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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:scrapper.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings scrapper_1.0.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/scrapper.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14)
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘scrapper/DESCRIPTION’ ... OK
* this is package ‘scrapper’ version ‘1.0.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘scrapper’ can be installed ... WARNING
Found the following significant warnings:
  /home/biocbuild/R/R-4.4.1/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]
  /home/biocbuild/R/R-4.4.1/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]
See ‘/home/biocbuild/bbs-3.20-bioc/meat/scrapper.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++ (conda-forge gcc 14.2.0-1) 14.2.0’
* checking installed package size ... NOTE
  installed size is 109.0Mb
  sub-directories of 1Mb or more:
    libs  108.7Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
runAllNeighborSteps 0.106  0.008   7.025
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/scrapper.Rcheck/00check.log’
for details.

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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-4.4.1/site-library’
* installing *source* package ‘scrapper’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (conda-forge gcc 14.2.0-1) 14.2.0’
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/assorthead/include' -I'/home/biocbuild/R/R-4.4.1/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.4.1/site-library/BiocNeighbors/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/assorthead/include' -I'/home/biocbuild/R/R-4.4.1/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.4.1/site-library/BiocNeighbors/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c adt_quality_control.cpp -o adt_quality_control.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/assorthead/include' -I'/home/biocbuild/R/R-4.4.1/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.4.1/site-library/BiocNeighbors/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c aggregate_across_cells.cpp -o aggregate_across_cells.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/assorthead/include' -I'/home/biocbuild/R/R-4.4.1/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.4.1/site-library/BiocNeighbors/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c build_snn_graph.cpp -o build_snn_graph.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/assorthead/include' -I'/home/biocbuild/R/R-4.4.1/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.4.1/site-library/BiocNeighbors/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c center_size_factors.cpp -o center_size_factors.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/assorthead/include' -I'/home/biocbuild/R/R-4.4.1/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.4.1/site-library/BiocNeighbors/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c choose_highly_variable_genes.cpp -o choose_highly_variable_genes.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/assorthead/include' -I'/home/biocbuild/R/R-4.4.1/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.4.1/site-library/BiocNeighbors/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c choose_pseudo_count.cpp -o choose_pseudo_count.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/assorthead/include' -I'/home/biocbuild/R/R-4.4.1/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.4.1/site-library/BiocNeighbors/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c cluster_graph.cpp -o cluster_graph.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/assorthead/include' -I'/home/biocbuild/R/R-4.4.1/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.4.1/site-library/BiocNeighbors/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c cluster_kmeans.cpp -o cluster_kmeans.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/assorthead/include' -I'/home/biocbuild/R/R-4.4.1/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.4.1/site-library/BiocNeighbors/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c combine_factors.cpp -o combine_factors.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/assorthead/include' -I'/home/biocbuild/R/R-4.4.1/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.4.1/site-library/BiocNeighbors/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c compute_clrm1_factors.cpp -o compute_clrm1_factors.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/assorthead/include' -I'/home/biocbuild/R/R-4.4.1/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.4.1/site-library/BiocNeighbors/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c correct_mnn.cpp -o correct_mnn.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/assorthead/include' -I'/home/biocbuild/R/R-4.4.1/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.4.1/site-library/BiocNeighbors/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c crispr_quality_control.cpp -o crispr_quality_control.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/assorthead/include' -I'/home/biocbuild/R/R-4.4.1/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.4.1/site-library/BiocNeighbors/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c fit_variance_trend.cpp -o fit_variance_trend.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/assorthead/include' -I'/home/biocbuild/R/R-4.4.1/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.4.1/site-library/BiocNeighbors/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c model_gene_variances.cpp -o model_gene_variances.o
In file included from /home/biocbuild/R/R-4.4.1/site-library/assorthead/include/tatami_stats/grouped_variances.hpp:6,
                 from /home/biocbuild/R/R-4.4.1/site-library/assorthead/include/tatami_stats/tatami_stats.hpp:7,
                 from /home/biocbuild/R/R-4.4.1/site-library/assorthead/include/scran_variances/model_gene_variances.hpp:5,
                 from /home/biocbuild/R/R-4.4.1/site-library/assorthead/include/scran_variances/scran_variances.hpp:5,
                 from model_gene_variances.cpp:8:
/home/biocbuild/R/R-4.4.1/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-4.4.1/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-4.4.1/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-4.4.1/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-4.4.1/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) {
