Aaron Lun
| Snapshot Date: 2025-10-13 13:40 -0400 (Mon, 13 Oct 2025) |
| git_url: https://git.bioconductor.org/packages/alabaster.base |
| git_branch: RELEASE_3_21 |
| git_last_commit: 7f04096 |
| git_last_commit_date: 2025-06-04 13:56:00 -0400 (Wed, 04 Jun 2025) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-10-16 11:41 -0400 (Thu, 16 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4833 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4614 |
| kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4555 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4586 |
| 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 41/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| alabaster.base 1.8.1 (landing page) Aaron Lun
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| merida1 | macOS 12.7.6 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson1 | macOS 13.7.5 Ventura / arm64 | OK | OK | WARNINGS | OK | | ||||||||
| kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | WARNINGS | ||||||||||
|
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. |
| Package: alabaster.base |
| Version: 1.8.1 |
| Command: /home/biocbuild/R/R/bin/R CMD INSTALL alabaster.base |
| StartedAt: 2025-10-13 20:25:25 -0000 (Mon, 13 Oct 2025) |
| EndedAt: 2025-10-13 20:27:48 -0000 (Mon, 13 Oct 2025) |
| EllapsedTime: 143.1 seconds |
| RetCode: 0 |
| Status: OK |
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### Running command:
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### /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)