Bioconductor Single Package Builder - Build History

Snapshot Date:

URL: https://git.bioconductor.org/packages/beachmat.hdf5

Last Changed Rev: / Revision:

Last Changed Date:

Hostname	OS /Arch	BUILD	CHECK	BUILD BIN	POST-PROCESSING
lconway	macOS 12.6.5 Monterey/x86_64	ERROR	skipped	skipped	skipped
nebbiolo2	Linux (Ubuntu 22.04.2 LTS)/x86_64	ERROR	skipped	skipped	skipped

lconway Summary

[top]

Package: beachmat.hdf5

Version: 0.99.0

RVersion: 4.3

BiocVersion: 3.18

BuildCommand: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data beachmat.hdf5

BuildTime: 0 minutes 4.92 seconds

CheckCommand:

CheckTime:

BuildBinCommand:

BuildBinTime:

PackageFileSize: -1.00 KiB

BuildID:: beachmat.hdf5_20230804140720

PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: beachmat.hdf5. Starting Build package.

PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 0. Checking git clone status: 0. Installing package status: 1. Build Package status: 1.

lconway BUILD SRC output

[top]

===============================

 R CMD BUILD

===============================

* checking for file ‘beachmat.hdf5/DESCRIPTION’ ... OK
* preparing ‘beachmat.hdf5’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
      -----------------------------------
* installing *source* package ‘beachmat.hdf5’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using C++17
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/beachmat/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rhdf5lib/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c initialize_from_hdf5.cpp -o initialize_from_hdf5.o
In file included from initialize_from_hdf5.cpp:1:
In file included from ../inst/include/Rtatami_hdf5.h:24:
In file included from ../inst/include/tatami_hdf5/tatami_hdf5.hpp:16:
../inst/include/tatami_hdf5/Hdf5DenseMatrix.hpp:179:17: error: no template named 'OracleChunkCache' in namespace 'tatami'
        tatami::OracleChunkCache<Index_, Index_, std::vector<CachedValue_> > cache;
        ~~~~~~~~^
../inst/include/tatami_hdf5/Hdf5DenseMatrix.hpp:183:21: error: no template named 'LruChunkCache' in namespace 'tatami'
    typedef tatami::LruChunkCache<Index_, std::vector<CachedValue_> > LruCache;
            ~~~~~~~~^
2 errors generated.
make: *** [initialize_from_hdf5.o] Error 1
ERROR: compilation failed for package ‘beachmat.hdf5’
* removing ‘/private/var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T/Rtmpp3oZYp/Rinst1064a6a78ada8/beachmat.hdf5’
      -----------------------------------
ERROR: package installation failed

lconway CHECK output

[top]

lconway BUILD BIN output

[top]

nebbiolo2 Summary

[top]

Package: beachmat.hdf5

Version: 0.99.0

RVersion: 4.3

BiocVersion: 3.18

BuildCommand: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data beachmat.hdf5

BuildTime: 0 minutes 8.46 seconds

CheckCommand:

CheckTime:

BuildBinCommand:

BuildBinTime:

PackageFileSize: -1.00 KiB

BuildID:: beachmat.hdf5_20230804140720

PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: beachmat.hdf5. Starting Build package.

PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 0. Checking git clone status: 0. Installing package status: 1. Build Package status: 1.

nebbiolo2 BUILD SRC output

[top]

