Aaron Lun
| Snapshot Date: 2025-10-13 13:40 -0400 (Mon, 13 Oct 2025) |
| git_url: https://git.bioconductor.org/packages/scrapper |
| git_branch: RELEASE_3_21 |
| git_last_commit: e2b419e |
| git_last_commit_date: 2025-05-13 16:05:58 -0400 (Tue, 13 May 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 1933/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| scrapper 1.2.1 (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 | OK | 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 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: 1.2.1 |
| Command: /home/biocbuild/R/R/bin/R CMD INSTALL scrapper |
| StartedAt: 2025-10-13 20:35:41 -0000 (Mon, 13 Oct 2025) |
| EndedAt: 2025-10-13 20:45:04 -0000 (Mon, 13 Oct 2025) |
| EllapsedTime: 562.7 seconds |
| RetCode: 0 |
| Status: OK |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD INSTALL scrapper
###
##############################################################################
##############################################################################
* installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-library’
* installing *source* package ‘scrapper’ ...
** this is package ‘scrapper’ version ‘1.2.1’
** 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'/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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:6,
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:5,
from /home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/scran_variances/scran_variances.hpp:5,
from model_gene_variances.cpp:8:
/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:272:60: 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]’
272 | 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:392:41: 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]’
392 | 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:474:36: 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]’
474 | internal::compute_variances(mat, buffers.per_block, block, block_size, options.num_threads);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
model_gene_variances.cpp:81:54: required from here
81 | 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:95:29: 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
95 | 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/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/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/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/Eigen/Core:214,
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/compute.hpp:4,
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/scran_pca/simple_pca.hpp:6,
from /home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/scran_pca/scran_pca.hpp:4,
from run_pca.cpp:10:
/home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/Eigen/src/Core/arch/NEON/PacketMath.h: In function ‘Packet Eigen::internal::pload(const typename unpacket_traits<T>::type*) [with Packet = eigen_packet_wrapper<int, 2>; typename unpacket_traits<T>::type = signed char]’:
/home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/Eigen/src/Core/arch/NEON/PacketMath.h:1671:9: warning: ‘void* memcpy(void*, const void*, size_t)’ copying an object of non-trivial type ‘Eigen::internal::Packet4c’ {aka ‘struct Eigen::internal::eigen_packet_wrapper<int, 2>’} from an array of ‘const int8_t’ {aka ‘const signed char’} [-Wclass-memaccess]
1671 | memcpy(&res, from, sizeof(Packet4c));
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/Eigen/Core:172:
/home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/Eigen/src/Core/GenericPacketMath.h:159:8: note: ‘Eigen::internal::Packet4c’ {aka ‘struct Eigen::internal::eigen_packet_wrapper<int, 2>’} declared here
159 | struct eigen_packet_wrapper
| ^~~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/Eigen/src/Core/arch/NEON/PacketMath.h: In function ‘Packet Eigen::internal::ploadu(const typename unpacket_traits<T>::type*) [with Packet = eigen_packet_wrapper<int, 2>; typename unpacket_traits<T>::type = signed char]’:
/home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/Eigen/src/Core/arch/NEON/PacketMath.h:1716:9: warning: ‘void* memcpy(void*, const void*, size_t)’ copying an object of non-trivial type ‘Eigen::internal::Packet4c’ {aka ‘struct Eigen::internal::eigen_packet_wrapper<int, 2>’} from an array of ‘const int8_t’ {aka ‘const signed char’} [-Wclass-memaccess]
