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Merge branch 'master' of https://github.com/jMotif/jmotif-R
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@seninp
seninp committed Feb 8, 2018
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# Version 1.0.3
* Fixed memory leaks in RRA.
* Fixed vector overruns in RRA.

# Version 1.0.2.9000

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inst/site/classifier_test.R:18:24: style: Do not place spaces around code in parentheses or square brackets.

​tfidf <- bags_to_tfidf( list("cylinder" = cylinder, "bell" = bell, "funnel" = funnel) )
                       ^

inst/site/classifier_test.R:18:86: style: Do not place spaces around code in parentheses or square brackets.

​tfidf <- bags_to_tfidf( list("cylinder" = cylinder, "bell" = bell, "funnel" = funnel) )
                                                                                     ^

inst/site/classifier_test.R:38:17: style: Do not place spaces around code in parentheses or square brackets.

​error <- length( which(labels_test != labels_predicted)) / length(labels_test)
                ^

inst/site/direct_optimizer_test.R:17:15: warning: no visible binding for global variable ‘train_labels’

​  m <- length(train_labels)
              ^~~~~~~~~~~~

inst/site/direct_optimizer_test.R:18:22: warning: no visible binding for global variable ‘train_labels’

​  c <- length(unique(train_labels))
                     ^~~~~~~~~~~~

inst/site/direct_optimizer_test.R:20:12: warning: no visible global function definition for ‘cvFolds’

​  folds <- cvFolds(m, K = nfolds, type = "random")
           ^~~~~~~

inst/site/direct_optimizer_test.R:20:27: warning: no visible binding for global variable ‘nfolds’, Did you mean 'folds'?

​  folds <- cvFolds(m, K = nfolds, type = "random")
                          ^~~~~~

inst/site/direct_optimizer_test.R:28:32: warning: no visible binding for global variable ‘train_labels’

​    bags <- plyr::alply(unique(train_labels), 1, function(x){x})
                               ^~~~~~~~~~~~

inst/site/direct_optimizer_test.R:28:61: style: Opening curly braces should never go on their own line and should always be followed by a new line.

​    bags <- plyr::alply(unique(train_labels), 1, function(x){x})
                                                            ^

inst/site/direct_optimizer_test.R:30:19: warning: no visible binding for global variable ‘train_labels’

​      ll <- which(train_labels[set_train] == unique(train_labels)[j])
                  ^~~~~~~~~~~~

inst/site/direct_optimizer_test.R:30:19: warning: no visible binding for global variable ‘train_labels’

​      ll <- which(train_labels[set_train] == unique(train_labels)[j])
                  ^~~~~~~~~~~~

inst/site/direct_optimizer_test.R:32:41: style: Do not place spaces around code in parentheses or square brackets.

​                  manyseries_to_wordbag( (train_data[set_train, ])[ll,], w, p, a, "exact", 0.01)
                                        ^

inst/site/direct_optimizer_test.R:32:71: style: Commas should always have a space after.

​                  manyseries_to_wordbag( (train_data[set_train, ])[ll,], w, p, a, "exact", 0.01)
                                                                      ^

inst/site/direct_optimizer_test.R:34:36: style: Do not place spaces around code in parentheses or square brackets.

​    tfidf <- jmotif::bags_to_tfidf( bags )
                                   ^

inst/site/direct_optimizer_test.R:34:41: style: Do not place spaces around code in parentheses or square brackets.

​    tfidf <- jmotif::bags_to_tfidf( bags )
                                        ^

inst/site/direct_optimizer_test.R:37:20: warning: no visible binding for global variable ‘train_labels’

​    labels_test <- train_labels[set_test]
                   ^~~~~~~~~~~~

inst/site/direct_optimizer_test.R:38:18: warning: no visible binding for global variable ‘train_data’

​    data_test <- train_data[set_test, ]
                 ^~~~~~~~~~

inst/site/direct_optimizer_test.R:43:16: warning: no visible global function definition for ‘series_to_wordbag’

​        bag <- series_to_wordbag(data_test[j, ], w, p, a, "exact", 0.01)
               ^~~~~~~~~~~~~~~~~

inst/site/direct_optimizer_test.R:45:16: warning: no visible global function definition for ‘series_to_wordbag’

​        bag <- series_to_wordbag(data_test, w, p, a, "exact", 0.01)
               ^~~~~~~~~~~~~~~~~

inst/site/direct_optimizer_test.R:47:18: warning: no visible global function definition for ‘cosine_sim’

​      cosines <- cosine_sim(list("bag" = bag, "tfidf" = tfidf))
                 ^~~~~~~~~~

inst/site/direct_optimizer_test.R:55:27: style: Place a space before left parenthesis, except in a function call.

​    error <- length(which((labels_test != labels_predicted))) / length(labels_test)
                          ^

inst/site/direct_optimizer_test.R:60:15: warning: no visible global function definition for ‘laply’, Did you mean 'lapply'?

​  err <- mean(laply(errors,function(x){x}))
              ^~~~~

inst/site/direct_optimizer_test.R:60:28: style: Commas should always have a space after.

​  err <- mean(laply(errors,function(x){x}))
                           ^

inst/site/direct_optimizer_test.R:60:39: style: Opening curly braces should never go on their own line and should always be followed by a new line.

​  err <- mean(laply(errors,function(x){x}))
                                      ^

inst/site/direct_optimizer_test.R:71:1: style: Variable or function name should be snake_case.

​S <- directL(cverror, rep(c(10, 2, 2)), rep(c(120, 60, 12)),
^

inst/site/direct_optimizer_test.R:77:1: style: Variable or function name should be snake_case.

​S <- directL(cverror, rep(c(10, 2, 2)), rep(c(140, 50, 12)),
^

inst/site/direct_optimizer_test.R:79:9: style: Do not place spaces around code in parentheses or square brackets.

​cverror( S$par)
        ^

inst/site/direct_optimizer_test.R:86:1: style: Variable or function name should be snake_case.

​S <- directL(cverror, rep(c(10, 2, 2)), rep(c(470, 100, 16)),
^

inst/site/direct_optimizer_test.R:89:9: style: Do not place spaces around code in parentheses or square brackets.

​cverror( S$par)
        ^

inst/site/direct_optimizer_test.R:92:3: style: Commented code should be removed.

​# nloptr.print.options()
  ^~~~~~~~~~~~~~~~~~~~~~

inst/site/makedata.R:8:14: style: Use <-, not =, for assignment.

​labels_train = unlist(dtrain[,1])
             ^

inst/site/makedata.R:8:31: style: Commas should always have a space after.

​labels_train = unlist(dtrain[,1])
                              ^

inst/site/makedata.R:9:13: style: Use <-, not =, for assignment.

​labels_test = unlist(dtest[,1])
            ^

inst/site/makedata.R:9:29: style: Commas should always have a space after.

​labels_test = unlist(dtest[,1])
                            ^

inst/site/makedata.R:11:37: style: Commas should always have a space after.

​data_train <- matrix(unlist(dtrain[,-1]), nrow = length(labels_train))
                                    ^

inst/site/makedata.R:12:35: style: Commas should always have a space after.

​data_test <- matrix(unlist(dtest[,-1]), nrow = length(labels_test))
                                  ^

inst/site/makedata.R:14:1: style: Variable or function name should be snake_case.

​Gun_Point <- list("labels_train" = labels_train, "data_train" = data_train,
^~~~~~~~~

inst/site/makedata.R:24:32: style: Commas should always have a space after.

​labels_train <- unlist(dtrain[,1])
                               ^

inst/site/makedata.R:25:30: style: Commas should always have a space after.

​labels_test <- unlist(dtest[,1])
                             ^

inst/site/makedata.R:27:37: style: Commas should always have a space after.

​data_train <- matrix(unlist(dtrain[,-1]), nrow = length(labels_train))
                                    ^

inst/site/makedata.R:28:35: style: Commas should always have a space after.

