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Old 06-27-2011, 12:42 AM   #1
crazy_dog
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Location: Japan

Join Date: Feb 2011
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Default tophat install errors

Could you please give me some advice for handling tophat installation errors?

I am installing tophat following manual's instruction. When I run ./configure, everything seems okay and there is no error. However, when I run make, I get following errors.

Any advice would be greatly appreciated.

PHP Code:
make  all-recursive
make
[1]: Entering directory `/home/seo/Desktop/NGS_related/programs/tophat-1.3.1'
Making all in src
make[2]: Entering directory 
`/home/seo/Desktop/NGS_related/programs/tophat-1.3.1/src'
if g++ -DHAVE_CONFIG_H -I. -I. -I..   -I/usr/local/include -Wall -Wno-strict-aliasing -march=i686 -O3  -DNDEBUG -I/usr/local/include -I./SeqAn-1.2 -Wall -Wno-strict-aliasing -march=i686 -O3  -DNDEBUG -I/usr/local/include -MT extract_reads.o -MD -MP -MF ".deps/extract_reads.Tpo" -c -o extract_reads.o extract_reads.cpp; \
    then mv -f ".deps/extract_reads.Tpo" ".deps/extract_reads.Po"; else rm -f ".deps/extract_reads.Tpo"; exit 1; fi
In file included from /usr/local/include/bam/bgzf.h:29:0,
                 from /usr/local/include/bam/bam.h:52,
                 from common.h:18,
                 from reads.h:15,
                 from extract_reads.cpp:17:
/usr/local/include/zlib.h:1583:39: error: declaration of C function ‘off_t gzseek64(void*, off_t, int)’ conflicts with
/usr/local/include/zlib.h:1567:30: error: previous declaration ‘off64_t gzseek64(void*, off64_t, int)’ here
/usr/local/include/zlib.h:1584:39: error: declaration of C function ‘off_t gztell64(void*)’ conflicts with
/usr/local/include/zlib.h:1568:30: error: previous declaration ‘off64_t gztell64(void*)’ here
/usr/local/include/zlib.h:1585:41: error: declaration of C function ‘off_t gzoffset64(void*)’ conflicts with
/usr/local/include/zlib.h:1569:30: error: previous declaration ‘off64_t gzoffset64(void*)’ here
/usr/local/include/zlib.h:1586:46: error: declaration of C function ‘uLong adler32_combine64(uLong, uLong, off_t)’ conflicts with
/usr/local/include/zlib.h:1570:26: error: previous declaration ‘uLong adler32_combine64(uLong, uLong, off64_t)’ here
/usr/local/include/zlib.h:1587:44: error: declaration of C function ‘uLong crc32_combine64(uLong, uLong, off_t)’ conflicts with
/usr/local/include/zlib.h:1571:26: error: previous declaration ‘uLong crc32_combine64(uLong, uLong, off64_t)’ here
make[2]: *** [extract_reads.o] Error 1
make[2]: Leaving directory `/home/seo/Desktop/NGS_related/programs/tophat-1.3.1/src'
make[1]: *** [all-recursiveError 1
make
[1]: Leaving directory `/home/seo/Desktop/NGS_related/programs/tophat-1.3.1'
make: *** [all] Error 2 
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Old 06-28-2011, 03:33 AM   #2
crazy_dog
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Location: Japan

Join Date: Feb 2011
Posts: 2
Default

I found that this is caused by a bug of zlib 1.2.5.

http://forum.tinycorelinux.net/index.php?topic=6403.0

I solved this problem by downgrading zlib from 1.2.5 to 1.2.4. Now tophat works perfectly!!
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Old 12-15-2011, 08:57 AM   #3
jordi
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Location: València, Spain

Join Date: Apr 2009
Posts: 48
Default

Hi all!
I'm trying to install tophat but I get exactly the same error:

/usr/local/include/zlib.h:1583:39: error: declaration of C function ‘off_t gzseek64(void*, off_t, int)’ conflicts with
/usr/local/include/zlib.h:1567:30: error: previous declaration ‘off64_t gzseek64(void*, off64_t, int)’ here
/usr/local/include/zlib.h:1584:39: error: declaration of C function ‘off_t gztell64(void*)’ conflicts with
/usr/local/include/zlib.h:1568:30: error: previous declaration ‘off64_t gztell64(void*)’ here
/usr/local/include/zlib.h:1585:41: error: declaration of C function ‘off_t gzoffset64(void*)’ conflicts with
/usr/local/include/zlib.h:1569:30: error: previous declaration ‘off64_t gzoffset64(void*)’ here
/usr/local/include/zlib.h:1586:46: error: declaration of C function ‘uLong adler32_combine64(uLong, uLong, off_t)’ conflicts with
/usr/local/include/zlib.h:1570:26: error: previous declaration ‘uLong adler32_combine64(uLong, uLong, off64_t)’ here
/usr/local/include/zlib.h:1587:44: error: declaration of C function ‘uLong crc32_combine64(uLong, uLong, off_t)’ conflicts with
/usr/local/include/zlib.h:1571:26: error: previous declaration ‘uLong crc32_combine64(uLong, uLong, off64_t)’ her

I've no idea how dowgrading zlib library and I've just installed zlib-1.2.5 as I think the bug was solved...
According to tophat "getting started" I copied libbam.a file in /usr/local/lib and a bam directory in /usr/local/include so I just did ./configure in order to install tophat.
Could anyone help me?
Thanks a lot in advance.
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