Daniel Jones
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/seqbias |
| git_branch: master |
| git_last_commit: b3b6bc6 |
| git_last_commit_date: 2021-10-26 11:57:52 -0400 (Tue, 26 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:08:40 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| 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 | ||||
|
To the developers/maintainers of the seqbias package: - Please 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 How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1771/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| seqbias 1.43.0 (landing page) Daniel Jones
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | WARNINGS | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: seqbias |
| Version: 1.43.0 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:seqbias.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings seqbias_1.43.0.tar.gz |
| StartedAt: 2022-03-17 20:15:16 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 20:16:47 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 90.8 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: seqbias.Rcheck |
| Warnings: 1 |
##############################################################################
##############################################################################
###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:seqbias.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings seqbias_1.43.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/seqbias.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* 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 '1.43.0'
* 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 ... WARNING
Found the following significant warnings:
./yaml-cpp/parser.h:45:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
./yaml-cpp/parser.h:46:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
./yaml-cpp/iterator.h:20:17: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
./yaml-cpp/iterator.h:36:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
./yaml-cpp/node.h:43:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
./yaml-cpp/node.h:115:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
./yaml-cpp/emitter.h:98:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
yaml-cpp/ptr_stack.h:29:17: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
yaml-cpp/ptr_stack.h:33:7: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
yaml-cpp/ptr_stack.h:34:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
yaml-cpp/setting.h:24:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
yaml-cpp/setting.h:59:14: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
yaml-cpp/setting.h:60:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
yaml-cpp/setting.h:84:18: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
yaml-cpp/emitterstate.cpp:51:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
yaml-cpp/emitterstate.cpp:71:9: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
yaml-cpp/iterator.cpp:11:26: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
yaml-cpp/ptr_vector.h:31:23: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
yaml-cpp/node.cpp:54:7: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
yaml-cpp/node.cpp:56:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
yaml-cpp/node.cpp:148:26: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
yaml-cpp/node.cpp:150:26: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
yaml-cpp/node.cpp:166:26: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
yaml-cpp/node.cpp:168:26: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
yaml-cpp/nodeownership.cpp:18:26: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
yaml-cpp/singledocparser.h:56:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
yaml-cpp/scanner.cpp:237:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
yaml-cpp/scanner.cpp:284:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
See 'D:/biocbuild/bbs-3.15-bioc/meat/seqbias.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' call to 'GenomicRanges' which was already attached by Depends.
Please remove these calls from your code.
Packages in Depends field not imported from:
'Biostrings' 'GenomicRanges' 'methods'
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
count.reads: no visible global function definition for 'is'
count.reads : <anonymous>: no visible global function definition for
'seqnames'
count.reads : <anonymous>: no visible global function definition for
'start'
count.reads : <anonymous>: no visible global function definition for
'end'
count.reads : <anonymous>: no visible global function definition for
'strand'
random.intervals: no visible global function definition for 'is'
random.intervals : uniform_ints : <anonymous>: no visible global
function definition for 'runif'
random.intervals: no visible global function definition for 'GRanges'
random.intervals: no visible global function definition for 'IRanges'
seqbias.fit: no visible global function definition for 'new'
seqbias.load: no visible global function definition for 'new'
seqbias.predict: no visible global function definition for 'is'
seqbias.predict : <anonymous>: no visible global function definition
for 'seqnames'
seqbias.predict : <anonymous>: no visible global function definition
for 'start'
seqbias.predict : <anonymous>: no visible global function definition
for 'end'
seqbias.predict : <anonymous>: no visible global function definition
for 'strand'
Undefined global functions or variables:
GRanges IRanges end is new runif seqnames start strand
Consider adding
importFrom("methods", "is", "new")
importFrom("stats", "end", "runif", "start")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... 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 ... NOTE
Note: information on .o files for x64 is not available
File 'D:/biocbuild/bbs-3.15-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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
seqbias_save 4.03 1.91 5.94
seqbias_load 3.61 2.06 5.68
* 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: 1 WARNING, 4 NOTEs
See
'D:/biocbuild/bbs-3.15-bioc/meat/seqbias.Rcheck/00check.log'
for details.
seqbias.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL seqbias
###
##############################################################################
##############################################################################
* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'seqbias' ...
