Aaron Lun
| Snapshot Date: 2026-04-17 13:40 -0400 (Fri, 17 Apr 2026) |
| git_url: https://git.bioconductor.org/packages/scrapper |
| git_branch: devel |
| git_last_commit: 8a77890 |
| git_last_commit_date: 2026-04-17 00:29:31 -0400 (Fri, 17 Apr 2026) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-04-18 11:37 -0400 (Sat, 18 Apr 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) | x86_64 | 4.6.0 alpha (2026-04-05 r89794) | 4957 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.6.0 alpha (2026-04-08 r89818) | 4686 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4627 |
| 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 1983/2404 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| scrapper 1.5.18 (landing page) Aaron Lun
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | WARNINGS | OK | | ||||||||
| kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | ERROR | skipped | ||||||||||
| See other builds for scrapper in R Universe. | ||||||||||||||
|
To the developers/maintainers of the scrapper package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/scrapper.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: scrapper |
| Version: 1.5.17 |
| Command: /home/biocbuild/R/R/bin/R CMD INSTALL scrapper |
| StartedAt: 2026-04-16 20:42:32 -0000 (Thu, 16 Apr 2026) |
| EndedAt: 2026-04-16 20:50:28 -0000 (Thu, 16 Apr 2026) |
| EllapsedTime: 475.7 seconds |
| RetCode: 0 |
| Status: OK |
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### Running command:
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### /home/biocbuild/R/R/bin/R CMD INSTALL scrapper
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* installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-library’
* installing *source* package ‘scrapper’ ...
** this is package ‘scrapper’ version ‘1.5.17’
** 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'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rigraphlib/igraph/include/igraph' -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/beachmat/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/BiocNeighbors/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rigraphlib/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'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rigraphlib/igraph/include/igraph' -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/beachmat/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/BiocNeighbors/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rigraphlib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c adt_quality_control.cpp -o adt_quality_control.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'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rigraphlib/igraph/include/igraph' -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/beachmat/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/BiocNeighbors/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rigraphlib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c aggregate_across_cells.cpp -o aggregate_across_cells.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'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rigraphlib/igraph/include/igraph' -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/beachmat/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/BiocNeighbors/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rigraphlib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c aggregate_across_genes.cpp -o aggregate_across_genes.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'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rigraphlib/igraph/include/igraph' -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/beachmat/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/BiocNeighbors/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rigraphlib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c build_snn_graph.cpp -o build_snn_graph.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'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rigraphlib/igraph/include/igraph' -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/beachmat/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/BiocNeighbors/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rigraphlib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c center_size_factors.cpp -o center_size_factors.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'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rigraphlib/igraph/include/igraph' -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/beachmat/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/BiocNeighbors/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rigraphlib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c choose_highly_variable_genes.cpp -o choose_highly_variable_genes.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'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rigraphlib/igraph/include/igraph' -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/beachmat/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/BiocNeighbors/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rigraphlib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c choose_pseudo_count.cpp -o choose_pseudo_count.