Daniel Jones
| Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021) |
| URL: https://git.bioconductor.org/packages/seqbias |
| Branch: RELEASE_3_12 |
| Last Commit: b5490ca |
| Last Changed Date: 2020-10-27 10:39:54 -0400 (Tue, 27 Oct 2020) |
| Back to Multiple platform build/check report for BioC 3.12 |
|
This page was generated on 2021-05-06 12:36:46 -0400 (Thu, 06 May 2021).
|
To the developers/maintainers of the seqbias package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1676/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| seqbias 1.38.0 (landing page) Daniel Jones
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | ERROR | |||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: seqbias |
| Version: 1.38.0 |
| Command: rm -rf seqbias.buildbin-libdir && mkdir seqbias.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh seqbias_1.38.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R seqbias.buildbin-libdir |
| StartedAt: 2021-05-06 09:59:00 -0400 (Thu, 06 May 2021) |
| EndedAt: 2021-05-06 10:00:48 -0400 (Thu, 06 May 2021) |
| EllapsedTime: 108.4 seconds |
| RetCode: 0 |
| Status: OK |
| PackageFile: seqbias_1.38.0.tgz |
| PackageFileSize: 1.036 MiB |
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###
### Running command:
###
### rm -rf seqbias.buildbin-libdir && mkdir seqbias.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh seqbias_1.38.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R seqbias.buildbin-libdir
###
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>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=seqbias.buildbin-libdir seqbias_1.38.0.tar.gz'
>>>>>>>
* installing *source* package ‘seqbias’ ...
** using staged installation
** libs
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -I/usr/local/include -Wall -Wextra -I. -fPIC -Wall -g -O2 -c sam.c -o sam.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -I/usr/local/include -Wall -Wextra -I. -fPIC -Wall -g -O2 -c bam_plbuf.c -o bam_plbuf.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -I/usr/local/include -Wall -Wextra -I. -fPIC -Wall -g -O2 -c bam_aux.c -o bam_aux.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -I/usr/local/include -Wall -Wextra -I. -fPIC -Wall -g -O2 -c common.c -o common.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -I/usr/local/include -Wall -Wextra -I. -fPIC -Wall -g -O2 -c miscmath.c -o miscmath.o
miscmath.c:21:12: warning: 'finite' is deprecated: first deprecated in macOS 10.9 - Use `isfinite((double)x)` instead. [-Wdeprecated-declarations]
return finite(a) && 0.0 <= a && a <= 1.0;
^
/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/math.h:749:12: note: 'finite' has been explicitly marked deprecated here
extern int finite(double)
^
miscmath.c:47:9: warning: 'finite' is deprecated: first deprecated in macOS 10.9 - Use `isfinite((double)x)` instead. [-Wdeprecated-declarations]
if (finite(u)) return x + log1p(-exp(u));
^
/Library/Developer/CommandLineTools/SDKs/MacOSX10.14.sdk/usr/include/math.h:749:12: note: 'finite' has been explicitly marked deprecated here
extern int finite(double)
^
2 warnings generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -I/usr/local/include -Wall -Wextra -I. -fPIC -Wall -g -O2 -c pos_table.c -o pos_table.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -I/usr/local/include -Wall -Wextra -I. -fPIC -Wall -g -O2 -c kmer_matrix.cpp -o kmer_matrix.o
In file included from kmer_matrix.cpp:8:
In file included from ./kmer_matrix.hpp:13:
In file included from ./yaml-cpp/yaml.h:9:
./yaml-cpp/parser.h:45:8: warning: 'auto_ptr<YAML::Scanner>' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<Scanner> m_pScanner;
^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<YAML::Scanner>' 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 kmer_matrix.cpp:8:
In file included from ./kmer_matrix.hpp:13:
In file included from ./yaml-cpp/yaml.h:9:
./yaml-cpp/parser.h:46:8: warning: 'auto_ptr<YAML::Directives>' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<Directives> m_pDirectives;
^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<YAML::Directives>' 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 kmer_matrix.cpp:8:
In file included from ./kmer_matrix.hpp:13:
In file included from ./yaml-cpp/yaml.h:10:
In file included from ./yaml-cpp/node.h:12:
./yaml-cpp/iterator.h:20:17: warning: 'auto_ptr<YAML::IterPriv>' is deprecated [-Wdeprecated-declarations]
Iterator(std::auto_ptr<IterPriv> pData);
^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<YAML::IterPriv>' 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 kmer_matrix.cpp:8:
In file included from ./kmer_matrix.hpp:13:
In file included from ./yaml-cpp/yaml.h:10:
In file included from ./yaml-cpp/node.h:12:
./yaml-cpp/iterator.h:36:8: warning: 'auto_ptr<YAML::IterPriv>' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<IterPriv> m_pData;
^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<YAML::IterPriv>' 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 kmer_matrix.cpp:8:
In file included from ./kmer_matrix.hpp:13:
In file included from ./yaml-cpp/yaml.h:10:
./yaml-cpp/node.h:43:8: warning: 'auto_ptr<YAML::Node>' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<Node> Clone() const;
^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<YAML::Node>' 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 kmer_matrix.cpp:8:
In file included from ./kmer_matrix.hpp:13:
In file included from ./yaml-cpp/yaml.h:10:
./yaml-cpp/node.h:115:8: warning: 'auto_ptr<YAML::NodeOwnership>' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<NodeOwnership> m_pOwnership;
^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<YAML::NodeOwnership>' 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 kmer_matrix.cpp:8:
In file included from ./kmer_matrix.hpp:13:
In file included from ./yaml-cpp/yaml.h:13:
./yaml-cpp/emitter.h:98:8: warning: 'auto_ptr<YAML::EmitterState>' is deprecated [-Wdeprecated-declarations]
std::auto_ptr <EmitterState> m_pState;
^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<YAML::EmitterState>' 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))
^
