* installing *source* package ‘blaster’ ...
** package ‘blaster’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-14 (GCC) 14.2.0’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/blaster/src'
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -DR_NO_REMAP -c ReadFasta.cpp -o ReadFasta.o
ReadFasta.cpp: In function 'std::string process_sequence(std::string, std::string, std::unordered_set<char>)':
ReadFasta.cpp:19:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
19 | for (int i = 0; i < sequence.size(); ++i)
| ~~^~~~~~~~~~~~~~~~~
ReadFasta.cpp:25:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
25 | for (int i = 0; i < sequence.size(); ++i)
| ~~^~~~~~~~~~~~~~~~~
ReadFasta.cpp:25:5: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
25 | for (int i = 0; i < sequence.size(); ++i)
| ^~~
ReadFasta.cpp:28:7: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
28 | str_acc = sequence;
| ^~~~~~~
In file included from Alnout/../Database/Search.h:3,
from Alnout/../Database/HitWriter.h:3,
from Alnout/Writer.h:3,
from FileFormat.h:14,
from ReadFasta.cpp:8:
Alnout/../Database/../Alignment/Cigar.h: At global scope:
Alnout/../Database/../Alignment/Cigar.h:144:22: warning: 'std::ostream& operator<<(std::ostream&, const Cigar&)' defined but not used [-Wunused-function]
144 | static std::ostream& operator<<( std::ostream& os, const Cigar& cigar ) {
| ^~~~~~~~
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -DR_NO_REMAP -c TextReader.cpp -o TextReader.o
In file included from TextReader.cpp:2:
Utils.h:9:13: warning: 'void UpcaseString(std::string&)' defined but not used [-Wunused-function]
9 | static void UpcaseString( std::string& str ) {
| ^~~~~~~~~~~~
g++-14 -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I/usr/local/include -DC99_INLINE_SEMANTICS=0 -fpic -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -DR_NO_REMAP -c blast.cpp -o blast.o
blast.cpp: In function 'std::string DFtoSeq(Rcpp::DataFrame)':
blast.cpp:121:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
121 | for (int i{0}; i < ids.size(); ++i) {
| ~~^~~~~~~~~~~~
In file included from blast.cpp:17:
WorkerQueue.h: In instantiation of 'WorkerQueue<Worker, QueueItem, Args>::WorkerQueue(int, Args ...) [with Worker = SearchResultsWriterWorker<DNA>; QueueItem = std::deque<std::pair<Sequence<DNA>, std::deque<Hit<DNA>, std::allocator<Hit<DNA> > > >, std::allocator<std::pair<Sequence<DNA>, std::deque<Hit<DNA>, std::allocator<Hit<DNA> > > > > >; Args = {const std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&}]':
blast.cpp:212:55: required from here
212 | SearchResultsWriter< DNA > writer( 1, output_file );
| ^
WorkerQueue.h:30:23: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
30 | for( int i = 0; i < actualWorkers; i++ ) {
| ~~^~~~~~~~~~~~~~~
WorkerQueue.h: In instantiation of 'WorkerQueue<Worker, QueueItem, Args>::WorkerQueue(int, Args ...) [with Worker = QueryDatabaseSearcherWorker<DNA>; QueueItem = std::deque<Sequence<DNA>, std::allocator<Sequence<DNA> > >; Args = {WorkerQueue<SearchResultsWriterWorker<DNA>, std::deque<std::pair<Sequence<DNA>, std::deque<Hit<DNA>, std::allocator<Hit<DNA> > > >, std::allocator<std::pair<Sequence<DNA>, std::deque<Hit<DNA>, std::allocator<Hit<DNA> > > > > >, const std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&>*, const Database<DNA>*, const SearchParams<DNA>&}]':
blast.cpp:213:73: required from here
213 | QueryDatabaseSearcher< DNA > searcher( -1, &writer, &db, searchParams );
| ^
WorkerQueue.h:30:23: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
30 | for( int i = 0; i < actualWorkers; i++ ) {
| ~~^~~~~~~~~~~~~~~
WorkerQueue.h: In instantiation of 'WorkerQueue<Worker, QueueItem, Args>::WorkerQueue(int, Args ...) [with Worker = SearchResultsWriterWorker<Protein>; QueueItem = std::deque<std::pair<Sequence<Protein>, std::deque<Hit<Protein>, std::allocator<Hit<Protein> > > >, std::allocator<std::pair<Sequence<Protein>, std::deque<Hit<Protein>, std::allocator<Hit<Protein> > > > > >; Args = {const std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&}]':
blast.cpp:320:59: required from here