** using staged installation
**********************************************
WARNING: this package has a configure script
It probably needs manual configuration
**********************************************
** libs
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -Wall -Wextra -I. -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c sam.c -o sam.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -Wall -Wextra -I. -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c bam_plbuf.c -o bam_plbuf.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -Wall -Wextra -I. -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c bam_aux.c -o bam_aux.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -Wall -Wextra -I. -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c common.c -o common.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -Wall -Wextra -I. -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c miscmath.c -o miscmath.o
"C:/rtools40/mingw64/bin/"gcc -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -Wall -Wextra -I. -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c pos_table.c -o pos_table.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -Wall -Wextra -I. -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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:45:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<Scanner> m_pScanner;
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
from ./yaml-cpp/parser.h:12,
from yaml-cpp/yaml.h:9,
from kmer_matrix.hpp:13,
from kmer_matrix.cpp:8:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
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:46:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<Directives> m_pDirectives;
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
from ./yaml-cpp/parser.h:12,
from yaml-cpp/yaml.h:9,
from kmer_matrix.hpp:13,
from kmer_matrix.cpp:8:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
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:20:17: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
Iterator(std::auto_ptr<IterPriv> pData);
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
from ./yaml-cpp/parser.h:12,
from yaml-cpp/yaml.h:9,
from kmer_matrix.hpp:13,
from kmer_matrix.cpp:8:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
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:36:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<IterPriv> m_pData;
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
from ./yaml-cpp/parser.h:12,
from yaml-cpp/yaml.h:9,
from kmer_matrix.hpp:13,
from kmer_matrix.cpp:8:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
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:43:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<Node> Clone() const;
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
from ./yaml-cpp/parser.h:12,
from yaml-cpp/yaml.h:9,
from kmer_matrix.hpp:13,
from kmer_matrix.cpp:8:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
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:115:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<NodeOwnership> m_pOwnership;
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
from ./yaml-cpp/parser.h:12,
from yaml-cpp/yaml.h:9,
from kmer_matrix.hpp:13,
from kmer_matrix.cpp:8:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
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:98:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
std::auto_ptr <EmitterState> m_pState;
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
from ./yaml-cpp/parser.h:12,
from yaml-cpp/yaml.h:9,
from kmer_matrix.hpp:13,
from kmer_matrix.cpp:8:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -Wall -Wextra -I. -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c logger.cpp -o logger.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -Wall -Wextra -I. -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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:45:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<Scanner> m_pScanner;
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
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:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
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:46:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<Directives> m_pDirectives;
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
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:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
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:20:17: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
Iterator(std::auto_ptr<IterPriv> pData);
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
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:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
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:36:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<IterPriv> m_pData;
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
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:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
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:43:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<Node> Clone() const;
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
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:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
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:115:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<NodeOwnership> m_pOwnership;
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
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:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
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:98:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
