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CHECK report for seqbias on tokay1

This page was generated on 2020-04-15 12:19:38 -0400 (Wed, 15 Apr 2020).

Package 1560/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
seqbias 1.34.0
Daniel Jones
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/seqbias
Branch: RELEASE_3_10
Last Commit: 9d5b1f7
Last Changed Date: 2019-10-29 13:08:18 -0400 (Tue, 29 Oct 2019)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] ERROR 
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: seqbias
Version: 1.34.0
Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:seqbias.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings seqbias_1.34.0.tar.gz
StartedAt: 2020-04-15 06:31:39 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 06:34:32 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 173.4 seconds
RetCode: 0
Status:  OK  
CheckDir: seqbias.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:seqbias.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings seqbias_1.34.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/seqbias.Rcheck'
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'seqbias/DESCRIPTION' ... OK
* this is package 'seqbias' version '1.34.0'
* 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 whether package 'seqbias' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  8.2Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' call to 'GenomicRanges' which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'Biostrings' 'GenomicRanges' 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
count.reads: no visible global function definition for 'is'
count.reads : <anonymous>: no visible global function definition for
  'seqnames'
count.reads : <anonymous>: no visible global function definition for
  'start'
count.reads : <anonymous>: no visible global function definition for
  'end'
count.reads : <anonymous>: no visible global function definition for
  'strand'
random.intervals: no visible global function definition for 'is'
random.intervals : uniform_ints : <anonymous>: no visible global
  function definition for 'runif'
random.intervals: no visible global function definition for 'GRanges'
random.intervals: no visible global function definition for 'IRanges'
seqbias.fit: no visible global function definition for 'new'
seqbias.load: no visible global function definition for 'new'
seqbias.predict: no visible global function definition for 'is'
seqbias.predict : <anonymous>: no visible global function definition
  for 'seqnames'
seqbias.predict : <anonymous>: no visible global function definition
  for 'start'
seqbias.predict : <anonymous>: no visible global function definition
  for 'end'
seqbias.predict : <anonymous>: no visible global function definition
  for 'strand'
Undefined global functions or variables:
  GRanges IRanges end is new runif seqnames start strand
Consider adding
  importFrom("methods", "is", "new")
  importFrom("stats", "end", "runif", "start")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.10-bioc/R/library/seqbias/libs/i386/seqbias.dll':
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
  Found 'putchar', possibly from 'putchar' (C)
  Found 'puts', possibly from 'printf' (C), 'puts' (C)
  Found 'rand', possibly from 'rand' (C)
File 'C:/Users/biocbuild/bbs-3.10-bioc/R/library/seqbias/libs/x64/seqbias.dll':
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
  Found 'putchar', possibly from 'putchar' (C)
  Found 'puts', possibly from 'printf' (C), 'puts' (C)
  Found 'rand', possibly from 'rand' (C)

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
             user system elapsed
seqbias_save 8.83   4.17   13.00
seqbias_load 7.67   3.18   10.86
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
             user system elapsed
seqbias_load 8.30   3.72   12.04
seqbias_save 6.47   3.56   10.19
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 5 NOTEs
See
  'C:/Users/biocbuild/bbs-3.10-bioc/meat/seqbias.Rcheck/00check.log'
for details.



Installation output

seqbias.Rcheck/00install.out

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##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/seqbias_1.34.0.tar.gz && rm -rf seqbias.buildbin-libdir && mkdir seqbias.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=seqbias.buildbin-libdir seqbias_1.34.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL seqbias_1.34.0.zip && rm seqbias_1.34.0.tar.gz seqbias_1.34.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  586k  100  586k    0     0  15.5M      0 --:--:-- --:--:-- --:--:-- 17.3M

