##############################################################################
##############################################################################
###
### Running command:
###
###   /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD check --install=check:alabaster.base.install-out.txt --library=/home/rapidbuild/bbs-3.21-bioc-rapid/R/site-library --timings alabaster.base_1.7.8.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/alabaster.base.Rcheck’
* using R Under development (unstable) (2025-01-20 r87609)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘alabaster.base/DESCRIPTION’ ... OK
* this is package ‘alabaster.base’ version ‘1.7.8’
* 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 hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘alabaster.base’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* checking C++ specification ... OK
* checking installed package size ... INFO
  installed size is 33.7Mb
  sub-directories of 1Mb or more:
    libs  33.2Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Versioned 'LinkingTo' value for ‘assorthead’ is only usable in R >= 3.0.2
* 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 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 ... OK
* checking Rd files ... OK
* checking Rd metadata ... 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 line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... INFO
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... WARNING
Note: information on .o files is not available
File ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/alabaster.base/libs/alabaster.base.so’:
  Found ‘_ZSt4cerr’, possibly from ‘std::cerr’ (C++)
  Found ‘__sprintf_chk’, possibly from ‘sprintf’ (C)
  Found ‘abort’, possibly from ‘abort’ (C)
  Found ‘exit’, possibly from ‘exit’ (C)
  Found ‘rand_r’, possibly from ‘rand_r’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (C)
  Found ‘stdout’, possibly from ‘stdout’ (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  Backtrace:
      ▆
   1. ├─alabaster.base::saveObject(input, file.path(tmp, "foo")) at test-vector.R:52:5
   2. └─alabaster.base::saveObject(input, file.path(tmp, "foo"))
   3.   └─alabaster.base (local) .local(x, path, ...)
   4.     └─rhdf5::H5Fcreate(ofile, "H5F_ACC_TRUNC")
  
  [ FAIL 41 | WARN 135 | SKIP 0 | PASS 546 ]
  Error: Test failures
  Execution halted
  
   *** caught segfault ***
  address 0x558, cause 'memory not mapped'
  An irrecoverable exception occurred. R is aborting now ...
  Segmentation fault (core dumped)
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 WARNING, 1 NOTE
See
  ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/meat/alabaster.base.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD INSTALL alabaster.base
###
##############################################################################
##############################################################################


* installing to library ‘/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library’
* installing *source* package ‘alabaster.base’ ...
** this is package ‘alabaster.base’ version ‘1.7.8’
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
using C++17
g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I../inst/include -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/assorthead/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I../inst/include -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/assorthead/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -DR_NO_REMAP -c check_csv.cpp -o check_csv.o
g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I../inst/include -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/assorthead/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -DR_NO_REMAP -c check_list.cpp -o check_list.o
g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I../inst/include -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/assorthead/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -DR_NO_REMAP -c choose_numeric_missing_placeholder.cpp -o choose_numeric_missing_placeholder.o
g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I../inst/include -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/assorthead/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -DR_NO_REMAP -c is_rfc3339.cpp -o is_rfc3339.o
g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I../inst/include -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/assorthead/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -DR_NO_REMAP -c load_csv.cpp -o load_csv.o
g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I../inst/include -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/assorthead/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -DR_NO_REMAP -c load_list.cpp -o load_list.o
g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I../inst/include -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/assorthead/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -DR_NO_REMAP -c validate.cpp -o validate.o