std::auto_ptr <EmitterState> m_pState;
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
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:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -Wall -Wextra -I. -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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:45:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<Scanner> m_pScanner;
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
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:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
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:46:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<Directives> m_pDirectives;
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
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:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
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:20:17: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
Iterator(std::auto_ptr<IterPriv> pData);
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
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:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
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:36:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<IterPriv> m_pData;
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
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:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
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:43:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<Node> Clone() const;
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
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:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
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:115:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<NodeOwnership> m_pOwnership;
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
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:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
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:98:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
std::auto_ptr <EmitterState> m_pState;
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
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:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
seqbias.cpp: In function 'void R_init_seqbias(DllInfo*)':
seqbias.cpp:493:45: 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]
{ "seqbias_fit", (DL_FUNC) &seqbias_fit, 5 },
^~~~~~~~~~~
seqbias.cpp:494:45: 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]
{ "seqbias_predict", (DL_FUNC) &seqbias_predict, 5 },
^~~~~~~~~~~~~~~
seqbias.cpp:495:45: warning: cast between incompatible function types from 'SEXPREC* (*)(SEXP, SEXP)' {aka 'SEXPREC* (*)(SEXPREC*, SEXPREC*)'} to 'DL_FUNC' {aka 'void* (*)()'} [-Wcast-function-type]
{ "seqbias_load", (DL_FUNC) &seqbias_load, 2 },
^~~~~~~~~~~~
seqbias.cpp:496:45: warning: cast between incompatible function types from 'SEXPREC* (*)(SEXP, SEXP)' {aka 'SEXPREC* (*)(SEXPREC*, SEXPREC*)'} to 'DL_FUNC' {aka 'void* (*)()'} [-Wcast-function-type]
{ "seqbias_save", (DL_FUNC) &seqbias_save, 2 },
^~~~~~~~~~~~
seqbias.cpp:497:48: warning: cast between incompatible function types from 'SEXPREC* (*)(SEXP)' {aka 'SEXPREC* (*)(SEXPREC*)'} to 'DL_FUNC' {aka 'void* (*)()'} [-Wcast-function-type]
{ "seqbias_open_bam", (DL_FUNC) &seqbias_open_bam, 1 },
^~~~~~~~~~~~~~~~
seqbias.cpp:498:48: 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]
{ "seqbias_count_reads", (DL_FUNC) &seqbias_count_reads, 7 },
^~~~~~~~~~~~~~~~~~~
seqbias.cpp:499:60: warning: cast between incompatible function types from 'SEXPREC* (*)(SEXP, SEXP)' {aka 'SEXPREC* (*)(SEXPREC*, SEXPREC*)'} to 'DL_FUNC' {aka 'void* (*)()'} [-Wcast-function-type]
{ "seqbias_alloc_kmer_matrix", (DL_FUNC) &seqbias_alloc_kmer_matrix, 2 },
^~~~~~~~~~~~~~~~~~~~~~~~~
seqbias.cpp:500:60: 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]
{ "seqbias_tally_kmers", (DL_FUNC) &seqbias_tally_kmers, 4 },
^~~~~~~~~~~~~~~~~~~
seqbias.cpp:501:60: warning: cast between incompatible function types from 'SEXPREC* (*)(SEXP, SEXP)' {aka 'SEXPREC* (*)(SEXPREC*, SEXPREC*)'} to 'DL_FUNC' {aka 'void* (*)()'} [-Wcast-function-type]
{ "sebqias_dataframe_from_kmer_matrix", (DL_FUNC) &seqbias_dataframe_from_kmer_matrix, 2 },
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -Wall -Wextra -I. -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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:45:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<Scanner> m_pScanner;
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
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:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
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:46:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<Directives> m_pDirectives;
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
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:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
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:20:17: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
Iterator(std::auto_ptr<IterPriv> pData);
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
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:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
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:36:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<IterPriv> m_pData;
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
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:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
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:43:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<Node> Clone() const;
