* using log directory ‘/data/gannet/ripley/R/packages/tests-LENGTH1/ffbase.Rcheck’ * using R Under development (unstable) (2022-04-03 r82074) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-stop-on-test-error’ * checking for file ‘ffbase/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘ffbase’ version ‘0.13.3’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘ffbase’ can be installed ... [11s/16s] OK * checking package directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking use of S3 registration ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... [20s/25s] OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd line widths ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking pragmas in C/C++ headers and code ... OK * checking compilation flags used ... OK * checking compiled code ... OK * checking examples ... ERROR Running examples in ‘ffbase-Ex.R’ failed The error most likely occurred in: > ### Name: is.na.ff > ### Title: 'Not Available' / Missing Values for ff vectors > ### Aliases: is.na.ff is.na<-.ff > > ### ** Examples > > is.na.ff(ff(c(NA, 1:100)), BATCHBYTES=20) ff (open) logical length=101 (112) [1] [2] [3] [4] [5] [6] [7] [8] [94] [95] [96] [97] TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE : FALSE FALSE FALSE FALSE [98] [99] [100] [101] FALSE FALSE FALSE FALSE > ## S3 generic > is.na(ff(c(NA, 1:100))) ff (open) logical length=101 (112) [1] [2] [3] [4] [5] [6] [7] [8] [94] [95] [96] [97] TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE : FALSE FALSE FALSE FALSE [98] [99] [100] [101] FALSE FALSE FALSE FALSE > ## Assign a missing value > x <- ff(c(NA, 1:100)) > is.na(x) <- ff(c(3,5)) ----------- FAILURE REPORT -------------- --- failure: length > 1 in coercion to logical --- --- srcref --- : --- package (from environment) --- ff --- call from context --- set.ff(x = x, i = value[i], value = NA, add = FALSE) --- call from argument --- !is.integer(i) || i < 1 --- R stacktrace --- where 1: set.ff(x = x, i = value[i], value = NA, add = FALSE) where 2: `is.na<-.ff`(`*tmp*`, value = list()) where 3: `is.na<-`(`*tmp*`, value = list()) --- value of length: 2 type: logical --- [1] FALSE FALSE --- function from context --- function (x, i, value, add = FALSE) { open(x, assert = TRUE) if (is.readonly(x)) stop("ff is readonly") if (length(i)) { if (is.double(i)) i <- as.integer(i) if (!is.integer(i) || i < 1 || i > length(x)) stop("illegal index") if (!is.null(vw(x))) stop("please use '[' to access ff with vw") if (!is.null(physical(x)$na.count)) stop("use readwrite.ff instead to maintain na.count (or deactivate na.count(x)<-NULL)") vm <- vmode(x) if (add) attr(x, "physical") <- .Call(C_addset_vec, .ffmode[vm], attr(x, "physical"), i, length(i), as.vmode(value, vm), PACKAGE = "ff") else attr(x, "physical") <- .Call(C_set_vec, .ffmode[vm], attr(x, "physical"), i, length(i), as.vmode(value, vm), PACKAGE = "ff") } x } --- function search by body --- Function set.ff in namespace ff has this body. ----------- END OF FAILURE REPORT -------------- Fatal error: length > 1 in coercion to logical * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ [8s/10s] [8s/11s] ERROR Running the tests in ‘tests/testthat.R’ failed. Complete output: > #library(ffbase) > library(testthat) > > test_check("ffbase") Loading required package: ffbase Loading required package: ff Loading required package: bit Attaching package: 'bit' The following object is masked from 'package:base': xor Attaching package ff - getOption("fftempdir")=="/tmp/Rtmp8mg79t/working_dir/RtmpzEygFN/ff" - getOption("ffextension")=="ff" - getOption("ffdrop")==TRUE - getOption("fffinonexit")==TRUE - getOption("ffpagesize")==65536 - getOption("ffcaching")=="mmnoflush" -- consider "ffeachflush" if your system stalls on large writes - getOption("ffbatchbytes")==16777216 -- consider a different value for tuning your system - getOption("ffmaxbytes")==536870912 -- consider a different value for tuning your system Attaching package: 'ff' The following objects are masked from 'package:utils': write.csv, write.csv2 The following objects are masked from 'package:base': is.factor, is.ordered Registered S3 methods overwritten by 'ffbase': method from [.ff ff [.ffdf ff [<-.ff ff [<-.ffdf ff Attaching package: 'ffbase' The following objects are masked from 'package:base': %in%, table ----------- FAILURE REPORT -------------- --- failure: length > 1 in coercion to logical --- --- srcref --- : --- package (from environment) --- ff --- call from context --- set.ff(x = x, i = value, value = NA, add = FALSE) --- call from argument --- !is.integer(i) || i < 1 --- R stacktrace --- where 1: set.ff(x = x, i = value, value = NA, add = FALSE) where 2: `is.na<-.ff`(`*tmp*`, value = c(54L, 29L, 58L, 87L, 75L, 56L, 51L, 50L, 48L, 3L, 33L, 34L, 66L, 64L, 40L, 98L, 20L, 78L, 25L, 71L, 86L, 61L, 22L, 95L, 90L, 97L, 53L, 31L, 46L, 24L, 60L, 30L, 23L, 17L, 59L, 57L, 43L, 68L, 26L, 36L, 45L, 8L, 15L, 79L, 70L, 91L, 39L, 76L, 38L, 77L)) where 3 at testisna.R#17: `is.na<-`(`*tmp*`, value = c(54L, 29L, 58L, 87L, 75L, 56L, 51L, 50L, 