##############################################################################
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###
### 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_1.8.1.tar.gz
###
##############################################################################
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* 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 ‘1.8.1’
* 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.

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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL alabaster.base
###
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* installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-library’
* installing *source* package ‘alabaster.base’ ...
** this is package ‘alabaster.base’ version ‘1.8.1’
** 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 -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)

R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

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Type 'license()' or 'licence()' for distribution details.

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> library(testthat)
> library(alabaster.base)
> test_check("alabaster.base")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 732 ]
> 
> proc.time()
   user  system elapsed 
 96.675   2.534 115.247