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
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:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
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:115:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<NodeOwnership> m_pOwnership;
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
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:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
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:98:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
std::auto_ptr <EmitterState> m_pState;
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
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:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -Wall -Wextra -I. -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c twobitseq.cpp -o twobitseq.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -Wall -Wextra -I. -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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:20:17: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
Iterator(std::auto_ptr<IterPriv> pData);
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
from ./yaml-cpp/iterator.h:9,
from ./yaml-cpp/node.h:12,
from yaml-cpp/aliasmanager.cpp:2:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from ./yaml-cpp/node.h:12,
from yaml-cpp/aliasmanager.cpp:2:
./yaml-cpp/iterator.h:36:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<IterPriv> m_pData;
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
from ./yaml-cpp/iterator.h:9,
from ./yaml-cpp/node.h:12,
from yaml-cpp/aliasmanager.cpp:2:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from yaml-cpp/aliasmanager.cpp:2:
./yaml-cpp/node.h:43:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<Node> Clone() const;
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
from ./yaml-cpp/iterator.h:9,
from ./yaml-cpp/node.h:12,
from yaml-cpp/aliasmanager.cpp:2:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from yaml-cpp/aliasmanager.cpp:2:
./yaml-cpp/node.h:115:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<NodeOwnership> m_pOwnership;
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
from ./yaml-cpp/iterator.h:9,
from ./yaml-cpp/node.h:12,
from yaml-cpp/aliasmanager.cpp:2:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -Wall -Wextra -I. -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c yaml-cpp/conversion.cpp -o yaml-cpp/conversion.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -Wall -Wextra -I. -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c yaml-cpp/directives.cpp -o yaml-cpp/directives.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -Wall -Wextra -I. -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c yaml-cpp/emitfromevents.cpp -o yaml-cpp/emitfromevents.o
In file included from yaml-cpp/emitfromevents.cpp:2:
./yaml-cpp/emitter.h:98:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
std::auto_ptr <EmitterState> m_pState;
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
from ./yaml-cpp/emitter.h:14,
from yaml-cpp/emitfromevents.cpp:2:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -Wall -Wextra -I. -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c yaml-cpp/emitter.cpp -o yaml-cpp/emitter.o
In file included from yaml-cpp/emitter.cpp:1:
./yaml-cpp/emitter.h:98:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
std::auto_ptr <EmitterState> m_pState;
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
from ./yaml-cpp/emitter.h:14,
from yaml-cpp/emitter.cpp:1:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
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:29:17: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
void push(std::auto_ptr<T> t) {
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
from ./yaml-cpp/emitter.h:14,
from yaml-cpp/emitter.cpp:1:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
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:33:7: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<T> pop() {
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
from ./yaml-cpp/emitter.h:14,
from yaml-cpp/emitter.cpp:1:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
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:34:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<T> t(m_data.back());
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
from ./yaml-cpp/emitter.h:14,
from yaml-cpp/emitter.cpp:1:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
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:24:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
std::auto_ptr <SettingChangeBase> set(const T& value);
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
from ./yaml-cpp/emitter.h:14,
from yaml-cpp/emitter.cpp:1:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from yaml-cpp/emitterstate.h:10,
from yaml-cpp/emitter.cpp:2:
yaml-cpp/setting.h:59:14: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
inline std::auto_ptr <SettingChangeBase> Setting<T>::set(const T& value) {
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
from ./yaml-cpp/emitter.h:14,
from yaml-cpp/emitter.cpp:1:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
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:60:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
std::auto_ptr <SettingChangeBase> pChange(new SettingChange<T> (this));
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
from ./yaml-cpp/emitter.h:14,
from yaml-cpp/emitter.cpp:1:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
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:84:18: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
void push(std::auto_ptr <SettingChangeBase> pSettingChange) {
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
from ./yaml-cpp/emitter.h:14,
