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### Running command:
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### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL qckitfastq
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* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘qckitfastq’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
using C++14
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/RSeqAn/include' -I/usr/local/include -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/RSeqAn/include' -I/usr/local/include -fpic -g -O2 -Wall -c calc_adapter_content.cpp -o calc_adapter_content.o
In file included from /home/biocbuild/bbs-3.20-bioc/R/site-library/RSeqAn/include/seqan/modifier.h:74,
from /home/biocbuild/bbs-3.20-bioc/R/site-library/RSeqAn/include/seqan/find.h:44,
from calc_adapter_content.cpp:7:
/home/biocbuild/bbs-3.20-bioc/R/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 /usr/include/c++/13/string:49,
from /usr/include/c++/13/bits/locale_classes.h:40,
from /usr/include/c++/13/bits/ios_base.h:41,
from /usr/include/c++/13/ios:44,
from /usr/include/c++/13/ostream:40,
from /usr/include/c++/13/iostream:41,
from calc_adapter_content.cpp:1:
/usr/include/c++/13/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
/home/biocbuild/bbs-3.20-bioc/R/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>
| ^~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
/home/biocbuild/bbs-3.20-bioc/R/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>
| ^~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
/home/biocbuild/bbs-3.20-bioc/R/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>
| ^~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
/home/biocbuild/bbs-3.20-bioc/R/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>
| ^~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
/home/biocbuild/bbs-3.20-bioc/R/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>
| ^~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
/home/biocbuild/bbs-3.20-bioc/R/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>
| ^~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
/home/biocbuild/bbs-3.20-bioc/R/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>
| ^~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
/home/biocbuild/bbs-3.20-bioc/R/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>
| ^~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
/home/biocbuild/bbs-3.20-bioc/R/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>
| ^~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
/home/biocbuild/bbs-3.20-bioc/R/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>
| ^~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.20-bioc/R/site-library/RSeqAn/include/seqan/modifier.h:79:
/home/biocbuild/bbs-3.20-bioc/R/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>
| ^~~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.20-bioc/R/site-library/RSeqAn/include/seqan/file.h:101,
from /home/biocbuild/bbs-3.20-bioc/R/site-library/RSeqAn/include/seqan/stream.h:62,
from /home/biocbuild/bbs-3.20-bioc/R/site-library/RSeqAn/include/seqan/score.h:43,
from /home/biocbuild/bbs-3.20-bioc/R/site-library/RSeqAn/include/seqan/find.h:45:
/home/biocbuild/bbs-3.20-bioc/R/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>
| ^~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.20-bioc/R/site-library/RSeqAn/include/seqan/graph_algorithms.h:48,
from /home/biocbuild/bbs-3.20-bioc/R/site-library/RSeqAn/include/seqan/find.h:47:
/home/biocbuild/bbs-3.20-bioc/R/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>
| ^~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
In file included from /home/biocbuild/bbs-3.20-bioc/R/site-library/RSeqAn/include/seqan/graph_algorithms.h:62:
/home/biocbuild/bbs-3.20-bioc/R/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>
| ^~~~~~~~~~~~~~
/usr/include/c++/13/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/RSeqAn/include' -I/usr/local/include -fpic -g -O2 -Wall -c gzstream.cpp -o gzstream.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/RSeqAn/include' -I/usr/local/include -fpic -g -O2 -Wall -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()) {
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++14 -shared -L/home/biocbuild/bbs-3.20-bioc/R/lib -L/usr/local/lib -o qckitfastq.so RcppExports.o calc_adapter_content.o gzstream.o read_fastq.o -lz -L/home/biocbuild/bbs-3.20-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.20-bioc/R/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)
