CRAN Package Check Results for Package icosa

Last updated on 2020-02-15 01:01:27 CET.

Check Details

Version: 0.9.81
Check: whether package can be installed
Result: WARN
    Found the following significant warnings:
     RccpSource_.cpp:978:54: warning: explicitly assigning value of variable of type 'Rcpp::NumericVector' (aka 'Vector<14>') to itself [-Wself-assign-overloaded]
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-fedora-clang

Version: 0.9.81
Check: examples
Result: ERROR
    Running examples in 'icosa-Ex.R' failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: PolToCar
    > ### Title: Conversion of spherical coordinates to 3d Cartesian coordinates
    > ### Aliases: PolToCar
    >
    > ### ** Examples
    >
    > longLat <- rbind(
    + c(0,0),
    + #note the precision here!
    + c(0, 90),
    + c(-45,12)
    + )
    >
    > xyz <- PolToCar(longLat)
     ----------- FAILURE REPORT --------------
     --- failure: the condition has length > 1 ---
     --- srcref ---
    :
     --- package (from environment) ---
    icosa
     --- call from context ---
    PolToCar(longLat)
     --- call from argument ---
    if (!class(longLatMat) %in% c("matrix", "data.frame")) {
     stop("Invalid input.")
    }
     --- R stacktrace ---
    where 1: PolToCar(longLat)
    
     --- value of length: 2 type: logical ---
    [1] FALSE TRUE
     --- function from context ---
    function (longLatMat, radius = authRadius, origin = c(0, 0, 0))
    {
     if (!class(longLatMat) %in% c("matrix", "data.frame")) {
     stop("Invalid input.")
     }
     if ((class(longLatMat[, 1]) == "numeric") + (class(longLatMat[,
     2]) == "numeric") != 2) {
     stop("Invalid input matrix or data frame.")
     }
     boolNA <- (is.na(longLatMat[, 1]) | is.na(longLatMat[, 2]))
     longLat <- longLatMat[!boolNA, , drop = FALSE]
     if (length(radius) != 1 | !is.numeric(radius))
     stop("Invalid 'radius' value.")
     if (max(abs(longLat[, 2])) > 90)
     stop("Latitudinal data should be in the second column of the matrix.")
     x <- cos(longLat[, 2]/180 * pi) * cos(longLat[, 1]/180 *
     pi)
     y <- cos(longLat[, 2]/180 * pi) * sin(longLat[, 1]/180 *
     pi)
     z <- sin(longLat[, 2]/180 * pi)
     newMat <- matrix(NA, ncol = 3, nrow = nrow(longLatMat))
     newMat[!boolNA, ] <- cbind(x, y, z)
     colnames(newMat) <- c("x", "y", "z")
     endRes <- newMat * radius
     endRes[, 1] <- endRes[, 1] + origin[1]
     endRes[, 2] <- endRes[, 2] + origin[2]
     endRes[, 3] <- endRes[, 3] + origin[3]
     return(endRes)
    }
    <bytecode: 0xa017ae0>
    <environment: namespace:icosa>
     --- function search by body ---
    Function PolToCar in namespace icosa has this body.
     ----------- END OF FAILURE REPORT --------------
    Error in if (!class(longLatMat) %in% c("matrix", "data.frame")) { :
     the condition has length > 1
    Calls: PolToCar
    Execution halted
Flavor: r-devel-linux-x86_64-debian-clang

