##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Rdisop.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings Rdisop_1.59.0.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/Rdisop.Rcheck'
* using R Under development (unstable) (2022-12-25 r83502 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 10.4.0
    GNU Fortran (GCC) 10.4.0
* running under: Windows Server x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'Rdisop/DESCRIPTION' ... OK
* this is package 'Rdisop' version '1.59.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .travis.yml
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'Rdisop' can be installed ... WARNING
Found the following significant warnings:
  ./imslib/src/ims/composedelement.h:204:72: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  ./imslib/src/ims/decomp/realmassdecomposer.h:103:22: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  disop.cpp:325:48: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = multiplies<double>; _Tp = double]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations]
  imslib/src/ims/composedelement.cpp:26:14: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  imslib/src/ims/composedelement.cpp:28:31: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  imslib/src/ims/composedelement.cpp:30:31: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  imslib/src/ims/composedelement.cpp:116:73: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  ./imslib/src/ims/utils/compose_f_gx_t.h:66:16: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
  ./imslib/src/ims/utils/compose_f_gx_hy_t.h:57:16: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
  imslib/src/ims/alphabet.cpp:33:42: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = equal_to<__cxx11::basic_string<char> >; _Tp = __cxx11::basic_string<char>]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations]
  imslib/src/ims/alphabet.cpp:34:33: warning: 'std::const_mem_fun_ref_t<_Ret, _Tp> std::mem_fun_ref(_Ret (_Tp::*)() const) [with _Ret = const __cxx11::basic_string<char>&; _Tp = ims::Element]' is deprecated: use 'std::mem_fn' instead [-Wdeprecated-declarations]
  imslib/src/ims/alphabet.cpp:74:57: warning: 'std::const_mem_fun_ref_t<_Ret, _Tp> std::mem_fun_ref(_Ret (_Tp::*)() const) [with _Ret = const __cxx11::basic_string<char>&; _Tp = ims::Element]' is deprecated: use 'std::mem_fn' instead [-Wdeprecated-declarations]
  imslib/src/ims/alphabet.cpp:75:57: warning: 'std::const_mem_fun_ref_t<_Ret, _Tp> std::mem_fun_ref(_Ret (_Tp::*)() const) [with _Ret = const __cxx11::basic_string<char>&; _Tp = ims::Element]' is deprecated: use 'std::mem_fn' instead [-Wdeprecated-declarations]
  ./imslib/src/ims/calib/matchmatrix.h:61:14: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  ./imslib/src/ims/calib/matchmatrix.h:65:14: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  imslib/src/ims/calib/matchmatrix.cpp:81:6: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  imslib/src/ims/calib/matchmatrix.cpp:82:14: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  imslib/src/ims/calib/matchmatrix.cpp:102:6: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  imslib/src/ims/calib/matchmatrix.cpp:103:14: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  ./imslib/src/ims/calib/linearpointsetmatcher.h:146:14: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  ./imslib/src/ims/calib/linearpointsetmatcher.h:169:22: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  ./imslib/src/ims/calib/linearpointsetmatcher.h:281:22: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  ./imslib/src/ims/calib/linearpointsetmatcher.h:324:40: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  ./imslib/src/ims/calib/linearpointsetmatcher.h:326:40: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  imslib/src/ims/calib/linearpointsetmatcher.cpp:84:6: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  imslib/src/ims/calib/linearpointsetmatcher.cpp:86:29: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  imslib/src/ims/calib/linearpointsetmatcher.cpp:89:29: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  imslib/src/ims/decomp/realmassdecomposer.cpp:21:27: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
See 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/Rdisop.Rcheck/00install.out' for details.
* used C++ compiler: 'G__~1.EXE (GCC) 12.2.0'
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files for x64 is not available
File 'F:/biocbuild/bbs-3.17-bioc/R/library/Rdisop/libs/x64/Rdisop.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'rand', possibly from 'rand' (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking sizes of PDF files under 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'doRUnit.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 2 NOTEs
See
  'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/Rdisop.Rcheck/00check.log'
for details.