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'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rigraphlib/igraph/include/igraph' -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/beachmat/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/BiocNeighbors/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rigraphlib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c cluster_graph.cpp -o cluster_graph.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'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rigraphlib/igraph/include/igraph' -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/beachmat/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/BiocNeighbors/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rigraphlib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c cluster_kmeans.cpp -o cluster_kmeans.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'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rigraphlib/igraph/include/igraph' -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/beachmat/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/BiocNeighbors/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rigraphlib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c combine_factors.cpp -o combine_factors.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'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rigraphlib/igraph/include/igraph' -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/beachmat/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/BiocNeighbors/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rigraphlib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c compute_block_weights.cpp -o compute_block_weights.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'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rigraphlib/igraph/include/igraph' -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/beachmat/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/BiocNeighbors/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rigraphlib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c compute_clrm1_factors.cpp -o compute_clrm1_factors.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'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rigraphlib/igraph/include/igraph' -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/beachmat/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/BiocNeighbors/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rigraphlib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c correct_mnn.cpp -o correct_mnn.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'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rigraphlib/igraph/include/igraph' -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/beachmat/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/BiocNeighbors/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rigraphlib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c crispr_quality_control.cpp -o crispr_quality_control.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'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rigraphlib/igraph/include/igraph' -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/beachmat/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/BiocNeighbors/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rigraphlib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c fit_variance_trend.cpp -o fit_variance_trend.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'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rigraphlib/igraph/include/igraph' -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/beachmat/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/BiocNeighbors/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rigraphlib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c model_gene_variances.cpp -o model_gene_variances.o
In file included from /home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/tatami_stats/grouped_variances.hpp:5,
from /home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/tatami_stats/tatami_stats.hpp:7,
from /home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/scran_variances/model_gene_variances.hpp:10,
from /home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/scran_variances/scran_variances.hpp:5,
from model_gene_variances.cpp:7:
/home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/tatami_stats/variances.hpp: In instantiation of ‘std::pair<_FIter, _FIter> tatami_stats::variances::direct(const Value_*, Index_, Index_, bool) [with Output_ = double; Value_ = double; Index_ = int]’:
/home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/scran_variances/model_gene_variances.hpp:332:66: required from ‘void scran_variances::internal::compute_variances_sparse_row(const tatami::Matrix<Value_, Index_>&, const std::vector<scran_variances::ModelGeneVariancesBuffers<Stat_> >&, const Block_*, const std::vector<Index_, std::allocator<_T2> >&, int) [with Value_ = double; Index_ = int; Stat_ = double; Block_ = int]’