from yaml-cpp/emitter.cpp:1:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -Wall -Wextra -I. -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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:29:17: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
void push(std::auto_ptr<T> t) {
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
from yaml-cpp/ptr_stack.h:9,
from yaml-cpp/emitterstate.h:9,
from yaml-cpp/emitterstate.cpp:1:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
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:33:7: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<T> pop() {
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
from yaml-cpp/ptr_stack.h:9,
from yaml-cpp/emitterstate.h:9,
from yaml-cpp/emitterstate.cpp:1:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
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:34:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<T> t(m_data.back());
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
from yaml-cpp/ptr_stack.h:9,
from yaml-cpp/emitterstate.h:9,
from yaml-cpp/emitterstate.cpp:1:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
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:24:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
std::auto_ptr <SettingChangeBase> set(const T& value);
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
from yaml-cpp/ptr_stack.h:9,
from yaml-cpp/emitterstate.h:9,
from yaml-cpp/emitterstate.cpp:1:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from yaml-cpp/emitterstate.h:10,
from yaml-cpp/emitterstate.cpp:1:
yaml-cpp/setting.h:59:14: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
inline std::auto_ptr <SettingChangeBase> Setting<T>::set(const T& value) {
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
from yaml-cpp/ptr_stack.h:9,
from yaml-cpp/emitterstate.h:9,
from yaml-cpp/emitterstate.cpp:1:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
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:60:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
std::auto_ptr <SettingChangeBase> pChange(new SettingChange<T> (this));
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
from yaml-cpp/ptr_stack.h:9,
from yaml-cpp/emitterstate.h:9,
from yaml-cpp/emitterstate.cpp:1:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
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:84:18: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
void push(std::auto_ptr <SettingChangeBase> pSettingChange) {
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
from yaml-cpp/ptr_stack.h:9,
from yaml-cpp/emitterstate.h:9,
from yaml-cpp/emitterstate.cpp:1:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
yaml-cpp/emitterstate.cpp: In member function 'void YAML::EmitterState::BeginGroup(YAML::GROUP_TYPE)':
yaml-cpp/emitterstate.cpp:51:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<Group> pGroup(new Group(type));
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
from yaml-cpp/ptr_stack.h:9,
from yaml-cpp/emitterstate.h:9,
from yaml-cpp/emitterstate.cpp:1:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
yaml-cpp/emitterstate.cpp: In member function 'void YAML::EmitterState::EndGroup(YAML::GROUP_TYPE)':
yaml-cpp/emitterstate.cpp:71:9: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<Group> pFinishedGroup = m_groups.pop();
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
from yaml-cpp/ptr_stack.h:9,
from yaml-cpp/emitterstate.h:9,
from yaml-cpp/emitterstate.cpp:1:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -Wall -Wextra -I. -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c yaml-cpp/emitterutils.cpp -o yaml-cpp/emitterutils.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -Wall -Wextra -I. -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c yaml-cpp/exp.cpp -o yaml-cpp/exp.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -Wall -Wextra -I. -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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:20:17: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
Iterator(std::auto_ptr<IterPriv> pData);
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
from ./yaml-cpp/iterator.h:9,
from ./yaml-cpp/node.h:12,
from yaml-cpp/iterator.cpp:1:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from ./yaml-cpp/node.h:12,
from yaml-cpp/iterator.cpp:1:
./yaml-cpp/iterator.h:36:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<IterPriv> m_pData;
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
from ./yaml-cpp/iterator.h:9,
from ./yaml-cpp/node.h:12,
from yaml-cpp/iterator.cpp:1:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from yaml-cpp/iterator.cpp:1:
./yaml-cpp/node.h:43:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<Node> Clone() const;
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
from ./yaml-cpp/iterator.h:9,
from ./yaml-cpp/node.h:12,
from yaml-cpp/iterator.cpp:1:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from yaml-cpp/iterator.cpp:1:
./yaml-cpp/node.h:115:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<NodeOwnership> m_pOwnership;
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
from ./yaml-cpp/iterator.h:9,
from ./yaml-cpp/node.h:12,
from yaml-cpp/iterator.cpp:1:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
yaml-cpp/iterator.cpp:11:26: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
Iterator::Iterator(std::auto_ptr<IterPriv> pData): m_pData(pData)
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
from ./yaml-cpp/iterator.h:9,
from ./yaml-cpp/node.h:12,
from yaml-cpp/iterator.cpp:1:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -Wall -Wextra -I. -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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:20:17: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
