CRAN Package Check Results for Package batchtools

Last updated on 2018-04-29 01:46:32 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.9.8 10.27 101.60 111.87 OK
r-devel-linux-x86_64-debian-gcc 0.9.8 7.84 84.11 91.95 OK
r-devel-linux-x86_64-fedora-clang 0.9.8 131.83 OK
r-devel-linux-x86_64-fedora-gcc 0.9.8 125.97 OK
r-devel-windows-ix86+x86_64 0.9.8 23.00 230.00 253.00 ERROR
r-patched-linux-x86_64 0.9.8 8.92 101.38 110.30 OK
r-patched-solaris-x86 0.9.8 210.70 OK
r-release-linux-x86_64 0.9.8 8.01 101.89 109.90 OK
r-release-windows-ix86+x86_64 0.9.8 23.00 230.00 253.00 ERROR
r-release-osx-x86_64 0.9.8 NOTE
r-oldrel-windows-ix86+x86_64 0.9.8 18.00 198.00 216.00 OK
r-oldrel-osx-x86_64 0.9.8 NOTE

Check Details

Version: 0.9.8
Check: running examples for arch ‘i386’
Result: ERROR
    Running examples in 'batchtools-Ex.R' failed
    The error most likely occurred in:
    
    > ### Name: addExperiments
    > ### Title: Add Experiments to the Registry
    > ### Aliases: addExperiments
    >
    > ### ** Examples
    >
    > tmp = makeExperimentRegistry(file.dir = NA, make.default = FALSE)
    No configuration file found
    Created registry in 'D:/temp/RtmpmALh4o/registryae745e5c485d' using cluster functions 'Interactive'
    >
    > # add first problem
    > fun = function(job, data, n, mean, sd, ...) rnorm(n, mean = mean, sd = sd)
    > addProblem("rnorm", fun = fun, reg = tmp)
    Adding problem 'rnorm'
    >
    > # add second problem
    > fun = function(job, data, n, lambda, ...) rexp(n, rate = lambda)
    > addProblem("rexp", fun = fun, reg = tmp)
    Adding problem 'rexp'
    >
    > # add first algorithm
    > fun = function(instance, method, ...) if (method == "mean") mean(instance) else median(instance)
    > addAlgorithm("average", fun = fun, reg = tmp)
    Adding algorithm 'average'
    >
    > # add second algorithm
    > fun = function(instance, ...) sd(instance)
    > addAlgorithm("deviation", fun = fun, reg = tmp)
    Adding algorithm 'deviation'
    >
    > # define problem and algorithm designs
    > prob.designs = algo.designs = list()
    > prob.designs$rnorm = CJ(n = 100, mean = -1:1, sd = 1:5)
    > prob.designs$rexp = data.table(n = 100, lambda = 1:5)
    > algo.designs$average = data.table(method = c("mean", "median"))
    > algo.designs$deviation = data.table()
    >
    > # add experiments and submit
    > addExperiments(prob.designs, algo.designs, reg = tmp)
    Adding 30 experiments ('rnorm'[15] x 'average'[2] x repls[1]) ...
    Error in length(ans$indices) : type must be LANGSXP at this point
    Calls: addExperiments ... merge -> merge.data.table -> [ -> [.data.table -> length
    Execution halted
Flavors: r-devel-windows-ix86+x86_64, r-release-windows-ix86+x86_64

Version: 0.9.8
Check: running tests for arch ‘i386’
Result: ERROR
     Running 'testthat.R' [29s]
    Running the tests in 'tests/testthat.R' failed.
    Complete output:
     > # setting R_TESTS to empty string because of
     > # https://github.com/hadley/testthat/issues/144
     > # revert this when that issue in R is fixed.
     > Sys.setenv("R_TESTS" = "")
     >
     > library(testthat)
     > library(batchtools)
     Loading required package: data.table
     Breaking change introduced in batchtools v0.9.6: The format of the returned data.table of the functions `reduceResultsDataTable()`, getJobTable()`, `getJobPars()`, and `getJobResources()` has changed. List columns are not unnested automatically anymore. To manually unnest tables, batchtools provides the helper function `unwrap()` now, e.g. `unwrap(getJobPars())`. The previously introduced helper function `flatten()` will be deprecated due to a name clash with `purrr::flatten()`.
     >
     > test_check("batchtools")
     -- 1. Error: addAlgorithm (@test_Algorithm.R#13) ------------------------------
     type must be LANGSXP at this point
     1: addExperiments(list(p1 = data.table()), algo.designs = list(a1 = data.table(), a2 = data.table()),
     repls = 2, reg = reg) at testthat/test_Algorithm.R:13
     2: merge(reg$defs[, !c("problem", "algorithm", "prob.pars", "algo.pars")], tab, by = "pars.hash",
     all.x = FALSE, all.y = TRUE, sort = FALSE)
     3: merge.data.table(reg$defs[, !c("problem", "algorithm", "prob.pars", "algo.pars")],
     tab, by = "pars.hash", all.x = FALSE, all.y = TRUE, sort = FALSE)
     4: y[x, nomatch = if (all.x) NA else 0, on = by, allow.cartesian = allow.cartesian]
     5: `[.data.table`(y, x, nomatch = if (all.x) NA else 0, on = by, allow.cartesian = allow.cartesian)
     6: length(ans$indices)
    