332 | const auto stat = tatami_stats::variances::direct(range.value, range.number, NC, false);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/scran_variances/model_gene_variances.hpp:453:41: required from ‘void scran_variances::internal::compute_variances(const tatami::Matrix<Value_, Index_>&, const std::vector<scran_variances::ModelGeneVariancesBuffers<Stat_> >&, const Block_*, const std::vector<Index_, std::allocator<_T2> >&, int) [with Value_ = double; Index_ = int; Stat_ = double; Block_ = int]’
453 | compute_variances_sparse_row(mat, buffers, block, block_size, num_threads);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/scran_variances/model_gene_variances.hpp:543:36: required from ‘void scran_variances::model_gene_variances_blocked(const tatami::Matrix<Value_, Index_>&, const Block_*, const ModelGeneVariancesBlockedBuffers<Stat_>&, const ModelGeneVariancesOptions&) [with Value_ = double; Index_ = int; Block_ = int; Stat_ = double]’
543 | internal::compute_variances(mat, buffers.per_block, block, block_size, options.num_threads);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
model_gene_variances.cpp:94:54: required from here
94 | scran_variances::model_gene_variances_blocked(*mat, ptr, bbuffers, opt);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/tatami_stats/variances.hpp:100:29: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
100 | std::pair<Output_, Output_> direct(const Value_* value, Index_ num_nonzero, Index_ num_all, bool skip_nan) {
| ^~~~~~
/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'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rigraphlib/igraph/include/igraph' -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/beachmat/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/BiocNeighbors/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rigraphlib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c normalize_counts.cpp -o normalize_counts.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'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rigraphlib/igraph/include/igraph' -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/beachmat/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/BiocNeighbors/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rigraphlib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c rna_quality_control.cpp -o rna_quality_control.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'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rigraphlib/igraph/include/igraph' -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/beachmat/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/BiocNeighbors/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rigraphlib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c run_pca.cpp -o run_pca.o
In file included from /home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/scran_pca/scran_pca.hpp:4,
from run_pca.cpp:8:
/home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/scran_pca/simple_pca.hpp: In instantiation of ‘void scran_pca::compute_row_means_and_variances(const tatami::Matrix<Value_, Index_>&, int, EigenVector_&, EigenVector_&) [with bool sparse_ = true; Value_ = double; Index_ = int; EigenVector_ = Eigen::Matrix<double, -1, 1>]’:
/home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/scran_pca/subset_pca.hpp:174:54: required from ‘void scran_pca::subset_pca(const tatami::Matrix<Value_, Index_>&, const SubsetVector_&, const SubsetPcaOptions&, SubsetPcaResults<EigenMatrix_, EigenVector_>&) [with Value_ = double; Index_ = int; SubsetVector_ = Rcpp::Vector<13>; EigenMatrix_ = Eigen::Matrix<double, -1, -1>; EigenVector_ = Eigen::Matrix<double, -1, 1>; SubsetPcaOptions = SimplePcaOptions; SubsetPcaResults<EigenMatrix_, EigenVector_> = SimplePcaResults<Eigen::Matrix<double, -1, -1>, Eigen::Matrix<double, -1, 1> >]’
174 | compute_row_means_and_variances<true>(inv_mat, options.num_threads, inv_center, inv_scale);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/scran_pca/subset_pca.hpp:256:15: required from ‘scran_pca::SubsetPcaResults<EigenMatrix_, EigenVector_> scran_pca::subset_pca(const tatami::Matrix<Value_, Index_>&, const SubsetVector_&, const SubsetPcaOptions&) [with EigenMatrix_ = Eigen::Matrix<double, -1, -1>; EigenVector_ = Eigen::Matrix<double, -1, 1>; Value_ = double; Index_ = int; SubsetVector_ = Rcpp::Vector<13>; SubsetPcaResults<EigenMatrix_, EigenVector_> = SimplePcaResults<Eigen::Matrix<double, -1, -1>, Eigen::Matrix<double, -1, 1> >; SubsetPcaOptions = SimplePcaOptions]’
256 | subset_pca(mat, subset, options, output);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
run_pca.cpp:106:45: required from here
106 | auto res = scran_pca::subset_pca(*(mat->ptr), Rcpp::IntegerVector(subset), opt);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/scran_pca/simple_pca.hpp:100:121: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
100 | return tatami_stats::variances::direct(range.value, range.number, ncells, /* skip_nan = */ false);
