I'm running Cygwin on a Windows 7 machine and trying to build Tophat from source following this tutorial:
I installed everything available through the cygwin installer. I've successfully (I think) installed Boost, SamTools, and Bowtie, and added all of them to my Path variable.
Configure seems to run without complaint:
Make returns these errors:
The problem seems to be that aio.h is missing. I'm not terribly experienced with Unix or Cygwin and I've been looking all over the place for a workaround without success.
Does anyone have a solution?
I installed everything available through the cygwin installer. I've successfully (I think) installed Boost, SamTools, and Bowtie, and added all of them to my Path variable.
Configure seems to run without complaint:
Code:
checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for gawk... gawk checking whether make sets $(MAKE)... yes checking for gawk... (cached) gawk checking for g++... g++ checking for C++ compiler default output file name... a.exe checking whether the C++ compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... .exe checking for suffix of object files... o checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking for style of include used by make... GNU checking dependency style of g++... gcc3 checking for gcc... gcc checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ANSI C... none needed checking dependency style of gcc... gcc3 checking whether make sets $(MAKE)... (cached) yes checking for ranlib... ranlib checking for a BSD-compatible install... /usr/bin/install -c checking for a Python interpreter with version >= 2.4... python checking for python... /usr/bin/python checking for python version... 2.6 checking for python platform... cygwin checking for python script directory... ${prefix}/lib/python2.6/site-packages checking for python extension module directory... ${exec_prefix}/lib/python2.6/site-packages checking for boostlib >= 1.38.0... yes checking for bamlib... yes checking build system type... i686-pc-cygwin checking whether the Boost::Thread library is available... yes checking for exit in -lboost_thread-mt... yes checking for exit in -lboost_system-mt... yes checking how to run the C preprocessor... gcc -E checking for egrep... grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for unistd.h... (cached) yes checking for ANSI C header files... (cached) yes checking for stdbool.h that conforms to C99... yes checking for _Bool... yes checking for inline... inline checking for pid_t... yes checking for size_t... yes checking for ptrdiff_t... yes checking for an ANSI C-conforming const... yes checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no checking for _LARGE_FILES value needed for large files... no checking for gzread in -lz... yes checking for stdlib.h... (cached) yes checking for GNU libc compatible malloc... yes checking for memset... yes checking for strdup... yes checking for strrchr... yes checking for strtol... yes checking for strsep... yes checking host system type... i686-pc-cygwin checking how to create a pax tar archive... gnutar checking dependency style of gcc... (cached) gcc3 checking dependency style of g++... (cached) gcc3 configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating config.h config.status: config.h is unchanged config.status: executing depfiles commands -- tophat 2.0.6 Configuration Results -- C++ compiler: g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -DNDEBUG -pthread -I/usr/include -I/usr/include -I./SeqAn-1.3 Linker flags: GCC version: gcc (GCC) 4.5.3 Host System type: i686-pc-cygwin Install prefix: /usr/local Install eprefix: ${prefix} See config.h for further configuration information. Email <[email protected], [email protected]> with questions and bug reports.
Code:
make all-recursive make[1]: Entering directory `/cygdrive/c/cygwin/home/mayars1/tophat-2.0.6' Making all in src make[2]: Entering directory `/cygdrive/c/cygwin/home/mayars1/tophat-2.0.6/src' if g++ -DHAVE_CONFIG_H -I. -I. -I.. -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -DNDEBUG -pthread -I/usr/include -I/usr/include -I./SeqAn-1.3 -MT reads.o -MD -MP -MF ".deps/reads.Tpo" -c -o reads.o reads.cpp; \ then mv -f ".deps/reads.Tpo" ".deps/reads.Po"; else rm -f ".deps/reads.Tpo"; exit 1; fi g++: unrecognized option '-pthread' In file included from ./SeqAn-1.3/seqan/file.h:70:0, from ./SeqAn-1.3/seqan/score/score_matrix.h:40, from ./SeqAn-1.3/seqan/score.h:48, from ./SeqAn-1.3/seqan/find.h:45, from reads.cpp:21: ./SeqAn-1.3/seqan/system.h:57:17: fatal error: aio.h: No such file or directory compilation terminated. Makefile:1104: recipe for target `reads.o' failed make[2]: *** [reads.o] Error 1 make[2]: Leaving directory `/cygdrive/c/cygwin/home/mayars1/tophat-2.0.6/src' Makefile:246: recipe for target `all-recursive' failed make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory `/cygdrive/c/cygwin/home/mayars1/tophat-2.0.6' Makefile:184: recipe for target `all' failed make: *** [all] Error 2
Does anyone have a solution?
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