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###
### Running command:
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###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL Rdisop
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* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’
* installing *source* package ‘Rdisop’ ...
** using staged installation
** libs
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include  -I./imslib/src/ -fpic  -g -O2  -Wall -c disop.cpp -o disop.o
In file included from ./imslib/src/ims/alphabet.h:8,
                 from disop.cpp:18:
./imslib/src/ims/element.h: In member function ‘ims::Element::mass_type ims::Element::getMass(ims::Element::size_type) const’:
./imslib/src/ims/element.h:166:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘ims::IsotopeDistribution::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  166 |       for (int i=0; i < IsotopeDistribution::SIZE; i++) {
      |                     ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from disop.cpp:22:
./imslib/src/ims/composedelement.h: At global scope:
./imslib/src/ims/composedelement.h:204:58: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  204 |   void initializeElements(const Alphabet& alphabet, std::auto_ptr<sequence_parser_type> parser)
      |                                                          ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
                 from /usr/include/c++/9/locale:43,
                 from /usr/include/c++/9/iomanip:43,
                 from disop.cpp:5:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from disop.cpp:26:
./imslib/src/ims/decomp/realmassdecomposer.h:103:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  103 |   std::auto_ptr<integer_decomposer_type> decomposer;
      |        ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
                 from /usr/include/c++/9/locale:43,
                 from /usr/include/c++/9/iomanip:43,
                 from disop.cpp:5:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from disop.cpp:28:
./imslib/src/ims/decomp/decomputils.h: In function ‘std::pair<typename DecompositionWeights::alphabet_mass_type, typename DecompositionWeights::alphabet_mass_type> ims::DecompUtils::getMinMaxWeightsRoundingErrors(const DecompositionWeights&)’:
./imslib/src/ims/decomp/decomputils.h:92:53: warning: typedef ‘weight_type’ locally defined but not used [-Wunused-local-typedefs]
   92 |  typedef typename DecompositionWeights::weight_type weight_type;
      |                                                     ^~~~~~~~~~~
disop.cpp: In function ‘bool isValidMyNitrogenRule(const ims::ComposedElement&, int)’:
disop.cpp:106:8: warning: unused variable ‘parityeven’ [-Wunused-variable]
  106 |   bool parityeven = !parityodd;
      |        ^~~~~~~~~~
disop.cpp: In function ‘SEXPREC* decomposeIsotopes(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
disop.cpp:228:43: warning: comparison of integer expressions of different signedness: ‘std::vector<ims::IsotopeDistribution::Peak>::size_type’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
  228 |  for (peaks_container::size_type i = 0; i < abundances.size(); ++i) {
      |                                         ~~^~~~~~~~~~~~~~~~~~~
disop.cpp:231:43: warning: comparison of integer expressions of different signedness: ‘std::vector<ims::IsotopeDistribution::Peak>::size_type’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
  231 |  for (peaks_container::size_type i = 0; i < abundances.size(); ++i) {
      |                                         ~~^~~~~~~~~~~~~~~~~~~
disop.cpp:239:46: warning: comparison of integer expressions of different signedness: ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
  239 |  for (masses_container::size_type mi = 0; mi < masses.size() && mi < abundances.size(); ++mi) {
      |                                           ~~~^~~~~~~~~~~~~~~
disop.cpp:239:68: warning: comparison of integer expressions of different signedness: ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
  239 |  for (masses_container::size_type mi = 0; mi < masses.size() && mi < abundances.size(); ++mi) {
      |                                                                 ~~~^~~~~~~~~~~~~~~~~~~
disop.cpp:191:6: warning: unused variable ‘number_molecules_shown’ [-Wunused-variable]
  191 |  int number_molecules_shown = 100;
      |      ^~~~~~~~~~~~~~~~~~~~~~