     -- 2. Error: addAlgorithm overwrites old algo (@test_Algorithm.R#31) ----------
     type must be LANGSXP at this point
     1: addExperiments(list(p1 = data.table()), list(a1 = data.table()), reg = reg) at testthat/test_Algorithm.R:31
     2: merge(reg$defs[, !c("problem", "algorithm", "prob.pars", "algo.pars")], tab, by = "pars.hash",
     all.x = FALSE, all.y = TRUE, sort = FALSE)
     3: merge.data.table(reg$defs[, !c("problem", "algorithm", "prob.pars", "algo.pars")],
     tab, by = "pars.hash", all.x = FALSE, all.y = TRUE, sort = FALSE)
     4: y[x, nomatch = if (all.x) NA else 0, on = by, allow.cartesian = allow.cartesian]
     5: `[.data.table`(y, x, nomatch = if (all.x) NA else 0, on = by, allow.cartesian = allow.cartesian)
     6: length(ans$indices)
    
     Loading required package: methods
     -- 3. Error: makeTestExperimentRegistry (@test_ExperimentRegistry.R#18) -------
     type must be LANGSXP at this point
     1: checkTables(reg, any.missing = FALSE, nrows = 0L) at testthat/test_ExperimentRegistry.R:18
     2: expect_key_set_equal(reg$defs, reg$status, by = "def.id") at d:\RCompile\CRANpkg\local\3.5\batchtools.Rcheck\tests_i386\testthat\helper.R:99
     3: expect_true(nrow(ajoin(x, y, by = by)) == 0 && nrow(ajoin(y, x, by = by)) == 0) at d:\RCompile\CRANpkg\local\3.5\batchtools.Rcheck\tests_i386\testthat\helper.R:128
     4: quasi_label(enquo(object), label)
     5: eval_bare(get_expr(quo), get_env(quo))
     6: nrow(ajoin(x, y, by = by))
     7: ajoin(x, y, by = by)
     8: setKey(x[!y, on = by], by)
     9: key(res)
     10: x[!y, on = by]
     11: `[.data.table`(x, !y, on = by)
     12: length(ans$indices)
    
     -- 4. Error: Experiment (@test_Job.R#33) --------------------------------------
     type must be LANGSXP at this point
     1: addExperiments(list(p1 = data.table(i = 1:3)), list(a1 = data.table()), reg = reg) at testthat/test_Job.R:33
     2: merge(reg$defs[, !c("problem", "algorithm", "prob.pars", "algo.pars")], tab, by = "pars.hash",
     all.x = FALSE, all.y = TRUE, sort = FALSE)
     3: merge.data.table(reg$defs[, !c("problem", "algorithm", "prob.pars", "algo.pars")],
     tab, by = "pars.hash", all.x = FALSE, all.y = TRUE, sort = FALSE)
     4: y[x, nomatch = if (all.x) NA else 0, on = by, allow.cartesian = allow.cartesian]
     5: `[.data.table`(y, x, nomatch = if (all.x) NA else 0, on = by, allow.cartesian = allow.cartesian)
     6: length(ans$indices)
    
     -- 5. Error: External directory is created (@test_Job.R#71) -------------------
     type must be LANGSXP at this point
     1: addExperiments(list(p1 = data.table(i = 1:3)), list(a1 = data.table()), reg = reg) at testthat/test_Job.R:71
     2: merge(reg$defs[, !c("problem", "algorithm", "prob.pars", "algo.pars")], tab, by = "pars.hash",
     all.x = FALSE, all.y = TRUE, sort = FALSE)
     3: merge.data.table(reg$defs[, !c("problem", "algorithm", "prob.pars", "algo.pars")],
     tab, by = "pars.hash", all.x = FALSE, all.y = TRUE, sort = FALSE)
     4: y[x, nomatch = if (all.x) NA else 0, on = by, allow.cartesian = allow.cartesian]
     5: `[.data.table`(y, x, nomatch = if (all.x) NA else 0, on = by, allow.cartesian = allow.cartesian)
     6: length(ans$indices)
    