In file included from /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/assorthead/include/chihaya/validate.hpp:13,
                 from /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/assorthead/include/chihaya/chihaya.hpp:10,
                 from /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/assorthead/include/takane/utils_public.hpp:13,
                 from /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/assorthead/include/takane/_validate.hpp:9,
                 from /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/assorthead/include/takane/takane.hpp:4,
                 from validate.cpp:2:
/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/assorthead/include/chihaya/sparse_matrix.hpp: In function ‘void chihaya::sparse_matrix::internal::validate_indices(const H5::DataSet&, const std::vector<long unsigned int>&, size_t, size_t, bool) [with Index_ = long unsigned int]’:
/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/assorthead/include/chihaya/sparse_matrix.hpp:51:32: warning: ‘previous’ may be used uninitialized [-Wmaybe-uninitialized]
   51 |             if (x > start && i <= previous) {
      |                              ~~^~~~~~~~~~~
/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/assorthead/include/chihaya/sparse_matrix.hpp:45:16: note: ‘previous’ was declared here
   45 |         Index_ previous;
      |                ^~~~~~~~
/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/assorthead/include/chihaya/sparse_matrix.hpp: In function ‘void chihaya::sparse_matrix::internal::validate_indices(const H5::DataSet&, const std::vector<long unsigned int>&, size_t, size_t, bool) [with Index_ = int]’:
/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/assorthead/include/chihaya/sparse_matrix.hpp:51:32: warning: ‘previous’ may be used uninitialized [-Wmaybe-uninitialized]
   51 |             if (x > start && i <= previous) {
      |                              ~~^~~~~~~~~~~
/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/assorthead/include/chihaya/sparse_matrix.hpp:45:16: note: ‘previous’ was declared here
   45 |         Index_ previous;
      |                ^~~~~~~~
g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I../inst/include -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/assorthead/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security -DR_NO_REMAP -c vls.cpp -o vls.o
g++ -std=gnu++17 -shared -L/usr/local/lib -o alabaster.base.so RcppExports.o check_csv.o check_list.o choose_numeric_missing_placeholder.o is_rfc3339.o load_csv.o load_list.o validate.o vls.o /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Rhdf5lib/lib/libhdf5_cpp.a /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Rhdf5lib/lib/libhdf5.a -L/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Rhdf5lib/lib -lcrypto -lcurl -lsz -laec -lz -ldl -lm -lz
installing to /media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/00LOCK-alabaster.base/00new/alabaster.base/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (alabaster.base)

R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(alabaster.base)
> test_check("alabaster.base")
[ FAIL 41 | WARN 135 | SKIP 0 | PASS 546 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-list.R:183:5'): data.frames cause dispatch to external objects ──
Error in `value[[3L]](cond)`: failed to stage list element 'Z'
  - failed to stage 'DFrame' entry inside a list
  - cannot open the connection
Backtrace:
    ▆
 1. ├─alabaster.base::stageObject(vals, tmp, path = "hstuff") at test-list.R:183:5
 2. └─alabaster.base::stageObject(vals, tmp, path = "hstuff")
 3.   └─alabaster.base (local) .local(x, dir, path, child, ...)
 4.     └─(function() {...
 5.       └─alabaster.base:::.transform_list_hdf5(...)
 6.         └─base::tryCatch(...)
 7.           └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 8.             └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 9.               └─value[[3L]](cond)
── Error ('test-list.R:183:5'): data.frames cause dispatch to external objects ──
Error in `H5Fclose(handle)`: HDF5. Object cache. Internal error detected.
Backtrace:
    ▆
 1. ├─alabaster.base::stageObject(vals, tmp, path = "hstuff") at test-list.R:183:5
 2. └─alabaster.base::stageObject(vals, tmp, path = "hstuff")
 3.   └─alabaster.base (local) .local(x, dir, path, child, ...)
 4.     └─(function() {...
 5.       └─rhdf5::H5Fclose(handle)
── Error ('test-list.R:209:5'): unnamed lists are properly supported ───────────
Error in `value[[3L]](cond)`: failed to stage list element 4
  - failed to stage list element 2
  - failed to stage list element 1
  - failed to stage 'DFrame' entry inside a list
  - cannot open the connection
Backtrace:
    ▆
 1. ├─alabaster.base::stageObject(vals, tmp, path = "stuff") at test-list.R:209:5
 2. └─alabaster.base::stageObject(vals, tmp, path = "stuff")
 3.   └─alabaster.base (local) .local(x, dir, path, child, ...)
 4.     └─alabaster.base:::.transform_list_json(...)
 5.       └─base::tryCatch(...)