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##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL Rdisop
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.17-bioc/R/library'
* installing *source* package 'Rdisop' ...
** using staged installation
** libs
using C++ compiler: 'G__~1.EXE (GCC) 12.2.0'
g++ -std=gnu++11  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include'   -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"  -I./imslib/src/   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -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(size_type) const':
./imslib/src/ims/element.h:166:37: warning: comparison of integer expressions of different signedness: 'int' and 'ims::IsotopeDistribution::size_type' {aka 'long 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:204:72: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  204 |                 void initializeElements(const Alphabet& alphabet, std::auto_ptr<sequence_parser_type> parser)
      |                                                                        ^~~~~~~~
In file included from c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\memory:76,
                 from ./imslib/src/ims/composedelement.h:6:
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
   64 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from disop.cpp:26:
./imslib/src/ims/decomp/realmassdecomposer.h:103:22: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  103 |                 std::auto_ptr<integer_decomposer_type> decomposer;
      |                      ^~~~~~~~
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
   64 |   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:92:60: 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:228:50: warning: comparison of integer expressions of different signedness: 'std::vector<ims::IsotopeDistribution::Peak>::size_type' {aka 'long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare]
  228 |         for (peaks_container::size_type i = 0; i < abundances.size(); ++i) {
      |                                                ~~^~~~~~~~~~~~~~~~~~~
disop.cpp:231:50: warning: comparison of integer expressions of different signedness: 'std::vector<ims::IsotopeDistribution::Peak>::size_type' {aka 'long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare]
  231 |         for (peaks_container::size_type i = 0; i < abundances.size(); ++i) {
      |                                                ~~^~~~~~~~~~~~~~~~~~~
disop.cpp:239:53: warning: comparison of integer expressions of different signedness: 'std::vector<double>::size_type' {aka 'long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare]
  239 |         for (masses_container::size_type mi = 0; mi < masses.size() && mi < abundances.size(); ++mi) {
      |                                                  ~~~^~~~~~~~~~~~~~~
disop.cpp:239:75: warning: comparison of integer expressions of different signedness: 'std::vector<double>::size_type' {aka 'long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare]
  239 |         for (masses_container::size_type mi = 0; mi < masses.size() && mi < abundances.size(); ++mi) {
      |                                                                        ~~~^~~~~~~~~~~~~~~~~~~
disop.cpp:325:48: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = multiplies<double>; _Tp = double]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations]
  325 |                                         bind2nd(multiplies<abundance_type>(), scale));  // operation (*scale)
      |                                         ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\stl_function.h:1438,
                 from c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\string:48,
                 from c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\locale_classes.h:40,
                 from c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\ios_base.h:41,
                 from c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\ios:42,
                 from c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\ostream:38,
                 from c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\iostream:39,
                 from disop.cpp:4:
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\backward\binders.h:172:5: note: declared here
  172 |     bind2nd(const _Operation& __fn, const _Tp& __x)
      |     ^~~~~~~
disop.cpp:191:13: 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:390:53: warning: comparison of integer expressions of different signedness: 'std::vector<double>::size_type' {aka 'long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare]
  390 |         for (masses_container::size_type mi = 0; mi < masses.size() && mi < abundances.size(); ++mi)
      |                                                  ~~~^~~~~~~~~~~~~~~
disop.cpp:390:75: warning: comparison of integer expressions of different signedness: 'std::vector<double>::size_type' {aka 'long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare]
  390 |         for (masses_container::size_type mi = 0; mi < masses.size() && mi < abundances.size(); ++mi)
      |                                                                        ~~~^~~~~~~~~~~~~~~~~~~
disop.cpp:407:50: warning: comparison of integer expressions of different signedness: 'std::vector<ims::IsotopeDistribution::Peak>::size_type' {aka 'long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare]
  407 |         for (peaks_container::size_type i = 0; i < abundances.size(); ++i) {
      |                                                ~~^~~~~~~~~~~~~~~~~~~
disop.cpp:410:50: warning: comparison of integer expressions of different signedness: 'std::vector<ims::IsotopeDistribution::Peak>::size_type' {aka 'long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare]
