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This page was generated on 2022-01-19 11:12:19 -0500 (Wed, 19 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4161
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4056
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 3998
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4115
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

INSTALL results for Rdisop on merida1


To the developers/maintainers of the Rdisop package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Rdisop.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1548/2074HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Rdisop 1.55.0  (landing page)
Steffen Neumann
Snapshot Date: 2022-01-18 13:55:18 -0500 (Tue, 18 Jan 2022)
git_url: https://git.bioconductor.org/packages/Rdisop
git_branch: master
git_last_commit: a46c8a5
git_last_commit_date: 2021-10-26 11:51:40 -0500 (Tue, 26 Oct 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    WARNINGS    OK  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: Rdisop
Version: 1.55.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL Rdisop
StartedAt: 2022-01-18 15:13:18 -0500 (Tue, 18 Jan 2022)
EndedAt: 2022-01-18 15:14:10 -0500 (Tue, 18 Jan 2022)
EllapsedTime: 52.3 seconds
RetCode: 0
Status:   OK  

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL Rdisop
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’
* installing *source* package ‘Rdisop’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include  -I./imslib/src/ -fPIC  -Wall -g -O2  -c disop.cpp -o disop.o
In file included from disop.cpp:22:
./imslib/src/ims/composedelement.h:204:58: warning: 'auto_ptr<ims::AbstractMoleculeSequenceParser>' is deprecated [-Wdeprecated-declarations]
                void initializeElements(const Alphabet& alphabet, std::auto_ptr<sequence_parser_type> parser)
                                                                       ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<ims::AbstractMoleculeSequenceParser>' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
                           ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1101:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
#  define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
                                      ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1090:48: note: expanded from macro '_LIBCPP_DEPRECATED'
#    define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
                                               ^
In file included from disop.cpp:26:
./imslib/src/ims/decomp/realmassdecomposer.h:103:8: warning: 'auto_ptr<ims::IntegerMassDecomposer<unsigned long, unsigned int> >' is deprecated [-Wdeprecated-declarations]
                std::auto_ptr<integer_decomposer_type> decomposer;
                     ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<ims::IntegerMassDecomposer<unsigned long, unsigned int> >' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
                           ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1101:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
#  define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
                                      ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1090:48: note: expanded from macro '_LIBCPP_DEPRECATED'
#    define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
                                               ^
disop.cpp:106:8: warning: unused variable 'parityeven' [-Wunused-variable]
  bool parityeven = !parityodd;
       ^
disop.cpp:325:6: warning: 'bind2nd<std::__1::multiplies<double>, double>' is deprecated [-Wdeprecated-declarations]
                                        bind2nd(multiplies<abundance_type>(), scale));  // operation (*scale)
                                        ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/functional:1079:1: note: 'bind2nd<std::__1::multiplies<double>, double>' has been explicitly marked deprecated here
_LIBCPP_DEPRECATED_IN_CXX11 inline _LIBCPP_INLINE_VISIBILITY
^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1101:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
#  define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
                                      ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1090:48: note: expanded from macro '_LIBCPP_DEPRECATED'
#    define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
                                               ^
disop.cpp:191:6: warning: unused variable 'number_molecules_shown' [-Wunused-variable]
        int number_molecules_shown = 100;
            ^
In file included from disop.cpp:28:
./imslib/src/ims/decomp/decomputils.h:92:53: warning: unused typedef 'weight_type' [-Wunused-local-typedef]
        typedef typename DecompositionWeights::weight_type weight_type;
                                                           ^
disop.cpp:169:39: warning: unused typedef 'mass_type' [-Wunused-local-typedef]
    typedef distribution_t::mass_type mass_type;
                                      ^
disop.cpp:171:47: warning: unused typedef 'nominal_mass_type' [-Wunused-local-typedef]
    typedef distribution_t::nominal_mass_type nominal_mass_type;
                                              ^
disop.cpp:174:42: warning: unused typedef 'decomposition_type' [-Wunused-local-typedef]
    typedef decompositions_t::value_type decomposition_type;
                                         ^
disop.cpp:377:40: warning: unused typedef 'mass_type' [-Wunused-local-typedef]