​data_test <- matrix(unlist(dtest[,-1]), nrow = length(labels_test))
                                  ^

inst/site/makedata.R:30:1: style: Variable or function name should be snake_case.

​CBF <- list("labels_train" = labels_train, "data_train" = data_train,
^~~

inst/site/readme_examples.R:14:16: style: Commas should always have a space after.

​abline(h = c(1,-1), lty = 2, col = "gray50")
               ^

inst/site/readme_examples.R:15:36: style: Commas should always have a space after.

​legend(0, -4, c("scaled sine wave","z-normalized wave"),
                                   ^

inst/site/readme_examples.R:16:18: style: Commas should always have a space after.

​       lty = c(1,1), lwd = c(1,1), col = c("blue","red"), cex = 0.8)
                 ^

inst/site/readme_examples.R:16:32: style: Commas should always have a space after.

​       lty = c(1,1), lwd = c(1,1), col = c("blue","red"), cex = 0.8)
                               ^

inst/site/readme_examples.R:16:51: style: Commas should always have a space after.

​       lty = c(1,1), lwd = c(1,1), col = c("blue","red"), cex = 0.8)
                                                  ^

inst/site/readme_examples.R:24:27: style: Commas should never have a space before.

​abline(v = c(1, 1 + 7 / 3 , 1 + 7 / 3 * 2, 8), lty = 3, lwd = 2, col = "gray50")
                         ~^

inst/site/readme_examples.R:38:13: style: Commas should always have a space after.

​y <- seq(-2,2, length = 100)
            ^

inst/site/readme_examples.R:40:9: style: Commas should always have a space after.

​lines(x,y, type = "l", lwd = 5, col = "magenta")
        ^

inst/site/readme_examples.R:62:82: style: Commas should always have a space after.

​cylinder <- manyseries_to_wordbag(CBF[["data_train"]][CBF[["labels_train"]] == 1,],
                                                                                 ^

inst/site/readme_examples.R:64:78: style: Commas should always have a space after.

​bell <- manyseries_to_wordbag(CBF[["data_train"]][CBF[["labels_train"]] == 2,],
                                                                             ^

inst/site/readme_examples.R:66:80: style: Commas should always have a space after.

​funnel <- manyseries_to_wordbag(CBF[["data_train"]][CBF[["labels_train"]] == 3,],
                                                                               ^

inst/site/readme_examples.R:71:7: style: Use <-, not =, for assignment.

​tfidf = bags_to_tfidf(
      ^

inst/site/readme_examples.R:72:64: style: Do not place spaces around code in parentheses or square brackets.

​  list("cylinder" = cylinder, "bell" = bell, "funnel" = funnel) )
                                                               ^

inst/site/readme_examples.R:77:59: style: Commas should always have a space after.

​sample <- (CBF[["data_train"]][CBF[["labels_train"]] == 3,])[1,]
                                                          ^

inst/site/readme_examples.R:77:64: style: Commas should always have a space after.

​sample <- (CBF[["data_train"]][CBF[["labels_train"]] == 3,])[1,]
                                                               ^

inst/site/readme_examples.R:87:34: style: Commas should always have a space after.

​  pattern <- weighted_patterns[i,]
                                 ^

inst/site/readme_examples.R:101:56: style: Commas should always have a space after.

​  scale_colour_gradientn(name = "Class specificity:  ",limits = c(0,1),
                                                       ^

inst/site/readme_examples.R:101:69: style: Commas should always have a space after.

​  scale_colour_gradientn(name = "Class specificity:  ",limits = c(0,1),
                                                                    ^

inst/site/readme_examples.R:109:47: style: Commas should always have a space after.

​        axis.text.x = element_text(size = 12),axis.text.y = element_blank(),
                                              ^

inst/site/readme_examples.R:118:33: style: Commas should always have a space after.

​for (i in c(1:length(data_test[,1]))) {
                                ^

inst/site/readme_examples.R:119:25: style: Commas should always have a space after.

​  series <- data_test[i,]
                        ^

inst/site/readme_examples.R:127:23: style: Place a space before left parenthesis, except in a function call.

​error <- length(which((labels_test != labels_predicted))) / length(labels_test)
                      ^

inst/site/readme_examples.R:132:7: style: Place a space before left parenthesis, except in a function call.

​which((labels_test != labels_predicted))
      ^

inst/site/SO46430559.R:12:41: style: Opening curly braces should never go on their own line and should always be followed by a new line.

​examplezn <- llply(example1, function(x){znorm(x, threshold = 0.01)})
                                        ^

inst/site/SO46430559.R:15:29: style: Opening curly braces should never go on their own line and should always be followed by a new line.

​llply(examplezn, function(x){paa(x, 3)})
                            ^

inst/site/SO46430559.R:18:43: style: Opening curly braces should never go on their own line and should always be followed by a new line.

​example_sax <- llply(example1, function(x){sax_via_window(x, 3, 2, 3, "none", 0.1)})
                                          ^

inst/site/test_RRA.R:15:25: style: Commas should always have a space after.

​sax_df <- ldply(ecg_sax,function(x){x})
                        ^

inst/site/test_RRA.R:15:36: style: Opening curly braces should never go on their own line and should always be followed by a new line.

​sax_df <- ldply(ecg_sax,function(x){x})
                                   ^

inst/site/test_RRA.R:16:26: style: Commas should always have a space after.

​names(sax_df) <- c("idx","word")
                         ^

inst/site/test_RRA.R:31:1: style: Trailing blank lines are superfluous.

​
^

inst/test_data/bugs.R:6:1: style: Lines should not be more than 100 characters.

​str_to_repair_grammar("adcc ccbb bbbd bbcb bdbb cbbc accb ccbb daba cbbc bbdb bcbb dabc bbcb adcc ccbc dabb	cbbd bbcb cdbb cbbc bbdc adcc cbcb bbbd bbcb bdbb cbbc accb cdbb dbbb cbbd bccb cdab cbbc accb ccbb dabb cbbd bbcb bdbb cbbc accb ccbb cbbd bbcb bdbb cbbc accb ccbb dabb cbbd bbcb bdbb cbbc accc ccbc dacb bbbd 	bbcb bdbb cbbc accb ccbc dbba cbbc bbdb bcbb dbbc bbcb adcc ccbc daba cbbc bbdb bcbb dbbc bbcb adcb bdac dcbb cbbd bbcb bdbb cbbc accb cdbb dbbb cbbd bccb bdab cbbc accb cdbb dbbb cbbd bbcb bdbb cbbc accc ccbb cbbd bbcb bdbb cbbc accb")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

inst/test_data/bugs.R:11:1: style: Lines should not be more than 100 characters.

​str_to_repair_grammar("dacb bbbd bbcb bdbb cbbc accb ccbc dbba cbbc bbdb bcbb dbbc bbcb adcc ccbc daba cbbc bbdb bcbb dbbc bbcb adcb bdac dcbb cbbd bbcb bdbb cbbc accb cdbb dbbb cbbd bccb bdab cbbc accb cdbb dbbb cbbd bbcb bdbb cbbc accc ccbb cbbd bbcb bdbb cbbc accb")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

inst/test_data/bugs.R:14:6: style: Use <-, not =, for assignment.

​data = fread("/Users/psenin/workspace/grammarviz2_src/data/mitdb__100_180.txt")
     ^

inst/test_data/bugs.R:15:5: style: Use <-, not =, for assignment.

​sax = sax_via_window(data$V1, 160, 4, 4, "exact", 0.001)
    ^

inst/test_data/bugs.R:16:5: style: Use <-, not =, for assignment.

​str = paste(unlist(sax), collapse =" ")
    ^

inst/test_data/bugs.R:16:35: style: Put spaces around all infix operators.

​str = paste(unlist(sax), collapse =" ")
                                  ^~

inst/test_data/bugs.R:17:9: style: Use <-, not =, for assignment.

​grammar = str_to_repair_grammar(str)
        ^

inst/test_data/bugs.R:19:6: style: Use <-, not =, for assignment.