 6.         └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 7.           └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 8.             └─value[[3L]](cond)
── Error ('test-list.R:260:5'): external references work correctly ─────────────
Error in `value[[3L]](cond)`: failed to stage list element 'B'
  - failed to stage list element 'C'
  - failed to stage 'DFrame' entry inside a list
  - cannot open the connection
Backtrace:
    ▆
 1. ├─alabaster.base::stageObject(vals, tmp, path = "stuff") at test-list.R:260:5
 2. └─alabaster.base::stageObject(vals, tmp, path = "stuff")
 3.   └─alabaster.base (local) .local(x, dir, path, child, ...)
 4.     └─alabaster.base:::.transform_list_json(...)
 5.       └─base::tryCatch(...)
 6.         └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 7.           └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 8.             └─value[[3L]](cond)
── Error ('test-list.R:300:5'): external references work correctly with lots of objects ──
Error in `value[[3L]](cond)`: failed to stage list element 1
  - failed to stage 'DFrame' entry inside a list
  - HDF5. File accessibility. Unable to open file.
Backtrace:
    ▆
 1. ├─alabaster.base::saveObject(vals, tmp) at test-list.R:300:5
 2. └─alabaster.base::saveObject(vals, tmp)
 3.   └─alabaster.base (local) .local(x, path, ...)
 4.     └─alabaster.base:::.transform_list_json(...)
 5.       └─base::tryCatch(...)
 6.         └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 7.           └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 8.             └─value[[3L]](cond)
── Error ('test-list.R:320:5'): we handle lists with NAs ───────────────────────
Error in `gzfile(fpath, open = "wb")`: cannot open the connection
Backtrace:
    ▆
 1. ├─alabaster.base::stageObject(vals, tmp, path = "stuff") at test-list.R:320:5
 2. └─alabaster.base::stageObject(vals, tmp, path = "stuff")
 3.   └─alabaster.base (local) .local(x, dir, path, child, ...)
 4.     └─base::gzfile(fpath, open = "wb")
── Error ('test-list.R:405:5'): we handle lists with minimum integers ──────────
Error in `gzfile(fpath, open = "wb")`: cannot open the connection
Backtrace:
    ▆
 1. ├─alabaster.base::stageObject(vals, tmp, path = "stuff") at test-list.R:405:5
 2. └─alabaster.base::stageObject(vals, tmp, path = "stuff")
 3.   └─alabaster.base (local) .local(x, dir, path, child, ...)
 4.     └─base::gzfile(fpath, open = "wb")
── Error ('test-list.R:444:5'): loaders work correctly from HDF5 with non-default placeholders ──
Error in `H5Fcreate(fpath, "H5F_ACC_TRUNC")`: HDF5. File accessibility. Unable to open file.
Backtrace:
    ▆
 1. ├─alabaster.base::stageObject(vals, tmp, path = "hstuff2") at test-list.R:444:5
 2. └─alabaster.base::stageObject(vals, tmp, path = "hstuff2")
 3.   └─alabaster.base (local) .local(x, dir, path, child, ...)
 4.     └─(function() {...
 5.       └─rhdf5::H5Fcreate(fpath, "H5F_ACC_TRUNC")
── Error ('test-list.R:477:5'): we handle the various float specials ───────────
Error in `gzfile(fpath, open = "wb")`: cannot open the connection
Backtrace:
    ▆
 1. ├─alabaster.base::saveObject(vals, tmp2) at test-list.R:477:5
 2. └─alabaster.base::saveObject(vals, tmp2)
 3.   └─alabaster.base (local) .local(x, path, ...)
 4.     └─base::gzfile(fpath, open = "wb")
── Error ('test-list.R:501:5'): we handle lists with NULLs ─────────────────────
Error in `gzfile(fpath, open = "wb")`: cannot open the connection
Backtrace:
    ▆
 1. ├─alabaster.base::stageObject(vals, tmp, path = "whee") at test-list.R:501:5
 2. └─alabaster.base::stageObject(vals, tmp, path = "whee")
 3.   └─alabaster.base (local) .local(x, dir, path, child, ...)