Iterator(std::auto_ptr<IterPriv> pData);
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
from yaml-cpp/nodebuilder.h:10,
from yaml-cpp/nodebuilder.cpp:1:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from ./yaml-cpp/node.h:12,
from yaml-cpp/nodebuilder.cpp:3:
./yaml-cpp/iterator.h:36:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<IterPriv> m_pData;
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
from yaml-cpp/nodebuilder.h:10,
from yaml-cpp/nodebuilder.cpp:1:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from yaml-cpp/nodebuilder.cpp:3:
./yaml-cpp/node.h:43:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<Node> Clone() const;
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
from yaml-cpp/nodebuilder.h:10,
from yaml-cpp/nodebuilder.cpp:1:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from yaml-cpp/nodebuilder.cpp:3:
./yaml-cpp/node.h:115:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<NodeOwnership> m_pOwnership;
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
from yaml-cpp/nodebuilder.h:10,
from yaml-cpp/nodebuilder.cpp:1:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -Wall -Wextra -I. -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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:20:17: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
Iterator(std::auto_ptr<IterPriv> pData);
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
from ./yaml-cpp/iterator.h:9,
from ./yaml-cpp/node.h:12,
from yaml-cpp/node.cpp:1:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from ./yaml-cpp/node.h:12,
from yaml-cpp/node.cpp:1:
./yaml-cpp/iterator.h:36:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<IterPriv> m_pData;
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
from ./yaml-cpp/iterator.h:9,
from ./yaml-cpp/node.h:12,
from yaml-cpp/node.cpp:1:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from yaml-cpp/node.cpp:1:
./yaml-cpp/node.h:43:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<Node> Clone() const;
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
from ./yaml-cpp/iterator.h:9,
from ./yaml-cpp/node.h:12,
from yaml-cpp/node.cpp:1:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from yaml-cpp/node.cpp:1:
./yaml-cpp/node.h:115:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<NodeOwnership> m_pOwnership;
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
from ./yaml-cpp/iterator.h:9,
from ./yaml-cpp/node.h:12,
from yaml-cpp/node.cpp:1:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
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:31:23: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
void push_back(std::auto_ptr<T> t) {
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
from ./yaml-cpp/iterator.h:9,
from ./yaml-cpp/node.h:12,
from yaml-cpp/node.cpp:1:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from yaml-cpp/node.cpp:10:
./yaml-cpp/emitter.h:98:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
std::auto_ptr <EmitterState> m_pState;
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
from ./yaml-cpp/iterator.h:9,
from ./yaml-cpp/node.h:12,
from yaml-cpp/node.cpp:1:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
yaml-cpp/node.cpp:54:7: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<Node> Node::Clone() const
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
from ./yaml-cpp/iterator.h:9,
from ./yaml-cpp/node.h:12,
from yaml-cpp/node.cpp:1:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
yaml-cpp/node.cpp: In member function 'std::auto_ptr<YAML::Node> YAML::Node::Clone() const':
yaml-cpp/node.cpp:56:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<Node> pNode(new Node);
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
from ./yaml-cpp/iterator.h:9,
from ./yaml-cpp/node.h:12,
from yaml-cpp/node.cpp:1:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
yaml-cpp/node.cpp: In member function 'YAML::Iterator YAML::Node::begin() const':
yaml-cpp/node.cpp:148:26: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
return Iterator(std::auto_ptr<IterPriv>(new IterPriv(m_seqData.begin())));
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
from ./yaml-cpp/iterator.h:9,
from ./yaml-cpp/node.h:12,
from yaml-cpp/node.cpp:1:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
yaml-cpp/node.cpp:150:26: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
return Iterator(std::auto_ptr<IterPriv>(new IterPriv(m_mapData.begin())));
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
from ./yaml-cpp/iterator.h:9,
from ./yaml-cpp/node.h:12,
from yaml-cpp/node.cpp:1:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
yaml-cpp/node.cpp: In member function 'YAML::Iterator YAML::Node::end() const':
yaml-cpp/node.cpp:166:26: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
return Iterator(std::auto_ptr<IterPriv>(new IterPriv(m_seqData.end())));
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
from ./yaml-cpp/iterator.h:9,
from ./yaml-cpp/node.h:12,
from yaml-cpp/node.cpp:1:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
yaml-cpp/node.cpp:168:26: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
return Iterator(std::auto_ptr<IterPriv>(new IterPriv(m_mapData.end())));
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
from ./yaml-cpp/iterator.h:9,
from ./yaml-cpp/node.h:12,
from yaml-cpp/node.cpp:1:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -Wall -Wextra -I. -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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:31:23: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
void push_back(std::auto_ptr<T> t) {
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
from yaml-cpp/ptr_vector.h:9,
from yaml-cpp/nodeownership.h:10,
from yaml-cpp/nodeownership.cpp:1:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from ./yaml-cpp/node.h:12,