​str1 = grammar[[1]]$rule_string
     ^

inst/test_data/bugs.R:20:4: style: Place a space before left parenthesis, except in a function call.

​for(i in c(2:95)){
   ^

inst/test_data/bugs.R:21:1: style: Lines should not be more than 100 characters.

​	str1 = gsub(paste(" R", i - 1, " ", sep = ""), paste(" ", grammar[[i]]$expanded_rule_string, " ", sep = ""), str1)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

inst/test_data/bugs.R:21:1: style: Use spaces to indent, not tabs.

​	str1 = gsub(paste(" R", i - 1, " ", sep = ""), paste(" ", grammar[[i]]$expanded_rule_string, " ", sep = ""), str1)
^

inst/test_data/bugs.R:21:7: style: Use <-, not =, for assignment.

​	str1 = gsub(paste(" R", i - 1, " ", sep = ""), paste(" ", grammar[[i]]$expanded_rule_string, " ", sep = ""), str1)
      ^

inst/test_data/bugs.R:26:1: error: unexpected '>'

​> library(jmotif)
^

R/jmotif.R:25:27: style: Commas should always have a space after.

​        distance_matrix[i,j] <- (cutlines[i] - cutlines[j - 1]) * (cutlines[i] - cutlines[j - 1])
                          ^

R/jmotif.R:27:27: style: Commas should always have a space after.

​        distance_matrix[j,i] <- distance_matrix[i,j]
                          ^

R/jmotif.R:27:51: style: Commas should always have a space after.

​        distance_matrix[j,i] <- distance_matrix[i,j]
                                                  ^

R/jmotif.R:34:72: style: Commas should always have a space after.

​    stop(paste("unable to get a distance matrix for the alphabet size",a_size))
                                                                       ^

R/jmotif.R:57:9: style: Do not place spaces around code in parentheses or square brackets.

​    if ( any(letters_to_idx(str1) > alphabet_size) |
        ^

R/jmotif.R:62:21: warning: no visible global function definition for ‘sax_distance_matrix’

​      dist_table <- sax_distance_matrix(alphabet_size)
                    ^~~~~~~~~~~~~~~~~~~

R/RcppExports.R:34:1: style: Lines should not be more than 100 characters.

​#' Finds the Euclidean distance between points, if distance is above the threshold, abandons the computation
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/RcppExports.R:67:1: style: Lines should not be more than 100 characters.

​    .Call('_jmotif_find_discords_hotsax', PACKAGE = 'jmotif', ts, w_size, paa_size, a_size, n_threshold, discords_num)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/RcppExports.R:123:1: style: Lines should not be more than 100 characters.

​find_discords_rra <- function(series, w_size, paa_size, a_size, nr_strategy, n_threshold, discords_num) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/RcppExports.R:124:1: style: Lines should not be more than 100 characters.

​    .Call('_jmotif_find_discords_rra', PACKAGE = 'jmotif', series, w_size, paa_size, a_size, nr_strategy, n_threshold, discords_num)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/RcppExports.R:127:1: style: Lines should not be more than 100 characters.

​#' Translates an alphabet size into the array of corresponding SAX cut-lines built using the Normal distribution.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/RcppExports.R:181:1: style: Lines should not be more than 100 characters.

​#' @param nr_strategy the Numerosity Reduction strategy, acceptable values are "exact" and "mindist" --
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/RcppExports.R:190:1: style: Lines should not be more than 100 characters.

​    .Call('_jmotif_sax_via_window', PACKAGE = 'jmotif', ts, w_size, paa_size, a_size, nr_strategy, n_threshold)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/RcppExports.R:224:1: style: Lines should not be more than 100 characters.

​    .Call('_jmotif_series_to_wordbag', PACKAGE = 'jmotif', ts, w_size, paa_size, a_size, nr_strategy, n_threshold)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/RcppExports.R:243:1: style: Lines should not be more than 100 characters.

​    .Call('_jmotif_manyseries_to_wordbag', PACKAGE = 'jmotif', data, w_size, paa_size, a_size, nr_strategy, n_threshold)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/RcppExports.R:381:1: style: Trailing blank lines are superfluous.

​
^

tests/testthat/test_cosine_sim.R:1:3: style: Use <-, not =, for assignment.

​a = c(2, 1, 0, 2, 0, 1, 1, 1)
  ^

tests/testthat/test_cosine_sim.R:6:58: style: Commas should always have a space after.

​  expect_equal(0.1784162, as.numeric(cosine_dist(rbind(a,b))), tolerance = 1e-6)
                                                         ^

tests/testthat/test_cosines.R:4:78: style: Commas should always have a space after.

​bag1 <- manyseries_to_wordbag(CBF[["data_train"]][CBF[["labels_train"]] == 1,],
                                                                             ^

tests/testthat/test_cosines.R:6:78: style: Commas should always have a space after.

​bag2 <- manyseries_to_wordbag(CBF[["data_train"]][CBF[["labels_train"]] == 2,],
                                                                             ^

tests/testthat/test_cosines.R:8:78: style: Commas should always have a space after.

​bag3 <- manyseries_to_wordbag(CBF[["data_train"]][CBF[["labels_train"]] == 3,],
                                                                             ^

tests/testthat/test_cosines.R:11:57: style: Commas should always have a space after.

​sample <- (CBF[["data_test"]][CBF[["labels_test"]] == 3,])[1,]
                                                        ^

tests/testthat/test_cosines.R:11:62: style: Commas should always have a space after.

​sample <- (CBF[["data_test"]][CBF[["labels_test"]] == 3,])[1,]
                                                             ^

tests/testthat/test_cosines.R:15:26: style: Do not place spaces around code in parentheses or square brackets.

​  tfidf <- bags_to_tfidf( list("cylinder" = bag1, "bell" = bag2, "funnel" = bag3) )
                         ^

tests/testthat/test_cosines.R:15:82: style: Do not place spaces around code in parentheses or square brackets.

​  tfidf <- bags_to_tfidf( list("cylinder" = bag1, "bell" = bag2, "funnel" = bag3) )
                                                                                 ^

tests/testthat/test_discord_brute_force.R:18:50: style: Commas should always have a space after.

​  expect_equal(discords[discords$position == 411,]$nn_distance, 1.5045846602966542)
                                                 ^

tests/testthat/test_discord_hot_sax.R:16:50: style: Commas should always have a space after.

​  expect_equal(discords[discords$position == 430,]$nn_distance, 5.252618285620532)
                                                 ^

tests/testthat/test_discord_hot_sax.R:17:50: style: Commas should always have a space after.

​  expect_equal(discords[discords$position == 318,]$nn_distance, 4.154825115936453)
                                                 ^

tests/testthat/test_discord_hot_sax.R:18:51: style: Commas should always have a space after.

​  expect_equal(discords[discords$position == 2080,]$nn_distance, 2.381003269560112)
                                                  ^

tests/testthat/test_discord_hot_sax.R:19:49: style: Commas should always have a space after.

​  expect_equal(discords[discords$position == 25,]$nn_distance, 2.363633774221037)
                                                ^

tests/testthat/test_discord_rra.R:3:26: style: Commas should always have a space after.

​  expect_true(discords[1,]$start < 420)
                         ^

tests/testthat/test_discord_rra.R:4:26: style: Commas should always have a space after.

​  expect_true(discords[1,]$end > 420)
                         ^

tests/testthat/test_early_abandoned_dist.R:3:38: style: Commas should always have a space after.

​test_dist <- as.numeric(dist(rbind(a,b)))
                                     ^

tests/testthat/test_early_abandoned_dist.R:7:44: style: Commas should always have a space after.

​  expect_error(early_abandoned_dist(a, c(1,2), 1))
                                           ^

tests/testthat/test_min_dist_equal.R:5:38: style: Do not place spaces around code in parentheses or square brackets.

​  expect_equal(m3[1, 3], 0.7421040279 )
                                     ^

tests/testthat/test_min_dist_equal.R:16:16: style: Do not place spaces around code in parentheses or square brackets.

