##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:seqbias.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings seqbias_1.38.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/seqbias.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘seqbias/DESCRIPTION’ ... OK
* this is package ‘seqbias’ version ‘1.38.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘seqbias’ can be installed ... WARNING
Found the following significant warnings:
  miscmath.c:21:12: warning: 'finite' is deprecated: first deprecated in macOS 10.9 - Use `isfinite((double)x)` instead. [-Wdeprecated-declarations]
  miscmath.c:47:9: warning: 'finite' is deprecated: first deprecated in macOS 10.9 - Use `isfinite((double)x)` instead. [-Wdeprecated-declarations]
  ./yaml-cpp/parser.h:45:8: warning: 'auto_ptr<YAML::Scanner>' is deprecated [-Wdeprecated-declarations]
  ./yaml-cpp/parser.h:46:8: warning: 'auto_ptr<YAML::Directives>' is deprecated [-Wdeprecated-declarations]
  ./yaml-cpp/iterator.h:20:17: warning: 'auto_ptr<YAML::IterPriv>' is deprecated [-Wdeprecated-declarations]
  ./yaml-cpp/iterator.h:36:8: warning: 'auto_ptr<YAML::IterPriv>' is deprecated [-Wdeprecated-declarations]
  ./yaml-cpp/node.h:43:8: warning: 'auto_ptr<YAML::Node>' is deprecated [-Wdeprecated-declarations]
  ./yaml-cpp/node.h:115:8: warning: 'auto_ptr<YAML::NodeOwnership>' is deprecated [-Wdeprecated-declarations]
  ./yaml-cpp/emitter.h:98:8: warning: 'auto_ptr<YAML::EmitterState>' is deprecated [-Wdeprecated-declarations]
  yaml-cpp/setting.h:24:8: warning: 'auto_ptr<YAML::SettingChangeBase>' is deprecated [-Wdeprecated-declarations]
  yaml-cpp/setting.h:59:14: warning: 'auto_ptr<YAML::SettingChangeBase>' is deprecated [-Wdeprecated-declarations]
  yaml-cpp/setting.h:60:8: warning: 'auto_ptr<YAML::SettingChangeBase>' is deprecated [-Wdeprecated-declarations]
  yaml-cpp/setting.h:84:18: warning: 'auto_ptr<YAML::SettingChangeBase>' is deprecated [-Wdeprecated-declarations]
  yaml-cpp/ptr_stack.h:29:17: warning: 'auto_ptr<YAML::EmitterState::Group>' is deprecated [-Wdeprecated-declarations]
  yaml-cpp/ptr_stack.h:33:7: warning: 'auto_ptr<YAML::EmitterState::Group>' is deprecated [-Wdeprecated-declarations]
  yaml-cpp/emitterstate.cpp:51:8: warning: 'auto_ptr<YAML::EmitterState::Group>' is deprecated [-Wdeprecated-declarations]
  yaml-cpp/emitterstate.cpp:71:9: warning: 'auto_ptr<YAML::EmitterState::Group>' is deprecated [-Wdeprecated-declarations]
  yaml-cpp/ptr_stack.h:34:8: warning: 'auto_ptr<YAML::EmitterState::Group>' is deprecated [-Wdeprecated-declarations]
  yaml-cpp/iterator.cpp:11:26: warning: 'auto_ptr<YAML::IterPriv>' is deprecated [-Wdeprecated-declarations]
  yaml-cpp/ptr_vector.h:31:23: warning: 'auto_ptr<YAML::Node>' is deprecated [-Wdeprecated-declarations]
  yaml-cpp/ptr_vector.h:31:23: warning: 'auto_ptr<YAML::Scanner::IndentMarker>' is deprecated [-Wdeprecated-declarations]
  yaml-cpp/node.cpp:54:7: warning: 'auto_ptr<YAML::Node>' is deprecated [-Wdeprecated-declarations]
  yaml-cpp/node.cpp:56:8: warning: 'auto_ptr<YAML::Node>' is deprecated [-Wdeprecated-declarations]
  yaml-cpp/node.cpp:148:26: warning: 'auto_ptr<YAML::IterPriv>' is deprecated [-Wdeprecated-declarations]
  yaml-cpp/node.cpp:150:26: warning: 'auto_ptr<YAML::IterPriv>' is deprecated [-Wdeprecated-declarations]
  yaml-cpp/node.cpp:166:26: warning: 'auto_ptr<YAML::IterPriv>' is deprecated [-Wdeprecated-declarations]