     -- 6. Error: addProblem / removeProblem (@test_Problem.R#28) ------------------
     type must be LANGSXP at this point
     1: addExperiments(prob.designs, algo.designs, repls = 2, reg = reg) at testthat/test_Problem.R:28
     2: merge(reg$defs[, !c("problem", "algorithm", "prob.pars", "algo.pars")], tab, by = "pars.hash",
     all.x = FALSE, all.y = TRUE, sort = FALSE)
     3: merge.data.table(reg$defs[, !c("problem", "algorithm", "prob.pars", "algo.pars")],
     tab, by = "pars.hash", all.x = FALSE, all.y = TRUE, sort = FALSE)
     4: y[x, nomatch = if (all.x) NA else 0, on = by, allow.cartesian = allow.cartesian]
     5: `[.data.table`(y, x, nomatch = if (all.x) NA else 0, on = by, allow.cartesian = allow.cartesian)
     6: length(ans$indices)
    
     -- 7. Error: instance caching (@test_Problem.R#50) ----------------------------
     type must be LANGSXP at this point
     1: addExperiments(prob.designs = list(p1 = data.table(param = 1:2)), repls = 2, reg = reg) at testthat/test_Problem.R:50
     2: merge(reg$defs[, !c("problem", "algorithm", "prob.pars", "algo.pars")], tab, by = "pars.hash",
     all.x = FALSE, all.y = TRUE, sort = FALSE)
     3: merge.data.table(reg$defs[, !c("problem", "algorithm", "prob.pars", "algo.pars")],
     tab, by = "pars.hash", all.x = FALSE, all.y = TRUE, sort = FALSE)
     4: y[x, nomatch = if (all.x) NA else 0, on = by, allow.cartesian = allow.cartesian]
     5: `[.data.table`(y, x, nomatch = if (all.x) NA else 0, on = by, allow.cartesian = allow.cartesian)
     6: length(ans$indices)
    
     -- 8. Error: makeRegistry (@test_Registry.R#17) -------------------------------
     type must be LANGSXP at this point
     1: checkTables(reg, any.missing = FALSE, nrows = 0L) at testthat/test_Registry.R:17
     2: expect_key_set_equal(reg$defs, reg$status, by = "def.id") at d:\RCompile\CRANpkg\local\3.5\batchtools.Rcheck\tests_i386\testthat\helper.R:99
     3: expect_true(nrow(ajoin(x, y, by = by)) == 0 && nrow(ajoin(y, x, by = by)) == 0) at d:\RCompile\CRANpkg\local\3.5\batchtools.Rcheck\tests_i386\testthat\helper.R:128
     4: quasi_label(enquo(object), label)
     5: eval_bare(get_expr(quo), get_env(quo))
     6: nrow(ajoin(x, y, by = by))
     7: ajoin(x, y, by = by)
     8: setKey(x[!y, on = by], by)
     9: key(res)
     10: x[!y, on = by]
     11: `[.data.table`(x, !y, on = by)
     12: length(ans$indices)
    
     -- 9. Error: loadRegistry (@test_Registry.R#88) -------------------------------
     type must be LANGSXP at this point
     1: checkTables(reg2) at testthat/test_Registry.R:88
     2: expect_key_set_equal(reg$defs, reg$status, by = "def.id") at d:\RCompile\CRANpkg\local\3.5\batchtools.Rcheck\tests_i386\testthat\helper.R:99
     3: expect_true(nrow(ajoin(x, y, by = by)) == 0 && nrow(ajoin(y, x, by = by)) == 0) at d:\RCompile\CRANpkg\local\3.5\batchtools.Rcheck\tests_i386\testthat\helper.R:128
     4: quasi_label(enquo(object), label)
     5: eval_bare(get_expr(quo), get_env(quo))
     6: nrow(ajoin(x, y, by = by))
     7: ajoin(x, y, by = by)
     8: setKey(x[!y, on = by], by)
     9: key(res)
     10: x[!y, on = by]
     11: `[.data.table`(x, !y, on = by)
     12: length(ans$indices)
    
     -- 10. Error: clearRegistry (@test_Registry.R#130) ----------------------------
     type must be LANGSXP at this point
     1: clearRegistry(reg) at testthat/test_Registry.R:130
     2: sweepRegistry(reg = reg)
     3: reg$resources[!reg$status, on = "resource.id", which = TRUE]
     4: `[.data.table`(reg$resources, !reg$status, on = "resource.id", which = TRUE)
     5: length(ans$indices)
    