​  expect_equal( sqrt((min_dist(str1, str2, 3)) ^ 2 / 2), 0.7421040279 )
               ^

tests/testthat/test_min_dist_equal.R:16:22: style: Place a space before left parenthesis, except in a function call.

​  expect_equal( sqrt((min_dist(str1, str2, 3)) ^ 2 / 2), 0.7421040279 )
                     ^

tests/testthat/test_min_dist_equal.R:16:70: style: Do not place spaces around code in parentheses or square brackets.

​  expect_equal( sqrt((min_dist(str1, str2, 3)) ^ 2 / 2), 0.7421040279 )
                                                                     ^

tests/testthat/test_min_dist_equal.R:18:16: style: Do not place spaces around code in parentheses or square brackets.

​  expect_equal( sqrt((min_dist(str2, str3, 3)) ^ 2), 0.7421040279 )
               ^

tests/testthat/test_min_dist_equal.R:18:22: style: Place a space before left parenthesis, except in a function call.

​  expect_equal( sqrt((min_dist(str2, str3, 3)) ^ 2), 0.7421040279 )
                     ^

tests/testthat/test_min_dist_equal.R:18:66: style: Do not place spaces around code in parentheses or square brackets.

​  expect_equal( sqrt((min_dist(str2, str3, 3)) ^ 2), 0.7421040279 )
                                                                 ^

tests/testthat/test_min_dist.R:3:15: style: Do not place spaces around code in parentheses or square brackets.

​  expect_true( is_equal_mindist("aaa", "bbb")  )
              ^

tests/testthat/test_min_dist.R:3:47: style: Do not place spaces around code in parentheses or square brackets.

​  expect_true( is_equal_mindist("aaa", "bbb")  )
                                              ^

tests/testthat/test_min_dist.R:5:16: style: Do not place spaces around code in parentheses or square brackets.

​  expect_false( is_equal_mindist("aaa", "bbba")  )
               ^

tests/testthat/test_min_dist.R:5:49: style: Do not place spaces around code in parentheses or square brackets.

​  expect_false( is_equal_mindist("aaa", "bbba")  )
                                                ^

tests/testthat/test_min_dist.R:7:16: style: Do not place spaces around code in parentheses or square brackets.

​  expect_false( is_equal_mindist("aaa", "aca")  )
               ^

tests/testthat/test_min_dist.R:7:48: style: Do not place spaces around code in parentheses or square brackets.

​  expect_false( is_equal_mindist("aaa", "aca")  )
                                               ^

tests/testthat/test_RePair_via_decompression.R:1:12: style: Use <-, not =, for assignment.

​sax_string = paste(
           ^

tests/testthat/test_RePair_via_decompression.R:10:3: style: Variable or function name should be snake_case.

​  uncompressed_R0 = paste(grammar[[1]]$rule_string, " ", sep = "")
  ^~~~~~~~~~~~~~~

tests/testthat/test_RePair_via_decompression.R:10:19: style: Use <-, not =, for assignment.

​  uncompressed_R0 = paste(grammar[[1]]$rule_string, " ", sep = "")
                  ^

tests/testthat/test_RePair_via_decompression.R:14:7: style: Variable or function name should be snake_case.

​      uncompressed_R0 = gsub(
      ^~~~~~~~~~~~~~~

tests/testthat/test_RePair_via_decompression.R:14:23: style: Use <-, not =, for assignment.

​      uncompressed_R0 = gsub(
                      ^

tests/testthat/test_SAX_simple.R:15:23: style: Do not place spaces around code in parentheses or square brackets.

​  str1_10_11 <- paste( matrix(unlist(sax_by_chunking(dat1, 10, 11, 0.01)),
                      ^

tests/testthat/test_SAX_simple.R:16:53: style: Commas should always have a space after.

​                             nrow = 10, byrow = T)[,1], collapse = "")
                                                    ^

tests/testthat/test_SAX_simple.R:17:23: style: Do not place spaces around code in parentheses or square brackets.

​  str1_14_10 <- paste( matrix(unlist(sax_by_chunking(dat1, 14, 10, 0.01)),
                      ^

tests/testthat/test_SAX_simple.R:18:53: style: Commas should always have a space after.

​                             nrow = 14, byrow = T)[,1], collapse = "")
                                                    ^

tests/testthat/test_SAX_simple.R:19:21: style: Do not place spaces around code in parentheses or square brackets.

​  str1_9_7 <- paste( matrix(unlist(sax_by_chunking(dat1, 9, 7, 0.01)),
                    ^

tests/testthat/test_SAX_simple.R:20:52: style: Commas should always have a space after.

​                             nrow = 9, byrow = T)[,1], collapse = "")
                                                   ^

tests/testthat/test_SAX_simple.R:34:23: style: Do not place spaces around code in parentheses or square brackets.

​  str2_10_11 <- paste( matrix(unlist(sax_by_chunking(dat2, 10, 11, 0.01)),
                      ^

tests/testthat/test_SAX_simple.R:36:23: style: Do not place spaces around code in parentheses or square brackets.

​  str2_14_10 <- paste( matrix(unlist(sax_by_chunking(dat2, 14, 10, 0.01)),
                      ^

tests/testthat/test_SAX_simple.R:38:21: style: Do not place spaces around code in parentheses or square brackets.

​  str2_9_7 <- paste( matrix(unlist(sax_by_chunking(dat2, 9, 7, 0.01)),
                    ^

tests/testthat/test_SAX_strategies.R:12:3: style: Commented code should be removed.

​# plot(as.numeric(dat),t="l")
  ^~~~~~~~~~~~~~~~~~~~~~~~~~~

tests/testthat/test_SAX_via_window.R:12:3: style: Commented code should be removed.

​# plot(as.numeric(dat),t="l")
  ^~~~~~~~~~~~~~~~~~~~~~~~~~~

tests/testthat/test_SAX_with_NAs.R:12:3: style: Commented code should be removed.

​# plot(as.numeric(dat),t="l")
  ^~~~~~~~~~~~~~~~~~~~~~~~~~~

tests/testthat/test_SAX_with_NAs.R:40:65: style: Commas should always have a space after.

​    cylinders <- CBF[["data_train"]][CBF[["labels_train"]] == 1,]
                                                                ^

tests/testthat/test_SAX_with_NAs.R:42:22: style: Commas should always have a space after.

​    c <- cylinders[2,]
                     ^

tests/testthat/test_wordbag.R:17:61: style: Commas should always have a space after.

​  words <- table(matrix(unlist(sax1), ncol = 1, byrow = T)[,1])
                                                            ^

tests/testthat/test_wordbag.R:22:44: style: Commas should always have a space after.

​                    wb1[wb1$words == "bca",]$counts)
                                           ^

tests/testthat/test_wordbag.R:30:46: style: Commas should always have a space after.

​  wb2 <- manyseries_to_wordbag(t(t(rbind(dat,dat))), 6, 3, 3, "none", 0.01)
                                             ^

tests/testthat/test_wordbag.R:41:61: style: Commas should always have a space after.

​  words <- table(matrix(unlist(sax1), ncol = 1, byrow = T)[,1])
                                                            ^

tests/testthat/test_wordbag.R:46:39: style: Commas should always have a space after.

​               wb1[wb1$words == "bca",]$counts)
                                      ^

tests/testthat/test_wordbag.R:54:46: style: Commas should always have a space after.

​  wb2 <- manyseries_to_wordbag(t(t(rbind(dat,dat))), 6, 3, 3, "mindist", 0.01)
                                             ^

tests/testthat/test_znorm.R:1:1: style: Variable or function name should be snake_case.

​X = c(-1, -2, -1, 0, 2, 1, 1, 0)
^

tests/testthat/test_znorm.R:1:3: style: Use <-, not =, for assignment.

​X = c(-1, -2, -1, 0, 2, 1, 1, 0)
  ^

tests/testthat/test_znorm.R:2:1: style: Variable or function name should be snake_case.