Version: 0.9.81
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
     ...
    --- re-building 'icosaIntroShort.Rmd' using rmarkdown
     ----------- FAILURE REPORT --------------
     --- failure: the condition has length > 1 ---
     --- srcref ---
    :
     --- package (from environment) ---
    icosa
     --- call from context ---
    PolToCar(merid, origin = origin, radius = radius)
     --- call from argument ---
    if (!class(longLatMat) %in% c("matrix", "data.frame")) {
     stop("Invalid input.")
    }
     --- R stacktrace ---
    where 1: PolToCar(merid, origin = origin, radius = radius)
    where 2: guides3d(col = "green", origin = x@center, radius = x@r, lwd = 2)
    where 3: .local(x, ...)
    where 4: plot3d(hLow)
    where 5: plot3d(hLow)
    where 6: eval(expr, envir, enclos)
    where 7: eval(expr, envir, enclos)
    where 8: withVisible(eval(expr, envir, enclos))
    where 9: withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler,
     error = eHandler, message = mHandler)
    where 10: handle(ev <- withCallingHandlers(withVisible(eval(expr, envir,
     enclos)), warning = wHandler, error = eHandler, message = mHandler))
    where 11: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval(expr,
     envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)))
    where 12: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos,
     debug = debug, last = i == length(out), use_try = stop_on_error !=
     2L, keep_warning = keep_warning, keep_message = keep_message,
     output_handler = output_handler, include_timing = include_timing)
    where 13: evaluate::evaluate(...)
    where 14: evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning),
     keep_message = !isFALSE(options$message), stop_on_error = if (options$error &&
     options$include) 0L else 2L, output_handler = knit_handlers(options$render,
     options))
    where 15: in_dir(input_dir(), evaluate(code, envir = env, new_device = FALSE,
     keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$message),
     stop_on_error = if (options$error && options$include) 0L else 2L,
     output_handler = knit_handlers(options$render, options)))
    where 16: block_exec(params)
    where 17: call_block(x)
    where 18: process_group.block(group)
    where 19: process_group(group)
    where 20: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
     error = function(e) {
     setwd(wd)
     cat(res, sep = "\n", file = output %n% "")
     message("Quitting from lines ", paste(current_lines(i),
     collapse = "-"), " (", knit_concord$get("infile"),
     ") ")
     })
    where 21: process_file(text, output)
    where 22: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
    where 23: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),
     output_dir = getwd(), ...)
    where 24: vweave_rmarkdown(...)
    where 25: engine$weave(file, quiet = quiet, encoding = enc)
    where 26: doTryCatch(return(expr), name, parentenv, handler)
    where 27: tryCatchOne(expr, names, parentenv, handlers[[1L]])
    where 28: tryCatchList(expr, classes, parentenv, handlers)
    where 29: tryCatch({
     engine$weave(file, quiet = quiet, encoding = enc)
     setwd(startdir)
     output <- find_vignette_product(name, by = "weave", engine = engine)
     if (!have.makefile && vignette_is_tex(output)) {
     texi2pdf(file = output, clean = FALSE, quiet = quiet)
     output <- find_vignette_product(name, by = "texi2pdf",
     engine = engine)
     }
     outputs <- c(outputs, output)
    }, error = function(e) {
     thisOK <<- FALSE
     fails <<- c(fails, file)
     message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s",
     file, conditionMessage(e)))
    })
    where 30: tools:::buildVignettes(dir = "/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/icosa.Rcheck/vign_test/icosa",
     ser_elibs = "/tmp/Rtmpt56XLw/file720619618372.rds")
    
     --- value of length: 2 type: logical ---
    [1] FALSE TRUE
     --- function from context ---
    function (longLatMat, radius = authRadius, origin = c(0, 0, 0))
    {
     if (!class(longLatMat) %in% c("matrix", "data.frame")) {
     stop("Invalid input.")
     }
     if ((class(longLatMat[, 1]) == "numeric") + (class(longLatMat[,
     2]) == "numeric") != 2) {
     stop("Invalid input matrix or data frame.")
     }
     boolNA <- (is.na(longLatMat[, 1]) | is.na(longLatMat[, 2]))
     longLat <- longLatMat[!boolNA, , drop = FALSE]
     if (length(radius) != 1 | !is.numeric(radius))
     stop("Invalid 'radius' value.")
     if (max(abs(longLat[, 2])) > 90)
     stop("Latitudinal data should be in the second column of the matrix.")
     x <- cos(longLat[, 2]/180 * pi) * cos(longLat[, 1]/180 *
     pi)
     y <- cos(longLat[, 2]/180 * pi) * sin(longLat[, 1]/180 *
     pi)
     z <- sin(longLat[, 2]/180 * pi)
     newMat <- matrix(NA, ncol = 3, nrow = nrow(longLatMat))
     newMat[!boolNA, ] <- cbind(x, y, z)
     colnames(newMat) <- c("x", "y", "z")
     endRes <- newMat * radius
     endRes[, 1] <- endRes[, 1] + origin[1]
     endRes[, 2] <- endRes[, 2] + origin[2]
     endRes[, 3] <- endRes[, 3] + origin[3]
     return(endRes)
    }
    <bytecode: 0x89b5a20>
    <environment: namespace:icosa>
     --- function search by body ---
    Function PolToCar in namespace icosa has this body.
     ----------- END OF FAILURE REPORT --------------
    Quitting from lines 86-91 (icosaIntroShort.Rmd)
    Error: processing vignette 'icosaIntroShort.Rmd' failed with diagnostics:
    the condition has length > 1
    --- failed re-building 'icosaIntroShort.Rmd'
    
    SUMMARY: processing the following file failed:
     'icosaIntroShort.Rmd'
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-devel-linux-x86_64-debian-clang

