Multiple platform build/check report for BioC 3.21 - INSTALL results for alabaster.base on palomino7

Hostname	OS	Arch (*)	R version	Installed pkgs
palomino7	Windows Server 2022 Datacenter	x64	R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences"	4545
lconway	macOS 12.7.1 Monterey	x86_64	R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences"	4576
kjohnson3	macOS 13.7.1 Ventura	arm64	R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences"	4528
kunpeng2	Linux (openEuler 24.03 LTS)	aarch64	R 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*

INSTALL results for alabaster.base on palomino7

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.

raw results

Summary

Package: alabaster.base

Version: 1.7.8

Command: E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL alabaster.base

StartedAt: 2025-03-16 15:42:19 -0400 (Sun, 16 Mar 2025)

EndedAt: 2025-03-16 15:45:48 -0400 (Sun, 16 Mar 2025)

EllapsedTime: 208.4 seconds

RetCode: 0

Status: OK

Command output

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### Running command:
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###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL alabaster.base
###
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* installing to library 'E:/biocbuild/bbs-3.21-bioc/R/library'
* installing *source* package 'alabaster.base' ...
** this is package 'alabaster.base' version '1.7.8'
** using staged installation
** libs
using C++ compiler: 'G__~1.EXE (GCC) 14.2.0'
using C++17
g++  -std=gnu++17 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I../inst/include -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/assorthead/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c RcppExports.cpp -o RcppExports.o
g++  -std=gnu++17 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I../inst/include -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/assorthead/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c check_csv.cpp -o check_csv.o
g++  -std=gnu++17 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I../inst/include -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/assorthead/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c check_list.cpp -o check_list.o
g++  -std=gnu++17 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I../inst/include -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/assorthead/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c choose_numeric_missing_placeholder.cpp -o choose_numeric_missing_placeholder.o
g++  -std=gnu++17 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I../inst/include -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/assorthead/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c is_rfc3339.cpp -o is_rfc3339.o
g++  -std=gnu++17 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I../inst/include -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/assorthead/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c load_csv.cpp -o load_csv.o
g++  -std=gnu++17 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I../inst/include -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/assorthead/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c load_list.cpp -o load_list.o
g++  -std=gnu++17 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I../inst/include -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/assorthead/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c validate.cpp -o validate.o
In file included from E:/biocbuild/bbs-3.21-bioc/R/library/assorthead/include/takane/_validate.hpp:12,
                 from E:/biocbuild/bbs-3.21-bioc/R/library/assorthead/include/takane/takane.hpp:4,
                 from validate.cpp:2:
E:/biocbuild/bbs-3.21-bioc/R/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&)':
E:/biocbuild/bbs-3.21-bioc/R/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");
      |                 ^~~~~~~
E:/biocbuild/bbs-3.21-bioc/R/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 E:/biocbuild/bbs-3.21-bioc/R/library/assorthead/include/takane/_validate.hpp:22:
E:/biocbuild/bbs-3.21-bioc/R/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&)':
E:/biocbuild/bbs-3.21-bioc/R/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");
      |                 ^~~~~
E:/biocbuild/bbs-3.21-bioc/R/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");
      |                         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