7 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -I/usr/local/include -Wall -Wextra -I. -fPIC -Wall -g -O2 -c logger.cpp -o logger.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -I/usr/local/include -Wall -Wextra -I. -fPIC -Wall -g -O2 -c motif.cpp -o motif.o
In file included from motif.cpp:8:
In file included from ./motif.hpp:13:
In file included from ./kmer_matrix.hpp:13:
In file included from ./yaml-cpp/yaml.h:9:
./yaml-cpp/parser.h:45:8: warning: 'auto_ptr<YAML::Scanner>' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<Scanner> m_pScanner;
^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<YAML::Scanner>' 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 motif.cpp:8:
In file included from ./motif.hpp:13:
In file included from ./kmer_matrix.hpp:13:
In file included from ./yaml-cpp/yaml.h:9:
./yaml-cpp/parser.h:46:8: warning: 'auto_ptr<YAML::Directives>' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<Directives> m_pDirectives;
^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<YAML::Directives>' 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 motif.cpp:8:
In file included from ./motif.hpp:13:
In file included from ./kmer_matrix.hpp:13:
In file included from ./yaml-cpp/yaml.h:10:
In file included from ./yaml-cpp/node.h:12:
./yaml-cpp/iterator.h:20:17: warning: 'auto_ptr<YAML::IterPriv>' is deprecated [-Wdeprecated-declarations]
Iterator(std::auto_ptr<IterPriv> pData);
^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<YAML::IterPriv>' 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 motif.cpp:8:
In file included from ./motif.hpp:13:
In file included from ./kmer_matrix.hpp:13:
In file included from ./yaml-cpp/yaml.h:10:
In file included from ./yaml-cpp/node.h:12:
./yaml-cpp/iterator.h:36:8: warning: 'auto_ptr<YAML::IterPriv>' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<IterPriv> m_pData;
^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<YAML::IterPriv>' 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 motif.cpp:8:
In file included from ./motif.hpp:13:
In file included from ./kmer_matrix.hpp:13:
In file included from ./yaml-cpp/yaml.h:10:
./yaml-cpp/node.h:43:8: warning: 'auto_ptr<YAML::Node>' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<Node> Clone() const;
^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<YAML::Node>' 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 motif.cpp:8:
In file included from ./motif.hpp:13:
In file included from ./kmer_matrix.hpp:13:
In file included from ./yaml-cpp/yaml.h:10:
./yaml-cpp/node.h:115:8: warning: 'auto_ptr<YAML::NodeOwnership>' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<NodeOwnership> m_pOwnership;
^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<YAML::NodeOwnership>' 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 motif.cpp:8:
In file included from ./motif.hpp:13:
In file included from ./kmer_matrix.hpp:13:
In file included from ./yaml-cpp/yaml.h:13:
./yaml-cpp/emitter.h:98:8: warning: 'auto_ptr<YAML::EmitterState>' is deprecated [-Wdeprecated-declarations]
std::auto_ptr <EmitterState> m_pState;
^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<YAML::EmitterState>' 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))
^
7 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -I/usr/local/include -Wall -Wextra -I. -fPIC -Wall -g -O2 -c seqbias.cpp -o seqbias.o
In file included from seqbias.cpp:2:
In file included from ./sequencing_bias.hpp:13:
In file included from ./motif.hpp:13:
In file included from ./kmer_matrix.hpp:13:
In file included from ./yaml-cpp/yaml.h:9:
./yaml-cpp/parser.h:45:8: warning: 'auto_ptr<YAML::Scanner>' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<Scanner> m_pScanner;
^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<YAML::Scanner>' 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 seqbias.cpp:2:
In file included from ./sequencing_bias.hpp:13:
In file included from ./motif.hpp:13:
In file included from ./kmer_matrix.hpp:13:
In file included from ./yaml-cpp/yaml.h:9:
./yaml-cpp/parser.h:46:8: warning: 'auto_ptr<YAML::Directives>' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<Directives> m_pDirectives;
^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<YAML::Directives>' 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 seqbias.cpp:2:
In file included from ./sequencing_bias.hpp:13:
In file included from ./motif.hpp:13:
In file included from ./kmer_matrix.hpp:13:
In file included from ./yaml-cpp/yaml.h:10:
In file included from ./yaml-cpp/node.h:12:
./yaml-cpp/iterator.h:20:17: warning: 'auto_ptr<YAML::IterPriv>' is deprecated [-Wdeprecated-declarations]
Iterator(std::auto_ptr<IterPriv> pData);
^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<YAML::IterPriv>' 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 seqbias.cpp:2:
In file included from ./sequencing_bias.hpp:13:
In file included from ./motif.hpp:13:
In file included from ./kmer_matrix.hpp:13:
In file included from ./yaml-cpp/yaml.h:10:
In file included from ./yaml-cpp/node.h:12:
./yaml-cpp/iterator.h:36:8: warning: 'auto_ptr<YAML::IterPriv>' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<IterPriv> m_pData;
^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<YAML::IterPriv>' 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 seqbias.cpp:2:
In file included from ./sequencing_bias.hpp:13:
In file included from ./motif.hpp:13:
In file included from ./kmer_matrix.hpp:13:
In file included from ./yaml-cpp/yaml.h:10:
./yaml-cpp/node.h:43:8: warning: 'auto_ptr<YAML::Node>' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<Node> Clone() const;
^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<YAML::Node>' 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 seqbias.cpp:2:
In file included from ./sequencing_bias.hpp:13:
In file included from ./motif.hpp:13:
In file included from ./kmer_matrix.hpp:13:
In file included from ./yaml-cpp/yaml.h:10:
./yaml-cpp/node.h:115:8: warning: 'auto_ptr<YAML::NodeOwnership>' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<NodeOwnership> m_pOwnership;
^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<YAML::NodeOwnership>' 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 seqbias.cpp:2:
In file included from ./sequencing_bias.hpp:13:
In file included from ./motif.hpp:13:
In file included from ./kmer_matrix.hpp:13:
In file included from ./yaml-cpp/yaml.h:13:
./yaml-cpp/emitter.h:98:8: warning: 'auto_ptr<YAML::EmitterState>' is deprecated [-Wdeprecated-declarations]
std::auto_ptr <EmitterState> m_pState;
^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<YAML::EmitterState>' 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))
^
7 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -I/usr/local/include -Wall -Wextra -I. -fPIC -Wall -g -O2 -c sequencing_bias.cpp -o sequencing_bias.o
In file included from sequencing_bias.cpp:8:
In file included from ./sequencing_bias.hpp:13:
In file included from ./motif.hpp:13:
In file included from ./kmer_matrix.hpp:13:
In file included from ./yaml-cpp/yaml.h:9:
./yaml-cpp/parser.h:45:8: warning: 'auto_ptr<YAML::Scanner>' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<Scanner> m_pScanner;
^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<YAML::Scanner>' 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 sequencing_bias.cpp:8:
In file included from ./sequencing_bias.hpp:13:
In file included from ./motif.hpp:13:
In file included from ./kmer_matrix.hpp:13:
In file included from ./yaml-cpp/yaml.h:9:
./yaml-cpp/parser.h:46:8: warning: 'auto_ptr<YAML::Directives>' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<Directives> m_pDirectives;
^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<YAML::Directives>' 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 sequencing_bias.cpp:8:
In file included from ./sequencing_bias.hpp:13:
In file included from ./motif.hpp:13:
In file included from ./kmer_matrix.hpp:13:
In file included from ./yaml-cpp/yaml.h:10:
In file included from ./yaml-cpp/node.h:12:
./yaml-cpp/iterator.h:20:17: warning: 'auto_ptr<YAML::IterPriv>' is deprecated [-Wdeprecated-declarations]
Iterator(std::auto_ptr<IterPriv> pData);
^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<YAML::IterPriv>' 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 sequencing_bias.cpp:8:
In file included from ./sequencing_bias.hpp:13:
In file included from ./motif.hpp:13:
In file included from ./kmer_matrix.hpp:13:
In file included from ./yaml-cpp/yaml.h:10:
In file included from ./yaml-cpp/node.h:12:
./yaml-cpp/iterator.h:36:8: warning: 'auto_ptr<YAML::IterPriv>' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<IterPriv> m_pData;
^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<YAML::IterPriv>' 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 sequencing_bias.cpp:8:
In file included from ./sequencing_bias.hpp:13:
In file included from ./motif.hpp:13:
In file included from ./kmer_matrix.hpp:13:
In file included from ./yaml-cpp/yaml.h:10:
./yaml-cpp/node.h:43:8: warning: 'auto_ptr<YAML::Node>' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<Node> Clone() const;
^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<YAML::Node>' 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 sequencing_bias.cpp:8:
In file included from ./sequencing_bias.hpp:13:
In file included from ./motif.hpp:13:
In file included from ./kmer_matrix.hpp:13:
In file included from ./yaml-cpp/yaml.h:10:
./yaml-cpp/node.h:115:8: warning: 'auto_ptr<YAML::NodeOwnership>' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<NodeOwnership> m_pOwnership;
^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<YAML::NodeOwnership>' 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 sequencing_bias.cpp:8:
In file included from ./sequencing_bias.hpp:13:
In file included from ./motif.hpp:13:
In file included from ./kmer_matrix.hpp:13:
In file included from ./yaml-cpp/yaml.h:13:
./yaml-cpp/emitter.h:98:8: warning: 'auto_ptr<YAML::EmitterState>' is deprecated [-Wdeprecated-declarations]
std::auto_ptr <EmitterState> m_pState;
^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<YAML::EmitterState>' 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))
^
7 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -I/usr/local/include -Wall -Wextra -I. -fPIC -Wall -g -O2 -c twobitseq.cpp -o twobitseq.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -I/usr/local/include -Wall -Wextra -I. -fPIC -Wall -g -O2 -c yaml-cpp/aliasmanager.cpp -o yaml-cpp/aliasmanager.o
In file included from yaml-cpp/aliasmanager.cpp:2:
In file included from ./yaml-cpp/node.h:12:
./yaml-cpp/iterator.h:20:17: warning: 'auto_ptr<YAML::IterPriv>' is deprecated [-Wdeprecated-declarations]
Iterator(std::auto_ptr<IterPriv> pData);
^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<YAML::IterPriv>' 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 yaml-cpp/aliasmanager.cpp:2:
In file included from ./yaml-cpp/node.h:12:
./yaml-cpp/iterator.h:36:8: warning: 'auto_ptr<YAML::IterPriv>' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<IterPriv> m_pData;
^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<YAML::IterPriv>' 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 yaml-cpp/aliasmanager.cpp:2:
./yaml-cpp/node.h:43:8: warning: 'auto_ptr<YAML::Node>' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<Node> Clone() const;
^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<YAML::Node>' 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 yaml-cpp/aliasmanager.cpp:2:
./yaml-cpp/node.h:115:8: warning: 'auto_ptr<YAML::NodeOwnership>' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<NodeOwnership> m_pOwnership;
^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<YAML::NodeOwnership>' 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))
^
4 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -I/usr/local/include -Wall -Wextra -I. -fPIC -Wall -g -O2 -c yaml-cpp/conversion.cpp -o yaml-cpp/conversion.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -I/usr/local/include -Wall -Wextra -I. -fPIC -Wall -g -O2 -c yaml-cpp/directives.cpp -o yaml-cpp/directives.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -I/usr/local/include -Wall -Wextra -I. -fPIC -Wall -g -O2 -c yaml-cpp/emitfromevents.cpp -o yaml-cpp/emitfromevents.o
In file included from yaml-cpp/emitfromevents.cpp:2:
./yaml-cpp/emitter.h:98:8: warning: 'auto_ptr<YAML::EmitterState>' is deprecated [-Wdeprecated-declarations]
std::auto_ptr <EmitterState> m_pState;
