Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-08-27 12:07 -0400 (Wed, 27 Aug 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4822 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4612 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4555 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4539 |
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 616/2319 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
DropletUtils 1.29.6 (landing page) Jonathan Griffiths
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | ERROR | ||||||||||
To the developers/maintainers of the DropletUtils package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/DropletUtils.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: DropletUtils |
Version: 1.29.6 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:DropletUtils.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings DropletUtils_1.29.6.tar.gz |
StartedAt: 2025-08-26 07:34:08 -0000 (Tue, 26 Aug 2025) |
EndedAt: 2025-08-26 07:39:56 -0000 (Tue, 26 Aug 2025) |
EllapsedTime: 348.4 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: DropletUtils.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:DropletUtils.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings DropletUtils_1.29.6.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/DropletUtils.Rcheck’ * using R version 4.5.0 (2025-04-11) * 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) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘DropletUtils/DESCRIPTION’ ... OK * this is package ‘DropletUtils’ version ‘1.29.6’ * 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 ... NOTE Found the following hidden files and directories: .BBSoptions These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘DropletUtils’ can be installed ... OK * used C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’ * checking C++ specification ... OK * checking installed package size ... INFO installed size is 30.9Mb sub-directories of 1Mb or more: libs 30.5Mb * 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 ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: ambientContribMaximum.Rd: SummarizedExperiment-class, BiocParallelParam-class ambientContribNegative.Rd: SummarizedExperiment-class ambientContribSparse.Rd: SummarizedExperiment-class, BiocParallelParam-class ambientProfileBimodal.Rd: SummarizedExperiment-class, medianSizeFactors ambientProfileEmpty.Rd: dgTMatrix-class, dgCMatrix-class, SummarizedExperiment-class, BiocParallelParam-class barcodeRanks.Rd: SummarizedExperiment-class, BiocParallelParam-class, DataFrame-class chimericDrops.Rd: DataFrame-class cleanTagCounts.Rd: SummarizedExperiment-class, isOutlier, DataFrame-class defaultDrops.Rd: SummarizedExperiment-class emptyDrops.Rd: dgTMatrix-class, dgCMatrix-class, SummarizedExperiment-class, BiocParallelParam-class, goodTuringProportions emptyDropsCellRanger.Rd: SummarizedExperiment-class, BiocParallelParam-class, DataFrame-class hashedDrops.Rd: SummarizedExperiment-class, DataFrame-class, metadata read10xCounts.Rd: SingleCellExperiment-class, DelayedArray-class, BiocParallelParam-class, TENxMatrix-class, splitAltExps read10xMolInfo.Rd: DataFrame-class removeAmbience.Rd: SummarizedExperiment-class, DataFrame-class, sumCountsAcrossCells, RealizationSink-class, BiocParallelParam-class swappedDrops.Rd: HDF5Matrix-class Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. * 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-4.5.0/site-library/DropletUtils/libs/DropletUtils.so’: Found ‘_ZSt4cerr’, possibly from ‘std::cerr’ (C++) Found ‘abort’, possibly from ‘abort’ (C) Found ‘exit’, possibly from ‘exit’ (C) Found ‘rand_r’, possibly from ‘rand_r’ (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 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’/home/biocbuild/R/R-4.5.0/bin/BATCH: line 60: 3131234 Segmentation fault (core dumped) ${R_HOME}/bin/R -f ${in} ${opts} ${R_BATCH_OPTIONS} > ${out} 2>&1 ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: 53: tryCatch(withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error), error = handle_fatal, skip = function(e) { }) 54: test_code(test = NULL, code = exprs, env = env, reporter = get_reporter() %||% StopReporter$new()) 55: source_file(path, env = env(env), desc = desc, error_call = error_call) 56: FUN(X[[i]], ...) 57: lapply(test_paths, test_one_file, env = env, desc = desc, error_call = error_call) 58: doTryCatch(return(expr), name, parentenv, handler) 59: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 60: tryCatchList(expr, classes, parentenv, handlers) 61: tryCatch(code, testthat_abort_reporter = function(cnd) { cat(conditionMessage(cnd), "\n") NULL}) 62: with_reporter(reporters$multi, lapply(test_paths, test_one_file, env = env, desc = desc, error_call = error_call)) 63: test_files_serial(test_dir = test_dir, test_package = test_package, test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, desc = desc, load_package = load_package, error_call = error_call) 64: test_files(test_dir = path, test_paths = test_paths, test_package = package, reporter = reporter, load_helpers = load_helpers, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, load_package = load_package, parallel = parallel) 65: test_dir("testthat", package = package, reporter = reporter, ..., load_package = "installed") 66: test_check("DropletUtils") An irrecoverable exception occurred. R is aborting now ... * 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 ERROR, 1 WARNING, 2 NOTEs See ‘/home/biocbuild/bbs-3.22-bioc/meat/DropletUtils.Rcheck/00check.log’ for details.
