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Old 09-07-2009, 03:12 AM   #1
henry
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Smile how to fix errors occuring in tophat-1.0.10 installation

I tried to install tophat-1.0.10. when I keyed in ./configure, it worked fine. But when I keyed in make, it unexpected popped up errors as follows:

In file included from FSA/sequence.h:20,
from FSA/sequence.cc:11:
FSA/fsa_alphabet.h: In member function ‘char fsa::Alphabet::get_nondegen_char(char) const’:
FSA/fsa_alphabet.h:234: error: ‘uint32_t’ was not declared in this scope
FSA/fsa_alphabet.h:238: error: ‘uint32_t’ was not declared in this scope
FSA/fsa_alphabet.h:252: error: ‘uint32_t’ was not declared in this scope
FSA/fsa_alphabet.h:256: error: ‘uint32_t’ was not declared in this scope
make[2]: *** [sequence.o] Error 1

Is there anyone who could kindly help me fix it? Thank you a lot.

btw, my operating system is fedora 11, on x64 machine.

Best wishes

Jing
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Old 09-07-2009, 09:21 AM   #2
Cole Trapnell
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Can you tell me what version of gcc you are using?
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Old 09-07-2009, 06:43 PM   #3
henry
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Quote:
Originally Posted by Cole Trapnell View Post
Can you tell me what version of gcc you are using?
Hi, Cole Trapnell,
Thank you for kindly responding to me. I keyed in gcc -v, and got all the information about gcc as follows:

Using built-in specs.
Target: x86_64-redhat-linux
Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-bootstrap --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-languages=c,c++,objc,obj-c++,java,fortran,ada --enable-java-awt=gtk --disable-dssi --enable-plugin --with-java-home=/usr/lib/jvm/java-1.5.0-gcj-1.5.0.0/jre --enable-libgcj-multifile --enable-java-maintainer-mode --with-ecj-jar=/usr/share/java/eclipse-ecj.jar --disable-libjava-multilib --with-ppl --with-cloog --with-tune=generic --with-arch_32=i586 --build=x86_64-redhat-linux
Thread model: posix
gcc version 4.4.0 20090506 (Red Hat 4.4.0-4) (GCC)

How can I fix the errors in tophat-1.0.10? Could you give me a hand? Thank you a lot.

Best

Jing
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Old 11-05-2009, 01:12 AM   #4
knoto
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Hi henry,

I ran into the same problem. Did you manage to fix the problem in the meantime?

Cheers

Knoto

Last edited by knoto; 11-05-2009 at 01:14 AM.
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Old 11-08-2009, 10:41 PM   #5
henry
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Quote:
Originally Posted by knoto View Post
Hi henry,

I ran into the same problem. Did you manage to fix the problem in the meantime?

Cheers

Knoto
Hi Knoto,

I didn't try to fix the problems. I ran into the problem, and then I left tophat behind. Why not try other applications that can also perform RNA-seq analysis?

Best wishes

Jing
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Old 11-09-2009, 06:08 AM   #6
Cole Trapnell
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Have either of you been able to reproduce this with 1.0.12? It appears to be specific to compiling TopHat with gcc 4.4.

I haven't yet had time to set up a virtual machine running Ubuntu to reproduce this - I develop and test with less bleeding-edge versions of gcc. You may have luck compiling TopHat on a Linux box using gcc 4.2 or earlier.
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Old 11-09-2009, 10:14 AM   #7
jmarshall
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The general problem here is that recent versions of GCC are more fussy about unexpected effects of standard include files than they used to be. For example, it used to be that #including <iostream> would also give you everything that #including <cstdio> would, as <iostream> included that header internally itself. These extra effects are being cleaned up, as such pollution is either forbidden by or at least not in the spirit of the C++ standard.

Henry's problem involves <stdint.h>, and (as I'm sure Cole recalls) that particular problem was fixed in 1.0.11. (The fix was to add #include <stdint.h> to the top of src/FSA/fsa_alphabet.h.)

knoto's problem is similar, and can be fixed by adding #include <cstdio> to the top of src/gff_juncs.cpp. With this single change, 1.0.12 can be compiled with GCC 4.4.1.
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Old 11-09-2009, 10:23 AM   #8
Cole Trapnell
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Thanks jmarshall, for the detailed response.

This is the last straw - time for me to set up that VM, so we don't get any of these compile issues in 1.0.13
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Old 11-09-2009, 11:26 PM   #9
knoto
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Default Thanks, jmarshall!

I wrote now #include <cstdio> into the gff_juncs.cpp. And it worked! So, thank you, jmarshall , that's great!
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Old 11-09-2009, 11:28 PM   #10
Wei-HD
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Default Installation of Tophat on mac

Hi everyone,

I am a totally beginner of Tophat. I am really sorry for this basic question, but I have suffered a long time and still do not know how to install it.

I use tophat on Mac OS X 10.5.8, and I download Bowtie 0.10.1 and Tophat 1.0.12 followed by extracting them.

