Back to Multiple platform build/check report for BioC 3.18:   simplified   long
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This page was generated on 2024-03-27 11:36:16 -0400 (Wed, 27 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4667
palomino4Windows Server 2022 Datacenterx644.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" 4403
merida1macOS 12.7.1 Montereyx86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4426
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 1922/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
seqbias 1.50.0  (landing page)
Daniel Jones
Snapshot Date: 2024-03-25 14:05:07 -0400 (Mon, 25 Mar 2024)
git_url: https://git.bioconductor.org/packages/seqbias
git_branch: RELEASE_3_18
git_last_commit: d82941c
git_last_commit_date: 2023-10-24 09:45:34 -0400 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 12.7.1 Monterey / x86_64  ERROR    ERROR  skippedskipped
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for seqbias on nebbiolo2


To the developers/maintainers of the seqbias package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/seqbias.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: seqbias
Version: 1.50.0
Command: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:seqbias.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings seqbias_1.50.0.tar.gz
StartedAt: 2024-03-26 02:25:54 -0400 (Tue, 26 Mar 2024)
EndedAt: 2024-03-26 02:27:02 -0400 (Tue, 26 Mar 2024)
EllapsedTime: 68.0 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: seqbias.Rcheck
Warnings: 2

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:seqbias.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings seqbias_1.50.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/seqbias.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘seqbias/DESCRIPTION’ ... OK
* this is package ‘seqbias’ version ‘1.50.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘seqbias’ can be installed ... WARNING
Found the following significant warnings:
  ./yaml-cpp/parser.h:45:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  ./yaml-cpp/parser.h:46:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  ./yaml-cpp/iterator.h:20:31: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  ./yaml-cpp/iterator.h:36:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  ./yaml-cpp/node.h:43:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  ./yaml-cpp/node.h:115:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  ./yaml-cpp/emitter.h:98:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  sequencing_bias.cpp:398:9: warning: ‘void free(void*)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
  sequencing_bias.cpp:628:9: warning: ‘void free(void*)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
  yaml-cpp/ptr_stack.h:29:24: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  yaml-cpp/ptr_stack.h:33:14: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  yaml-cpp/ptr_stack.h:34:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  yaml-cpp/setting.h:24:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  yaml-cpp/setting.h:59:21: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  yaml-cpp/setting.h:60:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  yaml-cpp/setting.h:84:32: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  yaml-cpp/emitterstate.cpp:51:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  yaml-cpp/emitterstate.cpp:71:30: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  yaml-cpp/iterator.cpp:11:33: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  yaml-cpp/ptr_vector.h:31:37: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  yaml-cpp/node.cpp:54:14: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  yaml-cpp/node.cpp:56:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  yaml-cpp/node.cpp:148:54: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  yaml-cpp/node.cpp:150:54: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  yaml-cpp/node.cpp:166:54: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  yaml-cpp/node.cpp:168:54: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  yaml-cpp/nodeownership.cpp:18:40: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  yaml-cpp/singledocparser.h:56:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  yaml-cpp/scanner.cpp:237:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  yaml-cpp/scanner.cpp:284:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  Warning: Package 'seqbias' is deprecated and will be removed from Bioconductor
See ‘/home/biocbuild/bbs-3.18-bioc/meat/seqbias.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
* used C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
* checking installed package size ... NOTE
  installed size is 10.4Mb
  sub-directories of 1Mb or more:
    libs   9.7Mb
* 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 loading without being on the library search path ... OK
* checking startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' call to ‘GenomicRanges’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘Biostrings’ ‘GenomicRanges’ ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
count.reads: no visible global function definition for ‘is’
count.reads : <anonymous>: no visible global function definition for
  ‘seqnames’
count.reads : <anonymous>: no visible global function definition for
  ‘start’
count.reads : <anonymous>: no visible global function definition for
  ‘end’
count.reads : <anonymous>: no visible global function definition for
  ‘strand’
random.intervals: no visible global function definition for ‘is’
random.intervals : uniform_ints : <anonymous>: no visible global
  function definition for ‘runif’
random.intervals: no visible global function definition for ‘GRanges’
random.intervals: no visible global function definition for ‘IRanges’
seqbias.fit: no visible global function definition for ‘new’
seqbias.load: no visible global function definition for ‘new’
seqbias.predict: no visible global function definition for ‘is’
seqbias.predict : <anonymous>: no visible global function definition
  for ‘seqnames’
seqbias.predict : <anonymous>: no visible global function definition
  for ‘start’
seqbias.predict : <anonymous>: no visible global function definition
  for ‘end’
seqbias.predict : <anonymous>: no visible global function definition
  for ‘strand’
Undefined global functions or variables:
  GRanges IRanges end is new runif seqnames start strand
Consider adding
  importFrom("methods", "is", "new")
  importFrom("stats", "end", "runif", "start")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... WARNING
Note: information on .o files is not available
File ‘/home/biocbuild/bbs-3.18-bioc/R/site-library/seqbias/libs/seqbias.so’:
  Found ‘__sprintf_chk’, possibly from ‘sprintf’ (C)
  Found ‘abort’, possibly from ‘abort’ (C)
  Found ‘exit’, possibly from ‘exit’ (C)
  Found ‘rand’, possibly from ‘rand’ (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 nor [v]sprintf. 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 ...
  ‘overview.Rnw’... OK
 OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 WARNINGs, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/seqbias.Rcheck/00check.log’
for details.



