Package: seqbias

Version: 1.32.0

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_1.32.0.tar.gz

StartedAt: 2019-10-16 04:56:04 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 04:57:25 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 80.9 seconds

RetCode: 0

Status:  OK

CheckDir: seqbias.Rcheck

Warnings: 0

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###
### 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_1.32.0.tar.gz
###
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##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/seqbias.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.32.0’
* 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 ... OK
* checking installed package size ... NOTE
  installed size is 10.0Mb
  sub-directories of 1Mb or more:
    libs   9.3Mb
* 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 : : no visible global function definition for
  ‘seqnames’
count.reads : : no visible global function definition for
  ‘start’
count.reads : : no visible global function definition for
  ‘end’
count.reads : : no visible global function definition for
  ‘strand’
random.intervals: no visible global function definition for ‘is’
random.intervals : uniform_ints : : 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 : : no visible global function definition
  for ‘seqnames’
seqbias.predict : : no visible global function definition
  for ‘start’
seqbias.predict : : no visible global function definition
  for ‘end’
seqbias.predict : : 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 ‘__assert_fail’, possibly from ‘assert’ (C)
  Found ‘abort’, possibly from ‘abort’ (C)
  Found ‘exit’, possibly from ‘exit’ (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)
  Found ‘stderr’, possibly from ‘stderr’ (C)
  Found ‘stdout’, possibly from ‘stdout’ (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.

