CRAN Package Check Results for Package ctsem

Last updated on 2018-08-17 21:48:01 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 2.6.5 495.81 1293.17 1788.98 NOTE
r-devel-linux-x86_64-debian-gcc 2.6.5 344.09 951.74 1295.83 WARN
r-devel-linux-x86_64-fedora-clang 2.6.5 2259.61 NOTE
r-devel-linux-x86_64-fedora-gcc 2.6.5 1998.53 NOTE
r-devel-windows-ix86+x86_64 2.6.5 519.00 278.00 797.00 NOTE --no-vignettes
r-patched-linux-x86_64 2.6.5 335.98 1277.99 1613.97 WARN
r-patched-solaris-x86 2.6.5 661.40 ERROR
r-release-linux-x86_64 2.6.5 347.60 1303.46 1651.06 WARN
r-release-windows-ix86+x86_64 2.6.5 418.00 342.00 760.00 NOTE --no-vignettes
r-release-osx-x86_64 2.6.5 NOTE
r-oldrel-windows-ix86+x86_64 2.6.5 408.00 357.00 765.00 NOTE --no-vignettes
r-oldrel-osx-x86_64 2.6.5 FAIL

Check Details

Version: 2.6.5
Check: for GNU extensions in Makefiles
Result: NOTE
    GNU make is a SystemRequirements.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-patched-linux-x86_64, r-patched-solaris-x86, r-release-linux-x86_64, r-release-osx-x86_64, r-oldrel-osx-x86_64

Version: 2.6.5
Check: whether package can be installed
Result: WARN
    Found the following significant warnings:
     Warning: S3 methods ‘[.fun_list’, ‘[.grouped_df’, ‘all.equal.tbl_df’, ‘anti_join.data.frame’, ‘anti_join.tbl_df’, ‘arrange.data.frame’, ‘arrange.default’, ‘arrange.grouped_df’, ‘arrange.tbl_df’, ‘arrange_.data.frame’, ‘arrange_.tbl_df’, ‘as.data.frame.grouped_df’, ‘as.data.frame.rowwise_df’, ‘as.data.frame.tbl_cube’, ‘as.data.frame.tbl_df’, ‘as.table.tbl_cube’, ‘as.tbl.data.frame’, ‘as.tbl.tbl’, ‘as.tbl_cube.array’, ‘as.tbl_cube.data.frame’, ‘as.tbl_cube.matrix’, ‘as.tbl_cube.table’, ‘as_data_frame.grouped_df’, ‘as_data_frame.tbl_cube’, ‘auto_copy.tbl_cube’, ‘auto_copy.tbl_df’, ‘cbind.grouped_df’, ‘collapse.data.frame’, ‘collect.data.frame’, ‘common_by.NULL’, ‘common_by.character’, ‘common_by.default’, ‘common_by.list’, ‘compute.data.frame’, ‘copy_to.DBIConnection’, ‘copy_to.src_local’, ‘default_missing.data.frame’, ‘default_missing.default’, ‘dim.tbl_cube’, ‘distinct.data.frame’, ‘distinct.default’, ‘distinct.grouped_df’, ‘distinct.tbl_df’, ‘distinct_.data.frame’, ‘distinct_.grouped_df’, ‘distinct_.tbl_df’, ‘do.NULL’, ‘do.data.frame’, ‘do.default’, ‘do.grouped_df’, ‘do.rowwise_df’, ‘do_.NULL’, ‘do_.data.frame’, ‘do_.grouped_df’, ‘do_.rowwise_df’, ‘filter.data.frame’, ‘filter.default’, ‘filter.tbl_cube’, ‘filter.tbl_df’, ‘filter.ts’, ‘filter_.data.frame’, ‘filter_.tbl_cube’, ‘filter_.tbl_df’, ‘format.src_local’, ‘full_join.data.frame’, ‘full_join.tbl_df’, ‘group_by.data.frame’, ‘group_by.default’, ‘group_by.rowwise_df’, ‘group_by.tbl_cube’, ‘group_by_.data.frame’, ‘group_by_.rowwise_df’, ‘group_by_.tbl_cube’, ‘group_indices.data.frame’, ‘group_indices.default’, ‘group_indices.grouped_df’, ‘group_indices_.data.frame’, ‘group_indices_.grouped_df’, ‘group_size.data.frame’, ‘group_size.grouped_df’, ‘group_size.rowwise_df’, ‘group_vars.default’, ‘group_vars.grouped_df’, ‘group_vars.tbl_cube’, ‘groups.data.frame’, ‘groups.grouped_df’, ‘groups.tbl_cube’, ‘inner_join.data.frame’, ‘inner_join.tbl_df’, ‘intersect.data.frame’, ‘intersect.default’, ‘left_join.data.frame’, ‘left_join.tbl_df’, ‘mutate.data.frame’, ‘mutate.default’, ‘mutate.tbl_df’, ‘mutate_.data.frame’, ‘mutate_.tbl_df’, ‘n_groups.data.frame’, ‘n_groups.grouped_df’, ‘n_groups.rowwise_df’, ‘print.BoolResult’, ‘print.all_vars’, ‘print.any_vars’, ‘print.fun_list’, ‘print.location’, ‘print.rowwise_df’, ‘print.src’, ‘print.tbl_cube’, ‘pull.data.frame’, ‘rbind.grouped_df’, ‘recode.character’, ‘recode.factor’, ‘recode.numeric’, ‘rename.data.frame’, ‘rename.default’, ‘rename.grouped_df’, ‘rename.tbl_cube’, ‘rename_.data.frame’, ‘rename_.grouped_df’, ‘rename_.tbl_cube’, ‘right_join.data.frame’, ‘right_join.tbl_df’, ‘same_src.data.frame’, ‘same_src.tbl_cube’, ‘sample_frac.data.frame’, ‘sample_frac.default’, ‘sample_frac.grouped_df’, ‘sample_n.data.frame’, ‘sample_n.default’, ‘sample_n.grouped_df’, ‘select.data.frame’, ‘select.default’, ‘select.grouped_df’, ‘select.tbl_cube’, ‘select_.data.frame’, ‘select_.grouped_df’, ‘select_.tbl_cube’, ‘semi_join.data.frame’, ‘semi_join.tbl_df’, ‘setdiff.data.frame’, ‘setdiff.default’, ‘setequal.data.frame’, ‘setequal.default’, ‘slice.data.frame’, ‘slice.default’, ‘slice.tbl_df’, ‘slice_.data.frame’, ‘slice_.tbl_df’, ‘src_tbls.src_local’, ‘summarise.data.frame’, ‘summarise.default’, ‘summarise.tbl_cube’, ‘summarise.tbl_df’, ‘summarise_.data.frame’, ‘summarise_.tbl_cube’, ‘summarise_.tbl_df’, ‘tbl.DBIConnection’, ‘tbl.src_local’, ‘tbl_sum.grouped_df’, ‘tbl_vars.data.frame’, ‘tbl_vars.tbl_cube’, ‘transmute.default’, ‘transmute.grouped_df’, ‘transmute_.default’, ‘transmute_.grouped_df’, ‘ungroup.data.frame’, ‘ungroup.grouped_df’, ‘ungroup.rowwise_df’, ‘union.data.frame’, ‘union.default’, ‘union_all.data.frame’, ‘union_all.default’ were declared in NAMESPACE but not found
Flavors: r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64, r-release-linux-x86_64

