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This page was generated on 2024-12-24 11:47 -0500 (Tue, 24 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4754
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" 4472
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4426
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4381
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" 4373
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 1883/2274HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
scrapper 1.1.8  (landing page)
Aaron Lun
Snapshot Date: 2024-12-23 13:40 -0500 (Mon, 23 Dec 2024)
git_url: https://git.bioconductor.org/packages/scrapper
git_branch: devel
git_last_commit: 2fb5c04
git_last_commit_date: 2024-12-21 13:39:18 -0500 (Sat, 21 Dec 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  ERROR    ERROR  skipped
palomino7Windows Server 2022 Datacenter / x64  ERROR    ERROR  skippedskipped
lconwaymacOS 12.7.1 Monterey / x86_64  ERROR    ERROR  skippedskipped
kjohnson3macOS 13.7.1 Ventura / arm64  ERROR    ERROR  skippedskipped
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  ERROR    ERROR  skipped

INSTALL results for scrapper on kunpeng2

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.

raw results


Summary

Package: scrapper
Version: 1.1.8
Command: /home/biocbuild/R/R/bin/R CMD INSTALL scrapper
StartedAt: 2024-12-23 19:39:46 -0000 (Mon, 23 Dec 2024)
EndedAt: 2024-12-23 19:43:04 -0000 (Mon, 23 Dec 2024)
EllapsedTime: 198.0 seconds
RetCode: 1
Status:   ERROR  

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL scrapper
###
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* installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’
* installing *source* package ‘scrapper’ ...
** using staged installation
** libs
using C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
/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-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BiocNeighbors/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -DR_NO_REMAP -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-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BiocNeighbors/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -DR_NO_REMAP -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-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BiocNeighbors/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -DR_NO_REMAP -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-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BiocNeighbors/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -DR_NO_REMAP -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-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BiocNeighbors/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -DR_NO_REMAP -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-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BiocNeighbors/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -DR_NO_REMAP -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-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BiocNeighbors/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -DR_NO_REMAP -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-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BiocNeighbors/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -DR_NO_REMAP -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-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BiocNeighbors/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -DR_NO_REMAP -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-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BiocNeighbors/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -DR_NO_REMAP -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-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BiocNeighbors/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -DR_NO_REMAP -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-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BiocNeighbors/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -DR_NO_REMAP -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-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BiocNeighbors/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -DR_NO_REMAP -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-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BiocNeighbors/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -DR_NO_REMAP -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-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BiocNeighbors/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -DR_NO_REMAP -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-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BiocNeighbors/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -DR_NO_REMAP -c model_gene_variances.cpp -o model_gene_variances.o
In file included from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/tatami_stats/grouped_variances.hpp:6,
                 from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/tatami_stats/tatami_stats.hpp:7,
                 from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/scran_variances/model_gene_variances.hpp:5,
                 from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/scran_variances/scran_variances.hpp:5,
                 from model_gene_variances.cpp:8:
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/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-4.5.0-devel_2024-11-24/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-4.5.0-devel_2024-11-24/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-4.5.0-devel_2024-11-24/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:76:54:   required from here
   76 |         scran_variances::model_gene_variances_blocked(*mat, ptr, bbuffers, opt);
      |         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/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-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BiocNeighbors/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -DR_NO_REMAP -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-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BiocNeighbors/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -DR_NO_REMAP -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-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BiocNeighbors/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security -DR_NO_REMAP -c run_pca.cpp -o run_pca.o
In file included from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/Eigen/Core:214,
                 from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/Eigen/Dense:1,
                 from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/irlba/irlba.hpp:4,
                 from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/scran_pca/simple_pca.hpp:6,
                 from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/scran_pca/scran_pca.hpp:4,
                 from run_pca.cpp:10:
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/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-4.5.0-devel_2024-11-24/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-4.5.0-devel_2024-11-24/site-library/assorthead/include/Eigen/Core:172:
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/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-4.5.0-devel_2024-11-24/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-4.5.0-devel_2024-11-24/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-4.5.0-devel_2024-11-24/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-4.5.0-devel_2024-11-24/site-library/assorthead/include/scran_pca/scran_pca.hpp:5:
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/scran_pca/blocked_pca.hpp: In function ‘void scran_pca::internal::project_matrix_realized_sparse(const IrlbaSparseMatrix_&, EigenMatrix_&, const EigenMatrix_&, int)’:
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/scran_pca/blocked_pca.hpp:514:16: error: ‘parallelize’ is not a member of ‘irlba’
  514 |         irlba::parallelize(nthreads, [&](size_t t) -> void {
      |                ^~~~~~~~~~~
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/scran_pca/blocked_pca.hpp:514:16: note: suggested alternatives:
In file included from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/beachmat/include/Rtatami.h:6,
                 from run_pca.cpp:9:
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/tatami_r/parallelize.hpp:61:6: note:   ‘tatami_r::parallelize’
   61 | void parallelize(Function_ fun, Index_ njobs, int nthreads) {
      |      ^~~~~~~~~~~
In file included from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/tatami/dense/convert_to_dense.hpp:8,
                 from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/tatami/tatami.hpp:5,
                 from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/tatami_r/UnknownMatrix.hpp:5,
                 from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/tatami_r/tatami_r.hpp:4,
                 from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/beachmat/include/Rtatami.h:8:
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/tatami/dense/../utils/parallelize.hpp:42:6: note:   ‘tatami::parallelize’
   42 | void parallelize(Function_ fun, Index_ tasks, int threads) {
      |      ^~~~~~~~~~~
In file included from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/subpar/subpar.hpp:5,
                 from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/tatami_stats/counts.hpp:5,
                 from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/tatami_stats/tatami_stats.hpp:4,
                 from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/scran_pca/simple_pca.hpp:5:
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/subpar/range.hpp:232:6: note:   ‘subpar::parallelize’
  232 | void parallelize(int num_workers, Task_ num_tasks, Run_ run_task_range) {
      |      ^~~~~~~~~~~
In file included from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/tatami_stats/grouped_variances.hpp:6,
                 from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/assorthead/include/tatami_stats/tatami_stats.hpp:7:
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/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-4.5.0-devel_2024-11-24/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-4.5.0-devel_2024-11-24/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-4.5.0-devel_2024-11-24/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:87:41:   required from here
   87 |         auto out = scran_pca::simple_pca(*(mat->ptr), opt);
      |                    ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/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) {
      |                             ^~~~~~
make: *** [/home/biocbuild/R/R/etc/Makeconf:204: run_pca.o] Error 1
ERROR: compilation failed for package ‘scrapper’
* removing ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/scrapper’
* restoring previous ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/scrapper’