  410 |         for (peaks_container::size_type i = 0; i < abundances.size(); ++i) {
      |                                                ~~^~~~~~~~~~~~~~~~~~~
disop.cpp:414:53: warning: comparison of integer expressions of different signedness: 'std::vector<double>::size_type' {aka 'long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare]
  414 |         for (masses_container::size_type mi = 0; mi < masses.size() && mi < abundances.size(); ++mi)
      |                                                  ~~~^~~~~~~~~~~~~~~
disop.cpp:414:75: warning: comparison of integer expressions of different signedness: 'std::vector<double>::size_type' {aka 'long long unsigned int'} and 'R_xlen_t' {aka 'long long int'} [-Wsign-compare]
  414 |         for (masses_container::size_type mi = 0; mi < masses.size() && mi < abundances.size(); ++mi)
      |                                                                        ~~~^~~~~~~~~~~~~~~~~~~
disop.cpp:377:43: 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:709:39: 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++11  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include'   -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"  -I./imslib/src/   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -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(size_type) const':
./imslib/src/ims/element.h:166:37: warning: comparison of integer expressions of different signedness: 'int' and 'ims::IsotopeDistribution::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
  166 |                     for (int i=0; i < IsotopeDistribution::SIZE; i++) {
      |                                   ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include'   -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"  -I./imslib/src/   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -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(size_type) const':
./imslib/src/ims/element.h:166:37: warning: comparison of integer expressions of different signedness: 'int' and 'ims::IsotopeDistribution::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
  166 |                     for (int i=0; i < IsotopeDistribution::SIZE; i++) {
      |                                   ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
./imslib/src/ims/composedelement.h: At global scope:
./imslib/src/ims/composedelement.h:204:72: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  204 |                 void initializeElements(const Alphabet& alphabet, std::auto_ptr<sequence_parser_type> parser)
      |                                                                        ^~~~~~~~
In file included from c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\memory:76,
                 from ./imslib/src/ims/composedelement.h:6:
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
   64 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
imslib/src/ims/composedelement.cpp: In constructor 'ims::ComposedElement::ComposedElement(const ims::Element::name_type&, const ims::Alphabet&, unsigned int)':
imslib/src/ims/composedelement.cpp:26:14: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   26 |         std::auto_ptr<sequence_parser_type> parser;
      |              ^~~~~~~~
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
   64 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
imslib/src/ims/composedelement.cpp:28:31: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   28 |                 parser = std::auto_ptr<sequence_parser_type>(new StandardMoleculeSequenceParser);
      |                               ^~~~~~~~
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
   64 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
imslib/src/ims/composedelement.cpp:30:31: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   30 |                 parser = std::auto_ptr<sequence_parser_type>(new MoleculeSequenceParser);
      |                               ^~~~~~~~
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
   64 |   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: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  116 | void ComposedElement::initializeElements(const Alphabet& alphabet, std::auto_ptr<sequence_parser_type> parser)
      |                                                                         ^~~~~~~~
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
   64 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
g++ -std=gnu++11  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include'   -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"  -I./imslib/src/   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c imslib/src/ims/isotopedistribution.cpp -o imslib/src/ims/isotopedistribution.o
g++ -std=gnu++11  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include'   -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"  -I./imslib/src/   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -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(size_type) const':
./imslib/src/ims/element.h:166:37: warning: comparison of integer expressions of different signedness: 'int' and 'ims::IsotopeDistribution::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
  166 |                     for (int i=0; i < IsotopeDistribution::SIZE; i++) {
      |                                   ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from imslib/src/ims/alphabet.cpp:7:
./imslib/src/ims/utils/compose_f_gx_t.h: At global scope:
./imslib/src/ims/utils/compose_f_gx_t.h:66:16: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
   66 |  : public std::unary_function<typename OP2::argument_type,
      |                ^~~~~~~~~~~~~~
In file included from c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\functional:49,
                 from imslib/src/ims/alphabet.cpp:4:
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\stl_function.h:117:12: note: declared here
  117 |     struct unary_function
      |            ^~~~~~~~~~~~~~
In file included from imslib/src/ims/alphabet.cpp:8:
./imslib/src/ims/utils/compose_f_gx_hy_t.h:57:16: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   57 |  : public std::binary_function<typename OP2::argument_type,
      |                ^~~~~~~~~~~~~~~
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\stl_function.h:131:12: note: declared here
  131 |     struct binary_function
      |            ^~~~~~~~~~~~~~~
imslib/src/ims/alphabet.cpp: In member function 'bool ims::Alphabet::hasName(const name_type&) const':
imslib/src/ims/alphabet.cpp:33:42: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = equal_to<__cxx11::basic_string<char> >; _Tp = __cxx11::basic_string<char>]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations]
   33 |                 compose_f_gx(std::bind2nd(std::equal_to<name_type>(), name),
      |                              ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\stl_function.h:1438:
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\backward\binders.h:172:5: note: declared here
  172 |     bind2nd(const _Operation& __fn, const _Tp& __x)
      |     ^~~~~~~
imslib/src/ims/alphabet.cpp:34:33: warning: 'std::const_mem_fun_ref_t<_Ret, _Tp> std::mem_fun_ref(_Ret (_Tp::*)() const) [with _Ret = const __cxx11::basic_string<char>&; _Tp = ims::Element]' is deprecated: use 'std::mem_fn' instead [-Wdeprecated-declarations]
   34 |                 std::mem_fun_ref(&element_type::getName))) < elements.end();
      |                 ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\stl_function.h:1389:5: note: declared here
 1389 |     mem_fun_ref(_Ret (_Tp::*__f)() const)
      |     ^~~~~~~~~~~
imslib/src/ims/alphabet.cpp: In member function 'virtual void ims::Alphabet::sortByNames()':
imslib/src/ims/alphabet.cpp:74:57: warning: 'std::const_mem_fun_ref_t<_Ret, _Tp> std::mem_fun_ref(_Ret (_Tp::*)() const) [with _Ret = const __cxx11::basic_string<char>&; _Tp = ims::Element]' is deprecated: use 'std::mem_fn' instead [-Wdeprecated-declarations]
   74 |                                         std::mem_fun_ref(&element_type::getName),
      |                                         ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\stl_function.h:1389:5: note: declared here
 1389 |     mem_fun_ref(_Ret (_Tp::*__f)() const)
      |     ^~~~~~~~~~~
imslib/src/ims/alphabet.cpp:75:57: warning: 'std::const_mem_fun_ref_t<_Ret, _Tp> std::mem_fun_ref(_Ret (_Tp::*)() const) [with _Ret = const __cxx11::basic_string<char>&; _Tp = ims::Element]' is deprecated: use 'std::mem_fn' instead [-Wdeprecated-declarations]
   75 |                                         std::mem_fun_ref(&element_type::getName)));
      |                                         ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\stl_function.h:1389:5: note: declared here
 1389 |     mem_fun_ref(_Ret (_Tp::*__f)() const)
      |     ^~~~~~~~~~~
g++ -std=gnu++11  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include'   -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"  -I./imslib/src/   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c imslib/src/ims/weights.cpp -o imslib/src/ims/weights.o
g++ -std=gnu++11  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include'   -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"  -I./imslib/src/   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -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(size_type) const':
./imslib/src/ims/element.h:166:37: warning: comparison of integer expressions of different signedness: 'int' and 'ims::IsotopeDistribution::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
  166 |                     for (int i=0; i < IsotopeDistribution::SIZE; i++) {
      |                                   ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include'   -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"  -I./imslib/src/   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c imslib/src/ims/transformation.cpp -o imslib/src/ims/transformation.o
g++ -std=gnu++11  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include'   -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"  -I./imslib/src/   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c imslib/src/ims/isotopespecies.cpp -o imslib/src/ims/isotopespecies.o
g++ -std=gnu++11  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include'   -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"  -I./imslib/src/   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c imslib/src/ims/base/parser/alphabettextparser.cpp -o imslib/src/ims/base/parser/alphabettextparser.o
g++ -std=gnu++11  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include'   -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"  -I./imslib/src/   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c imslib/src/ims/base/parser/distributedalphabettextparser.cpp -o imslib/src/ims/base/parser/distributedalphabettextparser.o
g++ -std=gnu++11  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include'   -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"  -I./imslib/src/   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c imslib/src/ims/base/parser/massestextparser.cpp -o imslib/src/ims/base/parser/massestextparser.o
g++ -std=gnu++11  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include'   -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"  -I./imslib/src/   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c imslib/src/ims/base/parser/moleculesequenceparser.cpp -o imslib/src/ims/base/parser/moleculesequenceparser.o