^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<YAML::EmitterState>' 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++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -I/usr/local/include -Wall -Wextra -I. -fPIC -Wall -g -O2 -c yaml-cpp/emitter.cpp -o yaml-cpp/emitter.o
In file included from yaml-cpp/emitter.cpp:1:
./yaml-cpp/emitter.h:98:8: warning: 'auto_ptr<YAML::EmitterState>' is deprecated [-Wdeprecated-declarations]
std::auto_ptr <EmitterState> m_pState;
^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<YAML::EmitterState>' 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 yaml-cpp/emitter.cpp:2:
In file included from yaml-cpp/emitterstate.h:10:
yaml-cpp/setting.h:24:8: warning: 'auto_ptr<YAML::SettingChangeBase>' is deprecated [-Wdeprecated-declarations]
std::auto_ptr <SettingChangeBase> set(const T& value);
^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<YAML::SettingChangeBase>' 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 yaml-cpp/emitter.cpp:2:
In file included from yaml-cpp/emitterstate.h:10:
yaml-cpp/setting.h:59:14: warning: 'auto_ptr<YAML::SettingChangeBase>' is deprecated [-Wdeprecated-declarations]
inline std::auto_ptr <SettingChangeBase> Setting<T>::set(const T& value) {
^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<YAML::SettingChangeBase>' 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 yaml-cpp/emitter.cpp:2:
In file included from yaml-cpp/emitterstate.h:10:
yaml-cpp/setting.h:60:8: warning: 'auto_ptr<YAML::SettingChangeBase>' is deprecated [-Wdeprecated-declarations]
std::auto_ptr <SettingChangeBase> pChange(new SettingChange<T> (this));
^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<YAML::SettingChangeBase>' 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 yaml-cpp/emitter.cpp:2:
In file included from yaml-cpp/emitterstate.h:10:
yaml-cpp/setting.h:84:18: warning: 'auto_ptr<YAML::SettingChangeBase>' is deprecated [-Wdeprecated-declarations]
void push(std::auto_ptr <SettingChangeBase> pSettingChange) {
^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<YAML::SettingChangeBase>' 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 yaml-cpp/emitter.cpp:2:
In file included from yaml-cpp/emitterstate.h:10:
yaml-cpp/setting.h:24:8: warning: 'auto_ptr<YAML::SettingChangeBase>' is deprecated [-Wdeprecated-declarations]
std::auto_ptr <SettingChangeBase> set(const T& value);
^
yaml-cpp/emitterstate.h:161:26: note: in instantiation of template class 'YAML::Setting<YAML::EMITTER_MANIP>' requested here
Setting<EMITTER_MANIP> m_charset;
^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<YAML::SettingChangeBase>' 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 yaml-cpp/emitter.cpp:2:
In file included from yaml-cpp/emitterstate.h:10:
yaml-cpp/setting.h:24:8: warning: 'auto_ptr<YAML::SettingChangeBase>' is deprecated [-Wdeprecated-declarations]
std::auto_ptr <SettingChangeBase> set(const T& value);
^
yaml-cpp/emitterstate.h:167:21: note: in instantiation of template class 'YAML::Setting<unsigned int>' requested here
Setting<unsigned> m_indent;
^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<YAML::SettingChangeBase>' 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 yaml-cpp/emitter.cpp:2:
In file included from yaml-cpp/emitterstate.h:9:
yaml-cpp/ptr_stack.h:29:17: warning: 'auto_ptr<YAML::EmitterState::Group>' is deprecated [-Wdeprecated-declarations]
void push(std::auto_ptr<T> t) {
^
yaml-cpp/emitterstate.h:187:20: note: in instantiation of template class 'ptr_stack<YAML::EmitterState::Group>' requested here
ptr_stack<Group> m_groups;
^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<YAML::EmitterState::Group>' 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 yaml-cpp/emitter.cpp:2:
In file included from yaml-cpp/emitterstate.h:9:
yaml-cpp/ptr_stack.h:33:7: warning: 'auto_ptr<YAML::EmitterState::Group>' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<T> pop() {
^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<YAML::EmitterState::Group>' 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))
^
9 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -I/usr/local/include -Wall -Wextra -I. -fPIC -Wall -g -O2 -c yaml-cpp/emitterstate.cpp -o yaml-cpp/emitterstate.o
In file included from yaml-cpp/emitterstate.cpp:1:
In file included from yaml-cpp/emitterstate.h:10:
yaml-cpp/setting.h:24:8: warning: 'auto_ptr<YAML::SettingChangeBase>' is deprecated [-Wdeprecated-declarations]
std::auto_ptr <SettingChangeBase> set(const T& value);
^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<YAML::SettingChangeBase>' 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 yaml-cpp/emitterstate.cpp:1:
In file included from yaml-cpp/emitterstate.h:10:
yaml-cpp/setting.h:59:14: warning: 'auto_ptr<YAML::SettingChangeBase>' is deprecated [-Wdeprecated-declarations]
inline std::auto_ptr <SettingChangeBase> Setting<T>::set(const T& value) {
^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<YAML::SettingChangeBase>' 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 yaml-cpp/emitterstate.cpp:1:
In file included from yaml-cpp/emitterstate.h:10:
yaml-cpp/setting.h:60:8: warning: 'auto_ptr<YAML::SettingChangeBase>' is deprecated [-Wdeprecated-declarations]
std::auto_ptr <SettingChangeBase> pChange(new SettingChange<T> (this));
^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<YAML::SettingChangeBase>' 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 yaml-cpp/emitterstate.cpp:1:
In file included from yaml-cpp/emitterstate.h:10:
yaml-cpp/setting.h:84:18: warning: 'auto_ptr<YAML::SettingChangeBase>' is deprecated [-Wdeprecated-declarations]
void push(std::auto_ptr <SettingChangeBase> pSettingChange) {
^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<YAML::SettingChangeBase>' 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 yaml-cpp/emitterstate.cpp:1:
In file included from yaml-cpp/emitterstate.h:10:
yaml-cpp/setting.h:24:8: warning: 'auto_ptr<YAML::SettingChangeBase>' is deprecated [-Wdeprecated-declarations]
std::auto_ptr <SettingChangeBase> set(const T& value);
^
yaml-cpp/emitterstate.h:161:26: note: in instantiation of template class 'YAML::Setting<YAML::EMITTER_MANIP>' requested here
Setting<EMITTER_MANIP> m_charset;
^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<YAML::SettingChangeBase>' 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 yaml-cpp/emitterstate.cpp:1:
In file included from yaml-cpp/emitterstate.h:10:
yaml-cpp/setting.h:24:8: warning: 'auto_ptr<YAML::SettingChangeBase>' is deprecated [-Wdeprecated-declarations]
std::auto_ptr <SettingChangeBase> set(const T& value);
^
yaml-cpp/emitterstate.h:167:21: note: in instantiation of template class 'YAML::Setting<unsigned int>' requested here
Setting<unsigned> m_indent;
^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<YAML::SettingChangeBase>' 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 yaml-cpp/emitterstate.cpp:1:
In file included from yaml-cpp/emitterstate.h:9:
yaml-cpp/ptr_stack.h:29:17: warning: 'auto_ptr<YAML::EmitterState::Group>' is deprecated [-Wdeprecated-declarations]
void push(std::auto_ptr<T> t) {
^
yaml-cpp/emitterstate.h:187:20: note: in instantiation of template class 'ptr_stack<YAML::EmitterState::Group>' requested here
ptr_stack<Group> m_groups;
^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<YAML::EmitterState::Group>' 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 yaml-cpp/emitterstate.cpp:1:
In file included from yaml-cpp/emitterstate.h:9:
yaml-cpp/ptr_stack.h:33:7: warning: 'auto_ptr<YAML::EmitterState::Group>' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<T> pop() {
^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<YAML::EmitterState::Group>' 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))
^
yaml-cpp/emitterstate.cpp:51:8: warning: 'auto_ptr<YAML::EmitterState::Group>' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<Group> pGroup(new Group(type));
^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<YAML::EmitterState::Group>' 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))
^
yaml-cpp/emitterstate.cpp:71:9: warning: 'auto_ptr<YAML::EmitterState::Group>' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<Group> pFinishedGroup = m_groups.pop();
^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<YAML::EmitterState::Group>' 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 yaml-cpp/emitterstate.cpp:1:
In file included from yaml-cpp/emitterstate.h:9:
yaml-cpp/ptr_stack.h:34:8: warning: 'auto_ptr<YAML::EmitterState::Group>' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<T> t(m_data.back());
^
yaml-cpp/emitterstate.cpp:71:51: note: in instantiation of member function 'ptr_stack<YAML::EmitterState::Group>::pop' requested here
std::auto_ptr<Group> pFinishedGroup = m_groups.pop();
^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<YAML::EmitterState::Group>' 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))
^
11 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -I/usr/local/include -Wall -Wextra -I. -fPIC -Wall -g -O2 -c yaml-cpp/emitterutils.cpp -o yaml-cpp/emitterutils.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -I/usr/local/include -Wall -Wextra -I. -fPIC -Wall -g -O2 -c yaml-cpp/exp.cpp -o yaml-cpp/exp.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -I/usr/local/include -Wall -Wextra -I. -fPIC -Wall -g -O2 -c yaml-cpp/iterator.cpp -o yaml-cpp/iterator.o
In file included from yaml-cpp/iterator.cpp:1:
In file included from ./yaml-cpp/node.h:12:
./yaml-cpp/iterator.h:20:17: warning: 'auto_ptr<YAML::IterPriv>' is deprecated [-Wdeprecated-declarations]
Iterator(std::auto_ptr<IterPriv> pData);
^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<YAML::IterPriv>' 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 yaml-cpp/iterator.cpp:1:
In file included from ./yaml-cpp/node.h:12:
./yaml-cpp/iterator.h:36:8: warning: 'auto_ptr<YAML::IterPriv>' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<IterPriv> m_pData;
^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<YAML::IterPriv>' 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 yaml-cpp/iterator.cpp:1:
./yaml-cpp/node.h:43:8: warning: 'auto_ptr<YAML::Node>' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<Node> Clone() const;
^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<YAML::Node>' 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 yaml-cpp/iterator.cpp:1:
./yaml-cpp/node.h:115:8: warning: 'auto_ptr<YAML::NodeOwnership>' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<NodeOwnership> m_pOwnership;
^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<YAML::NodeOwnership>' 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))
^
yaml-cpp/iterator.cpp:11:26: warning: 'auto_ptr<YAML::IterPriv>' is deprecated [-Wdeprecated-declarations]
Iterator::Iterator(std::auto_ptr<IterPriv> pData): m_pData(pData)
^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<YAML::IterPriv>' 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++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -I/usr/local/include -Wall -Wextra -I. -fPIC -Wall -g -O2 -c yaml-cpp/nodebuilder.cpp -o yaml-cpp/nodebuilder.o
In file included from yaml-cpp/nodebuilder.cpp:3:
In file included from ./yaml-cpp/node.h:12:
./yaml-cpp/iterator.h:20:17: warning: 'auto_ptr<YAML::IterPriv>' is deprecated [-Wdeprecated-declarations]
Iterator(std::auto_ptr<IterPriv> pData);
^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<YAML::IterPriv>' 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 yaml-cpp/nodebuilder.cpp:3:
In file included from ./yaml-cpp/node.h:12:
./yaml-cpp/iterator.h:36:8: warning: 'auto_ptr<YAML::IterPriv>' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<IterPriv> m_pData;
^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<YAML::IterPriv>' 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 yaml-cpp/nodebuilder.cpp:3:
./yaml-cpp/node.h:43:8: warning: 'auto_ptr<YAML::Node>' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<Node> Clone() const;
^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<YAML::Node>' 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 yaml-cpp/nodebuilder.cpp:3:
./yaml-cpp/node.h:115:8: warning: 'auto_ptr<YAML::NodeOwnership>' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<NodeOwnership> m_pOwnership;
^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<YAML::NodeOwnership>' 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))
^
4 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -I/usr/local/include -Wall -Wextra -I. -fPIC -Wall -g -O2 -c yaml-cpp/node.cpp -o yaml-cpp/node.o