Version: 2.6.5
Check: installed package size
Result: NOTE
     installed size is 74.4Mb
     sub-directories of 1Mb or more:
     data 5.3Mb
     doc 4.1Mb
     libs 64.1Mb
Flavors: r-devel-linux-x86_64-fedora-clang, r-patched-solaris-x86, r-release-osx-x86_64, r-oldrel-osx-x86_64

Version: 2.6.5
Flags: --no-vignettes
Check: installed package size
Result: NOTE
     installed size is 16.2Mb
     sub-directories of 1Mb or more:
     data 5.3Mb
     doc 4.1Mb
     libs 5.9Mb
Flavors: r-devel-windows-ix86+x86_64, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 2.6.5
Flags: --no-vignettes
Check: for GNU extensions in Makefiles
Result: NOTE
    GNU make is a SystemRequirements.
Flavors: r-devel-windows-ix86+x86_64, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 2.6.5
Check: examples
Result: ERROR
    Running examples in ‘ctsem-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: ctGenerateFromFit
    > ### Title: Generates data according to the model estimated in a ctsemFit
    > ### object.#'
    > ### Aliases: ctGenerateFromFit
    >
    > ### ** Examples
    >
    >
    > data(AnomAuth)
    > AnomAuthmodel <- ctModel(LAMBDA = matrix(c(1, 0, 0, 1), nrow = 2, ncol = 2),
    + Tpoints = 5, n.latent = 2, n.manifest = 2, MANIFESTVAR=diag(0, 2))
    > AnomAuthfit <- ctFit(AnomAuth, AnomAuthmodel)
    Running ctsemCarefulFit with 14 parameters
    
     *** caught segfault ***
    address 0, cause 'memory not mapped'
    
    Traceback:
     1: runHelper(model, frontendStart, intervals, silent, suppressWarnings, unsafe, checkpoint, useSocket, onlyFrontend, useOptimizer)
     2: OpenMx::mxRun(model)
     3: withCallingHandlers(expr, warning = function(w) invokeRestart("muffleWarning"))
     4: suppressWarnings(OpenMx::mxRun(model))
     5: doTryCatch(return(expr), name, parentenv, handler)
     6: tryCatchOne(expr, names, parentenv, handlers[[1L]])
     7: tryCatchList(expr, classes, parentenv, handlers)
     8: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call)[1L] prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})
     9: try(suppressWarnings(OpenMx::mxRun(model)))
    10: carefulFit(model, traitExtension = traitExtension, manifestTraitvarExtension = manifestTraitvarExtension, weighting = carefulFitWeight)
    11: ctFit(AnomAuth, AnomAuthmodel)
    An irrecoverable exception occurred. R is aborting now ...
Flavor: r-patched-solaris-x86