 4.     └─base::gzfile(fpath, open = "wb")
── Error ('test-list.R:543:5'): we handle lists with times ─────────────────────
Error in `gzfile(fpath, open = "wb")`: cannot open the connection
Backtrace:
    ▆
 1. ├─alabaster.base::stageObject(vals, tmp, path = "whee") at test-list.R:543:5
 2. └─alabaster.base::stageObject(vals, tmp, path = "whee")
 3.   └─alabaster.base (local) .local(x, dir, path, child, ...)
 4.     └─base::gzfile(fpath, open = "wb")
── Error ('test-list.R:602:5'): lists correctly distinguish between scalars and length-1 vectors ──
Error in `gzfile(fpath, open = "wb")`: cannot open the connection
Backtrace:
    ▆
 1. ├─alabaster.base::saveObject(ll, tmp) at test-list.R:602:5
 2. └─alabaster.base::saveObject(ll, tmp)
 3.   └─alabaster.base (local) .local(x, path, ...)
 4.     └─base::gzfile(fpath, open = "wb")
── Error ('test-list.R:657:5'): lists work correctly in legacy mode (JSON) ─────
Error in `gzfile(fpath, open = "wb")`: cannot open the connection
Backtrace:
    ▆
 1. ├─alabaster.base::stageObject(vals, tmp, path = "stuff", .version = 1) at test-list.R:657:5
 2. └─alabaster.base::stageObject(vals, tmp, path = "stuff", .version = 1)
 3.   └─alabaster.base (local) .local(x, dir, path, child, ...)
 4.     └─base::gzfile(fpath, open = "wb")
── Error ('test-list.R:670:5'): lists work correctly in legacy mode (HDF5) ─────
Error in `H5Fcreate(fpath, "H5F_ACC_TRUNC")`: HDF5. File accessibility. Unable to open file.
Backtrace:
    ▆
 1. ├─alabaster.base::stageObject(vals, tmp, path = "stuff", .version = 1) at test-list.R:670:5
 2. └─alabaster.base::stageObject(vals, tmp, path = "stuff", .version = 1)
 3.   └─alabaster.base (local) .local(x, dir, path, child, ...)
 4.     └─(function() {...
 5.       └─rhdf5::H5Fcreate(fpath, "H5F_ACC_TRUNC")
── Error ('test-list.R:697:5'): lists convert package versions to strings ──────
Error in `gzfile(fpath, open = "wb")`: cannot open the connection
Backtrace:
    ▆
 1. ├─alabaster.base::saveObject(vals, file.path(tmp, "gunk")) at test-list.R:697:5
 2. └─alabaster.base::saveObject(vals, file.path(tmp, "gunk"))
 3.   └─alabaster.base (local) .local(x, path, ...)
 4.     └─base::gzfile(fpath, open = "wb")
── Error ('test-list.R:711:5'): lists work in VLS mode ─────────────────────────
Error in `H5Fcreate(fpath, "H5F_ACC_TRUNC")`: HDF5. File accessibility. Unable to open file.
Backtrace:
    ▆
 1. ├─alabaster.base::saveObject(...) at test-list.R:711:5
 2. └─alabaster.base::saveObject(...)
 3.   └─alabaster.base (local) .local(x, path, ...)
 4.     └─rhdf5::H5Fcreate(fpath, "H5F_ACC_TRUNC")
── Error ('test-listDirectory.R:9:1'): (code run outside of `test_that()`) ─────
Error in `gzfile(path, "wb")`: cannot open the connection
Backtrace:
    ▆
 1. ├─alabaster.base::stageObject(df, tmp, path = "whee") at test-listDirectory.R:9:1
 2. └─alabaster.base::stageObject(df, tmp, path = "whee")
 3.   └─alabaster.base (local) .local(x, dir, path, child, ...)
 4.     └─alabaster.base::.quickWriteCsv(...)
 5.       └─alabaster.base::quickWriteCsv(...)
 6.         └─alabaster.base:::.quick_write_csv(...)
