Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-08-21 11:40 -0400 (Wed, 21 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4703 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4440 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4472 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4421 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4414 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
Package 302/2255 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
CellNOptR 1.51.0 (landing page) Attila Gabor
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the CellNOptR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CellNOptR.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: CellNOptR |
Version: 1.51.0 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:CellNOptR.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings CellNOptR_1.51.0.tar.gz |
StartedAt: 2024-08-20 23:14:00 -0400 (Tue, 20 Aug 2024) |
EndedAt: 2024-08-20 23:16:42 -0400 (Tue, 20 Aug 2024) |
EllapsedTime: 162.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: CellNOptR.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:CellNOptR.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings CellNOptR_1.51.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/CellNOptR.Rcheck' * using R version 4.4.1 (2024-06-14 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'CellNOptR/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'CellNOptR' version '1.51.0' * checking package namespace information ... OK * checking package dependencies ... NOTE Depends: includes the non-default packages: 'RBGL', 'graph', 'RCurl', 'Rgraphviz', 'XML', 'ggplot2', 'rmarkdown' Adding so many packages to the search path is excessive and importing selectively is preferable. * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking whether package 'CellNOptR' can be installed ... OK * used C compiler: 'gcc.exe (GCC) 13.2.0' * checking installed package size ... OK * checking package directory ... OK * checking 'build' directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking dependencies in R code ... NOTE Package in Depends field not imported from: 'rmarkdown' These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE .error.bar: no visible global function definition for 'arrows' CNORwrap: no visible global function definition for 'pdf' CNORwrap: no visible global function definition for 'dev.off' build_sif_table_from_rule : rename_gates: no visible binding for global variable 'node_in' build_sif_table_from_rule : rename_gates: no visible binding for global variable 'node_out' build_sif_table_from_rule : simplify_gates: no visible global function definition for 'filter' build_sif_table_from_rule : simplify_gates: no visible binding for global variable 'node_in' build_sif_table_from_rule : simplify_gates: no visible binding for global variable 'node_out' build_sif_table_from_rule : interpret_sif_list: no visible global function definition for 'setNames' build_sif_table_from_rule : interpret_sif_list: no visible binding for global variable 'num_or' build_sif_table_from_rule : interpret_sif_list: no visible binding for global variable 'node_out' build_sif_table_from_rule : interpret_sif_list: no visible binding for global variable 'new_node_out' build_sif_table_from_rule : interpret_sif_list: no visible binding for global variable 'node_in' build_sif_table_from_rule : interpret_sif_list: no visible binding for global variable 'new_node_in' build_sif_table_from_rule : interpret_sif_list: no visible global function definition for 'filter' build_sif_table_from_rule : interpret_sif_list: no visible global function definition for 'distinct' build_sif_table_from_rule : interpret_sif_list: no visible binding for global variable 'or_members' build_sif_table_from_rule : write_sif: no visible binding for global variable 'node_in' build_sif_table_from_rule : write_sif: no visible binding for global variable 'node_out' build_sif_table_from_rule : write_sif: no visible binding for global variable 'sign1' build_sif_table_from_rule : write_sif: no visible binding for global variable 'sign2' createEdgeAttrs: no visible global function definition for 'rgb' crossvalidateBoolean: no visible global function definition for 'error' expandGates: no visible global function definition for 'combn' gaBinaryT1: no visible global function definition for 'runif' gaBinaryTN: no visible global function definition for 'runif' graph2sif: no visible global function definition for 'write.table' makeCNOlist: no visible binding for global variable 'var' mapBack: no visible global function definition for 'write.table' plotCNOlist: no visible global function definition for 'par' plotCNOlist: no visible global function definition for 'text' plotCNOlist: no visible global function definition for 'axis' plotCNOlist: no visible global function definition for 'barplot' plotCNOlistLarge: no visible global function definition for 'par' plotCNOlistLarge: no visible global function definition for 'dev.new' plotCNOlistLarge: no visible global function definition for 'text' plotCNOlistLarge: no visible global function definition for 'axis' plotCNOlistLarge: no visible global function definition for 'image' plotCNOlistLargePDF: no visible global function definition for 'pdf' plotCNOlistLargePDF: no visible global function definition for 'dev.off' plotCNOlistPDF: no visible global function definition for 'pdf' plotCNOlistPDF: no visible global function definition for 'dev.off' plotFit: no visible global function definition for 'par' plotFit: no visible global function definition for 'pdf' plotFit: no visible global function definition for 'dev.off' plotModel: no visible global function definition for 'pdf' plotModel: no visible global function definition for 'png' plotModel: no visible global function definition for 'svg' plotModel: no visible global function definition for 'read.table' plotModel: no visible global function definition