In file included from yaml-cpp/node.cpp:1:
In file included from ./yaml-cpp/node.h:12:
./yaml-cpp/iterator.h:20:17: warning: 'auto_ptr<YAML::IterPriv>' is deprecated [-Wdeprecated-declarations]
Iterator(std::auto_ptr<IterPriv> pData);
^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<YAML::IterPriv>' 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 yaml-cpp/node.cpp:1:
In file included from ./yaml-cpp/node.h:12:
./yaml-cpp/iterator.h:36:8: warning: 'auto_ptr<YAML::IterPriv>' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<IterPriv> m_pData;
^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<YAML::IterPriv>' 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 yaml-cpp/node.cpp:1:
./yaml-cpp/node.h:43:8: warning: 'auto_ptr<YAML::Node>' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<Node> Clone() const;
^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<YAML::Node>' 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 yaml-cpp/node.cpp:1:
./yaml-cpp/node.h:115:8: warning: 'auto_ptr<YAML::NodeOwnership>' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<NodeOwnership> m_pOwnership;
^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<YAML::NodeOwnership>' 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 yaml-cpp/node.cpp:4:
In file included from yaml-cpp/nodeownership.h:10:
yaml-cpp/ptr_vector.h:31:23: warning: 'auto_ptr<YAML::Node>' is deprecated [-Wdeprecated-declarations]
void push_back(std::auto_ptr<T> t) {
^
yaml-cpp/nodeownership.h:33:20: note: in instantiation of template class 'YAML::ptr_vector<YAML::Node>' requested here
ptr_vector<Node> m_nodes;
^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<YAML::Node>' 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 yaml-cpp/node.cpp:4:
In file included from yaml-cpp/nodeownership.h:10:
yaml-cpp/ptr_vector.h:31:23: warning: 'auto_ptr<YAML::Scanner::IndentMarker>' is deprecated [-Wdeprecated-declarations]
void push_back(std::auto_ptr<T> t) {
^
yaml-cpp/scanner.h:126:28: note: in instantiation of template class 'YAML::ptr_vector<YAML::Scanner::IndentMarker>' requested here
ptr_vector<IndentMarker> m_indentRefs; // for "garbage collection"
^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<YAML::Scanner::IndentMarker>' 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 yaml-cpp/node.cpp:10:
./yaml-cpp/emitter.h:98:8: warning: 'auto_ptr<YAML::EmitterState>' is deprecated [-Wdeprecated-declarations]
std::auto_ptr <EmitterState> m_pState;
^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<YAML::EmitterState>' 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))
^
yaml-cpp/node.cpp:54:7: warning: 'auto_ptr<YAML::Node>' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<Node> Node::Clone() const
^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<YAML::Node>' 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))
^
yaml-cpp/node.cpp:56:8: warning: 'auto_ptr<YAML::Node>' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<Node> pNode(new Node);
^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<YAML::Node>' 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))
^
yaml-cpp/node.cpp:148:26: warning: 'auto_ptr<YAML::IterPriv>' is deprecated [-Wdeprecated-declarations]
return Iterator(std::auto_ptr<IterPriv>(new IterPriv(m_seqData.begin())));
^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<YAML::IterPriv>' 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))
^
yaml-cpp/node.cpp:150:26: warning: 'auto_ptr<YAML::IterPriv>' is deprecated [-Wdeprecated-declarations]
return Iterator(std::auto_ptr<IterPriv>(new IterPriv(m_mapData.begin())));
^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<YAML::IterPriv>' 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))
^
yaml-cpp/node.cpp:166:26: warning: 'auto_ptr<YAML::IterPriv>' is deprecated [-Wdeprecated-declarations]
return Iterator(std::auto_ptr<IterPriv>(new IterPriv(m_seqData.end())));
^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<YAML::IterPriv>' 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))
^
yaml-cpp/node.cpp:168:26: warning: 'auto_ptr<YAML::IterPriv>' is deprecated [-Wdeprecated-declarations]
return Iterator(std::auto_ptr<IterPriv>(new IterPriv(m_mapData.end())));
^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<YAML::IterPriv>' 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))
^
13 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -I/usr/local/include -Wall -Wextra -I. -fPIC -Wall -g -O2 -c yaml-cpp/nodeownership.cpp -o yaml-cpp/nodeownership.o
In file included from yaml-cpp/nodeownership.cpp:1:
In file included from yaml-cpp/nodeownership.h:10:
yaml-cpp/ptr_vector.h:31:23: warning: 'auto_ptr<YAML::Node>' is deprecated [-Wdeprecated-declarations]
void push_back(std::auto_ptr<T> t) {
^
yaml-cpp/nodeownership.h:33:20: note: in instantiation of template class 'YAML::ptr_vector<YAML::Node>' requested here
ptr_vector<Node> m_nodes;
^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<YAML::Node>' 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 yaml-cpp/nodeownership.cpp:2:
In file included from ./yaml-cpp/node.h:12:
./yaml-cpp/iterator.h:20:17: warning: 'auto_ptr<YAML::IterPriv>' is deprecated [-Wdeprecated-declarations]
Iterator(std::auto_ptr<IterPriv> pData);
^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<YAML::IterPriv>' 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 yaml-cpp/nodeownership.cpp:2:
In file included from ./yaml-cpp/node.h:12:
./yaml-cpp/iterator.h:36:8: warning: 'auto_ptr<YAML::IterPriv>' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<IterPriv> m_pData;
^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<YAML::IterPriv>' 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 yaml-cpp/nodeownership.cpp:2:
./yaml-cpp/node.h:43:8: warning: 'auto_ptr<YAML::Node>' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<Node> Clone() const;
^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<YAML::Node>' 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 yaml-cpp/nodeownership.cpp:2:
./yaml-cpp/node.h:115:8: warning: 'auto_ptr<YAML::NodeOwnership>' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<NodeOwnership> m_pOwnership;
^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<YAML::NodeOwnership>' 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))