 7.           └─base::gzfile(path, "wb")
── Error ('test-listObjects.R:9:5'): listObjects works as expected ─────────────
Error in `H5Fcreate(ofile, "H5F_ACC_TRUNC")`: HDF5. File accessibility. Unable to open file.
Backtrace:
    ▆
 1. ├─alabaster.base::saveObject(df, file.path(tmp, "whee")) at test-listObjects.R:9:5
 2. └─alabaster.base::saveObject(df, file.path(tmp, "whee"))
 3.   └─alabaster.base (local) .local(x, path, ...)
 4.     └─alabaster.base:::.write_hdf5_new(...)
 5.       └─rhdf5::H5Fcreate(ofile, "H5F_ACC_TRUNC")
── Error ('test-read.csv.R:20:5'): read.csv3 handles the different types correctly ──
<std::runtime_error/C++Error/error/condition>
Error: CSV file is empty
Backtrace:
    ▆
 1. └─alabaster.base:::read.csv3(path, compression = "none", nrows = nrow(df)) at test-read.csv.R:20:5
 2.   └─alabaster.base:::load_csv(...)
── Error ('test-read.csv.R:40:5'): read.csv3 handles missing values correctly ──
<std::runtime_error/C++Error/error/condition>
Error: CSV file is empty
Backtrace:
    ▆
 1. └─alabaster.base:::read.csv3(path, compression = "none", nrows = nrow(df)) at test-read.csv.R:40:5
 2.   └─alabaster.base:::load_csv(...)
── Error ('test-validate.R:7:5'): validation registration works as expected ────
Error in `file(file, ifelse(append, "a", "w"))`: cannot open the connection
Backtrace:
    ▆
 1. └─alabaster.base::saveObjectFile(tmp, "foobar") at test-validate.R:7:5
 2.   └─base::write(...)
 3.     └─base::cat(...)
 4.       └─base::file(file, ifelse(append, "a", "w"))
── Error ('test-validate.R:29:5'): height registration works as expected ───────
Error in `H5Fcreate(ofile, "H5F_ACC_TRUNC")`: HDF5. File accessibility. Unable to open file.
Backtrace:
    ▆
 1. ├─alabaster.base::saveObject(X, tmp) at test-validate.R:29:5
 2. └─alabaster.base::saveObject(X, tmp)
 3.   └─alabaster.base (local) .local(x, path, ...)
 4.     └─alabaster.base:::.write_hdf5_new(...)
 5.       └─rhdf5::H5Fcreate(ofile, "H5F_ACC_TRUNC")
── Error ('test-validate.R:59:5'): conversion from R list to C++ JSON during validation works as expected ──
Error in `H5Fcreate(ofile, "H5F_ACC_TRUNC")`: HDF5. File accessibility. Unable to open file.
Backtrace:
    ▆
 1. ├─alabaster.base::saveObject(df, tmp) at test-validate.R:59:5
 2. └─alabaster.base::saveObject(df, tmp)
 3.   └─alabaster.base (local) .local(x, path, ...)
 4.     └─alabaster.base:::.write_hdf5_new(...)
 5.       └─rhdf5::H5Fcreate(ofile, "H5F_ACC_TRUNC")
── Error ('test-validate.R:80:5'): conversion from C++ JSON to R list during validation works as expected ──
Error in `file(file, ifelse(append, "a", "w"))`: cannot open the connection
Backtrace:
    ▆
 1. └─alabaster.base::saveObjectFile(tmp, "foobar", list(foobar = 3)) at test-validate.R:80:5
 2.   └─base::write(...)
 3.     └─base::cat(...)
 4.       └─base::file(file, ifelse(append, "a", "w"))
── Error ('test-validate.R:91:5'): interface registration works as expected ────
Error in `H5Fcreate(ofile, "H5F_ACC_TRUNC")`: HDF5. File accessibility. Unable to open file.
Backtrace:
    ▆
 1. ├─alabaster.base::saveObject(X, tmp) at test-validate.R:91:5
 2. └─alabaster.base::saveObject(X, tmp)
 3.   └─alabaster.base (local) .local(x, path, ...)