DropletUtils.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL DropletUtils ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’ * installing *source* package ‘DropletUtils’ ... ** this is package ‘DropletUtils’ version ‘1.29.6’ ** 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-4.5.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.5.0/site-library/assorthead/include' -I'/home/biocbuild/R/R-4.5.0/site-library/Rhdf5lib/include' -I'/home/biocbuild/R/R-4.5.0/site-library/BH/include' -I'/home/biocbuild/R/R-4.5.0/site-library/dqrng/include' -I'/home/biocbuild/R/R-4.5.0/site-library/scuttle/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-4.5.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.5.0/site-library/assorthead/include' -I'/home/biocbuild/R/R-4.5.0/site-library/Rhdf5lib/include' -I'/home/biocbuild/R/R-4.5.0/site-library/BH/include' -I'/home/biocbuild/R/R-4.5.0/site-library/dqrng/include' -I'/home/biocbuild/R/R-4.5.0/site-library/scuttle/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c downsample_run.cpp -o downsample_run.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.5.0/site-library/assorthead/include' -I'/home/biocbuild/R/R-4.5.0/site-library/Rhdf5lib/include' -I'/home/biocbuild/R/R-4.5.0/site-library/BH/include' -I'/home/biocbuild/R/R-4.5.0/site-library/dqrng/include' -I'/home/biocbuild/R/R-4.5.0/site-library/scuttle/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c encode_sequences.cpp -o encode_sequences.o encode_sequences.cpp: In function ‘Rcpp::IntegerVector encode_sequences(Rcpp::StringVector)’: encode_sequences.cpp:8:23: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare] 8 | for (size_t i=0; i<output.size(); ++i) { | ~^~~~~~~~~~~~~~ /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.5.0/site-library/assorthead/include' -I'/home/biocbuild/R/R-4.5.0/site-library/Rhdf5lib/include' -I'/home/biocbuild/R/R-4.5.0/site-library/BH/include' -I'/home/biocbuild/R/R-4.5.0/site-library/dqrng/include' -I'/home/biocbuild/R/R-4.5.0/site-library/scuttle/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c find_chimeric.cpp -o find_chimeric.o find_chimeric.cpp: In function ‘Rcpp::List find_chimeric(Rcpp::StringVector, Rcpp::IntegerVector, Rcpp::IntegerVector, double, bool)’: find_chimeric.cpp:28:23: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘long int’ [-Wsign-compare] 28 | for (size_t i=0; i<nmolecules; ++i, ++uIt) { | ~^~~~~~~~~~~ /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.5.0/site-library/assorthead/include' -I'/home/biocbuild/R/R-4.5.0/site-library/Rhdf5lib/include' -I'/home/biocbuild/R/R-4.5.0/site-library/BH/include' -I'/home/biocbuild/R/R-4.5.0/site-library/dqrng/include' -I'/home/biocbuild/R/R-4.5.0/site-library/scuttle/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c find_swapped.cpp -o find_swapped.o In file included from /home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/lin_matrix.h:12, from /home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/read_lin_block.h:11, from /home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/beachmat.h:24, from find_swapped.cpp:2: /home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of ‘beachmat::SparseArraySeed_reader<V, TIT>::SparseArraySeed_reader(Rcpp::RObject) [with V = Rcpp::Vector<13>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’: /home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/lin_matrix.h:561:46: required from ‘beachmat::lin_SparseArraySeed<V, TIT>::lin_SparseArraySeed(Rcpp::RObject) [with V = Rcpp::Vector<13>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’ 561 | lin_SparseArraySeed(Rcpp::RObject mat) : reader(mat) { | ^~~~~~~~~~~ /home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/read_lin_block.h:36:39: required from ‘std::unique_ptr<_Tp> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’ 36 | return std::unique_ptr<M>(new integer_SparseArraySeed(block)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/read_lin_block.h:65:57: required from here 65 | auto ptr = read_lin_sparse_block_raw<lin_matrix>(block); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ /home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/Csparse_reader.h:535:17: warning: comparison of integer expressions of different signedness: ‘const size_t’ {aka ‘const long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare] 535 | if (nnz != x.size()) { | ~~~~^~~~~~~~~~~ /home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/Csparse_reader.h:551:45: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare] 551 | if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) { | ~~~~~~^~~~ /home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/Csparse_reader.h:551:73: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare] 551 | if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) { | ~~~~~~^~~~ /home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/Csparse_reader.h:593:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare] 593 | for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) { | ~~^~~~~ /home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of ‘beachmat::SparseArraySeed_reader<V, TIT>::SparseArraySeed_reader(Rcpp::RObject) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’: /home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/lin_matrix.h:561:46: required from ‘beachmat::lin_SparseArraySeed<V, TIT>::lin_SparseArraySeed(Rcpp::RObject) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’ 561 | lin_SparseArraySeed(Rcpp::RObject mat) : reader(mat) { | ^~~~~~~~~~~ /home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/read_lin_block.h:38:39: required from ‘std::unique_ptr<_Tp> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’ 38 | return std::unique_ptr<M>(new double_SparseArraySeed(block)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/read_lin_block.h:65:57: required from here 65 | auto ptr = read_lin_sparse_block_raw<lin_matrix>(block); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ /home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/Csparse_reader.h:535:17: warning: comparison of integer expressions of different signedness: ‘const size_t’ {aka ‘const long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare] 535 | if (nnz != x.size()) { | ~~~~^~~~~~~~~~~ /home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/Csparse_reader.h:551:45: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare] 551 | if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) { | ~~~~~~^~~~ /home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/Csparse_reader.h:551:73: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare] 