48L, 3L, 33L, 34L, 66L, 64L, 40L, 98L, 20L, 78L, 25L, 71L, 86L, 61L, 22L, 95L, 90L, 97L, 53L, 31L, 46L, 24L, 60L, 30L, 23L, 17L, 59L, 57L, 43L, 68L, 26L, 36L, 45L, 8L, 15L, 79L, 70L, 91L, 39L, 76L, 38L, 77L)) where 4: eval(code, test_env) where 5: eval(code, test_env) where 6: withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() } }, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error) where 7: doTryCatch(return(expr), name, parentenv, handler) where 8: tryCatchOne(expr, names, parentenv, handlers[[1L]]) where 9: tryCatchList(expr, names[-nh], parentenv, handlers[-nh]) where 10: doTryCatch(return(expr), name, parentenv, handler) where 11: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]]) where 12: tryCatchList(expr, classes, parentenv, handlers) where 13: tryCatch(withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() } }, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error), error = handle_fatal, skip = function(e) { }) where 14: test_code(desc, code, env = parent.frame(), reporter = reporter) where 15 at testisna.R#6: test_that("isna works", { size <- 100 x <- rnorm(size) x[sample(1:size, round(size/2))] <- NA test.ram <- is.na(x) test.ff <- is.na.ff(ff(x), by = 2) expect_equal(test.ram, test.ff[]) x <- rnorm(size) x.ff <- as.ff(x) idx <- sample(1:size, round(size/2)) is.na(x.ff) <- idx x[idx] <- NA test.ram <- is.na(x) test.ff <- is.na(x.ff) expect_equal(test.ram, test.ff[]) x <- rnorm(size) x.ff <- as.ff(x) idx <- sample(1:size, round(size/2)) x[idx] <- NA idx <- as.ff(idx) is.na(x.ff) <- idx test.ram <- is.na(x) test.ff <- is.na(x.ff) expect_equal(test.ram, test.ff[]) }) where 16: eval(code, test_env) where 17: eval(code, test_env) where 18: withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() } }, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error) where 19: doTryCatch(return(expr), name, parentenv, handler) where 20: tryCatchOne(expr, names, parentenv, handlers[[1L]]) where 21: tryCatchList(expr, names[-nh], parentenv, handlers[-nh]) where 22: doTryCatch(return(expr), name, parentenv, handler) where 23: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]]) where 24: tryCatchList(expr, classes, parentenv, handlers) where 25: tryCatch(withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() } }, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error), error = handle_fatal, skip = function(e) { }) where 26: test_code(NULL, exprs, env) where 27: source_file(path, child_env(env), wrap = wrap) where 28: FUN(X[[i]], ...) where 29: lapply(test_paths, test_one_file, env = env, wrap = wrap) where 30: doTryCatch(return(expr), name, parentenv, handler) where 31: tryCatchOne(expr, names, parentenv, handlers[[1L]]) where 32: tryCatchList(expr, classes, parentenv, handlers) where 33: tryCatch(code, testthat_abort_reporter = function(cnd) { cat(conditionMessage(cnd), "\n") NULL }) where 34: with_reporter(reporters$multi, lapply(test_paths, test_one_file, env = env, wrap = wrap)) where 35: test_files(test_dir = test_dir, test_package = test_package, test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, wrap = wrap, load_package = load_package) where 36: test_files(test_dir = path, test_paths = test_paths, test_package = package, reporter = reporter, load_helpers = load_helpers, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, wrap = wrap, load_package = load_package, parallel = parallel) where 37: test_dir("testthat", package = package, reporter = reporter, ..., load_package = "installed") where 38: test_check("ffbase") --- value of length: 50 type: logical --- [1] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE [13] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE [25] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE [37] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE [49] FALSE FALSE --- function from context --- function (x, i, value, add = FALSE) { open(x, assert = TRUE) if (is.readonly(x)) stop("ff is readonly") if (length(i)) { if (is.double(i)) i <- as.integer(i) if (!is.integer(i) || i < 1 || i > length(x)) stop("illegal index") if (!is.null(vw(x))) stop("please use '[' to access ff with vw") if (!is.null(physical(x)$na.count)) stop("use readwrite.ff instead to maintain na.count (or deactivate na.count(x)<-NULL)") vm <- vmode(x) if (add) attr(x, "physical") <- .Call(C_addset_vec, .ffmode[vm], attr(x, "physical"), i, length(i), as.vmode(value, vm), PACKAGE = "ff") else attr(x, "physical") <- .Call(C_set_vec, .ffmode[vm], attr(x, "physical"), i, length(i), as.vmode(value, vm), PACKAGE = "ff") } x } --- function search by body --- Function set.ff in namespace ff has this body. ----------- END OF FAILURE REPORT -------------- Fatal error: length > 1 in coercion to logical * checking PDF version of manual ... OK * checking for non-standard things in the check directory ... OK * checking for detritus in the temp directory ... OK * DONE Status: 2 ERRORs See ‘/data/gannet/ripley/R/packages/tests-LENGTH1/ffbase.Rcheck/00check.log’ for details. Command exited with non-zero status 1 Time 1:53.61, 71.86 + 7.83