​Xscaled <- X / 100
^~~~~~~

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inst/site/classifier_test.R:18:24: style: Do not place spaces around code in parentheses or square brackets.

​tfidf <- bags_to_tfidf( list("cylinder" = cylinder, "bell" = bell, "funnel" = funnel) )
                       ^

inst/site/classifier_test.R:18:86: style: Do not place spaces around code in parentheses or square brackets.

​tfidf <- bags_to_tfidf( list("cylinder" = cylinder, "bell" = bell, "funnel" = funnel) )
                                                                                     ^

inst/site/classifier_test.R:38:17: style: Do not place spaces around code in parentheses or square brackets.

​error <- length( which(labels_test != labels_predicted)) / length(labels_test)
                ^

inst/site/direct_optimizer_test.R:17:15: warning: no visible binding for global variable ‘train_labels’

​  m <- length(train_labels)
              ^~~~~~~~~~~~

inst/site/direct_optimizer_test.R:18:22: warning: no visible binding for global variable ‘train_labels’

​  c <- length(unique(train_labels))
                     ^~~~~~~~~~~~

inst/site/direct_optimizer_test.R:20:12: warning: no visible global function definition for ‘cvFolds’

​  folds <- cvFolds(m, K = nfolds, type = "random")
           ^~~~~~~

inst/site/direct_optimizer_test.R:20:27: warning: no visible binding for global variable ‘nfolds’, Did you mean 'folds'?

​  folds <- cvFolds(m, K = nfolds, type = "random")
                          ^~~~~~

inst/site/direct_optimizer_test.R:28:32: warning: no visible binding for global variable ‘train_labels’

​    bags <- plyr::alply(unique(train_labels), 1, function(x){x})
                               ^~~~~~~~~~~~

inst/site/direct_optimizer_test.R:28:61: style: Opening curly braces should never go on their own line and should always be followed by a new line.

​    bags <- plyr::alply(unique(train_labels), 1, function(x){x})
                                                            ^

inst/site/direct_optimizer_test.R:30:19: warning: no visible binding for global variable ‘train_labels’

​      ll <- which(train_labels[set_train] == unique(train_labels)[j])
                  ^~~~~~~~~~~~

inst/site/direct_optimizer_test.R:30:19: warning: no visible binding for global variable ‘train_labels’

​      ll <- which(train_labels[set_train] == unique(train_labels)[j])
                  ^~~~~~~~~~~~

inst/site/direct_optimizer_test.R:32:41: style: Do not place spaces around code in parentheses or square brackets.

​                  manyseries_to_wordbag( (train_data[set_train, ])[ll,], w, p, a, "exact", 0.01)
                                        ^

inst/site/direct_optimizer_test.R:32:71: style: Commas should always have a space after.

​                  manyseries_to_wordbag( (train_data[set_train, ])[ll,], w, p, a, "exact", 0.01)
                                                                      ^

inst/site/direct_optimizer_test.R:34:36: style: Do not place spaces around code in parentheses or square brackets.

​    tfidf <- jmotif::bags_to_tfidf( bags )
                                   ^

inst/site/direct_optimizer_test.R:34:41: style: Do not place spaces around code in parentheses or square brackets.

​    tfidf <- jmotif::bags_to_tfidf( bags )
                                        ^

inst/site/direct_optimizer_test.R:37:20: warning: no visible binding for global variable ‘train_labels’

​    labels_test <- train_labels[set_test]
                   ^~~~~~~~~~~~

inst/site/direct_optimizer_test.R:38:18: warning: no visible binding for global variable ‘train_data’

​    data_test <- train_data[set_test, ]
                 ^~~~~~~~~~

inst/site/direct_optimizer_test.R:43:16: warning: no visible global function definition for ‘series_to_wordbag’

​        bag <- series_to_wordbag(data_test[j, ], w, p, a, "exact", 0.01)
               ^~~~~~~~~~~~~~~~~

inst/site/direct_optimizer_test.R:45:16: warning: no visible global function definition for ‘series_to_wordbag’

​        bag <- series_to_wordbag(data_test, w, p, a, "exact", 0.01)
               ^~~~~~~~~~~~~~~~~

inst/site/direct_optimizer_test.R:47:18: warning: no visible global function definition for ‘cosine_sim’

​      cosines <- cosine_sim(list("bag" = bag, "tfidf" = tfidf))
                 ^~~~~~~~~~

inst/site/direct_optimizer_test.R:55:27: style: Place a space before left parenthesis, except in a function call.

​    error <- length(which((labels_test != labels_predicted))) / length(labels_test)
                          ^

inst/site/direct_optimizer_test.R:60:15: warning: no visible global function definition for ‘laply’, Did you mean 'lapply'?

​  err <- mean(laply(errors,function(x){x}))
              ^~~~~

inst/site/direct_optimizer_test.R:60:28: style: Commas should always have a space after.

​  err <- mean(laply(errors,function(x){x}))
                           ^

inst/site/direct_optimizer_test.R:60:39: style: Opening curly braces should never go on their own line and should always be followed by a new line.

​  err <- mean(laply(errors,function(x){x}))
                                      ^

inst/site/direct_optimizer_test.R:71:1: style: Variable or function name should be snake_case.

​S <- directL(cverror, rep(c(10, 2, 2)), rep(c(120, 60, 12)),
^

inst/site/direct_optimizer_test.R:77:1: style: Variable or function name should be snake_case.

​S <- directL(cverror, rep(c(10, 2, 2)), rep(c(140, 50, 12)),
^

inst/site/direct_optimizer_test.R:79:9: style: Do not place spaces around code in parentheses or square brackets.

​cverror( S$par)
        ^

inst/site/direct_optimizer_test.R:86:1: style: Variable or function name should be snake_case.

​S <- directL(cverror, rep(c(10, 2, 2)), rep(c(470, 100, 16)),
^

inst/site/direct_optimizer_test.R:89:9: style: Do not place spaces around code in parentheses or square brackets.

​cverror( S$par)
        ^

inst/site/direct_optimizer_test.R:92:3: style: Commented code should be removed.

​# nloptr.print.options()
  ^~~~~~~~~~~~~~~~~~~~~~

inst/site/makedata.R:8:14: style: Use <-, not =, for assignment.

​labels_train = unlist(dtrain[,1])
             ^

inst/site/makedata.R:8:31: style: Commas should always have a space after.

​labels_train = unlist(dtrain[,1])
                              ^

inst/site/makedata.R:9:13: style: Use <-, not =, for assignment.

​labels_test = unlist(dtest[,1])
            ^

inst/site/makedata.R:9:29: style: Commas should always have a space after.

​labels_test = unlist(dtest[,1])
                            ^

inst/site/makedata.R:11:37: style: Commas should always have a space after.

​data_train <- matrix(unlist(dtrain[,-1]), nrow = length(labels_train))
                                    ^

inst/site/makedata.R:12:35: style: Commas should always have a space after.

​data_test <- matrix(unlist(dtest[,-1]), nrow = length(labels_test))
                                  ^

inst/site/makedata.R:14:1: style: Variable or function name should be snake_case.

​Gun_Point <- list("labels_train" = labels_train, "data_train" = data_train,
^~~~~~~~~

inst/site/makedata.R:24:32: style: Commas should always have a space after.

​labels_train <- unlist(dtrain[,1])
                               ^

inst/site/makedata.R:25:30: style: Commas should always have a space after.

​labels_test <- unlist(dtest[,1])
                             ^

inst/site/makedata.R:27:37: style: Commas should always have a space after.

​data_train <- matrix(unlist(dtrain[,-1]), nrow = length(labels_train))
                                    ^

inst/site/makedata.R:28:35: style: Commas should always have a space after.

​data_test <- matrix(unlist(dtest[,-1]), nrow = length(labels_test))
                                  ^

inst/site/makedata.R:30:1: style: Variable or function name should be snake_case.