      |                             ^~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/assorthead/include' -I'/home/biocbuild/R/R-4.4.1/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.4.1/site-library/BiocNeighbors/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c normalize_counts.cpp -o normalize_counts.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/assorthead/include' -I'/home/biocbuild/R/R-4.4.1/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.4.1/site-library/BiocNeighbors/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c rna_quality_control.cpp -o rna_quality_control.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/assorthead/include' -I'/home/biocbuild/R/R-4.4.1/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.4.1/site-library/BiocNeighbors/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c run_pca.cpp -o run_pca.o
In file included from /home/biocbuild/R/R-4.4.1/site-library/assorthead/include/Eigen/Core:214,
                 from /home/biocbuild/R/R-4.4.1/site-library/assorthead/include/Eigen/Dense:1,
                 from /home/biocbuild/R/R-4.4.1/site-library/assorthead/include/irlba/irlba.hpp:4,
                 from /home/biocbuild/R/R-4.4.1/site-library/assorthead/include/scran_pca/simple_pca.hpp:6,
                 from /home/biocbuild/R/R-4.4.1/site-library/assorthead/include/scran_pca/scran_pca.hpp:4,
                 from run_pca.cpp:10:
/home/biocbuild/R/R-4.4.1/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-4.4.1/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-4.4.1/site-library/assorthead/include/Eigen/Core:172:
/home/biocbuild/R/R-4.4.1/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-4.4.1/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-4.4.1/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-4.4.1/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-4.4.1/site-library/assorthead/include/tatami_stats/grouped_variances.hpp:6,
                 from /home/biocbuild/R/R-4.4.1/site-library/assorthead/include/tatami_stats/tatami_stats.hpp:7,
                 from /home/biocbuild/R/R-4.4.1/site-library/assorthead/include/scran_pca/simple_pca.hpp:5:
/home/biocbuild/R/R-4.4.1/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-4.4.1/site-library/assorthead/include/scran_pca/simple_pca.hpp:200:63:   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&) [with Value_ = double; Index_ = int; EigenMatrix_ = Eigen::Matrix<double, -1, -1>; EigenVector_ = Eigen::Matrix<double, -1, 1>; typename EigenVector_::Scalar = double]'
  200 |                 auto results = tatami_stats::variances::direct(values.data() + offset, num_nonzero, ncells, /* skip_nan = */ false);
      |                                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-4.4.1/site-library/assorthead/include/scran_pca/simple_pca.hpp:359:29:   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>]'
  359 |         internal::run_sparse(mat, options, output.components, output.rotation, output.variance_explained, output.center, output.scale, output.total_variance);
      |         ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-4.4.1/site-library/assorthead/include/scran_pca/simple_pca.hpp:391:15:   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]'
  391 |     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-4.4.1/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-4.4.1/site-library/assorthead/include/Eigen/Core:341:
/home/biocbuild/R/R-4.4.1/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-4.4.1/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-4.4.1/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>
      |                        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/assorthead/include' -I'/home/biocbuild/R/R-4.4.1/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.4.1/site-library/BiocNeighbors/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c run_tsne.cpp -o run_tsne.o
In file included from /home/biocbuild/R/R-4.4.1/site-library/assorthead/include/kmeans/InitializeKmeanspp.hpp:9,
                 from /home/biocbuild/R/R-4.4.1/site-library/assorthead/include/kmeans/kmeans.hpp:9,
                 from /home/biocbuild/R/R-4.4.1/site-library/assorthead/include/knncolle/Kmknn.hpp:11,
                 from /home/biocbuild/R/R-4.4.1/site-library/assorthead/include/knncolle/knncolle.hpp:13,
                 from run_tsne.cpp:4:
/home/biocbuild/R/R-4.4.1/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-4.4.1/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-4.4.1/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) {
      |                 ^~~~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/assorthead/include' -I'/home/biocbuild/R/R-4.4.1/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.4.1/site-library/BiocNeighbors/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c run_umap.cpp -o run_umap.o
In file included from /home/biocbuild/R/R-4.4.1/site-library/assorthead/include/Eigen/Core:214,
                 from /home/biocbuild/R/R-4.4.1/site-library/assorthead/include/Eigen/Dense:1,
                 from /home/biocbuild/R/R-4.4.1/site-library/assorthead/include/irlba/irlba.hpp:4,
                 from /home/biocbuild/R/R-4.4.1/site-library/assorthead/include/umappp/spectral_init.hpp:4,
                 from /home/biocbuild/R/R-4.4.1/site-library/assorthead/include/umappp/initialize.hpp:8,
                 from /home/biocbuild/R/R-4.4.1/site-library/assorthead/include/umappp/umappp.hpp:11,
                 from run_umap.cpp:4:
/home/biocbuild/R/R-4.4.1/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-4.4.1/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-4.4.1/site-library/assorthead/include/Eigen/Core:172:
/home/biocbuild/R/R-4.4.1/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-4.4.1/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-4.4.1/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-4.4.1/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-4.4.1/site-library/assorthead/include/umappp/initialize.hpp:6:
/home/biocbuild/R/R-4.4.1/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-4.4.1/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-4.4.1/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-4.4.1/site-library/assorthead/include/Eigen/Core:341:
/home/biocbuild/R/R-4.4.1/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-4.4.1/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-4.4.1/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>
      |                        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/assorthead/include' -I'/home/biocbuild/R/R-4.4.1/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.4.1/site-library/BiocNeighbors/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c sanitize_size_factors.cpp -o sanitize_size_factors.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/assorthead/include' -I'/home/biocbuild/R/R-4.4.1/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.4.1/site-library/BiocNeighbors/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c scale_by_neighbors.cpp -o scale_by_neighbors.o
