CRAN Package Check Results for Package rstan

Last updated on 2019-12-06 05:46:50 CET.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 2.19.2 715.09 729.59 1444.68 ERROR
r-devel-linux-x86_64-debian-gcc 2.19.2 645.19 619.93 1265.12 NOTE
r-devel-linux-x86_64-fedora-clang 2.19.2 1909.99 NOTE
r-devel-linux-x86_64-fedora-gcc 2.19.2 1432.06 NOTE
r-devel-windows-ix86+x86_64 2.19.2 1257.00 856.00 2113.00 NOTE
r-devel-windows-ix86+x86_64-gcc8 2.19.2 1318.00 907.00 2225.00 NOTE
r-patched-linux-x86_64 2.19.2 680.59 706.74 1387.33 NOTE
r-patched-solaris-x86 2.19.2 1640.60 NOTE
r-release-linux-x86_64 2.19.2 679.46 710.79 1390.25 NOTE
r-release-windows-ix86+x86_64 2.19.2 1330.00 663.00 1993.00 NOTE
r-release-osx-x86_64 2.19.2 NOTE
r-oldrel-windows-ix86+x86_64 2.19.2 1260.00 734.00 1994.00 NOTE
r-oldrel-osx-x86_64 2.19.2 NOTE

Check Details

Version: 2.19.2
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-devel-windows-ix86+x86_64, r-devel-windows-ix86+x86_64-gcc8, r-patched-linux-x86_64, r-patched-solaris-x86, r-release-linux-x86_64, r-release-windows-ix86+x86_64, r-release-osx-x86_64, r-oldrel-windows-ix86+x86_64, r-oldrel-osx-x86_64

Version: 2.19.2
Check: examples
Result: ERROR
    Running examples in 'rstan-Ex.R' failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: extract_sparse_parts
    > ### Title: Extract the compressed representation of a sparse matrix
    > ### Aliases: extract_sparse_parts
    >
    > ### ** Examples
    >
    > A <- rbind(
    + c(19L, 27L, 0L, 0L),
    + c( 0L, 0L, 0L, 0L),
    + c( 0L, 0L, 0L, 52L),
    + c(81L, 0L, 95L, 33L)
    + )
    > str(extract_sparse_parts(A))
    Loading required namespace: Matrix
     ----------- FAILURE REPORT --------------
     --- failure: the condition has length > 1 ---
     --- srcref ---
    :
     --- package (from environment) ---
    rstan
     --- call from context ---
    extract_sparse_parts(A)
     --- call from argument ---
    if (class(A) == "matrix") A <- Matrix::Matrix(A, sparse = TRUE)
     --- R stacktrace ---
    where 1: extract_sparse_parts(A)
    where 2: str(extract_sparse_parts(A))
    
     --- value of length: 2 type: logical ---
    [1] TRUE FALSE
     --- function from context ---
    function (A)
    {
     if (!requireNamespace("Matrix"))
     stop("You have to install the Matrix package to call 'extract_sparse_parts'")
     if (class(A) == "matrix")
     A <- Matrix::Matrix(A, sparse = TRUE)
     A <- Matrix::t(A)
     A <- as(A, "dgCMatrix")
     return(.Call(extract_sparse_components, A))
    }
    <bytecode: 0x69de118>
    <environment: namespace:rstan>
     --- function search by body ---
    Function extract_sparse_parts in namespace rstan has this body.
     ----------- END OF FAILURE REPORT --------------
    Error in if (class(A) == "matrix") A <- Matrix::Matrix(A, sparse = TRUE) :
     the condition has length > 1
    Calls: str -> extract_sparse_parts
    Execution halted
Flavor: r-devel-linux-x86_64-debian-clang

Version: 2.19.2
Check: tests
Result: ERROR
     Running 'doRUnit.R' [6s/8s]
    Running the tests in 'tests/doRUnit.R' failed.
    Complete output:
     >
     > ## unit tests will not be done if RUnit is not available
     > if(!require("RUnit", quietly = TRUE)) {
     + warning("cannot run unit tests -- package RUnit is not available")
     + q('no');
     + }
     >
     >
     > pkg <- "rstan"
     >
     > path <- system.file(package = pkg, "unitTests")
     > source(file.path(path, "runRunitTests.R"), echo = TRUE)
    