install for i386

* installing *source* package 'seqbias' ...
** using staged installation

   **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************


** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O3 -Wall  -std=gnu99 -mtune=core2 -c sam.c -o sam.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O3 -Wall  -std=gnu99 -mtune=core2 -c bam_plbuf.c -o bam_plbuf.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O3 -Wall  -std=gnu99 -mtune=core2 -c bam_aux.c -o bam_aux.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O3 -Wall  -std=gnu99 -mtune=core2 -c common.c -o common.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O3 -Wall  -std=gnu99 -mtune=core2 -c miscmath.c -o miscmath.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O3 -Wall  -std=gnu99 -mtune=core2 -c pos_table.c -o pos_table.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -mtune=core2 -c kmer_matrix.cpp -o kmer_matrix.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -mtune=core2 -c logger.cpp -o logger.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -mtune=core2 -c motif.cpp -o motif.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -mtune=core2 -c seqbias.cpp -o seqbias.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -mtune=core2 -c sequencing_bias.cpp -o sequencing_bias.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -mtune=core2 -c twobitseq.cpp -o twobitseq.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -mtune=core2 -c yaml-cpp/aliasmanager.cpp -o yaml-cpp/aliasmanager.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -mtune=core2 -c yaml-cpp/conversion.cpp -o yaml-cpp/conversion.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -mtune=core2 -c yaml-cpp/directives.cpp -o yaml-cpp/directives.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -mtune=core2 -c yaml-cpp/emitfromevents.cpp -o yaml-cpp/emitfromevents.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -mtune=core2 -c yaml-cpp/emitter.cpp -o yaml-cpp/emitter.o
In file included from yaml-cpp/emitterstate.h:10:0,
                 from yaml-cpp/emitter.cpp:2:
yaml-cpp/setting.h: In member function 'std::auto_ptr<YAML::SettingChangeBase> YAML::Setting<T>::set(const T&)':
yaml-cpp/setting.h:60:44: warning: 'auto_ptr' is deprecated (declared at C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/backward/auto_ptr.h:87) [-Wdeprecated-declarations]
   std::auto_ptr <SettingChangeBase> pChange(new SettingChange<T> (this));
                                            ^
yaml-cpp/setting.h: At global scope:
yaml-cpp/setting.h:84:61: warning: 'auto_ptr' is deprecated (declared at C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/backward/auto_ptr.h:87) [-Wdeprecated-declarations]
   void push(std::auto_ptr <SettingChangeBase> pSettingChange) {
                                                             ^
C:/Rtools/mingw_32/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -mtune=core2 -c yaml-cpp/emitterstate.cpp -o yaml-cpp/emitterstate.o
In file included from yaml-cpp/emitterstate.h:10:0,
                 from yaml-cpp/emitterstate.cpp:1:
yaml-cpp/setting.h: In member function 'std::auto_ptr<YAML::SettingChangeBase> YAML::Setting<T>::set(const T&)':
yaml-cpp/setting.h:60:44: warning: 'auto_ptr' is deprecated (declared at C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/backward/auto_ptr.h:87) [-Wdeprecated-declarations]
   std::auto_ptr <SettingChangeBase> pChange(new SettingChange<T> (this));
                                            ^
yaml-cpp/setting.h: At global scope:
yaml-cpp/setting.h:84:61: warning: 'auto_ptr' is deprecated (declared at C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/backward/auto_ptr.h:87) [-Wdeprecated-declarations]
   void push(std::auto_ptr <SettingChangeBase> pSettingChange) {
                                                             ^
yaml-cpp/emitterstate.cpp: In member function 'void YAML::EmitterState::EndGroup(YAML::GROUP_TYPE)':
yaml-cpp/emitterstate.cpp:71:25: warning: 'auto_ptr' is deprecated (declared at C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/backward/auto_ptr.h:87) [-Wdeprecated-declarations]
    std::auto_ptr<Group> pFinishedGroup = m_groups.pop();
                         ^
C:/Rtools/mingw_32/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -mtune=core2 -c yaml-cpp/emitterutils.cpp -o yaml-cpp/emitterutils.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -mtune=core2 -c yaml-cpp/exp.cpp -o yaml-cpp/exp.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -mtune=core2 -c yaml-cpp/iterator.cpp -o yaml-cpp/iterator.o
yaml-cpp/iterator.cpp:11:50: warning: 'auto_ptr' is deprecated (declared at C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/backward/auto_ptr.h:87) [-Wdeprecated-declarations]
  Iterator::Iterator(std::auto_ptr<IterPriv> pData): m_pData(pData)
                                                  ^
C:/Rtools/mingw_32/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -mtune=core2 -c yaml-cpp/nodebuilder.cpp -o yaml-cpp/nodebuilder.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -mtune=core2 -c yaml-cpp/node.cpp -o yaml-cpp/node.o
yaml-cpp/node.cpp: In member function 'std::auto_ptr<YAML::Node> YAML::Node::Clone() const':
yaml-cpp/node.cpp:56:28: warning: 'auto_ptr' is deprecated (declared at C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/backward/auto_ptr.h:87) [-Wdeprecated-declarations]
   std::auto_ptr<Node> pNode(new Node);