| ^
/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'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rigraphlib/igraph/include/igraph' -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/beachmat/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/BiocNeighbors/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rigraphlib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c run_tsne.cpp -o run_tsne.o
In file included from /home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/qdtsne/utils.hpp:16,
from /home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/qdtsne/SPTree.hpp:43,
from /home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/qdtsne/Status.hpp:43,
from /home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/qdtsne/initialize.hpp:8,
from /home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/qdtsne/qdtsne.hpp:10,
from run_tsne.cpp:5:
/home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/aarand/aarand.hpp: In instantiation of ‘std::pair<_FIter, _FIter> aarand::standard_normal(Engine_&) [with Output_ = double; Engine_ = std::mersenne_twister_engine<long unsigned int, 64, 312, 156, 31, 13043109905998158313, 29, 6148914691236517205, 17, 8202884508482404352, 37, 18444473444759240704, 43, 6364136223846793005>]’:
/home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/qdtsne/utils.hpp:83:60: required from ‘void qdtsne::initialize_random(Float_*, std::size_t, std::mersenne_twister_engine<long unsigned int, 64, 312, 156, 31, 13043109905998158313, 29, 6148914691236517205, 17, 8202884508482404352, 37, 18444473444759240704, 43, 6364136223846793005>::result_type) [with long unsigned int num_dim_ = 2; Float_ = double; std::size_t = long unsigned int; std::mersenne_twister_engine<long unsigned int, 64, 312, 156, 31, 13043109905998158313, 29, 6148914691236517205, 17, 8202884508482404352, 37, 18444473444759240704, 43, 6364136223846793005>::result_type = long unsigned int]’
83 | const auto paired = aarand::standard_normal<Float_>(rng);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~
run_tsne.cpp:49:33: required from here
49 | qdtsne::initialize_random<2>(optr, sanisizer::cast<std::size_t>(nobs), sanisizer::from_float<unsigned long long>(seed));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/aarand/aarand.hpp:89:29: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
89 | std::pair<Output_, Output_> standard_normal(Engine_& eng) {
| ^~~~~~~~~~~~~~~
/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'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rigraphlib/igraph/include/igraph' -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/beachmat/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/BiocNeighbors/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rigraphlib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c run_umap.cpp -o run_umap.o
In file included from /home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/umappp/initialize.hpp:6,
from /home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/umappp/umappp.hpp:11,
from run_umap.cpp:8:
/home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/umappp/find_ab.hpp: In instantiation of ‘std::pair<_FIter, _FIter> umappp::find_ab(Float_, Float_) [with Float_ = double]’:
/home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/umappp/initialize.hpp:107:35: required from ‘umappp::Status<Index_, Float_> umappp::initialize(NeighborList<Index_, Float_>, std::size_t, Float_*, Options) [with Index_ = int; Float_ = float; NeighborList<Index_, Float_> = std::vector<std::vector<std::pair<int, float>, std::allocator<std::pair<int, float> > >, std::allocator<std::vector<std::pair<int, float>, std::allocator<std::pair<int, float> > > > >; std::size_t = long unsigned int]’
107 | const auto found = find_ab(options.spread, options.min_dist);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
run_umap.cpp:109:37: required from here
109 | auto status = umappp::initialize(std::move(neighbors), sanisizer::cast<std::size_t>(num_dim), embedding.data(), opt);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/umappp/find_ab.hpp:45:27: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
45 | std::pair<Float_, Float_> find_ab(const Float_ spread, const Float_ min_dist) {
| ^~~~~~~
/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'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rigraphlib/igraph/include/igraph' -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/beachmat/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/BiocNeighbors/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rigraphlib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c sanitize_size_factors.cpp -o sanitize_size_factors.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'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rigraphlib/igraph/include/igraph' -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/beachmat/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/BiocNeighbors/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rigraphlib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c scale_by_neighbors.cpp -o scale_by_neighbors.o