     > pkg <- "rstan"
    
     > if (!require("RUnit", quietly = TRUE)) {
     + stop("Package Runit is not found.")
     + }
    
     > if (exists("path")) {
     + reportfile <- file.path(getwd(), "report")
     + } else {
     + path <- getwd()
     + reportfile <- file.path(path, "report" .... [TRUNCATED]
    
     > stopifnot(file.exists(path), file.info(path.expand(path))$isdir)
    
     > library(package = pkg, character.only = TRUE)
     Loading required package: StanHeaders
     Loading required package: ggplot2
     rstan (Version 2.19.2, GitRev: 2e1f913d3ca3)
     For execution on a local, multicore CPU with excess RAM we recommend calling
     options(mc.cores = parallel::detectCores()).
     To avoid recompilation of unchanged Stan programs, we recommend calling
     rstan_options(auto_write = TRUE)
    
     > rstantest <- defineTestSuite("rstantest", dirs = path,
     + testFileRegexp = "^runit.+\\.R", testFuncRegexp = "^test_+",
     + rngKind = "Marsagl ..." ... [TRUNCATED]
    
     > testsres <- runTestSuite(rstantest)
    
    
     Executing test function test_ess2 ... Read 34 items
     Read 34 items
     done successfully.
    
    
    
     Executing test function test_essnrhat ... done successfully.
    
    
    
     Executing test function test_seq_perm ... done successfully.
    
    
    
     Executing test function test_extract_sparse_parts ... Loading required namespace: Matrix
     ----------- FAILURE REPORT --------------
     --- failure: the condition has length > 1 ---
     --- srcref ---
     :
     --- package (from environment) ---
     rstan
     --- call from context ---
     rstan::extract_sparse_parts(A)
     --- call from argument ---
     if (class(A) == "matrix") A <- Matrix::Matrix(A, sparse = TRUE)
     --- R stacktrace ---
     where 1: rstan::extract_sparse_parts(A)
     where 2: func()
     where 3: system.time(func(), gcFirst = RUnitEnv$.gcBeforeTest)
     where 4: doTryCatch(return(expr), name, parentenv, handler)
     where 5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
     where 6: tryCatchList(expr, classes, parentenv, handlers)
     where 7: tryCatch(expr, error = function(e) {
     call <- conditionCall(e)
     if (!is.null(call)) {
     if (identical(call[[1L]], quote(doTryCatch)))
     call <- sys.call(-4L)
     dcall <- deparse(call)[1L]
     prefix <- paste("Error in", dcall, ": ")
     LONG <- 75L
     sm <- strsplit(conditionMessage(e), "\n")[[1L]]
     w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")
     if (is.na(w))
     w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],
     type = "b")
     if (w > LONG)
     prefix <- paste0(prefix, "\n ")
     }
     else prefix <- "Error : "
     msg <- paste0(prefix, conditionMessage(e), "\n")
     .Internal(seterrmessage(msg[1L]))
     if (!silent && isTRUE(getOption("show.error.messages"))) {
     cat(msg, file = outFile)
     .Internal(printDeferredWarnings())
     }
     invisible(structure(msg, class = "try-error", condition = e))
     })
     where 8: try(system.time(func(), gcFirst = RUnitEnv$.gcBeforeTest))
     where 9: .executeTestCase(funcName, envir = sandbox, setUpFunc = .setUp,
     tearDownFunc = .tearDown)
     where 10: .sourceTestFile(testFile, testSuite$testFuncRegexp)
     where 11: runTestSuite(rstantest)
     where 12: eval(ei, envir)
     where 13: eval(ei, envir)
     where 14: withVisible(eval(ei, envir))
     where 15: source(file.path(path, "runRunitTests.R"), echo = TRUE)
    
     --- value of length: 2 type: logical ---
     [1] TRUE FALSE
     --- function from context ---
     function (A)
     {
     if (!requireNamespace("Matrix"))
     stop("You have to install the Matrix package to call 'extract_sparse_parts'")
     if (class(A) == "matrix")
     A <- Matrix::Matrix(A, sparse = TRUE)
     A <- Matrix::t(A)
     A <- as(A, "dgCMatrix")
     return(.Call(extract_sparse_components, A))
     }
     <bytecode: 0x3ecdc40>
     <environment: namespace:rstan>
     --- function search by body ---
     Function extract_sparse_parts in namespace rstan has this body.
     ----------- END OF FAILURE REPORT --------------
     Timing stopped at: 3.429 0.37 4.273
     Error in if (class(A) == "matrix") A <- Matrix::Matrix(A, sparse = TRUE) :
     the condition has length > 1
     done successfully.
    
