* installing *source* package ‘blaster’ ...
** package ‘blaster’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘clang version 18.1.4’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/blaster/src'
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3   -c RcppExports.cpp -o RcppExports.o
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3   -c ReadFasta.cpp -o ReadFasta.o
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3   -c TextReader.cpp -o TextReader.o
/usr/local/clang18/bin/clang++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang18/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3   -c blast.cpp -o blast.o
In file included from ReadFasta.cpp:8:
In file included from ./FileFormat.h:14:
./Alnout/Writer.h:177:12: warning: unused variable 'match' [-Wunused-variable]
  177 |     bool   match;
      |            ^~~~~
ReadFasta.cpp:28:7: warning: misleading indentation; statement is not part of the previous 'for' [-Wmisleading-indentation]
   28 |       str_acc = sequence;
      |       ^
ReadFasta.cpp:25:5: note: previous statement is here
   25 |     for (int i = 0; i < sequence.size(); ++i) 
      |     ^
In file included from ReadFasta.cpp:8:
In file included from ./FileFormat.h:14:
In file included from ./Alnout/Writer.h:3:
In file included from ./Alnout/../Database/HitWriter.h:3:
In file included from ./Alnout/../Database/Search.h:3:
./Alnout/../Database/../Alignment/Cigar.h:144:22: warning: unused function 'operator<<' [-Wunused-function]
  144 | static std::ostream& operator<<( std::ostream& os, const Cigar& cigar ) {
      |                      ^~~~~~~~
In file included from TextReader.cpp:2:
./Utils.h:9:13: warning: unused function 'UpcaseString' [-Wunused-function]
    9 | static void UpcaseString( std::string& str ) {
      |             ^~~~~~~~~~~~
1 warning generated.
3 warnings generated.
In file included from blast.cpp:7:
In file included from ./FileFormat.h:14:
./Alnout/Writer.h:177:12: warning: unused variable 'match' [-Wunused-variable]
  177 |     bool   match;
      |            ^~~~~
In file included from blast.cpp:10:
./Database/GlobalSearch.h:117:18: warning: variable 'length' set but not used [-Wunused-but-set-variable]
  117 |           size_t length = mDB.KmerLength();
      |                  ^
./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 blast.cpp:7:
In file included from ./FileFormat.h:14:
In file included from ./Alnout/Writer.h:3:
In file included from ./Alnout/../Database/HitWriter.h:3:
In file included from ./Alnout/../Database/Search.h:3:
./Alnout/../Database/../Alignment/Cigar.h:144:22: warning: unused function 'operator<<' [-Wunused-function]
  144 | static std::ostream& operator<<( std::ostream& os, const Cigar& cigar ) {
      |                      ^~~~~~~~
5 warnings generated.
/usr/local/clang18/bin/clang++ -std=gnu++17 -shared -L/usr/local/clang/lib64 -L/usr/local/clang18/lib -L/usr/local/clang18/lib/x86_64-unknown-linux-gnu -L/usr/local/gcc13/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-clang/blaster/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/blaster/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/blaster/src'
installing to /data/gannet/ripley/R/packages/tests-clang/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)