     -- 11. Error: addExperiments creates default designs (@test_addExperiments.R#27)
     type must be LANGSXP at this point
     1: addExperiments(reg = reg) at testthat/test_addExperiments.R:27
     2: merge(reg$defs[, !c("problem", "algorithm", "prob.pars", "algo.pars")], tab, by = "pars.hash",
     all.x = FALSE, all.y = TRUE, sort = FALSE)
     3: merge.data.table(reg$defs[, !c("problem", "algorithm", "prob.pars", "algo.pars")],
     tab, by = "pars.hash", all.x = FALSE, all.y = TRUE, sort = FALSE)
     4: y[x, nomatch = if (all.x) NA else 0, on = by, allow.cartesian = allow.cartesian]
     5: `[.data.table`(y, x, nomatch = if (all.x) NA else 0, on = by, allow.cartesian = allow.cartesian)
     6: length(ans$indices)
    
     -- 12. Error: addExperiments / user provided designs (@test_addExperiments.R#42)
     type must be LANGSXP at this point
     1: addExperiments(reg = reg, prob.designs = prob.designs, algo.designs = algo.designs,
     combine = "bind") at testthat/test_addExperiments.R:42
     2: merge(reg$defs[, !c("problem", "algorithm", "prob.pars", "algo.pars")], tab, by = "pars.hash",
     all.x = FALSE, all.y = TRUE, sort = FALSE)
     3: merge.data.table(reg$defs[, !c("problem", "algorithm", "prob.pars", "algo.pars")],
     tab, by = "pars.hash", all.x = FALSE, all.y = TRUE, sort = FALSE)
     4: y[x, nomatch = if (all.x) NA else 0, on = by, allow.cartesian = allow.cartesian]
     5: `[.data.table`(y, x, nomatch = if (all.x) NA else 0, on = by, allow.cartesian = allow.cartesian)
     6: length(ans$indices)
    
     -- 13. Error: caching works (@test_chunk.R#85) --------------------------------
     type must be LANGSXP at this point
     1: addExperiments(reg = reg) at testthat/test_chunk.R:85
     2: merge(reg$defs[, !c("problem", "algorithm", "prob.pars", "algo.pars")], tab, by = "pars.hash",
     all.x = FALSE, all.y = TRUE, sort = FALSE)
     3: merge.data.table(reg$defs[, !c("problem", "algorithm", "prob.pars", "algo.pars")],
     tab, by = "pars.hash", all.x = FALSE, all.y = TRUE, sort = FALSE)
     4: y[x, nomatch = if (all.x) NA else 0, on = by, allow.cartesian = allow.cartesian]
     5: `[.data.table`(y, x, nomatch = if (all.x) NA else 0, on = by, allow.cartesian = allow.cartesian)
     6: length(ans$indices)
    
     -- 14. Error: chunkIds (@test_chunkIds.R#11) ----------------------------------
     type must be LANGSXP at this point
     1: addExperiments(prob.designs, algo.designs, repls = repls, reg = reg) at testthat/test_chunkIds.R:11
     2: merge(reg$defs[, !c("problem", "algorithm", "prob.pars", "algo.pars")], tab, by = "pars.hash",
     all.x = FALSE, all.y = TRUE, sort = FALSE)
     3: merge.data.table(reg$defs[, !c("problem", "algorithm", "prob.pars", "algo.pars")],
     tab, by = "pars.hash", all.x = FALSE, all.y = TRUE, sort = FALSE)
     4: y[x, nomatch = if (all.x) NA else 0, on = by, allow.cartesian = allow.cartesian]
     5: `[.data.table`(y, x, nomatch = if (all.x) NA else 0, on = by, allow.cartesian = allow.cartesian)
     6: length(ans$indices)
    
     -- 15. Error: estimateRuntimes (@test_estimateRuntimes.R#8) -------------------
     type must be LANGSXP at this point
     1: addExperiments(algo.designs = list(nrow = CJ(x = 1:50, y = letters[1:5])), reg = reg) at testthat/test_estimateRuntimes.R:8
     2: merge(reg$defs[, !c("problem", "algorithm", "prob.pars", "algo.pars")], tab, by = "pars.hash",
     all.x = FALSE, all.y = TRUE, sort = FALSE)
     3: merge.data.table(reg$defs[, !c("problem", "algorithm", "prob.pars", "algo.pars")],
     tab, by = "pars.hash", all.x = FALSE, all.y = TRUE, sort = FALSE)
     4: y[x, nomatch = if (all.x) NA else 0, on = by, allow.cartesian = allow.cartesian]
     5: `[.data.table`(y, x, nomatch = if (all.x) NA else 0, on = by, allow.cartesian = allow.cartesian)
     6: length(ans$indices)
    