===============================

 R CMD BUILD

===============================

* checking for file ‘beachmat.hdf5/DESCRIPTION’ ... OK
* preparing ‘beachmat.hdf5’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
      -----------------------------------
* installing *source* package ‘beachmat.hdf5’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
using C++17
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I../inst/include -DNDEBUG -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I../inst/include -DNDEBUG -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/beachmat/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c initialize_from_hdf5.cpp -o initialize_from_hdf5.o
In file included from ../inst/include/tatami_hdf5/tatami_hdf5.hpp:16,
                 from ../inst/include/Rtatami_hdf5.h:24,
                 from initialize_from_hdf5.cpp:1:
../inst/include/tatami_hdf5/Hdf5DenseMatrix.hpp:179:17: error: ‘OracleChunkCache’ in namespace ‘tatami’ does not name a template type
  179 |         tatami::OracleChunkCache<Index_, Index_, std::vector<CachedValue_> > cache;
      |                 ^~~~~~~~~~~~~~~~
../inst/include/tatami_hdf5/Hdf5DenseMatrix.hpp:183:21: error: ‘LruChunkCache’ in namespace ‘tatami’ does not name a template type
  183 |     typedef tatami::LruChunkCache<Index_, std::vector<CachedValue_> > LruCache;
      |                     ^~~~~~~~~~~~~
../inst/include/tatami_hdf5/Hdf5DenseMatrix.hpp:202:25: error: ‘LruCache’ was not declared in this scope
  202 |         std::unique_ptr<LruCache> historian;
      |                         ^~~~~~~~
../inst/include/tatami_hdf5/Hdf5DenseMatrix.hpp:202:33: error: template argument 1 is invalid
  202 |         std::unique_ptr<LruCache> historian;
      |                                 ^
../inst/include/tatami_hdf5/Hdf5DenseMatrix.hpp:202:33: error: template argument 2 is invalid
../inst/include/tatami_hdf5/Hdf5DenseMatrix.hpp: In constructor ‘tatami_hdf5::Hdf5DenseMatrix<Value_, Index_, transpose_, CachedValue_>::OracleCache<accrow_>::OracleCache(Args_&& ...)’:
../inst/include/tatami_hdf5/Hdf5DenseMatrix.hpp:177:41: error: class ‘tatami_hdf5::Hdf5DenseMatrix<Value_, Index_, transpose_, CachedValue_>::OracleCache<accrow_>’ does not have any field named ‘cache’
  177 |         OracleCache(Args_&& ... args) : cache(std::forward<Args_>(args)...) {}
      |                                         ^~~~~
../inst/include/tatami_hdf5/Hdf5DenseMatrix.hpp: In member function ‘void tatami_hdf5::Hdf5DenseMatrix<Value_, Index_, transpose_, CachedValue_>::Hdf5Extractor<accrow_, selection_>::initialize_workspace(Index_)’:
../inst/include/tatami_hdf5/Hdf5DenseMatrix.hpp:506:43: error: expected type-specifier before ‘LruCache’
  506 |                 base->historian.reset(new LruCache(base->num_chunks_in_cache));
      |                                           ^~~~~~~~
In file included from ../inst/include/tatami_hdf5/tatami_hdf5.hpp:15,
                 from ../inst/include/Rtatami_hdf5.h:24,
                 from initialize_from_hdf5.cpp:1:
../inst/include/tatami_hdf5/Hdf5CompressedSparseMatrix.hpp: In instantiation of ‘tatami_hdf5::Hdf5CompressedSparseMatrix<row_, Value_, Index_, CachedValue_, CachedIndex_>::Hdf5CompressedSparseMatrix(Index_, Index_, std::string, std::string, std::string, std::string, const tatami_hdf5::Hdf5Options&) [with bool row_ = true; Value_ = double; Index_ = int; CachedValue_ = double; CachedIndex_ = int; std::string = std::__cxx11::basic_string<char>]’:
../inst/include/tatami_hdf5/Hdf5CompressedSparseMatrix.hpp:141:123:   required from ‘tatami_hdf5::Hdf5CompressedSparseMatrix<row_, Value_, Index_, CachedValue_, CachedIndex_>::Hdf5CompressedSparseMatrix(Index_, Index_, std::string, std::string, std::string, std::string) [with bool row_ = true; Value_ = double; Index_ = int; CachedValue_ = double; CachedIndex_ = int; std::string = std::__cxx11::basic_string<char>]’
initialize_from_hdf5.cpp:8:170:   required from here
../inst/include/tatami_hdf5/Hdf5CompressedSparseMatrix.hpp:92:56: warning: comparison of integer expressions of different signedness: ‘std::array<long long unsigned int, 1>::value_type’ {aka ‘long long unsigned int’} and ‘const int’ [-Wsign-compare]
   92 |         if (get_array_dimensions<1>(ihandle, "idx")[0] != nonzeros) {
../inst/include/tatami_hdf5/Hdf5CompressedSparseMatrix.hpp:99:22: warning: comparison of integer expressions of different signedness: ‘const int’ and ‘long unsigned int’ [-Wsign-compare]
   99 |         if (ptr_size != dim_p1) {
      |             ~~~~~~~~~^~~~~~~~~
../inst/include/tatami_hdf5/Hdf5CompressedSparseMatrix.hpp:109:29: warning: comparison of integer expressions of different signedness: ‘__gnu_cxx::__alloc_traits<std::allocator<long long unsigned int>, long long unsigned int>::value_type’ {aka ‘long long unsigned int’} and ‘const int’ [-Wsign-compare]
  109 |         if (pointers.back() != nonzeros) {
      |             ~~~~~~~~~~~~~~~~^~~~~~~~~~~
../inst/include/tatami_hdf5/Hdf5CompressedSparseMatrix.hpp: In instantiation of ‘tatami_hdf5::Hdf5CompressedSparseMatrix<row_, Value_, Index_, CachedValue_, CachedIndex_>::Hdf5CompressedSparseMatrix(Index_, Index_, std::string, std::string, std::string, std::string, const tatami_hdf5::Hdf5Options&) [with bool row_ = false; Value_ = double; Index_ = int; CachedValue_ = double; CachedIndex_ = int; std::string = std::__cxx11::basic_string<char>]’:
../inst/include/tatami_hdf5/Hdf5CompressedSparseMatrix.hpp:141:123:   required from ‘tatami_hdf5::Hdf5CompressedSparseMatrix<row_, Value_, Index_, CachedValue_, CachedIndex_>::Hdf5CompressedSparseMatrix(Index_, Index_, std::string, std::string, std::string, std::string) [with bool row_ = false; Value_ = double; Index_ = int; CachedValue_ = double; CachedIndex_ = int; std::string = std::__cxx11::basic_string<char>]’
initialize_from_hdf5.cpp:10:171:   required from here
../inst/include/tatami_hdf5/Hdf5CompressedSparseMatrix.hpp:92:56: warning: comparison of integer expressions of different signedness: ‘std::array<long long unsigned int, 1>::value_type’ {aka ‘long long unsigned int’} and ‘const int’ [-Wsign-compare]
   92 |         if (get_array_dimensions<1>(ihandle, "idx")[0] != nonzeros) {
../inst/include/tatami_hdf5/Hdf5CompressedSparseMatrix.hpp:99:22: warning: comparison of integer expressions of different signedness: ‘const int’ and ‘long unsigned int’ [-Wsign-compare]
   99 |         if (ptr_size != dim_p1) {
      |             ~~~~~~~~~^~~~~~~~~
../inst/include/tatami_hdf5/Hdf5CompressedSparseMatrix.hpp:109:29: warning: comparison of integer expressions of different signedness: ‘__gnu_cxx::__alloc_traits<std::allocator<long long unsigned int>, long long unsigned int>::value_type’ {aka ‘long long unsigned int’} and ‘const int’ [-Wsign-compare]
  109 |         if (pointers.back() != nonzeros) {
      |             ~~~~~~~~~~~~~~~~^~~~~~~~~~~
In file included from ../inst/include/tatami_hdf5/tatami_hdf5.hpp:16,
                 from ../inst/include/Rtatami_hdf5.h:24,
                 from initialize_from_hdf5.cpp:1:
../inst/include/tatami_hdf5/Hdf5DenseMatrix.hpp: In instantiation of ‘void tatami_hdf5::Hdf5DenseMatrix<Value_, Index_, transpose_, CachedValue_>::Hdf5Extractor<accrow_, selection_>::initialize_workspace(Index_) [with bool accrow_ = true; tatami::DimensionSelectionType selection_ = tatami::DimensionSelectionType::FULL; Value_ = double; Index_ = int; bool transpose_ = true; CachedValue_ = double]’:
../inst/include/tatami_hdf5/Hdf5DenseMatrix.hpp:424:17:   required from ‘tatami_hdf5::Hdf5DenseMatrix<Value_, Index_, transpose_, CachedValue_>::Hdf5Extractor<accrow_, selection_>::Hdf5Extractor(const tatami_hdf5::Hdf5DenseMatrix<Value_, Index_, transpose_, CachedValue_>*) [with bool accrow_ = true; tatami::DimensionSelectionType selection_ = tatami::DimensionSelectionType::FULL; Value_ = double; Index_ = int; bool transpose_ = true; CachedValue_ = double]’
../inst/include/tatami_hdf5/Hdf5DenseMatrix.hpp:544:87:   required from ‘std::unique_ptr<typename std::conditional<false, tatami::SparseExtractor<selection_, Value_, Index_>, tatami::DenseExtractor<selection_, Value_, Index_> >::type> tatami_hdf5::Hdf5DenseMatrix<Value_, Index_, transpose_, CachedValue_>::populate(const tatami::Options&, Args_&& ...) const [with bool accrow_ = true; tatami::DimensionSelectionType selection_ = tatami::DimensionSelectionType::FULL; Args_ = {}; Value_ = double; Index_ = int; bool transpose_ = true; CachedValue_ = double; typename std::conditional<false, tatami::SparseExtractor<selection_, Value_, Index_>, tatami::DenseExtractor<selection_, Value_, Index_> >::type = tatami::DenseExtractor<tatami::DimensionSelectionType::FULL, double, int>]’
../inst/include/tatami_hdf5/Hdf5DenseMatrix.hpp:549:68:   required from ‘std::unique_ptr<typename std::conditional<false, tatami::SparseExtractor<tatami::DimensionSelectionType::FULL, Value_, Index_>, tatami::DenseExtractor<tatami::DimensionSelectionType::FULL, Value_, Index_> >::type> tatami_hdf5::Hdf5DenseMatrix<Value_, Index_, transpose_, CachedValue_>::dense_row(const tatami::Options&) const [with Value_ = double; Index_ = int; bool transpose_ = true; CachedValue_ = double; typename std::conditional<false, tatami::SparseExtractor<tatami::DimensionSelectionType::FULL, Value_, Index_>, tatami::DenseExtractor<tatami::DimensionSelectionType::FULL, Value_, Index_> >::type = tatami::DenseExtractor<tatami::DimensionSelectionType::FULL, double, int>]’
../inst/include/tatami_hdf5/Hdf5DenseMatrix.hpp:548:66:   required from here
../inst/include/tatami_hdf5/Hdf5DenseMatrix.hpp:506:33: error: request for member ‘reset’ in ‘((tatami_hdf5::Hdf5DenseMatrix<double, int, true>::Hdf5Extractor<true, tatami::DimensionSelectionType::FULL>*)this)->tatami_hdf5::Hdf5DenseMatrix<double, int, true>::Hdf5Extractor<true, tatami::DimensionSelectionType::FULL>::base.std::unique_ptr<tatami_hdf5::Hdf5DenseMatrix<double, int, true>::Workspace<true>, std::default_delete<tatami_hdf5::Hdf5DenseMatrix<double, int, true>::Workspace<true> > >::operator->()->tatami_hdf5::Hdf5DenseMatrix<double, int, true>::Workspace<true>::historian’, which is of non-class type ‘int’
  506 |                 base->historian.reset(new LruCache(base->num_chunks_in_cache));
      |                 ~~~~~~~~~~~~~~~~^~~~~
../inst/include/tatami_hdf5/Hdf5DenseMatrix.hpp: In instantiation of ‘void tatami_hdf5::Hdf5DenseMatrix<Value_, Index_, transpose_, CachedValue_>::Hdf5Extractor<accrow_, selection_>::initialize_workspace(Index_) [with bool accrow_ = true; tatami::DimensionSelectionType selection_ = tatami::DimensionSelectionType::BLOCK; Value_ = double; Index_ = int; bool transpose_ = true; CachedValue_ = double]’:
../inst/include/tatami_hdf5/Hdf5DenseMatrix.hpp:432:17:   required from ‘tatami_hdf5::Hdf5DenseMatrix<Value_, Index_, transpose_, CachedValue_>::Hdf5Extractor<accrow_, selection_>::Hdf5Extractor(const tatami_hdf5::Hdf5DenseMatrix<Value_, Index_, transpose_, CachedValue_>*, Index_, Index_) [with bool accrow_ = true; tatami::DimensionSelectionType selection_ = tatami::DimensionSelectionType::BLOCK; Value_ = double; Index_ = int; bool transpose_ = true; CachedValue_ = double]’
../inst/include/tatami_hdf5/Hdf5DenseMatrix.hpp:544:87:   required from ‘std::unique_ptr<typename std::conditional<false, tatami::SparseExtractor<selection_, Value_, Index_>, tatami::DenseExtractor<selection_, Value_, Index_> >::type> tatami_hdf5::Hdf5DenseMatrix<Value_, Index_, transpose_, CachedValue_>::populate(const tatami::Options&, Args_&& ...) const [with bool accrow_ = true; tatami::DimensionSelectionType selection_ = tatami::DimensionSelectionType::BLOCK; Args_ = {int&, int&}; Value_ = double; Index_ = int; bool transpose_ = true; CachedValue_ = double; typename std::conditional<false, tatami::SparseExtractor<selection_, Value_, Index_>, tatami::DenseExtractor<selection_, Value_, Index_> >::type = tatami::DenseExtractor<tatami::DimensionSelectionType::BLOCK, double, int>]’