Version: 0.9.81
Check: examples
Result: ERROR
    Running examples in ‘icosa-Ex.R’ failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: PolToCar
    > ### Title: Conversion of spherical coordinates to 3d Cartesian coordinates
    > ### Aliases: PolToCar
    >
    > ### ** Examples
    >
    > longLat <- rbind(
    + c(0,0),
    + #note the precision here!
    + c(0, 90),
    + c(-45,12)
    + )
    >
    > xyz <- PolToCar(longLat)
     ----------- FAILURE REPORT --------------
     --- failure: the condition has length > 1 ---
     --- srcref ---
    :
     --- package (from environment) ---
    icosa
     --- call from context ---
    PolToCar(longLat)
     --- call from argument ---
    if (!class(longLatMat) %in% c("matrix", "data.frame")) {
     stop("Invalid input.")
    }
     --- R stacktrace ---
    where 1: PolToCar(longLat)
    
     --- value of length: 2 type: logical ---
    [1] FALSE TRUE
     --- function from context ---
    function (longLatMat, radius = authRadius, origin = c(0, 0, 0))
    {
     if (!class(longLatMat) %in% c("matrix", "data.frame")) {
     stop("Invalid input.")
     }
     if ((class(longLatMat[, 1]) == "numeric") + (class(longLatMat[,
     2]) == "numeric") != 2) {
     stop("Invalid input matrix or data frame.")
     }
     boolNA <- (is.na(longLatMat[, 1]) | is.na(longLatMat[, 2]))
     longLat <- longLatMat[!boolNA, , drop = FALSE]
     if (length(radius) != 1 | !is.numeric(radius))
     stop("Invalid 'radius' value.")
     if (max(abs(longLat[, 2])) > 90)
     stop("Latitudinal data should be in the second column of the matrix.")
     x <- cos(longLat[, 2]/180 * pi) * cos(longLat[, 1]/180 *
     pi)
     y <- cos(longLat[, 2]/180 * pi) * sin(longLat[, 1]/180 *
     pi)
     z <- sin(longLat[, 2]/180 * pi)
     newMat <- matrix(NA, ncol = 3, nrow = nrow(longLatMat))
     newMat[!boolNA, ] <- cbind(x, y, z)
     colnames(newMat) <- c("x", "y", "z")
     endRes <- newMat * radius
     endRes[, 1] <- endRes[, 1] + origin[1]
     endRes[, 2] <- endRes[, 2] + origin[2]
     endRes[, 3] <- endRes[, 3] + origin[3]
     return(endRes)
    }
    <bytecode: 0x5588b9c858f0>
    <environment: namespace:icosa>
     --- function search by body ---
    Function PolToCar in namespace icosa has this body.
     ----------- END OF FAILURE REPORT --------------
    Error in if (!class(longLatMat) %in% c("matrix", "data.frame")) { :
     the condition has length > 1
    Calls: PolToCar
    Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc

Version: 0.9.81
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
     ...
    --- re-building ‘icosaIntroShort.Rmd’ using rmarkdown
     ----------- FAILURE REPORT --------------
     --- failure: the condition has length > 1 ---
     --- srcref ---
    :
     --- package (from environment) ---
    icosa
     --- call from context ---
    PolToCar(merid, origin = origin, radius = radius)
     --- call from argument ---
    if (!class(longLatMat) %in% c("matrix", "data.frame")) {
     stop("Invalid input.")
    }
     --- R stacktrace ---
    where 1: PolToCar(merid, origin = origin, radius = radius)
    where 2: guides3d(col = "green", origin = x@center, radius = x@r, lwd = 2)
    where 3: .local(x, ...)
    where 4: plot3d(hLow)
    where 5: plot3d(hLow)
    where 6: eval(expr, envir, enclos)
    where 7: eval(expr, envir, enclos)
    where 8: withVisible(eval(expr, envir, enclos))
    where 9: withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler,
     error = eHandler, message = mHandler)
    where 10: handle(ev <- withCallingHandlers(withVisible(eval(expr, envir,
     enclos)), warning = wHandler, error = eHandler, message = mHandler))
    where 11: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval(expr,
     envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)))
    where 12: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos,
     debug = debug, last = i == length(out), use_try = stop_on_error !=
     2L, keep_warning = keep_warning, keep_message = keep_message,
     output_handler = output_handler, include_timing = include_timing)
    where 13: evaluate::evaluate(...)
    where 14: evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning),
     keep_message = !isFALSE(options$message), stop_on_error = if (options$error &&
     options$include) 0L else 2L, output_handler = knit_handlers(options$render,
     options))
    where 15: in_dir(input_dir(), evaluate(code, envir = env, new_device = FALSE,
     keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$message),
     stop_on_error = if (options$error && options$include) 0L else 2L,
     output_handler = knit_handlers(options$render, options)))
    where 16: block_exec(params)
    where 17: call_block(x)
    where 18: process_group.block(group)
    where 19: process_group(group)
    where 20: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
     error = function(e) {
     setwd(wd)
     cat(res, sep = "\n", file = output %n% "")
     message("Quitting from lines ", paste(current_lines(i),
     collapse = "-"), " (", knit_concord$get("infile"),
     ") ")
     })
    where 21: process_file(text, output)
    where 22: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
    where 23: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),
     output_dir = getwd(), ...)
    where 24: vweave_rmarkdown(...)
    where 25: engine$weave(file, quiet = quiet, encoding = enc)
    where 26: doTryCatch(return(expr), name, parentenv, handler)
    where 27: tryCatchOne(expr, names, parentenv, handlers[[1L]])
    where 28: tryCatchList(expr, classes, parentenv, handlers)
    where 29: tryCatch({
     engine$weave(file, quiet = quiet, encoding = enc)
     setwd(startdir)
     output <- find_vignette_product(name, by = "weave", engine = engine)
     if (!have.makefile && vignette_is_tex(output)) {
     texi2pdf(file = output, clean = FALSE, quiet = quiet)
     output <- find_vignette_product(name, by = "texi2pdf",
     engine = engine)
     }
     outputs <- c(outputs, output)
    }, error = function(e) {
     thisOK <<- FALSE
     fails <<- c(fails, file)
     message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s",
     file, conditionMessage(e)))
    })
    where 30: tools:::buildVignettes(dir = "/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/icosa.Rcheck/vign_test/icosa",
     ser_elibs = "/home/hornik/tmp/scratch/Rtmptmt0d2/file7ffb9f4789f.rds")
    
     --- value of length: 2 type: logical ---
    [1] FALSE TRUE
     --- function from context ---
    function (longLatMat, radius = authRadius, origin = c(0, 0, 0))
    {
     if (!class(longLatMat) %in% c("matrix", "data.frame")) {
     stop("Invalid input.")
     }
     if ((class(longLatMat[, 1]) == "numeric") + (class(longLatMat[,
     2]) == "numeric") != 2) {
     stop("Invalid input matrix or data frame.")
     }
     boolNA <- (is.na(longLatMat[, 1]) | is.na(longLatMat[, 2]))
     longLat <- longLatMat[!boolNA, , drop = FALSE]
     if (length(radius) != 1 | !is.numeric(radius))
     stop("Invalid 'radius' value.")
     if (max(abs(longLat[, 2])) > 90)
     stop("Latitudinal data should be in the second column of the matrix.")
     x <- cos(longLat[, 2]/180 * pi) * cos(longLat[, 1]/180 *
     pi)
     y <- cos(longLat[, 2]/180 * pi) * sin(longLat[, 1]/180 *
     pi)
     z <- sin(longLat[, 2]/180 * pi)
     newMat <- matrix(NA, ncol = 3, nrow = nrow(longLatMat))
     newMat[!boolNA, ] <- cbind(x, y, z)
     colnames(newMat) <- c("x", "y", "z")
     endRes <- newMat * radius
     endRes[, 1] <- endRes[, 1] + origin[1]
     endRes[, 2] <- endRes[, 2] + origin[2]
     endRes[, 3] <- endRes[, 3] + origin[3]
     return(endRes)
    }
    <bytecode: 0x55f045a343c8>
    <environment: namespace:icosa>
     --- function search by body ---
    Function PolToCar in namespace icosa has this body.
     ----------- END OF FAILURE REPORT --------------
    Quitting from lines 86-91 (icosaIntroShort.Rmd)
    Error: processing vignette 'icosaIntroShort.Rmd' failed with diagnostics:
    the condition has length > 1
    --- failed re-building ‘icosaIntroShort.Rmd’
    
    SUMMARY: processing the following file failed:
     ‘icosaIntroShort.Rmd’
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc

Version: 0.9.81
Check: installed package size
Result: NOTE
     installed size is 6.9Mb
     sub-directories of 1Mb or more:
     doc 1.9Mb
     extdata 1.4Mb
     libs 2.8Mb
Flavors: r-devel-linux-x86_64-fedora-clang, r-release-osx-x86_64, r-oldrel-osx-x86_64