for 'installed.packages' plotModel: no visible global function definition for 'dev.off' plotOptimResults: no visible global function definition for 'par' plotOptimResults: no visible global function definition for 'text' plotOptimResults: no visible global function definition for 'rect' plotOptimResults: no visible global function definition for 'points' plotOptimResults: no visible global function definition for 'axis' plotOptimResults: no visible global function definition for 'image' plotOptimResultsPDF: no visible global function definition for 'pdf' plotOptimResultsPDF: no visible global function definition for 'dev.off' plotOptimResultsPan: no visible global function definition for 'par' plotOptimResultsPan: no visible global function definition for 'split.screen' plotOptimResultsPan: no visible global function definition for 'heat.colors' plotOptimResultsPan: no visible global function definition for 'screen' plotOptimResultsPan: no visible global function definition for 'text' plotOptimResultsPan: no visible global function definition for 'rect' plotOptimResultsPan: no visible global function definition for 'points' plotOptimResultsPan: no visible global function definition for 'axis' plotOptimResultsPan: no visible global function definition for 'barplot' plotOptimResultsPan: no visible global function definition for 'image' plotOptimResultsPan: no visible global function definition for 'plot.new' plotOptimResultsPan: no visible global function definition for 'segments' plotOptimResultsPan: no visible global function definition for 'close.screen' plotOptimResultsPan: no visible global function definition for 'dev.off' randomizeCNOlist: no visible global function definition for 'rnorm' randomizeCNOlist: no visible global function definition for 'runif' readBND: no visible global function definition for 'write.table' readBNET: no visible global function definition for 'mutate' readBNET: no visible binding for global variable 'factors' readBNET: no visible binding for global variable 'i_and_gates' readBNET: no visible binding for global variable '.' readBNET: no visible binding for global variable 'sif_df' readBNET: no visible global function definition for 'write.table' readMIDAS: no visible global function definition for 'count.fields' readMIDAS: no visible global function definition for 'read.csv' readMIDAS: no visible global function definition for 'read.table' readSBMLQual: no visible global function definition for 'write.table' readSIF: no visible global function definition for 'read.table' sif2graph: no visible global function definition for 'read.table' writeMIDAS: no visible global function definition for 'write.table' writeNetworkW: no visible global function definition for 'write.table' writeSIF: no visible global function definition for 'write.table' writeScaffoldW: no visible global function definition for 'write.table' Undefined global functions or variables: . arrows axis barplot close.screen combn count.fields dev.new dev.off distinct error factors filter heat.colors i_and_gates image installed.packages mutate new_node_in new_node_out node_in node_out num_or or_members par pdf plot.new png points read.csv read.table rect rgb rnorm runif screen segments setNames sif_df sign1 sign2 split.screen svg text var write.table Consider adding importFrom("grDevices", "dev.new", "dev.off", "heat.colors", "pdf", "png", "rgb", "svg") importFrom("graphics", "arrows", "axis", "barplot", "close.screen", "image", "par", "plot.new", "points", "rect", "screen", "segments", "split.screen", "text") importFrom("stats", "filter", "rnorm", "runif", "setNames", "var") importFrom("utils", "combn", "count.fields", "installed.packages", "read.csv", "read.table", "write.table") to your NAMESPACE file. * checking Rd files ... NOTE checkRd: (-1) computeScoreT1.Rd:27: Lost braces 27 | a model structure, as created by code{readSIF}, normally pre-processed | ^ checkRd: (-1) computeScoreTN.Rd:26: Lost braces 26 | a model structure, as created by code{readSIF}, normally pre-processed | ^ checkRd: (-1) plotModel.Rd:59: Lost braces in \itemize; meant \describe ? checkRd: (-1) plotModel.Rd:60: Lost braces in \itemize; meant \describe ? checkRd: (-1) plotModel.Rd:61: Lost braces in \itemize; meant \describe ? checkRd: (-1) plotModel.Rd:62: Lost braces in \itemize; meant \describe ? checkRd: (-1) plotModel.Rd:63: Lost braces in \itemize; meant \describe ? checkRd: (-1) plotModel.Rd:64: Lost braces in \itemize; meant \describe ? checkRd: (-1) plotModel.Rd:65: Lost braces in \itemize; meant \describe ? checkRd: (-1) plotModel.Rd:66: Lost braces in \itemize; meant \describe ? checkRd: (-1) plotModel.Rd:67: Lost braces in \itemize; meant \describe ? checkRd: (-1) plotModel.Rd:68: Lost braces in \itemize; meant \describe ? checkRd: (-1) plotModel.Rd:69: Lost braces in \itemize; meant \describe ? * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of 'data' directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking compiled code ... NOTE Note: information on .o files for x64 is not available File 'F:/biocbuild/bbs-3.20-bioc/R/library/CellNOptR/libs/x64/CellNOptR.dll': Found '_exit', possibly from '_exit' (C) Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs nor [v]sprintf. The detected symbols are linked into the code but might come from libraries and not actually be called. See 'Writing portable packages' in the 'Writing R Extensions' manual. * checking files in 'vignettes' ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed crossvalidateBoolean 4.12 2.05 6.69 * checking for unstated dependencies in 'tests' ... OK * checking tests ... Running 'test_gaBinaryT1.R' Running 'test_gaBinaryT2.R' Running 'test_gaBinaryT3.R' Running 'test_import_rules.R' Running 'test_manySteadyStates.R' Running 'test_priorBitString.R' Running 'test_simulateTN.R' OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 5 NOTEs See 'F:/biocbuild/bbs-3.20-bioc/meat/CellNOptR.Rcheck/00check.log' for details.