../inst/include/tatami_hdf5/Hdf5DenseMatrix.hpp:553:69:   required from ‘std::unique_ptr<typename std::conditional<false, tatami::SparseExtractor<tatami::DimensionSelectionType::BLOCK, Value_, Index_>, tatami::DenseExtractor<tatami::DimensionSelectionType::BLOCK, Value_, Index_> >::type> tatami_hdf5::Hdf5DenseMatrix<Value_, Index_, transpose_, CachedValue_>::dense_row(Index_, Index_, const tatami::Options&) const [with Value_ = double; Index_ = int; bool transpose_ = true; CachedValue_ = double; typename std::conditional<false, tatami::SparseExtractor<tatami::DimensionSelectionType::BLOCK, Value_, Index_>, tatami::DenseExtractor<tatami::DimensionSelectionType::BLOCK, Value_, Index_> >::type = tatami::DenseExtractor<tatami::DimensionSelectionType::BLOCK, double, int>]’
../inst/include/tatami_hdf5/Hdf5DenseMatrix.hpp:552:67:   required from here
../inst/include/tatami_hdf5/Hdf5DenseMatrix.hpp:506:33: error: request for member ‘reset’ in ‘((tatami_hdf5::Hdf5DenseMatrix<double, int, true>::Hdf5Extractor<true, tatami::DimensionSelectionType::BLOCK>*)this)->tatami_hdf5::Hdf5DenseMatrix<double, int, true>::Hdf5Extractor<true, tatami::DimensionSelectionType::BLOCK>::base.std::unique_ptr<tatami_hdf5::Hdf5DenseMatrix<double, int, true>::Workspace<true>, std::default_delete<tatami_hdf5::Hdf5DenseMatrix<double, int, true>::Workspace<true> > >::operator->()->tatami_hdf5::Hdf5DenseMatrix<double, int, true>::Workspace<true>::historian’, which is of non-class type ‘int’
../inst/include/tatami_hdf5/Hdf5DenseMatrix.hpp: In instantiation of ‘void tatami_hdf5::Hdf5DenseMatrix<Value_, Index_, transpose_, CachedValue_>::Hdf5Extractor<accrow_, selection_>::initialize_workspace(Index_) [with bool accrow_ = true; tatami::DimensionSelectionType selection_ = tatami::DimensionSelectionType::INDEX; Value_ = double; Index_ = int; bool transpose_ = true; CachedValue_ = double]’:
../inst/include/tatami_hdf5/Hdf5DenseMatrix.hpp:440:17:   required from ‘tatami_hdf5::Hdf5DenseMatrix<Value_, Index_, transpose_, CachedValue_>::Hdf5Extractor<accrow_, selection_>::Hdf5Extractor(const tatami_hdf5::Hdf5DenseMatrix<Value_, Index_, transpose_, CachedValue_>*, std::vector<Index>) [with bool accrow_ = true; tatami::DimensionSelectionType selection_ = tatami::DimensionSelectionType::INDEX; Value_ = double; Index_ = int; bool transpose_ = true; CachedValue_ = double]’
../inst/include/tatami_hdf5/Hdf5DenseMatrix.hpp:544:87:   required from ‘std::unique_ptr<typename std::conditional<false, tatami::SparseExtractor<selection_, Value_, Index_>, tatami::DenseExtractor<selection_, Value_, Index_> >::type> tatami_hdf5::Hdf5DenseMatrix<Value_, Index_, transpose_, CachedValue_>::populate(const tatami::Options&, Args_&& ...) const [with bool accrow_ = true; tatami::DimensionSelectionType selection_ = tatami::DimensionSelectionType::INDEX; Args_ = {std::vector<int, std::allocator<int> >}; Value_ = double; Index_ = int; bool transpose_ = true; CachedValue_ = double; typename std::conditional<false, tatami::SparseExtractor<selection_, Value_, Index_>, tatami::DenseExtractor<selection_, Value_, Index_> >::type = tatami::DenseExtractor<tatami::DimensionSelectionType::INDEX, double, int>]’
../inst/include/tatami_hdf5/Hdf5DenseMatrix.hpp:557:69:   required from ‘std::unique_ptr<typename std::conditional<false, tatami::SparseExtractor<tatami::DimensionSelectionType::INDEX, Value_, Index_>, tatami::DenseExtractor<tatami::DimensionSelectionType::INDEX, Value_, Index_> >::type> tatami_hdf5::Hdf5DenseMatrix<Value_, Index_, transpose_, CachedValue_>::dense_row(std::vector<Index>, const tatami::Options&) const [with Value_ = double; Index_ = int; bool transpose_ = true; CachedValue_ = double; typename std::conditional<false, tatami::SparseExtractor<tatami::DimensionSelectionType::INDEX, Value_, Index_>, tatami::DenseExtractor<tatami::DimensionSelectionType::INDEX, Value_, Index_> >::type = tatami::DenseExtractor<tatami::DimensionSelectionType::INDEX, double, int>]’
../inst/include/tatami_hdf5/Hdf5DenseMatrix.hpp:556:67:   required from here
../inst/include/tatami_hdf5/Hdf5DenseMatrix.hpp:506:33: error: request for member ‘reset’ in ‘((tatami_hdf5::Hdf5DenseMatrix<double, int, true>::Hdf5Extractor<true, tatami::DimensionSelectionType::INDEX>*)this)->tatami_hdf5::Hdf5DenseMatrix<double, int, true>::Hdf5Extractor<true, tatami::DimensionSelectionType::INDEX>::base.std::unique_ptr<tatami_hdf5::Hdf5DenseMatrix<double, int, true>::Workspace<true>, std::default_delete<tatami_hdf5::Hdf5DenseMatrix<double, int, true>::Workspace<true> > >::operator->()->tatami_hdf5::Hdf5DenseMatrix<double, int, true>::Workspace<true>::historian’, which is of non-class type ‘int’
../inst/include/tatami_hdf5/Hdf5DenseMatrix.hpp: In instantiation of ‘void tatami_hdf5::Hdf5DenseMatrix<Value_, Index_, transpose_, CachedValue_>::Hdf5Extractor<accrow_, selection_>::initialize_workspace(Index_) [with bool accrow_ = false; tatami::DimensionSelectionType selection_ = tatami::DimensionSelectionType::FULL; Value_ = double; Index_ = int; bool transpose_ = true; CachedValue_ = double]’:
../inst/include/tatami_hdf5/Hdf5DenseMatrix.hpp:424:17:   required from ‘tatami_hdf5::Hdf5DenseMatrix<Value_, Index_, transpose_, CachedValue_>::Hdf5Extractor<accrow_, selection_>::Hdf5Extractor(const tatami_hdf5::Hdf5DenseMatrix<Value_, Index_, transpose_, CachedValue_>*) [with bool accrow_ = false; tatami::DimensionSelectionType selection_ = tatami::DimensionSelectionType::FULL; Value_ = double; Index_ = int; bool transpose_ = true; CachedValue_ = double]’
../inst/include/tatami_hdf5/Hdf5DenseMatrix.hpp:544:87:   required from ‘std::unique_ptr<typename std::conditional<false, tatami::SparseExtractor<selection_, Value_, Index_>, tatami::DenseExtractor<selection_, Value_, Index_> >::type> tatami_hdf5::Hdf5DenseMatrix<Value_, Index_, transpose_, CachedValue_>::populate(const tatami::Options&, Args_&& ...) const [with bool accrow_ = false; tatami::DimensionSelectionType selection_ = tatami::DimensionSelectionType::FULL; Args_ = {}; Value_ = double; Index_ = int; bool transpose_ = true; CachedValue_ = double; typename std::conditional<false, tatami::SparseExtractor<selection_, Value_, Index_>, tatami::DenseExtractor<selection_, Value_, Index_> >::type = tatami::DenseExtractor<tatami::DimensionSelectionType::FULL, double, int>]’
../inst/include/tatami_hdf5/Hdf5DenseMatrix.hpp:561:69:   required from ‘std::unique_ptr<typename std::conditional<false, tatami::SparseExtractor<tatami::DimensionSelectionType::FULL, Value_, Index_>, tatami::DenseExtractor<tatami::DimensionSelectionType::FULL, Value_, Index_> >::type> tatami_hdf5::Hdf5DenseMatrix<Value_, Index_, transpose_, CachedValue_>::dense_column(const tatami::Options&) const [with Value_ = double; Index_ = int; bool transpose_ = true; CachedValue_ = double; typename std::conditional<false, tatami::SparseExtractor<tatami::DimensionSelectionType::FULL, Value_, Index_>, tatami::DenseExtractor<tatami::DimensionSelectionType::FULL, Value_, Index_> >::type = tatami::DenseExtractor<tatami::DimensionSelectionType::FULL, double, int>]’
../inst/include/tatami_hdf5/Hdf5DenseMatrix.hpp:560:66:   required from here
../inst/include/tatami_hdf5/Hdf5DenseMatrix.hpp:506:33: error: request for member ‘reset’ in ‘((tatami_hdf5::Hdf5DenseMatrix<double, int, true>::Hdf5Extractor<false, tatami::DimensionSelectionType::FULL>*)this)->tatami_hdf5::Hdf5DenseMatrix<double, int, true>::Hdf5Extractor<false, tatami::DimensionSelectionType::FULL>::base.std::unique_ptr<tatami_hdf5::Hdf5DenseMatrix<double, int, true>::Workspace<false>, std::default_delete<tatami_hdf5::Hdf5DenseMatrix<double, int, true>::Workspace<false> > >::operator->()->tatami_hdf5::Hdf5DenseMatrix<double, int, true>::Workspace<false>::historian’, which is of non-class type ‘int’
../inst/include/tatami_hdf5/Hdf5DenseMatrix.hpp: In instantiation of ‘void tatami_hdf5::Hdf5DenseMatrix<Value_, Index_, transpose_, CachedValue_>::Hdf5Extractor<accrow_, selection_>::initialize_workspace(Index_) [with bool accrow_ = false; tatami::DimensionSelectionType selection_ = tatami::DimensionSelectionType::BLOCK; Value_ = double; Index_ = int; bool transpose_ = true; CachedValue_ = double]’:
../inst/include/tatami_hdf5/Hdf5DenseMatrix.hpp:432:17:   required from ‘tatami_hdf5::Hdf5DenseMatrix<Value_, Index_, transpose_, CachedValue_>::Hdf5Extractor<accrow_, selection_>::Hdf5Extractor(const tatami_hdf5::Hdf5DenseMatrix<Value_, Index_, transpose_, CachedValue_>*, Index_, Index_) [with bool accrow_ = false; tatami::DimensionSelectionType selection_ = tatami::DimensionSelectionType::BLOCK; Value_ = double; Index_ = int; bool transpose_ = true; CachedValue_ = double]’
../inst/include/tatami_hdf5/Hdf5DenseMatrix.hpp:544:87:   required from ‘std::unique_ptr<typename std::conditional<false, tatami::SparseExtractor<selection_, Value_, Index_>, tatami::DenseExtractor<selection_, Value_, Index_> >::type> tatami_hdf5::Hdf5DenseMatrix<Value_, Index_, transpose_, CachedValue_>::populate(const tatami::Options&, Args_&& ...) const [with bool accrow_ = false; tatami::DimensionSelectionType selection_ = tatami::DimensionSelectionType::BLOCK; Args_ = {int&, int&}; Value_ = double; Index_ = int; bool transpose_ = true; CachedValue_ = double; typename std::conditional<false, tatami::SparseExtractor<selection_, Value_, Index_>, tatami::DenseExtractor<selection_, Value_, Index_> >::type = tatami::DenseExtractor<tatami::DimensionSelectionType::BLOCK, double, int>]’
../inst/include/tatami_hdf5/Hdf5DenseMatrix.hpp:565:70:   required from ‘std::unique_ptr<typename std::conditional<false, tatami::SparseExtractor<tatami::DimensionSelectionType::BLOCK, Value_, Index_>, tatami::DenseExtractor<tatami::DimensionSelectionType::BLOCK, Value_, Index_> >::type> tatami_hdf5::Hdf5DenseMatrix<Value_, Index_, transpose_, CachedValue_>::dense_column(Index_, Index_, const tatami::Options&) const [with Value_ = double; Index_ = int; bool transpose_ = true; CachedValue_ = double; typename std::conditional<false, tatami::SparseExtractor<tatami::DimensionSelectionType::BLOCK, Value_, Index_>, tatami::DenseExtractor<tatami::DimensionSelectionType::BLOCK, Value_, Index_> >::type = tatami::DenseExtractor<tatami::DimensionSelectionType::BLOCK, double, int>]’
../inst/include/tatami_hdf5/Hdf5DenseMatrix.hpp:564:67:   required from here
../inst/include/tatami_hdf5/Hdf5DenseMatrix.hpp:506:33: error: request for member ‘reset’ in ‘((tatami_hdf5::Hdf5DenseMatrix<double, int, true>::Hdf5Extractor<false, tatami::DimensionSelectionType::BLOCK>*)this)->tatami_hdf5::Hdf5DenseMatrix<double, int, true>::Hdf5Extractor<false, tatami::DimensionSelectionType::BLOCK>::base.std::unique_ptr<tatami_hdf5::Hdf5DenseMatrix<double, int, true>::Workspace<false>, std::default_delete<tatami_hdf5::Hdf5DenseMatrix<double, int, true>::Workspace<false> > >::operator->()->tatami_hdf5::Hdf5DenseMatrix<double, int, true>::Workspace<false>::historian’, which is of non-class type ‘int’
../inst/include/tatami_hdf5/Hdf5DenseMatrix.hpp: In instantiation of ‘void tatami_hdf5::Hdf5DenseMatrix<Value_, Index_, transpose_, CachedValue_>::Hdf5Extractor<accrow_, selection_>::initialize_workspace(Index_) [with bool accrow_ = false; tatami::DimensionSelectionType selection_ = tatami::DimensionSelectionType::INDEX; Value_ = double; Index_ = int; bool transpose_ = true; CachedValue_ = double]’:
../inst/include/tatami_hdf5/Hdf5DenseMatrix.hpp:440:17:   required from ‘tatami_hdf5::Hdf5DenseMatrix<Value_, Index_, transpose_, CachedValue_>::Hdf5Extractor<accrow_, selection_>::Hdf5Extractor(const tatami_hdf5::Hdf5DenseMatrix<Value_, Index_, transpose_, CachedValue_>*, std::vector<Index>) [with bool accrow_ = false; tatami::DimensionSelectionType selection_ = tatami::DimensionSelectionType::INDEX; Value_ = double; Index_ = int; bool transpose_ = true; CachedValue_ = double]’
../inst/include/tatami_hdf5/Hdf5DenseMatrix.hpp:544:87:   required from ‘std::unique_ptr<typename std::conditional<false, tatami::SparseExtractor<selection_, Value_, Index_>, tatami::DenseExtractor<selection_, Value_, Index_> >::type> tatami_hdf5::Hdf5DenseMatrix<Value_, Index_, transpose_, CachedValue_>::populate(const tatami::Options&, Args_&& ...) const [with bool accrow_ = false; tatami::DimensionSelectionType selection_ = tatami::DimensionSelectionType::INDEX; Args_ = {std::vector<int, std::allocator<int> >}; Value_ = double; Index_ = int; bool transpose_ = true; CachedValue_ = double; typename std::conditional<false, tatami::SparseExtractor<selection_, Value_, Index_>, tatami::DenseExtractor<selection_, Value_, Index_> >::type = tatami::DenseExtractor<tatami::DimensionSelectionType::INDEX, double, int>]’
