A.Gabor
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/CellNOptR |
| Branch: RELEASE_3_9 |
| Last Commit: d0deb0e |
| Last Changed Date: 2019-05-02 11:53:33 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:00:42 -0400 (Wed, 16 Oct 2019).
| Package 232/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| CellNOptR 1.30.0 A.Gabor
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | [ WARNINGS ] | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
| Package: CellNOptR |
| Version: 1.30.0 |
| Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:CellNOptR.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings CellNOptR_1.30.0.tar.gz |
| StartedAt: 2019-10-16 00:22:15 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 00:24:35 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 140.5 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: CellNOptR.Rcheck |
| Warnings: 2 |
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### Running command:
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### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:CellNOptR.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings CellNOptR_1.30.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/CellNOptR.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.30.0’
* 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-3.9-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 ... OK
* 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 ‘%>%’
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 ‘%>%’
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 ‘%>%’
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 ‘%>%’
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’
readBND: no visible global function definition for ‘read_file’
readBNET: no visible global function definition for ‘%>%’
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:
%>% . distinct do 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 ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking installed files from ‘inst/doc’ ... NOTE
The following files should probably not be installed:
‘Fig1.png’, ‘Fig5.png’
Consider the use of a .Rinstignore file: see ‘Writing R Extensions’,
or move the vignette sources from ‘inst/doc’ to ‘vignettes’.
* checking files in ‘vignettes’ ... OK
* checking examples ... WARNING
Found the following significant warnings:
Warning: working directory was changed to ‘/tmp/RtmpW3Z5PG’, resetting
Warning: working directory was changed to ‘/tmp/RtmpW3Z5PG’, resetting
Warning: working directory was changed to ‘/tmp/RtmpW3Z5PG’, resetting
Warning: working directory was changed to ‘/tmp/RtmpW3Z5PG’, resetting
Warning: working directory was changed to ‘/tmp/RtmpW3Z5PG’, resetting
Warning: working directory was changed to ‘/tmp/RtmpW3Z5PG’, resetting
Warning: working directory was changed to ‘/tmp/RtmpW3Z5PG’, resetting
Warning: working directory was changed to ‘/tmp/RtmpW3Z5PG’, resetting
Warning: working directory was changed to ‘/tmp/RtmpW3Z5PG’, resetting
Warning: working directory was changed to ‘/tmp/RtmpW3Z5PG’, resetting
Warning: working directory was changed to ‘/tmp/RtmpW3Z5PG’, resetting
Warning: working directory was changed to ‘/tmp/RtmpW3Z5PG’, resetting
Warning: working directory was changed to ‘/tmp/RtmpW3Z5PG’, resetting
Warning: working directory was changed to ‘/tmp/RtmpW3Z5PG’, resetting
Examples with CPU or elapsed time > 5s
user system elapsed
CellNOptR-package 5.353 0.023 5.688
* 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: 2 WARNINGs, 4 NOTEs
See
‘/home/biocbuild/bbs-3.9-bioc/meat/CellNOptR.Rcheck/00check.log’
for details.
CellNOptR.Rcheck/00install.out
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### Running command:
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### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL CellNOptR
###
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘CellNOptR’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -c getFit.c -o getFit.o
getFit.c: In function ‘getFit’:
getFit.c:47:6: warning: unused variable ‘nReacs’ [-Wunused-variable]
int nReacs = INTEGER(nReacs_in)[0];
^~~~~~
getFit.c:42:6: warning: unused variable ‘selCounter’ [-Wunused-variable]
int selCounter = 0;
^~~~~~~~~~
getFit.c:41:6: warning: unused variable ‘selection’ [-Wunused-variable]
int selection[40];
^~~~~~~~~
getFit.c:40:6: warning: unused variable ‘or_max’ [-Wunused-variable]
int or_max = 0;
^~~~~~
getFit.c:39:6: warning: unused variable ‘curr_max’ [-Wunused-variable]
int curr_max = 0;
^~~~~~~~
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I/usr/local/include -I./include -fpic -g -O2 -Wall -c simulatorT1.c -o simulatorT1.o
simulatorT1.c: In function ‘simulatorT1’:
simulatorT1.c:502:20: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
if (MA[i][j]<0.95 & MA[i][j]>0.05) // actually we could check if they are exatly 0 or 1
~~~~~~~~^~~~~
gcc -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/lib -L/usr/local/lib -o CellNOptR.so getFit.o simulatorT1.o simulatorTN.o -L/home/biocbuild/bbs-3.9-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.9-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
‘CellNOptR-vignette.Rnw’
