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CHECK report for seqbias on malbec2

This page was generated on 2019-04-09 11:29:46 -0400 (Tue, 09 Apr 2019).

Package 1461/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
seqbias 1.31.1
Daniel Jones
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/seqbias
Branch: master
Last Commit: 30d6f83
Last Changed Date: 2019-03-22 16:05:41 -0400 (Fri, 22 Mar 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK 

Summary

Package: seqbias
Version: 1.31.1
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:seqbias.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings seqbias_1.31.1.tar.gz
StartedAt: 2019-04-09 03:34:00 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 03:35:25 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 84.9 seconds
RetCode: 0
Status:  OK 
CheckDir: seqbias.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:seqbias.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings seqbias_1.31.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/seqbias.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘seqbias/DESCRIPTION’ ... OK
* this is package ‘seqbias’ version ‘1.31.1’
* 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 ... OK
* checking installed package size ... NOTE
  installed size is  7.9Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
* 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 ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
File ‘/home/biocbuild/bbs-3.9-bioc/R/library/seqbias/libs/seqbias.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (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 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: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.9-bioc/meat/seqbias.Rcheck/00check.log’
for details.



Installation output

seqbias.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL seqbias
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘seqbias’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/home/biocbuild/bbs-3.9-bioc/R/bin/R" --vanilla --slave` -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I/usr/local/include -Wall -Wextra -I. -fpic  -g -O2  -Wall -c sam.c -o sam.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/home/biocbuild/bbs-3.9-bioc/R/bin/R" --vanilla --slave` -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I/usr/local/include -Wall -Wextra -I. -fpic  -g -O2  -Wall -c bam_plbuf.c -o bam_plbuf.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/home/biocbuild/bbs-3.9-bioc/R/bin/R" --vanilla --slave` -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I/usr/local/include -Wall -Wextra -I. -fpic  -g -O2  -Wall -c bam_aux.c -o bam_aux.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/home/biocbuild/bbs-3.9-bioc/R/bin/R" --vanilla --slave` -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I/usr/local/include -Wall -Wextra -I. -fpic  -g -O2  -Wall -c common.c -o common.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/home/biocbuild/bbs-3.9-bioc/R/bin/R" --vanilla --slave` -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I/usr/local/include -Wall -Wextra -I. -fpic  -g -O2  -Wall -c miscmath.c -o miscmath.o
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/home/biocbuild/bbs-3.9-bioc/R/bin/R" --vanilla --slave` -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I/usr/local/include -Wall -Wextra -I. -fpic  -g -O2  -Wall -c pos_table.c -o pos_table.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/home/biocbuild/bbs-3.9-bioc/R/bin/R" --vanilla --slave` -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I/usr/local/include -Wall -Wextra -I. -fpic  -g -O2  -Wall -c kmer_matrix.cpp -o kmer_matrix.o
In file included from yaml-cpp/yaml.h:9:0,
                 from kmer_matrix.hpp:13,
                 from kmer_matrix.cpp:8:
./yaml-cpp/parser.h:45:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   std::auto_ptr<Scanner> m_pScanner;
        ^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
                 from ./yaml-cpp/parser.h:12,
                 from yaml-cpp/yaml.h:9,
                 from kmer_matrix.hpp:13,
                 from kmer_matrix.cpp:8:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^˜˜˜˜˜˜˜
In file included from yaml-cpp/yaml.h:9:0,
                 from kmer_matrix.hpp:13,
                 from kmer_matrix.cpp:8:
./yaml-cpp/parser.h:46:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   std::auto_ptr<Directives> m_pDirectives;
        ^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
                 from ./yaml-cpp/parser.h:12,
                 from yaml-cpp/yaml.h:9,
                 from kmer_matrix.hpp:13,
                 from kmer_matrix.cpp:8:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^˜˜˜˜˜˜˜
In file included from ./yaml-cpp/node.h:12:0,
                 from yaml-cpp/yaml.h:10,
                 from kmer_matrix.hpp:13,
                 from kmer_matrix.cpp:8:
./yaml-cpp/iterator.h:20:17: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   Iterator(std::auto_ptr<IterPriv> pData);
                 ^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
                 from ./yaml-cpp/parser.h:12,
                 from yaml-cpp/yaml.h:9,
                 from kmer_matrix.hpp:13,
                 from kmer_matrix.cpp:8:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^˜˜˜˜˜˜˜
In file included from ./yaml-cpp/node.h:12:0,
                 from yaml-cpp/yaml.h:10,
                 from kmer_matrix.hpp:13,
                 from kmer_matrix.cpp:8:
./yaml-cpp/iterator.h:36:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   std::auto_ptr<IterPriv> m_pData;
        ^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
                 from ./yaml-cpp/parser.h:12,
                 from yaml-cpp/yaml.h:9,
                 from kmer_matrix.hpp:13,
                 from kmer_matrix.cpp:8:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^˜˜˜˜˜˜˜
In file included from yaml-cpp/yaml.h:10:0,
                 from kmer_matrix.hpp:13,
                 from kmer_matrix.cpp:8:
./yaml-cpp/node.h:43:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   std::auto_ptr<Node> Clone() const;
        ^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
                 from ./yaml-cpp/parser.h:12,
                 from yaml-cpp/yaml.h:9,
                 from kmer_matrix.hpp:13,
                 from kmer_matrix.cpp:8:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^˜˜˜˜˜˜˜
In file included from yaml-cpp/yaml.h:10:0,
                 from kmer_matrix.hpp:13,
                 from kmer_matrix.cpp:8:
./yaml-cpp/node.h:115:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   std::auto_ptr<NodeOwnership> m_pOwnership;
        ^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
                 from ./yaml-cpp/parser.h:12,
                 from yaml-cpp/yaml.h:9,
                 from kmer_matrix.hpp:13,
                 from kmer_matrix.cpp:8:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^˜˜˜˜˜˜˜
In file included from yaml-cpp/yaml.h:13:0,
                 from kmer_matrix.hpp:13,
                 from kmer_matrix.cpp:8:
./yaml-cpp/emitter.h:98:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   std::auto_ptr <EmitterState> m_pState;
        ^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
                 from ./yaml-cpp/parser.h:12,
                 from yaml-cpp/yaml.h:9,
                 from kmer_matrix.hpp:13,
                 from kmer_matrix.cpp:8:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^˜˜˜˜˜˜˜
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/home/biocbuild/bbs-3.9-bioc/R/bin/R" --vanilla --slave` -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I/usr/local/include -Wall -Wextra -I. -fpic  -g -O2  -Wall -c logger.cpp -o logger.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/home/biocbuild/bbs-3.9-bioc/R/bin/R" --vanilla --slave` -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I/usr/local/include -Wall -Wextra -I. -fpic  -g -O2  -Wall -c motif.cpp -o motif.o