Version: 0.9.81
Check: dependencies in R code
Result: NOTE
    Namespace in Imports field not imported from: ‘rgdal’
     All declared Imports should be used.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-patched-solaris-x86, r-release-osx-x86_64, r-oldrel-osx-x86_64

Version: 0.9.81
Check: examples
Result: ERROR
    Running examples in ‘icosa-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: PolToCar
    > ### Title: Conversion of spherical coordinates to 3d Cartesian coordinates
    > ### Aliases: PolToCar
    >
    > ### ** Examples
    >
    > longLat <- rbind(
    + c(0,0),
    + #note the precision here!
    + c(0, 90),
    + c(-45,12)
    + )
    >
    > xyz <- PolToCar(longLat)
     ----------- FAILURE REPORT --------------
     --- failure: the condition has length > 1 ---
     --- srcref ---
    :
     --- package (from environment) ---
    icosa
     --- call from context ---
    PolToCar(longLat)
     --- call from argument ---
    if (!class(longLatMat) %in% c("matrix", "data.frame")) {
     stop("Invalid input.")
    }
     --- R stacktrace ---
    where 1: PolToCar(longLat)
    
     --- value of length: 2 type: logical ---
    [1] FALSE TRUE
     --- function from context ---
    function (longLatMat, radius = authRadius, origin = c(0, 0, 0))
    {
     if (!class(longLatMat) %in% c("matrix", "data.frame")) {
     stop("Invalid input.")
     }
     if ((class(longLatMat[, 1]) == "numeric") + (class(longLatMat[,
     2]) == "numeric") != 2) {
     stop("Invalid input matrix or data frame.")
     }
     boolNA <- (is.na(longLatMat[, 1]) | is.na(longLatMat[, 2]))
     longLat <- longLatMat[!boolNA, , drop = FALSE]
     if (length(radius) != 1 | !is.numeric(radius))
     stop("Invalid 'radius' value.")
     if (max(abs(longLat[, 2])) > 90)
     stop("Latitudinal data should be in the second column of the matrix.")
     x <- cos(longLat[, 2]/180 * pi) * cos(longLat[, 1]/180 *
     pi)
     y <- cos(longLat[, 2]/180 * pi) * sin(longLat[, 1]/180 *
     pi)
     z <- sin(longLat[, 2]/180 * pi)
     newMat <- matrix(NA, ncol = 3, nrow = nrow(longLatMat))
     newMat[!boolNA, ] <- cbind(x, y, z)
     colnames(newMat) <- c("x", "y", "z")
     endRes <- newMat * radius
     endRes[, 1] <- endRes[, 1] + origin[1]
     endRes[, 2] <- endRes[, 2] + origin[2]
     endRes[, 3] <- endRes[, 3] + origin[3]
     return(endRes)
    }
    <bytecode: 0xa9d0060>
    <environment: namespace:icosa>
     --- function search by body ---
    Function PolToCar in namespace icosa has this body.
     ----------- END OF FAILURE REPORT --------------
    Error in if (!class(longLatMat) %in% c("matrix", "data.frame")) { :
     the condition has length > 1
    Calls: PolToCar
    Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang

Version: 0.9.81
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
    --- re-building ‘icosaIntroShort.Rmd’ using rmarkdown
     ----------- FAILURE REPORT --------------
     --- failure: the condition has length > 1 ---
     --- srcref ---
    :
     --- package (from environment) ---
    icosa
     --- call from context ---
    PolToCar(merid, origin = origin, radius = radius)
     --- call from argument ---
    if (!class(longLatMat) %in% c("matrix", "data.frame")) {
     stop("Invalid input.")
    }
     --- R stacktrace ---
    where 1: PolToCar(merid, origin = origin, radius = radius)
    where 2: guides3d(col = "green", origin = x@center, radius = x@r, lwd = 2)
    where 3: .local(x, ...)
    where 4: plot3d(hLow)
    where 5: plot3d(hLow)
    where 6: eval(expr, envir, enclos)
    where 7: eval(expr, envir, enclos)
    where 8: withVisible(eval(expr, envir, enclos))
    where 9: withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler,
     error = eHandler, message = mHandler)
    where 10: handle(ev <- withCallingHandlers(withVisible(eval(expr, envir,
     enclos)), warning = wHandler, error = eHandler, message = mHandler))
    where 11: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval(expr,
     envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)))
    where 12: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos,
     debug = debug, last = i == length(out), use_try = stop_on_error !=
     2L, keep_warning = keep_warning, keep_message = keep_message,
     output_handler = output_handler, include_timing = include_timing)
    where 13: evaluate::evaluate(...)
    where 14: evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning),
     keep_message = !isFALSE(options$message), stop_on_error = if (options$error &&
     options$include) 0L else 2L, output_handler = knit_handlers(options$render,
     options))
    where 15: in_dir(input_dir(), evaluate(code, envir = env, new_device = FALSE,
     keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$message),
     stop_on_error = if (options$error && options$include) 0L else 2L,
     output_handler = knit_handlers(options$render, options)))
    where 16: block_exec(params)
    where 17: call_block(x)
    where 18: process_group.block(group)
    where 19: process_group(group)
    where 20: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
     error = function(e) {
     setwd(wd)
     cat(res, sep = "\n", file = output %n% "")
     message("Quitting from lines ", paste(current_lines(i),
     collapse = "-"), " (", knit_concord$get("infile"),
     ") ")
     })
    where 21: process_file(text, output)
    where 22: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
    where 23: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),
     output_dir = getwd(), ...)
    where 24: vweave_rmarkdown(...)
    where 25: engine$weave(file, quiet = quiet, encoding = enc)
    where 26: doTryCatch(return(expr), name, parentenv, handler)
    where 27: tryCatchOne(expr, names, parentenv, handlers[[1L]])
    where 28: tryCatchList(expr, classes, parentenv, handlers)
    where 29: tryCatch({
     engine$weave(file, quiet = quiet, encoding = enc)
     setwd(startdir)
     output <- find_vignette_product(name, by = "weave", engine = engine)
     if (!have.makefile && vignette_is_tex(output)) {
     texi2pdf(file = output, clean = FALSE, quiet = quiet)
     output <- find_vignette_product(name, by = "texi2pdf",
     engine = engine)
     }
     outputs <- c(outputs, output)
    }, error = function(e) {
     thisOK <<- FALSE
     fails <<- c(fails, file)
     message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s",
     file, conditionMessage(e)))
    })
    where 30: tools:::buildVignettes(dir = "/data/gannet/ripley/R/packages/tests-clang/icosa.Rcheck/vign_test/icosa",
     ser_elibs = "/tmp/Rtmp7yqDQC/file1ce71ac72fcd.rds")
    
     --- value of length: 2 type: logical ---
    [1] FALSE TRUE
     --- function from context ---
    function (longLatMat, radius = authRadius, origin = c(0, 0, 0))
    {
     if (!class(longLatMat) %in% c("matrix", "data.frame")) {
     stop("Invalid input.")
     }
     if ((class(longLatMat[, 1]) == "numeric") + (class(longLatMat[,
     2]) == "numeric") != 2) {
     stop("Invalid input matrix or data frame.")
     }
     boolNA <- (is.na(longLatMat[, 1]) | is.na(longLatMat[, 2]))
     longLat <- longLatMat[!boolNA, , drop = FALSE]
     if (length(radius) != 1 | !is.numeric(radius))
     stop("Invalid 'radius' value.")
     if (max(abs(longLat[, 2])) > 90)
     stop("Latitudinal data should be in the second column of the matrix.")
     x <- cos(longLat[, 2]/180 * pi) * cos(longLat[, 1]/180 *
     pi)
     y <- cos(longLat[, 2]/180 * pi) * sin(longLat[, 1]/180 *
     pi)
     z <- sin(longLat[, 2]/180 * pi)
     newMat <- matrix(NA, ncol = 3, nrow = nrow(longLatMat))
     newMat[!boolNA, ] <- cbind(x, y, z)
     colnames(newMat) <- c("x", "y", "z")
     endRes <- newMat * radius
     endRes[, 1] <- endRes[, 1] + origin[1]
     endRes[, 2] <- endRes[, 2] + origin[2]
     endRes[, 3] <- endRes[, 3] + origin[3]
     return(endRes)
    }
    <bytecode: 0x87e9158>
    <environment: namespace:icosa>
     --- function search by body ---
    Function PolToCar in namespace icosa has this body.
     ----------- END OF FAILURE REPORT --------------
    Quitting from lines 86-91 (icosaIntroShort.Rmd)
    Error: processing vignette 'icosaIntroShort.Rmd' failed with diagnostics:
    the condition has length > 1
    --- failed re-building ‘icosaIntroShort.Rmd’
    
    SUMMARY: processing the following file failed:
     ‘icosaIntroShort.Rmd’
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang

Version: 0.9.81
Check: examples
Result: ERROR
    Running examples in ‘icosa-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: PolToCar
    > ### Title: Conversion of spherical coordinates to 3d Cartesian coordinates
    > ### Aliases: PolToCar
    >
    > ### ** Examples
    >
    > longLat <- rbind(
    + c(0,0),
    + #note the precision here!
    + c(0, 90),
    + c(-45,12)
    + )
    >
    > xyz <- PolToCar(longLat)
     ----------- FAILURE REPORT --------------
     --- failure: the condition has length > 1 ---
     --- srcref ---
    :
     --- package (from environment) ---
    icosa
     --- call from context ---
    PolToCar(longLat)
     --- call from argument ---
    if (!class(longLatMat) %in% c("matrix", "data.frame")) {
     stop("Invalid input.")
    }
     --- R stacktrace ---
    where 1: PolToCar(longLat)
    
     --- value of length: 2 type: logical ---
    [1] FALSE TRUE
     --- function from context ---
    function (longLatMat, radius = authRadius, origin = c(0, 0, 0))
    {
     if (!class(longLatMat) %in% c("matrix", "data.frame")) {
     stop("Invalid input.")
     }
     if ((class(longLatMat[, 1]) == "numeric") + (class(longLatMat[,
     2]) == "numeric") != 2) {
     stop("Invalid input matrix or data frame.")
     }
     boolNA <- (is.na(longLatMat[, 1]) | is.na(longLatMat[, 2]))
     longLat <- longLatMat[!boolNA, , drop = FALSE]
     if (length(radius) != 1 | !is.numeric(radius))
     stop("Invalid 'radius' value.")
     if (max(abs(longLat[, 2])) > 90)
     stop("Latitudinal data should be in the second column of the matrix.")
     x <- cos(longLat[, 2]/180 * pi) * cos(longLat[, 1]/180 *
     pi)
     y <- cos(longLat[, 2]/180 * pi) * sin(longLat[, 1]/180 *
     pi)
     z <- sin(longLat[, 2]/180 * pi)
     newMat <- matrix(NA, ncol = 3, nrow = nrow(longLatMat))
     newMat[!boolNA, ] <- cbind(x, y, z)
     colnames(newMat) <- c("x", "y", "z")
     endRes <- newMat * radius
     endRes[, 1] <- endRes[, 1] + origin[1]
     endRes[, 2] <- endRes[, 2] + origin[2]
     endRes[, 3] <- endRes[, 3] + origin[3]
     return(endRes)
    }
    <bytecode: 0xade8790>
    <environment: namespace:icosa>
     --- function search by body ---
    Function PolToCar in namespace icosa has this body.
     ----------- END OF FAILURE REPORT --------------
    Error in if (!class(longLatMat) %in% c("matrix", "data.frame")) { :
     the condition has length > 1
    Calls: PolToCar
    Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc

Version: 0.9.81
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
    --- re-building ‘icosaIntroShort.Rmd’ using rmarkdown
     ----------- FAILURE REPORT --------------
     --- failure: the condition has length > 1 ---
     --- srcref ---
    :
     --- package (from environment) ---
    icosa
     --- call from context ---
    PolToCar(merid, origin = origin, radius = radius)
     --- call from argument ---
    if (!class(longLatMat) %in% c("matrix", "data.frame")) {
     stop("Invalid input.")
    }
     --- R stacktrace ---
    where 1: PolToCar(merid, origin = origin, radius = radius)
    where 2: guides3d(col = "green", origin = x@center, radius = x@r, lwd = 2)
    where 3: .local(x, ...)
    where 4: plot3d(hLow)
    where 5: plot3d(hLow)
    where 6: eval(expr, envir, enclos)
    where 7: eval(expr, envir, enclos)
    where 8: withVisible(eval(expr, envir, enclos))
    where 9: withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler,
     error = eHandler, message = mHandler)
    where 10: handle(ev <- withCallingHandlers(withVisible(eval(expr, envir,
     enclos)), warning = wHandler, error = eHandler, message = mHandler))
    where 11: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval(expr,
     envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)))
    where 12: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos,
     debug = debug, last = i == length(out), use_try = stop_on_error !=
     2L, keep_warning = keep_warning, keep_message = keep_message,
     output_handler = output_handler, include_timing = include_timing)
    where 13: evaluate::evaluate(...)
    where 14: evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning),
     keep_message = !isFALSE(options$message), stop_on_error = if (options$error &&
     options$include) 0L else 2L, output_handler = knit_handlers(options$render,
     options))
    where 15: in_dir(input_dir(), evaluate(code, envir = env, new_device = FALSE,
     keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$message),
     stop_on_error = if (options$error && options$include) 0L else 2L,
     output_handler = knit_handlers(options$render, options)))
    where 16: block_exec(params)
    where 17: call_block(x)
    where 18: process_group.block(group)
    where 19: process_group(group)
    where 20: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
     error = function(e) {
     setwd(wd)
     cat(res, sep = "\n", file = output %n% "")
     message("Quitting from lines ", paste(current_lines(i),
     collapse = "-"), " (", knit_concord$get("infile"),
     ") ")
     })
    where 21: process_file(text, output)
    where 22: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
    where 23: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),
     output_dir = getwd(), ...)
    where 24: vweave_rmarkdown(...)
    where 25: engine$weave(file, quiet = quiet, encoding = enc)
    where 26: doTryCatch(return(expr), name, parentenv, handler)
    where 27: tryCatchOne(expr, names, parentenv, handlers[[1L]])
    where 28: tryCatchList(expr, classes, parentenv, handlers)
    where 29: tryCatch({
     engine$weave(file, quiet = quiet, encoding = enc)
     setwd(startdir)
     output <- find_vignette_product(name, by = "weave", engine = engine)
     if (!have.makefile && vignette_is_tex(output)) {
     texi2pdf(file = output, clean = FALSE, quiet = quiet)
     output <- find_vignette_product(name, by = "texi2pdf",
     engine = engine)
     }
     outputs <- c(outputs, output)
    }, error = function(e) {
     thisOK <<- FALSE
     fails <<- c(fails, file)
     message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s",
     file, conditionMessage(e)))
    })
    where 30: tools:::buildVignettes(dir = "/data/gannet/ripley/R/packages/tests-devel/icosa.Rcheck/vign_test/icosa",
     ser_elibs = "/tmp/RtmpK2nTNA/file2e7cf74c8e.rds")
    
