Back to Multiple platform build/check report for BioC 3.21:   simplified   long
[A]BCDEFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2025-03-17 11:41 -0400 (Mon, 17 Mar 2025).

HostnameOSArch (*)R versionInstalled pkgs
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences" 4545
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" 4576
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" 4528
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4459
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 41/2313HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
alabaster.base 1.7.8  (landing page)
Aaron Lun
Snapshot Date: 2025-03-16 13:40 -0400 (Sun, 16 Mar 2025)
git_url: https://git.bioconductor.org/packages/alabaster.base
git_branch: devel
git_last_commit: 1677a4d
git_last_commit_date: 2025-03-05 01:55:08 -0400 (Wed, 05 Mar 2025)
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    WARNINGS  


CHECK results for alabaster.base on kunpeng2

To the developers/maintainers of the alabaster.base package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/alabaster.base.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: alabaster.base
Version: 1.7.8
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:alabaster.base.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings alabaster.base_1.7.8.tar.gz
StartedAt: 2025-03-17 03:43:24 -0000 (Mon, 17 Mar 2025)
EndedAt: 2025-03-17 03:46:37 -0000 (Mon, 17 Mar 2025)
EllapsedTime: 192.4 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: alabaster.base.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:alabaster.base.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings alabaster.base_1.7.8.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/alabaster.base.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* 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: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
* checking C++ specification ... OK
* checking installed package size ... INFO
  installed size is 35.4Mb
  sub-directories of 1Mb or more:
    libs  34.9Mb
* 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 ‘/home/biocbuild/R/R-devel_2025-02-19/site-library/alabaster.base/libs/alabaster.base.so’:
  Found ‘_ZSt4cerr’, possibly from ‘std::cerr’ (C++)
  Found ‘abort’, possibly from ‘abort’ (C)
  Found ‘exit’, possibly from ‘exit’ (C)
  Found ‘rand_r’, possibly from ‘rand_r’ (C)
  Found ‘sprintf’, possibly from ‘sprintf’ (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’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/alabaster.base.Rcheck/00check.log’
for details.