CellNOptR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL CellNOptR ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'CellNOptR' ... ** using staged installation ** libs using C compiler: 'gcc.exe (GCC) 13.2.0' gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -I./include -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c simulatorT1.c -o simulatorT1.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -I./include -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c simulatorTN.c -o simulatorTN.o gcc -shared -s -static-libgcc -o CellNOptR.dll tmp.def simulatorT1.o simulatorTN.o -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.20-bioc/R/library/00LOCK-CellNOptR/00new/CellNOptR/libs/x64 ** 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 ** 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 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > # > # This file is part of the CNO software > # > # Copyright (c) 2011-2012 - EBI > # > # File author(s): CNO developers (cno-dev@ebi.ac.uk) > # > # Distributed under the GPLv2 License. > # See accompanying file LICENSE.txt or copy at > # http://www.gnu.org/licenses/gpl-2.0.html > # > # CNO website: http://www.ebi.ac.uk/saezrodriguez/cno > # > ############################################################################## > # $Id$ > > # This is a test of the ToyModel and gaBinaryT1 > library(CellNOptR) Loading required package: RBGL Loading required package: graph Loading required package: BiocGenerics Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: RCurl Loading required package: Rgraphviz Loading required package: grid Loading required package: XML Attaching package: 'XML' The following object is masked from 'package:graph': addNode Loading required package: ggplot2 Loading required package: rmarkdown > > # read data > pknmodel = readSIF(system.file("ToyModel/ToyPKNMMB.sif", package="CellNOptR")) > data = readMIDAS(system.file("ToyModel/ToyDataMMB.csv", package="CellNOptR")) [1] "Your data set comprises 18 conditions (i.e. combinations of time point and treatment)" [1] "Your data set comprises measurements on 7 different species" [1] "Your data set comprises 4 stimuli/inhibitors and 1 cell line(s) ( mock )" [1] "Please be aware that CNO only handles measurements on one cell line at this time." [1] "Your data file contained 'NaN'. We have assumed that these were missing values and replaced them by NAs." > cnolist = makeCNOlist(data, subfield=FALSE) [1] "Please be aware that if you only have some conditions at time zero (e.g.only inhibitor/no inhibitor), the measurements for these conditions will be copied across matching conditions at t=0" > > # preprocessing > model = preprocessing(cnolist, pknmodel, verbose=FALSE) > > # optimisation > T1opt<-gaBinaryT1(CNOlist=cnolist,model=model,verbose=FALSE) > > truebs =c(1, 1, 0, 1, 1, 0, 1, 1, 0, 0, 1, 1, 1, 0, 0, 0) > print(truebs) [1] 1 1 0 1 1 0 1 1 0 0 1 1 1 0 0 0 > print(T1opt$bString) [1] 1 1 0 1 1 0 1 1 0 0 1 1 1 0 0 0 > > # testing valid output > if (dist(rbind(T1opt$bString, truebs))>2){ + stop("something wrong going on") + } > > # extra call to simulateTN > SimT1<-simulateTN(CNOlist=cnolist,model=model, bStrings=list(truebs)) > > > proc.time() user system elapsed 3.03 0.32 3.37
CellNOptR.Rcheck/tests/test_gaBinaryT2.Rout
R version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > # > # This file is part of the CNO software > # > # Copyright (c) 2011-2012 - EBI > # > # File author(s): CNO developers (cno-dev@ebi.ac.uk) > # > # Distributed under the GPLv2 License. > # See accompanying file LICENSE.txt or copy at > # http://www.gnu.org/licenses/gpl-2.0.html > # > # CNO website: http://www.ebi.ac.uk/saezrodriguez/cno > # > ############################################################################## > # $Id$ > > # This is a test of the ToyModel and gaBinaryT1 > # > > library(CellNOptR) Loading required package: RBGL Loading required package: graph Loading required package: BiocGenerics Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: RCurl Loading required package: Rgraphviz Loading required package: grid Loading required package: XML Attaching package: 'XML' The following object is masked from 'package:graph': addNode Loading required package: ggplot2 Loading required package: rmarkdown > data(CNOlistToy2, package="CellNOptR") > data(ToyModel2, package="CellNOptR") > cnolist = CNOlistToy2 > pknmodel = ToyModel2 > > model = preprocessing(cnolist, pknmodel, verbose=FALSE) > T1opt<-gaBinaryT1(CNOlist=cnolist,model=model,verbose=FALSE) > print(T1opt$bString) [1] 1 1 1 1 1 0 1 1 0 0 1 1 1 1 0 0 0 0 > > truebs = c(1, 1, 1, 1, 1, 0, 1, 1, 0, 0, 1, 1, 1, 1, 0, 0, 0, 0) > > > T2opt<-gaBinaryTN(CNOlist=cnolist,model=model,bStrings=list(truebs),verbose=FALSE) > truebs2 = c(0, 0, 0, 1, 0, 0, 0) > > print(T2opt$bString) [1] 0 0 0 1 0 0 0 > > proc.time() user system elapsed 4.20 0.51 4.68