1716 | memcpy(&res, from, sizeof(Packet4c));
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/Eigen/src/Core/GenericPacketMath.h:159:8: note: ‘Eigen::internal::Packet4c’ {aka ‘struct Eigen::internal::eigen_packet_wrapper<int, 2>’} declared here
159 | struct eigen_packet_wrapper
| ^~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/tatami_stats/grouped_variances.hpp:6,
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:5:
/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:203:63: required from ‘void scran_pca::internal::run_sparse(const tatami::Matrix<Value_, Index_>&, const scran_pca::SimplePcaOptions&, EigenMatrix_&, EigenMatrix_&, EigenVector_&, EigenVector_&, EigenVector_&, typename EigenVector_::Scalar&, bool&) [with Value_ = double; Index_ = int; EigenMatrix_ = Eigen::Matrix<double, -1, -1>; EigenVector_ = Eigen::Matrix<double, -1, 1>; typename EigenVector_::Scalar = double]’
203 | 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:378:29: 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>]’
378 | internal::run_sparse(mat, options, output.components, output.rotation, output.variance_explained, output.center, output.scale, output.total_variance, output.converged);
| ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/scran_pca/simple_pca.hpp:411:15: 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]’
411 | simple_pca(mat, options, output);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
run_pca.cpp:88:41: required from here
88 | auto out = scran_pca::simple_pca(*(mat->ptr), opt);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/tatami_stats/variances.hpp:95:29: 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
95 | 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:341:
/home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/Eigen/src/Core/products/TriangularMatrixVector.h: In function ‘static void Eigen::internal::trmv_selector<Mode, 1>::run(const Lhs&, const Rhs&, Dest&, const typename Dest::Scalar&) [with Lhs = Eigen::Transpose<const Eigen::Block<const Eigen::Block<Eigen::Matrix<double, -1, -1>, -1, -1, false>, -1, -1, false> >; Rhs = Eigen::Transpose<const Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<double, double>, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, const Eigen::Matrix<double, 1, -1> >, const Eigen::Transpose<const Eigen::Block<const Eigen::Block<const Eigen::Block<Eigen::Matrix<double, -1, -1>, -1, -1, false>, -1, 1, true>, -1, 1, false> > > >; Dest = Eigen::Transpose<Eigen::Block<Eigen::Block<Eigen::Matrix<double, -1, -1, 1, -1, -1>, 1, -1, true>, 1, -1, false> >; int Mode = 6]’:
/home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/Eigen/src/Core/products/TriangularMatrixVector.h:332:12: warning: ‘result’ may be used uninitialized [-Wmaybe-uninitialized]
327 | internal::triangular_matrix_vector_product
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
328 | <Index,Mode,
| ~~~~~~~~~~~~
329 | LhsScalar, LhsBlasTraits::NeedToConjugate,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
330 | RhsScalar, RhsBlasTraits::NeedToConjugate,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
331 | RowMajor>
| ~~~~~~~~~
332 | ::run(actualLhs.rows(),actualLhs.cols(),
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
333 | actualLhs.data(),actualLhs.outerStride(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
334 | actualRhsPtr,1,
| ~~~~~~~~~~~~~~~
335 | dest.data(),dest.innerStride(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
336 | actualAlpha);
| ~~~~~~~~~~~~
/home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/Eigen/src/Core/products/TriangularMatrixVector.h:105:24: note: by argument 5 of type ‘const double*’ to ‘static void Eigen::internal::triangular_matrix_vector_product<Index, Mode, LhsScalar, ConjLhs, RhsScalar, ConjRhs, 1, Version>::run(Index, Index, const LhsScalar*, Index, const RhsScalar*, Index, ResScalar*, Index, const ResScalar&) [with Index = long int; int Mode = 6; LhsScalar = double; bool ConjLhs = false; RhsScalar = double; bool ConjRhs = false; int Version = 0]’ declared here
105 | EIGEN_DONT_INLINE void triangular_matrix_vector_product<Index,Mode,LhsScalar,ConjLhs,RhsScalar,ConjRhs,RowMajor,Version>