320 | SearchResultsWriter< Protein > writer( 1, output_file );
| ^
WorkerQueue.h:30:23: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
30 | for( int i = 0; i < actualWorkers; i++ ) {
| ~~^~~~~~~~~~~~~~~
WorkerQueue.h: In instantiation of 'WorkerQueue<Worker, QueueItem, Args>::WorkerQueue(int, Args ...) [with Worker = QueryDatabaseSearcherWorker<Protein>; QueueItem = std::deque<Sequence<Protein>, std::allocator<Sequence<Protein> > >; Args = {WorkerQueue<SearchResultsWriterWorker<Protein>, std::deque<std::pair<Sequence<Protein>, std::deque<Hit<Protein>, std::allocator<Hit<Protein> > > >, std::allocator<std::pair<Sequence<Protein>, std::deque<Hit<Protein>, std::allocator<Hit<Protein> > > > > >, const std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&>*, const Database<Protein>*, const SearchParams<Protein>&}]':
blast.cpp:321:77: required from here
321 | QueryDatabaseSearcher< Protein > searcher( -1, &writer, &db, searchParams );
| ^
WorkerQueue.h:30:23: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
30 | for( int i = 0; i < actualWorkers; i++ ) {
| ~~^~~~~~~~~~~~~~~
In file included from blast.cpp:10:
Database/GlobalSearch.h: In instantiation of 'void GlobalSearch<Alphabet>::SearchForHits(const Sequence<Alphabet>&, SearchForHitsCallback<Alphabet>&) [with Alphabet = Protein; SearchForHitsCallback<Alphabet> = std::function<void(const Sequence<Protein>&, const Cigar&)>]':
Database/GlobalSearch.h:40:6: required from here
40 | void GlobalSearch< A >::SearchForHits( const Sequence< A >& query,
| ^~~~~~~~~~~~~~~~~
Database/GlobalSearch.h:155:14: warning: unused variable 'rightQuery' [-Wunused-variable]
155 | size_t rightQuery, rightCandidate;
| ^~~~~~~~~~
Database/GlobalSearch.h:155:26: warning: unused variable 'rightCandidate' [-Wunused-variable]
155 | size_t rightQuery, rightCandidate;
| ^~~~~~~~~~~~~~
Database/GlobalSearch.h: In instantiation of 'void GlobalSearch<Alphabet>::SearchForHits(const Sequence<Alphabet>&, SearchForHitsCallback<Alphabet>&) [with Alphabet = DNA; SearchForHitsCallback<Alphabet> = std::function<void(const Sequence<DNA>&, const Cigar&)>]':
Database/GlobalSearch.h:40:6: required from here
40 | void GlobalSearch< A >::SearchForHits( const Sequence< A >& query,
| ^~~~~~~~~~~~~~~~~
Database/GlobalSearch.h:155:14: warning: unused variable 'rightQuery' [-Wunused-variable]
155 | size_t rightQuery, rightCandidate;
| ^~~~~~~~~~
Database/GlobalSearch.h:155:26: warning: unused variable 'rightCandidate' [-Wunused-variable]
155 | size_t rightQuery, rightCandidate;
| ^~~~~~~~~~~~~~
In file included from FileFormat.h:14,
from blast.cpp:7:
Alnout/Writer.h: In instantiation of 'static Alnout::Writer<Alphabet>::AlignmentLines Alnout::Writer<Alphabet>::ExtractAlignmentLines(const Sequence<Alphabet>&, const Sequence<Alphabet>&, const Cigar&, size_t*, size_t*, size_t*) [with Alphabet = Protein; AlignmentLines = std::deque<Alnout::Writer<Protein>::<unnamed struct>, std::allocator<Alnout::Writer<Protein>::<unnamed struct> > >; size_t = long unsigned int]':
Alnout/Writer.h:50:43: required from 'HitWriter<Alphabet>& Alnout::Writer<Alphabet>::operator<<(QueryHitsPair<Alphabet>&) [with Alphabet = Protein; QueryHitsPair<Alphabet> = std::pair<Sequence<Protein>, std::deque<Hit<Protein>, std::allocator<Hit<Protein> > > >]'
50 | auto lines = ExtractAlignmentLines(
| ~~~~~~~~~~~~~~~~~~~~~^
51 | QueryForAlignment( hit, query ), TargetForAlignment( hit, query ), hit.alignment,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
52 | &numCols, &numMatches, &numGaps );
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Alnout/Writer.h:18:3: required from here
18 | operator<<( const QueryHitsPair< Alphabet >& queryWithHits ) {
| ^~~~~~~~
Alnout/Writer.h:177:12: warning: unused variable 'match' [-Wunused-variable]
177 | bool match;
| ^~~~~
Alnout/Writer.h: In instantiation of 'static Alnout::Writer<Alphabet>::AlignmentLines Alnout::Writer<Alphabet>::ExtractAlignmentLines(const Sequence<Alphabet>&, const Sequence<Alphabet>&, const Cigar&, size_t*, size_t*, size_t*) [with Alphabet = DNA; AlignmentLines = std::deque<Alnout::Writer<DNA>::<unnamed struct>, std::allocator<Alnout::Writer<DNA>::<unnamed struct> > >; size_t = long unsigned int]':