Installation output

alabaster.base.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL alabaster.base
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-library’
* installing *source* package ‘alabaster.base’ ...
** this is package ‘alabaster.base’ version ‘1.7.8’
** using staged installation
** libs
using C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
using C++17
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -I../inst/include -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rhdf5lib/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c RcppExports.cpp -o RcppExports.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -I../inst/include -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rhdf5lib/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c check_csv.cpp -o check_csv.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -I../inst/include -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rhdf5lib/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c check_list.cpp -o check_list.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -I../inst/include -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rhdf5lib/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c choose_numeric_missing_placeholder.cpp -o choose_numeric_missing_placeholder.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -I../inst/include -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rhdf5lib/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c is_rfc3339.cpp -o is_rfc3339.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -I../inst/include -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rhdf5lib/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c load_csv.cpp -o load_csv.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -I../inst/include -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rhdf5lib/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c load_list.cpp -o load_list.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -I../inst/include -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rhdf5lib/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c validate.cpp -o validate.o
In file included from /home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/takane/_validate.hpp:12,
                 from /home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/takane/takane.hpp:4,
                 from validate.cpp:2:
/home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/takane/simple_list.hpp: In function ‘size_t takane::simple_list::height(const std::filesystem::__cxx11::path&, const takane::ObjectMetadata&, takane::Options&)’:
/home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/takane/simple_list.hpp:145:17: warning: possibly dangling reference to a temporary [-Wdangling-reference]
  145 |     const auto& metamap = internal_json::extract_typed_object_from_metadata(metadata.other, "simple_list");
      |                 ^~~~~~~
/home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/takane/simple_list.hpp:145:76: note: the temporary was destroyed at the end of the full expression ‘takane::internal_json::extract_typed_object_from_metadata(metadata.takane::ObjectMetadata::other, std::__cxx11::basic_string<char>(((const char*)"simple_list"), std::allocator<char>()))’
  145 |     const auto& metamap = internal_json::extract_typed_object_from_metadata(metadata.other, "simple_list");
      |                           ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/takane/_validate.hpp:22:
/home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/takane/summarized_experiment.hpp: In function ‘size_t takane::summarized_experiment::height(const std::filesystem::__cxx11::path&, const takane::ObjectMetadata&, takane::Options&)’:
/home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/takane/summarized_experiment.hpp:124:17: warning: possibly dangling reference to a temporary [-Wdangling-reference]
  124 |     const auto& semap = internal_json::extract_object(metadata.other, "summarized_experiment");
      |                 ^~~~~
/home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/takane/summarized_experiment.hpp:124:54: note: the temporary was destroyed at the end of the full expression ‘takane::internal_json::extract_object(metadata.takane::ObjectMetadata::other, std::__cxx11::basic_string<char>(((const char*)"summarized_experiment"), std::allocator<char>()))’
  124 |     const auto& semap = internal_json::extract_object(metadata.other, "summarized_experiment");
      |                         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/takane/summarized_experiment.hpp: In function ‘std::vector<long unsigned int> takane::summarized_experiment::dimensions(const std::filesystem::__cxx11::path&, const takane::ObjectMetadata&, takane::Options&)’:
/home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/takane/summarized_experiment.hpp:137:17: warning: possibly dangling reference to a temporary [-Wdangling-reference]
  137 |     const auto& semap = internal_json::extract_object(metadata.other, "summarized_experiment");
      |                 ^~~~~
/home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/takane/summarized_experiment.hpp:137:54: note: the temporary was destroyed at the end of the full expression ‘takane::internal_json::extract_object(metadata.takane::ObjectMetadata::other, std::__cxx11::basic_string<char>(((const char*)"summarized_experiment"), std::allocator<char>()))’
  137 |     const auto& semap = internal_json::extract_object(metadata.other, "summarized_experiment");
      |                         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/takane/_validate.hpp:27:
/home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/takane/sequence_string_set.hpp: In function ‘size_t takane::sequence_string_set::height(const std::filesystem::__cxx11::path&, const takane::ObjectMetadata&, takane::Options&)’:
/home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/takane/sequence_string_set.hpp:366:17: warning: possibly dangling reference to a temporary [-Wdangling-reference]
  366 |     const auto& obj = internal_json::extract_typed_object_from_metadata(metadata.other, "sequence_string_set");
      |                 ^~~
/home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/takane/sequence_string_set.hpp:366:72: note: the temporary was destroyed at the end of the full expression ‘takane::internal_json::extract_typed_object_from_metadata(metadata.takane::ObjectMetadata::other, std::__cxx11::basic_string<char>(((const char*)"sequence_string_set"), std::allocator<char>()))’
  366 |     const auto& obj = internal_json::extract_typed_object_from_metadata(metadata.other, "sequence_string_set");
      |                       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/takane/_validate.hpp:40:
/home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/takane/vcf_experiment.hpp: In function ‘size_t takane::vcf_experiment::height(const std::filesystem::__cxx11::path&, const takane::ObjectMetadata&, takane::Options&)’:
/home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/takane/vcf_experiment.hpp:241:17: warning: possibly dangling reference to a temporary [-Wdangling-reference]
  241 |     const auto& vcfmap = internal_json::extract_typed_object_from_metadata(metadata.other, "vcf_experiment");
      |                 ^~~~~~
/home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/takane/vcf_experiment.hpp:241:75: note: the temporary was destroyed at the end of the full expression ‘takane::internal_json::extract_typed_object_from_metadata(metadata.takane::ObjectMetadata::other, std::__cxx11::basic_string<char>(((const char*)"vcf_experiment"), std::allocator<char>()))’
  241 |     const auto& vcfmap = internal_json::extract_typed_object_from_metadata(metadata.other, "vcf_experiment");
      |                          ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/takane/vcf_experiment.hpp: In function ‘std::vector<long unsigned int> takane::vcf_experiment::dimensions(const std::filesystem::__cxx11::path&, const takane::ObjectMetadata&, takane::Options&)’:
/home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/takane/vcf_experiment.hpp:253:17: warning: possibly dangling reference to a temporary [-Wdangling-reference]
  253 |     const auto& vcfmap = internal_json::extract_typed_object_from_metadata(metadata.other, "vcf_experiment");
      |                 ^~~~~~
/home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/takane/vcf_experiment.hpp:253:75: note: the temporary was destroyed at the end of the full expression ‘takane::internal_json::extract_typed_object_from_metadata(metadata.takane::ObjectMetadata::other, std::__cxx11::basic_string<char>(((const char*)"vcf_experiment"), std::allocator<char>()))’
  253 |     const auto& vcfmap = internal_json::extract_typed_object_from_metadata(metadata.other, "vcf_experiment");
      |                          ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/chihaya/validate.hpp:13,
                 from /home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/chihaya/chihaya.hpp:10,
                 from /home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/takane/utils_public.hpp:13,
                 from /home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/takane/_validate.hpp:9:
/home/biocbuild/R/R-devel_2025-02-19/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]’:
/home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/chihaya/sparse_matrix.hpp:51:32: warning: ‘previous’ may be used uninitialized [-Wmaybe-uninitialized]
   51 |             if (x > start && i <= previous) {
      |                              ~~^~~~~~~~~~~
/home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/chihaya/sparse_matrix.hpp:45:16: note: ‘previous’ was declared here
   45 |         Index_ previous;
      |                ^~~~~~~~
/home/biocbuild/R/R-devel_2025-02-19/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]’:
/home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/chihaya/sparse_matrix.hpp:51:32: warning: ‘previous’ may be used uninitialized [-Wmaybe-uninitialized]
   51 |             if (x > start && i <= previous) {
      |                              ~~^~~~~~~~~~~
/home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/chihaya/sparse_matrix.hpp:45:16: note: ‘previous’ was declared here
   45 |         Index_ previous;
      |                ^~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -I../inst/include -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rhdf5lib/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c vls.cpp -o vls.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -shared -L/home/biocbuild/R/R/lib -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 /home/biocbuild/R/R-devel_2025-02-19/site-library/Rhdf5lib/lib/libhdf5_cpp.a /home/biocbuild/R/R-devel_2025-02-19/site-library/Rhdf5lib/lib/libhdf5.a -L/home/biocbuild/R/R-devel_2025-02-19/site-library/Rhdf5lib/lib -lcrypto -lcurl -lsz -laec -lz -ldl -lm -lz -L/home/biocbuild/R/R/lib -lR
installing to /home/biocbuild/R/R-devel_2025-02-19/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)