In file included from yaml-cpp/yaml.h:9:0,
                 from kmer_matrix.hpp:13,
                 from motif.hpp:13,
                 from motif.cpp:8:
./yaml-cpp/parser.h:45:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   std::auto_ptr<Scanner> m_pScanner;
        ^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
                 from ./yaml-cpp/parser.h:12,
                 from yaml-cpp/yaml.h:9,
                 from kmer_matrix.hpp:13,
                 from motif.hpp:13,
                 from motif.cpp:8:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^˜˜˜˜˜˜˜
In file included from yaml-cpp/yaml.h:9:0,
                 from kmer_matrix.hpp:13,
                 from motif.hpp:13,
                 from motif.cpp:8:
./yaml-cpp/parser.h:46:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   std::auto_ptr<Directives> m_pDirectives;
        ^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
                 from ./yaml-cpp/parser.h:12,
                 from yaml-cpp/yaml.h:9,
                 from kmer_matrix.hpp:13,
                 from motif.hpp:13,
                 from motif.cpp:8:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^˜˜˜˜˜˜˜
In file included from ./yaml-cpp/node.h:12:0,
                 from yaml-cpp/yaml.h:10,
                 from kmer_matrix.hpp:13,
                 from motif.hpp:13,
                 from motif.cpp:8:
./yaml-cpp/iterator.h:20:17: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   Iterator(std::auto_ptr<IterPriv> pData);
                 ^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
                 from ./yaml-cpp/parser.h:12,
                 from yaml-cpp/yaml.h:9,
                 from kmer_matrix.hpp:13,
                 from motif.hpp:13,
                 from motif.cpp:8:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^˜˜˜˜˜˜˜
In file included from ./yaml-cpp/node.h:12:0,
                 from yaml-cpp/yaml.h:10,
                 from kmer_matrix.hpp:13,
                 from motif.hpp:13,
                 from motif.cpp:8:
./yaml-cpp/iterator.h:36:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   std::auto_ptr<IterPriv> m_pData;
        ^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
                 from ./yaml-cpp/parser.h:12,
                 from yaml-cpp/yaml.h:9,
                 from kmer_matrix.hpp:13,
                 from motif.hpp:13,
                 from motif.cpp:8:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^˜˜˜˜˜˜˜
In file included from yaml-cpp/yaml.h:10:0,
                 from kmer_matrix.hpp:13,
                 from motif.hpp:13,
                 from motif.cpp:8:
./yaml-cpp/node.h:43:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   std::auto_ptr<Node> Clone() const;
        ^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
                 from ./yaml-cpp/parser.h:12,
                 from yaml-cpp/yaml.h:9,
                 from kmer_matrix.hpp:13,
                 from motif.hpp:13,
                 from motif.cpp:8:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^˜˜˜˜˜˜˜
In file included from yaml-cpp/yaml.h:10:0,
                 from kmer_matrix.hpp:13,
                 from motif.hpp:13,
                 from motif.cpp:8:
./yaml-cpp/node.h:115:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   std::auto_ptr<NodeOwnership> m_pOwnership;
        ^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
                 from ./yaml-cpp/parser.h:12,
                 from yaml-cpp/yaml.h:9,
                 from kmer_matrix.hpp:13,
                 from motif.hpp:13,
                 from motif.cpp:8:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^˜˜˜˜˜˜˜
In file included from yaml-cpp/yaml.h:13:0,
                 from kmer_matrix.hpp:13,
                 from motif.hpp:13,
                 from motif.cpp:8:
./yaml-cpp/emitter.h:98:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   std::auto_ptr <EmitterState> m_pState;
        ^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
                 from ./yaml-cpp/parser.h:12,
                 from yaml-cpp/yaml.h:9,
                 from kmer_matrix.hpp:13,
                 from motif.hpp:13,
                 from motif.cpp:8:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^˜˜˜˜˜˜˜
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/home/biocbuild/bbs-3.9-bioc/R/bin/R" --vanilla --slave` -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I/usr/local/include -Wall -Wextra -I. -fpic  -g -O2  -Wall -c seqbias.cpp -o seqbias.o
In file included from yaml-cpp/yaml.h:9:0,
                 from kmer_matrix.hpp:13,
                 from motif.hpp:13,
                 from sequencing_bias.hpp:13,
                 from seqbias.cpp:2:
./yaml-cpp/parser.h:45:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   std::auto_ptr<Scanner> m_pScanner;
        ^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
                 from ./yaml-cpp/parser.h:12,
                 from yaml-cpp/yaml.h:9,
                 from kmer_matrix.hpp:13,
                 from motif.hpp:13,
                 from sequencing_bias.hpp:13,
                 from seqbias.cpp:2:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^˜˜˜˜˜˜˜
In file included from yaml-cpp/yaml.h:9:0,
                 from kmer_matrix.hpp:13,
                 from motif.hpp:13,
                 from sequencing_bias.hpp:13,
                 from seqbias.cpp:2:
./yaml-cpp/parser.h:46:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   std::auto_ptr<Directives> m_pDirectives;
        ^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
                 from ./yaml-cpp/parser.h:12,
                 from yaml-cpp/yaml.h:9,
                 from kmer_matrix.hpp:13,
                 from motif.hpp:13,
                 from sequencing_bias.hpp:13,
                 from seqbias.cpp:2:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^˜˜˜˜˜˜˜
In file included from ./yaml-cpp/node.h:12:0,
                 from yaml-cpp/yaml.h:10,
                 from kmer_matrix.hpp:13,
                 from motif.hpp:13,
                 from sequencing_bias.hpp:13,
                 from seqbias.cpp:2:
./yaml-cpp/iterator.h:20:17: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   Iterator(std::auto_ptr<IterPriv> pData);
                 ^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
                 from ./yaml-cpp/parser.h:12,
                 from yaml-cpp/yaml.h:9,
                 from kmer_matrix.hpp:13,
                 from motif.hpp:13,
                 from sequencing_bias.hpp:13,
                 from seqbias.cpp:2:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^˜˜˜˜˜˜˜
In file included from ./yaml-cpp/node.h:12:0,
                 from yaml-cpp/yaml.h:10,
                 from kmer_matrix.hpp:13,
                 from motif.hpp:13,
                 from sequencing_bias.hpp:13,
                 from seqbias.cpp:2:
./yaml-cpp/iterator.h:36:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   std::auto_ptr<IterPriv> m_pData;
        ^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
                 from ./yaml-cpp/parser.h:12,
                 from yaml-cpp/yaml.h:9,
                 from kmer_matrix.hpp:13,
                 from motif.hpp:13,
                 from sequencing_bias.hpp:13,
                 from seqbias.cpp:2:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^˜˜˜˜˜˜˜
In file included from yaml-cpp/yaml.h:10:0,
                 from kmer_matrix.hpp:13,
                 from motif.hpp:13,
                 from sequencing_bias.hpp:13,
                 from seqbias.cpp:2:
