* using log directory ‘/data/gannet/ripley/R/packages/tests-MKL/data.table.Rcheck’
* using R Under development (unstable) (2025-12-24 r89227)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)
    GNU Fortran (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)
* running under: Fedora Linux 42 (Workstation Edition)
* using session charset: UTF-8
* using option ‘--no-stop-on-test-error’
* checking for file ‘data.table/DESCRIPTION’ ... OK
* this is package ‘data.table’ version ‘1.18.0’
* 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 ‘data.table’ can be installed ... [84s/56s] OK
* used C compiler: ‘gcc (GCC) 15.1.1 20250521 (Red Hat 15.1.1-2)’
* checking package directory ... OK
* checking ‘build’ 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 code 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 whether startup messages can be suppressed ... 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 ... [55s/58s] 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 shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... NOTE
File ‘data.table/libs/data_table.so’:
  Found non-API calls to R: ‘ATTRIB’, ‘SET_ATTRIB’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘S4.R’
  Running ‘autoprint.R’
  Comparing ‘autoprint.Rout’ to ‘autoprint.Rout.save’ ... OK
  Running ‘froll.R’
  Running ‘knitr.R’
  Comparing ‘knitr.Rout’ to ‘knitr.Rout.save’ ... OK
  Running ‘main.R’/data/gannet/ripley/R/MKL/bin/BATCH: line 60: 2207123 Segmentation fault      (core dumped) ${R_HOME}/bin/R -f ${in} ${opts} ${R_BATCH_OPTIONS} > ${out} 2>&1
 [21s/25s]
  Running ‘mergelist.R’
  Running ‘nafill.R’
  Running ‘other.R’
  Running ‘programming.R’
  Running ‘types.R’
 [43s/46s] ERROR
Running the tests in ‘tests/main.R’ failed.
Complete output:
  > Sys.setenv(OMP_THREAD_LIMIT = Sys.getenv("OMP_THREAD_LIMIT", "2"))
  > require(data.table)
  Loading required package: data.table
  
  Attaching package: 'data.table'
  
  The following object is masked from 'package:base':
  
      %notin%
  
  > 
  > test.data.table()  # runs the main test suite of 5,000+ tests in /inst/tests/tests.Rraw
  getDTthreads(verbose=TRUE):
    OpenMP version (_OPENMP)       201511
    omp_get_num_procs()            24
    R_DATATABLE_NUM_PROCS_PERCENT  unset (default 50)
    R_DATATABLE_NUM_THREADS        unset
    R_DATATABLE_THROTTLE           unset (default 1024)
    omp_get_thread_limit()         2
    omp_get_max_threads()          24
    OMP_THREAD_LIMIT               2
    OMP_NUM_THREADS                unset
    RestoreAfterFork               true
    data.table is using 2 threads with throttle==1024. See ?setDTthreads.
  test.data.table() running: /data/gannet/ripley/R/packages/tests-MKL/data.table.Rcheck/data.table/tests/tests.Rraw.bz2
  
