Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:06:22 -0400 (Fri, 15 Oct 2021).
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 1732/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
seqbias 1.40.0 (landing page) Daniel Jones
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | ERROR | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | |||||||||
Package: seqbias |
Version: 1.40.0 |
Command: rm -rf seqbias.buildbin-libdir && mkdir seqbias.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=seqbias.buildbin-libdir seqbias_1.40.0.tar.gz |
StartedAt: 2021-10-15 11:44:27 -0400 (Fri, 15 Oct 2021) |
EndedAt: 2021-10-15 11:45:53 -0400 (Fri, 15 Oct 2021) |
EllapsedTime: 85.4 seconds |
RetCode: 1 |
Status: ERROR |
PackageFile: None |
PackageFileSize: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf seqbias.buildbin-libdir && mkdir seqbias.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=seqbias.buildbin-libdir seqbias_1.40.0.tar.gz ### ############################################################################## ############################################################################## install for i386 * installing *source* package 'seqbias' ... ** using staged installation ********************************************** WARNING: this package has a configure script It probably needs manual configuration ********************************************** ** libs "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I"c:/extsoft/include" -Wall -Wextra -I. -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sam.c -o sam.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I"c:/extsoft/include" -Wall -Wextra -I. -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c bam_plbuf.c -o bam_plbuf.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I"c:/extsoft/include" -Wall -Wextra -I. -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c bam_aux.c -o bam_aux.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I"c:/extsoft/include" -Wall -Wextra -I. -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c common.c -o common.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I"c:/extsoft/include" -Wall -Wextra -I. -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c miscmath.c -o miscmath.o "C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I"c:/extsoft/include" -Wall -Wextra -I. -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c pos_table.c -o pos_table.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I"c:/extsoft/include" -Wall -Wextra -I. -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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/mingw32/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/mingw32/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/mingw32/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/mingw32/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/mingw32/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/mingw32/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/mingw32/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/mingw32/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/mingw32/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/mingw32/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/mingw32/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/mingw32/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/mingw32/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/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template<typename> class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I"c:/extsoft/include" -Wall -Wextra -I. -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c logger.cpp -o logger.o "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I"c:/extsoft/include" -Wall -Wextra -I. -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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/mingw32/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/mingw32/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/mingw32/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/mingw32/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/mingw32/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/mingw32/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/mingw32/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/mingw32/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/mingw32/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/mingw32/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/mingw32/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/mingw32/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/mingw32/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/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template<typename> class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I"c:/extsoft/include" -Wall -Wextra -I. -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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/mingw32/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/mingw32/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/mingw32/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/mingw32/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/mingw32/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/mingw32/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/mingw32/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/mingw32/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/mingw32/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/mingw32/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/mingw32/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/mingw32/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/mingw32/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/mingw32/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/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I"c:/extsoft/include" -Wall -Wextra -I. -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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/mingw32/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/mingw32/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/mingw32/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/mingw32/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/mingw32/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/mingw32/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/mingw32/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/mingw32/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/mingw32/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/mingw32/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/mingw32/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/mingw32/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/mingw32/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/mingw32/include/c++/8.3.0/bits/unique_ptr.h:53:28: note: declared here template<typename> class auto_ptr; ^~~~~~~~ "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rhtslib/include' -I"c:/extsoft/include" -Wall -Wextra -I. -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c twobitseq.cpp -o twobitseq.o C:\rtools40\mingw32\bin\nm.exe: yaml-cpp/aliasmanager.o: file format not recognized C:\rtools40\mingw32\bin\nm.exe: yaml-cpp/conversion.o: file format not recognized C:\rtools40\mingw32\bin\nm.exe: yaml-cpp/directives.o: file format not recognized C:\rtools40\mingw32\bin\nm.exe: yaml-cpp/emitfromevents.o: file format not recognized C:\rtools40\mingw32\bin\nm.exe: yaml-cpp/emitter.o: file format not recognized C:\rtools40\mingw32\bin\nm.exe: yaml-cpp/emitterstate.o: file format not recognized C:\rtools40\mingw32\bin\nm.exe: yaml-cpp/emitterutils.o: file format not recognized C:\rtools40\mingw32\bin\nm.exe: yaml-cpp/exp.o: file format not recognized C:\rtools40\mingw32\bin\nm.exe: yaml-cpp/iterator.o: file format not recognized C:\rtools40\mingw32\bin\nm.exe: yaml-cpp/nodebuilder.o: file format not recognized C:\rtools40\mingw32\bin\nm.exe: yaml-cpp/node.o: file format not recognized C:\rtools40\mingw32\bin\nm.exe: yaml-cpp/nodeownership.o: file format not recognized C:\rtools40\mingw32\bin\nm.exe: yaml-cpp/null.o: file format not recognized C:\rtools40\mingw32\bin\nm.exe: yaml-cpp/ostream.o: file format not recognized C:\rtools40\mingw32\bin\nm.exe: yaml-cpp/parser.o: file format not recognized C:\rtools40\mingw32\bin\nm.exe: yaml-cpp/regex.o: file format not recognized C:\rtools40\mingw32\bin\nm.exe: yaml-cpp/scanner.o: file format not recognized C:\rtools40\mingw32\bin\nm.exe: yaml-cpp/scanscalar.o: file format not recognized C:\rtools40\mingw32\bin\nm.exe: yaml-cpp/scantag.o: file format not recognized C:\rtools40\mingw32\bin\nm.exe: yaml-cpp/scantoken.o: file format not recognized C:\rtools40\mingw32\bin\nm.exe: yaml-cpp/simplekey.o: file format not recognized C:\rtools40\mingw32\bin\nm.exe: yaml-cpp/singledocparser.o: file format not recognized C:\rtools40\mingw32\bin\nm.exe: yaml-cpp/stream.o: file format not recognized C:\rtools40\mingw32\bin\nm.exe: yaml-cpp/tag.o: file format not recognized C:/rtools40/mingw32/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-3.13-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-3~1.13-/R/bin/i386 -lR yaml-cpp/aliasmanager.o: file not recognized: file format not recognized collect2.exe: error: ld returned 1 exit status no DLL was created ERROR: compilation failed for package 'seqbias' * removing 'C:/Users/biocbuild/bbs-3.13-bioc/meat/seqbias.buildbin-libdir/seqbias'