        typedef distribution_t::mass_type mass_type;
                                          ^
disop.cpp:626:43: warning: unused typedef 'scorer_type' [-Wunused-local-typedef]
    typedef DistributionProbabilityScorer scorer_type;
                                          ^
disop.cpp:709:32: warning: unused typedef 'elements_type' [-Wunused-local-typedef]
        typedef alphabet_t::container elements_type;
                                      ^
disop.cpp:814:33: warning: unused typedef 'elements_type' [-Wunused-local-typedef]
  typedef alphabet_t::container elements_type;
                                ^
13 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include  -I./imslib/src/ -fPIC  -Wall -g -O2  -c imslib/src/ims/element.cpp -o imslib/src/ims/element.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include  -I./imslib/src/ -fPIC  -Wall -g -O2  -c imslib/src/ims/composedelement.cpp -o imslib/src/ims/composedelement.o
In file included from imslib/src/ims/composedelement.cpp:8:
./imslib/src/ims/composedelement.h:204:58: warning: 'auto_ptr<ims::AbstractMoleculeSequenceParser>' is deprecated [-Wdeprecated-declarations]
                void initializeElements(const Alphabet& alphabet, std::auto_ptr<sequence_parser_type> parser)
                                                                       ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<ims::AbstractMoleculeSequenceParser>' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
                           ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1101:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
#  define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
                                      ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1090:48: note: expanded from macro '_LIBCPP_DEPRECATED'
#    define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
                                               ^
imslib/src/ims/composedelement.cpp:26:7: warning: 'auto_ptr<ims::AbstractMoleculeSequenceParser>' is deprecated [-Wdeprecated-declarations]
        std::auto_ptr<sequence_parser_type> parser;
             ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<ims::AbstractMoleculeSequenceParser>' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
                           ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1101:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
#  define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
                                      ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1090:48: note: expanded from macro '_LIBCPP_DEPRECATED'
#    define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
                                               ^
imslib/src/ims/composedelement.cpp:28:17: warning: 'auto_ptr<ims::AbstractMoleculeSequenceParser>' is deprecated [-Wdeprecated-declarations]
                parser = std::auto_ptr<sequence_parser_type>(new StandardMoleculeSequenceParser);
                              ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<ims::AbstractMoleculeSequenceParser>' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
                           ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1101:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
#  define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
                                      ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1090:48: note: expanded from macro '_LIBCPP_DEPRECATED'
#    define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
                                               ^
imslib/src/ims/composedelement.cpp:30:17: warning: 'auto_ptr<ims::AbstractMoleculeSequenceParser>' is deprecated [-Wdeprecated-declarations]
                parser = std::auto_ptr<sequence_parser_type>(new MoleculeSequenceParser);
                              ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<ims::AbstractMoleculeSequenceParser>' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
                           ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1101:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
#  define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
                                      ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1090:48: note: expanded from macro '_LIBCPP_DEPRECATED'
#    define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
                                               ^
imslib/src/ims/composedelement.cpp:116:73: warning: 'auto_ptr<ims::AbstractMoleculeSequenceParser>' is deprecated [-Wdeprecated-declarations]
void ComposedElement::initializeElements(const Alphabet& alphabet, std::auto_ptr<sequence_parser_type> parser)
                                                                        ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<ims::AbstractMoleculeSequenceParser>' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
                           ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1101:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
#  define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
                                      ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1090:48: note: expanded from macro '_LIBCPP_DEPRECATED'
#    define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
                                               ^