./yaml-cpp/node.h:43:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   std::auto_ptr<Node> Clone() const;
        ^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
                 from ./yaml-cpp/parser.h:12,
                 from yaml-cpp/yaml.h:9,
                 from kmer_matrix.hpp:13,
                 from motif.hpp:13,
                 from sequencing_bias.hpp:13,
                 from seqbias.cpp:2:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^˜˜˜˜˜˜˜
In file included from yaml-cpp/yaml.h:10:0,
                 from kmer_matrix.hpp:13,
                 from motif.hpp:13,
                 from sequencing_bias.hpp:13,
                 from seqbias.cpp:2:
./yaml-cpp/node.h:115:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   std::auto_ptr<NodeOwnership> m_pOwnership;
        ^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
                 from ./yaml-cpp/parser.h:12,
                 from yaml-cpp/yaml.h:9,
                 from kmer_matrix.hpp:13,
                 from motif.hpp:13,
                 from sequencing_bias.hpp:13,
                 from seqbias.cpp:2:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^˜˜˜˜˜˜˜
In file included from yaml-cpp/yaml.h:13:0,
                 from kmer_matrix.hpp:13,
                 from motif.hpp:13,
                 from sequencing_bias.hpp:13,
                 from seqbias.cpp:2:
./yaml-cpp/emitter.h:98:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   std::auto_ptr <EmitterState> m_pState;
        ^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
                 from ./yaml-cpp/parser.h:12,
                 from yaml-cpp/yaml.h:9,
                 from kmer_matrix.hpp:13,
                 from motif.hpp:13,
                 from sequencing_bias.hpp:13,
                 from seqbias.cpp:2:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^˜˜˜˜˜˜˜
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/home/biocbuild/bbs-3.9-bioc/R/bin/R" --vanilla --slave` -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I/usr/local/include -Wall -Wextra -I. -fpic  -g -O2  -Wall -c sequencing_bias.cpp -o sequencing_bias.o
In file included from yaml-cpp/yaml.h:9:0,
                 from kmer_matrix.hpp:13,
                 from motif.hpp:13,
                 from sequencing_bias.hpp:13,
                 from sequencing_bias.cpp:8:
./yaml-cpp/parser.h:45:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   std::auto_ptr<Scanner> m_pScanner;
        ^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
                 from ./yaml-cpp/parser.h:12,
                 from yaml-cpp/yaml.h:9,
                 from kmer_matrix.hpp:13,
                 from motif.hpp:13,
                 from sequencing_bias.hpp:13,
                 from sequencing_bias.cpp:8:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^˜˜˜˜˜˜˜
In file included from yaml-cpp/yaml.h:9:0,
                 from kmer_matrix.hpp:13,
                 from motif.hpp:13,
                 from sequencing_bias.hpp:13,
                 from sequencing_bias.cpp:8:
./yaml-cpp/parser.h:46:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   std::auto_ptr<Directives> m_pDirectives;
        ^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
                 from ./yaml-cpp/parser.h:12,
                 from yaml-cpp/yaml.h:9,
                 from kmer_matrix.hpp:13,
                 from motif.hpp:13,
                 from sequencing_bias.hpp:13,
                 from sequencing_bias.cpp:8:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^˜˜˜˜˜˜˜
In file included from ./yaml-cpp/node.h:12:0,
                 from yaml-cpp/yaml.h:10,
                 from kmer_matrix.hpp:13,
                 from motif.hpp:13,
                 from sequencing_bias.hpp:13,
                 from sequencing_bias.cpp:8:
./yaml-cpp/iterator.h:20:17: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   Iterator(std::auto_ptr<IterPriv> pData);
                 ^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
                 from ./yaml-cpp/parser.h:12,
                 from yaml-cpp/yaml.h:9,
                 from kmer_matrix.hpp:13,
                 from motif.hpp:13,
                 from sequencing_bias.hpp:13,
                 from sequencing_bias.cpp:8:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^˜˜˜˜˜˜˜
In file included from ./yaml-cpp/node.h:12:0,
                 from yaml-cpp/yaml.h:10,
                 from kmer_matrix.hpp:13,
                 from motif.hpp:13,
                 from sequencing_bias.hpp:13,
                 from sequencing_bias.cpp:8:
./yaml-cpp/iterator.h:36:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   std::auto_ptr<IterPriv> m_pData;
        ^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
                 from ./yaml-cpp/parser.h:12,
                 from yaml-cpp/yaml.h:9,
                 from kmer_matrix.hpp:13,
                 from motif.hpp:13,
                 from sequencing_bias.hpp:13,
                 from sequencing_bias.cpp:8:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^˜˜˜˜˜˜˜
In file included from yaml-cpp/yaml.h:10:0,
                 from kmer_matrix.hpp:13,
                 from motif.hpp:13,
                 from sequencing_bias.hpp:13,
                 from sequencing_bias.cpp:8:
./yaml-cpp/node.h:43:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   std::auto_ptr<Node> Clone() const;
        ^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
                 from ./yaml-cpp/parser.h:12,
                 from yaml-cpp/yaml.h:9,
                 from kmer_matrix.hpp:13,
                 from motif.hpp:13,
                 from sequencing_bias.hpp:13,
                 from sequencing_bias.cpp:8:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^˜˜˜˜˜˜˜
In file included from yaml-cpp/yaml.h:10:0,
                 from kmer_matrix.hpp:13,
                 from motif.hpp:13,
                 from sequencing_bias.hpp:13,
                 from sequencing_bias.cpp:8:
./yaml-cpp/node.h:115:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   std::auto_ptr<NodeOwnership> m_pOwnership;
        ^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
                 from ./yaml-cpp/parser.h:12,
                 from yaml-cpp/yaml.h:9,
                 from kmer_matrix.hpp:13,
                 from motif.hpp:13,
                 from sequencing_bias.hpp:13,
                 from sequencing_bias.cpp:8:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^˜˜˜˜˜˜˜
In file included from yaml-cpp/yaml.h:13:0,
                 from kmer_matrix.hpp:13,
                 from motif.hpp:13,
                 from sequencing_bias.hpp:13,
                 from sequencing_bias.cpp:8:
./yaml-cpp/emitter.h:98:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   std::auto_ptr <EmitterState> m_pState;
        ^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
                 from ./yaml-cpp/parser.h:12,
                 from yaml-cpp/yaml.h:9,
                 from kmer_matrix.hpp:13,
                 from motif.hpp:13,
                 from sequencing_bias.hpp:13,
                 from sequencing_bias.cpp:8:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^˜˜˜˜˜˜˜
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/home/biocbuild/bbs-3.9-bioc/R/bin/R" --vanilla --slave` -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I/usr/local/include -Wall -Wextra -I. -fpic  -g -O2  -Wall -c twobitseq.cpp -o twobitseq.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/home/biocbuild/bbs-3.9-bioc/R/bin/R" --vanilla --slave` -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I/usr/local/include -Wall -Wextra -I. -fpic  -g -O2  -Wall -c yaml-cpp/aliasmanager.cpp -o yaml-cpp/aliasmanager.o
In file included from ./yaml-cpp/node.h:12:0,
                 from yaml-cpp/aliasmanager.cpp:2:
./yaml-cpp/iterator.h:20:17: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   Iterator(std::auto_ptr<IterPriv> pData);