 4.     └─alabaster.base:::.write_hdf5_new(...)
 5.       └─rhdf5::H5Fcreate(ofile, "H5F_ACC_TRUNC")
── Error ('test-validateDirectory.R:17:5'): validateDirectory works as expected ──
Error in `value[[3L]](cond)`: failed to stage column 'Z'
  - cannot open the connection
Backtrace:
     ▆
  1. ├─alabaster.base::writeMetadata(stageObject(df, tmp, "foo"), tmp) at test-validateDirectory.R:17:5
  2. │ └─alabaster.base:::.strip_null_from_list(meta)
  3. │   └─base::logical(length(x))
  4. ├─alabaster.base::stageObject(df, tmp, "foo")
  5. └─alabaster.base::stageObject(df, tmp, "foo")
  6.   └─alabaster.base (local) .local(x, dir, path, child, ...)
  7.     └─alabaster.base:::.sanitize_df_columns(x, dir, path, .version.df)
  8.       └─base::tryCatch(...)
  9.         └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 10.           └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 11.             └─value[[3L]](cond)
── Error ('test-validateDirectory.R:31:5'): validateDirectory works as expected in the new world ──
Error in `H5Fcreate(ofile, "H5F_ACC_TRUNC")`: HDF5. File accessibility. Unable to open file.
Backtrace:
    ▆
 1. ├─alabaster.base::saveObject(df, file.path(tmp, "foo")) at test-validateDirectory.R:31:5
 2. └─alabaster.base::saveObject(df, file.path(tmp, "foo"))
 3.   └─alabaster.base (local) .local(x, path, ...)
 4.     └─alabaster.base:::.write_hdf5_new(...)
 5.       └─rhdf5::H5Fcreate(ofile, "H5F_ACC_TRUNC")
── Error ('test-validateDirectory.R:41:5'): validateDirectory throws with invalid metadata ──
Error in `value[[3L]](cond)`: failed to stage column 'Z'
  - cannot open the connection
Backtrace:
    ▆
 1. ├─alabaster.base::stageObject(df, tmp, "foo") at test-validateDirectory.R:41:5
 2. └─alabaster.base::stageObject(df, tmp, "foo")
 3.   └─alabaster.base (local) .local(x, dir, path, child, ...)
 4.     └─alabaster.base:::.sanitize_df_columns(x, dir, path, .version.df)
 5.       └─base::tryCatch(...)
 6.         └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 7.           └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 8.             └─value[[3L]](cond)
── Error ('test-validateDirectory.R:54:5'): validateDirectory throws with invalid objects ──
Error in `value[[3L]](cond)`: failed to stage column 'Z'
  - cannot open the connection
Backtrace:
    ▆
 1. ├─alabaster.base::stageObject(df, tmp, "foo") at test-validateDirectory.R:54:5
 2. └─alabaster.base::stageObject(df, tmp, "foo")
 3.   └─alabaster.base (local) .local(x, dir, path, child, ...)
 4.     └─alabaster.base:::.sanitize_df_columns(x, dir, path, .version.df)
 5.       └─base::tryCatch(...)
 6.         └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 7.           └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 8.             └─value[[3L]](cond)
── Error ('test-validateDirectory.R:67:5'): validateDirectory throws in the new world ──
Error in `H5Fcreate(ofile, "H5F_ACC_TRUNC")`: HDF5. File accessibility. Unable to open file.
Backtrace:
    ▆
 1. ├─alabaster.base::saveObject(df, file.path(tmp, "foo")) at test-validateDirectory.R:67:5
 2. └─alabaster.base::saveObject(df, file.path(tmp, "foo"))
 3.   └─alabaster.base (local) .local(x, path, ...)
 4.     └─alabaster.base:::.write_hdf5_new(...)
