- using R Under development (unstable) (2026-02-08 r89382)
- using platform: x86_64-pc-linux-gnu
- R was compiled by
Debian clang version 21.1.8 (3)
Debian flang version 21.1.8 (3)
- running under: Debian GNU/Linux forky/sid
- using session charset: UTF-8
* current time: 2026-02-10 09:25:04 UTC
- checking for file ‘tiledb/DESCRIPTION’ ... OK
- checking extension type ... Package
- this is package ‘tiledb’ version ‘0.33.0’
- package encoding: UTF-8
- checking CRAN incoming feasibility ... [4s/7s] OK
- 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 ‘tiledb’ can be installed ... OK
See the install log for details.
- used C compiler: ‘Debian clang version 21.1.8 (3)’
- used C++ compiler: ‘Debian clang version 21.1.8 (3)’
- checking C++ specification ... INFO
specified C++17
- checking package directory ... OK
- checking for future file timestamps ... 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 ... [2s/2s] OK
- checking whether the package can be loaded with stated dependencies ... [2s/2s] OK
- checking whether the package can be unloaded cleanly ... [1s/2s] OK
- checking whether the namespace can be loaded with stated dependencies ... [1s/2s] OK
- checking whether the namespace can be unloaded cleanly ... [2s/2s] OK
- checking loading without being on the library search path ... [1s/2s] OK
- checking whether startup messages can be suppressed ... [1s/2s] 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 ... [24s/31s] OK
- checking Rd files ... [2s/2s] 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 $(LAPACK_LIBS) ... OK
- checking use of PKG_*FLAGS in Makefiles ... OK
- checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
- checking pragmas in C/C++ headers and code ... OK
- checking compilation flags used ... OK
- checking compiled code ... OK
- checking installed files from ‘inst/doc’ ... OK
- checking files in ‘vignettes’ ... OK
- checking examples ... [2s/3s] ERROR
Running examples in ‘tiledb-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: fromDataFrame
> ### Title: Create a TileDB dense or sparse array from a given 'data.frame'
> ### Object
> ### Aliases: fromDataFrame
>
> ### ** Examples
>
> ## Don't show:
> ctx <- tiledb_ctx(limitTileDBCores())
> ## End(Don't show)
> uri <- tempfile()
> fromDataFrame(iris, uri)
*** caught segfault ***
address 0x7ffc0bb3b000, cause 'memory not mapped'
Traceback:
1: RcppSpdlog::formatter(s, v)
2: fmt(s, ...)
3: RcppSpdlog::log_debug(fmt(s, ...))
4: spdl::debug("[tiledb_array] query is {}", query_type)
5: tiledb_array(uri, query_type = "WRITE")
6: fromDataFrame(iris, uri)
An irrecoverable exception occurred. R is aborting now ...
Segmentation fault
- checking for unstated dependencies in ‘tests’ ... OK
- checking tests ... [4s/7s] ERROR
Running ‘pkgconfig-test.R’ [2s/2s]
Running ‘tinytest.R’ [3s/4s]
Running the tests in ‘tests/tinytest.R’ failed.
Complete output:
> if (requireNamespace("tinytest", quietly = TRUE)) {
+ if (R.Version()$minor >= "2.0" && Sys.getenv("MY_UNIVERSE", "") == "") {
+ tinytest::test_package("tiledb")
+ }
+ }
test_aggregates.R............. 0 tests
test_aggregates.R............. 0 tests
test_aggregates.R............. 0 tests
test_aggregates.R............. 0 tests
test_aggregates.R............. 0 tests
Attaching package: 'palmerpenguins'
The following objects are masked from 'package:datasets':
penguins, penguins_raw
test_aggregates.R............. 0 tests
test_aggregates.R............. 0 tests
*** caught segfault ***
address 0x7ffe3ac6d000, cause 'memory not mapped'
Traceback:
1: RcppSpdlog::formatter(s, v)
2: fmt(s, ...)
3: RcppSpdlog::log_debug(fmt(s, ...))
4: spdl::debug("[tiledb_array] query is {}", query_type)
5: tiledb_array(uri, query_type = "WRITE")
6: fromDataFrame(penguins, uri, sparse = TRUE)
7: doTryCatch(return(expr), name, parentenv, handler)
8: tryCatchOne(expr, names, parentenv, handlers[[1L]])
9: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
10: doTryCatch(return(expr), name, parentenv, handler)
11: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]])
12: tryCatchList(expr, classes, parentenv, handlers)
13: tryCatch(current, error = function(e) { result <<- FALSE msg <<- e$message type <<- "An error"}, warning = function(w) { result <<- FALSE msg <<- w$message type <<- "A warning"})
14: fun(...)
15: expect_silent(fromDataFrame(penguins, uri, sparse = TRUE))
16: eval(expr, envir = e)
17: eval(expr, envir = e)
18: FUN(X[[i]], ...)
19: lapply(basename(testfiles), run_test_file, at_home = at_home, verbose = verbose, color = color, remove_side_effects = remove_side_effects, ...)
20: run_test_dir(testdir, at_home = at_home, cluster = cluster, ...)
21: tinytest::test_package("tiledb")
An irrecoverable exception occurred. R is aborting now ...
Segmentation fault
- checking for unstated dependencies in vignettes ... OK
- checking package vignettes ... OK
- checking re-building of vignette outputs ... [6s/9s] OK
- checking PDF version of manual ... [14s/18s] OK
- checking HTML version of manual ... [15s/24s] OK
- checking for non-standard things in the check directory ... OK
- DONE
Status: 2 ERRORs