Fix broken test · stewid/EpiContactTrace@78387ba

lintr-bot · 2019-11-02T09:45:53Z

R/network-structure.R:135:1: style: Lines should not be more than 80 characters.

              i <- tmp[seq_len(length(tmp) - 1)] != tmp[seq_len(length(tmp))[-1]]
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/network-summary.R:248:1: style: Lines should not be more than 80 characters.

                     inDays = as.integer(x@ingoingContacts@tEnd - x@ingoingContacts@tBegin),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/network-summary.R:251:1: style: Lines should not be more than 80 characters.

                     outDays = as.integer(x@outgoingContacts@tEnd - x@outgoingContacts@tBegin),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/network-summary.R:254:1: style: Lines should not be more than 80 characters.

                     ingoingContactChain = IngoingContactChain(x@ingoingContacts),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/network-summary.R:255:1: style: Lines should not be more than 80 characters.

                     outgoingContactChain = OutgoingContactChain(x@outgoingContacts))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/network-summary.R:261:1: style: functions should have cyclomatic complexity of less than 15, this has 38.

setMethod("NetworkSummary",
^

R/network-summary.R:315:1: style: Lines should not be more than 80 characters.

              ## so test that root is a integer the same way as binom.test test x
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/network-summary.R:323:20: style: Only use double-quotes.

              stop('invalid class of root')
                   ^~~~~~~~~~~~~~~~~~~~~~~

R/network-summary.R:331:1: style: Lines should not be more than 80 characters.

              if (!all(is.null(inBegin), is.null(inEnd), is.null(outBegin), is.null(outEnd))) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/network-summary.R:332:1: style: Lines should not be more than 80 characters.

                  stop("Use either tEnd and days or inBegin, inEnd, outBegin and outEnd in call to NetworkSummary")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/network-summary.R:343:1: style: Lines should not be more than 80 characters.

              ## Test that days is a nonnegative integer the same way as binom.test test x
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/network-summary.R:345:1: style: Lines should not be more than 80 characters.

              if (any(is.na(days) | (days < 0)) || max(abs(days - daysr)) > 1e-07) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/network-summary.R:365:1: style: Lines should not be more than 80 characters.

          } else if (all(!is.null(inBegin), !is.null(inEnd), !is.null(outBegin), !is.null(outEnd))) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/network-summary.R:370:1: style: Lines should not be more than 80 characters.

                  stop("Use either tEnd and days or inBegin, inEnd, outBegin and outEnd in call to NetworkSummary")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/network-summary.R:373:1: style: Lines should not be more than 80 characters.

              stop("Use either tEnd and days or inBegin, inEnd, outBegin and outEnd in call to NetworkSummary")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/network-summary.R:456:1: style: Lines should not be more than 80 characters.

              stop("root, inBegin, inEnd, outBegin and outEnd must have equal length")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/network-summary.R:468:24: style: Put spaces around all infix operators.

          contact_chain<- .Call("networkSummary",
                      ~^

R/network-summary.R:469:1: style: Lines should not be more than 80 characters.

                                as.integer(factor(x$source, levels = levels(nodes))),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/network-summary.R:470:1: style: Lines should not be more than 80 characters.

                                as.integer(factor(x$destination, levels = levels(nodes))),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/network-summary.R:472:1: style: Lines should not be more than 80 characters.

                                as.integer(factor(root, levels = levels(nodes))),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/network-summary.R:489:1: style: Lines should not be more than 80 characters.

                            ingoingContactChain = contact_chain[["ingoingContactChain"]],
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/network-summary.R:490:1: style: Lines should not be more than 80 characters.

                            outgoingContactChain = contact_chain[["outgoingContactChain"]]))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/out-degree.R:119:1: style: Lines should not be more than 80 characters.

##'     Get the OutDegree for a data.frame with movements, see details and examples.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/outgoing-contact-chain.R:67:1: style: Lines should not be more than 80 characters.

##'     The \code{\link{OutgoingContactChain}} of the root within the time-interval
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/outgoing-contact-chain.R:77:1: style: Lines should not be more than 80 characters.