^
yaml-cpp/nodeownership.cpp:18:26: warning: 'auto_ptr<YAML::Node>' is deprecated [-Wdeprecated-declarations]
m_nodes.push_back(std::auto_ptr<Node>(new Node));
^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<YAML::Node>' 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++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -I/usr/local/include -Wall -Wextra -I. -fPIC -Wall -g -O2 -c yaml-cpp/null.cpp -o yaml-cpp/null.o
In file included from yaml-cpp/null.cpp:2:
In file included from ./yaml-cpp/node.h:12:
./yaml-cpp/iterator.h:20:17: warning: 'auto_ptr<YAML::IterPriv>' is deprecated [-Wdeprecated-declarations]
Iterator(std::auto_ptr<IterPriv> pData);
^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<YAML::IterPriv>' 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 yaml-cpp/null.cpp:2:
In file included from ./yaml-cpp/node.h:12:
./yaml-cpp/iterator.h:36:8: warning: 'auto_ptr<YAML::IterPriv>' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<IterPriv> m_pData;
^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<YAML::IterPriv>' 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 yaml-cpp/null.cpp:2:
./yaml-cpp/node.h:43:8: warning: 'auto_ptr<YAML::Node>' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<Node> Clone() const;
^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<YAML::Node>' 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 yaml-cpp/null.cpp:2:
./yaml-cpp/node.h:115:8: warning: 'auto_ptr<YAML::NodeOwnership>' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<NodeOwnership> m_pOwnership;
^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<YAML::NodeOwnership>' 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))
^
4 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -I/usr/local/include -Wall -Wextra -I. -fPIC -Wall -g -O2 -c yaml-cpp/ostream.cpp -o yaml-cpp/ostream.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -I/usr/local/include -Wall -Wextra -I. -fPIC -Wall -g -O2 -c yaml-cpp/parser.cpp -o yaml-cpp/parser.o
In file included from yaml-cpp/parser.cpp:1:
./yaml-cpp/parser.h:45:8: warning: 'auto_ptr<YAML::Scanner>' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<Scanner> m_pScanner;
^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<YAML::Scanner>' 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 yaml-cpp/parser.cpp:1:
./yaml-cpp/parser.h:46:8: warning: 'auto_ptr<YAML::Directives>' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<Directives> m_pDirectives;
^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<YAML::Directives>' 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 yaml-cpp/parser.cpp:5:
In file included from ./yaml-cpp/node.h:12:
./yaml-cpp/iterator.h:20:17: warning: 'auto_ptr<YAML::IterPriv>' is deprecated [-Wdeprecated-declarations]
Iterator(std::auto_ptr<IterPriv> pData);
^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<YAML::IterPriv>' 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 yaml-cpp/parser.cpp:5:
In file included from ./yaml-cpp/node.h:12:
./yaml-cpp/iterator.h:36:8: warning: 'auto_ptr<YAML::IterPriv>' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<IterPriv> m_pData;
^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<YAML::IterPriv>' 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 yaml-cpp/parser.cpp:5:
./yaml-cpp/node.h:43:8: warning: 'auto_ptr<YAML::Node>' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<Node> Clone() const;
^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<YAML::Node>' 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 yaml-cpp/parser.cpp:5:
./yaml-cpp/node.h:115:8: warning: 'auto_ptr<YAML::NodeOwnership>' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<NodeOwnership> m_pOwnership;
^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<YAML::NodeOwnership>' 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 yaml-cpp/parser.cpp:7:
In file included from yaml-cpp/scanner.h:15:
yaml-cpp/ptr_vector.h:31:23: warning: 'auto_ptr<YAML::Scanner::IndentMarker>' is deprecated [-Wdeprecated-declarations]
void push_back(std::auto_ptr<T> t) {
^
yaml-cpp/scanner.h:126:28: note: in instantiation of template class 'YAML::ptr_vector<YAML::Scanner::IndentMarker>' requested here
ptr_vector<IndentMarker> m_indentRefs; // for "garbage collection"
^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<YAML::Scanner::IndentMarker>' 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 yaml-cpp/parser.cpp:8:
yaml-cpp/singledocparser.h:56:8: warning: 'auto_ptr<YAML::CollectionStack>' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<CollectionStack> m_pCollectionStack;
^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<YAML::CollectionStack>' 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))
^
8 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -I/usr/local/include -Wall -Wextra -I. -fPIC -Wall -g -O2 -c yaml-cpp/regex.cpp -o yaml-cpp/regex.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -I/usr/local/include -Wall -Wextra -I. -fPIC -Wall -g -O2 -c yaml-cpp/scanner.cpp -o yaml-cpp/scanner.o
In file included from yaml-cpp/scanner.cpp:1:
In file included from yaml-cpp/scanner.h:15:
yaml-cpp/ptr_vector.h:31:23: warning: 'auto_ptr<YAML::Scanner::IndentMarker>' is deprecated [-Wdeprecated-declarations]
void push_back(std::auto_ptr<T> t) {
^
yaml-cpp/scanner.h:126:28: note: in instantiation of template class 'YAML::ptr_vector<YAML::Scanner::IndentMarker>' requested here
ptr_vector<IndentMarker> m_indentRefs; // for "garbage collection"
^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<YAML::Scanner::IndentMarker>' 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))
^
yaml-cpp/scanner.cpp:237:8: warning: 'auto_ptr<YAML::Scanner::IndentMarker>' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<IndentMarker> pIndent(new IndentMarker(-1, IndentMarker::NONE));
^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<YAML::Scanner::IndentMarker>' 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))
^
yaml-cpp/scanner.cpp:284:8: warning: 'auto_ptr<YAML::Scanner::IndentMarker>' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<IndentMarker> pIndent(new IndentMarker(column, type));
