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Old 01-26-2010, 04:16 PM   #1
deepsea
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Location: California

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Default tophat installing problem

Hi,

I have installed tophat (v1.0.12) on Mac (10.6, gcc 4.2.1) and it works fine. Now I need to install tophat on Linux boxes (Debian gcc4.4 and Redhat gcc4.1.2), all failed.

Here is the configure result:

======================

checking build system type... i686-pc-linux-gnu
checking host system type... i686-pc-linux-gnu
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
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 ISO C89... none needed
checking for g++... g++
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking for gawk... gawk
checking for a BSD-compatible install... /usr/bin/install -c
checking for ranlib... ranlib
checking for ar... ar
checking for perl... /usr/local/bin/perl
checking for bash... /bin/bash
checking for a Python interpreter with version >= 2.4... python
checking for python... /usr/bin/python
checking for python version... 2.4
checking for python platform... linux2
checking for python script directory... ${prefix}/lib/python2.4/site-packages
checking for python extension module directory... ${exec_prefix}/lib/python2.4/site-packages
checking if gcc accepts -m64... yes
checking for gzread in -lz... no
checking how to run the C++ preprocessor... g++ -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... no
checking for sys/types.h... no
checking for sys/stat.h... no
checking for stdlib.h... no
checking for string.h... no
checking for memory.h... no
checking for strings.h... no
checking for inttypes.h... no
checking for stdint.h... no
checking for unistd.h... no
checking for stdlib.h... (cached) no
checking for string.h... (cached) no
checking for unistd.h... (cached) no
checking for stdbool.h that conforms to C99... no
checking for _Bool... no
checking for an ANSI C-conforming const... no
checking for int32_t... no
checking for size_t... no
checking for uint32_t... no
checking for uint64_t... no
checking for uint8_t... no
checking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... unknown
checking for _LARGE_FILES value needed for large files... unknown
checking for stdlib.h... (cached) no
checking for GNU libc compatible malloc... no
checking for memset... no
checking for strdup... no
checking for strrchr... no
checking for strtol... no
checking for strsep... no
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking whether make sets $(MAKE)... yes
checking for style of include used by make... GNU
checking dependency style of gcc... gcc3
checking dependency style of g++... 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 1.0.12 Configuration Results --
C compiler: gcc -Wall -g -m64 -O3 -DNDEBUG
C++ compiler: g++ -Wall -g -m64 -O3 -DNDEBUG
GCC version: gcc (GCC) 4.1.2 20080704 (Red Hat 4.1.2-44)
Host System type: i686-pc-linux-gnu
Install prefix: /home/ds/software/tophat-1.0.12
Install eprefix: ${prefix}

See config.h for further configuration information.
Email <cole@cs.umd.edu> with questions and bug reports.

======================
Then make:

make all-recursive
make[1]: Entering directory `/home/ds/software/tophat-1.0.12'
Making all in src
make[2]: Entering directory `/home/ds/software/tophat-1.0.12/src'
g++ -DHAVE_CONFIG_H -I. -I.. -Wall -g -m64 -O3 -DNDEBUG -I./SeqAn-1.1 -Wall -g -m64 -O3 -DNDEBUG -MT reads.o -MD -MP -MF .deps/reads.Tpo -c -o reads.o reads.cpp
reads.cpp:1: sorry, unimplemented: 64-bit mode not compiled in
/usr/lib/gcc/i386-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstddef:55: error: expected unqualified-id before 'unsigned'
/usr/lib/gcc/i386-redhat-linux/4.1.2/../../../../include/c++/4.1.2/cstddef:55: error: expected `;' before 'unsigned'
....

======================


I found there were several posts about similar installation problems of tophat, but couldn't find a solution for my case.

Any suggestions? Thanks a lot!
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Old 01-28-2010, 03:41 PM   #2
ChrisL
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I have the same problem.

Installed fine on Mac, but same issue on current release of 64 bit Ubuntu.
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Old 02-02-2010, 09:15 PM   #3
deepsea
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Problem solved. I mean I don't know the exact reason but I found it works well on Ubuntu 8.04.