In file included from /home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/mumosa/mumosa.hpp:5,
from scale_by_neighbors.cpp:7:
/home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/mumosa/blocked.hpp: In instantiation of ‘std::pair<Index_, Index_> mumosa::compute_distance_blocked(const std::vector<std::shared_ptr<const knncolle::Prebuilt<Index_, Data_, Distance_> > >&, BlockedWorkspace<Distance_>&, const BlockedOptions&) [with Index_ = int; Input_ = double; Distance_ = double]’:
scale_by_neighbors.cpp:53:62: required from here
53 | values.push_back(mumosa::compute_distance_blocked(prebuilts, work, opt));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/mumosa/blocked.hpp:139:33: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
139 | std::pair<Distance_, Distance_> compute_distance_blocked(
| ^~~~~~~~~~~~~~~~~~~~~~~~
/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'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rigraphlib/igraph/include/igraph' -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/beachmat/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/BiocNeighbors/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rigraphlib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c score_gene_set.cpp -o score_gene_set.o
In file included from /home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/tatami_stats/grouped_variances.hpp:5,
from /home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/tatami_stats/tatami_stats.hpp:7,
from /home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/scran_pca/simple_pca.hpp:10,
from /home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/scran_pca/scran_pca.hpp:4,
from /home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/gsdecon/compute.hpp:9,
from /home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/gsdecon/gsdecon.hpp:4,
from score_gene_set.cpp:6:
/home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/tatami_stats/variances.hpp: In instantiation of ‘std::pair<_FIter, _FIter> tatami_stats::variances::direct(const Value_*, Index_, Index_, bool) [with Output_ = double; Value_ = double; Index_ = int]’:
/home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/scran_pca/simple_pca.hpp:225:69: required from ‘std::unique_ptr<irlba::Matrix<EigenVector_, EigenMatrix_> > scran_pca::prepare_sparse_matrix_for_irlba(const tatami::Matrix<Value_, Index_>&, const SimplePcaOptions&, EigenVector_&, EigenVector_&, typename EigenVector_::Scalar&) [with EigenMatrix_ = Eigen::Matrix<double, -1, -1>; Value_ = double; Index_ = int; EigenVector_ = Eigen::Matrix<double, -1, 1>; typename EigenVector_::Scalar = double]’
225 | const auto results = tatami_stats::variances::direct(values.data() + offset, num_nonzero, ncells, /* skip_nan = */ false);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/scran_pca/simple_pca.hpp:386:60: required from ‘void scran_pca::simple_pca_internal(const tatami::Matrix<Value_, Index_>&, const SimplePcaOptions&, SimplePcaResults<EigenMatrix_, EigenVector_>&, SubsetFunction_) [with Value_ = double; Index_ = int; EigenMatrix_ = Eigen::Matrix<double, -1, -1>; EigenVector_ = Eigen::Matrix<double, -1, 1>; SubsetFunction_ = simple_pca<double, int, Eigen::Matrix<double, -1, -1>, Eigen::Matrix<double, -1, 1> >(const tatami::Matrix<double, int>&, const SimplePcaOptions&, SimplePcaResults<Eigen::Matrix<double, -1, -1>, Eigen::Matrix<double, -1, 1> >&)::<lambda(const Eigen::Matrix<double, -1, -1>&, const Eigen::Matrix<double, -1, 1>&)>]’
386 | ptr = prepare_sparse_matrix_for_irlba<EigenMatrix_>(mat, options, output.center, output.scale, output.total_variance);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/scran_pca/simple_pca.hpp:434:24: required from ‘void scran_pca::simple_pca(const tatami::Matrix<Value_, Index_>&, const SimplePcaOptions&, SimplePcaResults<EigenMatrix_, EigenVector_>&) [with Value_ = double; Index_ = int; EigenMatrix_ = Eigen::Matrix<double, -1, -1>; EigenVector_ = Eigen::Matrix<double, -1, 1>]’
434 | simple_pca_internal(
| ~~~~~~~~~~~~~~~~~~~^
435 | mat,
| ~~~~
436 | options,
| ~~~~~~~~
437 | output,
| ~~~~~~~
438 | [](const EigenMatrix_&, const EigenVector_&) -> void {}
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
439 | );
| ~
/home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/scran_pca/simple_pca.hpp:460:15: required from ‘scran_pca::SimplePcaResults<EigenMatrix_, EigenVector_> scran_pca::simple_pca(const tatami::Matrix<Value_, Index_>&, const SimplePcaOptions&) [with EigenMatrix_ = Eigen::Matrix<double, -1, -1>; EigenVector_ = Eigen::Matrix<double, -1, 1>; Value_ = double; Index_ = int]’
460 | simple_pca(mat, options, output);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/gsdecon/compute.hpp:56:43: required from ‘void gsdecon::compute(const tatami::Matrix<Value_, Index_>&, const Options&, const Buffers<Float_>&) [with Value_ = double; Index_ = int; Float_ = double]’
56 | const auto res = scran_pca::simple_pca(matrix, sopt);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
