##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL qckitfastq
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-library’
* installing *source* package ‘qckitfastq’ ...
** this is package ‘qckitfastq’ version ‘1.24.0’
** using staged installation
** libs
using C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
using C++14
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++14 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/RSeqAn/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c RcppExports.cpp -o RcppExports.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++14 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/RSeqAn/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c calc_adapter_content.cpp -o calc_adapter_content.o
In file included from /home/biocbuild/R/R-devel_2025-02-19/site-library/RSeqAn/include/seqan/modifier.h:74,
                 from /home/biocbuild/R/R-devel_2025-02-19/site-library/RSeqAn/include/seqan/find.h:44,
                 from calc_adapter_content.cpp:7:
/home/biocbuild/R/R-devel_2025-02-19/site-library/RSeqAn/include/seqan/modifier/modifier_functors.h:79:36: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
   79 | struct FunctorUpcase : public std::unary_function<InType, Result>
      |                                    ^~~~~~~~~~~~~~
In file included from /opt/ohpc/pub/compiler/gcc/14.2.0/include/c++/14.2.0/string:49,
                 from /opt/ohpc/pub/compiler/gcc/14.2.0/include/c++/14.2.0/bits/locale_classes.h:40,
                 from /opt/ohpc/pub/compiler/gcc/14.2.0/include/c++/14.2.0/bits/ios_base.h:41,
                 from /opt/ohpc/pub/compiler/gcc/14.2.0/include/c++/14.2.0/ios:44,
                 from /opt/ohpc/pub/compiler/gcc/14.2.0/include/c++/14.2.0/ostream:40,
                 from /opt/ohpc/pub/compiler/gcc/14.2.0/include/c++/14.2.0/iostream:41,
                 from calc_adapter_content.cpp:1:
/opt/ohpc/pub/compiler/gcc/14.2.0/include/c++/14.2.0/bits/stl_function.h:117:12: note: declared here
  117 |     struct unary_function
      |            ^~~~~~~~~~~~~~
/home/biocbuild/R/R-devel_2025-02-19/site-library/RSeqAn/include/seqan/modifier/modifier_functors.h:113:37: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
  113 | struct FunctorLowcase : public std::unary_function<InType, Result>
      |                                     ^~~~~~~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/include/c++/14.2.0/bits/stl_function.h:117:12: note: declared here
  117 |     struct unary_function
      |            ^~~~~~~~~~~~~~
/home/biocbuild/R/R-devel_2025-02-19/site-library/RSeqAn/include/seqan/modifier/modifier_functors.h:147:37: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
  147 | struct FunctorConvert : public std::unary_function<InType,OutType>
      |                                     ^~~~~~~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/include/c++/14.2.0/bits/stl_function.h:117:12: note: declared here
  117 |     struct unary_function
      |            ^~~~~~~~~~~~~~
/home/biocbuild/R/R-devel_2025-02-19/site-library/RSeqAn/include/seqan/modifier/modifier_functors.h:219:46: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
  219 | struct FunctorComplement<char> : public std::unary_function<Dna5,Dna5>
      |                                              ^~~~~~~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/include/c++/14.2.0/bits/stl_function.h:117:12: note: declared here
  117 |     struct unary_function
      |            ^~~~~~~~~~~~~~
/home/biocbuild/R/R-devel_2025-02-19/site-library/RSeqAn/include/seqan/modifier/modifier_functors.h:228:45: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
  228 | struct FunctorComplement<Dna> : public std::unary_function<Dna,Dna>
      |                                             ^~~~~~~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/include/c++/14.2.0/bits/stl_function.h:117:12: note: declared here
  117 |     struct unary_function
      |            ^~~~~~~~~~~~~~
/home/biocbuild/R/R-devel_2025-02-19/site-library/RSeqAn/include/seqan/modifier/modifier_functors.h:237:46: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
  237 | struct FunctorComplement<Dna5> : public std::unary_function<Dna5,Dna5>
      |                                              ^~~~~~~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/include/c++/14.2.0/bits/stl_function.h:117:12: note: declared here
  117 |     struct unary_function
      |            ^~~~~~~~~~~~~~
/home/biocbuild/R/R-devel_2025-02-19/site-library/RSeqAn/include/seqan/modifier/modifier_functors.h:246:45: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
  246 | struct FunctorComplement<Rna> : public std::unary_function<Rna,Rna>
      |                                             ^~~~~~~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/include/c++/14.2.0/bits/stl_function.h:117:12: note: declared here
  117 |     struct unary_function
      |            ^~~~~~~~~~~~~~
/home/biocbuild/R/R-devel_2025-02-19/site-library/RSeqAn/include/seqan/modifier/modifier_functors.h:255:46: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
  255 | struct FunctorComplement<Rna5> : public std::unary_function<Rna5,Rna5>
      |                                              ^~~~~~~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/include/c++/14.2.0/bits/stl_function.h:117:12: note: declared here