551 | if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) { | ~~~~~~^~~~ /home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/Csparse_reader.h:593:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare] 593 | for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) { | ~~^~~~~ /home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of ‘beachmat::SparseArraySeed_reader<V, TIT>::SparseArraySeed_reader(Rcpp::RObject) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’: /home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/lin_matrix.h:561:46: required from ‘beachmat::lin_SparseArraySeed<V, TIT>::lin_SparseArraySeed(Rcpp::RObject) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’ 561 | lin_SparseArraySeed(Rcpp::RObject mat) : reader(mat) { | ^~~~~~~~~~~ /home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/read_lin_block.h:40:39: required from ‘std::unique_ptr<_Tp> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’ 40 | return std::unique_ptr<M>(new logical_SparseArraySeed(block)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/read_lin_block.h:65:57: required from here 65 | auto ptr = read_lin_sparse_block_raw<lin_matrix>(block); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ /home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/Csparse_reader.h:535:17: warning: comparison of integer expressions of different signedness: ‘const size_t’ {aka ‘const long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare] 535 | if (nnz != x.size()) { | ~~~~^~~~~~~~~~~ /home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/Csparse_reader.h:551:45: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare] 551 | if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) { | ~~~~~~^~~~ /home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/Csparse_reader.h:551:73: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare] 551 | if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) { | ~~~~~~^~~~ /home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/Csparse_reader.h:593:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare] 593 | for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) { | ~~^~~~~ /home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of ‘beachmat::sparse_index<OUT, I> beachmat::Csparse_core<TIT, I, P>::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const int*; ALT = int*; TIT = const double*; I = int; P = long unsigned int; size_t = long unsigned int]’: /home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/Csparse_reader.h:650:42: required from ‘beachmat::sparse_index<OUT, int> beachmat::SparseArraySeed_reader<V, TIT>::get_row(size_t, ALT, int*, size_t, size_t) [with OUT = const int*; ALT = int*; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; size_t = long unsigned int]’ 650 | return core.template get_row<OUT>(r, work_x, work_i, first, last); | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/lin_matrix.h:596:51: required from ‘beachmat::sparse_index<const int*, int> beachmat::lin_SparseArraySeed<V, TIT>::get_row(size_t, int*, int*, size_t, size_t) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; size_t = long unsigned int]’ 596 | return reader.template get_row<const int*>(r, work_x, work_i, first, last); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/lin_matrix.h:595:35: required from here 595 | sparse_index<const int*, int> get_row(size_t r, int* work_x, int* work_i, size_t first, size_t last) { | ^~~~~~~ /home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: ‘const int’ and ‘const long unsigned int’ [-Wsign-compare] 250 | if (idex != *pIt && static_cast<size_t>(i[idex]) == r) { | ~~~~~^~~~~~~ /home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of ‘beachmat::sparse_index<OUT, I> beachmat::Csparse_core<TIT, I, P>::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const double*; ALT = double*; TIT = const double*; I = int; P = long unsigned int; size_t = long unsigned int]’: /home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/Csparse_reader.h:650:42: required from ‘beachmat::sparse_index<OUT, int> beachmat::SparseArraySeed_reader<V, TIT>::get_row(size_t, ALT, int*, size_t, size_t) [with OUT = const double*; ALT = double*; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; size_t = long unsigned int]’ 650 | return core.template get_row<OUT>(r, work_x, work_i, first, last); | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/lin_matrix.h:602:54: required from ‘beachmat::sparse_index<const double*, int> beachmat::lin_SparseArraySeed<V, TIT>::get_row(size_t, double*, int*, size_t, size_t) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; size_t = long unsigned int]’ 602 | return reader.template get_row<const double*>(r, work_x, work_i, first, last); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/lin_matrix.h:601:38: required from here 601 | sparse_index<const double*, int> get_row(size_t r, double* work_x, int* work_i, size_t first, size_t last) { | ^~~~~~~ /home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: ‘const int’ and ‘const long unsigned int’ [-Wsign-compare] 250 | if (idex != *pIt && static_cast<size_t>(i[idex]) == r) { | ~~~~~^~~~~~~ /home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of ‘beachmat::sparse_index<OUT, I> beachmat::Csparse_core<TIT, I, P>::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const int*; ALT = int*; TIT = const int*; I = int; P = long unsigned int; size_t = long unsigned int]’: /home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/Csparse_reader.h:650:42: required from ‘beachmat::sparse_index<OUT, int> beachmat::SparseArraySeed_reader<V, TIT>::get_row(size_t, ALT, int*, size_t, size_t) [with OUT = const int*; ALT = int*; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; size_t = long unsigned int]’ 650 | return core.template get_row<OUT>(r, work_x, work_i, first, last); | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/lin_matrix.h:596:51: required from ‘beachmat::sparse_index<const int*, int> beachmat::lin_SparseArraySeed<V, TIT>::get_row(size_t, int*, int*, size_t, size_t) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; size_t = long unsigned int]’ 596 | return reader.template get_row<const int*>(r, work_x, work_i, first, last); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/lin_matrix.h:595:35: required from here 595 | sparse_index<const int*, int> get_row(size_t r, int* work_x, int* work_i, size_t first, size_t last) { | ^~~~~~~ /home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: ‘const int’ and ‘const long unsigned int’ [-Wsign-compare] 250 | if (idex != *pIt && static_cast<size_t>(i[idex]) == r) { | ~~~~~^~~~~~~ /home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of ‘beachmat::sparse_index<OUT, I> beachmat::Csparse_core<TIT, I, P>::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const double*; ALT = double*; TIT = const int*; I = int; P = long unsigned int; size_t = long unsigned int]’: /home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/Csparse_reader.h:650:42: required from ‘beachmat::sparse_index<OUT, int> beachmat::SparseArraySeed_reader<V, TIT>::get_row(size_t, ALT, int*, size_t, size_t) [with OUT = const double*; ALT = double*; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; size_t = long unsigned int]’ 650 | return core.template get_row<OUT>(r, work_x, work_i, first, last); | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/lin_matrix.h:602:54: required from ‘beachmat::sparse_index<const double*, int> beachmat::lin_SparseArraySeed<V, TIT>::get_row(size_t, double*, int*, size_t, size_t) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; size_t = long unsigned int]’ 602 | return reader.template get_row<const double*>(r, work_x, work_i, first, last); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/lin_matrix.h:601:38: required from here 601 | sparse_index<const double*, int> get_row(size_t r, double* work_x, int* work_i, size_t first, size_t last) { | ^~~~~~~ /home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: ‘const int’ and ‘const long unsigned int’ [-Wsign-compare] 250 | if (idex != *pIt && static_cast<size_t>(i[idex]) == r) { | ~~~~~^~~~~~~ /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.5.0/site-library/assorthead/include' -I'/home/biocbuild/R/R-4.5.0/site-library/Rhdf5lib/include' -I'/home/biocbuild/R/R-4.5.0/site-library/BH/include' -I'/home/biocbuild/R/R-4.5.0/site-library/dqrng/include' -I'/home/biocbuild/R/R-4.5.0/site-library/scuttle/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c get_cell_barcodes.cpp -o get_cell_barcodes.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.5.0/site-library/assorthead/include' -I'/home/biocbuild/R/R-4.5.0/site-library/Rhdf5lib/include' -I'/home/biocbuild/R/R-4.5.0/site-library/BH/include' -I'/home/biocbuild/R/R-4.5.0/site-library/dqrng/include' -I'/home/biocbuild/R/R-4.5.0/site-library/scuttle/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c group_cells.cpp -o group_cells.o group_cells.cpp: In function ‘Rcpp::List group_cells(Rcpp::StringVector, Rcpp::IntegerVector)’: group_cells.cpp:10:10: warning: comparison of integer expressions of different signedness: ‘const size_t’ {aka ‘const long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare] 10 | if (N!=gems.size()) { | ~^~~~~~~~~~~~~ /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.5.0/site-library/assorthead/include' -I'/home/biocbuild/R/R-4.5.0/site-library/Rhdf5lib/include' -I'/home/biocbuild/R/R-4.5.0/site-library/BH/include' -I'/home/biocbuild/R/R-4.5.0/site-library/dqrng/include' -I'/home/biocbuild/R/R-4.5.0/site-library/scuttle/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c hashed_deltas.cpp -o hashed_deltas.o In file included from /home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/lin_matrix.h:12, from /home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/read_lin_block.h:11, from /home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/beachmat.h:24, from hashed_deltas.cpp:2: /home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of ‘beachmat::SparseArraySeed_reader<V, TIT>::SparseArraySeed_reader(Rcpp::RObject) [with V = Rcpp::Vector<13>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’: /home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/lin_matrix.h:561:46: required from ‘beachmat::lin_SparseArraySeed<V, TIT>::lin_SparseArraySeed(Rcpp::RObject) [with V = Rcpp::Vector<13>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’ 561 | lin_SparseArraySeed(Rcpp::RObject mat) : reader(mat) { | ^~~~~~~~~~~ /home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/read_lin_block.h:36:39: required from ‘std::unique_ptr<_Tp> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’ 36 | return std::unique_ptr<M>(new integer_SparseArraySeed(block)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/read_lin_block.h:65:57: required from here 65 | auto ptr = read_lin_sparse_block_raw<lin_matrix>(block); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ /home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/Csparse_reader.h:535:17: warning: comparison of integer expressions of different signedness: ‘const size_t’ {aka ‘const long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare] 535 | if (nnz != x.size()) { | ~~~~^~~~~~~~~~~ /home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/Csparse_reader.h:551:45: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare] 551 | if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) { | ~~~~~~^~~~ /home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/Csparse_reader.h:551:73: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare] 551 | if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) { | ~~~~~~^~~~ /home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/Csparse_reader.h:593:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare] 593 | for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) { | ~~^~~~~ /home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of ‘beachmat::SparseArraySeed_reader<V, TIT>::SparseArraySeed_reader(Rcpp::RObject) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’: /home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/lin_matrix.h:561:46: required from ‘beachmat::lin_SparseArraySeed<V, TIT>::lin_SparseArraySeed(Rcpp::RObject) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’ 561 | lin_SparseArraySeed(Rcpp::RObject mat) : reader(mat) { | ^~~~~~~~~~~ /home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/read_lin_block.h:38:39: required from ‘std::unique_ptr<_Tp> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’ 38 | return std::unique_ptr<M>(new double_SparseArraySeed(block)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/read_lin_block.h:65:57: required from here 65 | auto ptr = read_lin_sparse_block_raw<lin_matrix>(block); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ /home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/Csparse_reader.h:535:17: warning: comparison of integer expressions of different signedness: ‘const size_t’ {aka ‘const long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare] 535 | if (nnz != x.size()) { | ~~~~^~~~~~~~~~~ /home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/Csparse_reader.h:551:45: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare] 551 | if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) { | ~~~~~~^~~~ /home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/Csparse_reader.h:551:73: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare] 551 | if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) { | ~~~~~~^~~~ /home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/Csparse_reader.h:593:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare] 593 | for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) { | ~~^~~~~ /home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of ‘beachmat::SparseArraySeed_reader<V, TIT>::SparseArraySeed_reader(Rcpp::RObject) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’: /home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/lin_matrix.h:561:46: required from ‘beachmat::lin_SparseArraySeed<V, TIT>::lin_SparseArraySeed(Rcpp::RObject) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’ 561 | lin_SparseArraySeed(Rcpp::RObject mat) : reader(mat) { | ^~~~~~~~~~~ /home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/read_lin_block.h:40:39: required from ‘std::unique_ptr<_Tp> beachmat::read_lin_sparse_block_raw(Rcpp::RObject) [with M = lin_matrix; Rcpp::RObject = Rcpp::RObject_Impl<Rcpp::PreserveStorage>]’ 40 | return std::unique_ptr<M>(new logical_SparseArraySeed(block)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/read_lin_block.h:65:57: required from here 65 | auto ptr = read_lin_sparse_block_raw<lin_matrix>(block); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ /home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/Csparse_reader.h:535:17: warning: comparison of integer expressions of different signedness: ‘const size_t’ {aka ‘const long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare] 535 | if (nnz != x.size()) { | ~~~~^~~~~~~~~~~ /home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/Csparse_reader.h:551:45: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare] 551 | if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) { | ~~~~~~^~~~ /home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/Csparse_reader.h:551:73: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare] 551 | if (lastR <= 0 || lastR > NR || lastC <= 0 || lastC > NC) { | ~~~~~~^~~~ /home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/Csparse_reader.h:593:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_t’ {aka ‘const long unsigned int’} [-Wsign-compare] 593 | for (int v = 0; v < nnz; ++v, ++rowIt, ++colIt, ++xIt) { | ~~^~~~~ /home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of ‘beachmat::sparse_index<OUT, I> beachmat::Csparse_core<TIT, I, P>::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const int*; ALT = int*; TIT = const double*; I = int; P = long unsigned int; size_t = long unsigned int]’: /home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/Csparse_reader.h:650:42: required from ‘beachmat::sparse_index<OUT, int> beachmat::SparseArraySeed_reader<V, TIT>::get_row(size_t, ALT, int*, size_t, size_t) [with OUT = const int*; ALT = int*; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; size_t = long unsigned int]’ 650 | return core.template get_row<OUT>(r, work_x, work_i, first, last); | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/lin_matrix.h:596:51: required from ‘beachmat::sparse_index<const int*, int> beachmat::lin_SparseArraySeed<V, TIT>::get_row(size_t, int*, int*, size_t, size_t) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; size_t = long unsigned int]’ 596 | return reader.template get_row<const int*>(r, work_x, work_i, first, last); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/lin_matrix.h:595:35: required from here 595 | sparse_index<const int*, int> get_row(size_t r, int* work_x, int* work_i, size_t first, size_t last) { | ^~~~~~~ /home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: ‘const int’ and ‘const long unsigned int’ [-Wsign-compare] 250 | if (idex != *pIt && static_cast<size_t>(i[idex]) == r) { | ~~~~~^~~~~~~ /home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of ‘beachmat::sparse_index<OUT, I> beachmat::Csparse_core<TIT, I, P>::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const double*; ALT = double*; TIT = const double*; I = int; P = long unsigned int; size_t = long unsigned int]’: /home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/Csparse_reader.h:650:42: required from ‘beachmat::sparse_index<OUT, int> beachmat::SparseArraySeed_reader<V, TIT>::get_row(size_t, ALT, int*, size_t, size_t) [with OUT = const double*; ALT = double*; V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; size_t = long unsigned int]’ 650 | return core.template get_row<OUT>(r, work_x, work_i, first, last); | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/lin_matrix.h:602:54: required from ‘beachmat::sparse_index<const double*, int> beachmat::lin_SparseArraySeed<V, TIT>::get_row(size_t, double*, int*, size_t, size_t) [with V = Rcpp::Vector<14, Rcpp::PreserveStorage>; TIT = const double*; size_t = long unsigned int]’ 602 | return reader.template get_row<const double*>(r, work_x, work_i, first, last); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/lin_matrix.h:601:38: required from here 601 | sparse_index<const double*, int> get_row(size_t r, double* work_x, int* work_i, size_t first, size_t last) { | ^~~~~~~ /home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: ‘const int’ and ‘const long unsigned int’ [-Wsign-compare] 250 | if (idex != *pIt && static_cast<size_t>(i[idex]) == r) { | ~~~~~^~~~~~~ /home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of ‘beachmat::sparse_index<OUT, I> beachmat::Csparse_core<TIT, I, P>::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const int*; ALT = int*; TIT = const int*; I = int; P = long unsigned int; size_t = long unsigned int]’: /home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/Csparse_reader.h:650:42: required from ‘beachmat::sparse_index<OUT, int> beachmat::SparseArraySeed_reader<V, TIT>::get_row(size_t, ALT, int*, size_t, size_t) [with OUT = const int*; ALT = int*; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; size_t = long unsigned int]’ 650 | return core.template get_row<OUT>(r, work_x, work_i, first, last); | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/lin_matrix.h:596:51: required from ‘beachmat::sparse_index<const