E:/biocbuild/bbs-3.21-bioc/R/library/assorthead/include/takane/summarized_experiment.hpp: In function 'std::vector<long long unsigned int> takane::summarized_experiment::dimensions(const std::filesystem::__cxx11::path&, const takane::ObjectMetadata&, takane::Options&)':
E:/biocbuild/bbs-3.21-bioc/R/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");
      |                 ^~~~~
E:/biocbuild/bbs-3.21-bioc/R/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 E:/biocbuild/bbs-3.21-bioc/R/library/assorthead/include/takane/_validate.hpp:27:
E:/biocbuild/bbs-3.21-bioc/R/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&)':
E:/biocbuild/bbs-3.21-bioc/R/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");
      |                 ^~~
E:/biocbuild/bbs-3.21-bioc/R/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 E:/biocbuild/bbs-3.21-bioc/R/library/assorthead/include/takane/_validate.hpp:40:
E:/biocbuild/bbs-3.21-bioc/R/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&)':
E:/biocbuild/bbs-3.21-bioc/R/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");
      |                 ^~~~~~
E:/biocbuild/bbs-3.21-bioc/R/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");
      |                          ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
E:/biocbuild/bbs-3.21-bioc/R/library/assorthead/include/takane/vcf_experiment.hpp: In function 'std::vector<long long unsigned int> takane::vcf_experiment::dimensions(const std::filesystem::__cxx11::path&, const takane::ObjectMetadata&, takane::Options&)':
E:/biocbuild/bbs-3.21-bioc/R/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");
      |                 ^~~~~~
E:/biocbuild/bbs-3.21-bioc/R/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 E:/biocbuild/bbs-3.21-bioc/R/library/assorthead/include/chihaya/validate.hpp:13,
                 from E:/biocbuild/bbs-3.21-bioc/R/library/assorthead/include/chihaya/chihaya.hpp:10,
                 from E:/biocbuild/bbs-3.21-bioc/R/library/assorthead/include/takane/utils_public.hpp:13,
                 from E:/biocbuild/bbs-3.21-bioc/R/library/assorthead/include/takane/_validate.hpp:9:
E:/biocbuild/bbs-3.21-bioc/R/library/assorthead/include/chihaya/sparse_matrix.hpp: In function 'void chihaya::sparse_matrix::internal::validate_indices(const H5::DataSet&, const std::vector<long long unsigned int>&, size_t, size_t, bool) [with Index_ = int]':
E:/biocbuild/bbs-3.21-bioc/R/library/assorthead/include/chihaya/sparse_matrix.hpp:51:32: warning: 'previous' may be used uninitialized [-Wmaybe-uninitialized]
   51 |             if (x > start && i <= previous) {
      |                              ~~^~~~~~~~~~~
E:/biocbuild/bbs-3.21-bioc/R/library/assorthead/include/chihaya/sparse_matrix.hpp:45:16: note: 'previous' was declared here
   45 |         Index_ previous;
      |                ^~~~~~~~
E:/biocbuild/bbs-3.21-bioc/R/library/assorthead/include/chihaya/sparse_matrix.hpp: In function 'void chihaya::sparse_matrix::internal::validate_indices(const H5::DataSet&, const std::vector<long long unsigned int>&, size_t, size_t, bool) [with Index_ = long long unsigned int]':
E:/biocbuild/bbs-3.21-bioc/R/library/assorthead/include/chihaya/sparse_matrix.hpp:51:32: warning: 'previous' may be used uninitialized [-Wmaybe-uninitialized]
   51 |             if (x > start && i <= previous) {
      |                              ~~^~~~~~~~~~~
E:/biocbuild/bbs-3.21-bioc/R/library/assorthead/include/chihaya/sparse_matrix.hpp:45:16: note: 'previous' was declared here
   45 |         Index_ previous;
      |                ^~~~~~~~
g++  -std=gnu++17 -I"E:/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I../inst/include -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rcpp/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/assorthead/include' -I'E:/biocbuild/bbs-3.21-bioc/R/library/Rhdf5lib/include'   -I"C:/rtools45/x86_64-w64-mingw32.static.posix/include"      -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign    -c vls.cpp -o vls.o
g++ -shared -s -static-libgcc -o alabaster.base.dll tmp.def 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 -LE:/biocbuild/bbs-3.21-bioc/R/library/Rhdf5lib/lib/x64-ucrt -lhdf5_cpp -lhdf5 -lcurl -lssh2 -lssl -lcrypto -lwldap32 -lws2_32 -lcrypt32 -lsz -laec -lz -lpsapi -lz -LC:/rtools45/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools45/x86_64-w64-mingw32.static.posix/lib -LE:/biocbuild/bbs-3.21-bioc/R/bin/x64 -lR
installing to E:/biocbuild/bbs-3.21-bioc/R/library/00LOCK-alabaster.base/00new/alabaster.base/libs/x64
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (alabaster.base)