** 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 3.6.1 (2019-07-05) -- "Action of the Toes" Copyright (C) 2019 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 ([email protected]) > # > # Distributed under the GPLv2 License. > # See accompanying file LICENSE.txt or copy at > # http://www.gnu.org/licenses/gpl-2.0.html > # > # CNO website: http://www.ebi.ac.uk/saezrodriguez/cno > # > ############################################################################## > # $Id$ > > # This is a test of the ToyModel and gaBinaryT1 > library(CellNOptR) Loading required package: RBGL Loading required package: graph Loading required package: BiocGenerics Loading required package: parallel Attaching package: 'BiocGenerics' The following objects are masked from 'package:parallel': clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which, which.max, which.min Loading required package: hash hash-2.2.6.1 provided by Decision Patterns Loading required package: RCurl Loading required package: bitops Loading required package: Rgraphviz Loading required package: grid Loading required package: XML Attaching package: 'XML' The following object is masked from 'package:graph': addNode Loading required package: ggplot2 > > # read data > pknmodel = readSIF(system.file("ToyModel/ToyPKNMMB.sif", package="CellNOptR")) > data = readMIDAS(system.file("ToyModel/ToyDataMMB.csv", package="CellNOptR")) [1] "Your data set comprises 18 conditions (i.e. combinations of time point and treatment)" [1] "Your data set comprises measurements on 7 different species" [1] "Your data set comprises 4 stimuli/inhibitors and 1 cell line(s) ( mock )" [1] "Please be aware that CNO only handles measurements on one cell line at this time." [1] "Your data file contained 'NaN'. We have assumed that these were missing values and replaced them by NAs." > cnolist = makeCNOlist(data, subfield=FALSE) [1] "Please be aware that if you only have some conditions at time zero (e.g.only inhibitor/no inhibitor), the measurements for these conditions will be copied across matching conditions at t=0" > > # preprocessing > model = preprocessing(cnolist, pknmodel, verbose=FALSE) > > # optimisation > T1opt<-gaBinaryT1(CNOlist=cnolist,model=model,verbose=FALSE) > > truebs =c(1, 1, 0, 1, 1, 0, 1, 1, 0, 0, 1, 1, 1, 0, 0, 0) > print(truebs) [1] 1 1 0 1 1 0 1 1 0 0 1 1 1 0 0 0 > print(T1opt$bString) [1] 1 1 0 1 1 0 1 1 0 0 1 1 1 0 0 0 > > # testing valid output > if (dist(rbind(T1opt$bString, truebs))>2){ + stop("something wrong going on") + } > > # extra call to simulateTN > SimT1<-simulateTN(CNOlist=cnolist,model=model, bStrings=list(truebs)) > > > proc.time() user system elapsed 3.705 0.131 3.820
CellNOptR.Rcheck/tests/test_gaBinaryT2.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes" Copyright (C) 2019 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 ([email protected]) > # > # Distributed under the GPLv2 License. > # See accompanying file LICENSE.txt or copy at > # http://www.gnu.org/licenses/gpl-2.0.html > # > # CNO website: http://www.ebi.ac.uk/saezrodriguez/cno > # > ############################################################################## > # $Id$ > > # This is a test of the ToyModel and gaBinaryT1 > # > > library(CellNOptR) Loading required package: RBGL Loading required package: graph Loading required package: BiocGenerics Loading required package: parallel Attaching package: 'BiocGenerics' The following objects are masked from 'package:parallel': clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which, which.max, which.min Loading required package: hash hash-2.2.6.1 provided by Decision Patterns Loading required package: RCurl Loading required package: bitops Loading required package: Rgraphviz Loading required package: grid Loading required package: XML Attaching package: 'XML' The following object is masked from 'package:graph': addNode 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 6.384 0.166 6.535
CellNOptR.Rcheck/tests/test_gaBinaryT3.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes" Copyright (C) 2019 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 ([email protected]) > # > # Distributed under the GPLv2 License. > # See accompanying file LICENSE.txt or copy at > # http://www.gnu.org/licenses/gpl-2.0.html > # > # CNO website: http://www.ebi.ac.uk/saezrodriguez/cno > # > ############################################################################## > # $Id$ > > # This is a test of the ToyModel and gaBinaryT1 > # > > library(CellNOptR) Loading required package: RBGL Loading required package: graph Loading required package: BiocGenerics Loading required package: parallel Attaching package: 'BiocGenerics' The following objects are masked from 'package:parallel': clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which, which.max, which.min Loading required package: hash hash-2.2.6.1 provided by Decision Patterns Loading required package: RCurl Loading required package: bitops Loading required package: Rgraphviz Loading required package: grid Loading required package: XML Attaching package: 'XML' The following object is masked from 'package:graph': addNode 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 6.421 0.149 6.588
CellNOptR.Rcheck/tests/test_import_rules.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(CellNOptR)
Loading required package: RBGL
Loading required package: graph
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which, which.max, which.min
Loading required package: hash
hash-2.2.6.1 provided by Decision Patterns
Loading required package: RCurl
Loading required package: bitops
Loading required package: Rgraphviz
Loading required package: grid
Loading required package: XML
Attaching package: 'XML'
The following object is masked from 'package:graph':
addNode
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.