from yaml-cpp/nodeownership.cpp:2:
./yaml-cpp/iterator.h:20:17: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
Iterator(std::auto_ptr<IterPriv> pData);
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
from yaml-cpp/ptr_vector.h:9,
from yaml-cpp/nodeownership.h:10,
from yaml-cpp/nodeownership.cpp:1:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from ./yaml-cpp/node.h:12,
from yaml-cpp/nodeownership.cpp:2:
./yaml-cpp/iterator.h:36:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<IterPriv> m_pData;
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
from yaml-cpp/ptr_vector.h:9,
from yaml-cpp/nodeownership.h:10,
from yaml-cpp/nodeownership.cpp:1:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from yaml-cpp/nodeownership.cpp:2:
./yaml-cpp/node.h:43:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<Node> Clone() const;
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
from yaml-cpp/ptr_vector.h:9,
from yaml-cpp/nodeownership.h:10,
from yaml-cpp/nodeownership.cpp:1:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from yaml-cpp/nodeownership.cpp:2:
./yaml-cpp/node.h:115:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<NodeOwnership> m_pOwnership;
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
from yaml-cpp/ptr_vector.h:9,
from yaml-cpp/nodeownership.h:10,
from yaml-cpp/nodeownership.cpp:1:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
yaml-cpp/nodeownership.cpp: In member function 'YAML::Node& YAML::NodeOwnership::_Create()':
yaml-cpp/nodeownership.cpp:18:26: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
m_nodes.push_back(std::auto_ptr<Node>(new Node));
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
from yaml-cpp/ptr_vector.h:9,
from yaml-cpp/nodeownership.h:10,
from yaml-cpp/nodeownership.cpp:1:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -Wall -Wextra -I. -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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:20:17: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
Iterator(std::auto_ptr<IterPriv> pData);
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
from ./yaml-cpp/iterator.h:9,
from ./yaml-cpp/node.h:12,
from yaml-cpp/null.cpp:2:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from ./yaml-cpp/node.h:12,
from yaml-cpp/null.cpp:2:
./yaml-cpp/iterator.h:36:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<IterPriv> m_pData;
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
from ./yaml-cpp/iterator.h:9,
from ./yaml-cpp/node.h:12,
from yaml-cpp/null.cpp:2:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from yaml-cpp/null.cpp:2:
./yaml-cpp/node.h:43:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<Node> Clone() const;
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
from ./yaml-cpp/iterator.h:9,
from ./yaml-cpp/node.h:12,
from yaml-cpp/null.cpp:2:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from yaml-cpp/null.cpp:2:
./yaml-cpp/node.h:115:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<NodeOwnership> m_pOwnership;
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
from ./yaml-cpp/iterator.h:9,
from ./yaml-cpp/node.h:12,
from yaml-cpp/null.cpp:2:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -Wall -Wextra -I. -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c yaml-cpp/ostream.cpp -o yaml-cpp/ostream.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -Wall -Wextra -I. -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c yaml-cpp/parser.cpp -o yaml-cpp/parser.o
In file included from yaml-cpp/parser.cpp:1:
./yaml-cpp/parser.h:45:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<Scanner> m_pScanner;
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
from ./yaml-cpp/parser.h:12,
from yaml-cpp/parser.cpp:1:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from yaml-cpp/parser.cpp:1:
./yaml-cpp/parser.h:46:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<Directives> m_pDirectives;
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
from ./yaml-cpp/parser.h:12,
from yaml-cpp/parser.cpp:1:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from ./yaml-cpp/node.h:12,
from yaml-cpp/parser.cpp:5:
./yaml-cpp/iterator.h:20:17: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
Iterator(std::auto_ptr<IterPriv> pData);
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
from ./yaml-cpp/parser.h:12,
from yaml-cpp/parser.cpp:1:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from ./yaml-cpp/node.h:12,
from yaml-cpp/parser.cpp:5:
./yaml-cpp/iterator.h:36:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<IterPriv> m_pData;
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
from ./yaml-cpp/parser.h:12,
from yaml-cpp/parser.cpp:1:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from yaml-cpp/parser.cpp:5:
./yaml-cpp/node.h:43:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<Node> Clone() const;
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
from ./yaml-cpp/parser.h:12,
from yaml-cpp/parser.cpp:1:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from yaml-cpp/parser.cpp:5:
./yaml-cpp/node.h:115:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<NodeOwnership> m_pOwnership;
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
from ./yaml-cpp/parser.h:12,
from yaml-cpp/parser.cpp:1:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
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:31:23: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
void push_back(std::auto_ptr<T> t) {
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
from ./yaml-cpp/parser.h:12,
from yaml-cpp/parser.cpp:1:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from yaml-cpp/parser.cpp:8:
yaml-cpp/singledocparser.h:56:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<CollectionStack> m_pCollectionStack;