   *** caught segfault ***
  address 0x6, cause 'memory not mapped'
  
  Traceback:
   1: all.equal(ax, ay, ..., check.attributes = check.attributes)
   2: attr.all.equal(target, current, tolerance = tolerance, scale = scale,     ...)
   3: all.equal.numeric(x, y, check.names = !isTRUE(y))
   4: all.equal(x, y, check.names = !isTRUE(y))
   5: isTRUE(all.equal.result <- all.equal(x, y, check.names = !isTRUE(y)))
   6: test(1252 + test_no * 0.001, ans1[ans1 != 0], with(DT, eval(ll)))
   7: FUN(newX[, i], ...)
   8: apply(cj, 1, function(y) {    test_no <<- test_no + 1L    ll = as.call(c(as.name("base_order"), method = "radix", lapply(seq_along(x),         function(j) {            if (y[j] == 1L) as.name(x[j]) else {                if (is.character(DT[[x[j]]])) as.call(c(as.name("-"),                   as.call(list(as.name("xtfrm"), as.name(x[j]))))) else as.call(list(as.name("-"),                   as.name(x[j])))            }        })))    ans1 = forderv(DT, by = x, order = y, na.last = TRUE)    test(1252 + test_no * 0.001, ans1, with(DT, eval(ll)))    test_no <<- test_no + 1L    ll <- as.call(c(as.list(ll), na.last = NA))    ans1 = forderv(DT, by = x, order = y, na.last = NA)    test(1252 + test_no * 0.001, ans1[ans1 != 0], with(DT, eval(ll)))})
   9: FUN(x[a], ...)
  10: combn(names(DT), i, function(x) {    tmp = apply(cj, 1, function(y) {        test_no <<- test_no + 1L        ll = as.call(c(as.name("base_order"), method = "radix",             lapply(seq_along(x), function(j) {                if (y[j] == 1L) as.name(x[j]) else {                  if (is.character(DT[[x[j]]])) as.call(c(as.name("-"),                     as.call(list(as.name("xtfrm"), as.name(x[j]))))) else as.call(list(as.name("-"),                     as.name(x[j])))                }            })))        ans1 = forderv(DT, by = x, order = y, na.last = TRUE)        test(1252 + test_no * 0.001, ans1, with(DT, eval(ll)))        test_no <<- test_no + 1L        ll <- as.call(c(as.list(ll), na.last = NA))        ans1 = forderv(DT, by = x, order = y, na.last = NA)        test(1252 + test_no * 0.001, ans1[ans1 != 0], with(DT,             eval(ll)))    })    dim(tmp) = NULL    list(tmp)})
  11: eval(exprs[i], envir)
  12: eval(exprs[i], envir)
  13: sys.source(fn, envir = env)
  14: withCallingHandlers(sys.source(fn, envir = env), warning = function(w) {    if (!silent && showProgress)         print(w)    env$warnings = c(env$warnings, list(list(`after test` = env$prevtest,         warning = conditionMessage(w), calls = paste(vapply_1c(sys.calls(),             function(call) {                if (is.name(call[[1]])) {                  as.character(call[[1]])                } else "..."            }), collapse = " -> "))))    invokeRestart("muffleWarning")})
  15: doTryCatch(return(expr), name, parentenv, handler)
  16: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  17: tryCatchList(expr, classes, parentenv, handlers)
  18: tryCatch(expr, error = function(e) {    call <- conditionCall(e)    if (!is.null(call)) {        if (identical(call[[1L]], quote(doTryCatch)))             call <- sys.call(-4L)        dcall <- deparse(call, nlines = 1L)        prefix <- paste("Error in", dcall, ": ")        LONG <- 75L        sm <- strsplit(conditionMessage(e), "\n")[[1L]]        w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")        if (is.na(w))             w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],                 type = "b")        if (w > LONG)             prefix <- paste0(prefix, "\n  ")    }    else prefix <- "Error : "    msg <- paste0(prefix, conditionMessage(e), "\n")    .Internal(seterrmessage(msg[1L]))    if (!silent && isTRUE(getOption("show.error.messages"))) {        cat(msg, file = outFile)        .Internal(printDeferredWarnings())    }    invisible(structure(msg, class = "try-error", condition = e))})
  19: try(withCallingHandlers(sys.source(fn, envir = env), warning = function(w) {    if (!silent && showProgress)         print(w)    env$warnings = c(env$warnings, list(list(`after test` = env$prevtest,         warning = conditionMessage(w), calls = paste(vapply_1c(sys.calls(),             function(call) {                if (is.name(call[[1]])) {                  as.character(call[[1]])                } else "..."            }), collapse = " -> "))))    invokeRestart("muffleWarning")}), silent = silent)
  20: test.data.table()
  An irrecoverable exception occurred. R is aborting now ...
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [88s/91s] OK
* checking PDF version of manual ... [22s/22s] OK
* checking HTML version of manual ... [23s/24s] OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE

Status: 1 ERROR, 1 NOTE
See
  ‘/data/gannet/ripley/R/packages/tests-MKL/data.table.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 5:58.77, 345.73 + 27.06