disop.cpp:169:39: warning: typedef ‘mass_type’ locally defined but not used [-Wunused-local-typedefs]
  169 |     typedef distribution_t::mass_type mass_type;
      |                                       ^~~~~~~~~
disop.cpp:171:47: warning: typedef ‘nominal_mass_type’ locally defined but not used [-Wunused-local-typedefs]
  171 |     typedef distribution_t::nominal_mass_type nominal_mass_type;
      |                                               ^~~~~~~~~~~~~~~~~
disop.cpp:174:42: warning: typedef ‘decomposition_type’ locally defined but not used [-Wunused-local-typedefs]
  174 |     typedef decompositions_t::value_type decomposition_type;
      |                                          ^~~~~~~~~~~~~~~~~~
disop.cpp: In function ‘SEXPREC* calculateScore(SEXP, SEXP, SEXP, SEXP)’:
disop.cpp:390:46: warning: comparison of integer expressions of different signedness: ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
  390 |  for (masses_container::size_type mi = 0; mi < masses.size() && mi < abundances.size(); ++mi)
      |                                           ~~~^~~~~~~~~~~~~~~
disop.cpp:390:68: warning: comparison of integer expressions of different signedness: ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
  390 |  for (masses_container::size_type mi = 0; mi < masses.size() && mi < abundances.size(); ++mi)
      |                                                                 ~~~^~~~~~~~~~~~~~~~~~~
disop.cpp:407:43: warning: comparison of integer expressions of different signedness: ‘std::vector<ims::IsotopeDistribution::Peak>::size_type’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
  407 |  for (peaks_container::size_type i = 0; i < abundances.size(); ++i) {
      |                                         ~~^~~~~~~~~~~~~~~~~~~
disop.cpp:410:43: warning: comparison of integer expressions of different signedness: ‘std::vector<ims::IsotopeDistribution::Peak>::size_type’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
  410 |  for (peaks_container::size_type i = 0; i < abundances.size(); ++i) {
      |                                         ~~^~~~~~~~~~~~~~~~~~~
disop.cpp:414:46: warning: comparison of integer expressions of different signedness: ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
  414 |  for (masses_container::size_type mi = 0; mi < masses.size() && mi < abundances.size(); ++mi)
      |                                           ~~~^~~~~~~~~~~~~~~
disop.cpp:414:68: warning: comparison of integer expressions of different signedness: ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} and ‘R_xlen_t’ {aka ‘long int’} [-Wsign-compare]
  414 |  for (masses_container::size_type mi = 0; mi < masses.size() && mi < abundances.size(); ++mi)
      |                                                                 ~~~^~~~~~~~~~~~~~~~~~~
disop.cpp:377:40: warning: typedef ‘mass_type’ locally defined but not used [-Wunused-local-typedefs]
  377 |      typedef distribution_t::mass_type mass_type;
      |                                        ^~~~~~~~~
disop.cpp: In function ‘SEXPREC* rlistScores(std::multimap<score_type, ims::ComposedElement, std::greater<score_type> >, int)’:
disop.cpp:626:43: warning: typedef ‘scorer_type’ locally defined but not used [-Wunused-local-typedefs]
  626 |     typedef DistributionProbabilityScorer scorer_type;
      |                                           ^~~~~~~~~~~
disop.cpp: In function ‘void initializeCHNOPS(alphabet_t&, int)’:
disop.cpp:709:32: warning: typedef ‘elements_type’ locally defined but not used [-Wunused-local-typedefs]
  709 |  typedef alphabet_t::container elements_type;
      |                                ^~~~~~~~~~~~~
disop.cpp: In function ‘void initializeAlphabet(SEXP, alphabet_t&, int)’:
disop.cpp:814:33: warning: typedef ‘elements_type’ locally defined but not used [-Wunused-local-typedefs]
  814 |   typedef alphabet_t::container elements_type;
      |                                 ^~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include  -I./imslib/src/ -fpic  -g -O2  -Wall -c imslib/src/ims/element.cpp -o imslib/src/ims/element.o
In file included from imslib/src/ims/element.cpp:6:
./imslib/src/ims/element.h: In member function ‘ims::Element::mass_type ims::Element::getMass(ims::Element::size_type) const’:
./imslib/src/ims/element.h:166:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘ims::IsotopeDistribution::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  166 |       for (int i=0; i < IsotopeDistribution::SIZE; i++) {