     --- value of length: 2 type: logical ---
    [1] FALSE TRUE
     --- function from context ---
    function (longLatMat, radius = authRadius, origin = c(0, 0, 0))
    {
     if (!class(longLatMat) %in% c("matrix", "data.frame")) {
     stop("Invalid input.")
     }
     if ((class(longLatMat[, 1]) == "numeric") + (class(longLatMat[,
     2]) == "numeric") != 2) {
     stop("Invalid input matrix or data frame.")
     }
     boolNA <- (is.na(longLatMat[, 1]) | is.na(longLatMat[, 2]))
     longLat <- longLatMat[!boolNA, , drop = FALSE]
     if (length(radius) != 1 | !is.numeric(radius))
     stop("Invalid 'radius' value.")
     if (max(abs(longLat[, 2])) > 90)
     stop("Latitudinal data should be in the second column of the matrix.")
     x <- cos(longLat[, 2]/180 * pi) * cos(longLat[, 1]/180 *
     pi)
     y <- cos(longLat[, 2]/180 * pi) * sin(longLat[, 1]/180 *
     pi)
     z <- sin(longLat[, 2]/180 * pi)
     newMat <- matrix(NA, ncol = 3, nrow = nrow(longLatMat))
     newMat[!boolNA, ] <- cbind(x, y, z)
     colnames(newMat) <- c("x", "y", "z")
     endRes <- newMat * radius
     endRes[, 1] <- endRes[, 1] + origin[1]
     endRes[, 2] <- endRes[, 2] + origin[2]
     endRes[, 3] <- endRes[, 3] + origin[3]
     return(endRes)
    }
    <bytecode: 0xa1acad0>
    <environment: namespace:icosa>
     --- function search by body ---
    Function PolToCar in namespace icosa has this body.
     ----------- END OF FAILURE REPORT --------------
    Quitting from lines 86-91 (icosaIntroShort.Rmd)
    Error: processing vignette 'icosaIntroShort.Rmd' failed with diagnostics:
    the condition has length > 1
    --- failed re-building ‘icosaIntroShort.Rmd’
    
    SUMMARY: processing the following file failed:
     ‘icosaIntroShort.Rmd’
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc

Version: 0.9.81
Flags: --no-vignettes
Check: installed package size
Result: NOTE
     installed size is 5.9Mb
     sub-directories of 1Mb or more:
     doc 1.9Mb
     extdata 1.4Mb
     libs 1.8Mb
Flavors: r-devel-windows-ix86+x86_64, r-devel-windows-ix86+x86_64-gcc8, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 0.9.81
Check: whether package can be installed
Result: WARN
    Found the following significant warnings:
     RccpSource_.cpp:978:54: warning: explicitly assigning value of variable of type 'Rcpp::NumericVector' (aka 'Vector<14>') to itself [-Wself-assign-overloaded]
     Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
Flavor: r-release-osx-x86_64