5 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include  -I./imslib/src/ -fPIC  -Wall -g -O2  -c imslib/src/ims/isotopedistribution.cpp -o imslib/src/ims/isotopedistribution.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include  -I./imslib/src/ -fPIC  -Wall -g -O2  -c imslib/src/ims/alphabet.cpp -o imslib/src/ims/alphabet.o
imslib/src/ims/alphabet.cpp:33:21: warning: 'bind2nd<std::__1::equal_to<std::__1::basic_string<char> >, std::__1::basic_string<char> >' is deprecated [-Wdeprecated-declarations]
                compose_f_gx(std::bind2nd(std::equal_to<name_type>(), name),
                                  ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/functional:1079:1: note: 'bind2nd<std::__1::equal_to<std::__1::basic_string<char> >, std::__1::basic_string<char> >' has been explicitly marked deprecated here
_LIBCPP_DEPRECATED_IN_CXX11 inline _LIBCPP_INLINE_VISIBILITY
^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1101:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
#  define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
                                      ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1090:48: note: expanded from macro '_LIBCPP_DEPRECATED'
#    define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
                                               ^
imslib/src/ims/alphabet.cpp:34:8: warning: 'mem_fun_ref<const std::__1::basic_string<char> &, ims::Element>' is deprecated [-Wdeprecated-declarations]
                std::mem_fun_ref(&element_type::getName))) < elements.end();
                     ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/functional:1253:1: note: 'mem_fun_ref<const std::__1::basic_string<char> &, ims::Element>' has been explicitly marked deprecated here
_LIBCPP_DEPRECATED_IN_CXX11 inline _LIBCPP_INLINE_VISIBILITY
^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1101:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
#  define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
                                      ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1090:48: note: expanded from macro '_LIBCPP_DEPRECATED'
#    define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
                                               ^
imslib/src/ims/alphabet.cpp:74:11: warning: 'mem_fun_ref<const std::__1::basic_string<char> &, ims::Element>' is deprecated [-Wdeprecated-declarations]
                                        std::mem_fun_ref(&element_type::getName),
                                             ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/functional:1253:1: note: 'mem_fun_ref<const std::__1::basic_string<char> &, ims::Element>' has been explicitly marked deprecated here
_LIBCPP_DEPRECATED_IN_CXX11 inline _LIBCPP_INLINE_VISIBILITY
^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1101:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
#  define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
                                      ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1090:48: note: expanded from macro '_LIBCPP_DEPRECATED'
#    define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
                                               ^
imslib/src/ims/alphabet.cpp:75:11: warning: 'mem_fun_ref<const std::__1::basic_string<char> &, ims::Element>' is deprecated [-Wdeprecated-declarations]
                                        std::mem_fun_ref(&element_type::getName)));
                                             ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/functional:1253:1: note: 'mem_fun_ref<const std::__1::basic_string<char> &, ims::Element>' has been explicitly marked deprecated here
_LIBCPP_DEPRECATED_IN_CXX11 inline _LIBCPP_INLINE_VISIBILITY
^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1101:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
#  define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
                                      ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1090:48: note: expanded from macro '_LIBCPP_DEPRECATED'
#    define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
                                               ^
4 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include  -I./imslib/src/ -fPIC  -Wall -g -O2  -c imslib/src/ims/weights.cpp -o imslib/src/ims/weights.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include  -I./imslib/src/ -fPIC  -Wall -g -O2  -c imslib/src/ims/distributedalphabet.cpp -o imslib/src/ims/distributedalphabet.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include  -I./imslib/src/ -fPIC  -Wall -g -O2  -c imslib/src/ims/transformation.cpp -o imslib/src/ims/transformation.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include  -I./imslib/src/ -fPIC  -Wall -g -O2  -c imslib/src/ims/isotopespecies.cpp -o imslib/src/ims/isotopespecies.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include  -I./imslib/src/ -fPIC  -Wall -g -O2  -c imslib/src/ims/base/parser/alphabettextparser.cpp -o imslib/src/ims/base/parser/alphabettextparser.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include  -I./imslib/src/ -fPIC  -Wall -g -O2  -c imslib/src/ims/base/parser/distributedalphabettextparser.cpp -o imslib/src/ims/base/parser/distributedalphabettextparser.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include  -I./imslib/src/ -fPIC  -Wall -g -O2  -c imslib/src/ims/base/parser/massestextparser.cpp -o imslib/src/ims/base/parser/massestextparser.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include  -I./imslib/src/ -fPIC  -Wall -g -O2  -c imslib/src/ims/base/parser/moleculesequenceparser.cpp -o imslib/src/ims/base/parser/moleculesequenceparser.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include  -I./imslib/src/ -fPIC  -Wall -g -O2  -c imslib/src/ims/base/parser/standardmoleculesequenceparser.cpp -o imslib/src/ims/base/parser/standardmoleculesequenceparser.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include  -I./imslib/src/ -fPIC  -Wall -g -O2  -c imslib/src/ims/base/parser/keggligandcompoundsparser.cpp -o imslib/src/ims/base/parser/keggligandcompoundsparser.o