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##############################################################################
###
### 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   std::auto_ptr 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 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   std::auto_ptr 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 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   Iterator(std::auto_ptr 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 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   std::auto_ptr 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 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   std::auto_ptr 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 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   std::auto_ptr 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 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   std::auto_ptr  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 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   std::auto_ptr 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 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   std::auto_ptr 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 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   Iterator(std::auto_ptr 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 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   std::auto_ptr 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 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   std::auto_ptr 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 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   std::auto_ptr 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 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   std::auto_ptr  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 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   std::auto_ptr 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 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   std::auto_ptr 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 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   Iterator(std::auto_ptr 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 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   std::auto_ptr 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 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   std::auto_ptr 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 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   std::auto_ptr 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 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   std::auto_ptr  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 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   std::auto_ptr 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 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   std::auto_ptr 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 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   Iterator(std::auto_ptr 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 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   std::auto_ptr 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 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   std::auto_ptr 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 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   std::auto_ptr 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 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   std::auto_ptr  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 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   Iterator(std::auto_ptr 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 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   std::auto_ptr 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 class auto_ptr;
                            ^~~~~~~~
In file included from yaml-cpp/aliasmanager.cpp:2:0:
./yaml-cpp/node.h:43:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   std::auto_ptr 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 class auto_ptr;
                            ^~~~~~~~
In file included from yaml-cpp/aliasmanager.cpp:2:0:
./yaml-cpp/node.h:115:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   std::auto_ptr 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 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   std::auto_ptr  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 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   std::auto_ptr  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 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  void push(std::auto_ptr 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 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  std::auto_ptr 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 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::pop()’:
yaml-cpp/ptr_stack.h:34:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   std::auto_ptr 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 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   std::auto_ptr  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 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  inline std::auto_ptr  Setting::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 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::Setting::set(const T&)’:
yaml-cpp/setting.h:60:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   std::auto_ptr  pChange(new SettingChange (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 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   void push(std::auto_ptr  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 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  void push(std::auto_ptr 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 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  std::auto_ptr 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 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 ptr_stack::pop()’:
yaml-cpp/ptr_stack.h:34:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   std::auto_ptr 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 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   std::auto_ptr  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 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  inline std::auto_ptr  Setting::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 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::Setting::set(const T&)’:
yaml-cpp/setting.h:60:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   std::auto_ptr  pChange(new SettingChange (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 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   void push(std::auto_ptr  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 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   std::auto_ptr 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 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
    std::auto_ptr 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 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   Iterator(std::auto_ptr 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 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   std::auto_ptr 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 class auto_ptr;
                            ^~~~~~~~
In file included from yaml-cpp/iterator.cpp:1:0:
./yaml-cpp/node.h:43:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   std::auto_ptr 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 class auto_ptr;
                            ^~~~~~~~
In file included from yaml-cpp/iterator.cpp:1:0:
./yaml-cpp/node.h:115:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   std::auto_ptr 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 class auto_ptr;
                            ^~~~~~~~
yaml-cpp/iterator.cpp:11:26: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
  Iterator::Iterator(std::auto_ptr 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 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   Iterator(std::auto_ptr 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 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   std::auto_ptr 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 class auto_ptr;
                            ^~~~~~~~
In file included from yaml-cpp/nodebuilder.cpp:3:0:
./yaml-cpp/node.h:43:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   std::auto_ptr 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 class auto_ptr;
                            ^~~~~~~~
In file included from yaml-cpp/nodebuilder.cpp:3:0:
./yaml-cpp/node.h:115:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   std::auto_ptr 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 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   Iterator(std::auto_ptr 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 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   std::auto_ptr 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 class auto_ptr;
                            ^~~~~~~~
In file included from yaml-cpp/node.cpp:1:0:
./yaml-cpp/node.h:43:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   std::auto_ptr 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 class auto_ptr;
                            ^~~~~~~~
In file included from yaml-cpp/node.cpp:1:0:
./yaml-cpp/node.h:115:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   std::auto_ptr 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 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   void push_back(std::auto_ptr 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 class auto_ptr;
                            ^~~~~~~~
In file included from yaml-cpp/node.cpp:10:0:
./yaml-cpp/emitter.h:98:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   std::auto_ptr  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 class auto_ptr;
                            ^~~~~~~~
yaml-cpp/node.cpp:54:7: warning: ‘template 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 class auto_ptr;
                            ^~~~~~~~
yaml-cpp/node.cpp: In member function ‘std::auto_ptr YAML::Node::Clone() const’:
yaml-cpp/node.cpp:56:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   std::auto_ptr 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 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     return Iterator(std::auto_ptr(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 class auto_ptr;
                            ^~~~~~~~
yaml-cpp/node.cpp:150:26: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     return Iterator(std::auto_ptr(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 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     return Iterator(std::auto_ptr(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 class auto_ptr;
                            ^~~~~~~~
yaml-cpp/node.cpp:168:26: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     return Iterator(std::auto_ptr(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 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   void push_back(std::auto_ptr 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 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   Iterator(std::auto_ptr 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 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   std::auto_ptr 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 class auto_ptr;
                            ^~~~~~~~
In file included from yaml-cpp/nodeownership.cpp:2:0:
./yaml-cpp/node.h:43:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   std::auto_ptr 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 class auto_ptr;
                            ^~~~~~~~
In file included from yaml-cpp/nodeownership.cpp:2:0:
./yaml-cpp/node.h:115:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   std::auto_ptr 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 class auto_ptr;
                            ^~~~~~~~
yaml-cpp/nodeownership.cpp: In member function ‘YAML::Node& YAML::NodeOwnership::_Create()’:
yaml-cpp/nodeownership.cpp:18:26: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   m_nodes.push_back(std::auto_ptr(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 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   Iterator(std::auto_ptr 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 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   std::auto_ptr 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 class auto_ptr;
                            ^~~~~~~~
In file included from yaml-cpp/null.cpp:2:0:
./yaml-cpp/node.h:43:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   std::auto_ptr 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 class auto_ptr;
                            ^~~~~~~~
In file included from yaml-cpp/null.cpp:2:0:
./yaml-cpp/node.h:115:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   std::auto_ptr 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 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   std::auto_ptr 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 class auto_ptr;
                            ^~~~~~~~
In file included from yaml-cpp/parser.cpp:1:0:
./yaml-cpp/parser.h:46:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   std::auto_ptr 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 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   Iterator(std::auto_ptr 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 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   std::auto_ptr 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 class auto_ptr;
                            ^~~~~~~~
In file included from yaml-cpp/parser.cpp:5:0:
./yaml-cpp/node.h:43:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   std::auto_ptr 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 class auto_ptr;
                            ^~~~~~~~
In file included from yaml-cpp/parser.cpp:5:0:
./yaml-cpp/node.h:115:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   std::auto_ptr 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 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   void push_back(std::auto_ptr 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 class auto_ptr;
                            ^~~~~~~~
In file included from yaml-cpp/parser.cpp:8:0:
yaml-cpp/singledocparser.h:56:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   std::auto_ptr 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 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   void push_back(std::auto_ptr 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 class auto_ptr;
                            ^~~~~~~~
yaml-cpp/scanner.cpp: In member function ‘void YAML::Scanner::StartStream()’:
yaml-cpp/scanner.cpp:237:8: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   std::auto_ptr 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 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   std::auto_ptr 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 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   void push_back(std::auto_ptr 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 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   void push_back(std::auto_ptr 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 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   void push_back(std::auto_ptr 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 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   void push_back(std::auto_ptr 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 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   std::auto_ptr 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 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 std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   void push_back(std::auto_ptr 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 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 /home/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/usrlib/libhts.a -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)

name	user	system	elapsed
count_reads	0.055	0.000	0.217
kmer_freq	0.343	0.000	0.350
random_intervals	0.048	0.004	0.052
seqbias_fit	1.600	0.012	1.619
seqbias_load	2.365	0.007	2.381
seqbias_predict	1.696	0.016	1.712
seqbias_save	1.938	0.004	1.943