##'     Get the OutgoingContactChain for a data.frame with movements, see examples.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/outgoing-contact-chain.R:137:1: style: Lines should not be more than 80 characters.

                  stop("Unable to determine OutgoingContactChain for ingoing contacts")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/plot.R:82:1: style: Lines should not be more than 80 characters.

              tree$ingoing$bg <- ifelse(tree$ingoing$level > 0, "white", "black")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/plot.R:95:1: style: Lines should not be more than 80 characters.

              tree$outgoing$bg <- ifelse(tree$outgoing$level > 0, "gray", "black")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/report.R:30:8: style: Place a space before left parenthesis, except in a function call.

    for(i in seq_len(nrow(contacts))) {
       ^

R/report.R:35:1: style: Lines should not be more than 80 characters.

                   paste(rep("<td>&nbsp;</td>", 2L * (contacts$distance[i] - 1L)), collapse = ""),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/report.R:44:1: style: Lines should not be more than 80 characters.

                             2L * (max(contacts$distance - 1L) - (contacts$distance[i] - 1L))),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/report.R:73:1: style: Lines should not be more than 80 characters.

    as.character(unlist(by(contacts, sprintf("%s - %s", contacts$lhs, contacts$rhs), function(x) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/report.R:78:1: style: Lines should not be more than 80 characters.

                   sprintf('<h3><a name="%s-%s-%s">%s %s %s</a></h3>', direction,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/report.R:81:1: style: Lines should not be more than 80 characters.

                   "<tr><th>Date</th><th>Id</th><th>N</th><th>Category</th><th>Source</th><th>Destination</th></tr>")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/report.R:83:12: style: Place a space before left parenthesis, except in a function call.

        for(i in seq_len(nrow(x))) {
           ^

R/report.R:112:1: style: Lines should not be more than 80 characters.

               sprintf("<h3 align='center'>Version: %s</h3>", packageVersion("EpiContactTrace")),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/report.R:117:1: style: Lines should not be more than 80 characters.

               sprintf("<tr><td>In begin date:</td><td>%s</td></tr>", x@ingoingContacts@tBegin),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/report.R:118:1: style: Lines should not be more than 80 characters.

               sprintf("<tr><td>In end date:</td><td>%s</td></tr>", x@ingoingContacts@tEnd),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/report.R:119:1: style: Lines should not be more than 80 characters.

               sprintf("<tr><td>In days:</td><td>%i</td></tr>", x@ingoingContacts@tEnd - x@ingoingContacts@tBegin),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/report.R:120:1: style: Lines should not be more than 80 characters.

               sprintf("<tr><td>In degree:</td><td>%i</td></tr>", InDegree(x@ingoingContacts)),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/report.R:121:1: style: Lines should not be more than 80 characters.

               sprintf("<tr><td>Ingoing contact chain:</td><td>%i</td></tr>", IngoingContactChain(x@ingoingContacts)),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/report.R:135:1: style: Lines should not be more than 80 characters.

        lines <- c(lines, "<p>No ingoing contacts during the search period.</p>")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/report.R:143:1: style: Lines should not be more than 80 characters.

               sprintf("<tr><td>Out begin date:</td><td>%s</td></tr>", x@outgoingContacts@tBegin),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/report.R:144:1: style: Lines should not be more than 80 characters.

               sprintf("<tr><td>Out end date:</td><td>%s</td></tr>", x@outgoingContacts@tEnd),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/report.R:145:1: style: Lines should not be more than 80 characters.

               sprintf("<tr><td>Out days:</td><td>%i</td></tr>", x@outgoingContacts@tEnd - x@outgoingContacts@tBegin),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/report.R:146:1: style: Lines should not be more than 80 characters.

               sprintf("<tr><td>Out degree:</td><td>%i</td></tr>", OutDegree(x@outgoingContacts)),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/report.R:147:1: style: Lines should not be more than 80 characters.

               sprintf("<tr><td>Outgoing contact chain:</td><td>%i</td></tr>", OutgoingContactChain(x@outgoingContacts)),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/report.R:161:1: style: Lines should not be more than 80 characters.

        lines <- c(lines, "<p>No outgoing contacts during the search period.</p>")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/report.R:237:1: style: Lines should not be more than 80 characters.