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
from ./yaml-cpp/parser.h:12,
from yaml-cpp/parser.cpp:1:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -Wall -Wextra -I. -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c yaml-cpp/regex.cpp -o yaml-cpp/regex.o
In file included from yaml-cpp/regex.cpp:1:
yaml-cpp/regex.h: In constructor 'YAML::RegEx::RegEx(const string&, YAML::REGEX_OP)':
yaml-cpp/regex.h:21:8: warning: '<anonymous>.YAML::RegEx::m_z' may be used uninitialized in this function [-Wmaybe-uninitialized]
class RegEx
^~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -Wall -Wextra -I. -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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:31:23: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
void push_back(std::auto_ptr<T> t) {
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
from yaml-cpp/ptr_vector.h:9,
from yaml-cpp/scanner.h:15,
from yaml-cpp/scanner.cpp:1:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
yaml-cpp/scanner.cpp: In member function 'void YAML::Scanner::StartStream()':
yaml-cpp/scanner.cpp:237:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<IndentMarker> pIndent(new IndentMarker(-1, IndentMarker::NONE));
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
from yaml-cpp/ptr_vector.h:9,
from yaml-cpp/scanner.h:15,
from yaml-cpp/scanner.cpp:1:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
yaml-cpp/scanner.cpp: In member function 'YAML::Scanner::IndentMarker* YAML::Scanner::PushIndentTo(int, YAML::Scanner::IndentMarker::INDENT_TYPE)':
yaml-cpp/scanner.cpp:284:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<IndentMarker> pIndent(new IndentMarker(column, type));
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
from yaml-cpp/ptr_vector.h:9,
from yaml-cpp/scanner.h:15,
from yaml-cpp/scanner.cpp:1:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -Wall -Wextra -I. -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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:31:23: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
void push_back(std::auto_ptr<T> t) {
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
from yaml-cpp/ptr_vector.h:9,
from yaml-cpp/scanner.h:15,
from yaml-cpp/scanscalar.cpp:2:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -Wall -Wextra -I. -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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:31:23: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
void push_back(std::auto_ptr<T> t) {
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
from yaml-cpp/ptr_vector.h:9,
from yaml-cpp/scanner.h:15,
from yaml-cpp/scantag.cpp:1:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -Wall -Wextra -I. -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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:31:23: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
void push_back(std::auto_ptr<T> t) {
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
from yaml-cpp/ptr_vector.h:9,
from yaml-cpp/scanner.h:15,
from yaml-cpp/scantoken.cpp:1:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -Wall -Wextra -I. -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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:31:23: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
void push_back(std::auto_ptr<T> t) {
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
from yaml-cpp/ptr_vector.h:9,
from yaml-cpp/scanner.h:15,
from yaml-cpp/simplekey.cpp:1:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -Wall -Wextra -I. -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c yaml-cpp/singledocparser.cpp -o yaml-cpp/singledocparser.o
In file included from yaml-cpp/singledocparser.cpp:1:
yaml-cpp/singledocparser.h:56:8: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<CollectionStack> m_pCollectionStack;
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
from yaml-cpp/singledocparser.h:13,
from yaml-cpp/singledocparser.cpp:1:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
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:28:48: warning: unused parameter 'type' [-Wunused-parameter]
void PopCollectionType(CollectionType::value type) { assert(type == GetCurCollectionType()); collectionStack.pop(); }
~~~~~~~~~~~~~~~~~~~~~~^~~~
In file included from yaml-cpp/scanner.h:15,
from yaml-cpp/singledocparser.cpp:6:
yaml-cpp/ptr_vector.h: At global scope:
yaml-cpp/ptr_vector.h:31:23: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
void push_back(std::auto_ptr<T> t) {
^~~~~~~~
In file included from C:/rtools40/mingw64/include/c++/8.3.0/memory:80,
from yaml-cpp/singledocparser.h:13,
from yaml-cpp/singledocparser.cpp:1:
C:/rtools40/mingw64/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -Wall -Wextra -I. -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c yaml-cpp/stream.cpp -o yaml-cpp/stream.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I"C:/extsoft/include" -Wall -Wextra -I. -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c yaml-cpp/tag.cpp -o yaml-cpp/tag.o
C:/rtools40/mingw64/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 D:/biocbuild/bbs-3.15-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 -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
installing to D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-seqbias/00new/seqbias/libs/x64
** 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
* DONE (seqbias)
Making 'packages.html' ... done
seqbias.Rcheck/seqbias-Ex.timings
| name | user | system | elapsed | |
| count_reads | 0.06 | 0.00 | 0.06 | |
| kmer_freq | 0.26 | 0.05 | 0.31 | |
| random_intervals | 0.04 | 0.00 | 0.05 | |
| seqbias_fit | 1.16 | 0.00 | 1.16 | |
| seqbias_load | 3.61 | 2.06 | 5.68 | |
| seqbias_predict | 0.75 | 0.00 | 0.75 | |
| seqbias_save | 4.03 | 1.91 | 5.94 | |