../inst/include/tatami_hdf5/Hdf5DenseMatrix.hpp:569:70:   required from ‘std::unique_ptr<typename std::conditional<false, tatami::SparseExtractor<tatami::DimensionSelectionType::INDEX, Value_, Index_>, tatami::DenseExtractor<tatami::DimensionSelectionType::INDEX, Value_, Index_> >::type> tatami_hdf5::Hdf5DenseMatrix<Value_, Index_, transpose_, CachedValue_>::dense_column(std::vector<Index>, const tatami::Options&) const [with Value_ = double; Index_ = int; bool transpose_ = true; CachedValue_ = double; typename std::conditional<false, tatami::SparseExtractor<tatami::DimensionSelectionType::INDEX, Value_, Index_>, tatami::DenseExtractor<tatami::DimensionSelectionType::INDEX, Value_, Index_> >::type = tatami::DenseExtractor<tatami::DimensionSelectionType::INDEX, double, int>]’
../inst/include/tatami_hdf5/Hdf5DenseMatrix.hpp:568:67:   required from here
../inst/include/tatami_hdf5/Hdf5DenseMatrix.hpp:506:33: error: request for member ‘reset’ in ‘((tatami_hdf5::Hdf5DenseMatrix<double, int, true>::Hdf5Extractor<false, tatami::DimensionSelectionType::INDEX>*)this)->tatami_hdf5::Hdf5DenseMatrix<double, int, true>::Hdf5Extractor<false, tatami::DimensionSelectionType::INDEX>::base.std::unique_ptr<tatami_hdf5::Hdf5DenseMatrix<double, int, true>::Workspace<false>, std::default_delete<tatami_hdf5::Hdf5DenseMatrix<double, int, true>::Workspace<false> > >::operator->()->tatami_hdf5::Hdf5DenseMatrix<double, int, true>::Workspace<false>::historian’, which is of non-class type ‘int’
../inst/include/tatami_hdf5/Hdf5DenseMatrix.hpp: In instantiation of ‘void tatami_hdf5::Hdf5DenseMatrix<Value_, Index_, transpose_, CachedValue_>::Hdf5Extractor<accrow_, selection_>::set_oracle(std::unique_ptr<tatami::Oracle<Index_> >) [with bool accrow_ = false; tatami::DimensionSelectionType selection_ = tatami::DimensionSelectionType::INDEX; Value_ = double; Index_ = int; bool transpose_ = true; CachedValue_ = double]’:
../inst/include/tatami_hdf5/Hdf5DenseMatrix.hpp:529:14:   required from here
../inst/include/tatami_hdf5/Hdf5DenseMatrix.hpp:537:33: error: request for member ‘reset’ in ‘((tatami_hdf5::Hdf5DenseMatrix<double, int, true>::Hdf5Extractor<false, tatami::DimensionSelectionType::INDEX>*)this)->tatami_hdf5::Hdf5DenseMatrix<double, int, true>::Hdf5Extractor<false, tatami::DimensionSelectionType::INDEX>::base.std::unique_ptr<tatami_hdf5::Hdf5DenseMatrix<double, int, true>::Workspace<false>, std::default_delete<tatami_hdf5::Hdf5DenseMatrix<double, int, true>::Workspace<false> > >::operator->()->tatami_hdf5::Hdf5DenseMatrix<double, int, true>::Workspace<false>::historian’, which is of non-class type ‘int’
  537 |                 base->historian.reset();
      |                 ~~~~~~~~~~~~~~~~^~~~~
../inst/include/tatami_hdf5/Hdf5DenseMatrix.hpp: In instantiation of ‘void tatami_hdf5::Hdf5DenseMatrix<Value_, Index_, transpose_, CachedValue_>::Hdf5Extractor<accrow_, selection_>::set_oracle(std::unique_ptr<tatami::Oracle<Index_> >) [with bool accrow_ = false; tatami::DimensionSelectionType selection_ = tatami::DimensionSelectionType::BLOCK; Value_ = double; Index_ = int; bool transpose_ = true; CachedValue_ = double]’:
../inst/include/tatami_hdf5/Hdf5DenseMatrix.hpp:529:14:   required from here
../inst/include/tatami_hdf5/Hdf5DenseMatrix.hpp:537:33: error: request for member ‘reset’ in ‘((tatami_hdf5::Hdf5DenseMatrix<double, int, true>::Hdf5Extractor<false, tatami::DimensionSelectionType::BLOCK>*)this)->tatami_hdf5::Hdf5DenseMatrix<double, int, true>::Hdf5Extractor<false, tatami::DimensionSelectionType::BLOCK>::base.std::unique_ptr<tatami_hdf5::Hdf5DenseMatrix<double, int, true>::Workspace<false>, std::default_delete<tatami_hdf5::Hdf5DenseMatrix<double, int, true>::Workspace<false> > >::operator->()->tatami_hdf5::Hdf5DenseMatrix<double, int, true>::Workspace<false>::historian’, which is of non-class type ‘int’
../inst/include/tatami_hdf5/Hdf5DenseMatrix.hpp: In instantiation of ‘void tatami_hdf5::Hdf5DenseMatrix<Value_, Index_, transpose_, CachedValue_>::Hdf5Extractor<accrow_, selection_>::set_oracle(std::unique_ptr<tatami::Oracle<Index_> >) [with bool accrow_ = false; tatami::DimensionSelectionType selection_ = tatami::DimensionSelectionType::FULL; Value_ = double; Index_ = int; bool transpose_ = true; CachedValue_ = double]’:
../inst/include/tatami_hdf5/Hdf5DenseMatrix.hpp:529:14:   required from here
../inst/include/tatami_hdf5/Hdf5DenseMatrix.hpp:537:33: error: request for member ‘reset’ in ‘((tatami_hdf5::Hdf5DenseMatrix<double, int, true>::Hdf5Extractor<false, tatami::DimensionSelectionType::FULL>*)this)->tatami_hdf5::Hdf5DenseMatrix<double, int, true>::Hdf5Extractor<false, tatami::DimensionSelectionType::FULL>::base.std::unique_ptr<tatami_hdf5::Hdf5DenseMatrix<double, int, true>::Workspace<false>, std::default_delete<tatami_hdf5::Hdf5DenseMatrix<double, int, true>::Workspace<false> > >::operator->()->tatami_hdf5::Hdf5DenseMatrix<double, int, true>::Workspace<false>::historian’, which is of non-class type ‘int’
../inst/include/tatami_hdf5/Hdf5DenseMatrix.hpp: In instantiation of ‘void tatami_hdf5::Hdf5DenseMatrix<Value_, Index_, transpose_, CachedValue_>::Hdf5Extractor<accrow_, selection_>::set_oracle(std::unique_ptr<tatami::Oracle<Index_> >) [with bool accrow_ = true; tatami::DimensionSelectionType selection_ = tatami::DimensionSelectionType::INDEX; Value_ = double; Index_ = int; bool transpose_ = true; CachedValue_ = double]’:
../inst/include/tatami_hdf5/Hdf5DenseMatrix.hpp:529:14:   required from here
../inst/include/tatami_hdf5/Hdf5DenseMatrix.hpp:537:33: error: request for member ‘reset’ in ‘((tatami_hdf5::Hdf5DenseMatrix<double, int, true>::Hdf5Extractor<true, tatami::DimensionSelectionType::INDEX>*)this)->tatami_hdf5::Hdf5DenseMatrix<double, int, true>::Hdf5Extractor<true, tatami::DimensionSelectionType::INDEX>::base.std::unique_ptr<tatami_hdf5::Hdf5DenseMatrix<double, int, true>::Workspace<true>, std::default_delete<tatami_hdf5::Hdf5DenseMatrix<double, int, true>::Workspace<true> > >::operator->()->tatami_hdf5::Hdf5DenseMatrix<double, int, true>::Workspace<true>::historian’, which is of non-class type ‘int’
../inst/include/tatami_hdf5/Hdf5DenseMatrix.hpp: In instantiation of ‘void tatami_hdf5::Hdf5DenseMatrix<Value_, Index_, transpose_, CachedValue_>::Hdf5Extractor<accrow_, selection_>::set_oracle(std::unique_ptr<tatami::Oracle<Index_> >) [with bool accrow_ = true; tatami::DimensionSelectionType selection_ = tatami::DimensionSelectionType::BLOCK; Value_ = double; Index_ = int; bool transpose_ = true; CachedValue_ = double]’:
../inst/include/tatami_hdf5/Hdf5DenseMatrix.hpp:529:14:   required from here
../inst/include/tatami_hdf5/Hdf5DenseMatrix.hpp:537:33: error: request for member ‘reset’ in ‘((tatami_hdf5::Hdf5DenseMatrix<double, int, true>::Hdf5Extractor<true, tatami::DimensionSelectionType::BLOCK>*)this)->tatami_hdf5::Hdf5DenseMatrix<double, int, true>::Hdf5Extractor<true, tatami::DimensionSelectionType::BLOCK>::base.std::unique_ptr<tatami_hdf5::Hdf5DenseMatrix<double, int, true>::Workspace<true>, std::default_delete<tatami_hdf5::Hdf5DenseMatrix<double, int, true>::Workspace<true> > >::operator->()->tatami_hdf5::Hdf5DenseMatrix<double, int, true>::Workspace<true>::historian’, which is of non-class type ‘int’
../inst/include/tatami_hdf5/Hdf5DenseMatrix.hpp: In instantiation of ‘void tatami_hdf5::Hdf5DenseMatrix<Value_, Index_, transpose_, CachedValue_>::Hdf5Extractor<accrow_, selection_>::set_oracle(std::unique_ptr<tatami::Oracle<Index_> >) [with bool accrow_ = true; tatami::DimensionSelectionType selection_ = tatami::DimensionSelectionType::FULL; Value_ = double; Index_ = int; bool transpose_ = true; CachedValue_ = double]’:
../inst/include/tatami_hdf5/Hdf5DenseMatrix.hpp:529:14:   required from here
../inst/include/tatami_hdf5/Hdf5DenseMatrix.hpp:537:33: error: request for member ‘reset’ in ‘((tatami_hdf5::Hdf5DenseMatrix<double, int, true>::Hdf5Extractor<true, tatami::DimensionSelectionType::FULL>*)this)->tatami_hdf5::Hdf5DenseMatrix<double, int, true>::Hdf5Extractor<true, tatami::DimensionSelectionType::FULL>::base.std::unique_ptr<tatami_hdf5::Hdf5DenseMatrix<double, int, true>::Workspace<true>, std::default_delete<tatami_hdf5::Hdf5DenseMatrix<double, int, true>::Workspace<true> > >::operator->()->tatami_hdf5::Hdf5DenseMatrix<double, int, true>::Workspace<true>::historian’, which is of non-class type ‘int’
In file included from ../inst/include/tatami_hdf5/tatami_hdf5.hpp:15,
                 from ../inst/include/Rtatami_hdf5.h:24,
                 from initialize_from_hdf5.cpp:1:
../inst/include/tatami_hdf5/Hdf5CompressedSparseMatrix.hpp: In instantiation of ‘void tatami_hdf5::Hdf5CompressedSparseMatrix<row_, Value_, Index_, CachedValue_, CachedIndex_>::extract_secondary_raw_loop(size_t, Function_, Index_, Index_, tatami_hdf5::Hdf5CompressedSparseMatrix<row_, Value_, Index_, CachedValue_, CachedIndex_>::SecondaryWorkspace&, bool) const [with Function_ = tatami_hdf5::Hdf5CompressedSparseMatrix<true, double, int>::extract_secondary(size_t, double*, int*, int, int, tatami_hdf5::Hdf5CompressedSparseMatrix<true, double, int>::SecondaryWorkspace&, bool, bool) const::<lambda(int, double)>; bool row_ = true; Value_ = double; Index_ = int; CachedValue_ = double; CachedIndex_ = int; size_t = long unsigned int]’:
../inst/include/tatami_hdf5/Hdf5CompressedSparseMatrix.hpp:878:35:   required from ‘tatami::SparseRange<Value_, Index_> tatami_hdf5::Hdf5CompressedSparseMatrix<row_, Value_, Index_, CachedValue_, CachedIndex_>::extract_secondary(size_t, Value_*, Index_*, Index_, Index_, tatami_hdf5::Hdf5CompressedSparseMatrix<row_, Value_, Index_, CachedValue_, CachedIndex_>::SecondaryWorkspace&, bool, bool) const [with bool row_ = true; Value_ = double; Index_ = int; CachedValue_ = double; CachedIndex_ = int; size_t = long unsigned int]’
../inst/include/tatami_hdf5/Hdf5CompressedSparseMatrix.hpp:1125:59:   required from ‘tatami::SparseRange<Value_, Index_> tatami_hdf5::Hdf5CompressedSparseMatrix<row_, Value_, Index_, CachedValue_, CachedIndex_>::SparseHdf5SparseExtractor<accrow_, selection_>::fetch(Index_, Value_*, Index_*) [with bool accrow_ = false; tatami::DimensionSelectionType selection_ = tatami::DimensionSelectionType::BLOCK; bool row_ = true; Value_ = double; Index_ = int; CachedValue_ = double; CachedIndex_ = int]’
../inst/include/tatami_hdf5/Hdf5CompressedSparseMatrix.hpp:1109:45:   required from here
../inst/include/tatami_hdf5/Hdf5CompressedSparseMatrix.hpp:848:34: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  848 |         for (size_t j = start; j < end; ++j) {
      |                                ~~^~~~~
../inst/include/tatami_hdf5/Hdf5CompressedSparseMatrix.hpp: In instantiation of ‘void tatami_hdf5::Hdf5CompressedSparseMatrix<row_, Value_, Index_, CachedValue_, CachedIndex_>::extract_primary_raw(size_t, Function_, Index_, tatami_hdf5::Hdf5CompressedSparseMatrix<row_, Value_, Index_, CachedValue_, CachedIndex_>::PrimaryWorkspace&, bool) const [with Function_ = tatami_hdf5::Hdf5CompressedSparseMatrix<true, double, int>::extract_primary(size_t, double*, int*, const std::vector<int>&, tatami_hdf5::Hdf5CompressedSparseMatrix<true, double, int>::PrimaryWorkspace&, bool, bool) const::<lambda(const int*, const int*, const double*)>; bool row_ = true; Value_ = double; Index_ = int; CachedValue_ = double; CachedIndex_ = int; size_t = long unsigned int]’:
../inst/include/tatami_hdf5/Hdf5CompressedSparseMatrix.hpp:754:32:   required from ‘tatami::SparseRange<Value_, Index_> tatami_hdf5::Hdf5CompressedSparseMatrix<row_, Value_, Index_, CachedValue_, CachedIndex_>::extract_primary(size_t, Value_*, Index_*, const std::vector<Index_>&, tatami_hdf5::Hdf5CompressedSparseMatrix<row_, Value_, Index_, CachedValue_, CachedIndex_>::PrimaryWorkspace&, bool, bool) const [with bool row_ = true; Value_ = double; Index_ = int; CachedValue_ = double; CachedIndex_ = int; size_t = long unsigned int]’