score_gene_set.cpp:57:25: required from here
57 | gsdecon::compute(matrix, opt, output);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/tatami_stats/variances.hpp:100:29: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
100 | std::pair<Output_, Output_> direct(const Value_* value, Index_ num_nonzero, Index_ num_all, bool skip_nan) {
| ^~~~~~
In file included from /home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/Eigen/Core:340,
from /home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/Eigen/Dense:1,
from /home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/irlba/utils.hpp:9,
from /home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/irlba/compute.hpp:10,
from /home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/irlba/irlba.hpp:4,
from /home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/gsdecon/compute.hpp:8:
In destructor ‘Eigen::internal::DenseStorage_impl<T, -1, -1, Cols, Options>::~DenseStorage_impl() [with T = double; int Cols = 1; int Options = 0]’,
inlined from ‘Eigen::DenseStorage<double, -1, -1, 1, 0, true>::~DenseStorage()’ at /home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/Eigen/src/Core/DenseStorage.h:536:7,
inlined from ‘Eigen::PlainObjectBase<Eigen::Matrix<double, -1, 1> >::~PlainObjectBase()’ at /home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/Eigen/src/Core/PlainObjectBase.h:95:7,
inlined from ‘Eigen::Matrix<double, -1, 1>::~Matrix()’ at /home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/Eigen/src/Core/Matrix.h:186:7,
inlined from ‘constexpr void std::_Optional_payload_base<_Tp>::_M_destroy() [with _Tp = Eigen::Matrix<double, -1, 1>]’ at /opt/ohpc/pub/compiler/gcc/14.2.0/include/c++/14.2.0/optional:283:35,
inlined from ‘constexpr void std::_Optional_payload_base<_Tp>::_M_reset() [with _Tp = Eigen::Matrix<double, -1, 1>]’ at /opt/ohpc/pub/compiler/gcc/14.2.0/include/c++/14.2.0/optional:314:14,
inlined from ‘constexpr void std::_Optional_payload_base<_Tp>::_M_reset() [with _Tp = Eigen::Matrix<double, -1, 1>]’ at /opt/ohpc/pub/compiler/gcc/14.2.0/include/c++/14.2.0/optional:311:7,
inlined from ‘std::_Optional_payload<_Tp, false, _Copy, _Move>::~_Optional_payload() [with _Tp = Eigen::Matrix<double, -1, 1>; bool _Copy = false; bool _Move = false]’ at /opt/ohpc/pub/compiler/gcc/14.2.0/include/c++/14.2.0/optional:437:65,
inlined from ‘std::_Optional_base<Eigen::Matrix<double, -1, 1>, false, false>::~_Optional_base()’ at /opt/ohpc/pub/compiler/gcc/14.2.0/include/c++/14.2.0/optional:508:12,
inlined from ‘std::optional<Eigen::Matrix<double, -1, 1> >::~optional()’ at /opt/ohpc/pub/compiler/gcc/14.2.0/include/c++/14.2.0/optional:703:11,
inlined from ‘irlba::Options<Eigen::Matrix<double, -1, 1> >::~Options()’ at /home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/irlba/Options.hpp:20:8,
inlined from ‘gsdecon::Options::~Options()’ at /home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/gsdecon/Options.hpp:18:8,
inlined from ‘Rcpp::List score_gene_set(SEXP, int, Rcpp::Nullable<Rcpp::Vector<13> >, std::string, Rcpp::NumericVector, bool, bool, int, int, double, int)’ at score_gene_set.cpp:64:1:
/home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/Eigen/src/Core/DenseStorage.h:363:85: warning: ‘*(Eigen::internal::DenseStorage_impl<double, -1, -1, 1, 0>*)((char*)&opt + offsetof(gsdecon::Options, gsdecon::Options::irlba_options.irlba::Options<Eigen::Matrix<double, -1, 1, 0, -1, 1> >::initial.std::optional<Eigen::Matrix<double, -1, 1, 0, -1, 1> >::<unnamed>.std::_Optional_base<Eigen::Matrix<double, -1, 1, 0, -1, 1>, false, false>::<unnamed>)).Eigen::internal::DenseStorage_impl<double, -1, -1, 1, 0>::m_data’ may be used uninitialized [-Wmaybe-uninitialized]
363 | EIGEN_DEVICE_FUNC ~DenseStorage_impl() { conditional_aligned_delete_auto<T, Align>(m_data, size()); }
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~
score_gene_set.cpp: In function ‘Rcpp::List score_gene_set(SEXP, int, Rcpp::Nullable<Rcpp::Vector<13> >, std::string, Rcpp::NumericVector, bool, bool, int, int, double, int)’:
score_gene_set.cpp:31:22: note: ‘opt’ declared here
31 | gsdecon::Options opt;
| ^~~
In destructor ‘Eigen::internal::DenseStorage_impl<T, -1, -1, Cols, Options>::~DenseStorage_impl() [with T = double; int Cols = 1; int Options = 0]’,
inlined from ‘Eigen::DenseStorage<double, -1, -1, 1, 0, true>::~DenseStorage()’ at /home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/Eigen/src/Core/DenseStorage.h:536:7,
inlined from ‘Eigen::PlainObjectBase<Eigen::Matrix<double, -1, 1> >::~PlainObjectBase()’ at /home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/Eigen/src/Core/PlainObjectBase.h:95:7,
inlined from ‘Eigen::Matrix<double, -1, 1>::~Matrix()’ at /home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/Eigen/src/Core/Matrix.h:186:7,
inlined from ‘constexpr void std::_Optional_payload_base<_Tp>::_M_destroy() [with _Tp = Eigen::Matrix<double, -1, 1>]’ at /opt/ohpc/pub/compiler/gcc/14.2.0/include/c++/14.2.0/optional:283:35,