Please use `cols = c(sif_df)`
>
>
>
> proc.time()
user system elapsed
3.199 0.158 3.745
CellNOptR.Rcheck/tests/test_manySteadyStates.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes" Copyright (C) 2019 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 ([email protected]) > # > # Distributed under the GPLv2 License. > # See accompanying file LICENSE.txt or copy at > # http://www.gnu.org/licenses/gpl-2.0.html > # > # CNO website: http://www.ebi.ac.uk/saezrodriguez/software.html > # > ############################################################################## > # $Id$ > > # This test runs optimisation using Boolean logic at different time points > # Author: S.Schrier, T.Cokelaer > > > > manySteadyStates <-function( + CNOlist, + model, + sizeFac=0.0001, + NAFac=1, + popSize=50, + pMutation=0.5, + maxTime=60, + maxGens=500, + stallGenMax=100, + selPress=1.2, + elitism=5, + relTol=0.1, + verbose=FALSE, + priorBitString=NULL){ + + + #initialize Opt array + Opt<-list() + #initialze a bString array + bStrings<-list() + simRes<-list() + + + T1opt<-gaBinaryT1(CNOlist=CNOlist, + model=model, + stallGenMax=stallGenMax, + sizeFac=sizeFac, + NAFac=NAFac, + popSize=popSize, + pMutation=pMutation, + maxTime=maxTime, + maxGens=maxGens, + selPress=selPress, + elitism=elitism, + relTol=relTol, + verbose=verbose, + priorBitString=priorBitString) + + Opt[[1]]<-T1opt + simT1<-simulateTN(CNOlist=CNOlist, model=model, bStrings=list(T1opt$bString)) + simRes[[1]]<-simT1 + bStrings[[1]] = T1opt$bString + + if (length(CNOlist@signals)>2){ + for(i in 3:length(CNOlist@signals)){ + Opt[[i-1]]<-gaBinaryTN(CNOlist=CNOlist, + model=model, + bStrings=bStrings, + stallGenMax=stallGenMax, + maxTime=maxTime, + sizeFac=sizeFac, + NAFac=NAFac, + popSize=popSize, + pMutation=pMutation, + maxGens=maxGens, + selPress=selPress, + elitism=elitism, + relTol=relTol, + verbose=verbose, + priorBitString=priorBitString) + + bStrings[[i-1]] = Opt[[i-1]]$bString + + simRes[[i]]<-simulateTN(CNOlist,model,bStrings) + } + } + return(list(bStrings=bStrings, Opt=Opt, simRes=simRes)) + } > > > > library(CellNOptR) Loading required package: RBGL Loading required package: graph Loading required package: BiocGenerics Loading required package: parallel Attaching package: 'BiocGenerics' The following objects are masked from 'package:parallel': clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which, which.max, which.min Loading required package: hash hash-2.2.6.1 provided by Decision Patterns Loading required package: RCurl Loading required package: bitops Loading required package: Rgraphviz Loading required package: grid Loading required package: XML Attaching package: 'XML' The following object is masked from 'package:graph': addNode Loading required package: ggplot2 > > # one steady state > data(CNOlistToy, package="CellNOptR") > cnolist = CNOlist(CNOlistToy) > data(ToyModel, package="CellNOptR") > results = manySteadyStates(cnolist, ToyModel) > print(results$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 12.227 0.186 12.451
CellNOptR.Rcheck/tests/test_priorBitString.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes" Copyright (C) 2019 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 ([email protected]) > # > # Distributed under the GPLv2 License. > # See accompanying file LICENSE.txt or copy at > # http://www.gnu.org/licenses/gpl-2.0.html > # > # CNO website: http://www.ebi.ac.uk/saezrodriguez/software.html > # > ############################################################################## > # $Id$ > # test if the priorBitString is used correctly in gaBinaryT1DO NOT MODIFY please (TC, June 2012) > > library(CellNOptR) Loading required package: RBGL Loading required package: graph Loading required package: BiocGenerics Loading required package: parallel Attaching package: 'BiocGenerics' The following objects are masked from 'package:parallel': clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which, which.max, which.min Loading required package: hash hash-2.2.6.1 provided by Decision Patterns Loading required package: RCurl Loading required package: bitops Loading required package: Rgraphviz Loading required package: grid Loading required package: XML Attaching package: 'XML' The following object is masked from 'package:graph': addNode 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 2.505 0.105 2.605