CellNOptR.Rcheck/tests/test_gaBinaryT3.Rout
R version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > # > # This file is part of the CNO software > # > # Copyright (c) 2011-2012 - EBI > # > # File author(s): CNO developers (cno-dev@ebi.ac.uk) > # > # Distributed under the GPLv2 License. > # See accompanying file LICENSE.txt or copy at > # http://www.gnu.org/licenses/gpl-2.0.html > # > # CNO website: http://www.ebi.ac.uk/saezrodriguez/cno > # > ############################################################################## > # $Id$ > > # This is a test of the ToyModel and gaBinaryT1 > # > > library(CellNOptR) Loading required package: RBGL Loading required package: graph Loading required package: BiocGenerics Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: RCurl Loading required package: Rgraphviz Loading required package: grid Loading required package: XML Attaching package: 'XML' The following object is masked from 'package:graph': addNode Loading required package: ggplot2 Loading required package: rmarkdown > > pknmodel = readSIF(system.file("ToyModelT3/ToyModelT3.sif", package="CellNOptR")) > cnolist = CNOlist(system.file("ToyModelT3/ToyDataT3.csv", package="CellNOptR")) > model = preprocessing(cnolist, pknmodel, verbose=FALSE) > > # expected values > bestBS = c(1, 1, 1, 0, 1, 1, 1, 1, 0, 1, 1, 1, 0, 0, 0, 0,0) > bestBS2 <- c(0,0,0,0,0,0,1) > bestBS3 <- c(0,0,1,0,0,0) > > # just to check that the simulateTN function works > SimT1<-simulateTN(CNOlist=cnolist, model=model, bString=list(bestBS)) > SimT2<-simulateTN(CNOlist=cnolist, model=model, bStrings=list(bestBS,bestBS2)) > SimT3<-simulateTN(CNOlist=cnolist, model=model, bStrings=list(bestBS, bestBS2, bestBS3)) > > > # again, just to check that gaBinary works > # run T1 first, > T1opt<-gaBinaryT1(CNOlist=cnolist,model=model,verbose=FALSE) > # run T2 > T2opt<-gaBinaryTN(CNOlist=cnolist,model=model,bStrings=list(T1opt$bString),verbose=FALSE) > # run T3 > T3opt<-gaBinaryTN(CNOlist=cnolist,model=model,bStrings=list(bestBS, bestBS2),verbose=FALSE) > > print( T1opt$bScore) 4.545455e-05 > print( T2opt$bScore) [1] 5.454545e-05 > print( T3opt$bScore) [1] 6.363636e-05 > # no using the hardcoded parameters, we can check the output of te scores that > # must be tiny. > score1 = computeScoreT1(cnolist, model, bString=bestBS) > score2 = computeScoreTN(cnolist, model, bStrings=list(bestBS,bestBS2)) > score3 = computeScoreTN(cnolist, model, bStrings=list(bestBS,bestBS2, bestBS3)) > > > print(score1) [1] 4.545455e-05 > print(score2) [1] 5.454545e-05 > print(score3) [1] 6.363636e-05 > if (score1>0.01 || score2>0.24 || score3>0.1){ + # ideally, the score should all be close to 0. In practice, it's about 1e-5 + # However, in the T3 case, once in while, the score is 0.0953 hence the + # score3>0.1 + stop("errore") + } > cutAndPlot(cnolist, model,bStrings=list(bestBS),plotPDF=TRUE, tag="test1") $filenames $filenames[[1]] [1] "test1_SimResultsT1_1_.pdf" $mse [,1] [,2] [,3] [,4] [,5] [,6] [1,] 0 0 0 0 0 0 [2,] 0 0 0 0 0 0 [3,] 0 0 0 0 0 0 [4,] 0 0 0 0 0 0 [5,] 0 0 0 0 0 0 [6,] 0 0 0 0 0 0 [7,] 0 0 0 0 0 0 $simResults $simResults[[1]] $simResults[[1]]$t0 [,1] [,2] [,3] [,4] [,5] [,6] [1,] 0 0 0 0 0 0 [2,] 0 0 0 0 0 0 [3,] 0 0 0 0 0 0 [4,] 0 0 0 0 0 0 [5,] 0 0 0 0 0 0 [6,] 0 0 0 0 0 0 [7,] 0 0 0 0 0 0 $simResults[[1]]$t1 [,1] [,2] [,3] [,4] [,5] [,6] [1,] 1 1 1 0 1 0 [2,] 1 1 1 1 1 1 [3,] 0 1 1 0 0 0 [4,] 1 0 0 0 1 0 [5,] 0 0 0 1 0 1 [6,] 1 0 0 1 1 1 [7,] 0 0 0 0 0 0 > cutAndPlot(cnolist, model,bStrings=list(bestBS,bestBS2),plotPDF=TRUE, tag="test2") $mse [,1] [,2] [,3] [,4] [,5] [,6] [1,] 0 0 0 0 0 0 [2,] 0 0 0 0 0 0 [3,] 0 0 0 0 0 0 [4,] 0 0 0 0 0 0 [5,] 0 0 0 0 0 0 [6,] 0 0 0 0 0 0 [7,] 0 0 0 0 0 0 $filenames list() $simResults $simResults[[1]] [,1] [,2] [,3] [,4] [,5] [,6] [1,] 0 0 0 0 0 0 [2,] 0 0 0 0 0 0 [3,] 0 0 0 0 0 0 [4,] 0 0 0 0 0 0 [5,] 0 0 0 0 0 0 [6,] 0 0 0 0 0 0 [7,] 0 0 0 0 0 0 $simResults[[2]] [,1] [,2] [,3] [,4] [,5] [,6] [1,] 1 1 1 0 1 0 [2,] 1 1 1 1 1 1 [3,] 0 1 1 0 0 0 [4,] 1 0 0 0 1 0 [5,] 0 0 0 1 0 1 [6,] 1 0 0 1 1 1 [7,] 0 0 0 0 0 0 $simResults[[3]] [,1] [,2] [,3] [,4] [,5] [,6] [1,] 1 1 1 0 1 0 [2,] 1 1 1 1 1 0 [3,] 0 1 1 0 0 0 [4,] 1 0 0 0 1 0 [5,] 0 0 0 1 0 0 [6,] 1 0 0 1 1 0 [7,] 0 0 0 0 0 0 > cutAndPlot(cnolist, model, bStrings=list(bestBS,bestBS2,bestBS3),plotPDF=TRUE, tag="test3") $mse [,1] [,2] [,3] [,4] [,5] [,6] [1,] 0 0 0 0 0 0 [2,] 0 0 0 0 0 0 [3,] 0 0 0 0 0 0 [4,] 0 0 0 0 0 0 [5,] 0 0 0 0 0 0 [6,] 0 0 0 0 0 0 [7,] 0 0 0 0 0 0 $filenames list() $simResults $simResults[[1]] [,1] [,2] [,3] [,4] [,5] [,6] [1,] 0 0 0 0 0 0 [2,] 0 0 0 0 0 0 [3,] 0 0 0 0 0 0 [4,] 0 0 0 0 0 0 [5,] 0 0 0 0 0 0 [6,] 0 0 0 0 0 0 [7,] 0 0 0 0 0 0 $simResults[[2]] [,1] [,2] [,3] [,4] [,5] [,6] [1,] 1 1 1 0 1 0 [2,] 1 1 1 1 1 1 [3,] 0 1 1 0 0 0 [4,] 1 0 0 0 1 0 [5,] 0 0 0 1 0 1 [6,] 1 0 0 1 1 1 [7,] 0 0 0 0 0 0 $simResults[[3]] [,1] [,2] [,3] [,4] [,5] [,6] [1,] 1 1 1 0 1 0 [2,] 1 1 1 1 1 0 [3,] 0 1 1 0 0 0 [4,] 1 0 0 0 1 0 [5,] 0 0 0 1 0 0 [6,] 1 0 0 1 1 0 [7,] 0 0 0 0 0 0 $simResults[[4]] [,1] [,2] [,3] [,4] [,5] [,6] [1,] 0 1 1 0 0 0 [2,] 0 0 0 1 0 1 [3,] 0 1 1 0 0 0 [4,] 0 0 0 0 0 0 [5,] 0 0 0 1 0 1 [6,] 0 0 0 1 0 1 [7,] 0 0 0 0 0 0 > > > > warnings() > > proc.time() user system elapsed 4.62 0.56 5.21
CellNOptR.Rcheck/tests/test_import_rules.Rout
R version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(CellNOptR) Loading required package: RBGL Loading required package: graph Loading required package: BiocGenerics Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: RCurl Loading required package: Rgraphviz Loading required package: grid Loading required package: XML Attaching package: 'XML' The following object is masked from 'package:graph': addNode Loading required package: ggplot2 Loading required package: rmarkdown > > # test readBND ------------------------------------------------------------------ > > required_pcks = list("dplyr","tidyr","readr") > > if(!all(unlist(lapply(required_pcks,requireNamespace)))){ + print("the following packages need to be installed to use readBND:") + print(unlist(required_pcks)) + print("Please, install the packages manually for this feature.") + + }else{ + #download.file("https://maboss.curie.fr/pub/example.bnd",destfile = "./tests/example.bnd") + + model = readBND("./data/example.bnd") + #model = readBND("https://maboss.curie.fr/pub/example1.bnd") + + # basic checks for being a CellNoptR model: + stopifnot(is.list(model)) + stopifnot(length(model)==4) + stopifnot(all(names(model) %in% c("reacID","namesSpecies","interMat","notMat"))) + stopifnot(length(model$reacID)==ncol(model$interMat)) + stopifnot(length(model$reacID)==ncol(model$notMat)) + stopifnot(length(model$namesSpecies)==nrow(model$interMat)) + stopifnot(length(model$namesSpecies)==nrow(model$notMat)) + + #plotModel(model) + + + + } Loading required namespace: tidyr Loading required namespace: readr Loading required package: dplyr Attaching package: 'dplyr' The following object is masked from 'package:graph': union The following objects are masked from 'package:BiocGenerics': combine, intersect, setdiff, union The following objects are masked from 'package:stats': filter, lag The following objects are masked from 'package:base': intersect, setdiff, setequal, union Loading required package: tidyr Attaching package: 'tidyr' The following object is masked from 'package:RCurl': complete Loading required package: readr > > > > proc.time() user system elapsed 2.92 0.40 3.29
CellNOptR.Rcheck/tests/test_manySteadyStates.Rout