​CBF <- list("labels_train" = labels_train, "data_train" = data_train,
^~~

inst/site/readme_examples.R:14:16: style: Commas should always have a space after.

​abline(h = c(1,-1), lty = 2, col = "gray50")
               ^

inst/site/readme_examples.R:15:36: style: Commas should always have a space after.

​legend(0, -4, c("scaled sine wave","z-normalized wave"),
                                   ^

inst/site/readme_examples.R:16:18: style: Commas should always have a space after.

​       lty = c(1,1), lwd = c(1,1), col = c("blue","red"), cex = 0.8)
                 ^

inst/site/readme_examples.R:16:32: style: Commas should always have a space after.

​       lty = c(1,1), lwd = c(1,1), col = c("blue","red"), cex = 0.8)
                               ^

inst/site/readme_examples.R:16:51: style: Commas should always have a space after.

​       lty = c(1,1), lwd = c(1,1), col = c("blue","red"), cex = 0.8)
                                                  ^

inst/site/readme_examples.R:24:27: style: Commas should never have a space before.

​abline(v = c(1, 1 + 7 / 3 , 1 + 7 / 3 * 2, 8), lty = 3, lwd = 2, col = "gray50")
                         ~^

inst/site/readme_examples.R:38:13: style: Commas should always have a space after.

​y <- seq(-2,2, length = 100)
            ^

inst/site/readme_examples.R:40:9: style: Commas should always have a space after.

​lines(x,y, type = "l", lwd = 5, col = "magenta")
        ^

inst/site/readme_examples.R:62:82: style: Commas should always have a space after.

​cylinder <- manyseries_to_wordbag(CBF[["data_train"]][CBF[["labels_train"]] == 1,],
                                                                                 ^

inst/site/readme_examples.R:64:78: style: Commas should always have a space after.

​bell <- manyseries_to_wordbag(CBF[["data_train"]][CBF[["labels_train"]] == 2,],
                                                                             ^

inst/site/readme_examples.R:66:80: style: Commas should always have a space after.

​funnel <- manyseries_to_wordbag(CBF[["data_train"]][CBF[["labels_train"]] == 3,],
                                                                               ^

inst/site/readme_examples.R:71:7: style: Use <-, not =, for assignment.

​tfidf = bags_to_tfidf(
      ^

inst/site/readme_examples.R:72:64: style: Do not place spaces around code in parentheses or square brackets.

​  list("cylinder" = cylinder, "bell" = bell, "funnel" = funnel) )
                                                               ^

inst/site/readme_examples.R:77:59: style: Commas should always have a space after.

​sample <- (CBF[["data_train"]][CBF[["labels_train"]] == 3,])[1,]
                                                          ^

inst/site/readme_examples.R:77:64: style: Commas should always have a space after.

​sample <- (CBF[["data_train"]][CBF[["labels_train"]] == 3,])[1,]
                                                               ^

inst/site/readme_examples.R:87:34: style: Commas should always have a space after.

​  pattern <- weighted_patterns[i,]
                                 ^

inst/site/readme_examples.R:101:56: style: Commas should always have a space after.

​  scale_colour_gradientn(name = "Class specificity:  ",limits = c(0,1),
                                                       ^

inst/site/readme_examples.R:101:69: style: Commas should always have a space after.

​  scale_colour_gradientn(name = "Class specificity:  ",limits = c(0,1),
                                                                    ^

inst/site/readme_examples.R:109:47: style: Commas should always have a space after.

​        axis.text.x = element_text(size = 12),axis.text.y = element_blank(),
                                              ^

inst/site/readme_examples.R:118:33: style: Commas should always have a space after.

​for (i in c(1:length(data_test[,1]))) {
                                ^

inst/site/readme_examples.R:119:25: style: Commas should always have a space after.

​  series <- data_test[i,]
                        ^

inst/site/readme_examples.R:127:23: style: Place a space before left parenthesis, except in a function call.

​error <- length(which((labels_test != labels_predicted))) / length(labels_test)
                      ^

inst/site/readme_examples.R:132:7: style: Place a space before left parenthesis, except in a function call.

​which((labels_test != labels_predicted))
      ^

inst/site/SO46430559.R:12:41: style: Opening curly braces should never go on their own line and should always be followed by a new line.

​examplezn <- llply(example1, function(x){znorm(x, threshold = 0.01)})
                                        ^

inst/site/SO46430559.R:15:29: style: Opening curly braces should never go on their own line and should always be followed by a new line.

​llply(examplezn, function(x){paa(x, 3)})
                            ^

inst/site/SO46430559.R:18:43: style: Opening curly braces should never go on their own line and should always be followed by a new line.

​example_sax <- llply(example1, function(x){sax_via_window(x, 3, 2, 3, "none", 0.1)})
                                          ^

inst/site/test_RRA.R:15:25: style: Commas should always have a space after.

​sax_df <- ldply(ecg_sax,function(x){x})
                        ^

inst/site/test_RRA.R:15:36: style: Opening curly braces should never go on their own line and should always be followed by a new line.

​sax_df <- ldply(ecg_sax,function(x){x})
                                   ^

inst/site/test_RRA.R:16:26: style: Commas should always have a space after.

​names(sax_df) <- c("idx","word")
                         ^

inst/site/test_RRA.R:31:1: style: Trailing blank lines are superfluous.

​
^

inst/test_data/bugs.R:6:1: style: Lines should not be more than 100 characters.

​str_to_repair_grammar("adcc ccbb bbbd bbcb bdbb cbbc accb ccbb daba cbbc bbdb bcbb dabc bbcb adcc ccbc dabb	cbbd bbcb cdbb cbbc bbdc adcc cbcb bbbd bbcb bdbb cbbc accb cdbb dbbb cbbd bccb cdab cbbc accb ccbb dabb cbbd bbcb bdbb cbbc accb ccbb cbbd bbcb bdbb cbbc accb ccbb dabb cbbd bbcb bdbb cbbc accc ccbc dacb bbbd 	bbcb bdbb cbbc accb ccbc dbba cbbc bbdb bcbb dbbc bbcb adcc ccbc daba cbbc bbdb bcbb dbbc bbcb adcb bdac dcbb cbbd bbcb bdbb cbbc accb cdbb dbbb cbbd bccb bdab cbbc accb cdbb dbbb cbbd bbcb bdbb cbbc accc ccbb cbbd bbcb bdbb cbbc accb")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

inst/test_data/bugs.R:11:1: style: Lines should not be more than 100 characters.

​str_to_repair_grammar("dacb bbbd bbcb bdbb cbbc accb ccbc dbba cbbc bbdb bcbb dbbc bbcb adcc ccbc daba cbbc bbdb bcbb dbbc bbcb adcb bdac dcbb cbbd bbcb bdbb cbbc accb cdbb dbbb cbbd bccb bdab cbbc accb cdbb dbbb cbbd bbcb bdbb cbbc accc ccbb cbbd bbcb bdbb cbbc accb")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

inst/test_data/bugs.R:14:6: style: Use <-, not =, for assignment.

​data = fread("/Users/psenin/workspace/grammarviz2_src/data/mitdb__100_180.txt")
     ^

inst/test_data/bugs.R:15:5: style: Use <-, not =, for assignment.

​sax = sax_via_window(data$V1, 160, 4, 4, "exact", 0.001)
    ^

inst/test_data/bugs.R:16:5: style: Use <-, not =, for assignment.

​str = paste(unlist(sax), collapse =" ")
    ^

inst/test_data/bugs.R:16:35: style: Put spaces around all infix operators.

​str = paste(unlist(sax), collapse =" ")
                                  ^~

inst/test_data/bugs.R:17:9: style: Use <-, not =, for assignment.

​grammar = str_to_repair_grammar(str)
        ^

inst/test_data/bugs.R:19:6: style: Use <-, not =, for assignment.

​str1 = grammar[[1]]$rule_string
     ^

inst/test_data/bugs.R:20:4: style: Place a space before left parenthesis, except in a function call.