CellNOptR.Rcheck/tests/test_simulateTN.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes" Copyright (C) 2019 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 ([email protected]) > # > # Distributed under the GPLv2 License. > # See accompanying file LICENSE.txt or copy at > # http://www.gnu.org/licenses/gpl-2.0.html > # > # CNO website: http://www.ebi.ac.uk/saezrodriguez/software.html > # > ############################################################################## > # $Id$ > # This test runs T3 data set to compute the scores (must be zero), and run > # cutAndPlot plot on each time points. > > # DO NOT MODIFY please (TC, June 2012) > > library(CellNOptR) Loading required package: RBGL Loading required package: graph Loading required package: BiocGenerics Loading required package: parallel Attaching package: 'BiocGenerics' The following objects are masked from 'package:parallel': clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which, which.max, which.min Loading required package: hash hash-2.2.6.1 provided by Decision Patterns Loading required package: RCurl Loading required package: bitops Loading required package: Rgraphviz Loading required package: grid Loading required package: XML Attaching package: 'XML' The following object is masked from 'package:graph': addNode 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 3.709 0.155 3.848
CellNOptR.Rcheck/CellNOptR-Ex.timings
| name | user | system | elapsed | |
| CNORbool | 2.478 | 0.052 | 2.574 | |
| CNOdata | 0 | 0 | 0 | |
| CNOlist-class | 0.100 | 0.000 | 0.105 | |
| CNOlist-methods | 0.078 | 0.000 | 0.077 | |
| CellNOptR-package | 5.353 | 0.023 | 5.688 | |
| buildBitString | 0.001 | 0.000 | 0.000 | |
| build_sif_table_from_rule | 1.640 | 0.008 | 1.648 | |
| checkSignals | 0.005 | 0.000 | 0.005 | |
| compressModel | 0.002 | 0.004 | 0.006 | |
| computeScoreT1 | 0.014 | 0.004 | 0.018 | |
| computeScoreTN | 0.031 | 0.000 | 0.031 | |
| crossInhibitedData | 0.004 | 0.000 | 0.005 | |
| cutAndPlot | 0.281 | 0.000 | 0.280 | |
| cutAndPlotResultsT1 | 0.370 | 0.004 | 0.374 | |
| cutAndPlotResultsTN | 0.522 | 0.008 | 0.531 | |
| cutNONC | 0.009 | 0.000 | 0.009 | |
| defaultParameters | 0.004 | 0.000 | 0.003 | |
| exhaustive | 0.731 | 0.000 | 0.732 | |
| expandGates | 0.015 | 0.000 | 0.014 | |
| findNONC | 0.009 | 0.000 | 0.009 | |
| gaBinaryT1 | 0.409 | 0.000 | 0.410 | |
| gaBinaryT2 | 0.195 | 0.000 | 0.195 | |
| gaBinaryTN | 0.227 | 0.000 | 0.226 | |
| getFit | 0.009 | 0.000 | 0.010 | |
| indexFinder | 0.005 | 0.000 | 0.004 | |
| normaliseCNOlist | 0.008 | 0.000 | 0.008 | |
| plot-methods | 0.122 | 0.000 | 0.122 | |
| plotCNOlist | 0.103 | 0.004 | 0.107 | |
| plotCNOlist2 | 2.613 | 0.000 | 2.614 | |
| plotCNOlistLarge | 0.153 | 0.000 | 0.153 | |
| plotFit | 0.068 | 0.000 | 0.069 | |
| plotModel | 2.098 | 0.104 | 2.202 | |
| plotOptimResultsPan | 0.3 | 0.0 | 0.3 | |
| prep4sim | 0.003 | 0.000 | 0.003 | |
| preprocessing | 0.01 | 0.00 | 0.01 | |
| randomizeCNOlist | 0.002 | 0.000 | 0.002 | |
| readSBMLQual | 0 | 0 | 0 | |
| residualError | 0.000 | 0.003 | 0.003 | |
| simulateT1 | 0.010 | 0.000 | 0.011 | |
| simulateTN | 0.008 | 0.000 | 0.007 | |
| simulatorT0 | 0.008 | 0.000 | 0.008 | |
| simulatorT1 | 0.007 | 0.000 | 0.007 | |
| simulatorT2 | 0.003 | 0.000 | 0.004 | |
| simulatorTN | 0.007 | 0.000 | 0.006 | |