ChrisL, you might want to the trick of adding a "#include <cstdio>" line in gff_juncs.cpp. Good luck!
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Old 02-02-2010, 11:00 PM   #4
jmarshall
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Quote:
Originally Posted by deepsea View Post
Here is the configure result:
======================
checking build system type... i686-pc-linux-gnu
checking host system type... i686-pc-linux-gnu
[...]
checking if gcc accepts -m64... yes
[...]
C compiler: gcc -Wall -g -m64 -O3 -DNDEBUG
C++ compiler: g++ -Wall -g -m64 -O3 -DNDEBUG
[...]
reads.cpp:1: sorry, unimplemented: 64-bit mode not compiled in
The problem is that you do not have an x86-64 compiler installed. The configure script should have detected this, but there is a bug that means it is not really "checking if gcc accepts -m64".

You can try changing CFLAGS="-m64" on line 4028 of configure to CXXFLAGS="-m64" and rerunning configure, which will hopefully cause different flags to be shown on the "C compiler" and "C++ compiler" lines shown above and will build a 32-bit executable, which you do have a compiler for.

(If you know autoconf, the bug is that it should be using CXXFLAGS before AC_COMPILE_IFELSE rather than CFLAGS due to AC_LANG(C++), and I've emailed Cole to that effect.)

-- John
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Old 02-08-2010, 10:58 AM   #5
deepsea
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Default Thanks John!

Now it works! Thank you so much! :-D
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Old 05-17-2010, 02:37 AM   #6
James
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I have tried to Install this on Mac however I seem unable to. I have moved all the bowtie files and installed Python. I get stuck on this bit:

./configure --prefix=/path/to/install/directory/

I get this:

./configure: No such file or directory

I'm a bit of a newbie to UNIX is there a different command for 'configure' and 'make' in bash on OSX?

I'm running bash on OS X Leopard.

Thanks, James
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Old 05-17-2010, 10:08 AM   #7
raela
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James, try running ./autogen.sh first, then proceed with ./configure.
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Old 06-17-2010, 03:48 AM   #8
sphil
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hey guys, want to install tophat on ubuntu 10.4 64 bit but get this freakin error:...

the configure seems to be well:
./configure CFLAGS="-m64" CXXFLAGS="-m64"
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
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 ISO C89... none needed
checking for g++... g++
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking for gawk... 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... /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... linux2
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 if gcc accepts -m64... yes
checking for gzread in -lz... no
checking how to run the C++ preprocessor... g++ -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/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 stdbool.h that conforms to C99... yes
checking for _Bool... no
checking for an ANSI C-conforming const... yes
checking for int32_t... yes
checking for size_t... yes
checking for uint32_t... yes
checking for uint64_t... yes
checking for uint8_t... 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 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 whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking whether make sets $(MAKE)... yes
checking for style of include used by make... GNU
checking dependency style of gcc... gcc3
checking dependency style of g++... 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 1.0.12 Configuration Results --
C compiler: gcc -Wall -g -m64 -O3 -m64 -DNDEBUG
C++ compiler: g++ -Wall -g -m64 -O3 -m64 -DNDEBUG
GCC version: gcc (Ubuntu 4.4.3-4ubuntu5) 4.4.3
Host System type: x86_64-unknown-linux-gnu
Install prefix: /home/lokadmin/.local/share/Trash/files/tophat-1.3.0.12
Install eprefix: ${prefix}

See config.h for further configuration information.
Email <cole@cs.umd.edu> with questions and bug reports.


but then when typing make error occurs:

lokadmin@mbt-pc1:~/Desktop/Mapping/tophat-1.0.12$ make
make all-recursive
make[1]: Betrete Verzeichnis '/home/lokadmin/.local/share/Trash/files/tophat-1.3.0.12'
Making all in src
make[2]: Betrete Verzeichnis '/home/lokadmin/.local/share/Trash/files/tophat-1.3.0.12/src'
g++ -DHAVE_CONFIG_H -I. -I.. -Wall -g -m64 -O3 -m64 -DNDEBUG -I./SeqAn-1.1 -Wall -g -m64 -O3 -m64 -DNDEBUG -MT gff_juncs.o -MD -MP -MF .deps/gff_juncs.Tpo -c -o gff_juncs.o gff_juncs.cpp
gff_juncs.cpp: In function ‘void print_usage()’:
gff_juncs.cpp:25: error: ‘stderr’ was not declared in this scope
gff_juncs.cpp:25: error: ‘fprintf’ was not declared in this scope
gff_juncs.cpp: In function ‘uint32_t get_junctions_from_gff(const fsa::GFF_database&)’:
gff_juncs.cpp:144: error: ‘stderr’ was not declared in this scope
gff_juncs.cpp:144: error: ‘fprintf’ was not declared in this scope
gff_juncs.cpp:153: error: ‘stdout’ was not declared in this scope
gff_juncs.cpp:157: error: ‘fprintf’ was not declared in this scope
gff_juncs.cpp: In function ‘int main(int, char**)’:
gff_juncs.cpp:189: error: ‘stderr’ was not declared in this scope
gff_juncs.cpp:189: error: ‘fprintf’ was not declared in this scope
make[2]: *** [gff_juncs.o] Fehler 1
make[2]: Verlasse Verzeichnis '/home/lokadmin/.local/share/Trash/files/tophat-1.3.0.12/src'
make[1]: *** [all-recursive] Fehler 1
make[1]: Verlasse Verzeichnis '/home/lokadmin/.local/share/Trash/files/tophat-1.3.0.12'
make: *** [all] Fehler 2


didnt know how to fix it, can u help me?


regards sphil
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Old 06-21-2010, 07:29 AM   #9
raela
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I believe the problem is the older version.. I think I had similar issues when I tried using that one. Instead try to install this one: http://tophat.cbcb.umd.edu/downloads...-1.0.13.tar.gz
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Old 08-12-2010, 03:37 PM   #10
doggysaywhat
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Hello Sphil I'm having a similar problem as you but I'm using the 1.0.14 version. The configure works just fine but after trying make I get this error

if g++ -DHAVE_CONFIG_H -I. -I. -I.. -Wall -m64 -O3 -DNDEBUG -I./SeqAn-1.1 -Wall -m64 -O3 -DNDEBUG -MT common.o -MD -MP -MF ".deps/common.Tpo" -c -o common.o common.cpp; \
then mv -f ".deps/common.Tpo" ".deps/common.Po"; else rm -f ".deps/common.Tpo"; exit 1; fi
common.cpp: In function ‘void err_exit(const char*, ...)’:
common.cpp:311: error: ‘stderr’ was not declared in this scope
common.cpp:311: error: ‘vfprintf’ was not declared in this scope
make[2]: *** [common.o] Error 1
make[2]: Leaving directory `/home/doggysaywhat/share/apps/tophat-1.0.14/src'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home/doggysaywhat/share/apps/tophat-1.0.14'
make: *** [all] Error 2

I did some reading looking for what could cause this in various programs and it could be a problem with the GCC compiler I was using. I went through the suggestion of adding the line
#include <cstdio> to each .cpp file but I kept getting the same error.

Where you ever able to find a solution to the problem?
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Old 08-12-2010, 10:20 PM   #11
sphil
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Hey,ya i was able to solve it, just tried the other version ,as mentioned to me ,and then it works fine. Currently i don't know where the problem is of u won't Change the version.

Cheers phil
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Old 08-13-2010, 08:39 AM   #12
doggysaywhat
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Hello Sphil, I also switched to version 1.0.13 and so far it seems to compile. Odd though that the newer version is having the problem but the older version runs fine. I noticed that they had a pre-compiled version 1.0.14 on their website and I'm probably going to try it since it was supposed to have improved error checking.

Thanks for the help,
Doggysaywhat
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Old 08-17-2010, 07:34 AM   #13
jmarshall
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Quote:
Originally Posted by doggysaywhat View Post
common.cpp:311: error: ‘stderr’ was not declared in this scope
common.cpp:311: error: ‘vfprintf’ was not declared in this scope

I went through the suggestion of adding the line #include <cstdio> to each .cpp file but I kept getting the same error.
I found adding #include <cstdio> to the top of src/common.cpp to be sufficient to make tophat 1.0.14 compile successfully with a recent version of GCC that doesn't let you get away with forgetting this header.

-- John
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Old 08-17-2010, 08:14 AM   #14
sphil
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oh, thanks a lot. this might be quiet helpful for further mappings...
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