##' available. To generate pdf files a TeX installation must exist to compile the
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/report.R:260:1: style: Lines should not be more than 80 characters.

##' @param template the Sweave template file to use. If none is provided, the default
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/report.R:345:1: style: Lines should not be more than 80 characters.

              writeLines(html_report(object), con = sprintf("%s.html", object@root))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/report.R:348:1: style: Lines should not be more than 80 characters.

                  template <- system.file("Sweave/speak-latex.rnw", package = "EpiContactTrace")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/report.R:351:45: style: Put spaces around all infix operators.

              utils::Sweave(template, syntax="SweaveSyntaxNoweb")
                                           ~^~

R/report.R:352:1: style: Lines should not be more than 80 characters.

              tools::texi2pdf(sub("rnw$", "tex", basename(template)), clean = TRUE)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/report.R:353:1: style: Lines should not be more than 80 characters.

              file.rename(sub("rnw$", "pdf", basename(template)), sprintf("%s.pdf", object@root))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/report.R:400:1: style: Opening curly braces should never go on their own line and should always be followed by a new line.

{
^

R/shortest-paths.R:168:1: style: functions should have cyclomatic complexity of less than 15, this has 41.

setMethod("ShortestPaths",
^

R/shortest-paths.R:239:1: style: Lines should not be more than 80 characters.

              if (!all(is.null(inBegin), is.null(inEnd), is.null(outBegin), is.null(outEnd))) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/shortest-paths.R:240:1: style: Lines should not be more than 80 characters.

                  stop("Use either tEnd and days or inBegin, inEnd, outBegin and outEnd in call to ShortestPaths")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/shortest-paths.R:254:1: style: Lines should not be more than 80 characters.

              if (any(is.na(days) | (days < 0)) || max(abs(days - daysr)) > 1e-07) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/shortest-paths.R:274:1: style: Lines should not be more than 80 characters.

          } else if (all(!is.null(inBegin), !is.null(inEnd), !is.null(outBegin), !is.null(outEnd))) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/shortest-paths.R:279:1: style: Lines should not be more than 80 characters.

                  stop("Use either tEnd and days or inBegin, inEnd, outBegin and outEnd in call to ShortestPaths")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/shortest-paths.R:282:1: style: Lines should not be more than 80 characters.

              stop("Use either tEnd and days or inBegin, inEnd, outBegin and outEnd in call to ShortestPaths")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/shortest-paths.R:365:1: style: Lines should not be more than 80 characters.

              stop("root, inBegin, inEnd, outBegin and outEnd must have equal length")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/shortest-paths.R:411:1: style: Lines should not be more than 80 characters.

                                         destination = x$destination[sp$outRowid],
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/show.R:76:7: style: Opening curly braces should never go on their own line and should always be followed by a new line.

      {
      ^

R/show.R:88:1: style: Lines should not be more than 80 characters.

              cat(sprintf("%sgoing contact chain: %i\n\n", prefix, OutgoingContactChain(object)))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/show.R:91:1: style: Lines should not be more than 80 characters.

              cat(sprintf("%sgoing contact chain: %i\n\n", prefix, IngoingContactChain(object)))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/show.R:102:1: style: Lines should not be more than 80 characters.

              ## Rename source and destination to lhs and rhs, with respect to direction
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/show.R:111:18: style: Place a space before left parenthesis, except in a function call.

              for(i in seq_len(nrow(ns))) {
                 ^

R/show.R:113:1: style: Lines should not be more than 80 characters.

                              paste(rep(" ", (ns$distance[i] - 1) * (width + 5)), collapse=""),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/show.R:113:91: style: Put spaces around all infix operators.