Installation output

seqbias.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL seqbias
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.18-bioc/R/site-library’
* installing *source* package ‘seqbias’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
$SEQBIAS_OBJ is [common.o miscmath.o pos_table.o kmer_matrix.o logger.o motif.o seqbias.o sequencing_bias.o twobitseq.o]
$YAML_CPP_OBJ is [aliasmanager.o conversion.o directives.o emitfromevents.o emitter.o emitterstate.o emitterutils.o exp.o iterator.o nodebuilder.o node.o nodeownership.o null.o ostream.o parser.o regex.o scanner.o scanscalar.o scantag.o scantoken.o simplekey.o singledocparser.o stream.o tag.o]
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/zlibbioc/include' -I/usr/local/include   -Wall -Wextra -I. -fpic  -g -O2  -Wall -c common.c -o common.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/zlibbioc/include' -I/usr/local/include   -Wall -Wextra -I. -fpic  -g -O2  -Wall -c miscmath.c -o miscmath.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/zlibbioc/include' -I/usr/local/include   -Wall -Wextra -I. -fpic  -g -O2  -Wall -c pos_table.c -o pos_table.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/zlibbioc/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,
                 from kmer_matrix.hpp:13,
                 from kmer_matrix.cpp:8:
./yaml-cpp/parser.h:45:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   45 |                 std::auto_ptr<Scanner> m_pScanner;
      |                      ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
                 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++/11/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from yaml-cpp/yaml.h:9,
                 from kmer_matrix.hpp:13,
                 from kmer_matrix.cpp:8:
./yaml-cpp/parser.h:46:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   46 |                 std::auto_ptr<Directives> m_pDirectives;
      |                      ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
                 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++/11/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from ./yaml-cpp/node.h:12,
                 from yaml-cpp/yaml.h:10,
                 from kmer_matrix.hpp:13,
                 from kmer_matrix.cpp:8:
./yaml-cpp/iterator.h:20:31: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   20 |                 Iterator(std::auto_ptr<IterPriv> pData);
      |                               ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
                 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++/11/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from ./yaml-cpp/node.h:12,
                 from yaml-cpp/yaml.h:10,
                 from kmer_matrix.hpp:13,
                 from kmer_matrix.cpp:8:
./yaml-cpp/iterator.h:36:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   36 |                 std::auto_ptr<IterPriv> m_pData;
      |                      ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
                 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++/11/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from yaml-cpp/yaml.h:10,
                 from kmer_matrix.hpp:13,
                 from kmer_matrix.cpp:8:
./yaml-cpp/node.h:43:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   43 |                 std::auto_ptr<Node> Clone() const;
      |                      ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
                 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++/11/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from yaml-cpp/yaml.h:10,
                 from kmer_matrix.hpp:13,
                 from kmer_matrix.cpp:8:
./yaml-cpp/node.h:115:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  115 |                 std::auto_ptr<NodeOwnership> m_pOwnership;
      |                      ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
                 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++/11/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from yaml-cpp/yaml.h:13,
                 from kmer_matrix.hpp:13,
                 from kmer_matrix.cpp:8:
./yaml-cpp/emitter.h:98:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   98 |                 std::auto_ptr <EmitterState> m_pState;
      |                      ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
                 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++/11/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/zlibbioc/include' -I/usr/local/include   -Wall -Wextra -I. -fpic  -g -O2  -Wall -c logger.cpp -o logger.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/zlibbioc/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,
                 from kmer_matrix.hpp:13,
                 from motif.hpp:13,
                 from motif.cpp:8:
./yaml-cpp/parser.h:45:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   45 |                 std::auto_ptr<Scanner> m_pScanner;
      |                      ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
                 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++/11/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from yaml-cpp/yaml.h:9,
                 from kmer_matrix.hpp:13,
                 from motif.hpp:13,
                 from motif.cpp:8:
./yaml-cpp/parser.h:46:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   46 |                 std::auto_ptr<Directives> m_pDirectives;
      |                      ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
                 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++/11/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from ./yaml-cpp/node.h:12,
                 from yaml-cpp/yaml.h:10,
                 from kmer_matrix.hpp:13,
                 from motif.hpp:13,
                 from motif.cpp:8:
./yaml-cpp/iterator.h:20:31: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   20 |                 Iterator(std::auto_ptr<IterPriv> pData);
      |                               ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
                 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++/11/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from ./yaml-cpp/node.h:12,
                 from yaml-cpp/yaml.h:10,
                 from kmer_matrix.hpp:13,
                 from motif.hpp:13,
                 from motif.cpp:8:
./yaml-cpp/iterator.h:36:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   36 |                 std::auto_ptr<IterPriv> m_pData;
      |                      ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
                 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++/11/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from yaml-cpp/yaml.h:10,
                 from kmer_matrix.hpp:13,
                 from motif.hpp:13,
                 from motif.cpp:8:
./yaml-cpp/node.h:43:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   43 |                 std::auto_ptr<Node> Clone() const;
      |                      ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
                 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++/11/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from yaml-cpp/yaml.h:10,
                 from kmer_matrix.hpp:13,
                 from motif.hpp:13,
                 from motif.cpp:8:
./yaml-cpp/node.h:115:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  115 |                 std::auto_ptr<NodeOwnership> m_pOwnership;
      |                      ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
                 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++/11/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from yaml-cpp/yaml.h:13,
                 from kmer_matrix.hpp:13,
                 from motif.hpp:13,
                 from motif.cpp:8:
./yaml-cpp/emitter.h:98:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   98 |                 std::auto_ptr <EmitterState> m_pState;
      |                      ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
                 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++/11/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/zlibbioc/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,
                 from kmer_matrix.hpp:13,
                 from motif.hpp:13,
                 from sequencing_bias.hpp:13,
                 from seqbias.cpp:2:
./yaml-cpp/parser.h:45:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   45 |                 std::auto_ptr<Scanner> m_pScanner;
      |                      ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
                 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++/11/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from yaml-cpp/yaml.h:9,
                 from kmer_matrix.hpp:13,
                 from motif.hpp:13,
                 from sequencing_bias.hpp:13,
                 from seqbias.cpp:2:
./yaml-cpp/parser.h:46:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   46 |                 std::auto_ptr<Directives> m_pDirectives;
      |                      ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
                 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++/11/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from ./yaml-cpp/node.h:12,
                 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:20:31: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   20 |                 Iterator(std::auto_ptr<IterPriv> pData);
      |                               ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
                 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++/11/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from ./yaml-cpp/node.h:12,
                 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:36:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   36 |                 std::auto_ptr<IterPriv> m_pData;
      |                      ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
                 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++/11/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included 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/node.h:43:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   43 |                 std::auto_ptr<Node> Clone() const;
      |                      ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
                 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++/11/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included 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/node.h:115:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  115 |                 std::auto_ptr<NodeOwnership> m_pOwnership;
      |                      ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
                 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++/11/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from yaml-cpp/yaml.h:13,
                 from kmer_matrix.hpp:13,
                 from motif.hpp:13,
                 from sequencing_bias.hpp:13,
                 from seqbias.cpp:2:
./yaml-cpp/emitter.h:98:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   98 |                 std::auto_ptr <EmitterState> m_pState;
      |                      ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
                 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++/11/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
seqbias.cpp: In function ‘void R_init_seqbias(DllInfo*)’:
seqbias.cpp:493:34: warning: cast between incompatible function types from ‘SEXPREC* (*)(SEXP, SEXP, SEXP, SEXP, SEXP)’ {aka ‘SEXPREC* (*)(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)’} to ‘DL_FUNC’ {aka ‘void* (*)()’} [-Wcast-function-type]
  493 |         { "seqbias_fit",         (DL_FUNC) &seqbias_fit, 5 },
      |                                  ^~~~~~~~~~~~~~~~~~~~~~
seqbias.cpp:494:34: warning: cast between incompatible function types from ‘SEXPREC* (*)(SEXP, SEXP, SEXP, SEXP, SEXP)’ {aka ‘SEXPREC* (*)(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)’} to ‘DL_FUNC’ {aka ‘void* (*)()’} [-Wcast-function-type]
  494 |         { "seqbias_predict",     (DL_FUNC) &seqbias_predict, 5 },
      |                                  ^~~~~~~~~~~~~~~~~~~~~~~~~~
seqbias.cpp:495:34: warning: cast between incompatible function types from ‘SEXPREC* (*)(SEXP, SEXP)’ {aka ‘SEXPREC* (*)(SEXPREC*, SEXPREC*)’} to ‘DL_FUNC’ {aka ‘void* (*)()’} [-Wcast-function-type]
  495 |         { "seqbias_load",        (DL_FUNC) &seqbias_load, 2 },
      |                                  ^~~~~~~~~~~~~~~~~~~~~~~
seqbias.cpp:496:34: warning: cast between incompatible function types from ‘SEXPREC* (*)(SEXP, SEXP)’ {aka ‘SEXPREC* (*)(SEXPREC*, SEXPREC*)’} to ‘DL_FUNC’ {aka ‘void* (*)()’} [-Wcast-function-type]
  496 |         { "seqbias_save",        (DL_FUNC) &seqbias_save, 2 },
      |                                  ^~~~~~~~~~~~~~~~~~~~~~~
seqbias.cpp:497:37: warning: cast between incompatible function types from ‘SEXPREC* (*)(SEXP)’ {aka ‘SEXPREC* (*)(SEXPREC*)’} to ‘DL_FUNC’ {aka ‘void* (*)()’} [-Wcast-function-type]
  497 |         { "seqbias_open_bam",       (DL_FUNC) &seqbias_open_bam, 1 },
      |                                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~
seqbias.cpp:498:37: warning: cast between incompatible function types from ‘SEXPREC* (*)(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’ {aka ‘SEXPREC* (*)(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)’} to ‘DL_FUNC’ {aka ‘void* (*)()’} [-Wcast-function-type]
  498 |         { "seqbias_count_reads",    (DL_FUNC) &seqbias_count_reads, 7 },
      |                                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
seqbias.cpp:499:49: warning: cast between incompatible function types from ‘SEXPREC* (*)(SEXP, SEXP)’ {aka ‘SEXPREC* (*)(SEXPREC*, SEXPREC*)’} to ‘DL_FUNC’ {aka ‘void* (*)()’} [-Wcast-function-type]
  499 |         { "seqbias_alloc_kmer_matrix",          (DL_FUNC) &seqbias_alloc_kmer_matrix, 2 },
      |                                                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
seqbias.cpp:500:49: warning: cast between incompatible function types from ‘SEXPREC* (*)(SEXP, SEXP, SEXP, SEXP)’ {aka ‘SEXPREC* (*)(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)’} to ‘DL_FUNC’ {aka ‘void* (*)()’} [-Wcast-function-type]
  500 |         { "seqbias_tally_kmers",                (DL_FUNC) &seqbias_tally_kmers, 4 },
      |                                                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
seqbias.cpp:501:49: warning: cast between incompatible function types from ‘SEXPREC* (*)(SEXP, SEXP)’ {aka ‘SEXPREC* (*)(SEXPREC*, SEXPREC*)’} to ‘DL_FUNC’ {aka ‘void* (*)()’} [-Wcast-function-type]
  501 |         { "sebqias_dataframe_from_kmer_matrix", (DL_FUNC) &seqbias_dataframe_from_kmer_matrix, 2 },
      |                                                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/zlibbioc/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,
                 from kmer_matrix.hpp:13,
                 from motif.hpp:13,
                 from sequencing_bias.hpp:13,
                 from sequencing_bias.cpp:8:
./yaml-cpp/parser.h:45:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   45 |                 std::auto_ptr<Scanner> m_pScanner;
      |                      ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
                 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++/11/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included 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:
./yaml-cpp/parser.h:46:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   46 |                 std::auto_ptr<Directives> m_pDirectives;
      |                      ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
                 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++/11/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from ./yaml-cpp/node.h:12,
                 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:20:31: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   20 |                 Iterator(std::auto_ptr<IterPriv> pData);
      |                               ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
                 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++/11/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from ./yaml-cpp/node.h:12,
                 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:36:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   36 |                 std::auto_ptr<IterPriv> m_pData;
      |                      ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
                 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++/11/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included 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/node.h:43:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   43 |                 std::auto_ptr<Node> Clone() const;
      |                      ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
                 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++/11/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included 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/node.h:115:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  115 |                 std::auto_ptr<NodeOwnership> m_pOwnership;
      |                      ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
                 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++/11/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from yaml-cpp/yaml.h:13,
                 from kmer_matrix.hpp:13,
                 from motif.hpp:13,
                 from sequencing_bias.hpp:13,
                 from sequencing_bias.cpp:8:
./yaml-cpp/emitter.h:98:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   98 |                 std::auto_ptr <EmitterState> m_pState;
      |                      ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
                 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++/11/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
sequencing_bias.cpp: In member function ‘void sequencing_bias::build(const char*, pos_table*, size_t, pos_t, pos_t, double)’:
sequencing_bias.cpp:398:9: warning: ‘void free(void*)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
  398 |     free(local_seq);
      |     ~~~~^~~~~~~~~~~
sequencing_bias.cpp:301:37: note: returned from ‘void* operator new [](std::size_t)’
  301 |     local_seq = new char[ L + R + 2 ];
      |                                     ^
sequencing_bias.cpp: In function ‘kmer_matrix tabulate_bias(double*, pos_t, pos_t, int, const char*, const char*, const char*)’:
sequencing_bias.cpp:628:9: warning: ‘void free(void*)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
  628 |     free(local_seq);
      |     ~~~~^~~~~~~~~~~
sequencing_bias.cpp:541:51: note: returned from ‘void* operator new [](std::size_t)’
  541 |     local_seq = new char[ (k - 1) + L + 1 + R + 1 ];
      |                                                   ^
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/zlibbioc/include' -I/usr/local/include   -Wall -Wextra -I. -fpic  -g -O2  -Wall -c twobitseq.cpp -o twobitseq.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/zlibbioc/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,
                 from yaml-cpp/aliasmanager.cpp:2:
./yaml-cpp/iterator.h:20:31: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   20 |                 Iterator(std::auto_ptr<IterPriv> pData);
      |                               ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
                 from ./yaml-cpp/iterator.h:9,
                 from ./yaml-cpp/node.h:12,
                 from yaml-cpp/aliasmanager.cpp:2:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from ./yaml-cpp/node.h:12,
                 from yaml-cpp/aliasmanager.cpp:2:
./yaml-cpp/iterator.h:36:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   36 |                 std::auto_ptr<IterPriv> m_pData;
      |                      ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
                 from ./yaml-cpp/iterator.h:9,
                 from ./yaml-cpp/node.h:12,
                 from yaml-cpp/aliasmanager.cpp:2:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from yaml-cpp/aliasmanager.cpp:2:
./yaml-cpp/node.h:43:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   43 |                 std::auto_ptr<Node> Clone() const;
      |                      ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
                 from ./yaml-cpp/iterator.h:9,
                 from ./yaml-cpp/node.h:12,
                 from yaml-cpp/aliasmanager.cpp:2:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from yaml-cpp/aliasmanager.cpp:2:
./yaml-cpp/node.h:115:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  115 |                 std::auto_ptr<NodeOwnership> m_pOwnership;
      |                      ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
                 from ./yaml-cpp/iterator.h:9,
                 from ./yaml-cpp/node.h:12,
                 from yaml-cpp/aliasmanager.cpp:2:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/zlibbioc/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++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/zlibbioc/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++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/zlibbioc/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:
./yaml-cpp/emitter.h:98:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   98 |                 std::auto_ptr <EmitterState> m_pState;
      |                      ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
                 from ./yaml-cpp/emitter.h:14,
                 from yaml-cpp/emitfromevents.cpp:2:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/zlibbioc/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:
./yaml-cpp/emitter.h:98:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   98 |                 std::auto_ptr <EmitterState> m_pState;
      |                      ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
                 from ./yaml-cpp/emitter.h:14,
                 from yaml-cpp/emitter.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from yaml-cpp/emitterstate.h:9,
                 from yaml-cpp/emitter.cpp:2:
yaml-cpp/ptr_stack.h:29:24: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   29 |         void push(std::auto_ptr<T> t) {
      |                        ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
                 from ./yaml-cpp/emitter.h:14,
                 from yaml-cpp/emitter.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from yaml-cpp/emitterstate.h:9,
                 from yaml-cpp/emitter.cpp:2:
yaml-cpp/ptr_stack.h:33:14: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   33 |         std::auto_ptr<T> pop() {
      |              ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
                 from ./yaml-cpp/emitter.h:14,
                 from yaml-cpp/emitter.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from yaml-cpp/emitterstate.h:9,
                 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:34:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   34 |                 std::auto_ptr<T> t(m_data.back());
      |                      ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