../inst/include/tatami_hdf5/Hdf5CompressedSparseMatrix.hpp:1129:57:   required from ‘tatami::SparseRange<Value_, Index_> tatami_hdf5::Hdf5CompressedSparseMatrix<row_, Value_, Index_, CachedValue_, CachedIndex_>::SparseHdf5SparseExtractor<accrow_, selection_>::fetch(Index_, Value_*, Index_*) [with bool accrow_ = true; tatami::DimensionSelectionType selection_ = tatami::DimensionSelectionType::INDEX; bool row_ = true; Value_ = double; Index_ = int; CachedValue_ = double; CachedIndex_ = int]’
../inst/include/tatami_hdf5/Hdf5CompressedSparseMatrix.hpp:1109:45:   required from here
../inst/include/tatami_hdf5/Hdf5CompressedSparseMatrix.hpp:592:34: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare]
  592 |                 if (target.first != -1) {
      |                     ~~~~~~~~~~~~~^~~~~
../inst/include/tatami_hdf5/Hdf5CompressedSparseMatrix.hpp:609:30: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare]
  609 |             if (target.first == -1) {
      |                 ~~~~~~~~~~~~~^~~~~
../inst/include/tatami_hdf5/Hdf5CompressedSparseMatrix.hpp: In instantiation of ‘void tatami_hdf5::Hdf5CompressedSparseMatrix<row_, Value_, Index_, CachedValue_, CachedIndex_>::extract_primary_raw(size_t, Function_, Index_, tatami_hdf5::Hdf5CompressedSparseMatrix<row_, Value_, Index_, CachedValue_, CachedIndex_>::PrimaryWorkspace&, bool) const [with Function_ = tatami_hdf5::Hdf5CompressedSparseMatrix<true, double, int>::extract_primary(size_t, double*, int*, int, int, tatami_hdf5::Hdf5CompressedSparseMatrix<true, double, int>::PrimaryWorkspace&, bool, bool) const::<lambda(const int*, const int*, const double*)>; bool row_ = true; Value_ = double; Index_ = int; CachedValue_ = double; CachedIndex_ = int; size_t = long unsigned int]’:
../inst/include/tatami_hdf5/Hdf5CompressedSparseMatrix.hpp:646:32:   required from ‘tatami::SparseRange<Value_, Index_> tatami_hdf5::Hdf5CompressedSparseMatrix<row_, Value_, Index_, CachedValue_, CachedIndex_>::extract_primary(size_t, Value_*, Index_*, Index_, Index_, tatami_hdf5::Hdf5CompressedSparseMatrix<row_, Value_, Index_, CachedValue_, CachedIndex_>::PrimaryWorkspace&, bool, bool) const [with bool row_ = true; Value_ = double; Index_ = int; CachedValue_ = double; CachedIndex_ = int; size_t = long unsigned int]’
../inst/include/tatami_hdf5/Hdf5CompressedSparseMatrix.hpp:1123:57:   required from ‘tatami::SparseRange<Value_, Index_> tatami_hdf5::Hdf5CompressedSparseMatrix<row_, Value_, Index_, CachedValue_, CachedIndex_>::SparseHdf5SparseExtractor<accrow_, selection_>::fetch(Index_, Value_*, Index_*) [with bool accrow_ = true; tatami::DimensionSelectionType selection_ = tatami::DimensionSelectionType::BLOCK; bool row_ = true; Value_ = double; Index_ = int; CachedValue_ = double; CachedIndex_ = int]’
../inst/include/tatami_hdf5/Hdf5CompressedSparseMatrix.hpp:1109:45:   required from here
../inst/include/tatami_hdf5/Hdf5CompressedSparseMatrix.hpp:592:34: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare]
  592 |                 if (target.first != -1) {
      |                     ~~~~~~~~~~~~~^~~~~
../inst/include/tatami_hdf5/Hdf5CompressedSparseMatrix.hpp:609:30: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare]
  609 |             if (target.first == -1) {
      |                 ~~~~~~~~~~~~~^~~~~
../inst/include/tatami_hdf5/Hdf5CompressedSparseMatrix.hpp: In instantiation of ‘void tatami_hdf5::Hdf5CompressedSparseMatrix<row_, Value_, Index_, CachedValue_, CachedIndex_>::extract_secondary_raw_loop(size_t, Function_, Index_, Index_, tatami_hdf5::Hdf5CompressedSparseMatrix<row_, Value_, Index_, CachedValue_, CachedIndex_>::SecondaryWorkspace&, bool) const [with Function_ = tatami_hdf5::Hdf5CompressedSparseMatrix<true, double, int>::extract_secondary(size_t, double*, int, int, tatami_hdf5::Hdf5CompressedSparseMatrix<true, double, int>::SecondaryWorkspace&) const::<lambda(int, double)>; bool row_ = true; Value_ = double; Index_ = int; CachedValue_ = double; CachedIndex_ = int; size_t = long unsigned int]’:
../inst/include/tatami_hdf5/Hdf5CompressedSparseMatrix.hpp:862:35:   required from ‘const Value_* tatami_hdf5::Hdf5CompressedSparseMatrix<row_, Value_, Index_, CachedValue_, CachedIndex_>::extract_secondary(size_t, Value_*, Index_, Index_, tatami_hdf5::Hdf5CompressedSparseMatrix<row_, Value_, Index_, CachedValue_, CachedIndex_>::SecondaryWorkspace&) const [with bool row_ = true; Value_ = double; Index_ = int; CachedValue_ = double; CachedIndex_ = int; size_t = long unsigned int]’
../inst/include/tatami_hdf5/Hdf5CompressedSparseMatrix.hpp:1091:59:   required from ‘const Value_* tatami_hdf5::Hdf5CompressedSparseMatrix<row_, Value_, Index_, CachedValue_, CachedIndex_>::DenseHdf5SparseExtractor<accrow_, selection_>::fetch(Index_, Value_*) [with bool accrow_ = false; tatami::DimensionSelectionType selection_ = tatami::DimensionSelectionType::BLOCK; bool row_ = true; Value_ = double; Index_ = int; CachedValue_ = double; CachedIndex_ = int]’
../inst/include/tatami_hdf5/Hdf5CompressedSparseMatrix.hpp:1080:23:   required from here
../inst/include/tatami_hdf5/Hdf5CompressedSparseMatrix.hpp:848:34: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  848 |         for (size_t j = start; j < end; ++j) {
      |                                ~~^~~~~
../inst/include/tatami_hdf5/Hdf5CompressedSparseMatrix.hpp: In instantiation of ‘void tatami_hdf5::Hdf5CompressedSparseMatrix<row_, Value_, Index_, CachedValue_, CachedIndex_>::extract_primary_raw(size_t, Function_, Index_, tatami_hdf5::Hdf5CompressedSparseMatrix<row_, Value_, Index_, CachedValue_, CachedIndex_>::PrimaryWorkspace&, bool) const [with Function_ = tatami_hdf5::Hdf5CompressedSparseMatrix<true, double, int>::extract_primary(size_t, double*, const std::vector<int>&, tatami_hdf5::Hdf5CompressedSparseMatrix<true, double, int>::PrimaryWorkspace&) const::<lambda(const int*, const int*, const double*)>; bool row_ = true; Value_ = double; Index_ = int; CachedValue_ = double; CachedIndex_ = int; size_t = long unsigned int]’:
../inst/include/tatami_hdf5/Hdf5CompressedSparseMatrix.hpp:727:32:   required from ‘const Value_* tatami_hdf5::Hdf5CompressedSparseMatrix<row_, Value_, Index_, CachedValue_, CachedIndex_>::extract_primary(size_t, Value_*, const std::vector<Index_>&, tatami_hdf5::Hdf5CompressedSparseMatrix<row_, Value_, Index_, CachedValue_, CachedIndex_>::PrimaryWorkspace&) const [with bool row_ = true; Value_ = double; Index_ = int; CachedValue_ = double; CachedIndex_ = int; size_t = long unsigned int]’
../inst/include/tatami_hdf5/Hdf5CompressedSparseMatrix.hpp:1095:57:   required from ‘const Value_* tatami_hdf5::Hdf5CompressedSparseMatrix<row_, Value_, Index_, CachedValue_, CachedIndex_>::DenseHdf5SparseExtractor<accrow_, selection_>::fetch(Index_, Value_*) [with bool accrow_ = true; tatami::DimensionSelectionType selection_ = tatami::DimensionSelectionType::INDEX; bool row_ = true; Value_ = double; Index_ = int; CachedValue_ = double; CachedIndex_ = int]’
../inst/include/tatami_hdf5/Hdf5CompressedSparseMatrix.hpp:1080:23:   required from here
../inst/include/tatami_hdf5/Hdf5CompressedSparseMatrix.hpp:592:34: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare]
  592 |                 if (target.first != -1) {
      |                     ~~~~~~~~~~~~~^~~~~
../inst/include/tatami_hdf5/Hdf5CompressedSparseMatrix.hpp:609:30: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare]
  609 |             if (target.first == -1) {
      |                 ~~~~~~~~~~~~~^~~~~
../inst/include/tatami_hdf5/Hdf5CompressedSparseMatrix.hpp: In instantiation of ‘void tatami_hdf5::Hdf5CompressedSparseMatrix<row_, Value_, Index_, CachedValue_, CachedIndex_>::extract_primary_raw(size_t, Function_, Index_, tatami_hdf5::Hdf5CompressedSparseMatrix<row_, Value_, Index_, CachedValue_, CachedIndex_>::PrimaryWorkspace&, bool) const [with Function_ = tatami_hdf5::Hdf5CompressedSparseMatrix<true, double, int>::extract_primary(size_t, double*, int, int, tatami_hdf5::Hdf5CompressedSparseMatrix<true, double, int>::PrimaryWorkspace&) const::<lambda(const int*, const int*, const double*)>; bool row_ = true; Value_ = double; Index_ = int; CachedValue_ = double; CachedIndex_ = int; size_t = long unsigned int]’:
../inst/include/tatami_hdf5/Hdf5CompressedSparseMatrix.hpp:622:32:   required from ‘const Value_* tatami_hdf5::Hdf5CompressedSparseMatrix<row_, Value_, Index_, CachedValue_, CachedIndex_>::extract_primary(size_t, Value_*, Index_, Index_, tatami_hdf5::Hdf5CompressedSparseMatrix<row_, Value_, Index_, CachedValue_, CachedIndex_>::PrimaryWorkspace&) const [with bool row_ = true; Value_ = double; Index_ = int; CachedValue_ = double; CachedIndex_ = int; size_t = long unsigned int]’
../inst/include/tatami_hdf5/Hdf5CompressedSparseMatrix.hpp:1089:57:   required from ‘const Value_* tatami_hdf5::Hdf5CompressedSparseMatrix<row_, Value_, Index_, CachedValue_, CachedIndex_>::DenseHdf5SparseExtractor<accrow_, selection_>::fetch(Index_, Value_*) [with bool accrow_ = true; tatami::DimensionSelectionType selection_ = tatami::DimensionSelectionType::BLOCK; bool row_ = true; Value_ = double; Index_ = int; CachedValue_ = double; CachedIndex_ = int]’
../inst/include/tatami_hdf5/Hdf5CompressedSparseMatrix.hpp:1080:23:   required from here
../inst/include/tatami_hdf5/Hdf5CompressedSparseMatrix.hpp:592:34: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare]
  592 |                 if (target.first != -1) {
      |                     ~~~~~~~~~~~~~^~~~~
../inst/include/tatami_hdf5/Hdf5CompressedSparseMatrix.hpp:609:30: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare]
  609 |             if (target.first == -1) {
      |                 ~~~~~~~~~~~~~^~~~~
../inst/include/tatami_hdf5/Hdf5CompressedSparseMatrix.hpp: In instantiation of ‘void tatami_hdf5::Hdf5CompressedSparseMatrix<row_, Value_, Index_, CachedValue_, CachedIndex_>::extract_primary_raw(size_t, Function_, Index_, tatami_hdf5::Hdf5CompressedSparseMatrix<row_, Value_, Index_, CachedValue_, CachedIndex_>::PrimaryWorkspace&, bool) const [with Function_ = tatami_hdf5::Hdf5CompressedSparseMatrix<false, double, int>::extract_primary(size_t, double*, int*, const std::vector<int>&, tatami_hdf5::Hdf5CompressedSparseMatrix<false, double, int>::PrimaryWorkspace&, bool, bool) const::<lambda(const int*, const int*, const double*)>; bool row_ = false; Value_ = double; Index_ = int; CachedValue_ = double; CachedIndex_ = int; size_t = long unsigned int]’:
../inst/include/tatami_hdf5/Hdf5CompressedSparseMatrix.hpp:754:32:   required from ‘tatami::SparseRange<Value_, Index_> tatami_hdf5::Hdf5CompressedSparseMatrix<row_, Value_, Index_, CachedValue_, CachedIndex_>::extract_primary(size_t, Value_*, Index_*, const std::vector<Index_>&, tatami_hdf5::Hdf5CompressedSparseMatrix<row_, Value_, Index_, CachedValue_, CachedIndex_>::PrimaryWorkspace&, bool, bool) const [with bool row_ = false; Value_ = double; Index_ = int; CachedValue_ = double; CachedIndex_ = int; size_t = long unsigned int]’
../inst/include/tatami_hdf5/Hdf5CompressedSparseMatrix.hpp:1129:57:   required from ‘tatami::SparseRange<Value_, Index_> tatami_hdf5::Hdf5CompressedSparseMatrix<row_, Value_, Index_, CachedValue_, CachedIndex_>::SparseHdf5SparseExtractor<accrow_, selection_>::fetch(Index_, Value_*, Index_*) [with bool accrow_ = false; tatami::DimensionSelectionType selection_ = tatami::DimensionSelectionType::INDEX; bool row_ = false; Value_ = double; Index_ = int; CachedValue_ = double; CachedIndex_ = int]’
../inst/include/tatami_hdf5/Hdf5CompressedSparseMatrix.hpp:1109:45:   required from here
../inst/include/tatami_hdf5/Hdf5CompressedSparseMatrix.hpp:592:34: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare]
  592 |                 if (target.first != -1) {
      |                     ~~~~~~~~~~~~~^~~~~
../inst/include/tatami_hdf5/Hdf5CompressedSparseMatrix.hpp:609:30: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare]
  609 |             if (target.first == -1) {
      |                 ~~~~~~~~~~~~~^~~~~