 5.       └─rhdf5::H5Fcreate(ofile, "H5F_ACC_TRUNC")
── Error ('test-validateDirectory.R:80:9'): validateDirectory throws with inconsistent paths ──
Error in `value[[3L]](cond)`: failed to stage column 'Z'
  - cannot open the connection
Backtrace:
     ▆
  1. ├─alabaster.base::writeMetadata(stageObject(df, tmp, "foo"), tmp) at test-validateDirectory.R:80:9
  2. │ └─alabaster.base:::.strip_null_from_list(meta)
  3. │   └─base::logical(length(x))
  4. ├─alabaster.base::stageObject(df, tmp, "foo")
  5. └─alabaster.base::stageObject(df, tmp, "foo")
  6.   └─alabaster.base (local) .local(x, dir, path, child, ...)
  7.     └─alabaster.base:::.sanitize_df_columns(x, dir, path, .version.df)
  8.       └─base::tryCatch(...)
  9.         └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 10.           └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 11.             └─value[[3L]](cond)
── Error ('test-validateDirectory.R:103:9'): validateDirectory throws with non-nested children ──
Error in `value[[3L]](cond)`: failed to stage column 'Z'
  - cannot open the connection
Backtrace:
    ▆
 1. ├─alabaster.base::stageObject(df, tmp, "foo") at test-validateDirectory.R:103:9
 2. └─alabaster.base::stageObject(df, tmp, "foo")
 3.   └─alabaster.base (local) .local(x, dir, path, child, ...)
 4.     └─alabaster.base:::.sanitize_df_columns(x, dir, path, .version.df)
 5.       └─base::tryCatch(...)
 6.         └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 7.           └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 8.             └─value[[3L]](cond)
── Error ('test-validateDirectory.R:138:5'): validateDirectory throws with non-child references ──
Error in `value[[3L]](cond)`: failed to stage column 'Z'
  - cannot open the connection
Backtrace:
    ▆
 1. ├─alabaster.base::stageObject(df, tmp, "foo") at test-validateDirectory.R:138:5
 2. └─alabaster.base::stageObject(df, tmp, "foo")
 3.   └─alabaster.base (local) .local(x, dir, path, child, ...)
 4.     └─alabaster.base:::.sanitize_df_columns(x, dir, path, .version.df)
 5.       └─base::tryCatch(...)
 6.         └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 7.           └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 8.             └─value[[3L]](cond)
── Error ('test-validateDirectory.R:152:5'): validateDirectory throws with multiple child references ──
Error in `value[[3L]](cond)`: failed to stage column 'Z'
  - cannot open the connection
Backtrace:
    ▆
 1. ├─alabaster.base::stageObject(df, tmp, "foo") at test-validateDirectory.R:152:5
 2. └─alabaster.base::stageObject(df, tmp, "foo")
 3.   └─alabaster.base (local) .local(x, dir, path, child, ...)
 4.     └─alabaster.base:::.sanitize_df_columns(x, dir, path, .version.df)
 5.       └─base::tryCatch(...)
 6.         └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 7.           └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 8.             └─value[[3L]](cond)
── Error ('test-validateDirectory.R:163:5'): validateDirectory throws with missing child object ──
Error in `value[[3L]](cond)`: failed to stage column 'Z'
  - cannot open the connection
Backtrace:
    ▆
 1. ├─alabaster.base::stageObject(df, tmp, "foo") at test-validateDirectory.R:163:5
 2. └─alabaster.base::stageObject(df, tmp, "foo")
 3.   └─alabaster.base (local) .local(x, dir, path, child, ...)
 4.     └─alabaster.base:::.sanitize_df_columns(x, dir, path, .version.df)
 5.       └─base::tryCatch(...)
 6.         └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 7.           └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 8.             └─value[[3L]](cond)
── Error ('test-validateDirectory.R:174:5'): validateDirectory throws with extra child object ──
Error in `value[[3L]](cond)`: failed to stage column 'Z'
  - cannot open the connection
Backtrace:
    ▆
 1. ├─alabaster.base::stageObject(df, tmp, "foo") at test-validateDirectory.R:174:5
 2. └─alabaster.base::stageObject(df, tmp, "foo")
 3.   └─alabaster.base (local) .local(x, dir, path, child, ...)