R version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > # > # This file is part of the CNO software > # > # Copyright (c) 2011-2012 - EBI > # > # File author(s): CNO developers (cno-dev@ebi.ac.uk) > # > # Distributed under the GPLv2 License. > # See accompanying file LICENSE.txt or copy at > # http://www.gnu.org/licenses/gpl-2.0.html > # > # CNO website: http://www.ebi.ac.uk/saezrodriguez/software.html > # > ############################################################################## > # $Id$ > > # This test runs optimisation using Boolean logic at different time points > # Author: S.Schrier, T.Cokelaer > > > > manySteadyStates <-function( + CNOlist, + model, + sizeFac=0.0001, + NAFac=1, + popSize=50, + pMutation=0.5, + maxTime=60, + maxGens=500, + stallGenMax=100, + selPress=1.2, + elitism=5, + relTol=0.1, + verbose=FALSE, + priorBitString=NULL){ + + + #initialize Opt array + Opt<-list() + #initialze a bString array + bStrings<-list() + simRes<-list() + + + T1opt<-gaBinaryT1(CNOlist=CNOlist, + model=model, + stallGenMax=stallGenMax, + sizeFac=sizeFac, + NAFac=NAFac, + popSize=popSize, + pMutation=pMutation, + maxTime=maxTime, + maxGens=maxGens, + selPress=selPress, + elitism=elitism, + relTol=relTol, + verbose=verbose, + priorBitString=priorBitString) + + Opt[[1]]<-T1opt + simT1<-simulateTN(CNOlist=CNOlist, model=model, bStrings=list(T1opt$bString)) + simRes[[1]]<-simT1 + bStrings[[1]] = T1opt$bString + + if (length(CNOlist@signals)>2){ + for(i in 3:length(CNOlist@signals)){ + Opt[[i-1]]<-gaBinaryTN(CNOlist=CNOlist, + model=model, + bStrings=bStrings, + stallGenMax=stallGenMax, + maxTime=maxTime, + sizeFac=sizeFac, + NAFac=NAFac, + popSize=popSize, + pMutation=pMutation, + maxGens=maxGens, + selPress=selPress, + elitism=elitism, + relTol=relTol, + verbose=verbose, + priorBitString=priorBitString) + + bStrings[[i-1]] = Opt[[i-1]]$bString + + simRes[[i]]<-simulateTN(CNOlist,model,bStrings) + } + } + return(list(bStrings=bStrings, Opt=Opt, simRes=simRes)) + } > > > > library(CellNOptR) Loading required package: RBGL Loading required package: graph Loading required package: BiocGenerics Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: RCurl Loading required package: Rgraphviz Loading required package: grid Loading required package: XML Attaching package: 'XML' The following object is masked from 'package:graph': addNode Loading required package: ggplot2 Loading required package: rmarkdown > > # one steady state > data(CNOlistToy, package="CellNOptR") > cnolist = CNOlist(CNOlistToy) > data(ToyModel, package="CellNOptR") > results = manySteadyStates(cnolist, ToyModel) > print(results$bStrings) [[1]] [1] 1 1 1 1 1 0 1 0 1 1 1 1 0 1 1 0 > > # two steady state > data(CNOlistToy2, package="CellNOptR") > cnolist = CNOlist(CNOlistToy2) > data(ToyModel2, package="CellNOptR") > results = manySteadyStates(cnolist, ToyModel2) > print(results$bStrings) [[1]] [1] 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 0 0 [[2]] [1] 0 0 1 > > # 3 steady state > ToyModel3 = readSIF(system.file("ToyModelT3/ToyModelT3.sif", package="CellNOptR")) > cnolist = CNOlist(system.file("ToyModelT3/ToyDataT3.csv", package="CellNOptR")) > results = manySteadyStates(cnolist, ToyModel3) > print(results$bStrings) [[1]] [1] 1 1 1 1 1 1 1 1 1 1 0 0 1 1 1 1 1 1 0 [[2]] [1] 0 0 0 [[3]] [1] 0 0 0 > > > > proc.time() user system elapsed 7.68 0.59 8.28
CellNOptR.Rcheck/tests/test_priorBitString.Rout
R version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > # > # This file is part of the CNO software > # > # Copyright (c) 2011-2012 - EBI > # > # File author(s): CNO developers (cno-dev@ebi.ac.uk) > # > # Distributed under the GPLv2 License. > # See accompanying file LICENSE.txt or copy at > # http://www.gnu.org/licenses/gpl-2.0.html > # > # CNO website: http://www.ebi.ac.uk/saezrodriguez/software.html > # > ############################################################################## > # $Id$ > # test if the priorBitString is used correctly in gaBinaryT1DO NOT MODIFY please (TC, June 2012) > > library(CellNOptR) Loading required package: RBGL Loading required package: graph Loading required package: BiocGenerics Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: RCurl Loading required package: Rgraphviz Loading required package: grid Loading required package: XML Attaching package: 'XML' The following object is masked from 'package:graph': addNode Loading required package: ggplot2 Loading required package: rmarkdown > > > # Load T1 and T2 data. Only T1 is used here below. > data(ToyModel, package="CellNOptR") > data(CNOlistToy, package="CellNOptR") > cnolist = CNOlistToy > pknmodel = ToyModel > > # preprocessing > model = preprocessing(cnolist, pknmodel) [1] "The following species are measured: Akt, Hsp27, NFkB, Erk, p90RSK, Jnk, cJun" [1] "The following species are stimulated: EGF, TNFa" [1] "The