imslib/src/ims/base/parser/keggligandcompoundsparser.cpp:53:31: warning: '&&' within '||' [-Wlogical-op-parentheses]
        for (;  letter_pos < last_pos && 
                ~~~~~~~~~~~~~~~~~~~~~~^~
imslib/src/ims/base/parser/keggligandcompoundsparser.cpp:53:31: note: place parentheses around the '&&' expression to silence this warning
        for (;  letter_pos < last_pos && 
                                      ^
                (
1 warning generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include  -I./imslib/src/ -fPIC  -Wall -g -O2  -c imslib/src/ims/base/parser/moleculeionchargemodificationparser.cpp -o imslib/src/ims/base/parser/moleculeionchargemodificationparser.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include  -I./imslib/src/ -fPIC  -Wall -g -O2  -c imslib/src/ims/calib/linepairstabber.cpp -o imslib/src/ims/calib/linepairstabber.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include  -I./imslib/src/ -fPIC  -Wall -g -O2  -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: 'auto_ptr<std::__1::map<int, int, std::__1::less<int>, std::__1::allocator<std::__1::pair<const int, int> > > >' is deprecated [-Wdeprecated-declarations]
        std::auto_ptr<std::map<int,int> > countMatches();
             ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<std::__1::map<int, int, std::__1::less<int>, std::__1::allocator<std::__1::pair<const int, int> > > >' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
                           ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1101:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
#  define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
                                      ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1090:48: note: expanded from macro '_LIBCPP_DEPRECATED'
#    define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
                                               ^
In file included from imslib/src/ims/calib/matchmatrix.cpp:1:
./imslib/src/ims/calib/matchmatrix.h:65:7: warning: 'auto_ptr<std::__1::map<int, int, std::__1::less<int>, std::__1::allocator<std::__1::pair<const int, int> > > >' is deprecated [-Wdeprecated-declarations]
        std::auto_ptr<std::map<int,int> > countMatchesRestrictive();
             ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<std::__1::map<int, int, std::__1::less<int>, std::__1::allocator<std::__1::pair<const int, int> > > >' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
                           ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1101:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
#  define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
                                      ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1090:48: note: expanded from macro '_LIBCPP_DEPRECATED'
#    define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
                                               ^
imslib/src/ims/calib/matchmatrix.cpp:81:6: warning: 'auto_ptr<std::__1::map<int, int, std::__1::less<int>, std::__1::allocator<std::__1::pair<const int, int> > > >' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<std::map<int,int> > MatchMatrix::countMatches() {
     ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<std::__1::map<int, int, std::__1::less<int>, std::__1::allocator<std::__1::pair<const int, int> > > >' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
                           ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1101:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
#  define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
                                      ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1090:48: note: expanded from macro '_LIBCPP_DEPRECATED'
#    define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
                                               ^
imslib/src/ims/calib/matchmatrix.cpp:82:7: warning: 'auto_ptr<std::__1::map<int, int, std::__1::less<int>, std::__1::allocator<std::__1::pair<const int, int> > > >' is deprecated [-Wdeprecated-declarations]
        std::auto_ptr<std::map<int,int> > m(new std::map<int,int>);
             ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<std::__1::map<int, int, std::__1::less<int>, std::__1::allocator<std::__1::pair<const int, int> > > >' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
                           ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1101:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
#  define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
                                      ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1090:48: note: expanded from macro '_LIBCPP_DEPRECATED'
#    define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
                                               ^
imslib/src/ims/calib/matchmatrix.cpp:102:6: warning: 'auto_ptr<std::__1::map<int, int, std::__1::less<int>, std::__1::allocator<std::__1::pair<const int, int> > > >' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<std::map<int,int> > MatchMatrix::countMatchesRestrictive() {
     ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<std::__1::map<int, int, std::__1::less<int>, std::__1::allocator<std::__1::pair<const int, int> > > >' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
                           ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1101:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
#  define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
                                      ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1090:48: note: expanded from macro '_LIBCPP_DEPRECATED'
#    define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
                                               ^
imslib/src/ims/calib/matchmatrix.cpp:103:7: warning: 'auto_ptr<std::__1::map<int, int, std::__1::less<int>, std::__1::allocator<std::__1::pair<const int, int> > > >' is deprecated [-Wdeprecated-declarations]
        std::auto_ptr<std::map<int,int> > m(new std::map<int,int>);
             ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<std::__1::map<int, int, std::__1::less<int>, std::__1::allocator<std::__1::pair<const int, int> > > >' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
                           ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1101:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
#  define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
                                      ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1090:48: note: expanded from macro '_LIBCPP_DEPRECATED'
#    define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
                                               ^
6 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include  -I./imslib/src/ -fPIC  -Wall -g -O2  -c imslib/src/ims/calib/linearpointsetmatcher.cpp -o imslib/src/ims/calib/linearpointsetmatcher.o
In file included from imslib/src/ims/calib/linearpointsetmatcher.cpp:11:
In file included from ./imslib/src/ims/calib/linearpointsetmatcher.h:13:
./imslib/src/ims/calib/matchmatrix.h:61:7: warning: 'auto_ptr<std::__1::map<int, int, std::__1::less<int>, std::__1::allocator<std::__1::pair<const int, int> > > >' is deprecated [-Wdeprecated-declarations]
        std::auto_ptr<std::map<int,int> > countMatches();
             ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<std::__1::map<int, int, std::__1::less<int>, std::__1::allocator<std::__1::pair<const int, int> > > >' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
                           ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1101:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
#  define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
                                      ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1090:48: note: expanded from macro '_LIBCPP_DEPRECATED'
#    define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
                                               ^
In file included from imslib/src/ims/calib/linearpointsetmatcher.cpp:11:
In file included from ./imslib/src/ims/calib/linearpointsetmatcher.h:13:
./imslib/src/ims/calib/matchmatrix.h:65:7: warning: 'auto_ptr<std::__1::map<int, int, std::__1::less<int>, std::__1::allocator<std::__1::pair<const int, int> > > >' is deprecated [-Wdeprecated-declarations]
        std::auto_ptr<std::map<int,int> > countMatchesRestrictive();
             ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<std::__1::map<int, int, std::__1::less<int>, std::__1::allocator<std::__1::pair<const int, int> > > >' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
                           ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1101:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
#  define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
                                      ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1090:48: note: expanded from macro '_LIBCPP_DEPRECATED'
#    define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
                                               ^
In file included from imslib/src/ims/calib/linearpointsetmatcher.cpp:11:
./imslib/src/ims/calib/linearpointsetmatcher.h:146:7: warning: 'auto_ptr<std::__1::map<int, int, std::__1::less<int>, std::__1::allocator<std::__1::pair<const int, int> > > >' is deprecated [-Wdeprecated-declarations]
        std::auto_ptr<std::map<int,int> > getMapping() const;
             ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<std::__1::map<int, int, std::__1::less<int>, std::__1::allocator<std::__1::pair<const int, int> > > >' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
                           ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1101:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
#  define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
                                      ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1090:48: note: expanded from macro '_LIBCPP_DEPRECATED'
#    define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
                                               ^
In file included from imslib/src/ims/calib/linearpointsetmatcher.cpp:11:
./imslib/src/ims/calib/linearpointsetmatcher.h:169:8: warning: 'auto_ptr<std::__1::map<int, int, std::__1::less<int>, std::__1::allocator<std::__1::pair<const int, int> > > >' is deprecated [-Wdeprecated-declarations]
                std::auto_ptr<std::map<int,int> > mapping;