int*, int> beachmat::lin_SparseArraySeed<V, TIT>::get_row(size_t, int*, int*, size_t, size_t) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; size_t = long unsigned int]’ 596 | return reader.template get_row<const int*>(r, work_x, work_i, first, last); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/lin_matrix.h:595:35: required from here 595 | sparse_index<const int*, int> get_row(size_t r, int* work_x, int* work_i, size_t first, size_t last) { | ^~~~~~~ /home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: ‘const int’ and ‘const long unsigned int’ [-Wsign-compare] 250 | if (idex != *pIt && static_cast<size_t>(i[idex]) == r) { | ~~~~~^~~~~~~ /home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/Csparse_reader.h: In instantiation of ‘beachmat::sparse_index<OUT, I> beachmat::Csparse_core<TIT, I, P>::get_row(size_t, ALT, I*, size_t, size_t) [with OUT = const double*; ALT = double*; TIT = const int*; I = int; P = long unsigned int; size_t = long unsigned int]’: /home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/Csparse_reader.h:650:42: required from ‘beachmat::sparse_index<OUT, int> beachmat::SparseArraySeed_reader<V, TIT>::get_row(size_t, ALT, int*, size_t, size_t) [with OUT = const double*; ALT = double*; V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; size_t = long unsigned int]’ 650 | return core.template get_row<OUT>(r, work_x, work_i, first, last); | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/lin_matrix.h:602:54: required from ‘beachmat::sparse_index<const double*, int> beachmat::lin_SparseArraySeed<V, TIT>::get_row(size_t, double*, int*, size_t, size_t) [with V = Rcpp::Vector<10, Rcpp::PreserveStorage>; TIT = const int*; size_t = long unsigned int]’ 602 | return reader.template get_row<const double*>(r, work_x, work_i, first, last); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/lin_matrix.h:601:38: required from here 601 | sparse_index<const double*, int> get_row(size_t r, double* work_x, int* work_i, size_t first, size_t last) { | ^~~~~~~ /home/biocbuild/R/R-4.5.0/site-library/beachmat/include/beachmat3/Csparse_reader.h:250:22: warning: comparison of integer expressions of different signedness: ‘const int’ and ‘const long unsigned int’ [-Wsign-compare] 250 | if (idex != *pIt && static_cast<size_t>(i[idex]) == r) { | ~~~~~^~~~~~~ /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.5.0/site-library/assorthead/include' -I'/home/biocbuild/R/R-4.5.0/site-library/Rhdf5lib/include' -I'/home/biocbuild/R/R-4.5.0/site-library/BH/include' -I'/home/biocbuild/R/R-4.5.0/site-library/dqrng/include' -I'/home/biocbuild/R/R-4.5.0/site-library/scuttle/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c montecarlo_pval.cpp -o montecarlo_pval.o In file included from /home/biocbuild/R/R-4.5.0/site-library/BH/include/boost/mpl/aux_/na_assert.hpp:23, from /home/biocbuild/R/R-4.5.0/site-library/BH/include/boost/mpl/arg.hpp:25, from /home/biocbuild/R/R-4.5.0/site-library/BH/include/boost/mpl/placeholders.hpp:24, from /home/biocbuild/R/R-4.5.0/site-library/BH/include/boost/iterator/iterator_categories.hpp:16, from /home/biocbuild/R/R-4.5.0/site-library/BH/include/boost/iterator/iterator_concepts.hpp:10, from /home/biocbuild/R/R-4.5.0/site-library/BH/include/boost/range/concepts.hpp:20, from /home/biocbuild/R/R-4.5.0/site-library/BH/include/boost/range/size_type.hpp:20, from /home/biocbuild/R/R-4.5.0/site-library/BH/include/boost/range/size.hpp:21, from /home/biocbuild/R/R-4.5.0/site-library/BH/include/boost/random/hyperexponential_distribution.hpp:30, from /home/biocbuild/R/R-4.5.0/site-library/BH/include/boost/random.hpp:71, from montecarlo_pval.cpp:3: /home/biocbuild/R/R-4.5.0/site-library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses] 194 | failed ************ (Pred::************ | ^~~~~~~~~~~~~~~~~~~ 195 | assert_arg( void (*)(Pred), typename assert_arg_pred<Pred>::type ) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 196 | ); | ~ /home/biocbuild/R/R-4.5.0/site-library/BH/include/boost/mpl/assert.hpp:194:21: note: remove parentheses 194 | failed ************ (Pred::************ | ^~~~~~~~~~~~~~~~~~~ | - 195 | assert_arg( void (*)(Pred), typename assert_arg_pred<Pred>::type ) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 196 | ); | ~ | - /home/biocbuild/R/R-4.5.0/site-library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses] 199 | failed ************ (boost::mpl::not_<Pred>::************ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 200 | assert_not_arg( void (*)(Pred), typename assert_arg_pred_not<Pred>::type ) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 201 | ); | ~ /home/biocbuild/R/R-4.5.0/site-library/BH/include/boost/mpl/assert.hpp:199:21: note: remove parentheses 199 | failed ************ (boost::mpl::not_<Pred>::************ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | - 200 | assert_not_arg( void (*)(Pred), typename assert_arg_pred_not<Pred>::type ) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 201 | ); | ~ | - montecarlo_pval.cpp: In function ‘Rcpp::IntegerVector montecarlo_pval(Rcpp::IntegerVector, Rcpp::IntegerVector, Rcpp::NumericVector, Rcpp::NumericVector, int, double, Rcpp::List, Rcpp::IntegerVector)’: montecarlo_pval.cpp:99:23: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘const int’ [-Wsign-compare] 99 | if (higher<curlen) { | ~~~~~~^~~~~~~ /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.5.0/site-library/assorthead/include' -I'/home/biocbuild/R/R-4.5.0/site-library/Rhdf5lib/include' -I'/home/biocbuild/R/R-4.5.0/site-library/BH/include' -I'/home/biocbuild/R/R-4.5.0/site-library/dqrng/include' -I'/home/biocbuild/R/R-4.5.0/site-library/scuttle/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c rand_custom.cpp -o rand_custom.o rand_custom.cpp: In function ‘void check_pcg_vectors(Rcpp::List, Rcpp::IntegerVector, size_t, const char*)’: rand_custom.cpp:8:21: warning: comparison of integer expressions of different signedness: ‘R_xlen_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 8 | if (seeds.size()!=N) { | ~~~~~~~~~~~~^~~ rand_custom.cpp:14:23: warning: comparison of integer expressions of different signedness: ‘R_xlen_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 14 | if (streams.size()!=N) { | ~~~~~~~~~~~~~~^~~ /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.5.0/site-library/assorthead/include' -I'/home/biocbuild/R/R-4.5.0/site-library/Rhdf5lib/include' -I'/home/biocbuild/R/R-4.5.0/site-library/BH/include' -I'/home/biocbuild/R/R-4.5.0/site-library/dqrng/include' -I'/home/biocbuild/R/R-4.5.0/site-library/scuttle/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c read_mm.cpp -o read_mm.