     -- 16. Error: findExperiments (@test_findJobs.R#100) --------------------------
     type must be LANGSXP at this point
     1: addExperiments(prob.designs, algo.designs, repls = repls, reg = reg) at testthat/test_findJobs.R:100
     2: merge(reg$defs[, !c("problem", "algorithm", "prob.pars", "algo.pars")], tab, by = "pars.hash",
     all.x = FALSE, all.y = TRUE, sort = FALSE)
     3: merge.data.table(reg$defs[, !c("problem", "algorithm", "prob.pars", "algo.pars")],
     tab, by = "pars.hash", all.x = FALSE, all.y = TRUE, sort = FALSE)
     4: y[x, nomatch = if (all.x) NA else 0, on = by, allow.cartesian = allow.cartesian]
     5: `[.data.table`(y, x, nomatch = if (all.x) NA else 0, on = by, allow.cartesian = allow.cartesian)
     6: length(ans$indices)
    
     -- 17. Error: getJobTable.ExperimentRegistry (@test_getJobTable.R#100) --------
     type must be LANGSXP at this point
     1: addExperiments(list(p1 = data.table(k = 1)), list(a1 = data.table(sq = 1:3)), reg = reg) at testthat/test_getJobTable.R:100
     2: merge(reg$defs[, !c("problem", "algorithm", "prob.pars", "algo.pars")], tab, by = "pars.hash",
     all.x = FALSE, all.y = TRUE, sort = FALSE)
     3: merge.data.table(reg$defs[, !c("problem", "algorithm", "prob.pars", "algo.pars")],
     tab, by = "pars.hash", all.x = FALSE, all.y = TRUE, sort = FALSE)
     4: y[x, nomatch = if (all.x) NA else 0, on = by, allow.cartesian = allow.cartesian]
     5: `[.data.table`(y, x, nomatch = if (all.x) NA else 0, on = by, allow.cartesian = allow.cartesian)
     6: length(ans$indices)
    
     -- 18. Error: experiment registry with vector parameters (@test_getJobTable.R#13
     type must be LANGSXP at this point
     1: addExperiments(prob.designs, algo.designs, reg = tmp) at testthat/test_getJobTable.R:138
     2: merge(reg$defs[, !c("problem", "algorithm", "prob.pars", "algo.pars")], tab, by = "pars.hash",
     all.x = FALSE, all.y = TRUE, sort = FALSE)
     3: merge.data.table(reg$defs[, !c("problem", "algorithm", "prob.pars", "algo.pars")],
     tab, by = "pars.hash", all.x = FALSE, all.y = TRUE, sort = FALSE)
     4: y[x, nomatch = if (all.x) NA else 0, on = by, allow.cartesian = allow.cartesian]
     5: `[.data.table`(y, x, nomatch = if (all.x) NA else 0, on = by, allow.cartesian = allow.cartesian)
     6: length(ans$indices)
    
     -- 19. Error: hooks (@test_hooks.R#12) ----------------------------------------
     type must be LANGSXP at this point
     1: makeJobCollection(1, reg = reg) at testthat/test_hooks.R:12
     2: makeJobCollection.Registry(1, reg = reg)
     3: createCollection(mergedJobs(reg, convertIds(reg, ids), c("job.id", "job.name", "job.pars")),
     resources, reg)
     4: setkeyv(jobs, "job.id")
     5: is.data.table(x)
     6: mergedJobs(reg, convertIds(reg, ids), c("job.id", "job.name", "job.pars"))
     7: reg$defs[reg$status[ids, nomatch = 0L, on = "job.id"], cols, on = "def.id", nomatch = 0L,
     with = missing(cols)]
     8: `[.data.table`(reg$defs, reg$status[ids, nomatch = 0L, on = "job.id"], cols, on = "def.id",
     nomatch = 0L, with = missing(cols))
     9: length(ans$indices)
Flavors: r-devel-windows-ix86+x86_64, r-release-windows-ix86+x86_64

Version: 0.9.8
Check: package dependencies
Result: NOTE
    Package suggested but not available for checking: ‘doMPI’
Flavors: r-release-osx-x86_64, r-oldrel-osx-x86_64

Version: 0.9.8
Check: Rd cross-references
Result: NOTE
    Package unavailable to check Rd xrefs: ‘Rmpi’
Flavors: r-release-osx-x86_64, r-oldrel-osx-x86_64