                 ^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
                 from ./yaml-cpp/iterator.h:9,
                 from ./yaml-cpp/node.h:12,
                 from yaml-cpp/aliasmanager.cpp:2:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^˜˜˜˜˜˜˜
In file included from ./yaml-cpp/node.h:12:0,
                 from yaml-cpp/aliasmanager.cpp:2:
./yaml-cpp/iterator.h:36:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   std::auto_ptr<IterPriv> m_pData;
        ^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
                 from ./yaml-cpp/iterator.h:9,
                 from ./yaml-cpp/node.h:12,
                 from yaml-cpp/aliasmanager.cpp:2:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^˜˜˜˜˜˜˜
In file included from yaml-cpp/aliasmanager.cpp:2:0:
./yaml-cpp/node.h:43:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   std::auto_ptr<Node> Clone() const;
        ^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
                 from ./yaml-cpp/iterator.h:9,
                 from ./yaml-cpp/node.h:12,
                 from yaml-cpp/aliasmanager.cpp:2:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^˜˜˜˜˜˜˜
In file included from yaml-cpp/aliasmanager.cpp:2:0:
./yaml-cpp/node.h:115:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   std::auto_ptr<NodeOwnership> m_pOwnership;
        ^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
                 from ./yaml-cpp/iterator.h:9,
                 from ./yaml-cpp/node.h:12,
                 from yaml-cpp/aliasmanager.cpp:2:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^˜˜˜˜˜˜˜
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/home/biocbuild/bbs-3.9-bioc/R/bin/R" --vanilla --slave` -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I/usr/local/include -Wall -Wextra -I. -fpic  -g -O2  -Wall -c yaml-cpp/conversion.cpp -o yaml-cpp/conversion.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/home/biocbuild/bbs-3.9-bioc/R/bin/R" --vanilla --slave` -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I/usr/local/include -Wall -Wextra -I. -fpic  -g -O2  -Wall -c yaml-cpp/directives.cpp -o yaml-cpp/directives.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/home/biocbuild/bbs-3.9-bioc/R/bin/R" --vanilla --slave` -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I/usr/local/include -Wall -Wextra -I. -fpic  -g -O2  -Wall -c yaml-cpp/emitfromevents.cpp -o yaml-cpp/emitfromevents.o
In file included from yaml-cpp/emitfromevents.cpp:2:0:
./yaml-cpp/emitter.h:98:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   std::auto_ptr <EmitterState> m_pState;
        ^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
                 from ./yaml-cpp/emitter.h:14,
                 from yaml-cpp/emitfromevents.cpp:2:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^˜˜˜˜˜˜˜
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/home/biocbuild/bbs-3.9-bioc/R/bin/R" --vanilla --slave` -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I/usr/local/include -Wall -Wextra -I. -fpic  -g -O2  -Wall -c yaml-cpp/emitter.cpp -o yaml-cpp/emitter.o
In file included from yaml-cpp/emitter.cpp:1:0:
./yaml-cpp/emitter.h:98:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   std::auto_ptr <EmitterState> m_pState;
        ^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
                 from ./yaml-cpp/emitter.h:14,
                 from yaml-cpp/emitter.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^˜˜˜˜˜˜˜
In file included from yaml-cpp/emitterstate.h:9:0,
                 from yaml-cpp/emitter.cpp:2:
yaml-cpp/ptr_stack.h:29:17: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  void push(std::auto_ptr<T> t) {
                 ^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
                 from ./yaml-cpp/emitter.h:14,
                 from yaml-cpp/emitter.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^˜˜˜˜˜˜˜
In file included from yaml-cpp/emitterstate.h:9:0,
                 from yaml-cpp/emitter.cpp:2:
yaml-cpp/ptr_stack.h:33:7: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  std::auto_ptr<T> pop() {
       ^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
                 from ./yaml-cpp/emitter.h:14,
                 from yaml-cpp/emitter.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^˜˜˜˜˜˜˜
In file included from yaml-cpp/emitterstate.h:9:0,
                 from yaml-cpp/emitter.cpp:2:
yaml-cpp/ptr_stack.h: In member function ‘std::auto_ptr<_Up> ptr_stack<T>::pop()’:
yaml-cpp/ptr_stack.h:34:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   std::auto_ptr<T> t(m_data.back());
        ^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
                 from ./yaml-cpp/emitter.h:14,
                 from yaml-cpp/emitter.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^˜˜˜˜˜˜˜
In file included from yaml-cpp/emitterstate.h:10:0,
                 from yaml-cpp/emitter.cpp:2:
yaml-cpp/setting.h: At global scope:
yaml-cpp/setting.h:24:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   std::auto_ptr <SettingChangeBase> set(const T& value);
        ^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
                 from ./yaml-cpp/emitter.h:14,
                 from yaml-cpp/emitter.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^˜˜˜˜˜˜˜
In file included from yaml-cpp/emitterstate.h:10:0,
                 from yaml-cpp/emitter.cpp:2:
yaml-cpp/setting.h:59:14: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  inline std::auto_ptr <SettingChangeBase> Setting<T>::set(const T& value) {
              ^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
                 from ./yaml-cpp/emitter.h:14,
                 from yaml-cpp/emitter.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^˜˜˜˜˜˜˜
In file included from yaml-cpp/emitterstate.h:10:0,
                 from yaml-cpp/emitter.cpp:2:
yaml-cpp/setting.h: In member function ‘std::auto_ptr<YAML::SettingChangeBase> YAML::Setting<T>::set(const T&)’:
yaml-cpp/setting.h:60:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   std::auto_ptr <SettingChangeBase> pChange(new SettingChange<T> (this));
        ^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
                 from ./yaml-cpp/emitter.h:14,
                 from yaml-cpp/emitter.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^˜˜˜˜˜˜˜
In file included from yaml-cpp/emitterstate.h:10:0,
                 from yaml-cpp/emitter.cpp:2:
yaml-cpp/setting.h: At global scope:
yaml-cpp/setting.h:84:18: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   void push(std::auto_ptr <SettingChangeBase> pSettingChange) {
                  ^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
                 from ./yaml-cpp/emitter.h:14,
                 from yaml-cpp/emitter.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^˜˜˜˜˜˜˜
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/home/biocbuild/bbs-3.9-bioc/R/bin/R" --vanilla --slave` -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I/usr/local/include -Wall -Wextra -I. -fpic  -g -O2  -Wall -c yaml-cpp/emitterstate.cpp -o yaml-cpp/emitterstate.o
In file included from yaml-cpp/emitterstate.h:9:0,
                 from yaml-cpp/emitterstate.cpp:1:
yaml-cpp/ptr_stack.h:29:17: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  void push(std::auto_ptr<T> t) {
                 ^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
                 from yaml-cpp/ptr_stack.h:9,
                 from yaml-cpp/emitterstate.h:9,
                 from yaml-cpp/emitterstate.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^˜˜˜˜˜˜˜
In file included from yaml-cpp/emitterstate.h:9:0,
                 from yaml-cpp/emitterstate.cpp:1:
yaml-cpp/ptr_stack.h:33:7: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  std::auto_ptr<T> pop() {