inlined from ‘constexpr void std::_Optional_payload_base<_Tp>::_M_reset() [with _Tp = Eigen::Matrix<double, -1, 1>]’ at /opt/ohpc/pub/compiler/gcc/14.2.0/include/c++/14.2.0/optional:314:14,
inlined from ‘constexpr void std::_Optional_payload_base<_Tp>::_M_reset() [with _Tp = Eigen::Matrix<double, -1, 1>]’ at /opt/ohpc/pub/compiler/gcc/14.2.0/include/c++/14.2.0/optional:311:7,
inlined from ‘std::_Optional_payload<_Tp, false, _Copy, _Move>::~_Optional_payload() [with _Tp = Eigen::Matrix<double, -1, 1>; bool _Copy = false; bool _Move = false]’ at /opt/ohpc/pub/compiler/gcc/14.2.0/include/c++/14.2.0/optional:437:65,
inlined from ‘std::_Optional_base<Eigen::Matrix<double, -1, 1>, false, false>::~_Optional_base()’ at /opt/ohpc/pub/compiler/gcc/14.2.0/include/c++/14.2.0/optional:508:12,
inlined from ‘std::optional<Eigen::Matrix<double, -1, 1> >::~optional()’ at /opt/ohpc/pub/compiler/gcc/14.2.0/include/c++/14.2.0/optional:703:11,
inlined from ‘irlba::Options<Eigen::Matrix<double, -1, 1> >::~Options()’ at /home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/irlba/Options.hpp:20:8,
inlined from ‘gsdecon::Options::~Options()’ at /home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/gsdecon/Options.hpp:18:8,
inlined from ‘Rcpp::List score_gene_set(SEXP, int, Rcpp::Nullable<Rcpp::Vector<13> >, std::string, Rcpp::NumericVector, bool, bool, int, int, double, int)’ at score_gene_set.cpp:64:1:
/home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/Eigen/src/Core/DenseStorage.h:363:85: warning: ‘*(Eigen::internal::DenseStorage_impl<double, -1, -1, 1, 0>*)((char*)&opt + offsetof(gsdecon::Options, gsdecon::Options::irlba_options.irlba::Options<Eigen::Matrix<double, -1, 1, 0, -1, 1> >::initial.std::optional<Eigen::Matrix<double, -1, 1, 0, -1, 1> >::<unnamed>.std::_Optional_base<Eigen::Matrix<double, -1, 1, 0, -1, 1>, false, false>::<unnamed>)).Eigen::internal::DenseStorage_impl<double, -1, -1, 1, 0>::m_data’ may be used uninitialized [-Wmaybe-uninitialized]
363 | EIGEN_DEVICE_FUNC ~DenseStorage_impl() { conditional_aligned_delete_auto<T, Align>(m_data, size()); }
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~
score_gene_set.cpp: In function ‘Rcpp::List score_gene_set(SEXP, int, Rcpp::Nullable<Rcpp::Vector<13> >, std::string, Rcpp::NumericVector, bool, bool, int, int, double, int)’:
score_gene_set.cpp:31:22: note: ‘opt’ declared here
31 | gsdecon::Options opt;
| ^~~
/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'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rigraphlib/igraph/include/igraph' -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/beachmat/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/BiocNeighbors/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rigraphlib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c score_markers.cpp -o score_markers.o
In file included from /home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/scran_markers/scan_matrix.hpp:13,
from /home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/scran_markers/score_markers_pairwise.hpp:13,
from /home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/scran_markers/scran_markers.hpp:4,
from score_markers.cpp:7:
/home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/scran_markers/cohens_d.hpp: In instantiation of ‘std::pair<_FIter, _FIter> scran_markers::internal::compute_cohens_d_blockmean(std::size_t, std::size_t, const Stat_*, const Stat_*, std::size_t, std::size_t, Stat_, const PrecomputedPairwiseWeights<Stat_>&) [with Stat_ = double; std::size_t = long unsigned int]’:
/home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/scran_markers/cohens_d.hpp:130:56: required from ‘void scran_markers::internal::compute_pairwise_cohens_d_blockmean(const Stat_*, const Stat_*, std::size_t, std::size_t, Stat_, const PrecomputedPairwiseWeights<Stat_>&, Stat_*) [with Stat_ = double; std::size_t = long unsigned int]’
130 | const auto tmp = compute_cohens_d_blockmean(g1, g2, means, vars, ngroups, nblocks, threshold, preweights);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/scran_markers/score_markers_summary.hpp:533:56: required from ‘void scran_markers::internal::process_simple_summary_effects(Index_, std::size_t, std::size_t, std::size_t, const std::vector<Index_, std::allocator<_T2> >&, const std::vector<Index_, std::allocator<_T2> >&, const std::vector<Index_, std::allocator<_T2> >&, double, const BlockAverageInfo<Stat_>&, const std::optional<std::vector<double> >&, Index_, bool, const scran_markers::ScoreMarkersSummaryBuffers<Stat_, Rank_>&, int) [with Index_ = int; Stat_ = double; Rank_ = int; std::size_t = long unsigned int]’
533 | compute_pairwise_cohens_d_blockmean(tmp_means, tmp_variances, ngroups, nblocks, threshold, *preweights, pairwise_buffer.data());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/scran_markers/score_markers_summary.hpp:808:35: required from ‘void scran_markers::internal::score_markers_summary(const tatami::Matrix<Value_, Index_>&, std::size_t, const Group_*, std::size_t, const Block_*, std::size_t, const std::size_t*, const std::vector<Index_, std::allocator<_Tp> >&, const scran_markers::ScoreMarkersSummaryOptions&, const scran_markers::ScoreMarkersSummaryBuffers<Stat_, Rank_>&) [with bool single_block_ = false; Value_ = double; Index_ = int; Group_ = int; Block_ = int; Stat_ = double; Rank_ = int; std::size_t = long unsigned int]’