                            ^
yaml-cpp/node.cpp: In member function 'YAML::Iterator YAML::Node::begin() const':
yaml-cpp/node.cpp:148:76: warning: 'auto_ptr' is deprecated (declared at C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/backward/auto_ptr.h:87) [-Wdeprecated-declarations]
     return Iterator(std::auto_ptr<IterPriv>(new IterPriv(m_seqData.begin())));
                                                                            ^
yaml-cpp/node.cpp:150:76: warning: 'auto_ptr' is deprecated (declared at C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/backward/auto_ptr.h:87) [-Wdeprecated-declarations]
     return Iterator(std::auto_ptr<IterPriv>(new IterPriv(m_mapData.begin())));
                                                                            ^
yaml-cpp/node.cpp: In member function 'YAML::Iterator YAML::Node::end() const':
yaml-cpp/node.cpp:166:74: warning: 'auto_ptr' is deprecated (declared at C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/backward/auto_ptr.h:87) [-Wdeprecated-declarations]
     return Iterator(std::auto_ptr<IterPriv>(new IterPriv(m_seqData.end())));
                                                                          ^
yaml-cpp/node.cpp:168:74: warning: 'auto_ptr' is deprecated (declared at C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/backward/auto_ptr.h:87) [-Wdeprecated-declarations]
     return Iterator(std::auto_ptr<IterPriv>(new IterPriv(m_mapData.end())));
                                                                          ^
C:/Rtools/mingw_32/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -mtune=core2 -c yaml-cpp/nodeownership.cpp -o yaml-cpp/nodeownership.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -mtune=core2 -c yaml-cpp/null.cpp -o yaml-cpp/null.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -mtune=core2 -c yaml-cpp/ostream.cpp -o yaml-cpp/ostream.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -mtune=core2 -c yaml-cpp/parser.cpp -o yaml-cpp/parser.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -mtune=core2 -c yaml-cpp/regex.cpp -o yaml-cpp/regex.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -mtune=core2 -c yaml-cpp/scanner.cpp -o yaml-cpp/scanner.o
yaml-cpp/scanner.cpp: In member function 'YAML::Scanner::IndentMarker* YAML::Scanner::PushIndentTo(int, YAML::Scanner::IndentMarker::INDENT_TYPE)':
yaml-cpp/scanner.cpp:284:38: warning: 'auto_ptr' is deprecated (declared at C:/Rtools/mingw_32/i686-w64-mingw32/include/c++/backward/auto_ptr.h:87) [-Wdeprecated-declarations]
   std::auto_ptr<IndentMarker> pIndent(new IndentMarker(column, type));
                                      ^
C:/Rtools/mingw_32/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -mtune=core2 -c yaml-cpp/scanscalar.cpp -o yaml-cpp/scanscalar.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -mtune=core2 -c yaml-cpp/scantag.cpp -o yaml-cpp/scantag.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -mtune=core2 -c yaml-cpp/scantoken.cpp -o yaml-cpp/scantoken.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -mtune=core2 -c yaml-cpp/simplekey.cpp -o yaml-cpp/simplekey.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -mtune=core2 -c yaml-cpp/singledocparser.cpp -o yaml-cpp/singledocparser.o
In file included from yaml-cpp/singledocparser.cpp:2:0:
yaml-cpp/collectionstack.h:28:48: warning: unused parameter 'type' [-Wunused-parameter]
   void PopCollectionType(CollectionType::value type) { assert(type == GetCurCollectionType()); collectionStack.pop(); }
                                                ^
C:/Rtools/mingw_32/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -mtune=core2 -c yaml-cpp/stream.cpp -o yaml-cpp/stream.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -mtune=core2 -c yaml-cpp/tag.cpp -o yaml-cpp/tag.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o seqbias.dll tmp.def sam.o bam_plbuf.o bam_aux.o common.o miscmath.o pos_table.o kmer_matrix.o logger.o motif.o seqbias.o sequencing_bias.o twobitseq.o yaml-cpp/aliasmanager.o yaml-cpp/conversion.o yaml-cpp/directives.o yaml-cpp/emitfromevents.o yaml-cpp/emitter.o yaml-cpp/emitterstate.o yaml-cpp/emitterutils.o yaml-cpp/exp.o yaml-cpp/iterator.o yaml-cpp/nodebuilder.o yaml-cpp/node.o yaml-cpp/nodeownership.o yaml-cpp/null.o yaml-cpp/ostream.o yaml-cpp/parser.o yaml-cpp/regex.o yaml-cpp/scanner.o yaml-cpp/scanscalar.o yaml-cpp/scantag.o yaml-cpp/scantoken.o yaml-cpp/simplekey.o yaml-cpp/singledocparser.o yaml-cpp/stream.o yaml-cpp/tag.o C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/usrlib/i386/libhts.a -LC:/extsoft/lib/i386 -lcurl -lrtmp -lssl -lssh2 -lcrypto -lgdi32 -lz -lws2_32 -lwldap32 -lwinmm -lidn -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.10-bioc/meat/seqbias.buildbin-libdir/00LOCK-seqbias/00new/seqbias/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'seqbias'
    finding HTML links ... done
    count_reads                             html  
    kmer_freq                               html  
    random_intervals                        html  
    seqbias-class                           html  
    seqbias-package                         html  
    seqbias_fit                             html  
    seqbias_load                            html  
    seqbias_predict                         html  
    seqbias_save                            html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'seqbias' ...