                 from ./yaml-cpp/emitter.h:14,
                 from yaml-cpp/emitter.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from yaml-cpp/emitterstate.h:10,
                 from yaml-cpp/emitter.cpp:2:
yaml-cpp/setting.h: At global scope:
yaml-cpp/setting.h:24:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   24 |                 std::auto_ptr <SettingChangeBase> set(const T& value);
      |                      ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
                 from ./yaml-cpp/emitter.h:14,
                 from yaml-cpp/emitter.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from yaml-cpp/emitterstate.h:10,
                 from yaml-cpp/emitter.cpp:2:
yaml-cpp/setting.h:59:21: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   59 |         inline std::auto_ptr <SettingChangeBase> Setting<T>::set(const T& value) {
      |                     ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
                 from ./yaml-cpp/emitter.h:14,
                 from yaml-cpp/emitter.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from yaml-cpp/emitterstate.h:10,
                 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:60:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   60 |                 std::auto_ptr <SettingChangeBase> pChange(new SettingChange<T> (this));
      |                      ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
                 from ./yaml-cpp/emitter.h:14,
                 from yaml-cpp/emitter.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from yaml-cpp/emitterstate.h:10,
                 from yaml-cpp/emitter.cpp:2:
yaml-cpp/setting.h: At global scope:
yaml-cpp/setting.h:84:32: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   84 |                 void push(std::auto_ptr <SettingChangeBase> pSettingChange) {
      |                                ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
                 from ./yaml-cpp/emitter.h:14,
                 from yaml-cpp/emitter.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/zlibbioc/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,
                 from yaml-cpp/emitterstate.cpp:1:
yaml-cpp/ptr_stack.h:29:24: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   29 |         void push(std::auto_ptr<T> t) {
      |                        ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
                 from yaml-cpp/ptr_stack.h:9,
                 from yaml-cpp/emitterstate.h:9,
                 from yaml-cpp/emitterstate.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from yaml-cpp/emitterstate.h:9,
                 from yaml-cpp/emitterstate.cpp:1:
yaml-cpp/ptr_stack.h:33:14: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   33 |         std::auto_ptr<T> pop() {
      |              ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
                 from yaml-cpp/ptr_stack.h:9,
                 from yaml-cpp/emitterstate.h:9,
                 from yaml-cpp/emitterstate.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from yaml-cpp/emitterstate.h:9,
                 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:34:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   34 |                 std::auto_ptr<T> t(m_data.back());
      |                      ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
                 from yaml-cpp/ptr_stack.h:9,
                 from yaml-cpp/emitterstate.h:9,
                 from yaml-cpp/emitterstate.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from yaml-cpp/emitterstate.h:10,
                 from yaml-cpp/emitterstate.cpp:1:
yaml-cpp/setting.h: At global scope:
yaml-cpp/setting.h:24:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   24 |                 std::auto_ptr <SettingChangeBase> set(const T& value);
      |                      ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
                 from yaml-cpp/ptr_stack.h:9,
                 from yaml-cpp/emitterstate.h:9,
                 from yaml-cpp/emitterstate.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from yaml-cpp/emitterstate.h:10,
                 from yaml-cpp/emitterstate.cpp:1:
yaml-cpp/setting.h:59:21: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   59 |         inline std::auto_ptr <SettingChangeBase> Setting<T>::set(const T& value) {
      |                     ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
                 from yaml-cpp/ptr_stack.h:9,
                 from yaml-cpp/emitterstate.h:9,
                 from yaml-cpp/emitterstate.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from yaml-cpp/emitterstate.h:10,
                 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:60:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   60 |                 std::auto_ptr <SettingChangeBase> pChange(new SettingChange<T> (this));
      |                      ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
                 from yaml-cpp/ptr_stack.h:9,
                 from yaml-cpp/emitterstate.h:9,
                 from yaml-cpp/emitterstate.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from yaml-cpp/emitterstate.h:10,
                 from yaml-cpp/emitterstate.cpp:1:
yaml-cpp/setting.h: At global scope:
yaml-cpp/setting.h:84:32: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   84 |                 void push(std::auto_ptr <SettingChangeBase> pSettingChange) {
      |                                ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
                 from yaml-cpp/ptr_stack.h:9,
                 from yaml-cpp/emitterstate.h:9,
                 from yaml-cpp/emitterstate.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
yaml-cpp/emitterstate.cpp: In member function ‘void YAML::EmitterState::BeginGroup(YAML::GROUP_TYPE)’:
yaml-cpp/emitterstate.cpp:51:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   51 |                 std::auto_ptr<Group> pGroup(new Group(type));
      |                      ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
                 from yaml-cpp/ptr_stack.h:9,
                 from yaml-cpp/emitterstate.h:9,
                 from yaml-cpp/emitterstate.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
yaml-cpp/emitterstate.cpp: In member function ‘void YAML::EmitterState::EndGroup(YAML::GROUP_TYPE)’:
yaml-cpp/emitterstate.cpp:71:30: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   71 |                         std::auto_ptr<Group> pFinishedGroup = m_groups.pop();
      |                              ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
                 from yaml-cpp/ptr_stack.h:9,
                 from yaml-cpp/emitterstate.h:9,
                 from yaml-cpp/emitterstate.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/zlibbioc/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++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/zlibbioc/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++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/zlibbioc/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,
                 from yaml-cpp/iterator.cpp:1:
./yaml-cpp/iterator.h:20:31: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   20 |                 Iterator(std::auto_ptr<IterPriv> pData);
      |                               ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
                 from ./yaml-cpp/iterator.h:9,
                 from ./yaml-cpp/node.h:12,
                 from yaml-cpp/iterator.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from ./yaml-cpp/node.h:12,
                 from yaml-cpp/iterator.cpp:1:
./yaml-cpp/iterator.h:36:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   36 |                 std::auto_ptr<IterPriv> m_pData;
      |                      ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
                 from ./yaml-cpp/iterator.h:9,