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/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/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/kmeans/InitializeKmeanspp.hpp:9,
from /home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/kmeans/kmeans.hpp:9,
from /home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/knncolle/Kmknn.hpp:11,
from /home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/knncolle/knncolle.hpp:13,
from run_tsne.cpp:4:
/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 T = 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:64:54: required from ‘void qdtsne::initialize_random(Float_*, size_t, int) [with int ndim_ = 2; Float_ = double; size_t = long unsigned int]’
64 | auto paired = aarand::standard_normal<Float_>(rng);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~
run_tsne.cpp:25:33: required from here
25 | qdtsne::initialize_random<2>(optr, nobs, seed);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/aarand/aarand.hpp:69:17: 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
69 | std::pair<T, T> 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/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/Eigen/Core:214,
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/compute.hpp:4,
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/umappp/spectral_init.hpp:4,
from /home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/umappp/initialize.hpp:8,
from /home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/umappp/umappp.hpp:11,
from run_umap.cpp:4:
/home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/Eigen/src/Core/arch/NEON/PacketMath.h: In function ‘Packet Eigen::internal::pload(const typename unpacket_traits<T>::type*) [with Packet = eigen_packet_wrapper<int, 2>; typename unpacket_traits<T>::type = signed char]’:
/home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/Eigen/src/Core/arch/NEON/PacketMath.h:1671:9: warning: ‘void* memcpy(void*, const void*, size_t)’ copying an object of non-trivial type ‘Eigen::internal::Packet4c’ {aka ‘struct Eigen::internal::eigen_packet_wrapper<int, 2>’} from an array of ‘const int8_t’ {aka ‘const signed char’} [-Wclass-memaccess]
1671 | memcpy(&res, from, sizeof(Packet4c));
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/Eigen/Core:172:
/home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/Eigen/src/Core/GenericPacketMath.h:159:8: note: ‘Eigen::internal::Packet4c’ {aka ‘struct Eigen::internal::eigen_packet_wrapper<int, 2>’} declared here
159 | struct eigen_packet_wrapper
| ^~~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/Eigen/src/Core/arch/NEON/PacketMath.h: In function ‘Packet Eigen::internal::ploadu(const typename unpacket_traits<T>::type*) [with Packet = eigen_packet_wrapper<int, 2>; typename unpacket_traits<T>::type = signed char]’:
/home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/Eigen/src/Core/arch/NEON/PacketMath.h:1716:9: warning: ‘void* memcpy(void*, const void*, size_t)’ copying an object of non-trivial type ‘Eigen::internal::Packet4c’ {aka ‘struct Eigen::internal::eigen_packet_wrapper<int, 2>’} from an array of ‘const int8_t’ {aka ‘const signed char’} [-Wclass-memaccess]
1716 | memcpy(&res, from, sizeof(Packet4c));
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/Eigen/src/Core/GenericPacketMath.h:159:8: note: ‘Eigen::internal::Packet4c’ {aka ‘struct Eigen::internal::eigen_packet_wrapper<int, 2>’} declared here
159 | struct eigen_packet_wrapper
| ^~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/umappp/initialize.hpp:6:
/home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/umappp/find_ab.hpp: In instantiation of ‘std::pair<_FIter, _FIter> umappp::internal::find_ab(Float_, Float_, Float_, Float_, int, Float_) [with Float_ = double]’:
/home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/umappp/initialize.hpp:87:39: required from ‘umappp::Status<Index_, Float_> umappp::initialize(NeighborList<Index_, Float_>, int, 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> > > > >]’
87 | auto found = internal::find_ab(options.spread, options.min_dist);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
run_umap.cpp:21:37: required from here
