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) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:19:38 -0400 (Wed, 15 Apr 2020).
| Package 1560/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| seqbias 1.34.0 Daniel Jones
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| 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 | |
| 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 |
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###
### 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
###
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* 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.
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
###
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% 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
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seqbias.Rcheck/examples_i386/seqbias-Ex.timings
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seqbias.Rcheck/examples_x64/seqbias-Ex.timings
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