      |                     ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include  -I./imslib/src/ -fpic  -g -O2  -Wall -c imslib/src/ims/composedelement.cpp -o imslib/src/ims/composedelement.o
In file included from ./imslib/src/ims/composedelement.h:7,
                 from imslib/src/ims/composedelement.cpp:8:
./imslib/src/ims/element.h: In member function ‘ims::Element::mass_type ims::Element::getMass(ims::Element::size_type) const’:
./imslib/src/ims/element.h:166:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘ims::IsotopeDistribution::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  166 |       for (int i=0; i < IsotopeDistribution::SIZE; i++) {
      |                     ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from imslib/src/ims/composedelement.cpp:8:
./imslib/src/ims/composedelement.h: At global scope:
./imslib/src/ims/composedelement.h:204:58: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  204 |   void initializeElements(const Alphabet& alphabet, std::auto_ptr<sequence_parser_type> parser)
      |                                                          ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from ./imslib/src/ims/composedelement.h:6,
                 from imslib/src/ims/composedelement.cpp:8:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
imslib/src/ims/composedelement.cpp: In constructor ‘ims::ComposedElement::ComposedElement(const name_type&, const ims::Alphabet&, unsigned int)’:
imslib/src/ims/composedelement.cpp:26:7: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   26 |  std::auto_ptr<sequence_parser_type> parser;
      |       ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from ./imslib/src/ims/composedelement.h:6,
                 from imslib/src/ims/composedelement.cpp:8:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
imslib/src/ims/composedelement.cpp:28:17: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   28 |   parser = std::auto_ptr<sequence_parser_type>(new StandardMoleculeSequenceParser);
      |                 ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from ./imslib/src/ims/composedelement.h:6,
                 from imslib/src/ims/composedelement.cpp:8:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
imslib/src/ims/composedelement.cpp:30:17: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   30 |   parser = std::auto_ptr<sequence_parser_type>(new MoleculeSequenceParser);
      |                 ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from ./imslib/src/ims/composedelement.h:6,
                 from imslib/src/ims/composedelement.cpp:8:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
imslib/src/ims/composedelement.cpp: At global scope:
imslib/src/ims/composedelement.cpp:116:73: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  116 | void ComposedElement::initializeElements(const Alphabet& alphabet, std::auto_ptr<sequence_parser_type> parser)
      |                                                                         ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from ./imslib/src/ims/composedelement.h:6,
                 from imslib/src/ims/composedelement.cpp:8:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include  -I./imslib/src/ -fpic  -g -O2  -Wall -c imslib/src/ims/isotopedistribution.cpp -o imslib/src/ims/isotopedistribution.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include  -I./imslib/src/ -fpic  -g -O2  -Wall -c imslib/src/ims/alphabet.cpp -o imslib/src/ims/alphabet.o
In file included from ./imslib/src/ims/alphabet.h:8,
                 from imslib/src/ims/alphabet.cpp:6:
./imslib/src/ims/element.h: In member function ‘ims::Element::mass_type ims::Element::getMass(ims::Element::size_type) const’:
./imslib/src/ims/element.h:166:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘ims::IsotopeDistribution::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  166 |       for (int i=0; i < IsotopeDistribution::SIZE; i++) {
      |                     ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include  -I./imslib/src/ -fpic  -g -O2  -Wall -c imslib/src/ims/weights.cpp -o imslib/src/ims/weights.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include  -I./imslib/src/ -fpic  -g -O2  -Wall -c imslib/src/ims/distributedalphabet.cpp -o imslib/src/ims/distributedalphabet.o
In file included from ./imslib/src/ims/alphabet.h:8,