21 | auto status = umappp::initialize(std::move(neighbors), ndim, embedding.data(), opt);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/umappp/find_ab.hpp:48:27: 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
48 | std::pair<Float_, Float_> find_ab(Float_ spread, Float_ min_dist, Float_ grid = 300, Float_ limit = 0.5, int iter = 50, Float_ tol = 1e-6) {
| ^~~~~~~
In file included from /home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/Eigen/Core:341:
/home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/Eigen/src/Core/products/TriangularMatrixVector.h: In function ‘static void Eigen::internal::trmv_selector<Mode, 1>::run(const Lhs&, const Rhs&, Dest&, const typename Dest::Scalar&) [with Lhs = Eigen::Transpose<const Eigen::Block<const Eigen::Block<Eigen::Matrix<double, -1, -1>, -1, -1, false>, -1, -1, false> >; Rhs = Eigen::Transpose<const Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<double, double>, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, const Eigen::Matrix<double, 1, -1> >, const Eigen::Transpose<const Eigen::Block<const Eigen::Block<const Eigen::Block<Eigen::Matrix<double, -1, -1>, -1, -1, false>, -1, 1, true>, -1, 1, false> > > >; Dest = Eigen::Transpose<Eigen::Block<Eigen::Block<Eigen::Matrix<double, -1, -1, 1, -1, -1>, 1, -1, true>, 1, -1, false> >; int Mode = 6]’:
/home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/Eigen/src/Core/products/TriangularMatrixVector.h:332:12: warning: ‘result’ may be used uninitialized [-Wmaybe-uninitialized]
327 | internal::triangular_matrix_vector_product
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
328 | <Index,Mode,
| ~~~~~~~~~~~~
329 | LhsScalar, LhsBlasTraits::NeedToConjugate,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
330 | RhsScalar, RhsBlasTraits::NeedToConjugate,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
331 | RowMajor>
| ~~~~~~~~~
332 | ::run(actualLhs.rows(),actualLhs.cols(),
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
333 | actualLhs.data(),actualLhs.outerStride(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
334 | actualRhsPtr,1,
| ~~~~~~~~~~~~~~~
335 | dest.data(),dest.innerStride(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
336 | actualAlpha);
| ~~~~~~~~~~~~
/home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/Eigen/src/Core/products/TriangularMatrixVector.h:105:24: note: by argument 5 of type ‘const double*’ to ‘static void Eigen::internal::triangular_matrix_vector_product<Index, Mode, LhsScalar, ConjLhs, RhsScalar, ConjRhs, 1, Version>::run(Index, Index, const LhsScalar*, Index, const RhsScalar*, Index, ResScalar*, Index, const ResScalar&) [with Index = long int; int Mode = 6; LhsScalar = double; bool ConjLhs = false; RhsScalar = double; bool ConjRhs = false; int Version = 0]’ declared here
105 | EIGEN_DONT_INLINE void triangular_matrix_vector_product<Index,Mode,LhsScalar,ConjLhs,RhsScalar,ConjRhs,RowMajor,Version>
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/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/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/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c scale_by_neighbors.cpp -o scale_by_neighbors.o
In file included from scale_by_neighbors.cpp:3:
/home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/mumosa/mumosa.hpp: In instantiation of ‘std::pair<_ForwardIterator, _ForwardIterator> mumosa::compute_distance(Index_, Float_*) [with Index_ = int; Float_ = double]’:
scale_by_neighbors.cpp:15:63: required from here
15 | values.push_back(mumosa::compute_distance<int, double>(copy.size(), copy.data()));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/mumosa/mumosa.hpp:54:27: 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
54 | std::pair<Float_, Float_> compute_distance(Index_ num_cells, Float_* distances) {
| ^~~~~~~~~~~~~~~~
/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/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/Eigen/Core:214,
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/compute.hpp:4,
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,
from /home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/gsdecon/gsdecon.hpp:4,
from score_gene_set.cpp:7:
/home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/Eigen/src/Core/arch/NEON/PacketMath.h: In function ‘Packet Eigen::internal::pload(const typename unpacket_traits<T>::type*) [with Packet = eigen_packet_wrapper<int, 2>; typename unpacket_traits<T>::type = signed char]’:
/home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/Eigen/src/Core/arch/NEON/PacketMath.h:1671:9: warning: ‘void* memcpy(void*, const void*, size_t)’ copying an object of non-trivial type ‘Eigen::internal::Packet4c’ {aka ‘struct Eigen::internal::eigen_packet_wrapper<int, 2>’} from an array of ‘const int8_t’ {aka ‘const signed char’} [-Wclass-memaccess]
1671 | memcpy(&res, from, sizeof(Packet4c));
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/Eigen/Core:172:
/home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/Eigen/src/Core/GenericPacketMath.h:159:8: note: ‘Eigen::internal::Packet4c’ {aka ‘struct Eigen::internal::eigen_packet_wrapper<int, 2>’} declared here
159 | struct eigen_packet_wrapper
| ^~~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/Eigen/src/Core/arch/NEON/PacketMath.h: In function ‘Packet Eigen::internal::ploadu(const typename unpacket_traits<T>::type*) [with Packet = eigen_packet_wrapper<int, 2>; typename unpacket_traits<T>::type = signed char]’:
/home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/Eigen/src/Core/arch/NEON/PacketMath.h:1716:9: warning: ‘void* memcpy(void*, const void*, size_t)’ copying an object of non-trivial type ‘Eigen::internal::Packet4c’ {aka ‘struct Eigen::internal::eigen_packet_wrapper<int, 2>’} from an array of ‘const int8_t’ {aka ‘const signed char’} [-Wclass-memaccess]
1716 | memcpy(&res, from, sizeof(Packet4c));
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/Eigen/src/Core/GenericPacketMath.h:159:8: note: ‘Eigen::internal::Packet4c’ {aka ‘struct Eigen::internal::eigen_packet_wrapper<int, 2>’} declared here
159 | struct eigen_packet_wrapper
| ^~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/tatami_stats/grouped_variances.hpp:6,
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:5,
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:
/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:203:63: required from ‘void scran_pca::internal::run_sparse(const tatami::Matrix<Value_, Index_>&, const scran_pca::SimplePcaOptions&, EigenMatrix_&, EigenMatrix_&, EigenVector_&, EigenVector_&, EigenVector_&, typename EigenVector_::Scalar&, bool&) [with Value_ = double; Index_ = int; EigenMatrix_ = Eigen::Matrix<double, -1, -1>; EigenVector_ = Eigen::Matrix<double, -1, 1>; typename EigenVector_::Scalar = double]’
203 | 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:378:29: 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>]’
378 | internal::run_sparse(mat, options, output.components, output.rotation, output.variance_explained, output.center, output.scale, output.total_variance, output.converged);
| ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/scran_pca/simple_pca.hpp:411:15: 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]’
411 | simple_pca(mat, options, output);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/gsdecon/compute.hpp:55:37: required from ‘void gsdecon::compute(const tatami::Matrix<Value_, Index_>&, const Options&, const Buffers<Float_>&) [with Value_ = double; Index_ = int; Float_ = double]’
55 | auto res = scran_pca::simple_pca(matrix, sopt);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
score_gene_set.cpp:56:25: required from here
56 | gsdecon::compute(matrix, opt, output);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/tatami_stats/variances.hpp:95:29: 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
95 | 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:341:
/home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/Eigen/src/Core/products/TriangularMatrixVector.h: In function ‘static void Eigen::internal::trmv_selector<Mode, 1>::run(const Lhs&, const Rhs&, Dest&, const typename Dest::Scalar&) [with Lhs = Eigen::Transpose<const Eigen::Block<const Eigen::Block<Eigen::Matrix<double, -1, -1>, -1, -1, false>, -1, -1, false> >; Rhs = Eigen::Transpose<const Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<double, double>, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, const Eigen::Matrix<double, 1, -1> >, const Eigen::Transpose<const Eigen::Block<const Eigen::Block<const Eigen::Block<Eigen::Matrix<double, -1, -1>, -1, -1, false>, -1, 1, true>, -1, 1, false> > > >; Dest = Eigen::Transpose<Eigen::Block<Eigen::Block<Eigen::Matrix<double, -1, -1, 1, -1, -1>, 1, -1, true>, 1, -1, false> >; int Mode = 6]’:
/home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/Eigen/src/Core/products/TriangularMatrixVector.h:332:12: warning: ‘result’ may be used uninitialized [-Wmaybe-uninitialized]
327 | internal::triangular_matrix_vector_product
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
328 | <Index,Mode,
| ~~~~~~~~~~~~
329 | LhsScalar, LhsBlasTraits::NeedToConjugate,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
330 | RhsScalar, RhsBlasTraits::NeedToConjugate,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
331 | RowMajor>
| ~~~~~~~~~
332 | ::run(actualLhs.rows(),actualLhs.cols(),
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
333 | actualLhs.data(),actualLhs.outerStride(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
334 | actualRhsPtr,1,
| ~~~~~~~~~~~~~~~
335 | dest.data(),dest.innerStride(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
336 | actualAlpha);
| ~~~~~~~~~~~~
/home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/Eigen/src/Core/products/TriangularMatrixVector.h:105:24: note: by argument 5 of type ‘const double*’ to ‘static void Eigen::internal::triangular_matrix_vector_product<Index, Mode, LhsScalar, ConjLhs, RhsScalar, ConjRhs, 1, Version>::run(Index, Index, const LhsScalar*, Index, const RhsScalar*, Index, ResScalar*, Index, const ResScalar&) [with Index = long int; int Mode = 6; LhsScalar = double; bool ConjLhs = false; RhsScalar = double; bool ConjRhs = false; int Version = 0]’ declared here
105 | EIGEN_DONT_INLINE void triangular_matrix_vector_product<Index,Mode,LhsScalar,ConjLhs,RhsScalar,ConjRhs,RowMajor,Version>
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/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/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/score_markers_pairwise.hpp:4,
from /home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/scran_markers/scran_markers.hpp:4,
from score_markers.cpp:10:
/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_pairwise_cohens_d_two_sided(size_t, size_t, const Stat_*, const Stat_*, size_t, size_t, const PrecomputedPairwiseWeights<Weight_>&, Stat_) [with Stat_ = double; Weight_ = double; size_t = long unsigned int]’:
/home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/scran_markers/score_markers_summary.hpp:466:75: required from ‘void scran_markers::internal::process_simple_summary_effects(size_t, size_t, size_t, size_t, const std::vector<T>&, const std::vector<T>&, const std::vector<T>&, const scran_markers::ScoreMarkersSummaryBuffers<Stat_, Rank_>&, const std::vector<T>&, double, size_t, int) [with Stat_ = double; Rank_ = int; size_t = long unsigned int]’
466 | auto tmp = compute_pairwise_cohens_d_two_sided(group, other, my_means, my_variances, ngroups, nblocks, preweights, threshold);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-devel_2025-02-19/site-library/assorthead/include/scran_markers/score_markers_summary.hpp:813:45: 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]’
813 | internal::process_simple_summary_effects(
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
814 | matrix.nrow(),
| ~~~~~~~~~~~~~~
815 | ngroups,
| ~~~~~~~~
816 | nblocks,
| ~~~~~~~~
817 | ncombos,
| ~~~~~~~~
818 | combo_means,
| ~~~~~~~~~~~~
819 | combo_vars,
| ~~~~~~~~~~~
820 | combo_detected,
| ~~~~~~~~~~~~~~~
821 | output,
| ~~~~~~~
822 | combo_weights,
| ~~~~~~~~~~~~~~
823 | options.threshold,
| ~~~~~~~~~~~~~~~~~~
824 | options.cache_size,
| ~~~~~~~~~~~~~~~~~~~
825 | options.num_threads
| ~~~~~~~~~~~~~~~~~~~
826 | );
| ~
score_markers.cpp:109:53: required from here
109 | 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:136:25: 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
136 | std::pair<Stat_, Stat_> compute_pairwise_cohens_d_two_sided(
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/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/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/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/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_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 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)