* installing *source* package ‘blaster’ ...
** package ‘blaster’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/blaster/src'
/usr/local/clang15/bin/clang++ -std=gnu++14 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang15/include    -fpic  -O3 -Wall -pedantic -frtti  -c RcppExports.cpp -o RcppExports.o
/usr/local/clang15/bin/clang++ -std=gnu++14 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang15/include    -fpic  -O3 -Wall -pedantic -frtti  -c ReadFasta.cpp -o ReadFasta.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]
    bool   match;
           ^
ReadFasta.cpp:28:7: warning: misleading indentation; statement is not part of the previous 'for' [-Wmisleading-indentation]
      str_acc = sequence;
      ^
ReadFasta.cpp:25:5: note: previous statement is here
    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 ./CSV/../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]
static std::ostream& operator<<( std::ostream& os, const Cigar& cigar ) {
                     ^
In file included from ReadFasta.cpp:8:
./FileFormat.h:32:19: warning: 'static' function 'InferFileFormat' declared in header file should be declared 'static inline' [-Wunneeded-internal-declaration]
static FileFormat InferFileFormat( const std::string& filepath, const FileFormat defaultFormat ) {
                  ^
4 warnings generated.
/usr/local/clang15/bin/clang++ -std=gnu++14 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang15/include    -fpic  -O3 -Wall -pedantic -frtti  -c TextReader.cpp -o TextReader.o
In file included from TextReader.cpp:2:
./Utils.h:9:13: warning: unused function 'UpcaseString' [-Wunused-function]
static void UpcaseString( std::string& str ) {
            ^
1 warning generated.
/usr/local/clang15/bin/clang++ -std=gnu++14 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-clang/Rcpp/include' -isystem /usr/local/clang15/include    -fpic  -O3 -Wall -pedantic -frtti  -c blast.cpp -o blast.o
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]
    bool   match;
           ^
In file included from blast.cpp:10:
In file included from ./Database/GlobalSearch.h:7:
./Alnout/../Database/../Alignment/ExtendAlign.h:10:15: warning: anonymous non-C-compatible type given name for linkage purposes by typedef declaration; add a tag name here [-Wnon-c-typedef-for-linkage]
typedef struct {
              ^
               ExtendAlignParams
./Alnout/../Database/../Alignment/ExtendAlign.h:11:15: note: type is not C-compatible due to this default member initializer
  int xDrop = 32;
              ^~
./Alnout/../Database/../Alignment/ExtendAlign.h:14:3: note: type is given name 'ExtendAlignParams' for linkage purposes by this typedef declaration
} ExtendAlignParams;
  ^
In file included from blast.cpp:10:
./Database/GlobalSearch.h:117:18: warning: variable 'length' set but not used [-Wunused-but-set-variable]
          size_t length = mDB.KmerLength();
                 ^
./Database/GlobalSearch.h:155:14: warning: unused variable 'rightQuery' [-Wunused-variable]
      size_t rightQuery, rightCandidate;
             ^
./Database/GlobalSearch.h:155:26: warning: unused variable 'rightCandidate' [-Wunused-variable]
      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 ./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]
static std::ostream& operator<<( std::ostream& os, const Cigar& cigar ) {
                     ^
6 warnings generated.
/usr/local/clang15/bin/clang++ -std=gnu++14 -shared -L/usr/local/clang/lib64 -L/usr/local/clang15/lib -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)