] [1,] 0 1 1 0 0 0 [2,] 0 0 0 1 0 1 [3,] 0 1 1 0 0 0 [4,] 0 0 0 0 0 0 [5,] 0 0 0 1 0 1 [6,] 0 0 0 1 0 1 [7,] 0 0 0 0 0 0 > > > > warnings() > > proc.time() user system elapsed 4.690 0.148 4.823
CellNOptR.Rcheck/tests/test_import_rules.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 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.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 2.313 0.103 3.649
CellNOptR.Rcheck/tests/test_manySteadyStates.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 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]]$bString + + simRes[[i]]<-simulateTN(CNOlist,model,bStrings) + } + } + return(list(bStrings=bStrings, Opt=Opt, simRes=simRes)) + } > > > > library(CellNOptR) Loading required package: RBGL Loading required package: graph Loading required package: BiocGenerics Loading required package: parallel Attaching package: 'BiocGenerics' The following objects are masked from 'package:parallel': clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: hash hash-2.2.6.1 provided by Decision Patterns Loading required package: RCurl Loading required package: Rgraphviz Loading required package: grid Loading required package: XML Attaching package: 'XML' The following object is masked from 'package:graph': addNode Loading required package: ggplot2 > > # one steady state > data(CNOlistToy, package="CellNOptR") > cnolist = CNOlist(CNOlistToy) > data(ToyModel, package="CellNOptR") > results = manySteadyStates(cnolist, ToyModel) > print(results$bStrings) [[1]] [1] 1 1 1 1 1 0 1 0 1 1 1 1 0 1 1 0 > > # two steady state > data(CNOlistToy2, package="CellNOptR") > cnolist = CNOlist(CNOlistToy2) > data(ToyModel2, package="CellNOptR") > results = manySteadyStates(cnolist, ToyModel2) > print(results$bStrings) [[1]] [1] 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 0 0 [[2]] [1] 0 0 1 > > # 3 steady state > ToyModel3 = readSIF(system.file("ToyModelT3/ToyModelT3.sif", package="CellNOptR")) > cnolist = CNOlist(system.file("ToyModelT3/ToyDataT3.csv", package="CellNOptR")) > results = manySteadyStates(cnolist, ToyModel3) > print(results$bStrings) [[1]] [1] 1 1 1 1 1 1 1 1 1 1 0 0 1 1 1 1 1 1 0 [[2]] [1] 0 0 0 [[3]] [1] 0 0 0 > > > > proc.time() user system elapsed 7.640 0.147 7.772
CellNOptR.Rcheck/tests/test_priorBitString.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 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.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 1.840 0.094 1.917
CellNOptR.Rcheck/tests/test_simulateTN.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 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.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 2.474 0.144 2.606
CellNOptR.Rcheck/CellNOptR-Ex.timings
name | user | system | elapsed | |
CNORbool | 1.433 | 0.012 | 1.445 | |
CNORwrap | 0.594 | 0.011 | 0.610 | |
CNOdata | 0.001 | 0.000 | 0.000 | |
CNOlist-class | 0.083 | 0.000 | 0.083 | |
CNOlist-methods | 0.057 | 0.000 | 0.058 | |
CellNOptR-package | 3.111 | 0.036 | 3.147 | |
buildBitString | 0.001 | 0.000 | 0.000 | |
build_sif_table_from_rule | 1.851 | 0.004 | 1.855 | |
checkSignals | 0.004 | 0.000 | 0.004 | |
compressModel | 0.005 | 0.000 | 0.005 | |
computeScoreT1 | 0.012 | 0.000 | 0.012 | |
computeScoreTN | 0.016 | 0.004 | 0.020 | |
crossInhibitedData | 0.000 | 0.004 | 0.004 | |
crossvalidateBoolean | 3.005 | 0.164 | 3.170 | |
cutAndPlot | 0.171 | 0.004 | 0.175 | |
cutAndPlotResultsT1 | 0.224 | 0.008 | 0.232 | |
cutAndPlotResultsTN | 0.301 | 0.016 | 0.317 | |
cutNONC | 0.006 | 0.000 | 0.006 | |
defaultParameters | 0.002 | 0.000 | 0.002 | |
exhaustive | 0.405 | 0.028 | 0.433 | |
expandGates | 0.005 | 0.007 | 0.013 | |
findNONC | 0.003 | 0.004 | 0.007 | |
gaBinaryT1 | 0.255 | 0.008 | 0.263 | |
gaBinaryT2 | 0.115 | 0.000 | 0.116 | |
gaBinaryTN | 0.113 | 0.008 | 0.121 | |
getFit | 0.007 | 0.000 | 0.006 | |
ilpBinaryT1 | 0.167 | 0.004 | 0.170 | |
ilpBinaryT2 | 0.167 | 0.000 | 0.166 | |
ilpBinaryTN | 0.167 | 0.008 | 0.176 | |
indexFinder | 0.004 | 0.000 | 0.003 | |
makeCNOlist | 0.013 | 0.000 | 0.013 | |
normaliseCNOlist | 0.006 | 0.000 | 0.005 | |
plot-methods | 0.07 | 0.00 | 0.07 | |
plotCNOlist | 0.068 | 0.000 | 0.068 | |
plotCNOlist2 | 1.748 | 0.024 | 1.773 | |
plotCNOlistLarge | 0.380 | 0.012 | 0.393 | |
plotCNOlistLargePDF | 0.145 | 0.008 | 0.153 | |
plotCNOlistPDF | 0.049 | 0.016 | 0.065 | |
plotFit | 0.045 | 0.000 | 0.046 | |
plotModel | 0.309 | 0.000 | 0.309 | |
plotOptimResults | 0.077 | 0.000 | 0.077 | |
plotOptimResultsPDF | 0.086 | 0.004 | 0.090 | |
plotOptimResultsPan | 0.141 | 0.004 | 0.145 | |
prep4sim | 0.002 | 0.000 | 0.002 | |
preprocessing | 0.006 | 0.000 | 0.006 | |
randomizeCNOlist | 0.001 | 0.000 | 0.001 | |
readMIDAS | 0.011 | 0.000 | 0.010 | |
readSBMLQual | 0 | 0 | 0 | |
readSIF | 0.001 | 0.002 | 0.003 | |
residualError | 0.002 | 0.000 | 0.002 | |
simulateT1 | 0.003 | 0.003 | 0.006 | |
simulateTN | 0.005 | 0.000 | 0.005 | |
simulatorT0 | 0.005 | 0.000 | 0.005 | |
simulatorT1 | 0.005 | 0.000 | 0.005 | |
simulatorT2 | 0.003 | 0.000 | 0.002 | |
simulatorTN | 0.005 | 0.000 | 0.005 | |
writeDot | 0.026 | 0.008 | 0.035 | |
writeMIDAS | 0.017 | 0.000 | 0.017 | |
writeNetwork | 0.031 | 0.008 | 0.039 | |
writeReport | 0.013 | 0.008 | 0.021 | |
writeSIF | 0.000 | 0.004 | 0.004 | |
writeScaffold | 0.026 | 0.012 | 0.038 | |