   **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************


** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -std=gnu99 -mtune=core2 -c sam.c -o sam.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -std=gnu99 -mtune=core2 -c bam_plbuf.c -o bam_plbuf.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -std=gnu99 -mtune=core2 -c bam_aux.c -o bam_aux.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -std=gnu99 -mtune=core2 -c common.c -o common.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -std=gnu99 -mtune=core2 -c miscmath.c -o miscmath.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -std=gnu99 -mtune=core2 -c pos_table.c -o pos_table.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -mtune=core2 -c kmer_matrix.cpp -o kmer_matrix.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -mtune=core2 -c logger.cpp -o logger.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -mtune=core2 -c motif.cpp -o motif.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -mtune=core2 -c seqbias.cpp -o seqbias.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -mtune=core2 -c sequencing_bias.cpp -o sequencing_bias.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -mtune=core2 -c twobitseq.cpp -o twobitseq.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -mtune=core2 -c yaml-cpp/aliasmanager.cpp -o yaml-cpp/aliasmanager.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -mtune=core2 -c yaml-cpp/conversion.cpp -o yaml-cpp/conversion.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -mtune=core2 -c yaml-cpp/directives.cpp -o yaml-cpp/directives.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -mtune=core2 -c yaml-cpp/emitfromevents.cpp -o yaml-cpp/emitfromevents.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -mtune=core2 -c yaml-cpp/emitter.cpp -o yaml-cpp/emitter.o
In file included from yaml-cpp/emitterstate.h:10:0,
                 from yaml-cpp/emitter.cpp:2:
yaml-cpp/setting.h: In member function 'std::auto_ptr<YAML::SettingChangeBase> YAML::Setting<T>::set(const T&)':
yaml-cpp/setting.h:60:44: warning: 'auto_ptr' is deprecated (declared at C:/Rtools/mingw_64/x86_64-w64-mingw32/include/c++/backward/auto_ptr.h:87) [-Wdeprecated-declarations]
   std::auto_ptr <SettingChangeBase> pChange(new SettingChange<T> (this));
                                            ^
yaml-cpp/setting.h: At global scope:
yaml-cpp/setting.h:84:61: warning: 'auto_ptr' is deprecated (declared at C:/Rtools/mingw_64/x86_64-w64-mingw32/include/c++/backward/auto_ptr.h:87) [-Wdeprecated-declarations]
   void push(std::auto_ptr <SettingChangeBase> pSettingChange) {
                                                             ^
C:/Rtools/mingw_64/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -mtune=core2 -c yaml-cpp/emitterstate.cpp -o yaml-cpp/emitterstate.o
In file included from yaml-cpp/emitterstate.h:10:0,
                 from yaml-cpp/emitterstate.cpp:1:
yaml-cpp/setting.h: In member function 'std::auto_ptr<YAML::SettingChangeBase> YAML::Setting<T>::set(const T&)':
yaml-cpp/setting.h:60:44: warning: 'auto_ptr' is deprecated (declared at C:/Rtools/mingw_64/x86_64-w64-mingw32/include/c++/backward/auto_ptr.h:87) [-Wdeprecated-declarations]
   std::auto_ptr <SettingChangeBase> pChange(new SettingChange<T> (this));
                                            ^
yaml-cpp/setting.h: At global scope:
yaml-cpp/setting.h:84:61: warning: 'auto_ptr' is deprecated (declared at C:/Rtools/mingw_64/x86_64-w64-mingw32/include/c++/backward/auto_ptr.h:87) [-Wdeprecated-declarations]
   void push(std::auto_ptr <SettingChangeBase> pSettingChange) {
