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### Running command:
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### rm -rf ChemmineR.buildbin-libdir && mkdir ChemmineR.buildbin-libdir && F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL --build --library=ChemmineR.buildbin-libdir ChemmineR_3.48.0.tar.gz
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* installing *source* package 'ChemmineR' ...
** using staged installation
** libs
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -DNO_MAIN -DNO_DEBUG -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c DisjointSets.cpp -o DisjointSets.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -DNO_MAIN -DNO_DEBUG -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c cluster.cc -o cluster.o
cluster.cc: In function 'int nbr_intersect(std::vector<int>&, std::vector<int>&)':
cluster.cc:118:11: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
118 | while (i < nbrs1.size() and j < nbrs2.size()) {
| ~~^~~~~~~~~~~~~~
cluster.cc:118:32: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
118 | while (i < nbrs1.size() and j < nbrs2.size()) {
| ~~^~~~~~~~~~~~~~
cluster.cc: In function 'int contains(int, std::vector<int>&)':
cluster.cc:131:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
131 | for(int i=0; i < list.size(); i++)
| ~~^~~~~~~~~~~~~
cluster.cc: In function 'DisjointSets cluster(int, int, int, int)':
cluster.cc:267:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
267 | for (int j = 0; j < nbr_list[i].size(); j ++) {
| ~~^~~~~~~~~~~~~~~~~~~~
cluster.cc: In function 'void loadNNMatrix(int, int, int, SEXP)':
cluster.cc:284:21: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
284 | for(unsigned i=0; i<N; i++) //rows
| ~^~
cluster.cc:298:18: warning: comparison of integer expressions of different signedness: 'std::vector<int>::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
298 | if(nbrs.size() < minNbrs) // will end up a singleton
| ~~~~~~~~~~~~^~~~~~~~~
cluster.cc: In function 'void loadNNList(int, int, SEXP)':
cluster.cc:314:21: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
314 | for(unsigned i=0; i<N; i++) //rows
| ~^~
cluster.cc:332:18: warning: comparison of integer expressions of different signedness: 'std::vector<int>::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
332 | if(nbrs.size() < minNbrs) // will end up a singleton
| ~~~~~~~~~~~~^~~~~~~~~
cluster.cc: In function 'SEXPREC* jarvis_patrick(SEXP, SEXP, SEXP, SEXP, SEXP)':
cluster.cc:390:21: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
390 | for(unsigned i=0; i<N; i++){
| ~^~
cluster.cc: At global scope:
cluster.cc:49:13: warning: 'void prepare_neighbors(const char*, int, int)' defined but not used [-Wunused-function]
49 | void static prepare_neighbors(const char* nbr_file, int skip, int p)
| ^~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -DNO_MAIN -DNO_DEBUG -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c cstrsplit.cc -o cstrsplit.o
In file included from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/range/iterator_range.hpp:13,
from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/range/as_literal.hpp:18,
from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/algorithm/string/trim.hpp:19,
from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/algorithm/string.hpp:19,
from cstrsplit.cc:7:
F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
194 | failed ************ (Pred::************
| ^
F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
199 | failed ************ (boost::mpl::not_<Pred>::************
| ^
In file included from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/bind/mem_fn.hpp:25,
from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mem_fn.hpp:22,
from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/function/detail/prologue.hpp:18,
from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/function.hpp:30,
from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18,
from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/algorithm/string/find_iterator.hpp:24,
from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/algorithm/string/iter_find.hpp:27,
from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/algorithm/string/split.hpp:16,
from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/algorithm/string.hpp:23,
from cstrsplit.cc:7:
F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/get_pointer.hpp:48:40: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
48 | template<class T> T * get_pointer(std::auto_ptr<T> const& p)
| ^~~~~~~~
In file included from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\bits\locale_conv.h:41,
from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\locale:43,
from c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\iomanip:43,
from F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include/RcppCommon.h:53,
from F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include/Rcpp.h:27,
from cstrsplit.cc:2:
c:\rtools42\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\10.3.0\include\c++\bits\unique_ptr.h:57:28: note: declared here
57 | template<typename> class auto_ptr;
| ^~~~~~~~
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -DNO_MAIN -DNO_DEBUG -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c desc.cc -o desc.o
desc.cc: In function 'SEXPREC* genAPDescriptor(SEXP)':
desc.cc:249:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<unsigned int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
249 | for(int i=0; i < descs.size(); i++)
| ~~^~~~~~~~~~~~~~
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -DNO_MAIN -DNO_DEBUG -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c fingerprints.cc -o fingerprints.o
fingerprints.cc: In function 'SEXPREC* uniquifyAtomPairs(SEXP)':
fingerprints.cc:138:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<IndexedValue*>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
138 | for(int i=0; i < aps.size(); i++)
| ~~^~~~~~~~~~~~
fingerprints.cc:145:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<IndexedValue*>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
145 | for(int i=0; i < aps.size(); i++){
| ~~^~~~~~~~~~~~
fingerprints.cc:158:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<IndexedValue*>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
158 | for(int i=0; i < aps.size(); i++){
| ~~^~~~~~~~~~~~
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -DNO_MAIN -DNO_DEBUG -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c formats.cc -o formats.o
formats.cc: In function 'int sdf_iter(std::fstream&, std::string&, int&)':
formats.cc:237:10: warning: 'char* strncpy(char*, const char*, size_t)' output may be truncated copying 4 bytes from a string of length 100001 [-Wstringop-truncation]
237 | strncpy(buf_4, line, 4);
| ~~~~~~~^~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -DNO_MAIN -DNO_DEBUG -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c molecule.cc -o molecule.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -DNO_MAIN -DNO_DEBUG -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c r_wrap.cc -o r_wrap.o
r_wrap.cc: In function 'SEXPREC* SWIG_MakePtr(void*, const char*, R_SWIG_Owner)':
r_wrap.cc:949:15: warning: variable 'p' set but not used [-Wunused-but-set-variable]
949 | const char *p = typeName;
| ^
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -DNO_MAIN -DNO_DEBUG -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c script.cc -o script.o
In file included from script.cc:2:
desc.h:39:13: warning: 'elements' defined but not used [-Wunused-variable]
39 | static char elements[112][3] = {
| ^~~~~~~~
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include" -DNO_MAIN -DNO_DEBUG -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c similarity.cc -o similarity.o
In file included from similarity.cc:1:
desc.h:39:13: warning: 'elements' defined but not used [-Wunused-variable]
39 | static char elements[112][3] = {
| ^~~~~~~~
g++ -std=gnu++11 -shared -s -static-libgcc -o ChemmineR.dll tmp.def DisjointSets.o cluster.o cstrsplit.o desc.o fingerprints.o formats.o molecule.o r_wrap.o script.o similarity.o -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.15-bioc/meat/ChemmineR.buildbin-libdir/00LOCK-ChemmineR/00new/ChemmineR/libs/x64
** R
** data
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* MD5 sums
packaged installation of 'ChemmineR' as ChemmineR_3.48.0.zip
* DONE (ChemmineR)