  yaml-cpp/node.cpp:168:26: warning: 'auto_ptr<YAML::IterPriv>' is deprecated [-Wdeprecated-declarations]
  yaml-cpp/nodeownership.cpp:18:26: warning: 'auto_ptr<YAML::Node>' is deprecated [-Wdeprecated-declarations]
  yaml-cpp/singledocparser.h:56:8: warning: 'auto_ptr<YAML::CollectionStack>' is deprecated [-Wdeprecated-declarations]
  yaml-cpp/scanner.cpp:237:8: warning: 'auto_ptr<YAML::Scanner::IndentMarker>' is deprecated [-Wdeprecated-declarations]
  yaml-cpp/scanner.cpp:284:8: warning: 'auto_ptr<YAML::Scanner::IndentMarker>' is deprecated [-Wdeprecated-declarations]
See ‘/Users/biocbuild/bbs-3.12-bioc/meat/seqbias.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' call to ‘GenomicRanges’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘Biostrings’ ‘GenomicRanges’ ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
count.reads: no visible global function definition for ‘is’
count.reads : <anonymous>: no visible global function definition for
  ‘seqnames’
count.reads : <anonymous>: no visible global function definition for
  ‘start’
count.reads : <anonymous>: no visible global function definition for
  ‘end’
count.reads : <anonymous>: no visible global function definition for
  ‘strand’
random.intervals: no visible global function definition for ‘is’
random.intervals : uniform_ints : <anonymous>: no visible global
  function definition for ‘runif’
random.intervals: no visible global function definition for ‘GRanges’
random.intervals: no visible global function definition for ‘IRanges’
seqbias.fit: no visible global function definition for ‘new’
seqbias.load: no visible global function definition for ‘new’
seqbias.predict: no visible global function definition for ‘is’
seqbias.predict : <anonymous>: no visible global function definition
  for ‘seqnames’
seqbias.predict : <anonymous>: no visible global function definition
  for ‘start’
seqbias.predict : <anonymous>: no visible global function definition
  for ‘end’
seqbias.predict : <anonymous>: no visible global function definition
  for ‘strand’
Undefined global functions or variables:
  GRanges IRanges end is new runif seqnames start strand
Consider adding
  importFrom("methods", "is", "new")
  importFrom("stats", "end", "runif", "start")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
File ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/seqbias/libs/seqbias.so’:
  Found ‘___assert_rtn’, possibly from ‘assert’ (C)
  Found ‘___stderrp’, possibly from ‘stderr’ (C)
  Found ‘___stdoutp’, possibly from ‘stdout’ (C)
  Found ‘_abort’, possibly from ‘abort’ (C)
  Found ‘_exit’, possibly from ‘exit’ (C)
  Found ‘_printf’, possibly from ‘printf’ (C)
  Found ‘_putchar’, possibly from ‘putchar’ (C)
  Found ‘_puts’, possibly from ‘printf’ (C), ‘puts’ (C)
  Found ‘_rand’, possibly from ‘rand’ (C)
  Found ‘_srand48’, possibly from ‘srand48’ (C)

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

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

Status: 1 WARNING, 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.12-bioc/meat/seqbias.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL seqbias
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* 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 /Library/Frameworks/R.framework/Versions/4.0/Resources/library/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)