g++ -std=gnu++11  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include'   -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"  -I./imslib/src/   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c imslib/src/ims/base/parser/standardmoleculesequenceparser.cpp -o imslib/src/ims/base/parser/standardmoleculesequenceparser.o
g++ -std=gnu++11  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include'   -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"  -I./imslib/src/   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -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 ims::AbstractMoleculeSequenceParser::sequence_type&)':
imslib/src/ims/base/parser/keggligandcompoundsparser.cpp:53:39: 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++11  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include'   -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"  -I./imslib/src/   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c imslib/src/ims/base/parser/moleculeionchargemodificationparser.cpp -o imslib/src/ims/base/parser/moleculeionchargemodificationparser.o
g++ -std=gnu++11  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include'   -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"  -I./imslib/src/   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c imslib/src/ims/calib/linepairstabber.cpp -o imslib/src/ims/calib/linepairstabber.o
g++ -std=gnu++11  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include'   -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"  -I./imslib/src/   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -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:61:14: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   61 |         std::auto_ptr<std::map<int,int> > countMatches();
      |              ^~~~~~~~
In file included from c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\memory:76,
                 from ./imslib/src/ims/calib/matchmatrix.h:4:
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
   64 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
./imslib/src/ims/calib/matchmatrix.h:65:14: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   65 |         std::auto_ptr<std::map<int,int> > countMatchesRestrictive();
      |              ^~~~~~~~
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
   64 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
imslib/src/ims/calib/matchmatrix.cpp:81:6: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   81 | std::auto_ptr<std::map<int,int> > MatchMatrix::countMatches() {
      |      ^~~~~~~~
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
   64 |   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:82:14: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   82 |         std::auto_ptr<std::map<int,int> > m(new std::map<int,int>);
      |              ^~~~~~~~
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
   64 |   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: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  102 | std::auto_ptr<std::map<int,int> > MatchMatrix::countMatchesRestrictive() {
      |      ^~~~~~~~
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
   64 |   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:103:14: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  103 |         std::auto_ptr<std::map<int,int> > m(new std::map<int,int>);
      |              ^~~~~~~~
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
   64 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
g++ -std=gnu++11  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include'   -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"  -I./imslib/src/   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -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:61:14: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   61 |         std::auto_ptr<std::map<int,int> > countMatches();
      |              ^~~~~~~~
In file included from c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\memory:76,
                 from ./imslib/src/ims/calib/linearpointsetmatcher.h:8:
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
   64 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
./imslib/src/ims/calib/matchmatrix.h:65:14: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   65 |         std::auto_ptr<std::map<int,int> > countMatchesRestrictive();
      |              ^~~~~~~~
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
   64 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
./imslib/src/ims/calib/linearpointsetmatcher.h:146:14: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  146 |         std::auto_ptr<std::map<int,int> > getMapping() const;
      |              ^~~~~~~~
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
   64 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
./imslib/src/ims/calib/linearpointsetmatcher.h:169:22: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  169 |                 std::auto_ptr<std::map<int,int> > mapping;
      |                      ^~~~~~~~
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
   64 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
./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:281:22: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  281 |                 std::auto_ptr<std::map<int,int> > mapping(0);
      |                      ^~~~~~~~
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
   64 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
./imslib/src/ims/calib/linearpointsetmatcher.h: In member function 'int ims::LinearPointSetMatcher::match(RandomAccessIterator, RandomAccessIterator, RandomAccessIterator, RandomAccessIterator)':
./imslib/src/ims/calib/linearpointsetmatcher.h:324:40: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  324 |                 results.mapping = std::auto_ptr<std::map<int,int> >(new std::map<int,int>);
      |                                        ^~~~~~~~