                     ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<std::__1::map<int, int, std::__1::less<int>, std::__1::allocator<std::__1::pair<const int, int> > > >' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
                           ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1101:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
#  define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
                                      ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1090:48: note: expanded from macro '_LIBCPP_DEPRECATED'
#    define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
                                               ^
In file included from imslib/src/ims/calib/linearpointsetmatcher.cpp:11:
./imslib/src/ims/calib/linearpointsetmatcher.h:281:8: warning: 'auto_ptr<std::__1::map<int, int, std::__1::less<int>, std::__1::allocator<std::__1::pair<const int, int> > > >' is deprecated [-Wdeprecated-declarations]
                std::auto_ptr<std::map<int,int> > mapping(0);
                     ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<std::__1::map<int, int, std::__1::less<int>, std::__1::allocator<std::__1::pair<const int, int> > > >' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
                           ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1101:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
#  define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
                                      ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1090:48: note: expanded from macro '_LIBCPP_DEPRECATED'
#    define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
                                               ^
In file included from imslib/src/ims/calib/linearpointsetmatcher.cpp:11:
./imslib/src/ims/calib/linearpointsetmatcher.h:324:26: warning: 'auto_ptr<std::__1::map<int, int, std::__1::less<int>, std::__1::allocator<std::__1::pair<const int, int> > > >' is deprecated [-Wdeprecated-declarations]
                results.mapping = std::auto_ptr<std::map<int,int> >(new std::map<int,int>);
                                       ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<std::__1::map<int, int, std::__1::less<int>, std::__1::allocator<std::__1::pair<const int, int> > > >' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
                           ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1101:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
#  define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
                                      ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1090:48: note: expanded from macro '_LIBCPP_DEPRECATED'
#    define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
                                               ^
In file included from imslib/src/ims/calib/linearpointsetmatcher.cpp:11:
./imslib/src/ims/calib/linearpointsetmatcher.h:326:26: warning: 'auto_ptr<std::__1::map<int, int, std::__1::less<int>, std::__1::allocator<std::__1::pair<const int, int> > > >' is deprecated [-Wdeprecated-declarations]
                results.mapping = std::auto_ptr<std::map<int,int> >(0);
                                       ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<std::__1::map<int, int, std::__1::less<int>, std::__1::allocator<std::__1::pair<const int, int> > > >' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
                           ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1101:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
#  define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
                                      ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1090:48: note: expanded from macro '_LIBCPP_DEPRECATED'
#    define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
                                               ^
imslib/src/ims/calib/linearpointsetmatcher.cpp:84:6: warning: 'auto_ptr<std::__1::map<int, int, std::__1::less<int>, std::__1::allocator<std::__1::pair<const int, int> > > >' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<std::map<int,int> > LinearPointSetMatcher::getMapping() const {
     ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<std::__1::map<int, int, std::__1::less<int>, std::__1::allocator<std::__1::pair<const int, int> > > >' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
                           ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1101:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
#  define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
                                      ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1090:48: note: expanded from macro '_LIBCPP_DEPRECATED'
#    define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
                                               ^
imslib/src/ims/calib/linearpointsetmatcher.cpp:86:15: warning: 'auto_ptr<std::__1::map<int, int, std::__1::less<int>, std::__1::allocator<std::__1::pair<const int, int> > > >' is deprecated [-Wdeprecated-declarations]
                return std::auto_ptr<std::map<int,int> >(0); // TODO throw sth. instead
                            ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<std::__1::map<int, int, std::__1::less<int>, std::__1::allocator<std::__1::pair<const int, int> > > >' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
                           ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1101:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