../inst/include/tatami_hdf5/Hdf5CompressedSparseMatrix.hpp: In instantiation of ‘void tatami_hdf5::Hdf5CompressedSparseMatrix<row_, Value_, Index_, CachedValue_, CachedIndex_>::extract_primary_raw(size_t, Function_, Index_, tatami_hdf5::Hdf5CompressedSparseMatrix<row_, Value_, Index_, CachedValue_, CachedIndex_>::PrimaryWorkspace&, bool) const [with Function_ = tatami_hdf5::Hdf5CompressedSparseMatrix<false, double, int>::extract_primary(size_t, double*, int*, int, int, tatami_hdf5::Hdf5CompressedSparseMatrix<false, double, int>::PrimaryWorkspace&, bool, bool) const::<lambda(const int*, const int*, const double*)>; bool row_ = false; Value_ = double; Index_ = int; CachedValue_ = double; CachedIndex_ = int; size_t = long unsigned int]’:
../inst/include/tatami_hdf5/Hdf5CompressedSparseMatrix.hpp:646:32:   required from ‘tatami::SparseRange<Value_, Index_> tatami_hdf5::Hdf5CompressedSparseMatrix<row_, Value_, Index_, CachedValue_, CachedIndex_>::extract_primary(size_t, Value_*, Index_*, Index_, Index_, tatami_hdf5::Hdf5CompressedSparseMatrix<row_, Value_, Index_, CachedValue_, CachedIndex_>::PrimaryWorkspace&, bool, bool) const [with bool row_ = false; Value_ = double; Index_ = int; CachedValue_ = double; CachedIndex_ = int; size_t = long unsigned int]’
../inst/include/tatami_hdf5/Hdf5CompressedSparseMatrix.hpp:1123:57:   required from ‘tatami::SparseRange<Value_, Index_> tatami_hdf5::Hdf5CompressedSparseMatrix<row_, Value_, Index_, CachedValue_, CachedIndex_>::SparseHdf5SparseExtractor<accrow_, selection_>::fetch(Index_, Value_*, Index_*) [with bool accrow_ = false; tatami::DimensionSelectionType selection_ = tatami::DimensionSelectionType::BLOCK; bool row_ = false; Value_ = double; Index_ = int; CachedValue_ = double; CachedIndex_ = int]’
../inst/include/tatami_hdf5/Hdf5CompressedSparseMatrix.hpp:1109:45:   required from here
../inst/include/tatami_hdf5/Hdf5CompressedSparseMatrix.hpp:592:34: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare]
  592 |                 if (target.first != -1) {
      |                     ~~~~~~~~~~~~~^~~~~
../inst/include/tatami_hdf5/Hdf5CompressedSparseMatrix.hpp:609:30: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare]
  609 |             if (target.first == -1) {
      |                 ~~~~~~~~~~~~~^~~~~
../inst/include/tatami_hdf5/Hdf5CompressedSparseMatrix.hpp: In instantiation of ‘void tatami_hdf5::Hdf5CompressedSparseMatrix<row_, Value_, Index_, CachedValue_, CachedIndex_>::extract_secondary_raw_loop(size_t, Function_, Index_, Index_, tatami_hdf5::Hdf5CompressedSparseMatrix<row_, Value_, Index_, CachedValue_, CachedIndex_>::SecondaryWorkspace&, bool) const [with Function_ = tatami_hdf5::Hdf5CompressedSparseMatrix<false, double, int>::extract_secondary(size_t, double*, int*, int, int, tatami_hdf5::Hdf5CompressedSparseMatrix<false, double, int>::SecondaryWorkspace&, bool, bool) const::<lambda(int, double)>; bool row_ = false; Value_ = double; Index_ = int; CachedValue_ = double; CachedIndex_ = int; size_t = long unsigned int]’:
../inst/include/tatami_hdf5/Hdf5CompressedSparseMatrix.hpp:878:35:   required from ‘tatami::SparseRange<Value_, Index_> tatami_hdf5::Hdf5CompressedSparseMatrix<row_, Value_, Index_, CachedValue_, CachedIndex_>::extract_secondary(size_t, Value_*, Index_*, Index_, Index_, tatami_hdf5::Hdf5CompressedSparseMatrix<row_, Value_, Index_, CachedValue_, CachedIndex_>::SecondaryWorkspace&, bool, bool) const [with bool row_ = false; Value_ = double; Index_ = int; CachedValue_ = double; CachedIndex_ = int; size_t = long unsigned int]’
../inst/include/tatami_hdf5/Hdf5CompressedSparseMatrix.hpp:1125:59:   required from ‘tatami::SparseRange<Value_, Index_> tatami_hdf5::Hdf5CompressedSparseMatrix<row_, Value_, Index_, CachedValue_, CachedIndex_>::SparseHdf5SparseExtractor<accrow_, selection_>::fetch(Index_, Value_*, Index_*) [with bool accrow_ = true; tatami::DimensionSelectionType selection_ = tatami::DimensionSelectionType::BLOCK; bool row_ = false; Value_ = double; Index_ = int; CachedValue_ = double; CachedIndex_ = int]’
../inst/include/tatami_hdf5/Hdf5CompressedSparseMatrix.hpp:1109:45:   required from here
../inst/include/tatami_hdf5/Hdf5CompressedSparseMatrix.hpp:848:34: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  848 |         for (size_t j = start; j < end; ++j) {
      |                                ~~^~~~~
../inst/include/tatami_hdf5/Hdf5CompressedSparseMatrix.hpp: In instantiation of ‘void tatami_hdf5::Hdf5CompressedSparseMatrix<row_, Value_, Index_, CachedValue_, CachedIndex_>::extract_primary_raw(size_t, Function_, Index_, tatami_hdf5::Hdf5CompressedSparseMatrix<row_, Value_, Index_, CachedValue_, CachedIndex_>::PrimaryWorkspace&, bool) const [with Function_ = tatami_hdf5::Hdf5CompressedSparseMatrix<false, double, int>::extract_primary(size_t, double*, const std::vector<int>&, tatami_hdf5::Hdf5CompressedSparseMatrix<false, double, int>::PrimaryWorkspace&) const::<lambda(const int*, const int*, const double*)>; bool row_ = false; Value_ = double; Index_ = int; CachedValue_ = double; CachedIndex_ = int; size_t = long unsigned int]’:
../inst/include/tatami_hdf5/Hdf5CompressedSparseMatrix.hpp:727:32:   required from ‘const Value_* tatami_hdf5::Hdf5CompressedSparseMatrix<row_, Value_, Index_, CachedValue_, CachedIndex_>::extract_primary(size_t, Value_*, const std::vector<Index_>&, tatami_hdf5::Hdf5CompressedSparseMatrix<row_, Value_, Index_, CachedValue_, CachedIndex_>::PrimaryWorkspace&) const [with bool row_ = false; Value_ = double; Index_ = int; CachedValue_ = double; CachedIndex_ = int; size_t = long unsigned int]’
../inst/include/tatami_hdf5/Hdf5CompressedSparseMatrix.hpp:1095:57:   required from ‘const Value_* tatami_hdf5::Hdf5CompressedSparseMatrix<row_, Value_, Index_, CachedValue_, CachedIndex_>::DenseHdf5SparseExtractor<accrow_, selection_>::fetch(Index_, Value_*) [with bool accrow_ = false; tatami::DimensionSelectionType selection_ = tatami::DimensionSelectionType::INDEX; bool row_ = false; Value_ = double; Index_ = int; CachedValue_ = double; CachedIndex_ = int]’
../inst/include/tatami_hdf5/Hdf5CompressedSparseMatrix.hpp:1080:23:   required from here
../inst/include/tatami_hdf5/Hdf5CompressedSparseMatrix.hpp:592:34: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare]
  592 |                 if (target.first != -1) {
      |                     ~~~~~~~~~~~~~^~~~~
../inst/include/tatami_hdf5/Hdf5CompressedSparseMatrix.hpp:609:30: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare]
  609 |             if (target.first == -1) {
      |                 ~~~~~~~~~~~~~^~~~~
../inst/include/tatami_hdf5/Hdf5CompressedSparseMatrix.hpp: In instantiation of ‘void tatami_hdf5::Hdf5CompressedSparseMatrix<row_, Value_, Index_, CachedValue_, CachedIndex_>::extract_primary_raw(size_t, Function_, Index_, tatami_hdf5::Hdf5CompressedSparseMatrix<row_, Value_, Index_, CachedValue_, CachedIndex_>::PrimaryWorkspace&, bool) const [with Function_ = tatami_hdf5::Hdf5CompressedSparseMatrix<false, double, int>::extract_primary(size_t, double*, int, int, tatami_hdf5::Hdf5CompressedSparseMatrix<false, double, int>::PrimaryWorkspace&) const::<lambda(const int*, const int*, const double*)>; bool row_ = false; Value_ = double; Index_ = int; CachedValue_ = double; CachedIndex_ = int; size_t = long unsigned int]’:
../inst/include/tatami_hdf5/Hdf5CompressedSparseMatrix.hpp:622:32:   required from ‘const Value_* tatami_hdf5::Hdf5CompressedSparseMatrix<row_, Value_, Index_, CachedValue_, CachedIndex_>::extract_primary(size_t, Value_*, Index_, Index_, tatami_hdf5::Hdf5CompressedSparseMatrix<row_, Value_, Index_, CachedValue_, CachedIndex_>::PrimaryWorkspace&) const [with bool row_ = false; Value_ = double; Index_ = int; CachedValue_ = double; CachedIndex_ = int; size_t = long unsigned int]’
../inst/include/tatami_hdf5/Hdf5CompressedSparseMatrix.hpp:1089:57:   required from ‘const Value_* tatami_hdf5::Hdf5CompressedSparseMatrix<row_, Value_, Index_, CachedValue_, CachedIndex_>::DenseHdf5SparseExtractor<accrow_, selection_>::fetch(Index_, Value_*) [with bool accrow_ = false; tatami::DimensionSelectionType selection_ = tatami::DimensionSelectionType::BLOCK; bool row_ = false; Value_ = double; Index_ = int; CachedValue_ = double; CachedIndex_ = int]’
../inst/include/tatami_hdf5/Hdf5CompressedSparseMatrix.hpp:1080:23:   required from here
../inst/include/tatami_hdf5/Hdf5CompressedSparseMatrix.hpp:592:34: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare]
  592 |                 if (target.first != -1) {
      |                     ~~~~~~~~~~~~~^~~~~
../inst/include/tatami_hdf5/Hdf5CompressedSparseMatrix.hpp:609:30: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare]
  609 |             if (target.first == -1) {
      |                 ~~~~~~~~~~~~~^~~~~
../inst/include/tatami_hdf5/Hdf5CompressedSparseMatrix.hpp: In instantiation of ‘void tatami_hdf5::Hdf5CompressedSparseMatrix<row_, Value_, Index_, CachedValue_, CachedIndex_>::extract_secondary_raw_loop(size_t, Function_, Index_, Index_, tatami_hdf5::Hdf5CompressedSparseMatrix<row_, Value_, Index_, CachedValue_, CachedIndex_>::SecondaryWorkspace&, bool) const [with Function_ = tatami_hdf5::Hdf5CompressedSparseMatrix<false, double, int>::extract_secondary(size_t, double*, int, int, tatami_hdf5::Hdf5CompressedSparseMatrix<false, double, int>::SecondaryWorkspace&) const::<lambda(int, double)>; bool row_ = false; Value_ = double; Index_ = int; CachedValue_ = double; CachedIndex_ = int; size_t = long unsigned int]’:
../inst/include/tatami_hdf5/Hdf5CompressedSparseMatrix.hpp:862:35:   required from ‘const Value_* tatami_hdf5::Hdf5CompressedSparseMatrix<row_, Value_, Index_, CachedValue_, CachedIndex_>::extract_secondary(size_t, Value_*, Index_, Index_, tatami_hdf5::Hdf5CompressedSparseMatrix<row_, Value_, Index_, CachedValue_, CachedIndex_>::SecondaryWorkspace&) const [with bool row_ = false; Value_ = double; Index_ = int; CachedValue_ = double; CachedIndex_ = int; size_t = long unsigned int]’
../inst/include/tatami_hdf5/Hdf5CompressedSparseMatrix.hpp:1091:59:   required from ‘const Value_* tatami_hdf5::Hdf5CompressedSparseMatrix<row_, Value_, Index_, CachedValue_, CachedIndex_>::DenseHdf5SparseExtractor<accrow_, selection_>::fetch(Index_, Value_*) [with bool accrow_ = true; tatami::DimensionSelectionType selection_ = tatami::DimensionSelectionType::BLOCK; bool row_ = false; Value_ = double; Index_ = int; CachedValue_ = double; CachedIndex_ = int]’
../inst/include/tatami_hdf5/Hdf5CompressedSparseMatrix.hpp:1080:23:   required from here
../inst/include/tatami_hdf5/Hdf5CompressedSparseMatrix.hpp:848:34: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  848 |         for (size_t j = start; j < end; ++j) {
      |                                ~~^~~~~
In file included from ../inst/include/tatami_hdf5/tatami_hdf5.hpp:16,
                 from ../inst/include/Rtatami_hdf5.h:24,
                 from initialize_from_hdf5.cpp:1:
../inst/include/tatami_hdf5/Hdf5DenseMatrix.hpp: In instantiation of ‘const CachedValue_* tatami_hdf5::Hdf5DenseMatrix<Value_, Index_, transpose_, CachedValue_>::extract_with_oracle(Index_, Index_, const ExtractType_&, Index_, tatami_hdf5::Hdf5DenseMatrix<Value_, Index_, transpose_, CachedValue_>::Workspace<accrow_>&) const [with bool accrow_ = false; ExtractType_ = std::vector<int>; Value_ = double; Index_ = int; bool transpose_ = true; CachedValue_ = double]’:
../inst/include/tatami_hdf5/Hdf5DenseMatrix.hpp:409:40:   required from ‘const Value_* tatami_hdf5::Hdf5DenseMatrix<Value_, Index_, transpose_, CachedValue_>::extract(Index_, Value_*, const ExtractType_&, Index_, tatami_hdf5::Hdf5DenseMatrix<Value_, Index_, transpose_, CachedValue_>::Workspace<accrow_>&) const [with bool accrow_ = false; ExtractType_ = std::vector<int>; Value_ = double; Index_ = int; bool transpose_ = true; CachedValue_ = double]’
../inst/include/tatami_hdf5/Hdf5DenseMatrix.hpp:525:48:   required from ‘const Value_* tatami_hdf5::Hdf5DenseMatrix<Value_, Index_, transpose_, CachedValue_>::Hdf5Extractor<accrow_, selection_>::fetch(Index_, Value_*) [with bool accrow_ = false; tatami::DimensionSelectionType selection_ = tatami::DimensionSelectionType::INDEX; Value_ = double; Index_ = int; bool transpose_ = true; CachedValue_ = double]’
../inst/include/tatami_hdf5/Hdf5DenseMatrix.hpp:519:23:   required from here
../inst/include/tatami_hdf5/Hdf5DenseMatrix.hpp:290:36: error: ‘struct tatami_hdf5::Hdf5DenseMatrix<double, int, true>::OracleCache<false>’ has no member named ‘cache’