                              paste(rep(" ", (ns$distance[i] - 1) * (width + 5)), collapse=""),
                                                                                         ~^~

R/show.R:119:1: style: Lines should not be more than 80 characters.

              cat(sprintf("No %sgoing contacts during the search period.\n", object@direction))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/trace.R:167:1: style: functions should have cyclomatic complexity of less than 15, this has 56.

Trace <- function(movements,
^

R/trace.R:207:1: style: Lines should not be more than 80 characters.

    if (any(is.factor(movements$destination), is.integer(movements$destination))) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/trace.R:252:1: style: Lines should not be more than 80 characters.

        if (any(is.factor(movements$category), is.integer(movements$category))) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/trace.R:306:1: style: Lines should not be more than 80 characters.

        if (!all(is.null(inBegin), is.null(inEnd), is.null(outBegin), is.null(outEnd))) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/trace.R:307:1: style: Lines should not be more than 80 characters.

            stop("Use either tEnd and days or inBegin, inEnd, outBegin and outEnd in call to Trace")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/trace.R:318:1: style: Lines should not be more than 80 characters.

        ## Test that days is a nonnegative integer the same way as binom.test test x
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/trace.R:335:31: style: Put spaces around all infix operators.

        root <- rep(root, each=n.tEnd*n.days, length.out=n)
                             ~^~

R/trace.R:335:38: style: Put spaces around all infix operators.

        root <- rep(root, each=n.tEnd*n.days, length.out=n)
                                    ~^~

R/trace.R:335:57: style: Put spaces around all infix operators.

        root <- rep(root, each=n.tEnd*n.days, length.out=n)
                                                       ~^~

R/trace.R:336:32: style: Put spaces around all infix operators.

        inEnd <- rep(tEnd, each=n.days, length.out=n)
                              ~^~

R/trace.R:336:51: style: Put spaces around all infix operators.

        inEnd <- rep(tEnd, each=n.days, length.out=n)
                                                 ~^~

R/trace.R:337:42: style: Put spaces around all infix operators.

        inBegin <- inEnd - rep(days, each=1, length.out=n)
                                        ~^~

R/trace.R:337:56: style: Put spaces around all infix operators.

        inBegin <- inEnd - rep(days, each=1, length.out=n)
                                                      ~^~

R/trace.R:340:1: style: Lines should not be more than 80 characters.

    } else if (all(!is.null(inBegin), !is.null(inEnd), !is.null(outBegin), !is.null(outEnd))) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/trace.R:345:1: style: Lines should not be more than 80 characters.

            stop("Use either tEnd and days or inBegin, inEnd, outBegin and outEnd in call to Trace")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/trace.R:348:1: style: Lines should not be more than 80 characters.

        stop("Use either tEnd and days or inBegin, inEnd, outBegin and outEnd in call to Trace")
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/trace.R:458:1: style: Lines should not be more than 80 characters.

                            as.integer(factor(movements$source, levels = levels(nodes))),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/trace.R:459:1: style: Lines should not be more than 80 characters.

                            as.integer(factor(movements$destination, levels = levels(nodes))),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/trace.R:471:16: style: Put spaces around all infix operators.

        j <- (i-1) * 4
              ~^~

R/trace.R:481:1: style: Lines should not be more than 80 characters.

        ## Create an index to contacts, so that the result matrix can be reconstructed
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/trace.R:483:12: style: Commented code should be removed.

        ## contacts_all <- cbind(contacts[index,], distance)
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/trace.R:484:1: style: Lines should not be more than 80 characters.

        index <- match(apply(contacts_all, 1, function(x) paste(x, collapse="\r")),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/trace.R:484:76: style: Put spaces around all infix operators.

        index <- match(apply(contacts_all, 1, function(x) paste(x, collapse="\r")),
                                                                          ~^~

R/trace.R:485:72: style: Put spaces around all infix operators.

                       apply(contacts, 1, function(x) paste(x, collapse="\r")))
                                                                      ~^~

R/trace.R:509:1: style: Lines should not be more than 80 characters.