                 from ./yaml-cpp/node.h:12,
                 from yaml-cpp/iterator.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from yaml-cpp/iterator.cpp:1:
./yaml-cpp/node.h:43:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   43 |                 std::auto_ptr<Node> Clone() const;
      |                      ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
                 from ./yaml-cpp/iterator.h:9,
                 from ./yaml-cpp/node.h:12,
                 from yaml-cpp/iterator.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from yaml-cpp/iterator.cpp:1:
./yaml-cpp/node.h:115:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  115 |                 std::auto_ptr<NodeOwnership> m_pOwnership;
      |                      ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
                 from ./yaml-cpp/iterator.h:9,
                 from ./yaml-cpp/node.h:12,
                 from yaml-cpp/iterator.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
yaml-cpp/iterator.cpp:11:33: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   11 |         Iterator::Iterator(std::auto_ptr<IterPriv> pData): m_pData(pData)
      |                                 ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
                 from ./yaml-cpp/iterator.h:9,
                 from ./yaml-cpp/node.h:12,
                 from yaml-cpp/iterator.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/zlibbioc/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,
                 from yaml-cpp/nodebuilder.cpp:3:
./yaml-cpp/iterator.h:20:31: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   20 |                 Iterator(std::auto_ptr<IterPriv> pData);
      |                               ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
                 from yaml-cpp/nodebuilder.h:10,
                 from yaml-cpp/nodebuilder.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from ./yaml-cpp/node.h:12,
                 from yaml-cpp/nodebuilder.cpp:3:
./yaml-cpp/iterator.h:36:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   36 |                 std::auto_ptr<IterPriv> m_pData;
      |                      ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
                 from yaml-cpp/nodebuilder.h:10,
                 from yaml-cpp/nodebuilder.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from yaml-cpp/nodebuilder.cpp:3:
./yaml-cpp/node.h:43:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   43 |                 std::auto_ptr<Node> Clone() const;
      |                      ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
                 from yaml-cpp/nodebuilder.h:10,
                 from yaml-cpp/nodebuilder.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from yaml-cpp/nodebuilder.cpp:3:
./yaml-cpp/node.h:115:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  115 |                 std::auto_ptr<NodeOwnership> m_pOwnership;
      |                      ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
                 from yaml-cpp/nodebuilder.h:10,
                 from yaml-cpp/nodebuilder.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/zlibbioc/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,
                 from yaml-cpp/node.cpp:1:
./yaml-cpp/iterator.h:20:31: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   20 |                 Iterator(std::auto_ptr<IterPriv> pData);
      |                               ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
                 from ./yaml-cpp/iterator.h:9,
                 from ./yaml-cpp/node.h:12,
                 from yaml-cpp/node.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from ./yaml-cpp/node.h:12,
                 from yaml-cpp/node.cpp:1:
./yaml-cpp/iterator.h:36:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   36 |                 std::auto_ptr<IterPriv> m_pData;
      |                      ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
                 from ./yaml-cpp/iterator.h:9,
                 from ./yaml-cpp/node.h:12,
                 from yaml-cpp/node.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from yaml-cpp/node.cpp:1:
./yaml-cpp/node.h:43:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   43 |                 std::auto_ptr<Node> Clone() const;
      |                      ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
                 from ./yaml-cpp/iterator.h:9,
                 from ./yaml-cpp/node.h:12,
                 from yaml-cpp/node.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from yaml-cpp/node.cpp:1:
./yaml-cpp/node.h:115:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  115 |                 std::auto_ptr<NodeOwnership> m_pOwnership;
      |                      ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
                 from ./yaml-cpp/iterator.h:9,
                 from ./yaml-cpp/node.h:12,
                 from yaml-cpp/node.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from yaml-cpp/nodeownership.h:10,
                 from yaml-cpp/node.cpp:4:
yaml-cpp/ptr_vector.h:31:37: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   31 |                 void push_back(std::auto_ptr<T> t) {
      |                                     ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
                 from ./yaml-cpp/iterator.h:9,
                 from ./yaml-cpp/node.h:12,
                 from yaml-cpp/node.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from yaml-cpp/node.cpp:10:
./yaml-cpp/emitter.h:98:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   98 |                 std::auto_ptr <EmitterState> m_pState;
      |                      ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
                 from ./yaml-cpp/iterator.h:9,
                 from ./yaml-cpp/node.h:12,
                 from yaml-cpp/node.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
yaml-cpp/node.cpp:54:14: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   54 |         std::auto_ptr<Node> Node::Clone() const
      |              ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
                 from ./yaml-cpp/iterator.h:9,
                 from ./yaml-cpp/node.h:12,
                 from yaml-cpp/node.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
   57 |   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:56:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   56 |                 std::auto_ptr<Node> pNode(new Node);
      |                      ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
                 from ./yaml-cpp/iterator.h:9,
                 from ./yaml-cpp/node.h:12,
                 from yaml-cpp/node.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
yaml-cpp/node.cpp: In member function ‘YAML::Iterator YAML::Node::begin() const’:
yaml-cpp/node.cpp:148:54: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  148 |                                 return Iterator(std::auto_ptr<IterPriv>(new IterPriv(m_seqData.begin())));
      |                                                      ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
                 from ./yaml-cpp/iterator.h:9,
                 from ./yaml-cpp/node.h:12,
                 from yaml-cpp/node.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
yaml-cpp/node.cpp:150:54: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  150 |                                 return Iterator(std::auto_ptr<IterPriv>(new IterPriv(m_mapData.begin())));
      |                                                      ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
                 from ./yaml-cpp/iterator.h:9,
                 from ./yaml-cpp/node.h:12,
                 from yaml-cpp/node.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
yaml-cpp/node.cpp: In member function ‘YAML::Iterator YAML::Node::end() const’:
yaml-cpp/node.cpp:166:54: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  166 |                                 return Iterator(std::auto_ptr<IterPriv>(new IterPriv(m_seqData.end())));
      |                                                      ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
                 from ./yaml-cpp/iterator.h:9,
                 from ./yaml-cpp/node.h:12,
                 from yaml-cpp/node.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
yaml-cpp/node.cpp:168:54: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  168 |                                 return Iterator(std::auto_ptr<IterPriv>(new IterPriv(m_mapData.end())));
      |                                                      ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
                 from ./yaml-cpp/iterator.h:9,
                 from ./yaml-cpp/node.h:12,
                 from yaml-cpp/node.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/zlibbioc/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,
                 from yaml-cpp/nodeownership.cpp:1:
yaml-cpp/ptr_vector.h:31:37: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   31 |                 void push_back(std::auto_ptr<T> t) {
      |                                     ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
                 from yaml-cpp/ptr_vector.h:9,
                 from yaml-cpp/nodeownership.h:10,
                 from yaml-cpp/nodeownership.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from ./yaml-cpp/node.h:12,
                 from yaml-cpp/nodeownership.cpp:2:
./yaml-cpp/iterator.h:20:31: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   20 |                 Iterator(std::auto_ptr<IterPriv> pData);
      |                               ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
                 from yaml-cpp/ptr_vector.h:9,
                 from yaml-cpp/nodeownership.h:10,
                 from yaml-cpp/nodeownership.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from ./yaml-cpp/node.h:12,
                 from yaml-cpp/nodeownership.cpp:2:
./yaml-cpp/iterator.h:36:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   36 |                 std::auto_ptr<IterPriv> m_pData;
      |                      ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
                 from yaml-cpp/ptr_vector.h:9,
                 from yaml-cpp/nodeownership.h:10,
                 from yaml-cpp/nodeownership.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from yaml-cpp/nodeownership.cpp:2:
./yaml-cpp/node.h:43:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   43 |                 std::auto_ptr<Node> Clone() const;
      |                      ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
                 from yaml-cpp/ptr_vector.h:9,
                 from yaml-cpp/nodeownership.h:10,
                 from yaml-cpp/nodeownership.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from yaml-cpp/nodeownership.cpp:2:
./yaml-cpp/node.h:115:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  115 |                 std::auto_ptr<NodeOwnership> m_pOwnership;
      |                      ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
                 from yaml-cpp/ptr_vector.h:9,
                 from yaml-cpp/nodeownership.h:10,
                 from yaml-cpp/nodeownership.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
yaml-cpp/nodeownership.cpp: In member function ‘YAML::Node& YAML::NodeOwnership::_Create()’:
yaml-cpp/nodeownership.cpp:18:40: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   18 |                 m_nodes.push_back(std::auto_ptr<Node>(new Node));
      |                                        ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
                 from yaml-cpp/ptr_vector.h:9,
                 from yaml-cpp/nodeownership.h:10,
                 from yaml-cpp/nodeownership.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/zlibbioc/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,
                 from yaml-cpp/null.cpp:2:
./yaml-cpp/iterator.h:20:31: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   20 |                 Iterator(std::auto_ptr<IterPriv> pData);
      |                               ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
                 from ./yaml-cpp/iterator.h:9,
                 from ./yaml-cpp/node.h:12,
                 from yaml-cpp/null.cpp:2:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from ./yaml-cpp/node.h:12,
                 from yaml-cpp/null.cpp:2:
./yaml-cpp/iterator.h:36:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   36 |                 std::auto_ptr<IterPriv> m_pData;
      |                      ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
                 from ./yaml-cpp/iterator.h:9,
                 from ./yaml-cpp/node.h:12,
                 from yaml-cpp/null.cpp:2:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from yaml-cpp/null.cpp:2:
./yaml-cpp/node.h:43:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   43 |                 std::auto_ptr<Node> Clone() const;
      |                      ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
                 from ./yaml-cpp/iterator.h:9,
                 from ./yaml-cpp/node.h:12,
                 from yaml-cpp/null.cpp:2:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from yaml-cpp/null.cpp:2:
./yaml-cpp/node.h:115:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  115 |                 std::auto_ptr<NodeOwnership> m_pOwnership;
      |                      ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
                 from ./yaml-cpp/iterator.h:9,
                 from ./yaml-cpp/node.h:12,
                 from yaml-cpp/null.cpp:2:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/zlibbioc/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++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/zlibbioc/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:
./yaml-cpp/parser.h:45:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   45 |                 std::auto_ptr<Scanner> m_pScanner;
      |                      ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
                 from ./yaml-cpp/parser.h:12,
                 from yaml-cpp/parser.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from yaml-cpp/parser.cpp:1:
./yaml-cpp/parser.h:46:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   46 |                 std::auto_ptr<Directives> m_pDirectives;
      |                      ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
                 from ./yaml-cpp/parser.h:12,
                 from yaml-cpp/parser.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from ./yaml-cpp/node.h:12,
                 from yaml-cpp/parser.cpp:5:
./yaml-cpp/iterator.h:20:31: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   20 |                 Iterator(std::auto_ptr<IterPriv> pData);
      |                               ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
                 from ./yaml-cpp/parser.h:12,
                 from yaml-cpp/parser.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from ./yaml-cpp/node.h:12,
                 from yaml-cpp/parser.cpp:5:
./yaml-cpp/iterator.h:36:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   36 |                 std::auto_ptr<IterPriv> m_pData;
      |                      ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
                 from ./yaml-cpp/parser.h:12,
                 from yaml-cpp/parser.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from yaml-cpp/parser.cpp:5:
./yaml-cpp/node.h:43:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   43 |                 std::auto_ptr<Node> Clone() const;
      |                      ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