  290 |         auto info = work.futurist->cache.next_chunk(
      |                     ~~~~~~~~~~~~~~~^~~~~
../inst/include/tatami_hdf5/Hdf5DenseMatrix.hpp: In instantiation of ‘const CachedValue_* tatami_hdf5::Hdf5DenseMatrix<Value_, Index_, transpose_, CachedValue_>::extract_without_oracle(Index_, Index_, Index_, const ExtractType_&, Index_, tatami_hdf5::Hdf5DenseMatrix<Value_, Index_, transpose_, CachedValue_>::Workspace<accrow_>&) const [with bool accrow_ = false; ExtractType_ = std::vector<int>; Value_ = double; Index_ = int; bool transpose_ = true; CachedValue_ = double]’:
../inst/include/tatami_hdf5/Hdf5DenseMatrix.hpp:411:43:   required from ‘const Value_* tatami_hdf5::Hdf5DenseMatrix<Value_, Index_, transpose_, CachedValue_>::extract(Index_, Value_*, const ExtractType_&, Index_, tatami_hdf5::Hdf5DenseMatrix<Value_, Index_, transpose_, CachedValue_>::Workspace<accrow_>&) const [with bool accrow_ = false; ExtractType_ = std::vector<int>; Value_ = double; Index_ = int; bool transpose_ = true; CachedValue_ = double]’
../inst/include/tatami_hdf5/Hdf5DenseMatrix.hpp:525:48:   required from ‘const Value_* tatami_hdf5::Hdf5DenseMatrix<Value_, Index_, transpose_, CachedValue_>::Hdf5Extractor<accrow_, selection_>::fetch(Index_, Value_*) [with bool accrow_ = false; tatami::DimensionSelectionType selection_ = tatami::DimensionSelectionType::INDEX; Value_ = double; Index_ = int; bool transpose_ = true; CachedValue_ = double]’
../inst/include/tatami_hdf5/Hdf5DenseMatrix.hpp:519:23:   required from here
../inst/include/tatami_hdf5/Hdf5DenseMatrix.hpp:346:36: error: base operand of ‘->’ is not a pointer
  346 |         const auto& cache_target = work.historian->find_chunk(
      |                                    ^~~~
../inst/include/tatami_hdf5/Hdf5DenseMatrix.hpp: In instantiation of ‘const CachedValue_* tatami_hdf5::Hdf5DenseMatrix<Value_, Index_, transpose_, CachedValue_>::extract_with_oracle(Index_, Index_, const ExtractType_&, Index_, tatami_hdf5::Hdf5DenseMatrix<Value_, Index_, transpose_, CachedValue_>::Workspace<accrow_>&) const [with bool accrow_ = false; ExtractType_ = int; Value_ = double; Index_ = int; bool transpose_ = true; CachedValue_ = double]’:
../inst/include/tatami_hdf5/Hdf5DenseMatrix.hpp:409:40:   required from ‘const Value_* tatami_hdf5::Hdf5DenseMatrix<Value_, Index_, transpose_, CachedValue_>::extract(Index_, Value_*, const ExtractType_&, Index_, tatami_hdf5::Hdf5DenseMatrix<Value_, Index_, transpose_, CachedValue_>::Workspace<accrow_>&) const [with bool accrow_ = false; ExtractType_ = int; Value_ = double; Index_ = int; bool transpose_ = true; CachedValue_ = double]’
../inst/include/tatami_hdf5/Hdf5DenseMatrix.hpp:523:48:   required from ‘const Value_* tatami_hdf5::Hdf5DenseMatrix<Value_, Index_, transpose_, CachedValue_>::Hdf5Extractor<accrow_, selection_>::fetch(Index_, Value_*) [with bool accrow_ = false; tatami::DimensionSelectionType selection_ = tatami::DimensionSelectionType::BLOCK; Value_ = double; Index_ = int; bool transpose_ = true; CachedValue_ = double]’
../inst/include/tatami_hdf5/Hdf5DenseMatrix.hpp:519:23:   required from here
../inst/include/tatami_hdf5/Hdf5DenseMatrix.hpp:290:36: error: ‘struct tatami_hdf5::Hdf5DenseMatrix<double, int, true>::OracleCache<false>’ has no member named ‘cache’
  290 |         auto info = work.futurist->cache.next_chunk(
      |                     ~~~~~~~~~~~~~~~^~~~~
../inst/include/tatami_hdf5/Hdf5DenseMatrix.hpp: In instantiation of ‘const CachedValue_* tatami_hdf5::Hdf5DenseMatrix<Value_, Index_, transpose_, CachedValue_>::extract_without_oracle(Index_, Index_, Index_, const ExtractType_&, Index_, tatami_hdf5::Hdf5DenseMatrix<Value_, Index_, transpose_, CachedValue_>::Workspace<accrow_>&) const [with bool accrow_ = false; ExtractType_ = int; Value_ = double; Index_ = int; bool transpose_ = true; CachedValue_ = double]’:
../inst/include/tatami_hdf5/Hdf5DenseMatrix.hpp:411:43:   required from ‘const Value_* tatami_hdf5::Hdf5DenseMatrix<Value_, Index_, transpose_, CachedValue_>::extract(Index_, Value_*, const ExtractType_&, Index_, tatami_hdf5::Hdf5DenseMatrix<Value_, Index_, transpose_, CachedValue_>::Workspace<accrow_>&) const [with bool accrow_ = false; ExtractType_ = int; Value_ = double; Index_ = int; bool transpose_ = true; CachedValue_ = double]’
../inst/include/tatami_hdf5/Hdf5DenseMatrix.hpp:523:48:   required from ‘const Value_* tatami_hdf5::Hdf5DenseMatrix<Value_, Index_, transpose_, CachedValue_>::Hdf5Extractor<accrow_, selection_>::fetch(Index_, Value_*) [with bool accrow_ = false; tatami::DimensionSelectionType selection_ = tatami::DimensionSelectionType::BLOCK; Value_ = double; Index_ = int; bool transpose_ = true; CachedValue_ = double]’
../inst/include/tatami_hdf5/Hdf5DenseMatrix.hpp:519:23:   required from here
../inst/include/tatami_hdf5/Hdf5DenseMatrix.hpp:346:36: error: base operand of ‘->’ is not a pointer
  346 |         const auto& cache_target = work.historian->find_chunk(
      |                                    ^~~~
../inst/include/tatami_hdf5/Hdf5DenseMatrix.hpp: In instantiation of ‘const CachedValue_* tatami_hdf5::Hdf5DenseMatrix<Value_, Index_, transpose_, CachedValue_>::extract_with_oracle(Index_, Index_, const ExtractType_&, Index_, tatami_hdf5::Hdf5DenseMatrix<Value_, Index_, transpose_, CachedValue_>::Workspace<accrow_>&) const [with bool accrow_ = true; ExtractType_ = std::vector<int>; Value_ = double; Index_ = int; bool transpose_ = true; CachedValue_ = double]’:
../inst/include/tatami_hdf5/Hdf5DenseMatrix.hpp:409:40:   required from ‘const Value_* tatami_hdf5::Hdf5DenseMatrix<Value_, Index_, transpose_, CachedValue_>::extract(Index_, Value_*, const ExtractType_&, Index_, tatami_hdf5::Hdf5DenseMatrix<Value_, Index_, transpose_, CachedValue_>::Workspace<accrow_>&) const [with bool accrow_ = true; ExtractType_ = std::vector<int>; Value_ = double; Index_ = int; bool transpose_ = true; CachedValue_ = double]’
../inst/include/tatami_hdf5/Hdf5DenseMatrix.hpp:525:48:   required from ‘const Value_* tatami_hdf5::Hdf5DenseMatrix<Value_, Index_, transpose_, CachedValue_>::Hdf5Extractor<accrow_, selection_>::fetch(Index_, Value_*) [with bool accrow_ = true; tatami::DimensionSelectionType selection_ = tatami::DimensionSelectionType::INDEX; Value_ = double; Index_ = int; bool transpose_ = true; CachedValue_ = double]’
../inst/include/tatami_hdf5/Hdf5DenseMatrix.hpp:519:23:   required from here
../inst/include/tatami_hdf5/Hdf5DenseMatrix.hpp:290:36: error: ‘struct tatami_hdf5::Hdf5DenseMatrix<double, int, true>::OracleCache<true>’ has no member named ‘cache’
  290 |         auto info = work.futurist->cache.next_chunk(
      |                     ~~~~~~~~~~~~~~~^~~~~
../inst/include/tatami_hdf5/Hdf5DenseMatrix.hpp: In instantiation of ‘const CachedValue_* tatami_hdf5::Hdf5DenseMatrix<Value_, Index_, transpose_, CachedValue_>::extract_without_oracle(Index_, Index_, Index_, const ExtractType_&, Index_, tatami_hdf5::Hdf5DenseMatrix<Value_, Index_, transpose_, CachedValue_>::Workspace<accrow_>&) const [with bool accrow_ = true; ExtractType_ = std::vector<int>; Value_ = double; Index_ = int; bool transpose_ = true; CachedValue_ = double]’:
../inst/include/tatami_hdf5/Hdf5DenseMatrix.hpp:411:43:   required from ‘const Value_* tatami_hdf5::Hdf5DenseMatrix<Value_, Index_, transpose_, CachedValue_>::extract(Index_, Value_*, const ExtractType_&, Index_, tatami_hdf5::Hdf5DenseMatrix<Value_, Index_, transpose_, CachedValue_>::Workspace<accrow_>&) const [with bool accrow_ = true; ExtractType_ = std::vector<int>; Value_ = double; Index_ = int; bool transpose_ = true; CachedValue_ = double]’
../inst/include/tatami_hdf5/Hdf5DenseMatrix.hpp:525:48:   required from ‘const Value_* tatami_hdf5::Hdf5DenseMatrix<Value_, Index_, transpose_, CachedValue_>::Hdf5Extractor<accrow_, selection_>::fetch(Index_, Value_*) [with bool accrow_ = true; tatami::DimensionSelectionType selection_ = tatami::DimensionSelectionType::INDEX; Value_ = double; Index_ = int; bool transpose_ = true; CachedValue_ = double]’
../inst/include/tatami_hdf5/Hdf5DenseMatrix.hpp:519:23:   required from here
../inst/include/tatami_hdf5/Hdf5DenseMatrix.hpp:346:36: error: base operand of ‘->’ is not a pointer
  346 |         const auto& cache_target = work.historian->find_chunk(
      |                                    ^~~~
../inst/include/tatami_hdf5/Hdf5DenseMatrix.hpp: In instantiation of ‘const CachedValue_* tatami_hdf5::Hdf5DenseMatrix<Value_, Index_, transpose_, CachedValue_>::extract_with_oracle(Index_, Index_, const ExtractType_&, Index_, tatami_hdf5::Hdf5DenseMatrix<Value_, Index_, transpose_, CachedValue_>::Workspace<accrow_>&) const [with bool accrow_ = true; ExtractType_ = int; Value_ = double; Index_ = int; bool transpose_ = true; CachedValue_ = double]’:
../inst/include/tatami_hdf5/Hdf5DenseMatrix.hpp:409:40:   required from ‘const Value_* tatami_hdf5::Hdf5DenseMatrix<Value_, Index_, transpose_, CachedValue_>::extract(Index_, Value_*, const ExtractType_&, Index_, tatami_hdf5::Hdf5DenseMatrix<Value_, Index_, transpose_, CachedValue_>::Workspace<accrow_>&) const [with bool accrow_ = true; ExtractType_ = int; Value_ = double; Index_ = int; bool transpose_ = true; CachedValue_ = double]’
../inst/include/tatami_hdf5/Hdf5DenseMatrix.hpp:523:48:   required from ‘const Value_* tatami_hdf5::Hdf5DenseMatrix<Value_, Index_, transpose_, CachedValue_>::Hdf5Extractor<accrow_, selection_>::fetch(Index_, Value_*) [with bool accrow_ = true; tatami::DimensionSelectionType selection_ = tatami::DimensionSelectionType::BLOCK; Value_ = double; Index_ = int; bool transpose_ = true; CachedValue_ = double]’
../inst/include/tatami_hdf5/Hdf5DenseMatrix.hpp:519:23:   required from here
../inst/include/tatami_hdf5/Hdf5DenseMatrix.hpp:290:36: error: ‘struct tatami_hdf5::Hdf5DenseMatrix<double, int, true>::OracleCache<true>’ has no member named ‘cache’
  290 |         auto info = work.futurist->cache.next_chunk(
      |                     ~~~~~~~~~~~~~~~^~~~~
../inst/include/tatami_hdf5/Hdf5DenseMatrix.hpp: In instantiation of ‘const CachedValue_* tatami_hdf5::Hdf5DenseMatrix<Value_, Index_, transpose_, CachedValue_>::extract_without_oracle(Index_, Index_, Index_, const ExtractType_&, Index_, tatami_hdf5::Hdf5DenseMatrix<Value_, Index_, transpose_, CachedValue_>::Workspace<accrow_>&) const [with bool accrow_ = true; ExtractType_ = int; Value_ = double; Index_ = int; bool transpose_ = true; CachedValue_ = double]’:
../inst/include/tatami_hdf5/Hdf5DenseMatrix.hpp:411:43:   required from ‘const Value_* tatami_hdf5::Hdf5DenseMatrix<Value_, Index_, transpose_, CachedValue_>::extract(Index_, Value_*, const ExtractType_&, Index_, tatami_hdf5::Hdf5DenseMatrix<Value_, Index_, transpose_, CachedValue_>::Workspace<accrow_>&) const [with bool accrow_ = true; ExtractType_ = int; Value_ = double; Index_ = int; bool transpose_ = true; CachedValue_ = double]’
../inst/include/tatami_hdf5/Hdf5DenseMatrix.hpp:523:48:   required from ‘const Value_* tatami_hdf5::Hdf5DenseMatrix<Value_, Index_, transpose_, CachedValue_>::Hdf5Extractor<accrow_, selection_>::fetch(Index_, Value_*) [with bool accrow_ = true; tatami::DimensionSelectionType selection_ = tatami::DimensionSelectionType::BLOCK; Value_ = double; Index_ = int; bool transpose_ = true; CachedValue_ = double]’
../inst/include/tatami_hdf5/Hdf5DenseMatrix.hpp:519:23:   required from here
../inst/include/tatami_hdf5/Hdf5DenseMatrix.hpp:346:36: error: base operand of ‘->’ is not a pointer
  346 |         const auto& cache_target = work.historian->find_chunk(
      |                                    ^~~~
In file included from ../inst/include/tatami_hdf5/tatami_hdf5.hpp:15,
                 from ../inst/include/Rtatami_hdf5.h:24,
                 from initialize_from_hdf5.cpp:1:
../inst/include/tatami_hdf5/Hdf5CompressedSparseMatrix.hpp: In instantiation of ‘tatami_hdf5::Hdf5CompressedSparseMatrix<row_, Value_, Index_, CachedValue_, CachedIndex_>::Extracted tatami_hdf5::Hdf5CompressedSparseMatrix<row_, Value_, Index_, CachedValue_, CachedIndex_>::extract_primary_with_oracle(tatami_hdf5::Hdf5CompressedSparseMatrix<row_, Value_, Index_, CachedValue_, CachedIndex_>::PrimaryWorkspace&, bool) const [with bool row_ = true; Value_ = double; Index_ = int; CachedValue_ = double; CachedIndex_ = int]’:
../inst/include/tatami_hdf5/Hdf5CompressedSparseMatrix.hpp:575:23:   required from ‘void tatami_hdf5::Hdf5CompressedSparseMatrix<row_, Value_, Index_, CachedValue_, CachedIndex_>::extract_primary_raw(size_t, Function_, Index_, tatami_hdf5::Hdf5CompressedSparseMatrix<row_, Value_, Index_, CachedValue_, CachedIndex_>::PrimaryWorkspace&, bool) const [with Function_ = tatami_hdf5::Hdf5CompressedSparseMatrix<true, double, int>::extract_primary(size_t, double*, int*, const std::vector<int>&, tatami_hdf5::Hdf5CompressedSparseMatrix<true, double, int>::PrimaryWorkspace&, bool, bool) const::<lambda(const int*, const int*, const double*)>; bool row_ = true; Value_ = double; Index_ = int; CachedValue_ = double; CachedIndex_ = int; size_t = long unsigned int]’
../inst/include/tatami_hdf5/Hdf5CompressedSparseMatrix.hpp:754:32:   required from ‘tatami::SparseRange<Value_, Index_> tatami_hdf5::Hdf5CompressedSparseMatrix<row_, Value_, Index_, CachedValue_, CachedIndex_>::extract_primary(size_t, Value_*, Index_*, const std::vector<Index_>&, tatami_hdf5::Hdf5CompressedSparseMatrix<row_, Value_, Index_, CachedValue_, CachedIndex_>::PrimaryWorkspace&, bool, bool) const [with bool row_ = true; Value_ = double; Index_ = int; CachedValue_ = double; CachedIndex_ = int; size_t = long unsigned int]’
../inst/include/tatami_hdf5/Hdf5CompressedSparseMatrix.hpp:1129:57:   required from ‘tatami::SparseRange<Value_, Index_> tatami_hdf5::Hdf5CompressedSparseMatrix<row_, Value_, Index_, CachedValue_, CachedIndex_>::SparseHdf5SparseExtractor<accrow_, selection_>::fetch(Index_, Value_*, Index_*) [with bool accrow_ = true; tatami::DimensionSelectionType selection_ = tatami::DimensionSelectionType::INDEX; bool row_ = true; Value_ = double; Index_ = int; CachedValue_ = double; CachedIndex_ = int]’
../inst/include/tatami_hdf5/Hdf5CompressedSparseMatrix.hpp:1109:45:   required from here
../inst/include/tatami_hdf5/Hdf5CompressedSparseMatrix.hpp:405:37: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  405 |         if (pred.max_cache_elements == -1) {
      |             ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~
../inst/include/tatami_hdf5/Hdf5CompressedSparseMatrix.hpp:407:41: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘const int’ [-Wsign-compare]
  407 |             if (pred.max_cache_elements < max_non_zeros) {
      |                 ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
../inst/include/tatami_hdf5/Hdf5CompressedSparseMatrix.hpp:455:34: warning: comparison of integer expressions of different signedness: ‘const long unsigned int’ and ‘int’ [-Wsign-compare]
  455 |                 if (bounds.first != -1) {
      |                     ~~~~~~~~~~~~~^~~~~
../inst/include/tatami_hdf5/Hdf5CompressedSparseMatrix.hpp: In instantiation of ‘tatami_hdf5::Hdf5CompressedSparseMatrix<row_, Value_, Index_, CachedValue_, CachedIndex_>::Extracted tatami_hdf5::Hdf5CompressedSparseMatrix<row_, Value_, Index_, CachedValue_, CachedIndex_>::extract_primary_without_oracle(Index_, tatami_hdf5::Hdf5CompressedSparseMatrix<row_, Value_, Index_, CachedValue_, CachedIndex_>::PrimaryWorkspace&, bool) const [with bool row_ = true; Value_ = double; Index_ = int; CachedValue_ = double; CachedIndex_ = int]’:
../inst/include/tatami_hdf5/Hdf5CompressedSparseMatrix.hpp:577:23:   required from ‘void tatami_hdf5::Hdf5CompressedSparseMatrix<row_, Value_, Index_, CachedValue_, CachedIndex_>::extract_primary_raw(size_t, Function_, Index_, tatami_hdf5::Hdf5CompressedSparseMatrix<row_, Value_, Index_, CachedValue_, CachedIndex_>::PrimaryWorkspace&, bool) const [with Function_ = tatami_hdf5::Hdf5CompressedSparseMatrix<true, double, int>::extract_primary(size_t, double*, int*, const std::vector<int>&, tatami_hdf5::Hdf5CompressedSparseMatrix<true, double, int>::PrimaryWorkspace&, bool, bool) const::<lambda(const int*, const int*, const double*)>; bool row_ = true; Value_ = double; Index_ = int; CachedValue_ = double; CachedIndex_ = int; size_t = long unsigned int]’
../inst/include/tatami_hdf5/Hdf5CompressedSparseMatrix.hpp:754:32:   required from ‘tatami::SparseRange<Value_, Index_> tatami_hdf5::Hdf5CompressedSparseMatrix<row_, Value_, Index_, CachedValue_, CachedIndex_>::extract_primary(size_t, Value_*, Index_*, const std::vector<Index_>&, tatami_hdf5::Hdf5CompressedSparseMatrix<row_, Value_, Index_, CachedValue_, CachedIndex_>::PrimaryWorkspace&, bool, bool) const [with bool row_ = true; Value_ = double; Index_ = int; CachedValue_ = double; CachedIndex_ = int; size_t = long unsigned int]’
../inst/include/tatami_hdf5/Hdf5CompressedSparseMatrix.hpp:1129:57:   required from ‘tatami::SparseRange<Value_, Index_> tatami_hdf5::Hdf5CompressedSparseMatrix<row_, Value_, Index_, CachedValue_, CachedIndex_>::SparseHdf5SparseExtractor<accrow_, selection_>::fetch(Index_, Value_*, Index_*) [with bool accrow_ = true; tatami::DimensionSelectionType selection_ = tatami::DimensionSelectionType::INDEX; bool row_ = true; Value_ = double; Index_ = int; CachedValue_ = double; CachedIndex_ = int]’
../inst/include/tatami_hdf5/Hdf5CompressedSparseMatrix.hpp:1109:45:   required from here
../inst/include/tatami_hdf5/Hdf5CompressedSparseMatrix.hpp:288:31: warning: comparison of integer expressions of different signedness: ‘const long unsigned int’ and ‘int’ [-Wsign-compare]
  288 |             if (current.first != -1) {
      |                 ~~~~~~~~~~~~~~^~~~~
../inst/include/tatami_hdf5/Hdf5CompressedSparseMatrix.hpp:306:40: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  306 |         if (historian.max_cache_number == -1) {
      |             ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~
../inst/include/tatami_hdf5/Hdf5CompressedSparseMatrix.hpp: In instantiation of ‘tatami_hdf5::Hdf5CompressedSparseMatrix<row_, Value_, Index_, CachedValue_, CachedIndex_>::Extracted tatami_hdf5::Hdf5CompressedSparseMatrix<row_, Value_, Index_, CachedValue_, CachedIndex_>::extract_primary_with_oracle(tatami_hdf5::Hdf5CompressedSparseMatrix<row_, Value_, Index_, CachedValue_, CachedIndex_>::PrimaryWorkspace&, bool) const [with bool row_ = false; Value_ = double; Index_ = int; CachedValue_ = double; CachedIndex_ = int]’:
../inst/include/tatami_hdf5/Hdf5CompressedSparseMatrix.hpp:575:23:   required from ‘void tatami_hdf5::Hdf5CompressedSparseMatrix<row_, Value_, Index_, CachedValue_, CachedIndex_>::extract_primary_raw(size_t, Function_, Index_, tatami_hdf5::Hdf5CompressedSparseMatrix<row_, Value_, Index_, CachedValue_, CachedIndex_>::PrimaryWorkspace&, bool) const [with Function_ = tatami_hdf5::Hdf5CompressedSparseMatrix<false, double, int>::extract_primary(size_t, double*, int*, const std::vector<int>&, tatami_hdf5::Hdf5CompressedSparseMatrix<false, double, int>::PrimaryWorkspace&, bool, bool) const::<lambda(const int*, const int*, const double*)>; bool row_ = false; Value_ = double; Index_ = int; CachedValue_ = double; CachedIndex_ = int; size_t = long unsigned int]’
../inst/include/tatami_hdf5/Hdf5CompressedSparseMatrix.hpp:754:32:   required from ‘tatami::SparseRange<Value_, Index_> tatami_hdf5::Hdf5CompressedSparseMatrix<row_, Value_, Index_, CachedValue_, CachedIndex_>::extract_primary(size_t, Value_*, Index_*, const std::vector<Index_>&, tatami_hdf5::Hdf5CompressedSparseMatrix<row_, Value_, Index_, CachedValue_, CachedIndex_>::PrimaryWorkspace&, bool, bool) const [with bool row_ = false; Value_ = double; Index_ = int; CachedValue_ = double; CachedIndex_ = int; size_t = long unsigned int]’
../inst/include/tatami_hdf5/Hdf5CompressedSparseMatrix.hpp:1129:57:   required from ‘tatami::SparseRange<Value_, Index_> tatami_hdf5::Hdf5CompressedSparseMatrix<row_, Value_, Index_, CachedValue_, CachedIndex_>::SparseHdf5SparseExtractor<accrow_, selection_>::fetch(Index_, Value_*, Index_*) [with bool accrow_ = false; tatami::DimensionSelectionType selection_ = tatami::DimensionSelectionType::INDEX; bool row_ = false; Value_ = double; Index_ = int; CachedValue_ = double; CachedIndex_ = int]’
../inst/include/tatami_hdf5/Hdf5CompressedSparseMatrix.hpp:1109:45:   required from here
../inst/include/tatami_hdf5/Hdf5CompressedSparseMatrix.hpp:405:37: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  405 |         if (pred.max_cache_elements == -1) {
      |             ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~
../inst/include/tatami_hdf5/Hdf5CompressedSparseMatrix.hpp:407:41: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘const int’ [-Wsign-compare]
  407 |             if (pred.max_cache_elements < max_non_zeros) {
      |                 ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
../inst/include/tatami_hdf5/Hdf5CompressedSparseMatrix.hpp:455:34: warning: comparison of integer expressions of different signedness: ‘const long unsigned int’ and ‘int’ [-Wsign-compare]
  455 |                 if (bounds.first != -1) {
      |                     ~~~~~~~~~~~~~^~~~~
../inst/include/tatami_hdf5/Hdf5CompressedSparseMatrix.hpp: In instantiation of ‘tatami_hdf5::Hdf5CompressedSparseMatrix<row_, Value_, Index_, CachedValue_, CachedIndex_>::Extracted tatami_hdf5::Hdf5CompressedSparseMatrix<row_, Value_, Index_, CachedValue_, CachedIndex_>::extract_primary_without_oracle(Index_, tatami_hdf5::Hdf5CompressedSparseMatrix<row_, Value_, Index_, CachedValue_, CachedIndex_>::PrimaryWorkspace&, bool) const [with bool row_ = false; Value_ = double; Index_ = int; CachedValue_ = double; CachedIndex_ = int]’:
../inst/include/tatami_hdf5/Hdf5CompressedSparseMatrix.hpp:577:23:   required from ‘void tatami_hdf5::Hdf5CompressedSparseMatrix<row_, Value_, Index_, CachedValue_, CachedIndex_>::extract_primary_raw(size_t, Function_, Index_, tatami_hdf5::Hdf5CompressedSparseMatrix<row_, Value_, Index_, CachedValue_, CachedIndex_>::PrimaryWorkspace&, bool) const [with Function_ = tatami_hdf5::Hdf5CompressedSparseMatrix<false, double, int>::extract_primary(size_t, double*, int*, const std::vector<int>&, tatami_hdf5::Hdf5CompressedSparseMatrix<false, double, int>::PrimaryWorkspace&, bool, bool) const::<lambda(const int*, const int*, const double*)>; bool row_ = false; Value_ = double; Index_ = int; CachedValue_ = double; CachedIndex_ = int; size_t = long unsigned int]’
../inst/include/tatami_hdf5/Hdf5CompressedSparseMatrix.hpp:754:32:   required from ‘tatami::SparseRange<Value_, Index_> tatami_hdf5::Hdf5CompressedSparseMatrix<row_, Value_, Index_, CachedValue_, CachedIndex_>::extract_primary(size_t, Value_*, Index_*, const std::vector<Index_>&, tatami_hdf5::Hdf5CompressedSparseMatrix<row_, Value_, Index_, CachedValue_, CachedIndex_>::PrimaryWorkspace&, bool, bool) const [with bool row_ = false; Value_ = double; Index_ = int; CachedValue_ = double; CachedIndex_ = int; size_t = long unsigned int]’
../inst/include/tatami_hdf5/Hdf5CompressedSparseMatrix.hpp:1129:57:   required from ‘tatami::SparseRange<Value_, Index_> tatami_hdf5::Hdf5CompressedSparseMatrix<row_, Value_, Index_, CachedValue_, CachedIndex_>::SparseHdf5SparseExtractor<accrow_, selection_>::fetch(Index_, Value_*, Index_*) [with bool accrow_ = false; tatami::DimensionSelectionType selection_ = tatami::DimensionSelectionType::INDEX; bool row_ = false; Value_ = double; Index_ = int; CachedValue_ = double; CachedIndex_ = int]’
../inst/include/tatami_hdf5/Hdf5CompressedSparseMatrix.hpp:1109:45:   required from here
../inst/include/tatami_hdf5/Hdf5CompressedSparseMatrix.hpp:288:31: warning: comparison of integer expressions of different signedness: ‘const long unsigned int’ and ‘int’ [-Wsign-compare]
  288 |             if (current.first != -1) {
      |                 ~~~~~~~~~~~~~~^~~~~
../inst/include/tatami_hdf5/Hdf5CompressedSparseMatrix.hpp:306:40: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  306 |         if (historian.max_cache_number == -1) {
      |             ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~
make: *** [/home/biocbuild/bbs-3.18-bioc/R/etc/Makeconf:198: initialize_from_hdf5.o] Error 1
ERROR: compilation failed for package ‘beachmat.hdf5’
* removing ‘/tmp/RtmpOmStzN/Rinst20e9e6257729e8/beachmat.hdf5’
      -----------------------------------
ERROR: package installation failed

nebbiolo2 CHECK output

[top]

nebbiolo2 BUILD BIN output

[top]