        ## Create an index to contacts, so that the result matrix can be reconstructed
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/trace.R:511:12: style: Commented code should be removed.

        ## contacts_all <- cbind(contacts[index,], distance)
           ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/trace.R:512:1: style: Lines should not be more than 80 characters.

        index <- match(apply(contacts_all, 1, function(x) paste(x, collapse="\r")),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/trace.R:512:76: style: Put spaces around all infix operators.

        index <- match(apply(contacts_all, 1, function(x) paste(x, collapse="\r")),
                                                                          ~^~

R/trace.R:513:72: style: Put spaces around all infix operators.

                       apply(contacts, 1, function(x) paste(x, collapse="\r")))
                                                                      ~^~

R/trace.R:535:1: style: Lines should not be more than 80 characters.

    ## Name each list item with ContactTrace objects to the name of the ContactTrace root.
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/trace.R:536:1: style: Lines should not be more than 80 characters.

    names(result) <-  sapply(result, function(listItem) listItem@ingoingContacts@root)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/tree.R:38:27: style: Put spaces around all infix operators.

    result <- list(ingoing=NULL, outgoing=NULL)
                         ~^~

R/tree.R:38:42: style: Put spaces around all infix operators.

    result <- list(ingoing=NULL, outgoing=NULL)
                                        ~^~

R/tree.R:53:12: style: Place a space before left parenthesis, except in a function call.

        for(lev in rev(seq_len(max(tree.in$level)))) {
           ^

R/tree.R:54:16: style: Place a space before left parenthesis, except in a function call.

            for(src in tree.in$node[tree.in$level == lev]) {
               ^

R/tree.R:64:38: style: Put spaces around all infix operators.

                stopifnot(length(dst)>0)
                                    ~^~

R/tree.R:83:12: style: Place a space before left parenthesis, except in a function call.

        for(lev in rev(seq_len(max(tree.out$level)))) {
           ^

R/tree.R:84:16: style: Place a space before left parenthesis, except in a function call.

            for(dst in tree.out$node[tree.out$level == lev]) {
               ^

R/tree.R:94:38: style: Put spaces around all infix operators.

                stopifnot(length(src)>0)
                                    ~^~

R/tree.R:131:1: style: Lines should not be more than 80 characters.

##'   \item John Q. Walker II, A node positioning algorithm for general tress.\cr
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/tree.R:134:1: style: functions should have cyclomatic complexity of less than 15, this has 48.

position_tree <- function(tree,
^

R/tree.R:152:14: style: Place a space before left parenthesis, except in a function call.

        while(all(!is.null(left_most),
             ^

R/tree.R:162:16: style: Place a space before left parenthesis, except in a function call.

            for(i in seq_len(compare_depth)) {
               ^

R/tree.R:182:22: style: Place a space before left parenthesis, except in a function call.

                while(all(!is.null(temp_node),
                     ^

R/tree.R:194:26: style: Place a space before left parenthesis, except in a function call.

                    while(!identical(temp_node, ancestor_neighbor)) {
                         ^

R/tree.R:196:1: style: Lines should not be more than 80 characters.

                        set_modifier(temp_node, modifier(temp_node) + move_distance)
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

R/tree.R:226:29: style: Put spaces around all infix operators.

        if (length(children)>0) {
                           ~^~

R/tree.R:241:18: style: Place a space before left parenthesis, except in a function call.

            while(all(is.null(left_most),
                 ^

R/tree.R:273:30: style: Put spaces around all infix operators.

                return(n[i[1]-1])
                            ~^~

R/tree.R:389:26: style: Put spaces around all infix operators.

            return(s[i[1]-1])
                        ~^~

R/tree.R:398:26: style: Put spaces around all infix operators.

            return(s[i[1]+1])
                        ~^~

R/tree.R:431:18: style: Place a space before left parenthesis, except in a function call.

            while(has_right_sibling(right_most)) {
                 ^

tests/arguments.R:172:1: style: Lines should not be more than 80 characters.