​for(i in c(2:95)){
   ^

inst/test_data/bugs.R:21:1: style: Lines should not be more than 100 characters.

​	str1 = gsub(paste(" R", i - 1, " ", sep = ""), paste(" ", grammar[[i]]$expanded_rule_string, " ", sep = ""), str1)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

inst/test_data/bugs.R:21:1: style: Use spaces to indent, not tabs.

​	str1 = gsub(paste(" R", i - 1, " ", sep = ""), paste(" ", grammar[[i]]$expanded_rule_string, " ", sep = ""), str1)
^

inst/test_data/bugs.R:21:7: style: Use <-, not =, for assignment.

​	str1 = gsub(paste(" R", i - 1, " ", sep = ""), paste(" ", grammar[[i]]$expanded_rule_string, " ", sep = ""), str1)
      ^

inst/test_data/bugs.R:26:1: error: unexpected '>'

​> library(jmotif)
^

R/jmotif.R:25:27: style: Commas should always have a space after.

​        distance_matrix[i,j] <- (cutlines[i] - cutlines[j - 1]) * (cutlines[i] - cutlines[j - 1])
                          ^

R/jmotif.R:27:27: style: Commas should always have a space after.

​        distance_matrix[j,i] <- distance_matrix[i,j]
                          ^

R/jmotif.R:27:51: style: Commas should always have a space after.

​        distance_matrix[j,i] <- distance_matrix[i,j]
                                                  ^

R/jmotif.R:34:72: style: Commas should always have a space after.

​    stop(paste("unable to get a distance matrix for the alphabet size",a_size))
                                                                       ^

R/jmotif.R:57:9: style: Do not place spaces around code in parentheses or square brackets.

​    if ( any(letters_to_idx(str1) > alphabet_size) |
        ^

R/jmotif.R:62:21: warning: no visible global function definition for ‘sax_distance_matrix’

​      dist_table <- sax_distance_matrix(alphabet_size)
                    ^~~~~~~~~~~~~~~~~~~

R/RcppExports.R:34:1: style: Lines should not be more than 100 characters.

​#' Finds the Euclidean distance between points, if distance is above the threshold, abandons the computation
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/RcppExports.R:67:1: style: Lines should not be more than 100 characters.

​    .Call('_jmotif_find_discords_hotsax', PACKAGE = 'jmotif', ts, w_size, paa_size, a_size, n_threshold, discords_num)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/RcppExports.R:123:1: style: Lines should not be more than 100 characters.

​find_discords_rra <- function(series, w_size, paa_size, a_size, nr_strategy, n_threshold, discords_num) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/RcppExports.R:124:1: style: Lines should not be more than 100 characters.

​    .Call('_jmotif_find_discords_rra', PACKAGE = 'jmotif', series, w_size, paa_size, a_size, nr_strategy, n_threshold, discords_num)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/RcppExports.R:127:1: style: Lines should not be more than 100 characters.

​#' Translates an alphabet size into the array of corresponding SAX cut-lines built using the Normal distribution.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/RcppExports.R:181:1: style: Lines should not be more than 100 characters.

​#' @param nr_strategy the Numerosity Reduction strategy, acceptable values are "exact" and "mindist" --
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/RcppExports.R:190:1: style: Lines should not be more than 100 characters.

​    .Call('_jmotif_sax_via_window', PACKAGE = 'jmotif', ts, w_size, paa_size, a_size, nr_strategy, n_threshold)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/RcppExports.R:224:1: style: Lines should not be more than 100 characters.

​    .Call('_jmotif_series_to_wordbag', PACKAGE = 'jmotif', ts, w_size, paa_size, a_size, nr_strategy, n_threshold)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/RcppExports.R:243:1: style: Lines should not be more than 100 characters.

​    .Call('_jmotif_manyseries_to_wordbag', PACKAGE = 'jmotif', data, w_size, paa_size, a_size, nr_strategy, n_threshold)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/RcppExports.R:381:1: style: Trailing blank lines are superfluous.

​
^

tests/testthat/test_cosine_sim.R:1:3: style: Use <-, not =, for assignment.

​a = c(2, 1, 0, 2, 0, 1, 1, 1)
  ^

tests/testthat/test_cosine_sim.R:6:58: style: Commas should always have a space after.

​  expect_equal(0.1784162, as.numeric(cosine_dist(rbind(a,b))), tolerance = 1e-6)
                                                         ^

tests/testthat/test_cosines.R:4:78: style: Commas should always have a space after.

​bag1 <- manyseries_to_wordbag(CBF[["data_train"]][CBF[["labels_train"]] == 1,],
                                                                             ^

tests/testthat/test_cosines.R:6:78: style: Commas should always have a space after.

​bag2 <- manyseries_to_wordbag(CBF[["data_train"]][CBF[["labels_train"]] == 2,],
                                                                             ^

tests/testthat/test_cosines.R:8:78: style: Commas should always have a space after.

​bag3 <- manyseries_to_wordbag(CBF[["data_train"]][CBF[["labels_train"]] == 3,],
                                                                             ^

tests/testthat/test_cosines.R:11:57: style: Commas should always have a space after.

​sample <- (CBF[["data_test"]][CBF[["labels_test"]] == 3,])[1,]
                                                        ^

tests/testthat/test_cosines.R:11:62: style: Commas should always have a space after.

​sample <- (CBF[["data_test"]][CBF[["labels_test"]] == 3,])[1,]
                                                             ^

tests/testthat/test_cosines.R:15:26: style: Do not place spaces around code in parentheses or square brackets.

​  tfidf <- bags_to_tfidf( list("cylinder" = bag1, "bell" = bag2, "funnel" = bag3) )
                         ^

tests/testthat/test_cosines.R:15:82: style: Do not place spaces around code in parentheses or square brackets.

​  tfidf <- bags_to_tfidf( list("cylinder" = bag1, "bell" = bag2, "funnel" = bag3) )
                                                                                 ^

tests/testthat/test_discord_brute_force.R:18:50: style: Commas should always have a space after.

​  expect_equal(discords[discords$position == 411,]$nn_distance, 1.5045846602966542)
                                                 ^

tests/testthat/test_discord_hot_sax.R:16:50: style: Commas should always have a space after.

​  expect_equal(discords[discords$position == 430,]$nn_distance, 5.252618285620532)
                                                 ^

tests/testthat/test_discord_hot_sax.R:17:50: style: Commas should always have a space after.

​  expect_equal(discords[discords$position == 318,]$nn_distance, 4.154825115936453)
                                                 ^

tests/testthat/test_discord_hot_sax.R:18:51: style: Commas should always have a space after.

​  expect_equal(discords[discords$position == 2080,]$nn_distance, 2.381003269560112)
                                                  ^

tests/testthat/test_discord_hot_sax.R:19:49: style: Commas should always have a space after.

​  expect_equal(discords[discords$position == 25,]$nn_distance, 2.363633774221037)
                                                ^

tests/testthat/test_discord_rra.R:3:26: style: Commas should always have a space after.

​  expect_true(discords[1,]$start < 420)
                         ^

tests/testthat/test_discord_rra.R:4:26: style: Commas should always have a space after.

​  expect_true(discords[1,]$end > 420)
                         ^

tests/testthat/test_early_abandoned_dist.R:3:38: style: Commas should always have a space after.

​test_dist <- as.numeric(dist(rbind(a,b)))
                                     ^

tests/testthat/test_early_abandoned_dist.R:7:44: style: Commas should always have a space after.

​  expect_error(early_abandoned_dist(a, c(1,2), 1))
                                           ^

tests/testthat/test_min_dist_equal.R:5:38: style: Do not place spaces around code in parentheses or square brackets.

​  expect_equal(m3[1, 3], 0.7421040279 )
                                     ^

tests/testthat/test_min_dist_equal.R:16:16: style: Do not place spaces around code in parentheses or square brackets.

