Aaron Lun
| Snapshot Date: 2025-03-18 13:40 -0400 (Tue, 18 Mar 2025) |
| git_url: https://git.bioconductor.org/packages/scrapper |
| git_branch: devel |
| git_last_commit: a8642ec |
| git_last_commit_date: 2025-03-17 13:12:05 -0400 (Mon, 17 Mar 2025) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-03-19 11:48 -0400 (Wed, 19 Mar 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2025-03-13 r87965) -- "Unsuffered Consequences" | 4742 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences" | 4545 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" | 4576 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" | 4528 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4459 |
| 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 1911/2313 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| scrapper 1.1.14 (landing page) Aaron Lun
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 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: 1.1.14 |
| 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_1.1.14.tar.gz |
| StartedAt: 2025-03-19 11:21:42 -0000 (Wed, 19 Mar 2025) |
| EndedAt: 2025-03-19 11:30:44 -0000 (Wed, 19 Mar 2025) |
| EllapsedTime: 541.9 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: scrapper.Rcheck |
| Warnings: 2 |
##############################################################################
##############################################################################
###
### 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_1.1.14.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/scrapper.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘scrapper/DESCRIPTION’ ... OK
* this is package ‘scrapper’ version ‘1.1.14’
* 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-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]
/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]
See ‘/home/biocbuild/bbs-3.21-bioc/meat/scrapper.Rcheck/00install.out’ for details.
* used C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
* checking C++ specification ... OK
* checking installed package size ... INFO
installed size is 116.4Mb
sub-directories of 1Mb or more:
libs 116.1Mb
* 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 ... NOTE
Namespace in Imports field not imported from: ‘Rigraphlib’
All declared Imports should be used.
* 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 line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... INFO
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... WARNING
Note: information on .o files is not available
File ‘/home/biocbuild/R/R-devel_2025-02-19/site-library/scrapper/libs/scrapper.so’:
Found ‘abort’, possibly from ‘abort’ (C)
Found ‘printf’, possibly from ‘printf’ (C)
Found ‘putchar’, possibly from ‘putchar’ (C)
Found ‘sprintf’, possibly from ‘sprintf’ (C)
Found ‘stderr’, possibly from ‘stderr’ (C)
Found ‘stdout’, possibly from ‘stdout’ (C)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
analyze 22.954 0.705 47.508
runAllNeighborSteps 0.095 0.000 12.963
* 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: 2 WARNINGs, 1 NOTE
See
‘/home/biocbuild/bbs-3.21-bioc/meat/scrapper.Rcheck/00check.log’
for details.
scrapper.Rcheck/00install.out
##############################################################################
##############################################################################
###
### 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 ‘1.1.14’
** 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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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)
scrapper.Rcheck/tests/testthat.Rout
R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(scrapper)
> test_check("scrapper")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 804 ]
>
> proc.time()
user system elapsed
59.751 2.208 262.060
scrapper.Rcheck/scrapper-Ex.timings
| name | user | system | elapsed | |
| adt_quality_control | 0.085 | 0.004 | 0.167 | |
| aggregateAcrossCells | 0.037 | 0.001 | 0.070 | |
| aggregateAcrossGenes | 0.023 | 0.000 | 0.044 | |
| analyze | 22.954 | 0.705 | 47.508 | |
| buildSnnGraph | 0.259 | 0.008 | 0.267 | |
| centerSizeFactors | 0.001 | 0.000 | 0.001 | |
| chooseHighlyVariableGenes | 0.002 | 0.000 | 0.002 | |
| choosePseudoCount | 0 | 0 | 0 | |
| clusterGraph | 1.663 | 0.028 | 2.094 | |
| clusterKmeans | 0.002 | 0.000 | 0.002 | |
| combineFactors | 0.004 | 0.000 | 0.005 | |
| computeClrm1Factors | 0.033 | 0.000 | 0.034 | |
| correctMnn | 0.417 | 0.003 | 0.430 | |
| crispr_quality_control | 0.028 | 0.000 | 0.056 | |
| fitVarianceTrend | 0.017 | 0.000 | 0.037 | |
| modelGeneVariances | 0.078 | 0.000 | 0.158 | |
| normalizeCounts | 0.133 | 0.008 | 0.281 | |
| rna_quality_control | 0.037 | 0.000 | 0.073 | |
| runAllNeighborSteps | 0.095 | 0.000 | 12.963 | |
| runPca | 0.171 | 0.005 | 0.358 | |
| runTsne | 0.282 | 0.000 | 0.563 | |
| runUmap | 0.223 | 0.008 | 0.467 | |
| sanitizeSizeFactors | 0.001 | 0.000 | 0.000 | |
| scaleByNeighbors | 0.119 | 0.000 | 0.239 | |
| scoreGeneSet | 0.083 | 0.004 | 0.176 | |
| scoreMarkers | 0.167 | 0.032 | 0.332 | |
| subsampleByNeighbors | 2.666 | 0.099 | 4.151 | |
| summarizeEffects | 0.106 | 0.000 | 0.215 | |
| testEnrichment | 0 | 0 | 0 | |