==569445== Memcheck, a memory error detector ==569445== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==569445== Using Valgrind-3.16.1 and LibVEX; rerun with -h for copyright info ==569445== Command: /data/blackswan/ripley/R/R-devel-vg/bin/exec/R --vanilla ==569445== R Under development (unstable) (2021-04-15 r80174) -- "Unsuffered Consequences" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale 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. > pkgname <- "alineR" > source(file.path(R.home("share"), "R", "examples-header.R")) > options(warn = 1) > library('alineR') > > base::assign(".oldSearch", base::search(), pos = 'CheckExEnv') > base::assign(".old_wd", base::getwd(), pos = 'CheckExEnv') > cleanEx() > nameEx("ALINE.map") > ### * ALINE.map > > flush(stderr()); flush(stdout()) > > ### Name: ALINE.map > ### Title: Aline IPA-ASCII character map > ### Aliases: ALINE.map > ### Keywords: datasets > > ### ** Examples > > data(ALINE.map) > > > > cleanEx() > nameEx("ALINE.segments") > ### * ALINE.segments > > flush(stderr()); flush(stdout()) > > ### Name: ALINE.segments > ### Title: Similarity scores of aligned segments > ### Aliases: ALINE.segments > ### Keywords: Similarity Score alignment > > ### ** Examples > > # align words > result<-raw.alignment(c("watu","dat")) ==569445== Invalid read of size 4 ==569445== at 0x48B3C88: exchange (packages/tests-vg/alineR/src/alineR.cpp:19) ==569445== by 0x49D33F: R_doDotCall (svn/R-devel/src/main/dotcode.c:604) ==569445== by 0x49D823: do_dotcall (svn/R-devel/src/main/dotcode.c:1281) ==569445== by 0x4DA78A: bcEval (svn/R-devel/src/main/eval.c:7671) ==569445== by 0x4F0237: Rf_eval (svn/R-devel/src/main/eval.c:727) ==569445== by 0x4F1C4D: R_execClosure (svn/R-devel/src/main/eval.c:1897) ==569445== by 0x4F2943: Rf_applyClosure (svn/R-devel/src/main/eval.c:1823) ==569445== by 0x4F0403: Rf_eval (svn/R-devel/src/main/eval.c:850) ==569445== by 0x4F4459: do_set (svn/R-devel/src/main/eval.c:2969) ==569445== by 0x4F0684: Rf_eval (svn/R-devel/src/main/eval.c:802) ==569445== by 0x5214EC: Rf_ReplIteration (svn/R-devel/src/main/main.c:264) ==569445== by 0x521837: R_ReplConsole (svn/R-devel/src/main/main.c:314) ==569445== Address 0xef5a168 is 1,448 bytes inside a block of size 7,960 alloc'd ==569445== at 0x483A809: malloc (/builddir/build/BUILD/valgrind-3.16.1/coregrind/m_replacemalloc/vg_replace_malloc.c:307) ==569445== by 0x52BC80: GetNewPage (svn/R-devel/src/main/memory.c:946) ==569445== by 0x52D91B: Rf_allocVector3 (svn/R-devel/src/main/memory.c:2784) ==569445== by 0x588B09: Rf_allocVector (svn/R-devel/src/include/Rinlinedfuns.h:595) ==569445== by 0x588B09: ReadItem (svn/R-devel/src/main/serialize.c:1943) ==569445== by 0x589E8C: ReadBC1 (svn/R-devel/src/main/serialize.c:2125) ==569445== by 0x58A045: ReadBCConsts (svn/R-devel/src/main/serialize.c:2098) ==569445== by 0x58A045: ReadBC1 (svn/R-devel/src/main/serialize.c:2129) ==569445== by 0x58A045: ReadBCConsts (svn/R-devel/src/main/serialize.c:2098) ==569445== by 0x58A045: ReadBC1 (svn/R-devel/src/main/serialize.c:2129) ==569445== by 0x5892F9: ReadBC (svn/R-devel/src/main/serialize.c:2140) ==569445== by 0x5892F9: ReadItem (svn/R-devel/src/main/serialize.c:1977) ==569445== by 0x588331: ReadItem (svn/R-devel/src/main/serialize.c:1884) ==569445== by 0x58C0C4: R_Unserialize (svn/R-devel/src/main/serialize.c:2192) ==569445== by 0x58D32F: R_unserialize (svn/R-devel/src/main/serialize.c:2907) ==569445== by 0x58D731: do_lazyLoadDBfetch (svn/R-devel/src/main/serialize.c:3207) ==569445== > > # print the alignment followed by the sim score > # for each pair of aligned segments > cat(result[[3]],result[[4]],sep='\n') | - w a t | u | d - a t | - > ALINE.segments(result) [1] 0 0 15 35 > > > > > cleanEx() > nameEx("aline") > ### * aline > > flush(stderr()); flush(stdout()) > > ### Name: aline > ### Title: Calculate aline distances > ### Aliases: aline > > ### ** Examples > > x<-c(intToUtf8(c(361,109,108,97,116,952)),intToUtf8(c(100,105,331,331,105,114,97))) > y<-c(intToUtf8(c(418,109,108,97,116,952)),intToUtf8(c(100,105,110,110,105,114,97))) > # For CRAN requirement, to see x and y, type x,y in R console > x [1] "ũmlatθ" "diŋŋira" > y [1] "Ƣmlatθ" "dinnira" > aline(w1=x,w2=y) # A warning is returned because of unknown character Invalid character: Ƣ in Ƣmlatθ [1] 0.04615385 0.10810811 > > # user substitution > aline(w1=x,w2=y,m1=intToUtf8(418),m2="o") [1] 0.07647059 0.10810811 > > > > cleanEx() > nameEx("decode.ALINE") > ### * decode.ALINE > > flush(stderr()); flush(stdout()) > > ### Name: decode.ALINE > ### Title: Decode ALINE ASCII output > ### Aliases: decode.ALINE > > ### ** Examples > > x<-intToUtf8(c(611,117,108,108,97)) > y<-"| gS u l l a | " > decode.ALINE(x,y) [1] "| ɣ u l l a | " > > # user-specified mapping. Should be consistent with encode.ALINE() function > x<-intToUtf8(c(418,109,108,97,116,952)) > y<-"| o m l a t tS | " > decode.ALINE(x,y,m1=intToUtf8(418), m2="o") [1] "| Ƣ m l a t θ | " > > > > cleanEx() > nameEx("encode.ALINE") > ### * encode.ALINE > > flush(stderr()); flush(stdout()) > > ### Name: encode.ALINE > ### Title: Encode IPA as ALINE ASCII notation > ### Aliases: encode.ALINE > > ### ** Examples > > y<-c(intToUtf8(c(418,109,108,97,116,952)),intToUtf8(c(100,105,110,110,105,114,97))) > y [1] "Ƣmlatθ" "dinnira" > encode.ALINE(y,m1=intToUtf8(418), m2="o") Ƣmlatθ dinnira "omlattS" "dinnira" > > > > cleanEx() > nameEx("features.plot") > ### * features.plot > > flush(stderr()); flush(stdout()) > > ### Name: features.plot > ### Title: Plot feature optimization result > ### Aliases: features.plot > > ### ** Examples > > data<-data.frame(dog=c('dog','perro'),cat=c('cat','gato'),rat=c('rat','rata')) > M1<-generate.training(raw.data=data,search.size=100,table=FALSE) > M2<-optimize.features(set=M1,ranking=c(1,1,1), + num=20,step=5,replication=2,list=TRUE) > features.plot(M2) > > > > cleanEx() > nameEx("generate.training") > ### * generate.training > > flush(stderr()); flush(stdout()) > > ### Name: generate.training > ### Title: Generate training dataset > ### Aliases: generate.training > ### Keywords: csv Table Candiate Alignments to Choose From > > ### ** Examples > > # some cognates > data<-data.frame(dog=c('dog','perro'),cat=c('cat','gato'),rat=c('rat','rata')) > > # write out a CSV file that can be openned in Excel and used for expert determinations > M<-generate.training(raw.data=data,search.size=100,file="open.with.excel.csv") > > > > > cleanEx() > nameEx("map") > ### * map > > flush(stderr()); flush(stdout()) > > ### Name: map > ### Title: User-defined Mappings > ### Aliases: map > > ### ** Examples > > map(intToUtf8(418),"dX") #valid Aline U.Val A.Val 1 dX 418 100 88 2 32 3 bS 66 98 83 4 oF 79 111 70 5 a 97 97 6 b 98 98 7 tP 99 116 80 8 d 100 100 9 e 101 101 10 f 102 102 11 g 103 103 12 h 104 104 13 i 105 105 14 y 106 121 15 k 107 107 16 l 108 108 17 m 109 109 18 n 110 110 19 o 111 111 20 p 112 112 21 k 113 107 22 r 114 114 23 s 115 115 24 t 116 116 25 u 117 117 26 v 118 118 27 w 119 119 28 x 120 120 29 uF 121 117 70 30 z 122 122 31 bS 223 98 83 32 a 225 97 33 a 226 97 34 aN 227 97 78 35 aF 230 97 70 36 e 233 101 37 e 234 101 38 i 236 105 39 i 237 105 40 i 238 105 41 dSD 240 100 83 68 42 o 243 111 43 o 244 111 44 oN 245 111 78 45 oF 248 111 70 46 u 249 117 47 u 250 117 48 u 251 117 49 iN 297 105 78 50 iH 299 105 72 51 gN 331 103 78 52 uN 361 117 78 53 a 592 97 54 a 593 97 55 a 594 97 56 b 595 98 57 o 596 111 58 sP 597 115 80 59 dX 598 100 88 60 eC 601 101 67 61 e 603 101 62 eC 604 101 67 63 dP 607 100 80 64 g 610 103 65 gS 611 103 83 66 h 614 104 67 iC 616 105 67 68 i 618 105 69 lA 620 108 65 70 lX 621 108 88 71 lS 622 108 83 72 w 624 119 73 fN 625 102 78 74 nP 626 110 80 75 nX 627 110 88 76 gN 628 103 78 77 oF 630 111 70 78 pS 632 112 83 79 rX 637 114 88 80 r 638 114 81 r 640 114 82 gS 641 103 83 83 sX 642 115 88 84 sV 643 115 86 85 tX 648 116 88 86 uC 649 117 67 87 u 650 117 88 v 651 118 89 eC 652 101 67 90 lP 654 108 80 91 zX 656 122 88 92 zP 657 122 80 93 zV 658 122 86 94 q 660 113 95 dSV 676 100 83 86 96 tSV 679 116 83 86 97 wF 687 119 70 98 A 688 65 99 y 690 121 100 w 695 119 101 x 739 120 102 tS 952 116 83 103 x 967 120 104 N 8319 78 > map(intToUtf8(361),"dM") #invalid Invalide mapping: ũ to dM Aline U.Val A.Val 1 32 2 bS 66 98 83 3 oF 79 111 70 4 a 97 97 5 b 98 98 6 tP 99 116 80 7 d 100 100 8 e 101 101 9 f 102 102 10 g 103 103 11 h 104 104 12 i 105 105 13 y 106 121 14 k 107 107 15 l 108 108 16 m 109 109 17 n 110 110 18 o 111 111 19 p 112 112 20 k 113 107 21 r 114 114 22 s 115 115 23 t 116 116 24 u 117 117 25 v 118 118 26 w 119 119 27 x 120 120 28 uF 121 117 70 29 z 122 122 30 bS 223 98 83 31 a 225 97 32 a 226 97 33 aN 227 97 78 34 aF 230 97 70 35 e 233 101 36 e 234 101 37 i 236 105 38 i 237 105 39 i 238 105 40 dSD 240 100 83 68 41 o 243 111 42 o 244 111 43 oN 245 111 78 44 oF 248 111 70 45 u 249 117 46 u 250 117 47 u 251 117 48 iN 297 105 78 49 iH 299 105 72 50 gN 331 103 78 51 uN 361 117 78 52 a 592 97 53 a 593 97 54 a 594 97 55 b 595 98 56 o 596 111 57 sP 597 115 80 58 dX 598 100 88 59 eC 601 101 67 60 e 603 101 61 eC 604 101 67 62 dP 607 100 