following species are inhibited: Raf, PI3K" [1] "The following species are not observable and/or not controllable: " > > # computeScoreT1 with init string made of ones > initBstring<-rep(1,length(model$reacID)) > > > > priorBitString = rep(NA, length(model$reacID)) > priorBitString[1] = 0 > priorBitString[2] = 0 > priorBitString[3] = 0 > priorBitString[4] = 0 > > # Second, you call the gaBinaryT1 function by providing the priorBitString > # argument: > ToyT1opt<-gaBinaryT1(CNOlist=CNOlistToy, model=model, + initBstring=initBstring, maxGens=10, popSize=5, + verbose=FALSE, priorBitString=priorBitString) > > > for (x in ToyT1opt$results[,7]){ + x = strsplit(x ,",")[[1]] + if (as.numeric(x[[1]]) != 0 ){ stop("first element must be 0")} + if (as.numeric(x[[2]]) != 0 ){ stop("second element must be 0")} + if (as.numeric(x[[3]]) != 0 ){ stop("tirdh element must be 0")} + if (as.numeric(x[[4]]) != 0 ){ stop("fourth element must be 0")} + } > > > > proc.time() user system elapsed 2.18 0.35 2.56
CellNOptR.Rcheck/tests/test_simulateTN.Rout
R version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > # > # This file is part of the CNO software > # > # Copyright (c) 2011-2012 - EBI > # > # File author(s): CNO developers (cno-dev@ebi.ac.uk) > # > # Distributed under the GPLv2 License. > # See accompanying file LICENSE.txt or copy at > # http://www.gnu.org/licenses/gpl-2.0.html > # > # CNO website: http://www.ebi.ac.uk/saezrodriguez/software.html > # > ############################################################################## > # $Id$ > # This test runs T3 data set to compute the scores (must be zero), and run > # cutAndPlot plot on each time points. > > # DO NOT MODIFY please (TC, June 2012) > > library(CellNOptR) Loading required package: RBGL Loading required package: graph Loading required package: BiocGenerics Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: RCurl Loading required package: Rgraphviz Loading required package: grid Loading required package: XML Attaching package: 'XML' The following object is masked from 'package:graph': addNode Loading required package: ggplot2 Loading required package: rmarkdown > pknmodel = readSIF(system.file("ToyModelT3/ToyModelT3.sif", package="CellNOptR")) > cnolist = CNOlist(system.file("ToyModelT3/ToyDataT3.csv", package="CellNOptR")) > > model = preprocessing(cnolist, pknmodel) [1] "The following species are measured: AKT, MEK, ERK, P38, JNK, NFKB" [1] "The following species are stimulated: TGFa, TNFa" [1] "The following species are inhibited: PI3K, MEK" [1] "The following species are not observable and/or not controllable: " > > # computeScoreT1 with init string made of ones > verbose = FALSE > initBstring<-rep(1,length(model$reacID)) > score = computeScoreT1(cnolist, model,bString=rep(1,length(model$reacID))) > bestBS = c(1, 1, 1, 0, 1, 1, 1, 1, 0, 1, 1, 1, 0, 0, 0, 0,0) > bestBS2 <- c(0,0,0,0,0,0,1) # given by running gaBinaryTN > bestBS3 <- c(0,0,1,0,0,0) # given by running gaBinaryTN > > > SimT1<-simulateTN(CNOlist=cnolist, model=model, bString=list(bestBS)) > SimT2<-simulateTN(CNOlist=cnolist, model=model, bStrings=list(bestBS, bestBS2)) > SimT3<-simulateTN(CNOlist=cnolist, model=model, bStrings=list(bestBS, bestBS2, bestBS3)) > > score1 = computeScoreT1(cnolist, model, bString=bestBS) > score2 = computeScoreTN(cnolist, model, bStrings=list(bestBS,bestBS2)) > score3 = computeScoreTN(cnolist, model, bStrings=list(bestBS,bestBS2, bestBS3)) > > print(score1) [1] 4.545455e-05 > print(score2) [1] 5.454545e-05 > print(score3) [1] 6.363636e-05 > if (score1>0.01 || score2>0.024){ + stop("errore") + } > cutAndPlot(cnolist, model,bStrings=list(bestBS),plotPDF=TRUE, tag="test1") $filenames $filenames[[1]] [1] "test1_SimResultsT1_1_.pdf" $mse [,1] [,2] [,3] [,4] [,5] [,6] [1,] 0 0 0 0 0 0 [2,] 0 0 0 0 0 0 [3,] 0 0 0 0 0 0 [4,] 0 0 0 0 0 0 [5,] 0 0 0 0 0 0 [6,] 0 0 0 0 0 0 [7,] 0 0 0 0 0 0 $simResults $simResults[[1]] $simResults[[1]]$t0 [,1] [,2] [,3] [,4] [,5] [,6] [1,] 0 0 0 0 0 0 [2,] 0 0 0 0 0 0 [3,] 0 0 0 0 0 0 [4,] 0 0 0 0 0 0 [5,] 0 0 0 0 0 0 [6,] 0 0 0 0 0 0 [7,] 0 0 0 0 0 0 $simResults[[1]]$t1 [,1] [,2] [,3] [,4] [,5] [,6] [1,] 1 1 1 0 1 0 [2,] 1 1 1 1 1 1 [3,] 0 1 1 0 0 0 [4,] 1 0 0 0 1 0 [5,] 0 0 0 1 0 1 [6,] 1 0 0 1 1 1 [7,] 0 0 0 0 0 0 > cutAndPlot(cnolist, model,bStrings=list(bestBS,bestBS2),plotPDF=TRUE, tag="test2") $mse [,1] [,2] [,3] [,4] [,5] [,6] [1,] 0 0 0 0 0 0 [2,] 0 0 0 0 0 0 [3,] 0 0 0 0 0 0 [4,] 0 0 0 0 0 0 [5,] 0 0 0 0 0 0 [6,] 0 0 0 0 0 0 [7,] 0 0 0 0 0 0 $filenames list() $simResults $simResults[[1]] [,1] [,2] [,3] [,4] [,5] [,6] [1,] 0 0 0 0 0 0 [2,] 0 0 0 0 0 0 [3,] 0 0 0 0 0 0 [4,] 0 0 0 0 0 0 [5,] 0 0 0 0 0 0 [6,] 0 0 0 0 0 0 [7,] 0 0 0 0 0 0 $simResults[[2]] [,1] [,2] [,3] [,4] [,5] [,6] [1,] 1 1 1 0 1 0 [2,] 1 1 1 1 1 1 [3,] 0 1 1 0 0 0 [4,] 1 0 0 0 1 0 [5,] 0 0 0 1 0 1 [6,] 1 0 0 1 1 1 [7,] 0 0 0 0 0 0 $simResults[[3]] [,1] [,2] [,3] [,4] [,5] [,6] [1,] 1 1 1 0 1 0 [2,] 1 1 1 1 1 0 [3,] 0 1 1 0 0 0 [4,] 1 0 0 0 1 0 [5,] 0 0 0 1 0 0 [6,] 1 0 0 1 1 0 [7,] 0 0 0 0 0 0 > cutAndPlot(cnolist, model, bStrings=list(bestBS,bestBS2,bestBS3),plotPDF=TRUE, tag="test3") $mse [,1] [,2] [,3] [,4] [,5] [,6] [1,] 0 0 0 0 0 0 [2,] 0 0 0 0 0 0 [3,] 0 0 0 0 0 0 [4,] 0 0 0 0 0 0 [5,] 0 0 0 0 0 0 [6,] 0 0 0 0 0 0 [7,] 0 0 0 0 0 0 $filenames list() $simResults $simResults[[1]] [,1] [,2] [,3] [,4] [,5] [,6] [1,] 0 0 0 0 0 0 [2,] 0 0 0 0 0 0 [3,] 0 0 0 0 0 0 [4,] 0 0 0 0 0 0 [5,] 0 0 0 0 0 0 [6,] 0 0 0 0 0 0 [7,] 0 0 0 0 0 0 $simResults[[2]] [,1] [,2] [,3] [,4] [,5] [,6] [1,] 1 1 1 0 1 0 [2,] 1 1 1 1 1 1 [3,] 0 1 1 0 0 0 [4,] 1 0 0 0 1 0 [5,] 0 0 0 1 0 1 [6,] 1 0 0 1 1 1 [7,] 0 0 0 0 0 0 $simResults[[3]] [,1] [,2] [,3] [,4] [,5] [,6] [1,] 1 1 1 0 1 0 [2,] 1 1 1 1 1 0 [3,] 0 1 1 0 0 0 [4,] 1 0 0 0 1 0 [5,] 0 0 0 1 0 0 [6,] 1 0 0 1 1 0 [7,] 0 0 0 0 0 0 $simResults[[4]] [,1] [,2] [,3] [,4] [,5] [,6] [1,] 0 1 1 0 0 0 [2,] 0 0 0 1 0 1 [3,] 0 1 1 0 0 0 [4,] 0 0 0 0 0 0 [5,] 0 0 0 1 0 1 [6,] 0 0 0 1 0 1 [7,] 0 0 0 0 0 0 > > > proc.time() user system elapsed 3.04 0.48 3.56
CellNOptR.Rcheck/CellNOptR-Ex.timings
name | user | system | elapsed | |
CNORbool | 1.43 | 0.06 | 1.50 | |
CNORwrap | 0.86 | 0.13 | 1.00 | |
CNOdata | 0 | 0 | 0 | |
CNOlist-class | 0.09 | 0.00 | 0.09 | |
CNOlist-methods | 0.08 | 0.02 | 0.10 | |
CellNOptR-package | 3.39 | 0.25 | 3.67 | |
buildBitString | 0 | 0 | 0 | |
build_sif_table_from_rule | 1.68 | 0.09 | 1.76 | |
checkSignals | 0 | 0 | 0 | |
compressModel | 0.02 | 0.00 | 0.02 | |
computeScoreT1 | 0.01 | 0.00 | 0.03 | |
computeScoreTN | 0.05 | 0.00 | 0.04 | |
crossInhibitedData | 0.00 | 0.01 | 0.02 | |
crossvalidateBoolean | 4.12 | 2.05 | 6.69 | |
cutAndPlot | 0.22 | 0.03 | 0.25 | |
cutAndPlotResultsT1 | 0.24 | 0.00 | 0.23 | |
cutAndPlotResultsTN | 0.45 | 0.00 | 0.45 | |
cutCNOlist | 0.00 | 0.02 | 0.02 | |
cutModel | 0 | 0 | 0 | |
cutNONC | 0.00 | 0.01 | 0.02 | |
defaultParameters | 0.00 | 0.02 | 0.01 | |
exhaustive | 0.69 | 0.03 | 0.72 | |
expandGates | 0.01 | 0.02 | 0.03 | |
findNONC | 0.02 | 0.00 | 0.02 | |
gaBinaryT1 | 0.26 | 0.01 | 0.28 | |
gaBinaryTN | 0.15 | 0.02 | 0.15 | |
getFit | 0 | 0 | 0 | |
graph2sif | 0.01 | 0.00 | 0.02 | |
ilpBinaryT1 | 0.31 | 0.02 | 0.33 | |
ilpBinaryT2 | 0.25 | 0.00 | 0.25 | |
ilpBinaryTN | 0.26 | 0.01 | 0.30 | |
indexFinder | 0.00 | 0.02 | 0.01 | |
makeCNOlist | 0.04 | 0.00 | 0.05 | |
model2igraph | 0.07 | 0.00 | 0.08 | |
model2sif | 0.00 | 0.02 | 0.01 | |
normaliseCNOlist | 0 | 0 | 0 | |
plot-methods | 0.13 | 0.01 | 0.14 | |
plotCNOlist | 0.08 | 0.00 | 0.08 | |
plotCNOlist2 | 2.62 | 0.03 | 2.66 | |
plotCNOlistLarge | 0.14 | 0.03 | 0.17 | |
plotCNOlistLargePDF | 0.21 | 0.02 | 0.22 | |
plotCNOlistPDF | 0.09 | 0.02 | 0.11 | |
plotFit | 0.06 | 0.00 | 0.06 | |
plotModel | 0.38 | 0.03 | 0.42 | |
plotOptimResults | 0.14 | 0.01 | 0.16 | |
plotOptimResultsPDF | 0.34 | 0.02 | 0.37 | |
plotOptimResultsPan | 0.16 | 0.00 | 0.15 | |
prep4sim | 0.00 | 0.02 | 0.02 | |
preprocessing | 0 | 0 | 0 | |
randomizeCNOlist | 0 | 0 | 0 | |
readBND | 0 | 0 | 0 | |
readMIDAS | 0.02 | 0.01 | 0.03 | |
readSBMLQual | 0 | 0 | 0 | |
readSIF | 0.00 | 0.00 | 0.01 | |
residualError | 0.01 | 0.00 | 0.02 | |
sif2graph | 0.00 | 0.02 | 0.03 | |
simulateT1 | 0.02 | 0.00 | 0.02 | |
simulateTN | 0.00 | 0.02 | 0.01 | |
simulatorT0 | 0.02 | 0.00 | 0.02 | |
simulatorT1 | 0.00 | 0.01 | 0.01 | |
simulatorT2 | 0.01 | 0.00 | 0.02 | |
simulatorTN | 0.00 | 0.00 | 0.01 | |
toSBML | 0.00 | 0.00 | 0.02 | |
writeDot | 0.05 | 0.08 | 0.12 | |
writeMIDAS | 0.00 | 0.03 | 0.07 | |
writeNetwork | 0.06 | 0.05 | 0.11 | |
writeReport | 0.02 | 0.03 | 0.06 | |
writeSIF | 0.00 | 0.00 | 0.01 | |
writeScaffold | 0.04 | 0.06 | 0.13 | |