​  expect_equal( sqrt((min_dist(str1, str2, 3)) ^ 2 / 2), 0.7421040279 )
               ^

tests/testthat/test_min_dist_equal.R:16:22: style: Place a space before left parenthesis, except in a function call.

​  expect_equal( sqrt((min_dist(str1, str2, 3)) ^ 2 / 2), 0.7421040279 )
                     ^

tests/testthat/test_min_dist_equal.R:16:70: style: Do not place spaces around code in parentheses or square brackets.

​  expect_equal( sqrt((min_dist(str1, str2, 3)) ^ 2 / 2), 0.7421040279 )
                                                                     ^

tests/testthat/test_min_dist_equal.R:18:16: style: Do not place spaces around code in parentheses or square brackets.

​  expect_equal( sqrt((min_dist(str2, str3, 3)) ^ 2), 0.7421040279 )
               ^

tests/testthat/test_min_dist_equal.R:18:22: style: Place a space before left parenthesis, except in a function call.

​  expect_equal( sqrt((min_dist(str2, str3, 3)) ^ 2), 0.7421040279 )
                     ^

tests/testthat/test_min_dist_equal.R:18:66: style: Do not place spaces around code in parentheses or square brackets.

​  expect_equal( sqrt((min_dist(str2, str3, 3)) ^ 2), 0.7421040279 )
                                                                 ^

tests/testthat/test_min_dist.R:3:15: style: Do not place spaces around code in parentheses or square brackets.

​  expect_true( is_equal_mindist("aaa", "bbb")  )
              ^

tests/testthat/test_min_dist.R:3:47: style: Do not place spaces around code in parentheses or square brackets.

​  expect_true( is_equal_mindist("aaa", "bbb")  )
                                              ^

tests/testthat/test_min_dist.R:5:16: style: Do not place spaces around code in parentheses or square brackets.

​  expect_false( is_equal_mindist("aaa", "bbba")  )
               ^

tests/testthat/test_min_dist.R:5:49: style: Do not place spaces around code in parentheses or square brackets.

​  expect_false( is_equal_mindist("aaa", "bbba")  )
                                                ^

tests/testthat/test_min_dist.R:7:16: style: Do not place spaces around code in parentheses or square brackets.

​  expect_false( is_equal_mindist("aaa", "aca")  )
               ^

tests/testthat/test_min_dist.R:7:48: style: Do not place spaces around code in parentheses or square brackets.

​  expect_false( is_equal_mindist("aaa", "aca")  )
                                               ^

tests/testthat/test_RePair_via_decompression.R:1:12: style: Use <-, not =, for assignment.

​sax_string = paste(
           ^

tests/testthat/test_RePair_via_decompression.R:10:3: style: Variable or function name should be snake_case.

​  uncompressed_R0 = paste(grammar[[1]]$rule_string, " ", sep = "")
  ^~~~~~~~~~~~~~~

tests/testthat/test_RePair_via_decompression.R:10:19: style: Use <-, not =, for assignment.

​  uncompressed_R0 = paste(grammar[[1]]$rule_string, " ", sep = "")
                  ^

tests/testthat/test_RePair_via_decompression.R:14:7: style: Variable or function name should be snake_case.

​      uncompressed_R0 = gsub(
      ^~~~~~~~~~~~~~~

tests/testthat/test_RePair_via_decompression.R:14:23: style: Use <-, not =, for assignment.

​      uncompressed_R0 = gsub(
                      ^

tests/testthat/test_SAX_simple.R:15:23: style: Do not place spaces around code in parentheses or square brackets.

​  str1_10_11 <- paste( matrix(unlist(sax_by_chunking(dat1, 10, 11, 0.01)),
                      ^

tests/testthat/test_SAX_simple.R:16:53: style: Commas should always have a space after.

​                             nrow = 10, byrow = T)[,1], collapse = "")
                                                    ^

tests/testthat/test_SAX_simple.R:17:23: style: Do not place spaces around code in parentheses or square brackets.

​  str1_14_10 <- paste( matrix(unlist(sax_by_chunking(dat1, 14, 10, 0.01)),
                      ^

tests/testthat/test_SAX_simple.R:18:53: style: Commas should always have a space after.

​                             nrow = 14, byrow = T)[,1], collapse = "")
                                                    ^

tests/testthat/test_SAX_simple.R:19:21: style: Do not place spaces around code in parentheses or square brackets.

​  str1_9_7 <- paste( matrix(unlist(sax_by_chunking(dat1, 9, 7, 0.01)),
                    ^

tests/testthat/test_SAX_simple.R:20:52: style: Commas should always have a space after.

​                             nrow = 9, byrow = T)[,1], collapse = "")
                                                   ^

tests/testthat/test_SAX_simple.R:34:23: style: Do not place spaces around code in parentheses or square brackets.

​  str2_10_11 <- paste( matrix(unlist(sax_by_chunking(dat2, 10, 11, 0.01)),
                      ^

tests/testthat/test_SAX_simple.R:36:23: style: Do not place spaces around code in parentheses or square brackets.

​  str2_14_10 <- paste( matrix(unlist(sax_by_chunking(dat2, 14, 10, 0.01)),
                      ^

tests/testthat/test_SAX_simple.R:38:21: style: Do not place spaces around code in parentheses or square brackets.

​  str2_9_7 <- paste( matrix(unlist(sax_by_chunking(dat2, 9, 7, 0.01)),
                    ^

tests/testthat/test_SAX_strategies.R:12:3: style: Commented code should be removed.

​# plot(as.numeric(dat),t="l")
  ^~~~~~~~~~~~~~~~~~~~~~~~~~~

tests/testthat/test_SAX_via_window.R:12:3: style: Commented code should be removed.

​# plot(as.numeric(dat),t="l")
  ^~~~~~~~~~~~~~~~~~~~~~~~~~~

tests/testthat/test_SAX_with_NAs.R:12:3: style: Commented code should be removed.

​# plot(as.numeric(dat),t="l")
  ^~~~~~~~~~~~~~~~~~~~~~~~~~~

tests/testthat/test_SAX_with_NAs.R:40:65: style: Commas should always have a space after.

​    cylinders <- CBF[["data_train"]][CBF[["labels_train"]] == 1,]
                                                                ^

tests/testthat/test_SAX_with_NAs.R:42:22: style: Commas should always have a space after.

​    c <- cylinders[2,]
                     ^

tests/testthat/test_wordbag.R:17:61: style: Commas should always have a space after.

​  words <- table(matrix(unlist(sax1), ncol = 1, byrow = T)[,1])
                                                            ^

tests/testthat/test_wordbag.R:22:44: style: Commas should always have a space after.

​                    wb1[wb1$words == "bca",]$counts)
                                           ^

tests/testthat/test_wordbag.R:30:46: style: Commas should always have a space after.

​  wb2 <- manyseries_to_wordbag(t(t(rbind(dat,dat))), 6, 3, 3, "none", 0.01)
                                             ^

tests/testthat/test_wordbag.R:41:61: style: Commas should always have a space after.

​  words <- table(matrix(unlist(sax1), ncol = 1, byrow = T)[,1])
                                                            ^

tests/testthat/test_wordbag.R:46:39: style: Commas should always have a space after.

​               wb1[wb1$words == "bca",]$counts)
                                      ^

tests/testthat/test_wordbag.R:54:46: style: Commas should always have a space after.

​  wb2 <- manyseries_to_wordbag(t(t(rbind(dat,dat))), 6, 3, 3, "mindist", 0.01)
                                             ^

tests/testthat/test_znorm.R:1:1: style: Variable or function name should be snake_case.

​X = c(-1, -2, -1, 0, 2, 1, 1, 0)
^

tests/testthat/test_znorm.R:1:3: style: Use <-, not =, for assignment.

​X = c(-1, -2, -1, 0, 2, 1, 1, 0)
  ^

tests/testthat/test_znorm.R:2:1: style: Variable or function name should be snake_case.

​Xscaled <- X / 100
^~~~~~~

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