80 63 g 610 103 64 gS 611 103 83 65 h 614 104 66 iC 616 105 67 67 i 618 105 68 lA 620 108 65 69 lX 621 108 88 70 lS 622 108 83 71 w 624 119 72 fN 625 102 78 73 nP 626 110 80 74 nX 627 110 88 75 gN 628 103 78 76 oF 630 111 70 77 pS 632 112 83 78 rX 637 114 88 79 r 638 114 80 r 640 114 81 gS 641 103 83 82 sX 642 115 88 83 sV 643 115 86 84 tX 648 116 88 85 uC 649 117 67 86 u 650 117 87 v 651 118 88 eC 652 101 67 89 lP 654 108 80 90 zX 656 122 88 91 zP 657 122 80 92 zV 658 122 86 93 q 660 113 94 dSV 676 100 83 86 95 tSV 679 116 83 86 96 wF 687 119 70 97 A 688 65 98 y 690 121 99 w 695 119 100 x 739 120 101 tS 952 116 83 102 x 967 120 103 N 8319 78 > map(intToUtf8(361),"dd") #invalid Invalide mapping: ũ to dd Aline U.Val A.Val 1 32 2 bS 66 98 83 3 oF 79 111 70 4 a 97 97 5 b 98 98 6 tP 99 116 80 7 d 100 100 8 e 101 101 9 f 102 102 10 g 103 103 11 h 104 104 12 i 105 105 13 y 106 121 14 k 107 107 15 l 108 108 16 m 109 109 17 n 110 110 18 o 111 111 19 p 112 112 20 k 113 107 21 r 114 114 22 s 115 115 23 t 116 116 24 u 117 117 25 v 118 118 26 w 119 119 27 x 120 120 28 uF 121 117 70 29 z 122 122 30 bS 223 98 83 31 a 225 97 32 a 226 97 33 aN 227 97 78 34 aF 230 97 70 35 e 233 101 36 e 234 101 37 i 236 105 38 i 237 105 39 i 238 105 40 dSD 240 100 83 68 41 o 243 111 42 o 244 111 43 oN 245 111 78 44 oF 248 111 70 45 u 249 117 46 u 250 117 47 u 251 117 48 iN 297 105 78 49 iH 299 105 72 50 gN 331 103 78 51 uN 361 117 78 52 a 592 97 53 a 593 97 54 a 594 97 55 b 595 98 56 o 596 111 57 sP 597 115 80 58 dX 598 100 88 59 eC 601 101 67 60 e 603 101 61 eC 604 101 67 62 dP 607 100 80 63 g 610 103 64 gS 611 103 83 65 h 614 104 66 iC 616 105 67 67 i 618 105 68 lA 620 108 65 69 lX 621 108 88 70 lS 622 108 83 71 w 624 119 72 fN 625 102 78 73 nP 626 110 80 74 nX 627 110 88 75 gN 628 103 78 76 oF 630 111 70 77 pS 632 112 83 78 rX 637 114 88 79 r 638 114 80 r 640 114 81 gS 641 103 83 82 sX 642 115 88 83 sV 643 115 86 84 tX 648 116 88 85 uC 649 117 67 86 u 650 117 87 v 651 118 88 eC 652 101 67 89 lP 654 108 80 90 zX 656 122 88 91 zP 657 122 80 92 zV 658 122 86 93 q 660 113 94 dSV 676 100 83 86 95 tSV 679 116 83 86 96 wF 687 119 70 97 A 688 65 98 y 690 121 99 w 695 119 100 x 739 120 101 tS 952 116 83 102 x 967 120 103 N 8319 78 > > > > cleanEx() > nameEx("optimization.GA") > ### * optimization.GA > > flush(stderr()); flush(stdout()) > > ### Name: optimization.GA > ### Title: Core optimization function for finding optimal weights. > ### Aliases: optimization.GA > > ### ** Examples > > data<-as.matrix(data.frame(dog=c('dog','perro'),cat=c('cat','gato'),rat=c('rat','rata'))) > M<-generate.training(raw.data=data,search.size=100,table=FALSE) > alignment<-rbind(M[[2]][4,],M[[2]][5,]) > optimization.GA(Al=alignment,data=data,num=5,step=3,plot=FALSE) $performance [1] 2 2 2 2 2 $optimized_parameters Syllabic Place Stop Voice Nasal Retroflex Lateral Aspirated 3 65 27 30 9 63 96 0 Long High Back Round SkipCost 32 65 85 2 98 > > > > cleanEx() > nameEx("optimize.features") > ### * optimize.features > > flush(stderr()); flush(stdout()) > > ### Name: optimize.features > ### Title: Supervised learning with a genetic algorithm > ### Aliases: optimize.features > ### Keywords: Optimal Parameter Genetic Algorithm > > ### ** Examples > > # This simplified example illustrates the supervised learning workflow > # some cognate data > data<-data.frame(dog=c('dog','perro'),cat=c('cat','gato'),rat=c('rat','rata')) > > # generate training data for linguist (not written) > M1<-generate.training(raw.data=data, search.size=100) > > # optimize features using expert determinations: 1,1,1 > optimize.features(set=M1, ranking=c(1,1,1), + num=20, step=5, replication=2, list=FALSE) [1] 43 41 43 87 39 33 71 7 78 66 81 37 64 > > > > > cleanEx() > nameEx("raw.alignment") > ### * raw.alignment > > flush(stderr()); flush(stdout()) > > ### Name: raw.alignment > ### Title: R/C++ Interface > ### Aliases: raw.alignment > > ### ** Examples > > s<-c("digNgNira","dinnira") > raw.alignment(s) $`word pair` [1] "digNgNira" "dinnira" $`similarity score` [1] 165 $alignment1 [1] "| d i gN gN i r a | " $alignment2 [1] "| d i n n i r a | " > > > > > cleanEx() > nameEx("show.map") > ### * show.map > > flush(stderr()); flush(stdout()) > > ### Name: show.map > ### Title: IPA-ASCII character map > ### Aliases: show.map > > ### ** Examples > > show.map() IPA Aline U.Val A.Val 1 32 2 B bS 66 98 83 3 O oF 79 111 70 4 a a 97 97 5 b b 98 98 6 c tP 99 116 80 7 d d 100 100 8 e e 101 101 9 f f 102 102 10 g g 103 103 11 h h 104 104 12 i i 105 105 13 j y 106 121 14 k k 107 107 15 l l 108 108 16 m m 109 109 17 n n 110 110 18 o o 111 111 19 p p 112 112 20 q k 113 107 21 r r 114 114 22 s s 115 115 23 t t 116 116 24 u u 117 117 25 v v 118 118 26 w w 119 119 27 x x 120 120 28 y uF 121 117 70 29 z z 122 122 30 ß bS 223 98 83 31 á a 225 97 32 â a 226 97 33 ã aN 227 97 78 34 æ aF 230 97 70 35 é e 233 101 36 ê e 234 101 37 ì i 236 105 38 í i 237 105 39 î i 238 105 40 ð dSD 240 100 83 68 41 ó o 243 111 42 ô o 244 111 43 õ oN 245 111 78 44 ø oF 248 111 70 45 ù u 249 117 46 ú u 250 117 47 û u 251 117 48 ĩ iN 297 105 78 49 ī iH 299 105 72 50 ŋ gN 331 103 78 51 ũ uN 361 117 78 52 ɐ a 592 97 53 ɑ a 593 97 54 ɒ a 594 97 55 ɓ b 595 98 56 ɔ o 596 111 57 ɕ sP 597 115 80 58 ɖ dX 598 100 88 59 ə eC 601 101 67 60 ɛ e 603 101 61 ɜ eC 604 101 67 62 ɟ dP 607 100 80 63 ɢ g 610 103 64 ɣ gS 611 103 83 65 ɦ h 614 104 66 ɨ iC 616 105 67 67 ɪ i 618 105 68 ɬ lA 620 108 65 69 ɭ lX 621 108 88 70 ɮ lS 622 108 83 71 ɰ w 624 119 72 ɱ fN 625 102 78 73 ɲ nP 626 110 80 74 ɳ nX 627 110 88 75 ɴ gN 628 103 78 76 ɶ oF 630 111 70 77 ɸ pS 632 112 83 78 ɽ rX 637 114 88 79 ɾ r 638 114 80 ʀ r 640 114 81 ʁ gS 641 103 83 82 ʂ sX 642 115 88 83 ʃ sV 643 115 86 84 ʈ tX 648 116 88 85 ʉ uC 649 117 67 86 ʊ u 650 117 87 ʋ v 651 118 88 ʌ eC 652 101 67 89 ʎ lP 654 108 80 90 ʐ zX 656 122 88 91 ʑ zP 657 122 80 92 ʒ zV 658 122 86 93 ʔ q 660 113 94 ʤ dSV 676 100 83 86 95 ʧ tSV 679 116 83 86 96 ʯ wF 687 119 70 97 ʰ A 688 65 98 ʲ y 690 121 99 ʷ w 695 119 100 ˣ x 739 120 101 θ tS 952 116 83 102 χ x 967 120 103 ⁿ N 8319 78 > > > > ### *