                 from ./imslib/src/ims/distributedalphabet.h:7,
                 from imslib/src/ims/distributedalphabet.cpp:7:
./imslib/src/ims/element.h: In member function ‘ims::Element::mass_type ims::Element::getMass(ims::Element::size_type) const’:
./imslib/src/ims/element.h:166:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘ims::IsotopeDistribution::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  166 |       for (int i=0; i < IsotopeDistribution::SIZE; i++) {
      |                     ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include  -I./imslib/src/ -fpic  -g -O2  -Wall -c imslib/src/ims/transformation.cpp -o imslib/src/ims/transformation.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include  -I./imslib/src/ -fpic  -g -O2  -Wall -c imslib/src/ims/isotopespecies.cpp -o imslib/src/ims/isotopespecies.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include  -I./imslib/src/ -fpic  -g -O2  -Wall -c imslib/src/ims/base/parser/alphabettextparser.cpp -o imslib/src/ims/base/parser/alphabettextparser.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include  -I./imslib/src/ -fpic  -g -O2  -Wall -c imslib/src/ims/base/parser/distributedalphabettextparser.cpp -o imslib/src/ims/base/parser/distributedalphabettextparser.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include  -I./imslib/src/ -fpic  -g -O2  -Wall -c imslib/src/ims/base/parser/massestextparser.cpp -o imslib/src/ims/base/parser/massestextparser.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include  -I./imslib/src/ -fpic  -g -O2  -Wall -c imslib/src/ims/base/parser/moleculesequenceparser.cpp -o imslib/src/ims/base/parser/moleculesequenceparser.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include  -I./imslib/src/ -fpic  -g -O2  -Wall -c imslib/src/ims/base/parser/standardmoleculesequenceparser.cpp -o imslib/src/ims/base/parser/standardmoleculesequenceparser.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include  -I./imslib/src/ -fpic  -g -O2  -Wall -c imslib/src/ims/base/parser/keggligandcompoundsparser.cpp -o imslib/src/ims/base/parser/keggligandcompoundsparser.o
imslib/src/ims/base/parser/keggligandcompoundsparser.cpp: In member function ‘virtual void ims::KeggLigandCompoundsParser::parse(const sequence_type&)’:
imslib/src/ims/base/parser/keggligandcompoundsparser.cpp:53:31: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses]
   53 |  for (; letter_pos < last_pos &&
      |         ~~~~~~~~~~~~~~~~~~~~~~^~
   54 |    ( std::isalpha(sequence[letter_pos]) && std::isupper(sequence[letter_pos])) ||
      |    ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include  -I./imslib/src/ -fpic  -g -O2  -Wall -c imslib/src/ims/base/parser/moleculeionchargemodificationparser.cpp -o imslib/src/ims/base/parser/moleculeionchargemodificationparser.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include  -I./imslib/src/ -fpic  -g -O2  -Wall -c imslib/src/ims/calib/linepairstabber.cpp -o imslib/src/ims/calib/linepairstabber.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include  -I./imslib/src/ -fpic  -g -O2  -Wall -c imslib/src/ims/calib/matchmatrix.cpp -o imslib/src/ims/calib/matchmatrix.o
In file included from imslib/src/ims/calib/matchmatrix.cpp:1:
./imslib/src/ims/calib/matchmatrix.h:61:7: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   61 |  std::auto_ptr<std::map<int,int> > countMatches();
      |       ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from ./imslib/src/ims/calib/matchmatrix.h:4,
                 from imslib/src/ims/calib/matchmatrix.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from imslib/src/ims/calib/matchmatrix.cpp:1:
./imslib/src/ims/calib/matchmatrix.h:65:7: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   65 |  std::auto_ptr<std::map<int,int> > countMatchesRestrictive();
      |       ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from ./imslib/src/ims/calib/matchmatrix.h:4,
                 from imslib/src/ims/calib/matchmatrix.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
imslib/src/ims/calib/matchmatrix.cpp:81:6: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   81 | std::auto_ptr<std::map<int,int> > MatchMatrix::countMatches() {
      |      ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from ./imslib/src/ims/calib/matchmatrix.h:4,
                 from imslib/src/ims/calib/matchmatrix.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