Tests output

alabaster.base.Rcheck/tests/testthat.Rout

R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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 0 | WARN 0 | SKIP 0 | PASS 725 ]
> 
> proc.time()
   user  system elapsed 
 96.067   2.151 110.724 

Example timings

alabaster.base.Rcheck/alabaster.base-Ex.timings

nameusersystemelapsed
Rfc33390.0040.0000.008
absolutizePath0.0010.0000.001
acquireFile0.7680.0301.439
altReadObject0.1270.0080.501
altSaveObject0.0950.0000.180
anyMissing0.0010.0000.000
chooseMissingPlaceholderForHdf50.0020.0000.001
cloneDirectory0.0020.0000.001
createDedupSession0.0640.0000.064
createRedirection0.6460.0460.877
getSaveEnvironment0.0230.0000.023
listObjects0.1450.0040.149
loadDirectory1.2090.0291.712
moveObject1.3590.0091.470
quickLoadObject1.1650.0281.560
quickReadCsv0.0650.0000.140
readAtomicVector0.0290.0000.057
readBaseFactor0.0290.0000.062
readBaseList0.1480.0040.237
readDataFrame0.0880.0000.090
readDataFrameFactor0.2730.0000.273
readObject0.1080.0120.120
readObjectFile0.0000.0020.001
removeObject1.0610.0341.093
saveAtomicVector0.0880.0000.180
saveBaseFactor0.0210.0000.041
saveBaseList0.0720.0000.072
saveDataFrameFactor0.1410.0000.141
saveFormats0.0010.0000.000
saveObject0.0800.0000.081
stageDataFrame0.0770.0000.077
transformVectorForHdf50.0010.0000.001
validateDirectory0.1260.0000.136
validateObject0.0870.0000.173
writeMetadata0.3550.0120.430