808 | process_simple_summary_effects(
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
809 | matrix.nrow(),
| ~~~~~~~~~~~~~~
810 | ngroups,
| ~~~~~~~~
811 | nblocks,
| ~~~~~~~~
812 | ncombos,
| ~~~~~~~~
813 | combo_means,
| ~~~~~~~~~~~~
814 | combo_vars,
| ~~~~~~~~~~~
815 | combo_detected,
| ~~~~~~~~~~~~~~~
816 | options.threshold,
| ~~~~~~~~~~~~~~~~~~
817 | average_info,
| ~~~~~~~~~~~~~
818 | options.compute_summary_quantiles,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
819 | minrank_limit,
| ~~~~~~~~~~~~~~
820 | options.min_rank_preserve_ties,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
821 | output,
| ~~~~~~~
822 | options.num_threads
| ~~~~~~~~~~~~~~~~~~~
823 | );
| ~
/home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/scran_markers/score_markers_summary.hpp:934:43: required from ‘void scran_markers::score_markers_summary_blocked(const tatami::Matrix<Value_, Index_>&, const Group_*, const Block_*, const ScoreMarkersSummaryOptions&, const ScoreMarkersSummaryBuffers<Stat_, Rank_>&) [with Value_ = double; Index_ = int; Group_ = int; Block_ = int; Stat_ = double; Rank_ = int]’
934 | internal::score_markers_summary<false>(
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
935 | matrix,
| ~~~~~~~
936 | sanisizer::cast<std::size_t>(ngroups),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
937 | group,
| ~~~~~~
938 | sanisizer::cast<std::size_t>(nblocks),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
939 | block,
| ~~~~~~
940 | sanisizer::cast<std::size_t>(ncombos),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
941 | combinations.data(),
| ~~~~~~~~~~~~~~~~~~~~
942 | combo_sizes,
| ~~~~~~~~~~~~
943 | options,
| ~~~~~~~~
944 | output
| ~~~~~~
945 | );
| ~
score_markers.cpp:183:53: required from here
183 | scran_markers::score_markers_summary_blocked(*mat, static_cast<const int*>(groups.begin()), ptr, opt, buffers);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/scran_markers/cohens_d.hpp:61:25: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
61 | std::pair<Stat_, Stat_> compute_cohens_d_blockmean(
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
/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'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rigraphlib/igraph/include/igraph' -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/beachmat/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/BiocNeighbors/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rigraphlib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c set_executor.cpp -o set_executor.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'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rigraphlib/igraph/include/igraph' -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/beachmat/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/BiocNeighbors/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rigraphlib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c subsample_by_neighbors.cpp -o subsample_by_neighbors.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'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rigraphlib/igraph/include/igraph' -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/beachmat/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/BiocNeighbors/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rigraphlib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c summarize_effects.cpp -o summarize_effects.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'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rigraphlib/igraph/include/igraph' -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/beachmat/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/BiocNeighbors/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rigraphlib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c test_enrichment.cpp -o test_enrichment.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 scrapper.so RcppExports.o adt_quality_control.o aggregate_across_cells.o aggregate_across_genes.o build_snn_graph.o center_size_factors.o choose_highly_variable_genes.o choose_pseudo_count.o cluster_graph.o cluster_kmeans.o combine_factors.o compute_block_weights.o compute_clrm1_factors.o correct_mnn.o crispr_quality_control.o fit_variance_trend.o model_gene_variances.o normalize_counts.o rna_quality_control.o run_pca.o run_tsne.o run_umap.o sanitize_size_factors.o scale_by_neighbors.o score_gene_set.o score_markers.o set_executor.o subsample_by_neighbors.o summarize_effects.o test_enrichment.o /home/biocbuild/R/R-devel_2025-02-19/site-library/Rigraphlib/igraph/lib64/libigraph.a -L/home/biocbuild/R/R/lib -lRlapack -L/home/biocbuild/R/R/lib -lRblas -lgfortran -lm -L/home/biocbuild/R/R/lib -lR
installing to /home/biocbuild/R/R-devel_2025-02-19/site-library/00LOCK-scrapper/00new/scrapper/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 (scrapper)