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
   64 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
./imslib/src/ims/calib/linearpointsetmatcher.h:326:40: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  326 |                 results.mapping = std::auto_ptr<std::map<int,int> >(0);
      |                                        ^~~~~~~~
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
   64 |   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: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   84 | std::auto_ptr<std::map<int,int> > LinearPointSetMatcher::getMapping() const {
      |      ^~~~~~~~
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
   64 |   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:86:29: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   86 |                 return std::auto_ptr<std::map<int,int> >(0); // TODO throw sth. instead
      |                             ^~~~~~~~
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
   64 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
imslib/src/ims/calib/linearpointsetmatcher.cpp:89:29: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   89 |                 return std::auto_ptr<std::map<int,int> >(new std::map<int,int>(*(results.mapping)));
      |                             ^~~~~~~~
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
   64 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
g++ -std=gnu++11  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include'   -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"  -I./imslib/src/   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -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:103:22: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  103 |                 std::auto_ptr<integer_decomposer_type> decomposer;
      |                      ^~~~~~~~
In file included from c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\memory:76,
                 from ./imslib/src/ims/decomp/realmassdecomposer.h:5:
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
   64 |   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(size_type) const':
./imslib/src/ims/element.h:166:37: warning: comparison of integer expressions of different signedness: 'int' and 'ims::IsotopeDistribution::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
  166 |                     for (int i=0; i < IsotopeDistribution::SIZE; i++) {
      |                                   ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
./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:92:60: 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:21:27: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   21 |         decomposer = std::auto_ptr<integer_decomposer_type>(
      |                           ^~~~~~~~
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
   64 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
g++ -std=gnu++11  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include'   -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"  -I./imslib/src/   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c imslib/src/ims/utils/distribution.cpp -o imslib/src/ims/utils/distribution.o
g++ -std=gnu++11  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include'   -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"  -I./imslib/src/   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c imslib/src/ims/distributionprobabilityscorer.cpp -o imslib/src/ims/distributionprobabilityscorer.o
g++ -std=gnu++11  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include'   -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"  -I./imslib/src/   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -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(size_type) const':
./imslib/src/ims/element.h:166:37: warning: comparison of integer expressions of different signedness: 'int' and 'ims::IsotopeDistribution::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
  166 |                     for (int i=0; i < IsotopeDistribution::SIZE; i++) {
      |                                   ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include'   -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"  -I./imslib/src/   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -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(size_type) const':
./imslib/src/ims/element.h:166:37: warning: comparison of integer expressions of different signedness: 'int' and 'ims::IsotopeDistribution::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
  166 |                     for (int i=0; i < IsotopeDistribution::SIZE; i++) {
      |                                   ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
./imslib/src/ims/composedelement.h: At global scope:
./imslib/src/ims/composedelement.h:204:72: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  204 |                 void initializeElements(const Alphabet& alphabet, std::auto_ptr<sequence_parser_type> parser)
      |                                                                        ^~~~~~~~
In file included from c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\memory:76,
                 from ./imslib/src/ims/composedelement.h:6:
c:\rtools43\x86_64-w64-mingw32.static.posix\lib\gcc\x86_64-w64-mingw32.static.posix\12.2.0\include\c++\bits\unique_ptr.h:64:28: note: declared here
   64 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
g++ -std=gnu++11 -shared -s -static-libgcc -o Rdisop.dll tmp.def 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 -Lc:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -Lc:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.17-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.17-bioc/R/library/00LOCK-Rdisop/00new/Rdisop/libs/x64
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (Rdisop)