Version: 2.6.5
Check: re-building of vignette outputs
Result: WARN
    Error in re-building vignettes:
     ...
    Observations with missing time information found - removing 1 rows
    Discrete time points created: 4
    Extracting first non-missing value for time independent predictors
    imputedefs==FALSE (default, recommended) so setting observations with no time value to NA
    Running ctsemCarefulFit with 16 parameters
    
     *** caught segfault ***
    address 0, cause 'memory not mapped'
    
    Traceback:
     1: runHelper(model, frontendStart, intervals, silent, suppressWarnings, unsafe, checkpoint, useSocket, onlyFrontend, useOptimizer)
     2: OpenMx::mxRun(model)
     3: withCallingHandlers(expr, warning = function(w) invokeRestart("muffleWarning"))
     4: suppressWarnings(OpenMx::mxRun(model))
     5: doTryCatch(return(expr), name, parentenv, handler)
     6: tryCatchOne(expr, names, parentenv, handlers[[1L]])
     7: tryCatchList(expr, classes, parentenv, handlers)
     8: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call)[1L] prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})
     9: try(suppressWarnings(OpenMx::mxRun(model)))
    10: carefulFit(model, traitExtension = traitExtension, manifestTraitvarExtension = manifestTraitvarExtension, weighting = carefulFitWeight)
    11: ctFit(dat = ctExample1, ctmodelobj = example1model)
    12: eval(expr, envir, enclos)
    13: eval(expr, envir, enclos)
    14: withVisible(eval(expr, envir, enclos))
    15: withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)
    16: handle(ev <- withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler))
    17: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)))
    18: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos, debug = debug, last = i == length(out), use_try = stop_on_error != 2L, keep_warning = keep_warning, keep_message = keep_message, output_handler = output_handler, include_timing = include_timing)
    19: evaluate::evaluate(...)
    20: evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$message), stop_on_error = if (options$error && options$include) 0L else 2L, output_handler = knit_handlers(options$render, options))
    21: 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$render, options)))
    22: block_exec(params)
    23: call_block(x)
    24: process_group.block(group)
    25: process_group(group)
    26: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { setwd(wd) cat(res, sep = "\n", file = output %n% "") message("Quitting from lines ", paste(current_lines(i), collapse = "-"), " (", knit_concord$get("infile"), ") ") })
    27: process_file(text, output)
    28: (if (grepl("\\.[Rr]md$", file)) knit2html_v1 else if (grepl("\\.[Rr]rst$", file)) knit2pandoc else knit)(file, encoding = encoding, quiet = quiet, envir = globalenv())
    29: engine$weave(file, quiet = quiet, encoding = enc)
    30: doTryCatch(return(expr), name, parentenv, handler)
    31: tryCatchOne(expr, names, parentenv, handlers[[1L]])
    32: tryCatchList(expr, classes, parentenv, handlers)
    33: tryCatch({ engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir) find_vignette_product(name, by = "weave", engine = engine)}, error = function(e) { stop(gettextf("processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)), domain = NA, call. = FALSE)})
    34: buildVignettes(dir = "/home/ripley/R/packages/tests32/ctsem.Rcheck/vign_test/ctsem")
    An irrecoverable exception occurred. R is aborting now ...
Flavor: r-patched-solaris-x86

Version: 2.6.5
Check: re-building of vignette outputs
Result: WARN
    Error in re-building vignettes:
     ...
     Lowest minimum so far: 4151.13132113271
    
    Solution found
    
    NPSOL optimizer not available - switching to CSOLNP - consider installing OpenMx using command: source('http://openmx.psyc.virginia.edu/getOpenMx.R')
    Running ctsem with 19 parameters
    Running ctsemCarefulFit with 19 parameters
    
    Begin fit attempt 1 of at maximum 16 tries
    
     Lowest minimum so far: 4203.3130332814
    
    Solution found
    
    NPSOL optimizer not available - switching to CSOLNP - consider installing OpenMx using command: source('http://openmx.psyc.virginia.edu/getOpenMx.R')
    Running ctsem with 19 parameters
    Linear model specified -- setting lineardynamics = TRUE
    Unique discreteDRIFT calculations per step required = 93
    Unique discreteCINT calculations per step required = 93
    Unique discreteDIFFUSION calculations per step required = 93
    Missingness in TDpreds! Replaced by zeroes...
    Missingness in TIpreds - sampling 1 values
    Sampling...
    
    Execution halted
Flavor: r-oldrel-osx-x86_64

Version: 2.6.5
Check: PDF version of manual
Result: FAIL
    
Flavor: r-oldrel-osx-x86_64