       ^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
                 from yaml-cpp/ptr_stack.h:9,
                 from yaml-cpp/emitterstate.h:9,
                 from yaml-cpp/emitterstate.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^˜˜˜˜˜˜˜
In file included from yaml-cpp/emitterstate.h:9:0,
                 from yaml-cpp/emitterstate.cpp:1:
yaml-cpp/ptr_stack.h: In member function ‘std::auto_ptr<T> ptr_stack<T>::pop()’:
yaml-cpp/ptr_stack.h:34:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   std::auto_ptr<T> t(m_data.back());
        ^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
                 from yaml-cpp/ptr_stack.h:9,
                 from yaml-cpp/emitterstate.h:9,
                 from yaml-cpp/emitterstate.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^˜˜˜˜˜˜˜
In file included from yaml-cpp/emitterstate.h:10:0,
                 from yaml-cpp/emitterstate.cpp:1:
yaml-cpp/setting.h: At global scope:
yaml-cpp/setting.h:24:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   std::auto_ptr <SettingChangeBase> set(const T& value);
        ^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
                 from yaml-cpp/ptr_stack.h:9,
                 from yaml-cpp/emitterstate.h:9,
                 from yaml-cpp/emitterstate.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^˜˜˜˜˜˜˜
In file included from yaml-cpp/emitterstate.h:10:0,
                 from yaml-cpp/emitterstate.cpp:1:
yaml-cpp/setting.h:59:14: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  inline std::auto_ptr <SettingChangeBase> Setting<T>::set(const T& value) {
              ^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
                 from yaml-cpp/ptr_stack.h:9,
                 from yaml-cpp/emitterstate.h:9,
                 from yaml-cpp/emitterstate.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^˜˜˜˜˜˜˜
In file included from yaml-cpp/emitterstate.h:10:0,
                 from yaml-cpp/emitterstate.cpp:1:
yaml-cpp/setting.h: In member function ‘std::auto_ptr<YAML::SettingChangeBase> YAML::Setting<T>::set(const T&)’:
yaml-cpp/setting.h:60:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   std::auto_ptr <SettingChangeBase> pChange(new SettingChange<T> (this));
        ^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
                 from yaml-cpp/ptr_stack.h:9,
                 from yaml-cpp/emitterstate.h:9,
                 from yaml-cpp/emitterstate.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^˜˜˜˜˜˜˜
In file included from yaml-cpp/emitterstate.h:10:0,
                 from yaml-cpp/emitterstate.cpp:1:
yaml-cpp/setting.h: At global scope:
yaml-cpp/setting.h:84:18: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   void push(std::auto_ptr <SettingChangeBase> pSettingChange) {
                  ^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
                 from yaml-cpp/ptr_stack.h:9,
                 from yaml-cpp/emitterstate.h:9,
                 from yaml-cpp/emitterstate.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^˜˜˜˜˜˜˜
yaml-cpp/emitterstate.cpp: In member function ‘void YAML::EmitterState::BeginGroup(YAML::GROUP_TYPE)’:
yaml-cpp/emitterstate.cpp:51:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   std::auto_ptr<Group> pGroup(new Group(type));
        ^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
                 from yaml-cpp/ptr_stack.h:9,
                 from yaml-cpp/emitterstate.h:9,
                 from yaml-cpp/emitterstate.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^˜˜˜˜˜˜˜
yaml-cpp/emitterstate.cpp: In member function ‘void YAML::EmitterState::EndGroup(YAML::GROUP_TYPE)’:
yaml-cpp/emitterstate.cpp:71:9: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
    std::auto_ptr<Group> pFinishedGroup = m_groups.pop();
         ^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
                 from yaml-cpp/ptr_stack.h:9,
                 from yaml-cpp/emitterstate.h:9,
                 from yaml-cpp/emitterstate.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^˜˜˜˜˜˜˜
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/home/biocbuild/bbs-3.9-bioc/R/bin/R" --vanilla --slave` -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I/usr/local/include -Wall -Wextra -I. -fpic  -g -O2  -Wall -c yaml-cpp/emitterutils.cpp -o yaml-cpp/emitterutils.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/home/biocbuild/bbs-3.9-bioc/R/bin/R" --vanilla --slave` -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I/usr/local/include -Wall -Wextra -I. -fpic  -g -O2  -Wall -c yaml-cpp/exp.cpp -o yaml-cpp/exp.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/home/biocbuild/bbs-3.9-bioc/R/bin/R" --vanilla --slave` -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I/usr/local/include -Wall -Wextra -I. -fpic  -g -O2  -Wall -c yaml-cpp/iterator.cpp -o yaml-cpp/iterator.o
In file included from ./yaml-cpp/node.h:12:0,
                 from yaml-cpp/iterator.cpp:1:
./yaml-cpp/iterator.h:20:17: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   Iterator(std::auto_ptr<IterPriv> pData);
                 ^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
                 from ./yaml-cpp/iterator.h:9,
                 from ./yaml-cpp/node.h:12,
                 from yaml-cpp/iterator.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^˜˜˜˜˜˜˜
In file included from ./yaml-cpp/node.h:12:0,
                 from yaml-cpp/iterator.cpp:1:
./yaml-cpp/iterator.h:36:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   std::auto_ptr<IterPriv> m_pData;
        ^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
                 from ./yaml-cpp/iterator.h:9,
                 from ./yaml-cpp/node.h:12,
                 from yaml-cpp/iterator.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^˜˜˜˜˜˜˜
In file included from yaml-cpp/iterator.cpp:1:0:
./yaml-cpp/node.h:43:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   std::auto_ptr<Node> Clone() const;
        ^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
                 from ./yaml-cpp/iterator.h:9,
                 from ./yaml-cpp/node.h:12,
                 from yaml-cpp/iterator.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^˜˜˜˜˜˜˜
In file included from yaml-cpp/iterator.cpp:1:0:
./yaml-cpp/node.h:115:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   std::auto_ptr<NodeOwnership> m_pOwnership;
        ^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
                 from ./yaml-cpp/iterator.h:9,
                 from ./yaml-cpp/node.h:12,
                 from yaml-cpp/iterator.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^˜˜˜˜˜˜˜
yaml-cpp/iterator.cpp:11:26: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  Iterator::Iterator(std::auto_ptr<IterPriv> pData): m_pData(pData)
                          ^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
                 from ./yaml-cpp/iterator.h:9,
                 from ./yaml-cpp/node.h:12,
                 from yaml-cpp/iterator.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^˜˜˜˜˜˜˜
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/home/biocbuild/bbs-3.9-bioc/R/bin/R" --vanilla --slave` -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I/usr/local/include -Wall -Wextra -I. -fpic  -g -O2  -Wall -c yaml-cpp/nodebuilder.cpp -o yaml-cpp/nodebuilder.o
In file included from ./yaml-cpp/node.h:12:0,
                 from yaml-cpp/nodebuilder.cpp:3:
./yaml-cpp/iterator.h:20:17: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   Iterator(std::auto_ptr<IterPriv> pData);
                 ^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
                 from yaml-cpp/nodebuilder.h:10,
                 from yaml-cpp/nodebuilder.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^˜˜˜˜˜˜˜