Alnout/Writer.h:50:43: required from 'HitWriter<Alphabet>& Alnout::Writer<Alphabet>::operator<<(QueryHitsPair<Alphabet>&) [with Alphabet = DNA; QueryHitsPair<Alphabet> = std::pair<Sequence<DNA>, std::deque<Hit<DNA>, std::allocator<Hit<DNA> > > >]'
50 | auto lines = ExtractAlignmentLines(
| ~~~~~~~~~~~~~~~~~~~~~^
51 | QueryForAlignment( hit, query ), TargetForAlignment( hit, query ), hit.alignment,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
52 | &numCols, &numMatches, &numGaps );
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Alnout/Writer.h:18:3: required from here
18 | operator<<( const QueryHitsPair< Alphabet >& queryWithHits ) {
| ^~~~~~~~
Alnout/Writer.h:177:12: warning: unused variable 'match' [-Wunused-variable]
177 | bool match;
| ^~~~~
In file included from Alnout/../Database/Search.h:3,
from Alnout/../Database/HitWriter.h:3,
from Alnout/Writer.h:3:
Alnout/../Database/../Alignment/Cigar.h: At global scope:
Alnout/../Database/../Alignment/Cigar.h:144:22: warning: 'std::ostream& operator<<(std::ostream&, const Cigar&)' defined but not used [-Wunused-function]
144 | static std::ostream& operator<<( std::ostream& os, const Cigar& cigar ) {
| ^~~~~~~~
In file included from Database/GlobalSearch.h:7:
Database/../Alignment/ExtendAlign.h: In member function 'int ExtendAlign<Alphabet>::Extend(const Sequence<Alphabet>&, const Sequence<Alphabet>&, size_t*, size_t*, Cigar*, AlignmentDirection, size_t, size_t) [with Alphabet = Protein]':
Database/../Alignment/ExtendAlign.h:184:24: warning: 'match' may be used uninitialized [-Wmaybe-uninitialized]
184 | op = match ? CigarOp::Match : CigarOp::Mismatch;
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Database/../Alignment/ExtendAlign.h:123:14: note: 'match' was declared here
123 | bool match;
| ^~~~~
Database/../Alignment/ExtendAlign.h: In member function 'int ExtendAlign<Alphabet>::Extend(const Sequence<Alphabet>&, const Sequence<Alphabet>&, size_t*, size_t*, Cigar*, AlignmentDirection, size_t, size_t) [with Alphabet = DNA]':
Database/../Alignment/ExtendAlign.h:184:24: warning: 'match' may be used uninitialized [-Wmaybe-uninitialized]
184 | op = match ? CigarOp::Match : CigarOp::Mismatch;
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Database/../Alignment/ExtendAlign.h:123:14: note: 'match' was declared here
123 | bool match;
| ^~~~~
In file included from Database/GlobalSearch.h:5:
Database/../Alignment/BandedAlign.h: In function 'int BandedAlign<Alphabet>::Align(const Sequence<Alphabet>&, const Sequence<Alphabet>&, Cigar*, AlignmentDirection, size_t, size_t, size_t, size_t) [with Alphabet = Protein]':
Database/../Alignment/BandedAlign.h:231:22: warning: 'match' may be used uninitialized [-Wmaybe-uninitialized]
231 | op = match ? CigarOp::Match : CigarOp::Mismatch;
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Database/../Alignment/BandedAlign.h:196:16: note: 'match' was declared here
196 | bool match;
| ^~~~~
Database/../Alignment/BandedAlign.h: In function 'int BandedAlign<Alphabet>::Align(const Sequence<Alphabet>&, const Sequence<Alphabet>&, Cigar*, AlignmentDirection, size_t, size_t, size_t, size_t) [with Alphabet = DNA]':
Database/../Alignment/BandedAlign.h:231:22: warning: 'match' may be used uninitialized [-Wmaybe-uninitialized]
231 | op = match ? CigarOp::Match : CigarOp::Mismatch;
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Database/../Alignment/BandedAlign.h:196:16: note: 'match' was declared here
196 | bool match;
| ^~~~~
g++-14 -std=gnu++17 -shared -L/usr/local/gcc14/lib64 -L/usr/local/lib64 -o blaster.so RcppExports.o ReadFasta.o TextReader.o blast.o
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/blaster/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/blaster/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/blaster/src'
installing to /data/gannet/ripley/R/packages/tests-devel/blaster.Rcheck/00LOCK-blaster/00new/blaster/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** 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 (blaster)