    
    
     Executing test function test_config_argss ... Error in rstan:::config_argss(3, 100, 10, 3, "random", 10, NA, algorithm = "NUTS", :
     chain_id has duplicated elements
     Error in check_seed(seed) : seed needs to be string of digits
     Error in check_seed(seed) : seed needs to be string of digits
     done successfully.
    
    
    
     Executing test function test_data_list2array ... done successfully.
    
    
    
     Executing test function test_data_preprocess ... Error in FUN(X[[i]], ...) : Stan does not support NA (in f) in data
     In addition: Warning message:
     In FUN(X[[i]], ...) : data with name h is not numeric and not used
     done successfully.
    
    
    
     Executing test function test_data_preprocess2 ... Error in data_list2array(x) : all elements of the list should be numeric
     done successfully.
    
    
    
     Executing test function test_dotfnames_fromto_sqrfnames ... done successfully.
    
    
    
     Executing test function test_flatnames ... done successfully.
    
    
    
     Executing test function test_get_dims_from_fnames ... done successfully.
    
    
    
     Executing test function test_get_model_strcode ... Error in rstan:::get_model_strcode() :
     model file missing and empty model_code
     In addition: Warning messages:
     1: In readLines(file, warn = TRUE) :
     incomplete final line found on 'tmp.stan'
     2: In readLines(file, warn = TRUE) :
     incomplete final line found on 'tmp.stan'
     done successfully.
    
    
    
     Executing test function test_idx_col2rowm ... done successfully.
    
    
    
     Executing test function test_idx_row2colm ... done successfully.
    
    
    
     Executing test function test_is_named_list ... done successfully.
    
    
    
     Executing test function test_is_valid_stan_name ... done successfully.
    
    
    
     Executing test function test_mklist ... Error in rstan:::mklist(c("x", "f")) :
     objects 'f' of mode numeric and list not found
     done successfully.
    
    
    
     Executing test function test_multi_idx_row2colm ... done successfully.
    
    
    
     Executing test function test_par_vector2list ... done successfully.
    
    
    
     Executing test function test_pars_total_indexes ... done successfully.
    
    
    
     Executing test function test_read_comments ... done successfully.
    
    
    
     Executing test function test_read_csv_header ... done successfully.
    
    
    
     Executing test function test_read_rdump ... done successfully.
    
    
    
     Executing test function test_remove_empty_pars ... done successfully.
    
    
    
     Executing test function test_seq_array_ind ... done successfully.
    
    
    
     Executing test function test_stan_rdump ... done successfully.
    
    
    
     Executing test function test_options1 ... done successfully.
    
    
    
     Executing test function test_options2 ... done successfully.
    
    
    
     Executing test function test_plot_rhat_breaks ... done successfully.
    
    
    
     Executing test function test_rstan_options ... done successfully.
    
    
    
     Executing test function test_paridx_fun ... done successfully.
    
    
    
     Executing test function test_parse_stancsv_comments3 ... done successfully.
    
    
     > printTextProtocol(testsres, showDetails = TRUE)
     RUNIT TEST PROTOCOL -- Fri Dec 6 02:11:22 2019
     ***********************************************
     Number of test functions: 32
     Number of errors: 1
     Number of failures: 0
    
    
     1 Test Suite :
     rstantest - 32 test functions, 1 error, 0 failures
     ERROR in test_extract_sparse_parts: Error in if (class(A) == "matrix") A <- Matrix::Matrix(A, sparse = TRUE) :
     the condition has length > 1
    
    
    