In file included from scale_by_neighbors.cpp:3:
/home/biocbuild/R/R-4.4.1/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:14:63:   required from here
   14 |         values.push_back(mumosa::compute_distance<int, double>(dist.size(), dist.begin()));
      |                          ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-4.4.1/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) {
      |                           ^~~~~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/assorthead/include' -I'/home/biocbuild/R/R-4.4.1/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.4.1/site-library/BiocNeighbors/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c score_gene_set.cpp -o score_gene_set.o
In file included from /home/biocbuild/R/R-4.4.1/site-library/assorthead/include/Eigen/Core:214,
                 from /home/biocbuild/R/R-4.4.1/site-library/assorthead/include/Eigen/Dense:1,
                 from /home/biocbuild/R/R-4.4.1/site-library/assorthead/include/irlba/irlba.hpp:4,
                 from /home/biocbuild/R/R-4.4.1/site-library/assorthead/include/gsdecon/compute.hpp:8,
                 from /home/biocbuild/R/R-4.4.1/site-library/assorthead/include/gsdecon/gsdecon.hpp:4,
                 from score_gene_set.cpp:7:
/home/biocbuild/R/R-4.4.1/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-4.4.1/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-4.4.1/site-library/assorthead/include/Eigen/Core:172:
/home/biocbuild/R/R-4.4.1/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-4.4.1/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-4.4.1/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-4.4.1/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-4.4.1/site-library/assorthead/include/tatami_stats/grouped_variances.hpp:6,
                 from /home/biocbuild/R/R-4.4.1/site-library/assorthead/include/tatami_stats/tatami_stats.hpp:7,
                 from /home/biocbuild/R/R-4.4.1/site-library/assorthead/include/scran_pca/simple_pca.hpp:5,
                 from /home/biocbuild/R/R-4.4.1/site-library/assorthead/include/scran_pca/scran_pca.hpp:4,
                 from /home/biocbuild/R/R-4.4.1/site-library/assorthead/include/gsdecon/compute.hpp:9:
/home/biocbuild/R/R-4.4.1/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-4.4.1/site-library/assorthead/include/scran_pca/simple_pca.hpp:200:63:   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&) [with Value_ = double; Index_ = int; EigenMatrix_ = Eigen::Matrix<double, -1, -1>; EigenVector_ = Eigen::Matrix<double, -1, 1>; typename EigenVector_::Scalar = double]'
  200 |                 auto results = tatami_stats::variances::direct(values.data() + offset, num_nonzero, ncells, /* skip_nan = */ false);
      |                                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-4.4.1/site-library/assorthead/include/scran_pca/simple_pca.hpp:359:29:   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>]'
  359 |         internal::run_sparse(mat, options, output.components, output.rotation, output.variance_explained, output.center, output.scale, output.total_variance);
      |         ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-4.4.1/site-library/assorthead/include/scran_pca/simple_pca.hpp:391:15:   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]'
  391 |     simple_pca(mat, options, output);
      |     ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-4.4.1/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-4.4.1/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-4.4.1/site-library/assorthead/include/Eigen/Core:341:
/home/biocbuild/R/R-4.4.1/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-4.4.1/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-4.4.1/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>
      |                        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/assorthead/include' -I'/home/biocbuild/R/R-4.4.1/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.4.1/site-library/BiocNeighbors/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c score_markers.cpp -o score_markers.o
In file included from /home/biocbuild/R/R-4.4.1/site-library/assorthead/include/scran_markers/score_markers_pairwise.hpp:4,
                 from /home/biocbuild/R/R-4.4.1/site-library/assorthead/include/scran_markers/scran_markers.hpp:4,
                 from score_markers.cpp:10:
/home/biocbuild/R/R-4.4.1/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-4.4.1/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-4.4.1/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:100:53:   required from here
  100 |         scran_markers::score_markers_summary_blocked(*mat, static_cast<const int*>(groups.begin()), ptr, opt, buffers);
      |         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-4.4.1/site-library/assorthead/include/scran_markers/cohens_d.hpp:135:25: 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
  135 | std::pair<Stat_, Stat_> compute_pairwise_cohens_d_two_sided(
      |                         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/assorthead/include' -I'/home/biocbuild/R/R-4.4.1/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.4.1/site-library/BiocNeighbors/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c subsample_by_neighbors.cpp -o subsample_by_neighbors.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/assorthead/include' -I'/home/biocbuild/R/R-4.4.1/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.4.1/site-library/BiocNeighbors/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c summarize_effects.cpp -o summarize_effects.o
g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-4.4.1/lib -L/usr/local/lib -o scrapper.so RcppExports.o adt_quality_control.o aggregate_across_cells.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 -L/home/biocbuild/R/R-4.4.1/lib -lR
installing to /home/biocbuild/R/R-4.4.1/site-library/00LOCK-scrapper/00new/scrapper/libs
** R
** 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)

R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

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Type 'license()' or 'licence()' for distribution details.

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> library(testthat)
> library(scrapper)
> test_check("scrapper")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 642 ]
> 
> proc.time()
   user  system elapsed 
 18.947   0.759  59.587