^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<YAML::Scanner::IndentMarker>' 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))
^
3 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -I/usr/local/include -Wall -Wextra -I. -fPIC -Wall -g -O2 -c yaml-cpp/scanscalar.cpp -o yaml-cpp/scanscalar.o
In file included from yaml-cpp/scanscalar.cpp:2:
In file included from yaml-cpp/scanner.h:15:
yaml-cpp/ptr_vector.h:31:23: warning: 'auto_ptr<YAML::Scanner::IndentMarker>' is deprecated [-Wdeprecated-declarations]
void push_back(std::auto_ptr<T> t) {
^
yaml-cpp/scanner.h:126:28: note: in instantiation of template class 'YAML::ptr_vector<YAML::Scanner::IndentMarker>' requested here
ptr_vector<IndentMarker> m_indentRefs; // for "garbage collection"
^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<YAML::Scanner::IndentMarker>' 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++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -I/usr/local/include -Wall -Wextra -I. -fPIC -Wall -g -O2 -c yaml-cpp/scantag.cpp -o yaml-cpp/scantag.o
In file included from yaml-cpp/scantag.cpp:1:
In file included from yaml-cpp/scanner.h:15:
yaml-cpp/ptr_vector.h:31:23: warning: 'auto_ptr<YAML::Scanner::IndentMarker>' is deprecated [-Wdeprecated-declarations]
void push_back(std::auto_ptr<T> t) {
^
yaml-cpp/scanner.h:126:28: note: in instantiation of template class 'YAML::ptr_vector<YAML::Scanner::IndentMarker>' requested here
ptr_vector<IndentMarker> m_indentRefs; // for "garbage collection"
^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<YAML::Scanner::IndentMarker>' 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++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -I/usr/local/include -Wall -Wextra -I. -fPIC -Wall -g -O2 -c yaml-cpp/scantoken.cpp -o yaml-cpp/scantoken.o
In file included from yaml-cpp/scantoken.cpp:1:
In file included from yaml-cpp/scanner.h:15:
yaml-cpp/ptr_vector.h:31:23: warning: 'auto_ptr<YAML::Scanner::IndentMarker>' is deprecated [-Wdeprecated-declarations]
void push_back(std::auto_ptr<T> t) {
^
yaml-cpp/scanner.h:126:28: note: in instantiation of template class 'YAML::ptr_vector<YAML::Scanner::IndentMarker>' requested here
ptr_vector<IndentMarker> m_indentRefs; // for "garbage collection"
^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<YAML::Scanner::IndentMarker>' 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++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -I/usr/local/include -Wall -Wextra -I. -fPIC -Wall -g -O2 -c yaml-cpp/simplekey.cpp -o yaml-cpp/simplekey.o
In file included from yaml-cpp/simplekey.cpp:1:
In file included from yaml-cpp/scanner.h:15:
yaml-cpp/ptr_vector.h:31:23: warning: 'auto_ptr<YAML::Scanner::IndentMarker>' is deprecated [-Wdeprecated-declarations]
void push_back(std::auto_ptr<T> t) {
^
yaml-cpp/scanner.h:126:28: note: in instantiation of template class 'YAML::ptr_vector<YAML::Scanner::IndentMarker>' requested here
ptr_vector<IndentMarker> m_indentRefs; // for "garbage collection"
^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<YAML::Scanner::IndentMarker>' 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++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -I/usr/local/include -Wall -Wextra -I. -fPIC -Wall -g -O2 -c yaml-cpp/singledocparser.cpp -o yaml-cpp/singledocparser.o
In file included from yaml-cpp/singledocparser.cpp:1:
yaml-cpp/singledocparser.h:56:8: warning: 'auto_ptr<YAML::CollectionStack>' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<CollectionStack> m_pCollectionStack;
^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<YAML::CollectionStack>' 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 yaml-cpp/singledocparser.cpp:2:
yaml-cpp/collectionstack.h:28:48: warning: unused parameter 'type' [-Wunused-parameter]
void PopCollectionType(CollectionType::value type) { assert(type == GetCurCollectionType()); collectionStack.pop(); }
^
In file included from yaml-cpp/singledocparser.cpp:6:
In file included from yaml-cpp/scanner.h:15:
yaml-cpp/ptr_vector.h:31:23: warning: 'auto_ptr<YAML::Scanner::IndentMarker>' is deprecated [-Wdeprecated-declarations]
void push_back(std::auto_ptr<T> t) {
^
yaml-cpp/scanner.h:126:28: note: in instantiation of template class 'YAML::ptr_vector<YAML::Scanner::IndentMarker>' requested here
ptr_vector<IndentMarker> m_indentRefs; // for "garbage collection"
^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:2080:28: note: 'auto_ptr<YAML::Scanner::IndentMarker>' 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))
^
3 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -I/usr/local/include -Wall -Wextra -I. -fPIC -Wall -g -O2 -c yaml-cpp/stream.cpp -o yaml-cpp/stream.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/include' -I/usr/local/include -Wall -Wextra -I. -fPIC -Wall -g -O2 -c yaml-cpp/tag.cpp -o yaml-cpp/tag.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -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 seqbias.so sam.o bam_plbuf.o bam_aux.o common.o miscmath.o pos_table.o kmer_matrix.o logger.o motif.o seqbias.o sequencing_bias.o twobitseq.o yaml-cpp/aliasmanager.o yaml-cpp/conversion.o yaml-cpp/directives.o yaml-cpp/emitfromevents.o yaml-cpp/emitter.o yaml-cpp/emitterstate.o yaml-cpp/emitterutils.o yaml-cpp/exp.o yaml-cpp/iterator.o yaml-cpp/nodebuilder.o yaml-cpp/node.o yaml-cpp/nodeownership.o yaml-cpp/null.o yaml-cpp/ostream.o yaml-cpp/parser.o yaml-cpp/regex.o yaml-cpp/scanner.o yaml-cpp/scanscalar.o yaml-cpp/scantag.o yaml-cpp/scantoken.o yaml-cpp/simplekey.o yaml-cpp/singledocparser.o yaml-cpp/stream.o yaml-cpp/tag.o /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhtslib/usrlib/libhts.a -lcurl -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.12-bioc/meat/seqbias.buildbin-libdir/00LOCK-seqbias/00new/seqbias/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 (seqbias)
>>>>>>>
>>>>>>> FIXING LINKS FOR seqbias.buildbin-libdir/seqbias/libs/seqbias.so
>>>>>>>
install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libgcc_s.1.dylib" "seqbias.buildbin-libdir/seqbias/libs/seqbias.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libgfortran.5.dylib" "seqbias.buildbin-libdir/seqbias/libs/seqbias.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libquadmath.0.dylib" "seqbias.buildbin-libdir/seqbias/libs/seqbias.so"