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.5.0/site-library/assorthead/include' -I'/home/biocbuild/R/R-4.5.0/site-library/Rhdf5lib/include' -I'/home/biocbuild/R/R-4.5.0/site-library/BH/include' -I'/home/biocbuild/R/R-4.5.0/site-library/dqrng/include' -I'/home/biocbuild/R/R-4.5.0/site-library/scuttle/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c utils.cpp -o utils.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-4.5.0/lib -L/usr/local/lib -o DropletUtils.so RcppExports.o downsample_run.o encode_sequences.o find_chimeric.o find_swapped.o get_cell_barcodes.o group_cells.o hashed_deltas.o montecarlo_pval.o rand_custom.o read_mm.o utils.o /home/biocbuild/R/R-4.5.0/site-library/Rhdf5lib/lib/libhdf5_cpp.a /home/biocbuild/R/R-4.5.0/site-library/Rhdf5lib/lib/libhdf5.a -L/home/biocbuild/R/R-4.5.0/site-library/Rhdf5lib/lib -lsz -laec -lz -ldl -lm -L/home/biocbuild/R/R-4.5.0/lib -lR installing to /home/biocbuild/R/R-4.5.0/site-library/00LOCK-DropletUtils/00new/DropletUtils/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 (DropletUtils)
DropletUtils.Rcheck/tests/testthat.Rout.fail
R version 4.5.0 (2025-04-11) -- "How About a Twenty-Six" 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(DropletUtils) Loading required package: SingleCellExperiment Loading required package: SummarizedExperiment Loading required package: MatrixGenerics Loading required package: matrixStats Attaching package: 'MatrixGenerics' The following objects are masked from 'package:matrixStats': colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse, colCounts, colCummaxs, colCummins, colCumprods, colCumsums, colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs, colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats, colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds, colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads, colWeightedMeans, colWeightedMedians, colWeightedSds, colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet, rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods, rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps, rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins, rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks, rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars, rowWeightedMads, rowWeightedMeans, rowWeightedMedians, rowWeightedSds, rowWeightedVars Loading required package: GenomicRanges Loading required package: stats4 Loading required package: BiocGenerics Loading required package: generics Attaching package: 'generics' The following objects are masked from 'package:base': as.difftime, as.factor, as.ordered, intersect, is.element, setdiff, setequal, union Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, saveRDS, table, tapply, unique, unsplit, which.max, which.min Loading required package: S4Vectors Attaching package: 'S4Vectors' The following object is masked from 'package:utils': findMatches The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: IRanges Loading required package: Seqinfo Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Attaching package: 'Biobase' The following object is masked from 'package:MatrixGenerics': rowMedians The following objects are masked from 'package:matrixStats': anyMissing, rowMedians > test_check("DropletUtils") *** caught segfault *** address 0x1, cause 'memory not mapped' Traceback: 1: read_mm(matrix.loc, two_pass = mtx.two.pass, class_name = mtx.class, threads = mtx.threads) 2: .read_from_sparse(run, version = version, is.prefix = FALSE, compressed = compressed, mtx.two.pass = mtx.two.pass, mtx.class = mtx.class, mtx.threads = mtx.threads) 3: FUN(...) 4: withCallingHandlers({ ERROR_CALL_DEPTH <<- (function() sys.nframe() - 1L)() FUN(...)}, error = function(e) { annotated_condition <- handle_error(e) stop(annotated_condition)}, warning = handle_warning) 5: doTryCatch(return(expr), name, parentenv, handler) 6: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 7: tryCatchList(expr, classes, parentenv, handlers) 8: tryCatch({ withCallingHandlers({ ERROR_CALL_DEPTH <<- (function() sys.nframe() - 1L)() FUN(...) }, error = function(e) { annotated_condition <- handle_error(e) stop(annotated_condition) }, warning = handle_warning)}, error = identity) 9: FUN(X[[i]], ...) 10: (function (X, FUN, ...) { FUN <- match.fun(FUN) if (!is.vector(X) || is.object(X)) X <- as.list(X) .Internal(lapply(X, FUN))})(X = "/home/biocbuild/tmp/RtmpYP1kcN/file2fc76229350200", FUN = function (...) { if (!identical(timeout, WORKER_TIMEOUT)) { setTimeLimit(timeout, timeout, TRUE) on.exit(setTimeLimit(Inf, Inf, FALSE)) } if (!is.null(globalOptions)) base::options(globalOptions) if (stop.on.error && ERROR_OCCURRED) { UNEVALUATED } else { .rng_reset_generator("L'Ecuyer-CMRG", SEED) output <- tryCatch({ withCallingHandlers({ ERROR_CALL_DEPTH <<- (function() sys.nframe() - 1L)() FUN(...) }, error = function(e) { annotated_condition <- handle_error(e) stop(annotated_condition) }, warning = handle_warning) }, error = identity) if (force.GC) gc(verbose = FALSE, full = FALSE) SEED <<- .rng_next_substream(SEED) output }}, type = "auto", version = "auto", genome = NULL, compressed = NULL, mtx.two.pass = TRUE, mtx.class = "CsparseMatrix", mtx.threads = 1) 11: do.call(lapply, args) 12: BiocParallel:::.workerLapply_impl(...) 13: (function (...) BiocParallel:::.workerLapply_impl(...))(X = "/home/biocbuild/tmp/RtmpYP1kcN/file2fc76229350200", FUN = function (run, type, version, genome, compressed, mtx.two.pass, mtx.class, mtx.threads) { cur.type <- .type_chooser(run, type) if (cur.type == "mtx") { .read_from_sparse(run, version = version, is.prefix = FALSE, compressed = compressed, mtx.two.pass = mtx.two.pass, mtx.class = mtx.class, mtx.threads = mtx.threads) } else if (cur.type == "prefix") { .read_from_sparse(run, version = version, is.prefix = TRUE, compressed = compressed, mtx.two.pass = mtx.two.pass, mtx.class = mtx.class, mtx.threads = mtx.threads) } else { .read_from_hdf5(run, genome = genome, version = version) } }, ARGS = list(type = "auto", version = "auto", genome = NULL, compressed = NULL, mtx.two.pass = TRUE, mtx.class = "CsparseMatrix", mtx.threads = 1), OPTIONS = list(log = FALSE, threshold = "INFO", stop.on.error = TRUE, as.error = TRUE, timeout = NA_integer_, force.GC = FALSE, globalOptions = NULL), BPRNGSEED = c(10407L, 1763172631L, -542487218L, -1784214123L, 377959037L, 1532812307L, -1263117200L), GLOBALS = list(), PACKAGES = character(0)) 14: do.call(msg$data$fun, msg$data$args) 15: doTryCatch(return(expr), name, parentenv, handler) 16: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 17: tryCatchList(expr, classes, parentenv, handlers) 18: tryCatch({ .autoload_s4_classes(msg$data$args$X) do.call(msg$data$fun, msg$data$args)}, error = function(e) { list(.error_worker_comm(e, "worker evaluation failed"))}) 19: .bpworker_EXEC(msg, bplog(backend$BPPARAM)) 20: .recv_any(manager$backend) 21: .recv_any(manager$backend) 22: .manager_recv(manager) 23: .manager_recv(manager) 24: .collect_result(manager, reducer, progress, BPPARAM) 25: .bploop_impl(ITER = ITER, FUN = FUN, ARGS = ARGS, BPPARAM = BPPARAM, BPOPTIONS = BPOPTIONS, BPREDO = BPREDO, reducer = reducer, progress.length = length(redo_index)) 26: bploop.lapply(manager, BPPARAM = BPPARAM, BPOPTIONS = BPOPTIONS, ...) 