Binary files /tmp/tmpWEQmqx/xu_ThnITCL/r-cran-boolnet-2.1.3/build/vignette.rds and /tmp/tmpWEQmqx/Mg2FcsQEdv/r-cran-boolnet-2.1.4/build/vignette.rds differ diff -Nru r-cran-boolnet-2.1.3/debian/changelog r-cran-boolnet-2.1.4/debian/changelog --- r-cran-boolnet-2.1.3/debian/changelog 2017-11-29 14:08:31.000000000 +0000 +++ r-cran-boolnet-2.1.4/debian/changelog 2018-06-14 06:46:46.000000000 +0000 @@ -1,3 +1,15 @@ +r-cran-boolnet (2.1.4-1) unstable; urgency=medium + + * New upstream version + * debhelper 11 + * Maintainer: Debian R Packages Maintainers + * Point Vcs fields to salsa.debian.org + * dh-update-R to update Build-Depends + * Remove redundant test depends + + -- Andreas Tille Thu, 14 Jun 2018 08:46:46 +0200 + r-cran-boolnet (2.1.3-2) unstable; urgency=medium * Moved packaging from SVN to Git diff -Nru r-cran-boolnet-2.1.3/debian/compat r-cran-boolnet-2.1.4/debian/compat --- r-cran-boolnet-2.1.3/debian/compat 2017-11-29 14:08:31.000000000 +0000 +++ r-cran-boolnet-2.1.4/debian/compat 2018-06-14 06:46:46.000000000 +0000 @@ -1 +1 @@ -10 +11 diff -Nru r-cran-boolnet-2.1.3/debian/control r-cran-boolnet-2.1.4/debian/control --- r-cran-boolnet-2.1.3/debian/control 2017-11-29 14:08:31.000000000 +0000 +++ r-cran-boolnet-2.1.4/debian/control 2018-06-14 06:46:46.000000000 +0000 @@ -1,23 +1,23 @@ Source: r-cran-boolnet -Maintainer: Debian Med Packaging Team +Maintainer: Debian R Packages Maintainers Uploaders: Andreas Tille Section: gnu-r Priority: optional -Build-Depends: debhelper (>= 10), - r-base-dev, +Build-Depends: debhelper (>= 11~), dh-r, + r-base-dev, r-cran-igraph, r-cran-xml -Standards-Version: 4.1.1 -Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/r-cran-boolnet.git -Vcs-Git: https://anonscm.debian.org/git/debian-med/r-cran-boolnet.git +Standards-Version: 4.1.4 +Vcs-Browser: https://salsa.debian.org/r-pkg-team/r-cran-boolnet +Vcs-Git: https://salsa.debian.org/r-pkg-team/r-cran-boolnet.git Homepage: https://cran.r-project.org/package=BoolNet Package: r-cran-boolnet Architecture: any -Depends: ${shlibs:Depends}, - ${misc:Depends}, - ${R:Depends} +Depends: ${R:Depends}, + ${shlibs:Depends}, + ${misc:Depends} Recommends: ${R:Recommends} Suggests: ${R:Suggests} Description: assembling, analyzing and visualizing Boolean networks diff -Nru r-cran-boolnet-2.1.3/debian/tests/control r-cran-boolnet-2.1.4/debian/tests/control --- r-cran-boolnet-2.1.3/debian/tests/control 2017-11-29 14:08:31.000000000 +0000 +++ r-cran-boolnet-2.1.4/debian/tests/control 2018-06-14 06:46:46.000000000 +0000 @@ -1,3 +1,3 @@ Tests: run-unit-test -Depends: @, r-cran-xml, r-cran-igraph +Depends: @ Restrictions: allow-stderr diff -Nru r-cran-boolnet-2.1.3/DESCRIPTION r-cran-boolnet-2.1.4/DESCRIPTION --- r-cran-boolnet-2.1.3/DESCRIPTION 2016-11-21 11:23:47.000000000 +0000 +++ r-cran-boolnet-2.1.4/DESCRIPTION 2018-06-07 17:43:58.000000000 +0000 @@ -1,8 +1,8 @@ Package: BoolNet Type: Package Title: Construction, Simulation and Analysis of Boolean Networks -Version: 2.1.3 -Date: 2016-06-21 +Version: 2.1.4 +Date: 2018-05-23 Authors@R: c(person("Christoph", "Müssel", role = "aut"), person("Martin", "Hopfensitz", role = "aut"), person("Dao", "Zhou", role = "aut"), @@ -18,7 +18,7 @@ ByteCompile: TRUE Encoding: UTF-8 NeedsCompilation: yes -Packaged: 2016-06-24 13:47:18 UTC; burkovae +Packaged: 2018-05-23 11:35:57 UTC; julian_schwab Author: Christoph Müssel [aut], Martin Hopfensitz [aut], Dao Zhou [aut], @@ -27,4 +27,4 @@ Troy D. Hanson [ctb] (contributed uthash macros) Maintainer: Hans A. Kestler Repository: CRAN -Date/Publication: 2016-11-21 12:23:47 +Date/Publication: 2018-06-07 17:43:58 UTC Binary files /tmp/tmpWEQmqx/xu_ThnITCL/r-cran-boolnet-2.1.3/inst/doc/BoolNet_package_vignette.pdf and /tmp/tmpWEQmqx/Mg2FcsQEdv/r-cran-boolnet-2.1.4/inst/doc/BoolNet_package_vignette.pdf differ diff -Nru r-cran-boolnet-2.1.3/inst/doc/BoolNet_package_vignette.R r-cran-boolnet-2.1.4/inst/doc/BoolNet_package_vignette.R --- r-cran-boolnet-2.1.3/inst/doc/BoolNet_package_vignette.R 2016-06-24 13:47:18.000000000 +0000 +++ r-cran-boolnet-2.1.4/inst/doc/BoolNet_package_vignette.R 2018-05-23 11:35:57.000000000 +0000 @@ -282,54 +282,56 @@ ################################################### -### code chunk number 38: BoolNet_package_vignette.Snw:496-500 +### code chunk number 38: BoolNet_package_vignette.Snw:496-501 ################################################### pdf("sequence.pdf") par(mar = c(1, 4, 2, 1)) -plotSequence(sequence = path) +path <- getPathToAttractor(cellcycle, rep(0,10)) +plotSequence(sequence=path) dev.off() ################################################### -### code chunk number 39: BoolNet_package_vignette.Snw:502-503 (eval = FALSE) +### code chunk number 39: BoolNet_package_vignette.Snw:503-505 (eval = FALSE) ################################################### +## path <- getPathToAttractor(cellcycle, rep(0,10)) ## plotSequence(sequence=path) ################################################### -### code chunk number 40: BoolNet_package_vignette.Snw:516-517 (eval = FALSE) +### code chunk number 40: BoolNet_package_vignette.Snw:518-519 (eval = FALSE) ################################################### ## sequenceToLaTeX(sequence=path, file="sequence.tex") ################################################### -### code chunk number 41: BoolNet_package_vignette.Snw:522-524 +### code chunk number 41: BoolNet_package_vignette.Snw:524-526 ################################################### startState <- generateState(cellcycle, specs=c("CycD"=1,"CycA"=1)) stateTransition(cellcycle,startState) ################################################### -### code chunk number 42: BoolNet_package_vignette.Snw:531-532 +### code chunk number 42: BoolNet_package_vignette.Snw:533-534 ################################################### data(igf) ################################################### -### code chunk number 43: BoolNet_package_vignette.Snw:537-539 +### code chunk number 43: BoolNet_package_vignette.Snw:539-541 ################################################### startState <- generateState(igf, specs=c("IGF"=1)) stateTransition(igf, startState) ################################################### -### code chunk number 44: BoolNet_package_vignette.Snw:542-543 +### code chunk number 44: BoolNet_package_vignette.Snw:544-545 ################################################### getPathToAttractor(network=igf,state=startState) ################################################### -### code chunk number 45: BoolNet_package_vignette.Snw:548-551 +### code chunk number 45: BoolNet_package_vignette.Snw:550-553 ################################################### startState <- generateState(igf, specs=list("IGF"=c(0,0,1))) @@ -337,7 +339,7 @@ ################################################### -### code chunk number 46: BoolNet_package_vignette.Snw:561-565 +### code chunk number 46: BoolNet_package_vignette.Snw:563-567 ################################################### pdf("sequence_igf.pdf") par(mar = c(1, 9, 2, 1)) @@ -346,65 +348,65 @@ ################################################### -### code chunk number 47: BoolNet_package_vignette.Snw:567-568 (eval = FALSE) +### code chunk number 47: BoolNet_package_vignette.Snw:569-570 (eval = FALSE) ################################################### ## plotSequence(network=igf, startState=startState) ################################################### -### code chunk number 48: BoolNet_package_vignette.Snw:574-575 +### code chunk number 48: BoolNet_package_vignette.Snw:576-577 ################################################### set.seed(54321) ################################################### -### code chunk number 49: BoolNet_package_vignette.Snw:577-578 +### code chunk number 49: BoolNet_package_vignette.Snw:579-580 ################################################### stateTransition(cellcycle, rep(1,10), type="asynchronous") ################################################### -### code chunk number 50: BoolNet_package_vignette.Snw:584-585 +### code chunk number 50: BoolNet_package_vignette.Snw:586-587 ################################################### set.seed(4321) ################################################### -### code chunk number 51: BoolNet_package_vignette.Snw:587-589 +### code chunk number 51: BoolNet_package_vignette.Snw:589-591 ################################################### stateTransition(cellcycle, rep(1,10), type="asynchronous", geneProbabilities=c(0.05,0.05,0.2,0.3,0.05,0.05,0.05,0.05,0.1,0.1)) ################################################### -### code chunk number 52: BoolNet_package_vignette.Snw:596-598 +### code chunk number 52: BoolNet_package_vignette.Snw:598-600 ################################################### stateTransition(cellcycle, rep(1,10), type="asynchronous", chosenGene="CycE") ################################################### -### code chunk number 53: BoolNet_package_vignette.Snw:602-603 +### code chunk number 53: BoolNet_package_vignette.Snw:604-605 ################################################### set.seed(432) ################################################### -### code chunk number 54: BoolNet_package_vignette.Snw:605-607 +### code chunk number 54: BoolNet_package_vignette.Snw:607-609 ################################################### data(examplePBN) stateTransition(examplePBN, c(0,1,1), type="probabilistic") ################################################### -### code chunk number 55: BoolNet_package_vignette.Snw:610-612 +### code chunk number 55: BoolNet_package_vignette.Snw:612-614 ################################################### stateTransition(examplePBN, c(0,1,1), type="probabilistic", chosenFunctions=c(2,1,2)) ################################################### -### code chunk number 56: BoolNet_package_vignette.Snw:630-633 (eval = FALSE) +### code chunk number 56: BoolNet_package_vignette.Snw:632-635 (eval = FALSE) ################################################### ## data(cellcycle) ## attr <- getAttractors(cellcycle) @@ -412,38 +414,38 @@ ################################################### -### code chunk number 57: BoolNet_package_vignette.Snw:636-638 +### code chunk number 57: BoolNet_package_vignette.Snw:638-640 ################################################### attr <- getAttractors(cellcycle) attr ################################################### -### code chunk number 58: BoolNet_package_vignette.Snw:644-645 (eval = FALSE) +### code chunk number 58: BoolNet_package_vignette.Snw:646-647 (eval = FALSE) ################################################### ## print(attr, activeOnly=TRUE) ################################################### -### code chunk number 59: BoolNet_package_vignette.Snw:648-649 +### code chunk number 59: BoolNet_package_vignette.Snw:650-651 ################################################### print(attr, activeOnly=TRUE) ################################################### -### code chunk number 60: BoolNet_package_vignette.Snw:658-659 +### code chunk number 60: BoolNet_package_vignette.Snw:660-661 ################################################### getAttractorSequence(attr, 2) ################################################### -### code chunk number 61: BoolNet_package_vignette.Snw:671-672 (eval = FALSE) +### code chunk number 61: BoolNet_package_vignette.Snw:673-674 (eval = FALSE) ################################################### ## plotAttractors(attr, subset=2) ################################################### -### code chunk number 62: BoolNet_package_vignette.Snw:674-678 +### code chunk number 62: BoolNet_package_vignette.Snw:676-680 ################################################### pdf("attractor1.pdf") par(mar=c(1,5,1,1)) @@ -452,32 +454,32 @@ ################################################### -### code chunk number 63: BoolNet_package_vignette.Snw:681-682 (eval = FALSE) +### code chunk number 63: BoolNet_package_vignette.Snw:683-684 (eval = FALSE) ################################################### ## attractorsToLaTeX(attr, subset=2, file="attractors.tex") ################################################### -### code chunk number 64: BoolNet_package_vignette.Snw:689-691 (eval = FALSE) +### code chunk number 64: BoolNet_package_vignette.Snw:691-693 (eval = FALSE) ################################################### ## tt <- getTransitionTable(attr) ## tt ################################################### -### code chunk number 65: BoolNet_package_vignette.Snw:705-706 (eval = FALSE) +### code chunk number 65: BoolNet_package_vignette.Snw:707-708 (eval = FALSE) ################################################### ## getBasinOfAttraction(attr, 1) ################################################### -### code chunk number 66: BoolNet_package_vignette.Snw:711-712 (eval = FALSE) +### code chunk number 66: BoolNet_package_vignette.Snw:713-714 (eval = FALSE) ################################################### ## getStateSummary(attr, c(1,1,1,1,1,1,1,1,1,1)) ################################################### -### code chunk number 67: BoolNet_package_vignette.Snw:724-729 +### code chunk number 67: BoolNet_package_vignette.Snw:726-731 ################################################### pdf("stategraph1.pdf") set.seed(43210) @@ -487,13 +489,13 @@ ################################################### -### code chunk number 68: BoolNet_package_vignette.Snw:731-732 (eval = FALSE) +### code chunk number 68: BoolNet_package_vignette.Snw:733-734 (eval = FALSE) ################################################### ## plotStateGraph(attr) ################################################### -### code chunk number 69: BoolNet_package_vignette.Snw:738-743 +### code chunk number 69: BoolNet_package_vignette.Snw:740-745 ################################################### pdf("piecewisestategraph.pdf") set.seed(43210) @@ -503,19 +505,19 @@ ################################################### -### code chunk number 70: BoolNet_package_vignette.Snw:745-746 (eval = FALSE) +### code chunk number 70: BoolNet_package_vignette.Snw:747-748 (eval = FALSE) ################################################### ## plotStateGraph(attr, piecewise=TRUE) ################################################### -### code chunk number 71: BoolNet_package_vignette.Snw:770-771 +### code chunk number 71: BoolNet_package_vignette.Snw:772-773 ################################################### attr <- getAttractors(cellcycle, method="random", startStates=100) ################################################### -### code chunk number 72: BoolNet_package_vignette.Snw:775-778 +### code chunk number 72: BoolNet_package_vignette.Snw:777-780 ################################################### attr <- getAttractors(cellcycle, method="chosen", @@ -523,14 +525,14 @@ ################################################### -### code chunk number 73: BoolNet_package_vignette.Snw:787-789 +### code chunk number 73: BoolNet_package_vignette.Snw:789-791 ################################################### attr <- getAttractors(cellcycle, method="sat.exhaustive") ################################################### -### code chunk number 74: BoolNet_package_vignette.Snw:794-797 +### code chunk number 74: BoolNet_package_vignette.Snw:796-799 ################################################### attr <- getAttractors(cellcycle, method="sat.restricted", @@ -538,19 +540,19 @@ ################################################### -### code chunk number 75: BoolNet_package_vignette.Snw:800-801 (eval = FALSE) +### code chunk number 75: BoolNet_package_vignette.Snw:802-803 (eval = FALSE) ################################################### ## attr ################################################### -### code chunk number 76: BoolNet_package_vignette.Snw:804-805 +### code chunk number 76: BoolNet_package_vignette.Snw:806-807 ################################################### attr ################################################### -### code chunk number 77: BoolNet_package_vignette.Snw:813-817 +### code chunk number 77: BoolNet_package_vignette.Snw:815-819 ################################################### attr <- getAttractors(cellcycle, type="asynchronous", @@ -559,13 +561,13 @@ ################################################### -### code chunk number 78: BoolNet_package_vignette.Snw:823-824 (eval = FALSE) +### code chunk number 78: BoolNet_package_vignette.Snw:825-826 (eval = FALSE) ################################################### ## attr ################################################### -### code chunk number 79: BoolNet_package_vignette.Snw:850-855 (eval = FALSE) +### code chunk number 79: BoolNet_package_vignette.Snw:852-857 (eval = FALSE) ################################################### ## attr <- getAttractors(cellcycle, ## type="asynchronous", @@ -575,7 +577,7 @@ ################################################### -### code chunk number 80: BoolNet_package_vignette.Snw:870-874 +### code chunk number 80: BoolNet_package_vignette.Snw:872-876 ################################################### pdf("attractor2.pdf") par(mar=c(1,1,1,1)) @@ -584,27 +586,27 @@ ################################################### -### code chunk number 81: BoolNet_package_vignette.Snw:876-877 (eval = FALSE) +### code chunk number 81: BoolNet_package_vignette.Snw:878-879 (eval = FALSE) ################################################### ## plotAttractors(attr, subset=2, mode="graph", drawLabels=FALSE) ################################################### -### code chunk number 82: BoolNet_package_vignette.Snw:885-887 (eval = FALSE) +### code chunk number 82: BoolNet_package_vignette.Snw:887-889 (eval = FALSE) ################################################### ## sim <- simulateSymbolicModel(igf) ## sim ################################################### -### code chunk number 83: BoolNet_package_vignette.Snw:890-892 +### code chunk number 83: BoolNet_package_vignette.Snw:892-894 ################################################### sim <- simulateSymbolicModel(igf) sim ################################################### -### code chunk number 84: BoolNet_package_vignette.Snw:906-914 +### code chunk number 84: BoolNet_package_vignette.Snw:908-916 ################################################### pdf("attractor3.pdf") par(mar=c(1,5,1,1)) @@ -617,49 +619,49 @@ ################################################### -### code chunk number 85: BoolNet_package_vignette.Snw:916-917 (eval = FALSE) +### code chunk number 85: BoolNet_package_vignette.Snw:918-919 (eval = FALSE) ################################################### ## plotAttractors(sim, subset=2) ################################################### -### code chunk number 86: BoolNet_package_vignette.Snw:920-921 (eval = FALSE) +### code chunk number 86: BoolNet_package_vignette.Snw:922-923 (eval = FALSE) ################################################### ## plotStateGraph(sim) ################################################### -### code chunk number 87: BoolNet_package_vignette.Snw:937-938 +### code chunk number 87: BoolNet_package_vignette.Snw:939-940 ################################################### set.seed(43851) ################################################### -### code chunk number 88: BoolNet_package_vignette.Snw:940-941 +### code chunk number 88: BoolNet_package_vignette.Snw:942-943 ################################################### sim <- simulateSymbolicModel(igf, method="random", startStates=2) ################################################### -### code chunk number 89: BoolNet_package_vignette.Snw:944-945 +### code chunk number 89: BoolNet_package_vignette.Snw:946-947 ################################################### sim$sequences ################################################### -### code chunk number 90: BoolNet_package_vignette.Snw:950-951 +### code chunk number 90: BoolNet_package_vignette.Snw:952-953 ################################################### sim <- simulateSymbolicModel(igf, method="sat.exhaustive") ################################################### -### code chunk number 91: BoolNet_package_vignette.Snw:954-955 +### code chunk number 91: BoolNet_package_vignette.Snw:956-957 ################################################### sim <- simulateSymbolicModel(igf, method="sat.restricted", maxAttractorLength=1) ################################################### -### code chunk number 92: BoolNet_package_vignette.Snw:971-974 +### code chunk number 92: BoolNet_package_vignette.Snw:973-976 ################################################### data(examplePBN) sim <- markovSimulation(examplePBN) @@ -667,13 +669,13 @@ ################################################### -### code chunk number 93: BoolNet_package_vignette.Snw:980-981 (eval = FALSE) +### code chunk number 93: BoolNet_package_vignette.Snw:982-983 (eval = FALSE) ################################################### ## plotPBNTransitions(sim) ################################################### -### code chunk number 94: BoolNet_package_vignette.Snw:983-988 +### code chunk number 94: BoolNet_package_vignette.Snw:985-990 ################################################### pdf("pbntransitions.pdf") set.seed(4961) @@ -683,7 +685,7 @@ ################################################### -### code chunk number 95: BoolNet_package_vignette.Snw:1001-1006 +### code chunk number 95: BoolNet_package_vignette.Snw:1003-1008 ################################################### data(cellcycle) sim <- markovSimulation(cellcycle, @@ -693,7 +695,7 @@ ################################################### -### code chunk number 96: BoolNet_package_vignette.Snw:1015-1020 +### code chunk number 96: BoolNet_package_vignette.Snw:1017-1022 ################################################### sim <- markovSimulation(cellcycle, numIterations=1024, @@ -703,13 +705,13 @@ ################################################### -### code chunk number 97: BoolNet_package_vignette.Snw:1032-1033 +### code chunk number 97: BoolNet_package_vignette.Snw:1034-1035 ################################################### set.seed(3361) ################################################### -### code chunk number 98: BoolNet_package_vignette.Snw:1035-1040 +### code chunk number 98: BoolNet_package_vignette.Snw:1037-1042 ################################################### data(cellcycle) r <- perturbTrajectories(cellcycle, @@ -719,13 +721,13 @@ ################################################### -### code chunk number 99: BoolNet_package_vignette.Snw:1044-1045 +### code chunk number 99: BoolNet_package_vignette.Snw:1046-1047 ################################################### r$value ################################################### -### code chunk number 100: BoolNet_package_vignette.Snw:1049-1054 +### code chunk number 100: BoolNet_package_vignette.Snw:1051-1056 ################################################### r <- perturbTrajectories(cellcycle, measure="sensitivity", @@ -735,13 +737,13 @@ ################################################### -### code chunk number 101: BoolNet_package_vignette.Snw:1056-1057 +### code chunk number 101: BoolNet_package_vignette.Snw:1058-1059 ################################################### r$value ################################################### -### code chunk number 102: BoolNet_package_vignette.Snw:1062-1067 +### code chunk number 102: BoolNet_package_vignette.Snw:1064-1069 ################################################### r <- perturbTrajectories(cellcycle, measure="attractor", @@ -751,7 +753,7 @@ ################################################### -### code chunk number 103: BoolNet_package_vignette.Snw:1074-1077 +### code chunk number 103: BoolNet_package_vignette.Snw:1076-1079 ################################################### perturbedNet <- perturbNetwork(cellcycle, perturb="functions", @@ -759,7 +761,7 @@ ################################################### -### code chunk number 104: BoolNet_package_vignette.Snw:1082-1085 +### code chunk number 104: BoolNet_package_vignette.Snw:1084-1087 ################################################### perturbedNet <- perturbNetwork(cellcycle, perturb="functions", @@ -767,7 +769,7 @@ ################################################### -### code chunk number 105: BoolNet_package_vignette.Snw:1091-1095 +### code chunk number 105: BoolNet_package_vignette.Snw:1093-1097 ################################################### perturbedNet <- perturbNetwork(cellcycle, perturb="transitions", @@ -776,7 +778,7 @@ ################################################### -### code chunk number 106: BoolNet_package_vignette.Snw:1103-1159 (eval = FALSE) +### code chunk number 106: BoolNet_package_vignette.Snw:1105-1161 (eval = FALSE) ################################################### ## # Perform a robustness test on a network ## # by counting the numbers of perturbed networks @@ -837,7 +839,7 @@ ################################################### -### code chunk number 107: BoolNet_package_vignette.Snw:1193-1198 (eval = FALSE) +### code chunk number 107: BoolNet_package_vignette.Snw:1195-1200 (eval = FALSE) ################################################### ## data(cellcycle) ## res <- testNetworkProperties(cellcycle, @@ -847,7 +849,7 @@ ################################################### -### code chunk number 108: BoolNet_package_vignette.Snw:1204-1213 +### code chunk number 108: BoolNet_package_vignette.Snw:1206-1215 ################################################### pdf("attractor_robustness.pdf") par(mar=c(4,4,2,1)) @@ -861,7 +863,7 @@ ################################################### -### code chunk number 109: BoolNet_package_vignette.Snw:1234-1239 (eval = FALSE) +### code chunk number 109: BoolNet_package_vignette.Snw:1236-1241 (eval = FALSE) ################################################### ## testNetworkProperties(cellcycle, ## numRandomNets=100, @@ -871,7 +873,7 @@ ################################################### -### code chunk number 110: BoolNet_package_vignette.Snw:1242-1252 +### code chunk number 110: BoolNet_package_vignette.Snw:1244-1254 ################################################### pdf("transition_robustness.pdf") par(mar=c(4,4,2,1)) @@ -886,7 +888,7 @@ ################################################### -### code chunk number 111: BoolNet_package_vignette.Snw:1257-1260 (eval = FALSE) +### code chunk number 111: BoolNet_package_vignette.Snw:1259-1262 (eval = FALSE) ################################################### ## testNetworkProperties(cellcycle, ## numRandomNets=100, @@ -894,7 +896,7 @@ ################################################### -### code chunk number 112: BoolNet_package_vignette.Snw:1262-1269 +### code chunk number 112: BoolNet_package_vignette.Snw:1264-1271 ################################################### pdf("indegree.pdf") par(mar=c(4,4,2,1)) @@ -906,7 +908,7 @@ ################################################### -### code chunk number 113: BoolNet_package_vignette.Snw:1286-1290 (eval = FALSE) +### code chunk number 113: BoolNet_package_vignette.Snw:1288-1292 (eval = FALSE) ################################################### ## testNetworkProperties(cellcycle, ## numRandomNets=100, @@ -915,7 +917,7 @@ ################################################### -### code chunk number 114: BoolNet_package_vignette.Snw:1292-1300 +### code chunk number 114: BoolNet_package_vignette.Snw:1294-1302 ################################################### pdf("indegree_kl.pdf") par(mar=c(4,4,2,1)) @@ -928,7 +930,7 @@ ################################################### -### code chunk number 115: BoolNet_package_vignette.Snw:1316-1328 +### code chunk number 115: BoolNet_package_vignette.Snw:1318-1330 ################################################### testBasinSizes <- function(network, accumulate=TRUE, params) { @@ -945,7 +947,7 @@ ################################################### -### code chunk number 116: BoolNet_package_vignette.Snw:1334-1338 (eval = FALSE) +### code chunk number 116: BoolNet_package_vignette.Snw:1336-1340 (eval = FALSE) ################################################### ## testNetworkProperties(cellcycle, ## numRandomNets=100, @@ -954,7 +956,7 @@ ################################################### -### code chunk number 117: BoolNet_package_vignette.Snw:1340-1348 +### code chunk number 117: BoolNet_package_vignette.Snw:1342-1350 ################################################### pdf("basinsize.pdf") par(mar=c(4,4,2,1)) @@ -967,20 +969,20 @@ ################################################### -### code chunk number 118: BoolNet_package_vignette.Snw:1371-1372 (eval = FALSE) +### code chunk number 118: BoolNet_package_vignette.Snw:1373-1374 (eval = FALSE) ################################################### ## saveNetwork(cellcycle, file="cellcycle.txt") ################################################### -### code chunk number 119: BoolNet_package_vignette.Snw:1377-1379 +### code chunk number 119: BoolNet_package_vignette.Snw:1379-1381 ################################################### net <- generateRandomNKNetwork(n=10, k=3, readableFunctions=FALSE) saveNetwork(net, file="randomnet.txt", generateDNF=TRUE) ################################################### -### code chunk number 120: BoolNet_package_vignette.Snw:1394-1397 +### code chunk number 120: BoolNet_package_vignette.Snw:1396-1399 ################################################### toSBML(cellcycle, file="cellcycle.sbml") sbml_cellcycle <- loadSBML("cellcycle.sbml") @@ -988,37 +990,37 @@ ################################################### -### code chunk number 121: BoolNet_package_vignette.Snw:1416-1417 (eval = FALSE) +### code chunk number 121: BoolNet_package_vignette.Snw:1418-1419 (eval = FALSE) ################################################### ## system.file("doc/example.btp", package="BoolNet") ################################################### -### code chunk number 122: BoolNet_package_vignette.Snw:1449-1450 +### code chunk number 122: BoolNet_package_vignette.Snw:1451-1452 ################################################### net <- loadBioTapestry(system.file("doc/example.btp", package="BoolNet")) ################################################### -### code chunk number 123: BoolNet_package_vignette.Snw:1452-1453 (eval = FALSE) +### code chunk number 123: BoolNet_package_vignette.Snw:1454-1455 (eval = FALSE) ################################################### ## net <- loadBioTapestry("example.btp") ################################################### -### code chunk number 124: BoolNet_package_vignette.Snw:1458-1459 (eval = FALSE) +### code chunk number 124: BoolNet_package_vignette.Snw:1460-1461 (eval = FALSE) ################################################### ## net ################################################### -### code chunk number 125: BoolNet_package_vignette.Snw:1482-1483 (eval = FALSE) +### code chunk number 125: BoolNet_package_vignette.Snw:1484-1485 (eval = FALSE) ################################################### ## plotNetworkWiring(net) ################################################### -### code chunk number 126: BoolNet_package_vignette.Snw:1485-1490 +### code chunk number 126: BoolNet_package_vignette.Snw:1487-1492 ################################################### pdf("wiring_biotap.pdf") par(mar=c(1,1,1,1)) @@ -1028,7 +1030,7 @@ ################################################### -### code chunk number 127: BoolNet_package_vignette.Snw:1511-1514 (eval = FALSE) +### code chunk number 127: BoolNet_package_vignette.Snw:1513-1516 (eval = FALSE) ################################################### ## data(cellcycle) ## attr <- getAttractors(cellcycle) @@ -1036,7 +1038,7 @@ ################################################### -### code chunk number 128: BoolNet_package_vignette.Snw:1518-1519 (eval = FALSE) +### code chunk number 128: BoolNet_package_vignette.Snw:1520-1521 (eval = FALSE) ################################################### ## toPajek(attr, file="cellcycle.net", includeLabels=TRUE) diff -Nru r-cran-boolnet-2.1.3/inst/doc/BoolNet_package_vignette.Snw r-cran-boolnet-2.1.4/inst/doc/BoolNet_package_vignette.Snw --- r-cran-boolnet-2.1.3/inst/doc/BoolNet_package_vignette.Snw 2016-06-24 13:47:18.000000000 +0000 +++ r-cran-boolnet-2.1.4/inst/doc/BoolNet_package_vignette.Snw 2018-05-23 09:02:15.000000000 +0000 @@ -496,10 +496,12 @@ <>= pdf("sequence.pdf") par(mar = c(1, 4, 2, 1)) -plotSequence(sequence = path) +path <- getPathToAttractor(cellcycle, rep(0,10)) +plotSequence(sequence=path) dev.off() @ <>= +path <- getPathToAttractor(cellcycle, rep(0,10)) plotSequence(sequence=path) @ diff -Nru r-cran-boolnet-2.1.3/inst/NEWS.Rd r-cran-boolnet-2.1.4/inst/NEWS.Rd --- r-cran-boolnet-2.1.3/inst/NEWS.Rd 2016-06-24 13:29:00.000000000 +0000 +++ r-cran-boolnet-2.1.4/inst/NEWS.Rd 2018-05-23 09:50:31.000000000 +0000 @@ -1,10 +1,9 @@ \name{NEWS} \title{NEWS file for the \pkg{BoolNet} package} -\section{Changes in version 2.1.1}{ +\section{Changes in version 2.1.4}{ \itemize{ -\item{Minor bug fixing in \code{plotStateGraph}.} -\item{Added cosmetic changes to \code{plotAttractors} and \code{plotSequence}.} +\item{\code{getAttractors()} now allows for plotting all attractors inside one plot. Fixed minor bugs.} } } diff -Nru r-cran-boolnet-2.1.3/man/BoolNet-package.Rd r-cran-boolnet-2.1.4/man/BoolNet-package.Rd --- r-cran-boolnet-2.1.3/man/BoolNet-package.Rd 2016-06-21 14:20:36.000000000 +0000 +++ r-cran-boolnet-2.1.4/man/BoolNet-package.Rd 2018-05-23 09:48:48.000000000 +0000 @@ -9,8 +9,8 @@ \tabular{ll}{ Package: \tab BoolNet\cr Type: \tab Package\cr -Version: \tab 2.1.2\cr -Date: \tab 2015-07-03\cr +Version: \tab 2.1.4\cr +Date: \tab 2018-05-23\cr License: \tab Artistic-2.0\cr LazyLoad: \tab yes\cr } diff -Nru r-cran-boolnet-2.1.3/man/plotAttractors.Rd r-cran-boolnet-2.1.4/man/plotAttractors.Rd --- r-cran-boolnet-2.1.3/man/plotAttractors.Rd 2016-06-24 13:35:05.000000000 +0000 +++ r-cran-boolnet-2.1.4/man/plotAttractors.Rd 2018-05-17 09:46:07.000000000 +0000 @@ -49,9 +49,9 @@ \item{plotFixed}{This optional parameter is only used if \code{mode="table"}. If this is true, genes with fixed values are included in the plot. Otherwise, these genes are not drawn. } - \item{onColor}{This optional parameter is only used if \code{mode="table"} and specifies the color value for the 1/ON values in the table. Defaults to greenish color. + \item{onColor}{This optional parameter is only used if \code{mode="table"} and specifies the color value for the 1/ON values in the table. Defaults to green. } - \item{offColor}{This optional parameter is only used if \code{mode="table"} and specifies the color value for the 0/OFF values in the table. Defaults to reddish color. + \item{offColor}{This optional parameter is only used if \code{mode="table"} and specifies the color value for the 0/OFF values in the table. Defaults to red. } \item{layout}{If \code{mode="graph"}, this parameter specifies a layouting function that determines the placement of the nodes in the graph. Please refer to the \code{\link[igraph]{layout}} manual entry in the \pkg{igraph} package for further details. By default, the circle layout is used. diff -Nru r-cran-boolnet-2.1.3/man/plotSequence.Rd r-cran-boolnet-2.1.4/man/plotSequence.Rd --- r-cran-boolnet-2.1.3/man/plotSequence.Rd 2016-06-24 13:34:51.000000000 +0000 +++ r-cran-boolnet-2.1.4/man/plotSequence.Rd 2018-05-23 08:59:58.000000000 +0000 @@ -14,8 +14,8 @@ title = "", mode=c("table","graph"), plotFixed = TRUE, grouping = list(), - onColor="#4daf4a", - offColor="#e41a1c", + onColor="#4daf4a", + offColor = "#e41a1c", layout, drawLabels=TRUE, drawLegend=TRUE, @@ -61,9 +61,9 @@ \item{index}{A list with the same length as \code{class}. Each element is a vector of gene names or gene indices belonging to the group.}} } - \item{onColor}{This optional parameter is only used if \code{mode="table"} and specifies the color value for the 1/ON values in the table. Defaults to greenish color. + \item{onColor}{This optional parameter is only used if \code{mode="table"} and specifies the color value for the 1/ON values in the table. Defaults to green. } - \item{offColor}{This optional parameter is only used if \code{mode="table"} and specifies the color value for the 0/OFF values in the table. Defaults to reddish color. + \item{offColor}{This optional parameter is only used if \code{mode="table"} and specifies the color value for the 0/OFF values in the table. Defaults to red. } \item{layout}{If \code{mode="graph"}, this parameter specifies a layouting function that determines the placement of the nodes in the graph. Please refer to the \code{\link[igraph]{layout}} manual entry in the \pkg{igraph} package for further details. By default, the nodes are placed in a horizontal line. diff -Nru r-cran-boolnet-2.1.3/MD5 r-cran-boolnet-2.1.4/MD5 --- r-cran-boolnet-2.1.3/MD5 2016-11-21 11:23:47.000000000 +0000 +++ r-cran-boolnet-2.1.4/MD5 2018-06-07 17:43:59.000000000 +0000 @@ -1,5 +1,5 @@ -ff810381b175b295970c5b706d6bf4de *DESCRIPTION -9f03faf9050bd5ddf3d3c1833207bb0a *NAMESPACE +379f5e8a5ba709f2ae276a04db45c56c *DESCRIPTION +9784bbd31ff5e76e9a8013fb1718d14d *NAMESPACE 57679970d38c17ac9c95478b9313aed0 *R/attractorsToLaTeX.R 0e037f01fa88a832cb43d3a9d5e9f5dd *R/binarizeTimeSeries.R ec2c323ef07745ec7b89339aa5a4433c *R/chooseNetwork.R @@ -16,7 +16,7 @@ 9637fc5badfec905a1d865d5e65d3839 *R/getStateSummary.R a45f67785e1846f8482c9ff10debd95c *R/getTransitionProbabilities.R d31c9950c1a42c23eb5585c23e98bb25 *R/getTransitionTable.R -fcedd10ae785f0be113ea1ea2e66b091 *R/helpers.R +553c3f023784f01d73c69c469d14ea53 *R/helpers.R 8e0fdeac893b8bfc8837c9d94e9ed1f9 *R/loadBioTapestry.R f1e4da50ef5dd5ea083b8fcd060b3f77 *R/loadNetwork.R aa19fa3aaa70362a5d5d18bb114c245c *R/loadSBML.R @@ -27,7 +27,7 @@ b3c6b0765a241bb1d4e4a150f47d3d8b *R/plotAttractors.R 20fd67145509cae5e9701fcfa93e210c *R/plotNetworkWiring.R 9f64811ec997a7aa2fc262725ae6f7e5 *R/plotPBNTransitions.R -da8b7350847b5c4715a67c34fe829f53 *R/plotSequence.R +6404119c6511b8c5741721d6cd237276 *R/plotSequence.R 3e92ac93c5ce1934d542b3eb7985aa44 *R/plotStateGraph.R 1d3e5b86636a5b54035d7062285e34e4 *R/print.AttractorInfo.R bd5b5182c9a4321e0051be7f40bcbf6f *R/print.BooleanNetwork.R @@ -50,19 +50,19 @@ 47bc51ada1eefa53c11e0171a589bc8b *R/toSBML.R dab752c2c82ef4e5e93224ad6934208c *R/truthTableToSymbolic.R 811f12cc71a25cbf23ade7eb93bb2162 *R/zeta.R -bcc619228d6f025ff8cd6e2a77f73def *build/vignette.rds +55c1fc26be7d0ac68b11f7e3568dd6aa *build/vignette.rds 6323b9a68ede50d320ceffa342711988 *data/cellcycle.rda 2162a3dfd9f29f06223413307dd177c8 *data/examplePBN.rda d58578f1cc7da58378f1617a6d8bb021 *data/igf.rda 8919de127f7ee2391900468a36c5dcd4 *data/yeastTimeSeries.rda 62409980eecaca8e52f1d495f499d6bd *inst/CITATION -313ba5036165b50314bb2ec3372150f6 *inst/NEWS.Rd -d9ed6c7ca4c6531245a460d64ef5281b *inst/doc/BoolNet_package_vignette.R -14df741a8cec94d3f34e4077bd665062 *inst/doc/BoolNet_package_vignette.Snw -c73445a79cd51131c37d631bb93be53a *inst/doc/BoolNet_package_vignette.pdf +064f1e9310a405f967a891c4a615d8e6 *inst/NEWS.Rd +afb80529a9bc54d2cc270ecf679e58d8 *inst/doc/BoolNet_package_vignette.R +4145b7d121ce7237afd95336a8c0e899 *inst/doc/BoolNet_package_vignette.Snw +077f49f4364c7c9356f17a11d813da06 *inst/doc/BoolNet_package_vignette.pdf fcb0ddc4a26eb5062f05b55032e5b151 *inst/doc/cellcycle.txt 27bccf40991bbe762bc274cbd7874f40 *inst/doc/example.btp -5fb48be5bfbec8ac6e8a2a6dadcc317e *man/BoolNet-package.Rd +cd4180d541f3f016d9b1c2a04b27a72d *man/BoolNet-package.Rd 67caa758b9f663491e69a3c18f4ee36f *man/attractorsToLaTeX.Rd 3461bfd43dd57a88d01d83df611f95c0 *man/binarizeTimeSeries.Rd 3623b2fe85476af5336cf7e220c1d60e *man/cellcycle.Rd @@ -87,10 +87,10 @@ c859af507471ba3da30d304d90622a83 *man/markovSimulation.Rd 1592f64ef13d306cbc4110ae2ce8f604 *man/perturbNetwork.Rd 196308b14d4adf113e9a71211c9018cf *man/perturbTrajectories.Rd -9484e9a7865353afdf2e1e79363890ff *man/plotAttractors.Rd +67a72a4ba20f295c1ac6df8beed67471 *man/plotAttractors.Rd c7904f48e78584e4ad19f1f88c897398 *man/plotNetworkWiring.Rd 2638a35d79eddce77b3cac8e6cd995b9 *man/plotPBNTransitions.Rd -246effe1700433b4173c699150802ee9 *man/plotSequence.Rd +14494768e2d21361527b3636273ed637 *man/plotSequence.Rd 4fd22acacd58b14152afe03320b8600f *man/plotStateGraph.Rd 5f379a9e2b4a9a418d8b665af74757be *man/print.AttractorInfo.Rd e0b2b98da9c074e4e30dd73d57dae9da *man/print.BooleanNetwork.Rd @@ -115,22 +115,23 @@ 8b25f0694d6279bba2e28c947e304524 *src/attractor_info.h 036826c4ebee96d5885709f10efbd391 *src/attractor_search_interface.c 8e4fdfd767d86b61f15c5c245e8dba77 *src/boolean_network.h -8bcc0d40927949da8d50a8b116fc45d9 *src/common.c -156f9c56866c9e7707594d1f0faf101b *src/common.h +7e1bc399f8290fba5715ae68f560e5eb *src/common.c +8b9a314ecf353576c5d9199a8fc9d97d *src/common.h +777df32f6a8cb6981deb459bde233165 *src/init.c 3ae7901969630cf0f1c12ac9024957eb *src/picosat.c 2c29607ee624151f84ac09f55535010e *src/picosat.h a869a6a74b9c0a1c4c796003c1251d60 *src/probabilistic_boolean_network.c 686e443cfcfa3f597ea866bc25c356e7 *src/random.h -58be262aa256be87d8d8cf3cf63abfb3 *src/reconstruct_network.c +a18cb9116413559c5438e6f25e8f7149 *src/reconstruct_network.c 22bc54f938607f08f72f1fbbf7289b7c *src/sat_search.c 0d6515ab8ff7605f16ca10eb5c6fc9e4 *src/sat_search.h 351d201ca2f926bdd1b5f4694de19902 *src/statespace_search.c c085761b2f853545febe7170a3715eb2 *src/statespace_search.h 4d4e389c0ff626a5e0db88416991e94e *src/symbolic_network.c dbbf4848847aefb8b756d749519bdf1d *src/symbolic_network.h -a92bedbf4bd0438dab983bd4713b6456 *src/symbolic_simulator.c +e6dbdce5060446eefdc62946f9cfdea5 *src/symbolic_simulator.c 460b4e88a7af5ba2c60231ca9f3644c8 *src/uthash.h -14df741a8cec94d3f34e4077bd665062 *vignettes/BoolNet_package_vignette.Snw +4145b7d121ce7237afd95336a8c0e899 *vignettes/BoolNet_package_vignette.Snw 45d3f76bd49d22f8d6e0ad5cc2a14c62 *vignettes/BoolNet_package_vignette.bib cbc02d945670e5381418720262b10955 *vignettes/biotap_initval.png 530409792bed5d5a53140e85554b9d61 *vignettes/biotap_logic.png diff -Nru r-cran-boolnet-2.1.3/NAMESPACE r-cran-boolnet-2.1.4/NAMESPACE --- r-cran-boolnet-2.1.3/NAMESPACE 2016-06-24 13:37:56.000000000 +0000 +++ r-cran-boolnet-2.1.4/NAMESPACE 2018-05-23 09:40:34.000000000 +0000 @@ -1,11 +1,11 @@ -useDynLib(BoolNet) +useDynLib(BoolNet, .registration = TRUE) import("igraph", "XML") importFrom("graphics", "abline", "arrows", "axis", "hist", "legend", "lines", "par", "plot", "rect", "text") +importFrom("grDevices", "adjustcolor") importFrom("grDevices", "dev.interactive") importFrom("stats", "dist", "kmeans", "quantile", "rnorm", "rpois", "runif") importFrom("utils", "installed.packages", "tail") -importFrom("grDevices", "adjustcolor") S3method(print, AttractorInfo) S3method(print, SymbolicSimulation) diff -Nru r-cran-boolnet-2.1.3/R/helpers.R r-cran-boolnet-2.1.4/R/helpers.R --- r-cran-boolnet-2.1.3/R/helpers.R 2016-06-21 14:20:36.000000000 +0000 +++ r-cran-boolnet-2.1.4/R/helpers.R 2018-05-23 11:30:37.000000000 +0000 @@ -10,7 +10,7 @@ dec = rep(0,numElts) - dec = .C("bin2dec",as.integer(dec),as.integer(bin),as.integer(len))[[1]] + dec = .C("bin2decC",as.integer(dec),as.integer(bin),as.integer(len))[[1]] } # Decode the low-order bits of to a vector of binary values, @@ -19,7 +19,7 @@ { bin = rep(0,len) - bin = .C("dec2bin",as.integer(bin),as.integer(dec),as.integer(len),NAOK=TRUE)[[1]] + bin = .C("dec2binC",as.integer(bin),as.integer(dec),as.integer(len),NAOK=TRUE)[[1]] } # Generate a list of all assignments of n variables with N possible values @@ -339,7 +339,7 @@ # Check whether the internal C pointer is null checkNullPointer <- function(ptr) { - return(.Call("checkNullPointer",ptr)) + return(.Call("checkNullPointerC",ptr)) } # Print a synchronous attractor specified by a data frame diff -Nru r-cran-boolnet-2.1.3/R/plotSequence.R r-cran-boolnet-2.1.4/R/plotSequence.R --- r-cran-boolnet-2.1.3/R/plotSequence.R 2016-06-24 12:38:50.000000000 +0000 +++ r-cran-boolnet-2.1.4/R/plotSequence.R 2018-05-23 09:10:47.000000000 +0000 @@ -26,9 +26,8 @@ } } else { - if (missing(sequence) || !missing(startState)) { + if (missing(sequence) || !missing(startState)) stop("Either \"network\" and \"startState\" or \"sequence\" must be provided!") - } } switch(match.arg(mode, c("table", "graph")), table = { totalMatrix <- t(sequence) @@ -95,8 +94,8 @@ } #if (drawLegend) legend(x = "bottomright", pch = c(15, 15), col = c(onColor, offColor), legend = c("active", "inactive"), cex = 0.7, horiz = T) if (drawLegend) legend(x = 0, y = -2, pch = c(15, 15), col = c(onColor, offColor), legend = c("active", "inactive"), cex = 0.7, horiz = T, xpd=T) - netGenes <- if (missing(network)) colnames(sequence) else network$genes - return(totalMatrix[netGenes,,drop=F]) + #return(totalMatrix[network$genes,]) + return(totalMatrix) }, graph = { if (installed.packages()["igraph", "Version"] < package_version("0.6")) bias <- 1 else bias <- 0 args <- list(...) diff -Nru r-cran-boolnet-2.1.3/src/common.c r-cran-boolnet-2.1.4/src/common.c --- r-cran-boolnet-2.1.3/src/common.c 2016-06-24 13:47:18.000000000 +0000 +++ r-cran-boolnet-2.1.4/src/common.c 2018-05-23 11:35:57.000000000 +0000 @@ -30,7 +30,7 @@ * is an array of elements, and points * to an integer to which the result is written. */ -void bin2dec(int *dec, int *bin, int *numBits) +void bin2decC(int *dec, int *bin, int *numBits) { // clear output first unsigned int numElts; @@ -57,7 +57,7 @@ * points to the result vector, is a number * to be decoded, and is the number of bits/elements in bin */ -void dec2bin(int *bin, int *dec, int *numBits) +void dec2binC(int *bin, int *dec, int *numBits) { unsigned int i; unsigned int * unsigned_dec = (unsigned int *) dec; @@ -100,7 +100,7 @@ } // re-encode Boolean array to integer value - bin2dec((int *)value,(int*)tmp,(int*)&numGenes); + bin2decC((int *)value,(int*)tmp,(int*)&numGenes); } /** @@ -129,7 +129,7 @@ } // re-encode Boolean array to integer value - bin2dec((int *)value,(int*)tmp,(int*)&numGenes); + bin2decC((int *)value,(int*)tmp,(int*)&numGenes); } diff -Nru r-cran-boolnet-2.1.3/src/common.h r-cran-boolnet-2.1.4/src/common.h --- r-cran-boolnet-2.1.3/src/common.h 2016-06-24 13:47:18.000000000 +0000 +++ r-cran-boolnet-2.1.4/src/common.h 2018-05-23 11:35:57.000000000 +0000 @@ -159,8 +159,9 @@ /** * Free all remaining memory blocks stored in * the global map. + * moved to init.c */ -extern void freeAllMemory(); +//extern void freeAllMemory(); /** * A structure that provides flexible @@ -203,16 +204,18 @@ * The rightmost element in is the leftmost bit in * is an array of elements, and points * to an integer to which the result is written. + * Moved to init.c */ -extern void bin2dec(int *dec, int *bin, int *numBits); +extern void bin2decC(int *dec, int *bin, int *numBits); /** * Decode an integer to a vector of binary values. * The rightmost element in is the leftmost bit in * points to the result vector, is a number * to be decoded, and is the number of bits/elements in bin + * moved to init.c */ -extern void dec2bin(int *bin, int *dec, int *numBits); +extern void dec2binC(int *bin, int *dec, int *numBits); /** * Inserts values of fixed genes into states - this is required as diff -Nru r-cran-boolnet-2.1.3/src/init.c r-cran-boolnet-2.1.4/src/init.c --- r-cran-boolnet-2.1.3/src/init.c 1970-01-01 00:00:00.000000000 +0000 +++ r-cran-boolnet-2.1.4/src/init.c 2018-05-23 11:35:57.000000000 +0000 @@ -0,0 +1,46 @@ +#include +#include +#include // for NULL +#include + +/* .C calls */ +extern void bin2decC(void *, void *, void *); +extern void dec2binC(void *, void *, void *); +extern void freeAllMemory(); + +/* .Call calls */ +extern SEXP checkNullPointerC(SEXP); +extern SEXP constructNetworkTrees_R(SEXP); +extern SEXP getAttractors_R(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP); +extern SEXP getTruthTable_R(SEXP, SEXP); +extern SEXP markovSimulation_R(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP); +extern SEXP reconstructNetwork_R(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP); +extern SEXP simulateStates_R(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP); +extern SEXP symbolicSATSearch_R(SEXP, SEXP, SEXP); +extern SEXP symbolicStateTransition_R(SEXP, SEXP, SEXP); + +static const R_CMethodDef CEntries[] = { + {"bin2decC", (DL_FUNC) &bin2decC, 3}, + {"dec2binC", (DL_FUNC) &dec2binC, 3}, + {"freeAllMemory", (DL_FUNC) &freeAllMemory, 0}, + {NULL, NULL, 0} +}; + +static const R_CallMethodDef CallEntries[] = { + {"checkNullPointerC", (DL_FUNC) &checkNullPointerC, 1}, + {"constructNetworkTrees_R", (DL_FUNC) &constructNetworkTrees_R, 1}, + {"getAttractors_R", (DL_FUNC) &getAttractors_R, 12}, + {"getTruthTable_R", (DL_FUNC) &getTruthTable_R, 2}, + {"markovSimulation_R", (DL_FUNC) &markovSimulation_R, 11}, + {"reconstructNetwork_R", (DL_FUNC) &reconstructNetwork_R, 10}, + {"simulateStates_R", (DL_FUNC) &simulateStates_R, 6}, + {"symbolicSATSearch_R", (DL_FUNC) &symbolicSATSearch_R, 3}, + {"symbolicStateTransition_R", (DL_FUNC) &symbolicStateTransition_R, 3}, + {NULL, NULL, 0} +}; + +void R_init_BoolNet(DllInfo *dll) +{ + R_registerRoutines(dll, CEntries, CallEntries, NULL, NULL); + R_useDynamicSymbols(dll, FALSE); +} diff -Nru r-cran-boolnet-2.1.3/src/reconstruct_network.c r-cran-boolnet-2.1.4/src/reconstruct_network.c --- r-cran-boolnet-2.1.3/src/reconstruct_network.c 2016-06-24 13:47:18.000000000 +0000 +++ r-cran-boolnet-2.1.4/src/reconstruct_network.c 2018-05-23 11:35:57.000000000 +0000 @@ -1065,7 +1065,7 @@ if (_returnPBN) // for PBN, functions are internally represented as bit vectors to save memory - dec2bin(array,(int*)cur->transitionFunction,(int*)&numBits); + dec2binC(array,(int*)cur->transitionFunction,(int*)&numBits); else // for incomplete truth tables, we need a third "don't care" value // hence, each bit is an integer in this case (but far fewer entries => less memory) diff -Nru r-cran-boolnet-2.1.3/src/symbolic_simulator.c r-cran-boolnet-2.1.4/src/symbolic_simulator.c --- r-cran-boolnet-2.1.3/src/symbolic_simulator.c 2016-06-24 13:47:18.000000000 +0000 +++ r-cran-boolnet-2.1.4/src/symbolic_simulator.c 2018-05-23 11:35:57.000000000 +0000 @@ -1379,7 +1379,7 @@ /** * Check whether is a null pointer. */ -SEXP checkNullPointer(SEXP ptr) +SEXP checkNullPointerC(SEXP ptr) { void * p = R_ExternalPtrAddr(ptr); diff -Nru r-cran-boolnet-2.1.3/vignettes/BoolNet_package_vignette.Snw r-cran-boolnet-2.1.4/vignettes/BoolNet_package_vignette.Snw --- r-cran-boolnet-2.1.3/vignettes/BoolNet_package_vignette.Snw 2016-06-24 12:40:18.000000000 +0000 +++ r-cran-boolnet-2.1.4/vignettes/BoolNet_package_vignette.Snw 2018-05-23 09:02:15.000000000 +0000 @@ -496,10 +496,12 @@ <>= pdf("sequence.pdf") par(mar = c(1, 4, 2, 1)) -plotSequence(sequence = path) +path <- getPathToAttractor(cellcycle, rep(0,10)) +plotSequence(sequence=path) dev.off() @ <>= +path <- getPathToAttractor(cellcycle, rep(0,10)) plotSequence(sequence=path) @