In file included from ./yaml-cpp/node.h:12:0,
                 from yaml-cpp/nodebuilder.cpp:3:
./yaml-cpp/iterator.h:36:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   std::auto_ptr<IterPriv> m_pData;
        ^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
                 from yaml-cpp/nodebuilder.h:10,
                 from yaml-cpp/nodebuilder.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^˜˜˜˜˜˜˜
In file included from yaml-cpp/nodebuilder.cpp:3:0:
./yaml-cpp/node.h:43:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   std::auto_ptr<Node> Clone() const;
        ^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
                 from yaml-cpp/nodebuilder.h:10,
                 from yaml-cpp/nodebuilder.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^˜˜˜˜˜˜˜
In file included from yaml-cpp/nodebuilder.cpp:3:0:
./yaml-cpp/node.h:115:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   std::auto_ptr<NodeOwnership> m_pOwnership;
        ^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
                 from yaml-cpp/nodebuilder.h:10,
                 from yaml-cpp/nodebuilder.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^˜˜˜˜˜˜˜
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/home/biocbuild/bbs-3.9-bioc/R/bin/R" --vanilla --slave` -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I/usr/local/include -Wall -Wextra -I. -fpic  -g -O2  -Wall -c yaml-cpp/node.cpp -o yaml-cpp/node.o
In file included from ./yaml-cpp/node.h:12:0,
                 from yaml-cpp/node.cpp:1:
./yaml-cpp/iterator.h:20:17: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   Iterator(std::auto_ptr<IterPriv> pData);
                 ^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
                 from ./yaml-cpp/iterator.h:9,
                 from ./yaml-cpp/node.h:12,
                 from yaml-cpp/node.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^˜˜˜˜˜˜˜
In file included from ./yaml-cpp/node.h:12:0,
                 from yaml-cpp/node.cpp:1:
./yaml-cpp/iterator.h:36:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   std::auto_ptr<IterPriv> m_pData;
        ^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
                 from ./yaml-cpp/iterator.h:9,
                 from ./yaml-cpp/node.h:12,
                 from yaml-cpp/node.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^˜˜˜˜˜˜˜
In file included from yaml-cpp/node.cpp:1:0:
./yaml-cpp/node.h:43:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   std::auto_ptr<Node> Clone() const;
        ^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
                 from ./yaml-cpp/iterator.h:9,
                 from ./yaml-cpp/node.h:12,
                 from yaml-cpp/node.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^˜˜˜˜˜˜˜
In file included from yaml-cpp/node.cpp:1:0:
./yaml-cpp/node.h:115:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   std::auto_ptr<NodeOwnership> m_pOwnership;
        ^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
                 from ./yaml-cpp/iterator.h:9,
                 from ./yaml-cpp/node.h:12,
                 from yaml-cpp/node.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^˜˜˜˜˜˜˜
In file included from yaml-cpp/nodeownership.h:10:0,
                 from yaml-cpp/node.cpp:4:
yaml-cpp/ptr_vector.h:31:23: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   void push_back(std::auto_ptr<T> t) {
                       ^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
                 from ./yaml-cpp/iterator.h:9,
                 from ./yaml-cpp/node.h:12,
                 from yaml-cpp/node.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^˜˜˜˜˜˜˜
In file included from yaml-cpp/node.cpp:10:0:
./yaml-cpp/emitter.h:98:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   std::auto_ptr <EmitterState> m_pState;
        ^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
                 from ./yaml-cpp/iterator.h:9,
                 from ./yaml-cpp/node.h:12,
                 from yaml-cpp/node.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^˜˜˜˜˜˜˜
yaml-cpp/node.cpp:54:7: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  std::auto_ptr<Node> Node::Clone() const
       ^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
                 from ./yaml-cpp/iterator.h:9,
                 from ./yaml-cpp/node.h:12,
                 from yaml-cpp/node.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^˜˜˜˜˜˜˜
yaml-cpp/node.cpp: In member function ‘std::auto_ptr<YAML::Node> YAML::Node::Clone() const’:
yaml-cpp/node.cpp:56:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   std::auto_ptr<Node> pNode(new Node);
        ^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
                 from ./yaml-cpp/iterator.h:9,
                 from ./yaml-cpp/node.h:12,
                 from yaml-cpp/node.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^˜˜˜˜˜˜˜
yaml-cpp/node.cpp: In member function ‘YAML::Iterator YAML::Node::begin() const’:
yaml-cpp/node.cpp:148:26: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     return Iterator(std::auto_ptr<IterPriv>(new IterPriv(m_seqData.begin())));
                          ^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
                 from ./yaml-cpp/iterator.h:9,
                 from ./yaml-cpp/node.h:12,
                 from yaml-cpp/node.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^˜˜˜˜˜˜˜
yaml-cpp/node.cpp:150:26: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     return Iterator(std::auto_ptr<IterPriv>(new IterPriv(m_mapData.begin())));
                          ^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
                 from ./yaml-cpp/iterator.h:9,
                 from ./yaml-cpp/node.h:12,
                 from yaml-cpp/node.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^˜˜˜˜˜˜˜
yaml-cpp/node.cpp: In member function ‘YAML::Iterator YAML::Node::end() const’:
yaml-cpp/node.cpp:166:26: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     return Iterator(std::auto_ptr<IterPriv>(new IterPriv(m_seqData.end())));
                          ^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
                 from ./yaml-cpp/iterator.h:9,
                 from ./yaml-cpp/node.h:12,
                 from yaml-cpp/node.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^˜˜˜˜˜˜˜
yaml-cpp/node.cpp:168:26: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     return Iterator(std::auto_ptr<IterPriv>(new IterPriv(m_mapData.end())));
                          ^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
                 from ./yaml-cpp/iterator.h:9,
                 from ./yaml-cpp/node.h:12,
                 from yaml-cpp/node.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^˜˜˜˜˜˜˜
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/home/biocbuild/bbs-3.9-bioc/R/bin/R" --vanilla --slave` -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I/usr/local/include -Wall -Wextra -I. -fpic  -g -O2  -Wall -c yaml-cpp/nodeownership.cpp -o yaml-cpp/nodeownership.o
In file included from yaml-cpp/nodeownership.h:10:0,
                 from yaml-cpp/nodeownership.cpp:1:
yaml-cpp/ptr_vector.h:31:23: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   void push_back(std::auto_ptr<T> t) {
                       ^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
                 from yaml-cpp/ptr_vector.h:9,
                 from yaml-cpp/nodeownership.h:10,
                 from yaml-cpp/nodeownership.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^˜˜˜˜˜˜˜
In file included from ./yaml-cpp/node.h:12:0,
                 from yaml-cpp/nodeownership.cpp:2:
./yaml-cpp/iterator.h:20:17: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   Iterator(std::auto_ptr<IterPriv> pData);
                 ^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