27: bploop(manager, BPPARAM = BPPARAM, BPOPTIONS = BPOPTIONS, ...) 28: .bpinit(manager = manager, X = X, FUN = FUN, ARGS = ARGS, BPPARAM = BPPARAM, BPOPTIONS = BPOPTIONS, BPREDO = BPREDO) 29: bplapply(samples, FUN = .tenx_loader, type = type, version = version, genome = genome, compressed = compressed, mtx.two.pass = mtx.two.pass, mtx.class = match.arg(mtx.class), mtx.threads = mtx.threads, BPPARAM = BPPARAM) 30: bplapply(samples, FUN = .tenx_loader, type = type, version = version, genome = genome, compressed = compressed, mtx.two.pass = mtx.two.pass, mtx.class = match.arg(mtx.class), mtx.threads = mtx.threads, BPPARAM = BPPARAM) 31: read10xCounts(tmpdir, mtx.two.pass = TRUE) 32: eval(code, test_env) 33: eval(code, test_env) 34: withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error) 35: doTryCatch(return(expr), name, parentenv, handler) 36: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 37: tryCatchList(expr, names[-nh], parentenv, handlers[-nh]) 38: doTryCatch(return(expr), name, parentenv, handler) 39: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]]) 40: tryCatchList(expr, classes, parentenv, handlers) 41: tryCatch(withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error), error = handle_fatal, skip = function(e) { }) 42: test_code(desc, code, env = parent.frame(), reporter = reporter) 43: test_that("read10xCounts works correctly for sparse counts, version < 3", { tmpdir <- tempfile() write10xCounts(path = tmpdir, my.counts, gene.id = gene.ids, gene.symbol = gene.symb, barcodes = cell.ids) sce10x <- read10xCounts(tmpdir) alt.counts <- my.counts rownames(alt.counts) <- gene.ids colnames(alt.counts) <- NULL expect_equal(counts(sce10x), alt.counts) expect_identical(rowData(sce10x)$ID, gene.ids) expect_identical(rowData(sce10x)$Symbol, gene.symb) expect_identical(sce10x$Sample, rep(tmpdir, ncol(my.counts))) expect_identical(sce10x$Barcode, cell.ids) sce10x.tp <- read10xCounts(tmpdir, mtx.two.pass = TRUE) expect_equal(counts(sce10x.tp), alt.counts) sce10x.svt <- read10xCounts(tmpdir, mtx.class = "SVT_SparseMatrix") svt.counts <- as(alt.counts, "SVT_SparseArray") expect_equal(counts(sce10x.svt), svt.counts) sce10x.tp.svt <- read10xCounts(tmpdir, mtx.two.pass = TRUE, mtx.class = "SVT_SparseMatrix") expect_equal(counts(sce10x.tp.svt), svt.counts) sce10x.mc <- read10xCounts(tmpdir, mtx.threads = 2) expect_equal(counts(sce10x.mc), alt.counts) sce10x.mc <- read10xCounts(tmpdir, mtx.threads = 2, mtx.two.pass = TRUE) expect_equal(counts(sce10x.mc), alt.counts) tmpdir2 <- tempfile() write10xCounts(path = tmpdir2, my.counts * 2, gene.id = gene.ids, gene.symbol = gene.symb, barcodes = cell.ids) sce10x2 <- read10xCounts(tmpdir2) expect_equal(assay(sce10x) * 2L, assay(sce10x2)) ref <- cbind(sce10x, sce10x2) colnames(ref) <- NULL combined <- read10xCounts(c(tmpdir, tmpdir2)) expect_equal(rowData(ref), rowData(combined)) expect_equal(colData(ref), colData(combined)) expect_equal(assay(ref), assay(combined)) }) 44: eval(code, test_env) 45: eval(code, test_env) 46: withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error) 47: doTryCatch(return(expr), name, parentenv, handler) 48: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 49: tryCatchList(expr, names[-nh], parentenv, handlers[-nh]) 50: doTryCatch(return(expr), name, parentenv, handler) 51: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]]) 52: tryCatchList(expr, classes, parentenv, handlers) 53: tryCatch(withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error), error = handle_fatal, skip = function(e) { }) 54: test_code(test = NULL, code = exprs, env = env, reporter = get_reporter() %||% StopReporter$new()) 55: source_file(path, env = env(env), desc = desc, error_call = error_call) 56: FUN(X[[i]], ...) 57: lapply(test_paths, test_one_file, env = env, desc = desc, error_call = error_call) 58: doTryCatch(return(expr), name, parentenv, handler) 59: tryCatchOne(expr, names, parentenv, handlers[[1L]]) 60: tryCatchList(expr, classes, parentenv, handlers) 61: tryCatch(code, testthat_abort_reporter = function(cnd) { cat(conditionMessage(cnd), "\n") NULL}) 62: with_reporter(reporters$multi, lapply(test_paths, test_one_file, env = env, desc = desc, error_call = error_call)) 63: test_files_serial(test_dir = test_dir, test_package = test_package, test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, desc = desc, load_package = load_package, error_call = error_call) 64: test_files(test_dir = path, test_paths = test_paths, test_package = package, reporter = reporter, load_helpers = load_helpers, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, load_package = load_package, parallel = parallel) 65: test_dir("testthat", package = package, reporter = reporter, ..., load_package = "installed") 66: test_check("DropletUtils") An irrecoverable exception occurred. R is aborting now ...
DropletUtils.Rcheck/DropletUtils-Ex.timings
name | user | system | elapsed | |
ambientContribMaximum | 1.240 | 0.004 | 1.248 | |
ambientContribNegative | 0.036 | 0.000 | 0.036 | |
ambientContribSparse | 0.047 | 0.000 | 0.047 | |
ambientProfileBimodal | 0.006 | 0.000 | 0.006 | |
ambientProfileEmpty | 0.093 | 0.012 | 0.106 | |
barcodeRanks | 0.202 | 0.012 | 0.215 | |
chimericDrops | 0.232 | 0.000 | 0.235 | |
cleanTagCounts | 0.079 | 0.000 | 0.080 | |
defaultDrops | 0.071 | 0.000 | 0.072 | |
downsampleReads | 0.168 | 0.000 | 0.169 | |
emptyDrops | 1.054 | 0.004 | 1.059 | |
emptyDropsCellRanger | 1.970 | 0.032 | 2.008 | |
encodeSequences | 0.000 | 0.000 | 0.001 | |
get10xMolInfoStats | 0.167 | 0.000 | 0.168 | |
hashedDrops | 0.144 | 0.004 | 0.148 | |
makeCountMatrix | 0.003 | 0.004 | 0.006 | |
read10xCounts | 0.480 | 0.000 | 0.483 | |
read10xMolInfo | 0.131 | 0.004 | 0.135 | |
removeAmbience | 0.371 | 0.028 | 0.400 | |
swappedDrops | 0.550 | 0.008 | 0.560 | |
write10xCounts | 0.133 | 0.012 | 0.145 | |