imslib/src/ims/calib/matchmatrix.cpp: In member function ‘std::auto_ptr<std::map<int, int> > ims::MatchMatrix::countMatches()’:
imslib/src/ims/calib/matchmatrix.cpp:82:7: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   82 |  std::auto_ptr<std::map<int,int> > m(new std::map<int,int>);
      |       ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from ./imslib/src/ims/calib/matchmatrix.h:4,
                 from imslib/src/ims/calib/matchmatrix.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
imslib/src/ims/calib/matchmatrix.cpp: At global scope:
imslib/src/ims/calib/matchmatrix.cpp:102:6: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  102 | std::auto_ptr<std::map<int,int> > MatchMatrix::countMatchesRestrictive() {
      |      ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from ./imslib/src/ims/calib/matchmatrix.h:4,
                 from imslib/src/ims/calib/matchmatrix.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
imslib/src/ims/calib/matchmatrix.cpp: In member function ‘std::auto_ptr<std::map<int, int> > ims::MatchMatrix::countMatchesRestrictive()’:
imslib/src/ims/calib/matchmatrix.cpp:103:7: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  103 |  std::auto_ptr<std::map<int,int> > m(new std::map<int,int>);
      |       ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from ./imslib/src/ims/calib/matchmatrix.h:4,
                 from imslib/src/ims/calib/matchmatrix.cpp:1:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include  -I./imslib/src/ -fpic  -g -O2  -Wall -c imslib/src/ims/calib/linearpointsetmatcher.cpp -o imslib/src/ims/calib/linearpointsetmatcher.o
In file included from ./imslib/src/ims/calib/linearpointsetmatcher.h:13,
                 from imslib/src/ims/calib/linearpointsetmatcher.cpp:11:
./imslib/src/ims/calib/matchmatrix.h:61:7: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   61 |  std::auto_ptr<std::map<int,int> > countMatches();
      |       ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from ./imslib/src/ims/calib/linearpointsetmatcher.h:8,
                 from imslib/src/ims/calib/linearpointsetmatcher.cpp:11:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from ./imslib/src/ims/calib/linearpointsetmatcher.h:13,
                 from imslib/src/ims/calib/linearpointsetmatcher.cpp:11:
./imslib/src/ims/calib/matchmatrix.h:65:7: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   65 |  std::auto_ptr<std::map<int,int> > countMatchesRestrictive();
      |       ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from ./imslib/src/ims/calib/linearpointsetmatcher.h:8,
                 from imslib/src/ims/calib/linearpointsetmatcher.cpp:11:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from imslib/src/ims/calib/linearpointsetmatcher.cpp:11:
./imslib/src/ims/calib/linearpointsetmatcher.h:146:7: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  146 |  std::auto_ptr<std::map<int,int> > getMapping() const;
      |       ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from ./imslib/src/ims/calib/linearpointsetmatcher.h:8,
                 from imslib/src/ims/calib/linearpointsetmatcher.cpp:11:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from imslib/src/ims/calib/linearpointsetmatcher.cpp:11:
./imslib/src/ims/calib/linearpointsetmatcher.h:169:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  169 |   std::auto_ptr<std::map<int,int> > mapping;
      |        ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from ./imslib/src/ims/calib/linearpointsetmatcher.h:8,
                 from imslib/src/ims/calib/linearpointsetmatcher.cpp:11:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from imslib/src/ims/calib/linearpointsetmatcher.cpp:11:
./imslib/src/ims/calib/linearpointsetmatcher.h: In member function ‘void ims::LinearPointSetMatcher::countMatchesOneToOne(RandomAccessIterator, RandomAccessIterator, RandomAccessIterator, RandomAccessIterator, const std::vector<ims::RepresentativeScale>&, int, int, float)’:
./imslib/src/ims/calib/linearpointsetmatcher.h:281:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  281 |   std::auto_ptr<std::map<int,int> > mapping(0);
      |        ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from ./imslib/src/ims/calib/linearpointsetmatcher.h:8,
                 from imslib/src/ims/calib/linearpointsetmatcher.cpp:11:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from imslib/src/ims/calib/linearpointsetmatcher.cpp:11:
./imslib/src/ims/calib/linearpointsetmatcher.h: In member function ‘int ims::LinearPointSetMatcher::match(RandomAccessIterator, RandomAccessIterator, RandomAccessIterator, RandomAccessIterator)’:
./imslib/src/ims/calib/linearpointsetmatcher.h:324:26: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  324 |   results.mapping = std::auto_ptr<std::map<int,int> >(new std::map<int,int>);
      |                          ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from ./imslib/src/ims/calib/linearpointsetmatcher.h:8,
                 from imslib/src/ims/calib/linearpointsetmatcher.cpp:11:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from imslib/src/ims/calib/linearpointsetmatcher.cpp:11:
./imslib/src/ims/calib/linearpointsetmatcher.h:326:26: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  326 |   results.mapping = std::auto_ptr<std::map<int,int> >(0);
      |                          ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from ./imslib/src/ims/calib/linearpointsetmatcher.h:8,
                 from imslib/src/ims/calib/linearpointsetmatcher.cpp:11:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
imslib/src/ims/calib/linearpointsetmatcher.cpp: At global scope:
imslib/src/ims/calib/linearpointsetmatcher.cpp:84:6: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   84 | std::auto_ptr<std::map<int,int> > LinearPointSetMatcher::getMapping() const {
      |      ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from ./imslib/src/ims/calib/linearpointsetmatcher.h:8,
                 from imslib/src/ims/calib/linearpointsetmatcher.cpp:11:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
imslib/src/ims/calib/linearpointsetmatcher.cpp: In member function ‘std::auto_ptr<std::map<int, int> > ims::LinearPointSetMatcher::getMapping() const’:
imslib/src/ims/calib/linearpointsetmatcher.cpp:86:15: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   86 |   return std::auto_ptr<std::map<int,int> >(0); // TODO throw sth. instead
      |               ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from ./imslib/src/ims/calib/linearpointsetmatcher.h:8,
                 from imslib/src/ims/calib/linearpointsetmatcher.cpp:11:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
imslib/src/ims/calib/linearpointsetmatcher.cpp:89:15: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   89 |   return std::auto_ptr<std::map<int,int> >(new std::map<int,int>(*(results.mapping)));
      |               ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from ./imslib/src/ims/calib/linearpointsetmatcher.h:8,
                 from imslib/src/ims/calib/linearpointsetmatcher.cpp:11:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include  -I./imslib/src/ -fpic  -g -O2  -Wall -c imslib/src/ims/decomp/realmassdecomposer.cpp -o imslib/src/ims/decomp/realmassdecomposer.o
In file included from imslib/src/ims/decomp/realmassdecomposer.cpp:8:
./imslib/src/ims/decomp/realmassdecomposer.h:103:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  103 |   std::auto_ptr<integer_decomposer_type> decomposer;
      |        ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from ./imslib/src/ims/decomp/realmassdecomposer.h:5,
                 from imslib/src/ims/decomp/realmassdecomposer.cpp:8:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from ./imslib/src/ims/alphabet.h:8,
                 from ./imslib/src/ims/decomp/decomputils.h:12,
                 from imslib/src/ims/decomp/realmassdecomposer.cpp:9:
./imslib/src/ims/element.h: In member function ‘ims::Element::mass_type ims::Element::getMass(ims::Element::size_type) const’:
./imslib/src/ims/element.h:166:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘ims::IsotopeDistribution::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  166 |       for (int i=0; i < IsotopeDistribution::SIZE; i++) {
      |                     ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from imslib/src/ims/decomp/realmassdecomposer.cpp:9:
./imslib/src/ims/decomp/decomputils.h: In function ‘std::pair<typename DecompositionWeights::alphabet_mass_type, typename DecompositionWeights::alphabet_mass_type> ims::DecompUtils::getMinMaxWeightsRoundingErrors(const DecompositionWeights&)’:
./imslib/src/ims/decomp/decomputils.h:92:53: warning: typedef ‘weight_type’ locally defined but not used [-Wunused-local-typedefs]
   92 |  typedef typename DecompositionWeights::weight_type weight_type;
      |                                                     ^~~~~~~~~~~