                 from yaml-cpp/ptr_vector.h:9,
                 from yaml-cpp/nodeownership.h:10,
                 from yaml-cpp/nodeownership.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^˜˜˜˜˜˜˜
In file included from ./yaml-cpp/node.h:12:0,
                 from yaml-cpp/nodeownership.cpp:2:
./yaml-cpp/iterator.h:36:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   std::auto_ptr<IterPriv> m_pData;
        ^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
                 from yaml-cpp/ptr_vector.h:9,
                 from yaml-cpp/nodeownership.h:10,
                 from yaml-cpp/nodeownership.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^˜˜˜˜˜˜˜
In file included from yaml-cpp/nodeownership.cpp:2:0:
./yaml-cpp/node.h:43:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   std::auto_ptr<Node> Clone() const;
        ^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
                 from yaml-cpp/ptr_vector.h:9,
                 from yaml-cpp/nodeownership.h:10,
                 from yaml-cpp/nodeownership.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^˜˜˜˜˜˜˜
In file included from yaml-cpp/nodeownership.cpp:2:0:
./yaml-cpp/node.h:115:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   std::auto_ptr<NodeOwnership> m_pOwnership;
        ^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
                 from yaml-cpp/ptr_vector.h:9,
                 from yaml-cpp/nodeownership.h:10,
                 from yaml-cpp/nodeownership.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^˜˜˜˜˜˜˜
yaml-cpp/nodeownership.cpp: In member function ‘YAML::Node& YAML::NodeOwnership::_Create()’:
yaml-cpp/nodeownership.cpp:18:26: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   m_nodes.push_back(std::auto_ptr<Node>(new Node));
                          ^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
                 from yaml-cpp/ptr_vector.h:9,
                 from yaml-cpp/nodeownership.h:10,
                 from yaml-cpp/nodeownership.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^˜˜˜˜˜˜˜
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/home/biocbuild/bbs-3.9-bioc/R/bin/R" --vanilla --slave` -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I/usr/local/include -Wall -Wextra -I. -fpic  -g -O2  -Wall -c yaml-cpp/null.cpp -o yaml-cpp/null.o
In file included from ./yaml-cpp/node.h:12:0,
                 from yaml-cpp/null.cpp:2:
./yaml-cpp/iterator.h:20:17: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   Iterator(std::auto_ptr<IterPriv> pData);
                 ^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
                 from ./yaml-cpp/iterator.h:9,
                 from ./yaml-cpp/node.h:12,
                 from yaml-cpp/null.cpp:2:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^˜˜˜˜˜˜˜
In file included from ./yaml-cpp/node.h:12:0,
                 from yaml-cpp/null.cpp:2:
./yaml-cpp/iterator.h:36:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   std::auto_ptr<IterPriv> m_pData;
        ^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
                 from ./yaml-cpp/iterator.h:9,
                 from ./yaml-cpp/node.h:12,
                 from yaml-cpp/null.cpp:2:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^˜˜˜˜˜˜˜
In file included from yaml-cpp/null.cpp:2:0:
./yaml-cpp/node.h:43:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   std::auto_ptr<Node> Clone() const;
        ^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
                 from ./yaml-cpp/iterator.h:9,
                 from ./yaml-cpp/node.h:12,
                 from yaml-cpp/null.cpp:2:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^˜˜˜˜˜˜˜
In file included from yaml-cpp/null.cpp:2:0:
./yaml-cpp/node.h:115:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   std::auto_ptr<NodeOwnership> m_pOwnership;
        ^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
                 from ./yaml-cpp/iterator.h:9,
                 from ./yaml-cpp/node.h:12,
                 from yaml-cpp/null.cpp:2:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^˜˜˜˜˜˜˜
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/home/biocbuild/bbs-3.9-bioc/R/bin/R" --vanilla --slave` -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I/usr/local/include -Wall -Wextra -I. -fpic  -g -O2  -Wall -c yaml-cpp/ostream.cpp -o yaml-cpp/ostream.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/home/biocbuild/bbs-3.9-bioc/R/bin/R" --vanilla --slave` -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I/usr/local/include -Wall -Wextra -I. -fpic  -g -O2  -Wall -c yaml-cpp/parser.cpp -o yaml-cpp/parser.o
In file included from yaml-cpp/parser.cpp:1:0:
./yaml-cpp/parser.h:45:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   std::auto_ptr<Scanner> m_pScanner;
        ^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
                 from ./yaml-cpp/parser.h:12,
                 from yaml-cpp/parser.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^˜˜˜˜˜˜˜
In file included from yaml-cpp/parser.cpp:1:0:
./yaml-cpp/parser.h:46:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   std::auto_ptr<Directives> m_pDirectives;
        ^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
                 from ./yaml-cpp/parser.h:12,
                 from yaml-cpp/parser.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^˜˜˜˜˜˜˜
In file included from ./yaml-cpp/node.h:12:0,
                 from yaml-cpp/parser.cpp:5:
./yaml-cpp/iterator.h:20:17: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   Iterator(std::auto_ptr<IterPriv> pData);
                 ^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
                 from ./yaml-cpp/parser.h:12,
                 from yaml-cpp/parser.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^˜˜˜˜˜˜˜
In file included from ./yaml-cpp/node.h:12:0,
                 from yaml-cpp/parser.cpp:5:
./yaml-cpp/iterator.h:36:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   std::auto_ptr<IterPriv> m_pData;
        ^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
                 from ./yaml-cpp/parser.h:12,
                 from yaml-cpp/parser.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^˜˜˜˜˜˜˜
In file included from yaml-cpp/parser.cpp:5:0:
./yaml-cpp/node.h:43:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   std::auto_ptr<Node> Clone() const;
        ^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
                 from ./yaml-cpp/parser.h:12,
                 from yaml-cpp/parser.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^˜˜˜˜˜˜˜
In file included from yaml-cpp/parser.cpp:5:0:
./yaml-cpp/node.h:115:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   std::auto_ptr<NodeOwnership> m_pOwnership;
        ^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
                 from ./yaml-cpp/parser.h:12,
                 from yaml-cpp/parser.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^˜˜˜˜˜˜˜
In file included from yaml-cpp/scanner.h:15:0,
                 from yaml-cpp/parser.cpp:7:
yaml-cpp/ptr_vector.h:31:23: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   void push_back(std::auto_ptr<T> t) {
                       ^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
                 from ./yaml-cpp/parser.h:12,
                 from yaml-cpp/parser.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^˜˜˜˜˜˜˜
In file included from yaml-cpp/parser.cpp:8:0:
yaml-cpp/singledocparser.h:56:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   std::auto_ptr<CollectionStack> m_pCollectionStack;
        ^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
                 from ./yaml-cpp/parser.h:12,
                 from yaml-cpp/parser.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^˜˜˜˜˜˜˜
