Jonathan Griffiths
| Snapshot Date: 2024-12-23 13:40 -0500 (Mon, 23 Dec 2024) |
| git_url: https://git.bioconductor.org/packages/DropletUtils |
| git_branch: devel |
| git_last_commit: 5aea486 |
| git_last_commit_date: 2024-12-10 17:50:38 -0500 (Tue, 10 Dec 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2024-12-24 11:46 -0500 (Tue, 24 Dec 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4373 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 601/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| DropletUtils 1.27.2 (landing page) Jonathan Griffiths
| 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 | WARNINGS | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | WARNINGS | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
|
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: 1.27.2 |
| Command: /home/biocbuild/R/R/bin/R CMD INSTALL DropletUtils |
| StartedAt: 2024-12-23 19:54:14 -0000 (Mon, 23 Dec 2024) |
| EndedAt: 2024-12-23 19:55:48 -0000 (Mon, 23 Dec 2024) |
| EllapsedTime: 93.8 seconds |
| RetCode: 0 |
| Status: OK |
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### Running command:
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### /home/biocbuild/R/R/bin/R CMD INSTALL DropletUtils
###
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* installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’
* installing *source* package ‘DropletUtils’ ...
** using staged installation
** libs
using C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
using C++11
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rhdf5lib/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/dqrng/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/scuttle/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rhdf5lib/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/dqrng/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/scuttle/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c downsample_run.cpp -o downsample_run.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rhdf5lib/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/dqrng/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/scuttle/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -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++11 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rhdf5lib/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/dqrng/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/scuttle/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -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++11 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rhdf5lib/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/dqrng/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/scuttle/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c find_swapped.cpp -o find_swapped.o
In file included from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/beachmat/include/beachmat3/lin_matrix.h:12,
from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/beachmat/include/beachmat3/read_lin_block.h:11,
from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/beachmat/include/beachmat3/beachmat.h:24,
from find_swapped.cpp:2:
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/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-devel_2024-11-24/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-devel_2024-11-24/site-library/beachmat/include/beachmat3/read_lin_block.h:36:39: required from ‘std::unique_ptr<M> 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-devel_2024-11-24/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-devel_2024-11-24/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-devel_2024-11-24/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-devel_2024-11-24/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-devel_2024-11-24/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-devel_2024-11-24/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-devel_2024-11-24/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-devel_2024-11-24/site-library/beachmat/include/beachmat3/read_lin_block.h:38:39: required from ‘std::unique_ptr<M> 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-devel_2024-11-24/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-devel_2024-11-24/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-devel_2024-11-24/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-devel_2024-11-24/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-devel_2024-11-24/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-devel_2024-11-24/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-devel_2024-11-24/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-devel_2024-11-24/site-library/beachmat/include/beachmat3/read_lin_block.h:40:39: required from ‘std::unique_ptr<M> 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-devel_2024-11-24/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-devel_2024-11-24/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-devel_2024-11-24/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-devel_2024-11-24/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-devel_2024-11-24/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-devel_2024-11-24/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-devel_2024-11-24/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-devel_2024-11-24/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-devel_2024-11-24/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-devel_2024-11-24/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-devel_2024-11-24/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-devel_2024-11-24/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-devel_2024-11-24/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-devel_2024-11-24/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-devel_2024-11-24/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-devel_2024-11-24/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-devel_2024-11-24/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-devel_2024-11-24/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-devel_2024-11-24/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-devel_2024-11-24/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-devel_2024-11-24/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-devel_2024-11-24/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-devel_2024-11-24/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-devel_2024-11-24/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-devel_2024-11-24/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++11 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rhdf5lib/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/dqrng/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/scuttle/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -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++11 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rhdf5lib/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/dqrng/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/scuttle/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -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++11 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rhdf5lib/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/dqrng/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/scuttle/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c hashed_deltas.cpp -o hashed_deltas.o
In file included from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/beachmat/include/beachmat3/lin_matrix.h:12,
from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/beachmat/include/beachmat3/read_lin_block.h:11,
from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/beachmat/include/beachmat3/beachmat.h:24,
from hashed_deltas.cpp:2:
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/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-devel_2024-11-24/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-devel_2024-11-24/site-library/beachmat/include/beachmat3/read_lin_block.h:36:39: required from ‘std::unique_ptr<M> 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-devel_2024-11-24/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-devel_2024-11-24/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-devel_2024-11-24/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-devel_2024-11-24/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-devel_2024-11-24/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-devel_2024-11-24/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-devel_2024-11-24/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-devel_2024-11-24/site-library/beachmat/include/beachmat3/read_lin_block.h:38:39: required from ‘std::unique_ptr<M> 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-devel_2024-11-24/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-devel_2024-11-24/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-devel_2024-11-24/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-devel_2024-11-24/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-devel_2024-11-24/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-devel_2024-11-24/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-devel_2024-11-24/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-devel_2024-11-24/site-library/beachmat/include/beachmat3/read_lin_block.h:40:39: required from ‘std::unique_ptr<M> 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-devel_2024-11-24/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-devel_2024-11-24/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-devel_2024-11-24/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-devel_2024-11-24/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-devel_2024-11-24/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-devel_2024-11-24/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-devel_2024-11-24/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-devel_2024-11-24/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-devel_2024-11-24/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-devel_2024-11-24/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-devel_2024-11-24/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-devel_2024-11-24/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-devel_2024-11-24/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-devel_2024-11-24/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-devel_2024-11-24/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-devel_2024-11-24/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-devel_2024-11-24/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-devel_2024-11-24/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-devel_2024-11-24/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-devel_2024-11-24/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-devel_2024-11-24/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-devel_2024-11-24/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-devel_2024-11-24/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-devel_2024-11-24/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-devel_2024-11-24/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++11 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rhdf5lib/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/dqrng/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/scuttle/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c montecarlo_pval.cpp -o montecarlo_pval.o
In file included from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include/boost/mpl/arg.hpp:25,
from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include/boost/mpl/placeholders.hpp:24,
from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include/boost/iterator/iterator_categories.hpp:16,
from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include/boost/iterator/iterator_concepts.hpp:10,
from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include/boost/range/concepts.hpp:20,
from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include/boost/range/size_type.hpp:20,
from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include/boost/range/size.hpp:21,
from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include/boost/random/hyperexponential_distribution.hpp:30,
from /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include/boost/random.hpp:71,
from montecarlo_pval.cpp:3:
/home/biocbuild/R/R-4.5.0-devel_2024-11-24/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-devel_2024-11-24/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-devel_2024-11-24/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-devel_2024-11-24/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++11 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rhdf5lib/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/dqrng/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/scuttle/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -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++11 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/beachmat/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rhdf5lib/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/BH/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/dqrng/include' -I'/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/scuttle/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c utils.cpp -o utils.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -shared -L/home/biocbuild/R/R/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 utils.o /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rhdf5lib/lib/libhdf5_cpp.a /home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rhdf5lib/lib/libhdf5.a -L/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/Rhdf5lib/lib -lcrypto -lcurl -lsz -laec -lz -ldl -lm -L/home/biocbuild/R/R/lib -lR
installing to /home/biocbuild/R/R-4.5.0-devel_2024-11-24/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)