R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

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> ## unit tests will not be done if RUnit is not available
> if(require("RUnit", quietly=TRUE)) {
+ 
+   ## --- Setup ---
+ 
+   pkg <- "Rdisop" # <-- Change to package name!
+   if(Sys.getenv("RCMDCHECK") == "FALSE") {
+     ## Path to unit tests for standalone running under Makefile (not R CMD check)
+     ## PKG/tests/../inst/unitTests
+     path <- file.path(getwd(), "..", "inst", "unitTests")
+   } else {
+     ## Path to unit tests for R CMD check
+     ## PKG.Rcheck/tests/../PKG/unitTests
+     path <- system.file(package=pkg, "unitTests")
+   }
+   cat("\nRunning unit tests\n")
+   print(list(pkg=pkg, getwd=getwd(), pathToUnitTests=path))
+ 
+   library(package=pkg, character.only=TRUE)
+ ##  attr(faahko, "filepaths") <- sapply(as.list(basename(attr(faahko, "filepaths"))), 
+ ##    function(x) system.file("cdf", if (length(grep("ko",x)) > 0) "KO" else  "WT" ,x, package = "faahKO"))
+ 
+   ## If desired, load the name space to allow testing of private functions
+   ## if (is.element(pkg, loadedNamespaces()))
+   ##     attach(loadNamespace(pkg), name=paste("namespace", pkg, sep=":"), pos=3)
+   ##
+   ## or simply call PKG:::myPrivateFunction() in tests
+ 
+   ## --- Testing ---
+ 
+   ## Define tests
+   testSuite <- defineTestSuite(name=paste(pkg, "unit testing"),
+                                           dirs=path)
+   ## Run
+   tests <- runTestSuite(testSuite)
+ 
+   ## Default report name
+   pathReport <- file.path(path, "report")
+ 
+   ## Report to stdout and text files
+   cat("------------------- UNIT TEST SUMMARY ---------------------\n\n")
+   printTextProtocol(tests, showDetails=FALSE)
+   printTextProtocol(tests, showDetails=FALSE,
+                     fileName=paste(pathReport, "Summary.txt", sep=""))
+   printTextProtocol(tests, showDetails=TRUE,
+                     fileName=paste(pathReport, ".txt", sep=""))
+ 
+   ## Report to HTML file
+   printHTMLProtocol(tests, fileName=paste(pathReport, ".html", sep=""))
+ 
+   ## Return stop() to cause R CMD check stop in case of
+   ##  - failures i.e. FALSE to unit tests or
+   ##  - errors i.e. R errors
+   tmp <- getErrors(tests)
+   if(tmp$nFail > 0 | tmp$nErr > 0) {
+     stop(paste("\n\nunit testing failed (#test failures: ", tmp$nFail,
+                ", #R errors: ",  tmp$nErr, ")\n\n", sep=""))
+   }
+ } else {
+   warning("cannot run unit tests -- package RUnit is not available")
+ }

Running unit tests
$pkg
[1] "Rdisop"

$getwd
[1] "F:/biocbuild/bbs-3.17-bioc-rtools43/meat/Rdisop.Rcheck/tests"

$pathToUnitTests
[1] "F:/biocbuild/bbs-3.17-bioc/R/library/Rdisop/unitTests"

Loading required package: Rcpp


Executing test function test.addformula1  ...  done successfully.



Executing test function test.addformula2  ...  done successfully.



Executing test function test.subformula1  ...  done successfully.



Executing test function test.subformula2  ...  done successfully.



Executing test function test.cid24892761  ...  done successfully.



Executing test function test.cid46173807  ...  done successfully.



Executing test function test.empty  ...  done successfully.



Executing test function test.exact  ...  done successfully.



Executing test function test.remove  ...  done successfully.



Executing test function test.minmaxElements1  ...  done successfully.



Executing test function test.minmaxElements2  ...  done successfully.



Executing test function test.minmaxElements3  ...  done successfully.



Executing test function test.minmaxElements4  ...  done successfully.



Executing test function test.minmaxElements5  ...  done successfully.



Executing test function test.minmaxElements6  ...  done successfully.



Executing test function test.minmaxElements7  ...  done successfully.



Executing test function test.monoisotopicMasses  ...  done successfully.

------------------- UNIT TEST SUMMARY ---------------------

RUNIT TEST PROTOCOL -- Thu Dec 29 02:41:42 2022 
*********************************************** 
Number of test functions: 17 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
Rdisop unit testing - 17 test functions, 0 errors, 0 failures
Warning messages:
1: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
  RNGkind: Marsaglia-Multicarry has poor statistical properties
2: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
  RNGkind: severe deviations from normality for Kinderman-Ramage + Marsaglia-Multicarry
3: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
  RNGkind: Marsaglia-Multicarry has poor statistical properties
4: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
  RNGkind: severe deviations from normality for Kinderman-Ramage + Marsaglia-Multicarry
5: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
  RNGkind: Marsaglia-Multicarry has poor statistical properties
6: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
  RNGkind: severe deviations from normality for Kinderman-Ramage + Marsaglia-Multicarry
7: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
  RNGkind: Marsaglia-Multicarry has poor statistical properties
8: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
  RNGkind: severe deviations from normality for Kinderman-Ramage + Marsaglia-Multicarry
9: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
  RNGkind: Marsaglia-Multicarry has poor statistical properties
10: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
  RNGkind: severe deviations from normality for Kinderman-Ramage + Marsaglia-Multicarry
> 
> proc.time()
   user  system elapsed 
   0.42    0.15    0.54