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/home/biocbuild/bbs-3.9-bioc/R/bin/R" --vanilla --slave` -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I/usr/local/include -Wall -Wextra -I. -fpic  -g -O2  -Wall -c yaml-cpp/regex.cpp -o yaml-cpp/regex.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/home/biocbuild/bbs-3.9-bioc/R/bin/R" --vanilla --slave` -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I/usr/local/include -Wall -Wextra -I. -fpic  -g -O2  -Wall -c yaml-cpp/scanner.cpp -o yaml-cpp/scanner.o
In file included from yaml-cpp/scanner.h:15:0,
                 from yaml-cpp/scanner.cpp:1:
yaml-cpp/ptr_vector.h:31:23: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   void push_back(std::auto_ptr<T> t) {
                       ^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
                 from yaml-cpp/ptr_vector.h:9,
                 from yaml-cpp/scanner.h:15,
                 from yaml-cpp/scanner.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^˜˜˜˜˜˜˜
yaml-cpp/scanner.cpp: In member function ‘void YAML::Scanner::StartStream()’:
yaml-cpp/scanner.cpp:237:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   std::auto_ptr<IndentMarker> pIndent(new IndentMarker(-1, IndentMarker::NONE));
        ^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
                 from yaml-cpp/ptr_vector.h:9,
                 from yaml-cpp/scanner.h:15,
                 from yaml-cpp/scanner.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^˜˜˜˜˜˜˜
yaml-cpp/scanner.cpp: In member function ‘YAML::Scanner::IndentMarker* YAML::Scanner::PushIndentTo(int, YAML::Scanner::IndentMarker::INDENT_TYPE)’:
yaml-cpp/scanner.cpp:284:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   std::auto_ptr<IndentMarker> pIndent(new IndentMarker(column, type));
        ^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
                 from yaml-cpp/ptr_vector.h:9,
                 from yaml-cpp/scanner.h:15,
                 from yaml-cpp/scanner.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^˜˜˜˜˜˜˜
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/home/biocbuild/bbs-3.9-bioc/R/bin/R" --vanilla --slave` -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I/usr/local/include -Wall -Wextra -I. -fpic  -g -O2  -Wall -c yaml-cpp/scanscalar.cpp -o yaml-cpp/scanscalar.o
In file included from yaml-cpp/scanner.h:15:0,
                 from yaml-cpp/scanscalar.cpp:2:
yaml-cpp/ptr_vector.h:31:23: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   void push_back(std::auto_ptr<T> t) {
                       ^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
                 from yaml-cpp/ptr_vector.h:9,
                 from yaml-cpp/scanner.h:15,
                 from yaml-cpp/scanscalar.cpp:2:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^˜˜˜˜˜˜˜
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/home/biocbuild/bbs-3.9-bioc/R/bin/R" --vanilla --slave` -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I/usr/local/include -Wall -Wextra -I. -fpic  -g -O2  -Wall -c yaml-cpp/scantag.cpp -o yaml-cpp/scantag.o
In file included from yaml-cpp/scanner.h:15:0,
                 from yaml-cpp/scantag.cpp:1:
yaml-cpp/ptr_vector.h:31:23: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   void push_back(std::auto_ptr<T> t) {
                       ^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
                 from yaml-cpp/ptr_vector.h:9,
                 from yaml-cpp/scanner.h:15,
                 from yaml-cpp/scantag.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^˜˜˜˜˜˜˜
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/home/biocbuild/bbs-3.9-bioc/R/bin/R" --vanilla --slave` -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I/usr/local/include -Wall -Wextra -I. -fpic  -g -O2  -Wall -c yaml-cpp/scantoken.cpp -o yaml-cpp/scantoken.o
In file included from yaml-cpp/scanner.h:15:0,
                 from yaml-cpp/scantoken.cpp:1:
yaml-cpp/ptr_vector.h:31:23: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   void push_back(std::auto_ptr<T> t) {
                       ^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
                 from yaml-cpp/ptr_vector.h:9,
                 from yaml-cpp/scanner.h:15,
                 from yaml-cpp/scantoken.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^˜˜˜˜˜˜˜
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/home/biocbuild/bbs-3.9-bioc/R/bin/R" --vanilla --slave` -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I/usr/local/include -Wall -Wextra -I. -fpic  -g -O2  -Wall -c yaml-cpp/simplekey.cpp -o yaml-cpp/simplekey.o
In file included from yaml-cpp/scanner.h:15:0,
                 from yaml-cpp/simplekey.cpp:1:
yaml-cpp/ptr_vector.h:31:23: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   void push_back(std::auto_ptr<T> t) {
                       ^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
                 from yaml-cpp/ptr_vector.h:9,
                 from yaml-cpp/scanner.h:15,
                 from yaml-cpp/simplekey.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^˜˜˜˜˜˜˜
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/home/biocbuild/bbs-3.9-bioc/R/bin/R" --vanilla --slave` -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I/usr/local/include -Wall -Wextra -I. -fpic  -g -O2  -Wall -c yaml-cpp/singledocparser.cpp -o yaml-cpp/singledocparser.o
In file included from yaml-cpp/singledocparser.cpp:1:0:
yaml-cpp/singledocparser.h:56:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   std::auto_ptr<CollectionStack> m_pCollectionStack;
        ^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
                 from yaml-cpp/singledocparser.h:13,
                 from yaml-cpp/singledocparser.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^˜˜˜˜˜˜˜
In file included from yaml-cpp/singledocparser.cpp:2:0:
yaml-cpp/collectionstack.h: In member function ‘void YAML::CollectionStack::PopCollectionType(YAML::CollectionType::value)’:
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/scanner.h:15:0,
                 from yaml-cpp/singledocparser.cpp:6:
yaml-cpp/ptr_vector.h: At global scope:
yaml-cpp/ptr_vector.h:31:23: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   void push_back(std::auto_ptr<T> t) {
                       ^˜˜˜˜˜˜˜
In file included from /usr/include/c++/7/memory:80:0,
                 from yaml-cpp/singledocparser.h:13,
                 from yaml-cpp/singledocparser.cpp:1:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
   template<typename> class auto_ptr;
                            ^˜˜˜˜˜˜˜
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/home/biocbuild/bbs-3.9-bioc/R/bin/R" --vanilla --slave` -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I/usr/local/include -Wall -Wextra -I. -fpic  -g -O2  -Wall -c yaml-cpp/stream.cpp -o yaml-cpp/stream.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG `echo 'Rhtslib::pkgconfig("PKG_CPPFLAGS")'| "/home/biocbuild/bbs-3.9-bioc/R/bin/R" --vanilla --slave` -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I/usr/local/include -Wall -Wextra -I. -fpic  -g -O2  -Wall -c yaml-cpp/tag.cpp -o yaml-cpp/tag.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.9-bioc/R/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 -L/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/usrlib -Wl,-rpath,/home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/usrlib -lhts -lz -lm -lbz2 -llzma -lpthread -L/home/biocbuild/bbs-3.9-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.9-bioc/R/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)

Tests output


Example timings

seqbias.Rcheck/seqbias-Ex.timings

nameusersystemelapsed
count_reads0.0410.0120.155
kmer_freq0.5730.0080.588
random_intervals0.0760.0120.087
seqbias_fit2.2860.0202.306
seqbias_load2.7930.0282.874
seqbias_predict1.1310.0041.135
seqbias_save2.3970.0162.412