imslib/src/ims/decomp/realmassdecomposer.cpp: In constructor ‘ims::RealMassDecomposer::RealMassDecomposer(const ims::Weights&)’:
imslib/src/ims/decomp/realmassdecomposer.cpp:21:20: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   21 |  decomposer = std::auto_ptr<integer_decomposer_type>(
      |                    ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from ./imslib/src/ims/decomp/realmassdecomposer.h:5,
                 from imslib/src/ims/decomp/realmassdecomposer.cpp:8:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include  -I./imslib/src/ -fpic  -g -O2  -Wall -c imslib/src/ims/utils/distribution.cpp -o imslib/src/ims/utils/distribution.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include  -I./imslib/src/ -fpic  -g -O2  -Wall -c imslib/src/ims/distributionprobabilityscorer.cpp -o imslib/src/ims/distributionprobabilityscorer.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include  -I./imslib/src/ -fpic  -g -O2  -Wall -c imslib/src/ims/characteralphabet.cpp -o imslib/src/ims/characteralphabet.o
In file included from ./imslib/src/ims/alphabet.h:8,
                 from ./imslib/src/ims/characteralphabet.h:6,
                 from imslib/src/ims/characteralphabet.cpp:3:
./imslib/src/ims/element.h: In member function ‘ims::Element::mass_type ims::Element::getMass(ims::Element::size_type) const’:
./imslib/src/ims/element.h:166:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘ims::IsotopeDistribution::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  166 |       for (int i=0; i < IsotopeDistribution::SIZE; i++) {
      |                     ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include  -I./imslib/src/ -fpic  -g -O2  -Wall -c imslib/src/ims/nitrogenrulefilter.cpp -o imslib/src/ims/nitrogenrulefilter.o
In file included from ./imslib/src/ims/composedelement.h:7,
                 from ./imslib/src/ims/nitrogenrulefilter.h:4,
                 from imslib/src/ims/nitrogenrulefilter.cpp:5:
./imslib/src/ims/element.h: In member function ‘ims::Element::mass_type ims::Element::getMass(ims::Element::size_type) const’:
./imslib/src/ims/element.h:166:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘ims::IsotopeDistribution::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  166 |       for (int i=0; i < IsotopeDistribution::SIZE; i++) {
      |                     ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ./imslib/src/ims/nitrogenrulefilter.h:4,
                 from imslib/src/ims/nitrogenrulefilter.cpp:5:
./imslib/src/ims/composedelement.h: At global scope:
./imslib/src/ims/composedelement.h:204:58: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  204 |   void initializeElements(const Alphabet& alphabet, std::auto_ptr<sequence_parser_type> parser)
      |                                                          ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
                 from ./imslib/src/ims/composedelement.h:6,
                 from ./imslib/src/ims/nitrogenrulefilter.h:4,
                 from imslib/src/ims/nitrogenrulefilter.cpp:5:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
   53 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
g++ -std=gnu++14 -shared -L/home/biocbuild/bbs-3.14-bioc/R/lib -L/usr/local/lib -o Rdisop.so disop.o imslib/src/ims/element.o imslib/src/ims/composedelement.o imslib/src/ims/isotopedistribution.o imslib/src/ims/alphabet.o imslib/src/ims/weights.o imslib/src/ims/distributedalphabet.o imslib/src/ims/transformation.o imslib/src/ims/isotopespecies.o imslib/src/ims/base/parser/alphabettextparser.o imslib/src/ims/base/parser/distributedalphabettextparser.o imslib/src/ims/base/parser/massestextparser.o imslib/src/ims/base/parser/moleculesequenceparser.o imslib/src/ims/base/parser/standardmoleculesequenceparser.o imslib/src/ims/base/parser/keggligandcompoundsparser.o imslib/src/ims/base/parser/moleculeionchargemodificationparser.o imslib/src/ims/calib/linepairstabber.o imslib/src/ims/calib/matchmatrix.o imslib/src/ims/calib/linearpointsetmatcher.o imslib/src/ims/decomp/realmassdecomposer.o imslib/src/ims/utils/distribution.o imslib/src/ims/distributionprobabilityscorer.o imslib/src/ims/characteralphabet.o imslib/src/ims/nitrogenrulefilter.o -L/home/biocbuild/bbs-3.14-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.14-bioc/R/library/00LOCK-Rdisop/00new/Rdisop/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 (Rdisop)