Tophat Cygwin Build from source error: aio.h

[Kolamite]

I'm running Cygwin on a Windows 7 machine and trying to build Tophat from source following this tutorial:

http://tophat.cbcb.umd.edu/tutorial.html

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:

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.

Make returns these errors:

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

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?

[mbblack]

I think your problem is more than that. TopHat is a 64-bit program with 64-bit dependencies, and it (like most short read genomic aligners) will require far more memory than can be addressed by Cygwin's 32-bit limited DLL emulation library.

Cygwin, and anything running within its emulation layer, is restricted to 32-bit memory only. You need a real 64-bit Linux box (or OS X box) and preferable with a bare minimum of 8Gb RAM, or better 16-32Gb's.

P.S. note it does not matter if your Windows release is 64-bit or your machine has tons of RAM - Cygwin, and everything that runs under it, is limited to 32-bit memory addressing only.

[Kolamite]

Gotcha, I was misinformed.

Thanks!