                                                             ^
yaml-cpp/emitterstate.cpp: In member function 'void YAML::EmitterState::EndGroup(YAML::GROUP_TYPE)':
yaml-cpp/emitterstate.cpp:71:25: warning: 'auto_ptr' is deprecated (declared at C:/Rtools/mingw_64/x86_64-w64-mingw32/include/c++/backward/auto_ptr.h:87) [-Wdeprecated-declarations]
    std::auto_ptr<Group> pFinishedGroup = m_groups.pop();
                         ^
C:/Rtools/mingw_64/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -mtune=core2 -c yaml-cpp/emitterutils.cpp -o yaml-cpp/emitterutils.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -mtune=core2 -c yaml-cpp/exp.cpp -o yaml-cpp/exp.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -mtune=core2 -c yaml-cpp/iterator.cpp -o yaml-cpp/iterator.o
yaml-cpp/iterator.cpp:11:50: warning: 'auto_ptr' is deprecated (declared at C:/Rtools/mingw_64/x86_64-w64-mingw32/include/c++/backward/auto_ptr.h:87) [-Wdeprecated-declarations]
  Iterator::Iterator(std::auto_ptr<IterPriv> pData): m_pData(pData)
                                                  ^
C:/Rtools/mingw_64/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -mtune=core2 -c yaml-cpp/nodebuilder.cpp -o yaml-cpp/nodebuilder.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -mtune=core2 -c yaml-cpp/node.cpp -o yaml-cpp/node.o
yaml-cpp/node.cpp: In member function 'std::auto_ptr<YAML::Node> YAML::Node::Clone() const':
yaml-cpp/node.cpp:56:28: warning: 'auto_ptr' is deprecated (declared at C:/Rtools/mingw_64/x86_64-w64-mingw32/include/c++/backward/auto_ptr.h:87) [-Wdeprecated-declarations]
   std::auto_ptr<Node> pNode(new Node);
                            ^
yaml-cpp/node.cpp: In member function 'YAML::Iterator YAML::Node::begin() const':
yaml-cpp/node.cpp:148:76: warning: 'auto_ptr' is deprecated (declared at C:/Rtools/mingw_64/x86_64-w64-mingw32/include/c++/backward/auto_ptr.h:87) [-Wdeprecated-declarations]
     return Iterator(std::auto_ptr<IterPriv>(new IterPriv(m_seqData.begin())));
                                                                            ^
yaml-cpp/node.cpp:150:76: warning: 'auto_ptr' is deprecated (declared at C:/Rtools/mingw_64/x86_64-w64-mingw32/include/c++/backward/auto_ptr.h:87) [-Wdeprecated-declarations]
     return Iterator(std::auto_ptr<IterPriv>(new IterPriv(m_mapData.begin())));
                                                                            ^
yaml-cpp/node.cpp: In member function 'YAML::Iterator YAML::Node::end() const':
yaml-cpp/node.cpp:166:74: warning: 'auto_ptr' is deprecated (declared at C:/Rtools/mingw_64/x86_64-w64-mingw32/include/c++/backward/auto_ptr.h:87) [-Wdeprecated-declarations]
     return Iterator(std::auto_ptr<IterPriv>(new IterPriv(m_seqData.end())));
                                                                          ^
yaml-cpp/node.cpp:168:74: warning: 'auto_ptr' is deprecated (declared at C:/Rtools/mingw_64/x86_64-w64-mingw32/include/c++/backward/auto_ptr.h:87) [-Wdeprecated-declarations]
     return Iterator(std::auto_ptr<IterPriv>(new IterPriv(m_mapData.end())));
                                                                          ^
C:/Rtools/mingw_64/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -mtune=core2 -c yaml-cpp/nodeownership.cpp -o yaml-cpp/nodeownership.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -mtune=core2 -c yaml-cpp/null.cpp -o yaml-cpp/null.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -mtune=core2 -c yaml-cpp/ostream.cpp -o yaml-cpp/ostream.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -mtune=core2 -c yaml-cpp/parser.cpp -o yaml-cpp/parser.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -mtune=core2 -c yaml-cpp/regex.cpp -o yaml-cpp/regex.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -mtune=core2 -c yaml-cpp/scanner.cpp -o yaml-cpp/scanner.o