     Details
     ***************************
     Test Suite: rstantest
     Test function regexp: ^test_+
     Test file regexp: ^runit.+\.R
     Involved directory:
     /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/rstan/unitTests
     ---------------------------
     Test file: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/rstan/unitTests/runit.test.chains.R
     test_ess2: (1 checks) ... OK (0 seconds)
     test_essnrhat: (4 checks) ... OK (0.24 seconds)
     test_seq_perm: (4 checks) ... OK (0 seconds)
     ---------------------------
     Test file: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/rstan/unitTests/runit.test.extract_sparse_parts.R
     test_extract_sparse_parts: ERROR !!
     Error in if (class(A) == "matrix") A <- Matrix::Matrix(A, sparse = TRUE) :
     the condition has length > 1
     ---------------------------
     Test file: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/rstan/unitTests/runit.test.misc.R
     test_config_argss: (13 checks) ... OK (0.01 seconds)
     test_data_list2array: (9 checks) ... OK (0 seconds)
     test_data_preprocess: (5 checks) ... OK (0 seconds)
     test_data_preprocess2: (6 checks) ... OK (0 seconds)
     test_dotfnames_fromto_sqrfnames: (1 checks) ... OK (0 seconds)
     test_flatnames: (2 checks) ... OK (0 seconds)
     test_get_dims_from_fnames: (1 checks) ... OK (0.01 seconds)
     test_get_model_strcode: (11 checks) ... OK (0 seconds)
     test_idx_col2rowm: (3 checks) ... OK (0 seconds)
     test_idx_row2colm: (3 checks) ... OK (0 seconds)
     test_is_named_list: (4 checks) ... OK (0 seconds)
     test_is_valid_stan_name: (5 checks) ... OK (0 seconds)
     test_mklist: (5 checks) ... OK (0 seconds)
     test_multi_idx_row2colm: (3 checks) ... OK (0 seconds)
     test_par_vector2list: (5 checks) ... OK (0 seconds)
     test_pars_total_indexes: (6 checks) ... OK (0 seconds)
     test_read_comments: (4 checks) ... OK (0 seconds)
     test_read_csv_header: (2 checks) ... OK (0 seconds)
     test_read_rdump: (3 checks) ... OK (0 seconds)
     test_remove_empty_pars: (4 checks) ... OK (0 seconds)
     test_seq_array_ind: (4 checks) ... OK (0 seconds)
     test_stan_rdump: (8 checks) ... OK (0 seconds)
     ---------------------------
     Test file: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/rstan/unitTests/runit.test.options.R
     test_options1: (2 checks) ... OK (0 seconds)
     test_options2: (7 checks) ... OK (0.01 seconds)
     test_plot_rhat_breaks: (2 checks) ... OK (0 seconds)
     test_rstan_options: (0 checks) ... OK (0 seconds)
     ---------------------------
     Test file: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/rstan/unitTests/runit.test.stan_csv.R
     test_paridx_fun: (3 checks) ... OK (0 seconds)
     test_parse_stancsv_comments3: (6 checks) ... OK (0 seconds)
    
     > printTextProtocol(testsres, showDetails = TRUE, fileName = paste(reportfile,
     + ".txt", sep = ""))
    
     > printHTMLProtocol(testsres, fileName = paste(reportfile,
     + ".html", sep = ""))
    
     > tmp <- getErrors(testsres)
    
     > if (tmp$nFail > 0 | tmp$nErr > 0) {
     + stop(paste("\n\nUnit testing failed (#test failures: ", tmp$nFail,
     + ", #R errors: ", tmp$nErr, " ..." ... [TRUNCATED]
     Error in eval(ei, envir) :
    
     Unit testing failed (#test failures: 0, #R errors: 1)
    
     Calls: source -> withVisible -> eval -> eval
     In addition: Warning messages:
     1: In (function (x) : rstan option 'c' not found
     2: In (function (x) : rstan option 'c' not found
     Execution halted
Flavor: r-devel-linux-x86_64-debian-clang

Version: 2.19.2
Check: installed package size
Result: NOTE
     installed size is 172.6Mb
     sub-directories of 1Mb or more:
     libs 169.8Mb
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-windows-ix86+x86_64, r-devel-windows-ix86+x86_64-gcc8, r-patched-solaris-x86, r-release-windows-ix86+x86_64, r-release-osx-x86_64, r-oldrel-windows-ix86+x86_64, r-oldrel-osx-x86_64