  117 |     struct unary_function
      |            ^~~~~~~~~~~~~~
/home/biocbuild/R/R-devel_2025-02-19/site-library/RSeqAn/include/seqan/modifier/modifier_functors.h:264:46: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
  264 | struct FunctorComplement<DnaQ> : public std::unary_function<DnaQ,DnaQ>
      |                                              ^~~~~~~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/include/c++/14.2.0/bits/stl_function.h:117:12: note: declared here
  117 |     struct unary_function
      |            ^~~~~~~~~~~~~~
/home/biocbuild/R/R-devel_2025-02-19/site-library/RSeqAn/include/seqan/modifier/modifier_functors.h:276:47: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
  276 | struct FunctorComplement<Dna5Q> : public std::unary_function<Dna5Q,Dna5Q>
      |                                               ^~~~~~~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/include/c++/14.2.0/bits/stl_function.h:117:12: note: declared here
  117 |     struct unary_function
      |            ^~~~~~~~~~~~~~
/home/biocbuild/R/R-devel_2025-02-19/site-library/RSeqAn/include/seqan/modifier/modifier_functors.h:287:47: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
  287 | struct FunctorComplement<Iupac> : public std::unary_function<Iupac,Iupac>
      |                                               ^~~~~~~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/include/c++/14.2.0/bits/stl_function.h:117:12: note: declared here
  117 |     struct unary_function
      |            ^~~~~~~~~~~~~~
In file included from /home/biocbuild/R/R-devel_2025-02-19/site-library/RSeqAn/include/seqan/modifier.h:79:
/home/biocbuild/R/R-devel_2025-02-19/site-library/RSeqAn/include/seqan/modifier/modifier_position.h:393:31: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations]
  393 | struct PosLess_ : public std::binary_function<TPos, TPos, bool>
      |                               ^~~~~~~~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/include/c++/14.2.0/bits/stl_function.h:131:12: note: declared here
  131 |     struct binary_function
      |            ^~~~~~~~~~~~~~~
In file included from /home/biocbuild/R/R-devel_2025-02-19/site-library/RSeqAn/include/seqan/file.h:101,
                 from /home/biocbuild/R/R-devel_2025-02-19/site-library/RSeqAn/include/seqan/stream.h:62,
                 from /home/biocbuild/R/R-devel_2025-02-19/site-library/RSeqAn/include/seqan/score.h:43,
                 from /home/biocbuild/R/R-devel_2025-02-19/site-library/RSeqAn/include/seqan/find.h:45:
/home/biocbuild/R/R-devel_2025-02-19/site-library/RSeqAn/include/seqan/file/string_external.h:1338:41: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
 1338 |         struct testIODone : public std::unary_function<TPageFrame&,bool>
      |                                         ^~~~~~~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/include/c++/14.2.0/bits/stl_function.h:117:12: note: declared here
  117 |     struct unary_function
      |            ^~~~~~~~~~~~~~
In file included from /home/biocbuild/R/R-devel_2025-02-19/site-library/RSeqAn/include/seqan/graph_algorithms.h:48,
                 from /home/biocbuild/R/R-devel_2025-02-19/site-library/RSeqAn/include/seqan/find.h:47:
/home/biocbuild/R/R-devel_2025-02-19/site-library/RSeqAn/include/seqan/graph_algorithms/graph_algorithm_heap_tree.h:325:17: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
  325 |     public std::unary_function<Pair<TKey, TValue>, bool>
      |                 ^~~~~~~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/include/c++/14.2.0/bits/stl_function.h:117:12: note: declared here
  117 |     struct unary_function
      |            ^~~~~~~~~~~~~~
In file included from /home/biocbuild/R/R-devel_2025-02-19/site-library/RSeqAn/include/seqan/graph_algorithms.h:62:
/home/biocbuild/R/R-devel_2025-02-19/site-library/RSeqAn/include/seqan/graph_algorithms/kruskal.h:63:34: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations]
   63 | struct LessPairI1_ : public std::unary_function<Pair<TWeight, TPair>, bool>
      |                                  ^~~~~~~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/include/c++/14.2.0/bits/stl_function.h:117:12: note: declared here
  117 |     struct unary_function
      |            ^~~~~~~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++14 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/RSeqAn/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c gzstream.cpp -o gzstream.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++14 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/RSeqAn/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c read_fastq.cpp -o read_fastq.o
read_fastq.cpp: In function ‘Rcpp::List qual_score_per_read(std::string)’:
read_fastq.cpp:181:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::map<int, std::vector<unsigned char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  181 |                 if (pos_counter <= qual_score_matrix.size()) {
      |                     ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++14 -shared -L/home/biocbuild/R/R/lib -L/usr/local/lib -o qckitfastq.so RcppExports.o calc_adapter_content.o gzstream.o read_fastq.o -lz -L/home/biocbuild/R/R/lib -lR
installing to /home/biocbuild/R/R-devel_2025-02-19/site-library/00LOCK-qckitfastq/00new/qckitfastq/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (qckitfastq)