yaml-cpp/scanner.cpp: In member function 'YAML::Scanner::IndentMarker* YAML::Scanner::PushIndentTo(int, YAML::Scanner::IndentMarker::INDENT_TYPE)':
yaml-cpp/scanner.cpp:284:38: warning: 'auto_ptr' is deprecated (declared at C:/Rtools/mingw_64/x86_64-w64-mingw32/include/c++/backward/auto_ptr.h:87) [-Wdeprecated-declarations]
   std::auto_ptr<IndentMarker> pIndent(new IndentMarker(column, type));
                                      ^
C:/Rtools/mingw_64/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -mtune=core2 -c yaml-cpp/scanscalar.cpp -o yaml-cpp/scanscalar.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -mtune=core2 -c yaml-cpp/scantag.cpp -o yaml-cpp/scantag.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -mtune=core2 -c yaml-cpp/scantoken.cpp -o yaml-cpp/scantoken.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -mtune=core2 -c yaml-cpp/simplekey.cpp -o yaml-cpp/simplekey.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -mtune=core2 -c yaml-cpp/singledocparser.cpp -o yaml-cpp/singledocparser.o
In file included from yaml-cpp/singledocparser.cpp:2:0:
yaml-cpp/collectionstack.h:28:48: warning: unused parameter 'type' [-Wunused-parameter]
   void PopCollectionType(CollectionType::value type) { assert(type == GetCurCollectionType()); collectionStack.pop(); }
                                                ^
C:/Rtools/mingw_64/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -mtune=core2 -c yaml-cpp/stream.cpp -o yaml-cpp/stream.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/include"   -I"C:/extsoft/include"  -Wall -Wextra -I.   -O2 -Wall  -mtune=core2 -c yaml-cpp/tag.cpp -o yaml-cpp/tag.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o seqbias.dll tmp.def sam.o bam_plbuf.o bam_aux.o common.o miscmath.o pos_table.o kmer_matrix.o logger.o motif.o seqbias.o sequencing_bias.o twobitseq.o yaml-cpp/aliasmanager.o yaml-cpp/conversion.o yaml-cpp/directives.o yaml-cpp/emitfromevents.o yaml-cpp/emitter.o yaml-cpp/emitterstate.o yaml-cpp/emitterutils.o yaml-cpp/exp.o yaml-cpp/iterator.o yaml-cpp/nodebuilder.o yaml-cpp/node.o yaml-cpp/nodeownership.o yaml-cpp/null.o yaml-cpp/ostream.o yaml-cpp/parser.o yaml-cpp/regex.o yaml-cpp/scanner.o yaml-cpp/scanscalar.o yaml-cpp/scantag.o yaml-cpp/scantoken.o yaml-cpp/simplekey.o yaml-cpp/singledocparser.o yaml-cpp/stream.o yaml-cpp/tag.o C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rhtslib/usrlib/x64/libhts.a -LC:/extsoft/lib/x64 -lcurl -lrtmp -lssl -lssh2 -lcrypto -lgdi32 -lz -lws2_32 -lwldap32 -lwinmm -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.10-bioc/meat/seqbias.buildbin-libdir/seqbias/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'seqbias' as seqbias_1.34.0.zip
* DONE (seqbias)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'seqbias' successfully unpacked and MD5 sums checked

Tests output


Example timings

seqbias.Rcheck/examples_i386/seqbias-Ex.timings

nameusersystemelapsed
count_reads0.070.020.08
kmer_freq0.390.050.43
random_intervals0.070.000.06
seqbias_fit0.980.001.00
seqbias_load 7.67 3.1810.86
seqbias_predict1.530.021.55
seqbias_save 8.83 4.1713.00

seqbias.Rcheck/examples_x64/seqbias-Ex.timings

nameusersystemelapsed
count_reads0.080.000.15
kmer_freq0.610.040.65
random_intervals0.090.000.09
seqbias_fit1.530.011.61
seqbias_load 8.30 3.7212.04
seqbias_predict2.130.022.14
seqbias_save 6.47 3.5610.19