Having a problem installing TopHat v.1.1.x onto a PC using cygwin. I have Bowtie 0.12.7 and Samtools 0.1.9 properly (as far as I can tell) installed and configured. Running ./configure for tophat I get :
Running make I get:
Any suggestions? I'm relatively new to all this computer stuff, so dumbed down answers would be appreciated. Thanks.
# ./configure --prefix=/path/to/install/directory/
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 build system type... i686-pc-cygwin
checking host system type... i686-pc-cygwin
checking for gcc... gcc
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 gcc accepts -g... yes
checking for gcc option to accept ANSI C... none needed
checking for style of include used by make... GNU
checking dependency style of gcc... gcc3
checking for g++... g++
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking dependency style of g++... gcc3
checking for gawk... (cached) gawk
checking for a BSD-compatible install... /usr/bin/install -c
checking for ranlib... ranlib
checking for ar... ar
checking for perl... /usr/bin/perl
checking for bash... /usr/bin/bash
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/s
ite-packages
checking for bamlib... 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 if zlib is wanted... yes
checking for inflateEnd in -lz... yes
checking zlib.h usability... yes
checking zlib.h presence... yes
checking for zlib.h... yes
checking for inflateEnd in -lz... (cached) yes
checking zlib in /usr... ok
checking how to run the C++ preprocessor... g++ -E
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 stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking for unistd.h... (cached) yes
checking for stdbool.h that conforms to C99... yes
checking for _Bool... no
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 if gcc accepts -m64... yes
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 1.1.0 Configuration Results --
C compiler: gcc -Wall -m64 -O3 -DNDEBUG
C++ compiler: g++ -Wall -m64 -O3 -DNDEBUG -I/usr/local/include
GCC version: gcc (GCC) 3.4.4 (cygming special, gdc 0.12, using dmd 0.1
25)
Host System type: i686-pc-cygwin
Install prefix: /path/to/install/directory/
Install eprefix: ${prefix}
See config.h for further configuration information.
Email <[email protected]> with questions and bug reports.
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 build system type... i686-pc-cygwin
checking host system type... i686-pc-cygwin
checking for gcc... gcc
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 gcc accepts -g... yes
checking for gcc option to accept ANSI C... none needed
checking for style of include used by make... GNU
checking dependency style of gcc... gcc3
checking for g++... g++
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking dependency style of g++... gcc3
checking for gawk... (cached) gawk
checking for a BSD-compatible install... /usr/bin/install -c
checking for ranlib... ranlib
checking for ar... ar
checking for perl... /usr/bin/perl
checking for bash... /usr/bin/bash
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/s
ite-packages
checking for bamlib... 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 if zlib is wanted... yes
checking for inflateEnd in -lz... yes
checking zlib.h usability... yes
checking zlib.h presence... yes
checking for zlib.h... yes
checking for inflateEnd in -lz... (cached) yes
checking zlib in /usr... ok
checking how to run the C++ preprocessor... g++ -E
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 stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking for unistd.h... (cached) yes
checking for stdbool.h that conforms to C99... yes
checking for _Bool... no
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 if gcc accepts -m64... yes
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 1.1.0 Configuration Results --
C compiler: gcc -Wall -m64 -O3 -DNDEBUG
C++ compiler: g++ -Wall -m64 -O3 -DNDEBUG -I/usr/local/include
GCC version: gcc (GCC) 3.4.4 (cygming special, gdc 0.12, using dmd 0.1
25)
Host System type: i686-pc-cygwin
Install prefix: /path/to/install/directory/
Install eprefix: ${prefix}
See config.h for further configuration information.
Email <[email protected]> with questions and bug reports.
Running make I get:
# make
make all-recursive
make[1]: Entering directory `/cygdrive/c/Users/jfontana/Desktop/tophat-1.1.0'
Making all in src
make[2]: Entering directory `/cygdrive/c/Users/jfontana/Desktop/tophat-1.1.0/src
'
if g++ -DHAVE_CONFIG_H -I. -I. -I.. -I/usr/include -Wall -m64 -O3 -DNDEBUG -I
/usr/local/include -I./SeqAn-1.1 -Wall -m64 -O3 -DNDEBUG -I/usr/local/include -
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.T
po"; exit 1; fi
reads.cpp:1: sorry, unimplemented: 64-bit mode not compiled in
In file included from reads.cpp:20:
bwt_map.h: In constructor `RefSequenceTable::RefSequenceTable(const std::string&
, bool, bool)':
bwt_map.h:332: warning: comparison between signed and unsigned integer expressio
ns
make[2]: *** [reads.o] Error 1
make[2]: Leaving directory `/cygdrive/c/Users/jfontana/Desktop/tophat-1.1.0/src'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/cygdrive/c/Users/jfontana/Desktop/tophat-1.1.0'
make: *** [all] Error 2
make all-recursive
make[1]: Entering directory `/cygdrive/c/Users/jfontana/Desktop/tophat-1.1.0'
Making all in src
make[2]: Entering directory `/cygdrive/c/Users/jfontana/Desktop/tophat-1.1.0/src
'
if g++ -DHAVE_CONFIG_H -I. -I. -I.. -I/usr/include -Wall -m64 -O3 -DNDEBUG -I
/usr/local/include -I./SeqAn-1.1 -Wall -m64 -O3 -DNDEBUG -I/usr/local/include -
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.T
po"; exit 1; fi
reads.cpp:1: sorry, unimplemented: 64-bit mode not compiled in
In file included from reads.cpp:20:
bwt_map.h: In constructor `RefSequenceTable::RefSequenceTable(const std::string&
, bool, bool)':
bwt_map.h:332: warning: comparison between signed and unsigned integer expressio
ns
make[2]: *** [reads.o] Error 1
make[2]: Leaving directory `/cygdrive/c/Users/jfontana/Desktop/tophat-1.1.0/src'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/cygdrive/c/Users/jfontana/Desktop/tophat-1.1.0'
make: *** [all] Error 2
Any suggestions? I'm relatively new to all this computer stuff, so dumbed down answers would be appreciated. Thanks.
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