## Use either tEnd and days or inBegin, inEnd, outBegin and outEnd in call to Trace
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

tests/arguments.R:224:1: style: Lines should not be more than 80 characters.

tools::assertError(Trace(movements = data.frame(source = 1L, destination = 2L, t = 1),
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

tests/arguments.R:235:44: style: Commas should always have a space after.

                             source = c(1L,NA),
                                           ^

tests/arguments.R:236:49: style: Commas should always have a space after.

                             destination = c(2L,3L),
                                                ^

tests/arguments.R:248:44: style: Commas should always have a space after.

                             source = c(1L,2L),
                                           ^

tests/arguments.R:249:49: style: Commas should always have a space after.

                             destination = c(2L,NA),
                                                ^

tests/arguments.R:261:44: style: Commas should always have a space after.

                             source = c(1L,2L),
                                           ^

tests/arguments.R:262:49: style: Commas should always have a space after.

                             destination = c(2L,3L),
                                                ^

tests/arguments.R:274:44: style: Commas should always have a space after.

                             source = c(1L,2L),
                                           ^

tests/arguments.R:275:49: style: Commas should always have a space after.

                             destination = c(2L,3L),
                                                ^

tests/arguments.R:394:4: style: Commented code should be removed.

## inEnd < inBegin
   ^~~~~~~~~~~~~~~

tests/arguments.R:407:4: style: Commented code should be removed.

## outEnd < outBegin
   ^~~~~~~~~~~~~~~~~

tests/contact-chain.R:51:1: style: Put spaces around all infix operators.

= "Date"), individual = c(NA_character_, NA_character_, NA_character_,
^

tests/contact-chain.R:71:31: style: Do not place spaces around code in parentheses or square brackets.

c(NA_character_, NA_character_ ), n = c(NA_integer_, NA_integer_)),
                              ^

tests/contact-chain.R:73:1: style: Put spaces around all infix operators.

= c(NA, -2L), class = "data.frame")
^

tests/contact-chain.R:91:1: style: Put spaces around all infix operators.

= c(NA_character_, NA_character_, NA_character_, NA_character_,
^

tests/contact-chain.R:95:28: style: Do not place spaces around code in parentheses or square brackets.

"n"), row.names = c(NA, -7L ), class = "data.frame")
                           ^

tests/contact-chain.R:112:31: style: Do not place spaces around code in parentheses or square brackets.

c(NA_character_, NA_character_ ), n = c(NA_integer_, NA_integer_)),
                              ^

tests/contact-chain.R:114:1: style: Put spaces around all infix operators.

= c(NA, -2L), class = "data.frame")
^

tests/contact-chain.R:156:37: style: Put spaces around all infix operators.

ns <- NetworkSummary(movements, root=1, tEnd="2010-10-20", days=10)
                                   ~^~

tests/contact-chain.R:156:45: style: Put spaces around all infix operators.

ns <- NetworkSummary(movements, root=1, tEnd="2010-10-20", days=10)
                                           ~^~

tests/contact-chain.R:156:64: style: Put spaces around all infix operators.

ns <- NetworkSummary(movements, root=1, tEnd="2010-10-20", days=10)
                                                              ~^~

tests/misc.R:329:44: style: Commas should always have a space after.

                         ct_1_df$category),]
                                           ^

tests/misc.R:336:44: style: Commas should always have a space after.

                         ct_2_df$category),]
                                           ^

tests/network-summary.R:31:10: style: Put spaces around all infix operators.

load(file=system.file("extdata", "ns.rda", package = "EpiContactTrace"))
        ~^~

-Original file line number
+Diff line change
@@ Expand Up / @@ -80,4 +80,4 @@ sp_out <- sp_out[sp_out$direction == "out", @@
     sp_out <- sp_out[order(as.numeric(sp_out$destination)), ]
     rownames(sp_out) <- NULL
-    stopifnot(identical(sp_out, sp_out.exp))
+    stopifnot(identical(sp_out, sp_out_exp))

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lintr-bot commented on `78387ba` Nov 2, 2019