                 from ./yaml-cpp/parser.h:12,
                 from yaml-cpp/parser.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from yaml-cpp/parser.cpp:5:
./yaml-cpp/node.h:115:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  115 |                 std::auto_ptr<NodeOwnership> m_pOwnership;
      |                      ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
                 from ./yaml-cpp/parser.h:12,
                 from yaml-cpp/parser.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from yaml-cpp/scanner.h:15,
                 from yaml-cpp/parser.cpp:7:
yaml-cpp/ptr_vector.h:31:37: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   31 |                 void push_back(std::auto_ptr<T> t) {
      |                                     ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
                 from ./yaml-cpp/parser.h:12,
                 from yaml-cpp/parser.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from yaml-cpp/parser.cpp:8:
yaml-cpp/singledocparser.h:56:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   56 |                 std::auto_ptr<CollectionStack> m_pCollectionStack;
      |                      ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
                 from ./yaml-cpp/parser.h:12,
                 from yaml-cpp/parser.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/zlibbioc/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++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/zlibbioc/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,
                 from yaml-cpp/scanner.cpp:1:
yaml-cpp/ptr_vector.h:31:37: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   31 |                 void push_back(std::auto_ptr<T> t) {
      |                                     ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
                 from yaml-cpp/ptr_vector.h:9,
                 from yaml-cpp/scanner.h:15,
                 from yaml-cpp/scanner.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
yaml-cpp/scanner.cpp: In member function ‘void YAML::Scanner::StartStream()’:
yaml-cpp/scanner.cpp:237:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  237 |                 std::auto_ptr<IndentMarker> pIndent(new IndentMarker(-1, IndentMarker::NONE));
      |                      ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
                 from yaml-cpp/ptr_vector.h:9,
                 from yaml-cpp/scanner.h:15,
                 from yaml-cpp/scanner.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
   57 |   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:284:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  284 |                 std::auto_ptr<IndentMarker> pIndent(new IndentMarker(column, type));
      |                      ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
                 from yaml-cpp/ptr_vector.h:9,
                 from yaml-cpp/scanner.h:15,
                 from yaml-cpp/scanner.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/zlibbioc/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,
                 from yaml-cpp/scanscalar.cpp:2:
yaml-cpp/ptr_vector.h:31:37: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   31 |                 void push_back(std::auto_ptr<T> t) {
      |                                     ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
                 from yaml-cpp/ptr_vector.h:9,
                 from yaml-cpp/scanner.h:15,
                 from yaml-cpp/scanscalar.cpp:2:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/zlibbioc/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,
                 from yaml-cpp/scantag.cpp:1:
yaml-cpp/ptr_vector.h:31:37: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   31 |                 void push_back(std::auto_ptr<T> t) {
      |                                     ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
                 from yaml-cpp/ptr_vector.h:9,
                 from yaml-cpp/scanner.h:15,
                 from yaml-cpp/scantag.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/zlibbioc/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,
                 from yaml-cpp/scantoken.cpp:1:
yaml-cpp/ptr_vector.h:31:37: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   31 |                 void push_back(std::auto_ptr<T> t) {
      |                                     ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
                 from yaml-cpp/ptr_vector.h:9,
                 from yaml-cpp/scanner.h:15,
                 from yaml-cpp/scantoken.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/zlibbioc/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,
                 from yaml-cpp/simplekey.cpp:1:
yaml-cpp/ptr_vector.h:31:37: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   31 |                 void push_back(std::auto_ptr<T> t) {
      |                                     ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
                 from yaml-cpp/ptr_vector.h:9,
                 from yaml-cpp/scanner.h:15,
                 from yaml-cpp/simplekey.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/zlibbioc/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:
yaml-cpp/singledocparser.h:56:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   56 |                 std::auto_ptr<CollectionStack> m_pCollectionStack;
      |                      ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
                 from yaml-cpp/singledocparser.h:13,
                 from yaml-cpp/singledocparser.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from yaml-cpp/singledocparser.cpp:2:
yaml-cpp/collectionstack.h: In member function ‘void YAML::CollectionStack::PopCollectionType(YAML::CollectionType::value)’:
yaml-cpp/collectionstack.h:28:62: warning: unused parameter ‘type’ [-Wunused-parameter]
   28 |                 void PopCollectionType(CollectionType::value type) { assert(type == GetCurCollectionType()); collectionStack.pop(); }
      |                                        ~~~~~~~~~~~~~~~~~~~~~~^~~~
In file included from yaml-cpp/scanner.h:15,
                 from yaml-cpp/singledocparser.cpp:6:
yaml-cpp/ptr_vector.h: At global scope:
yaml-cpp/ptr_vector.h:31:37: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   31 |                 void push_back(std::auto_ptr<T> t) {
      |                                     ^~~~~~~~
In file included from /usr/include/c++/11/memory:76,
                 from yaml-cpp/singledocparser.h:13,
                 from yaml-cpp/singledocparser.cpp:1:
/usr/include/c++/11/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/zlibbioc/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++17 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rhtslib/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/zlibbioc/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++17 -shared -L/home/biocbuild/bbs-3.18-bioc/R/lib -L/usr/local/lib -o seqbias.so 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-3.18-bioc/R/site-library/Rhtslib/usrlib/libhts.a -lcurl -lbz2 -llzma -lz -L/home/biocbuild/bbs-3.18-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.18-bioc/R/site-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
Warning: Package 'seqbias' is deprecated and will be removed from Bioconductor
  version 3.19
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
Warning: Package 'seqbias' is deprecated and will be removed from Bioconductor
  version 3.19
** testing if installed package keeps a record of temporary installation path
* DONE (seqbias)

Tests output


Example timings

seqbias.Rcheck/seqbias-Ex.timings

nameusersystemelapsed
count_reads0.0450.0150.063
kmer_freq0.3850.0090.393
random_intervals0.030.000.03
seqbias_fit1.2830.0111.294
seqbias_load1.6350.0161.651
seqbias_predict0.6960.0080.704
seqbias_save1.6360.0041.641