 4.     └─alabaster.base:::.sanitize_df_columns(x, dir, path, .version.df)
 5.       └─base::tryCatch(...)
 6.         └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 7.           └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 8.             └─value[[3L]](cond)
── Error ('test-validateDirectory.R:185:5'): validateDirectory throws with nested non-child object ──
Error in `value[[3L]](cond)`: failed to stage column 'Z'
  - cannot open the connection
Backtrace:
    ▆
 1. ├─alabaster.base::stageObject(df, tmp, "foo") at test-validateDirectory.R:185:5
 2. └─alabaster.base::stageObject(df, tmp, "foo")
 3.   └─alabaster.base (local) .local(x, dir, path, child, ...)
 4.     └─alabaster.base:::.sanitize_df_columns(x, dir, path, .version.df)
 5.       └─base::tryCatch(...)
 6.         └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 7.           └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 8.             └─value[[3L]](cond)
── Error ('test-validateDirectory.R:201:5'): validateDirectory throws with random extra objects ──
Error in `value[[3L]](cond)`: failed to stage column 'Z'
  - cannot open the connection
Backtrace:
    ▆
 1. ├─alabaster.base::stageObject(df, tmp, "foo") at test-validateDirectory.R:201:5
 2. └─alabaster.base::stageObject(df, tmp, "foo")
 3.   └─alabaster.base (local) .local(x, dir, path, child, ...)
 4.     └─alabaster.base:::.sanitize_df_columns(x, dir, path, .version.df)
 5.       └─base::tryCatch(...)
 6.         └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 7.           └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 8.             └─value[[3L]](cond)
── Error ('test-validateDirectory.R:214:9'): validateDirectory handles redirects correctly ──
Error in `value[[3L]](cond)`: failed to stage column 'Z'
  - cannot open the connection
Backtrace:
     ▆
  1. ├─alabaster.base::writeMetadata(stageObject(df, tmp, "foo"), tmp) at test-validateDirectory.R:214:9
  2. │ └─alabaster.base:::.strip_null_from_list(meta)
  3. │   └─base::logical(length(x))
  4. ├─alabaster.base::stageObject(df, tmp, "foo")
  5. └─alabaster.base::stageObject(df, tmp, "foo")
  6.   └─alabaster.base (local) .local(x, dir, path, child, ...)
  7.     └─alabaster.base:::.sanitize_df_columns(x, dir, path, .version.df)
  8.       └─base::tryCatch(...)
  9.         └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 10.           └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 11.             └─value[[3L]](cond)
── Error ('test-vector.R:9:5'): vectors work correctly without names ───────────
Error in `gzfile(path, "wb")`: cannot open the connection
Backtrace:
    ▆
 1. ├─alabaster.base::stageObject(input, tmp, path = "foo") at test-vector.R:9:5
 2. └─alabaster.base::stageObject(input, tmp, path = "foo")
 3.   └─alabaster.base::quickWriteCsv(...)
 4.     └─alabaster.base:::.quick_write_csv(...)
 5.       └─base::gzfile(path, "wb")
── Error ('test-vector.R:52:5'): vectors work correctly without names in the new world ──
Error in `H5Fcreate(ofile, "H5F_ACC_TRUNC")`: HDF5. File accessibility. Unable to open file.
Backtrace:
    ▆
 1. ├─alabaster.base::saveObject(input, file.path(tmp, "foo")) at test-vector.R:52:5
 2. └─alabaster.base::saveObject(input, file.path(tmp, "foo"))
 3.   └─alabaster.base (local) .local(x, path, ...)
 4.     └─rhdf5::H5Fcreate(ofile, "H5F_ACC_TRUNC")

[ FAIL 41 | WARN 135 | SKIP 0 | PASS 546 ]
Error: Test failures
Execution halted

 *** caught segfault ***
address 0x558, cause 'memory not mapped'
An irrecoverable exception occurred. R is aborting now ...
Segmentation fault (core dumped)