#  define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
                                      ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1090:48: note: expanded from macro '_LIBCPP_DEPRECATED'
#    define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
                                               ^
imslib/src/ims/calib/linearpointsetmatcher.cpp:89:15: warning: 'auto_ptr<std::__1::map<int, int, std::__1::less<int>, std::__1::allocator<std::__1::pair<const int, int> > > >' is deprecated [-Wdeprecated-declarations]
                return std::auto_ptr<std::map<int,int> >(new std::map<int,int>(*(results.mapping)));
                            ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<std::__1::map<int, int, std::__1::less<int>, std::__1::allocator<std::__1::pair<const int, int> > > >' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
                           ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1101:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
#  define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
                                      ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1090:48: note: expanded from macro '_LIBCPP_DEPRECATED'
#    define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
                                               ^
10 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include  -I./imslib/src/ -fPIC  -Wall -g -O2  -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: 'auto_ptr<ims::IntegerMassDecomposer<unsigned long, unsigned int> >' is deprecated [-Wdeprecated-declarations]
                std::auto_ptr<integer_decomposer_type> decomposer;
                     ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<ims::IntegerMassDecomposer<unsigned long, unsigned int> >' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
                           ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1101:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
#  define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
                                      ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1090:48: note: expanded from macro '_LIBCPP_DEPRECATED'
#    define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
                                               ^
imslib/src/ims/decomp/realmassdecomposer.cpp:21:20: warning: 'auto_ptr<ims::IntegerMassDecomposer<unsigned long, unsigned int> >' is deprecated [-Wdeprecated-declarations]
        decomposer = std::auto_ptr<integer_decomposer_type>(
                          ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<ims::IntegerMassDecomposer<unsigned long, unsigned int> >' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
                           ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1101:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
#  define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
                                      ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1090:48: note: expanded from macro '_LIBCPP_DEPRECATED'
#    define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
                                               ^
In file included from imslib/src/ims/decomp/realmassdecomposer.cpp:9:
./imslib/src/ims/decomp/decomputils.h:92:53: warning: unused typedef 'weight_type' [-Wunused-local-typedef]
        typedef typename DecompositionWeights::weight_type weight_type;
                                                           ^
3 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include  -I./imslib/src/ -fPIC  -Wall -g -O2  -c imslib/src/ims/utils/distribution.cpp -o imslib/src/ims/utils/distribution.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include  -I./imslib/src/ -fPIC  -Wall -g -O2  -c imslib/src/ims/distributionprobabilityscorer.cpp -o imslib/src/ims/distributionprobabilityscorer.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include  -I./imslib/src/ -fPIC  -Wall -g -O2  -c imslib/src/ims/characteralphabet.cpp -o imslib/src/ims/characteralphabet.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include  -I./imslib/src/ -fPIC  -Wall -g -O2  -c imslib/src/ims/nitrogenrulefilter.cpp -o imslib/src/ims/nitrogenrulefilter.o
In file included from imslib/src/ims/nitrogenrulefilter.cpp:5:
In file included from ./imslib/src/ims/nitrogenrulefilter.h:4:
./imslib/src/ims/composedelement.h:204:58: warning: 'auto_ptr<ims::AbstractMoleculeSequenceParser>' is deprecated [-Wdeprecated-declarations]
                void initializeElements(const Alphabet& alphabet, std::auto_ptr<sequence_parser_type> parser)
                                                                       ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<ims::AbstractMoleculeSequenceParser>' has been explicitly marked deprecated here
class _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 auto_ptr
                           ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1101:39: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
#  define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
                                      ^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__config:1090:48: note: expanded from macro '_LIBCPP_DEPRECATED'
#    define _LIBCPP_DEPRECATED __attribute__ ((deprecated))
                                               ^
1 warning generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/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 -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.2/Resources/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)