I copied these three bowtie in usr/bin,

bowtie
bowtie-build
bowtie-inspect

Then I should change the directory of tophat, here I do not know where I should write the script. I tried to input following script in Terminal:

tar zxvf tophat-1.0.11_OSX.tar.gz

It returns as followed:

tar (child): tophat-1.0.11_OSX.tar.gz: Cannot open: No such file or directory
tar (child): Error is not recoverable: exiting now
tar: Child returned status 2
tar: Error exit delayed from previous errors

Is there anyone who can give me some hints concerning about installing of
Tophat on Mac? I really appreciate your kind help.

Thanks so much!
Wei
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Old 11-11-2009, 12:36 PM   #11
madsen
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Default compile problems tophat 1.0.12

Hi all

Seems like I got a similar problem. Wanted to update/install the newest version of tophat 1.0.12 (has already 1.0.11 running) and ran apparently into some compiling problems. It seems like the ./configure commands runs without any problems, but the make (and make install) results in errors. Since I installed tophat 1.0.11 I've updated my system from Ubuntu 9.09 to 9.10, thus I wondered if the gcc compiler in Ubuntu 9.10 somehow doesn't work with tophat. I've add #include <cstdio> to the top of src/gff_juncs.cpp as suggested by jmarshall and also tried with older versions of GCC (4.1; 4.2 and 4.3) but this gave the same errors.

Hope some can help. Thanks

Some output:
summary ./configure:
-- 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 (Ubuntu 4.4.1-4ubuntu8) 4.4.1
Host System type: x86_64-unknown-linux-gnu
Install prefix: /home/ole/tophat/tophat-1.0.12
Install eprefix: ${prefix}

the first couple (of many) warnings with make:
ole@ole-desktop:~/tophat/tophat-1.0.12$ make
make all-recursive
make[1]: Entering directory `/home/ole/tophat/tophat-1.0.12'
Making all in src
make[2]: Entering directory `/home/ole/tophat/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
In file included from reads.cpp:20:
bwt_map.h: In member function ‘bool HitStream::next_read_hits(HitsForRead&)’:
bwt_map.h:586: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result
mv -f .deps/reads.Tpo .deps/reads.Po
gcc -DHAVE_CONFIG_H -I. -I.. -Wall -g -m64 -O3 -DNDEBUG -MT alphabet.o -MD -MP -MF .deps/alphabet.Tpo -c -o alphabet.o alphabet.c
mv -f .deps/alphabet.Tpo .deps/alphabet.Po
g++ -DHAVE_CONFIG_H -I. -I.. -Wall -g -m64 -O3 -DNDEBUG -I./SeqAn-1.1 -Wall -g -m64 -O3 -DNDEBUG -MT bwt_map.o -MD -MP -MF .deps/bwt_map.Tpo -c -o bwt_map.o bwt_map.cpp
In file included from bwt_map.cpp:21:
bwt_map.h: In member function ‘bool HitStream::next_read_hits(HitsForRead&)’:
bwt_map.h:586: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result
mv -f .deps/bwt_map.Tpo .deps/bwt_map.Po
g++ -DHAVE_CONFIG_H -I. -I.. -Wall -g -m64 -O3 -DNDEBUG -I./SeqAn-1.1 -Wall -g -m64 -O3 -DNDEBUG -MT common.o -MD -MP -MF .deps/common.Tpo -c -o common.o common.cpp
mv -f .deps/common.Tpo .deps/common.Po
g++ -DHAVE_CONFIG_H -I. -I.. -Wall -g -m64 -O3 -DNDEBUG -I./SeqAn-1.1 -Wall -g -m64 -O3 -DNDEBUG -MT junctions.o -MD -MP -MF .deps/junctions.Tpo -c -o junctions.o junctions.cpp
In file included from junctions.h:26,
from junctions.cpp:16:
bwt_map.h: In member function ‘bool HitStream::next_read_hits(HitsForRead&)’:
bwt_map.h:586: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result
mv -f .deps/junctions.Tpo .deps/junctions.Po

the make install output:
ole@ole-desktop:~/tophat/tophat-1.0.12$ make install
Making install in src
make[1]: Entering directory `/home/ole/tophat/tophat-1.0.12/src'
make[2]: Entering directory `/home/ole/tophat/tophat-1.0.12/src'
test -z "/home/ole/tophat/tophat-1.0.12/bin" || /bin/mkdir -p "/home/ole/tophat/tophat-1.0.12/bin"
/usr/bin/install -c 'prep_reads' '/home/ole/tophat/tophat-1.0.12/bin/prep_reads'
/usr/bin/install -c 'tophat_reports' '/home/ole/tophat/tophat-1.0.12/bin/tophat_reports'
/usr/bin/install -c 'juncs_db' '/home/ole/tophat/tophat-1.0.12/bin/juncs_db'
/usr/bin/install -c 'gff_juncs' '/home/ole/tophat/tophat-1.0.12/bin/gff_juncs'
/usr/bin/install -c 'extract_reads' '/home/ole/tophat/tophat-1.0.12/bin/extract_reads'
/usr/bin/install -c 'segment_juncs' '/home/ole/tophat/tophat-1.0.12/bin/segment_juncs'
/usr/bin/install -c 'closure_juncs' '/home/ole/tophat/tophat-1.0.12/bin/closure_juncs'
/usr/bin/install -c 'long_spanning_reads' '/home/ole/tophat/tophat-1.0.12/bin/long_spanning_reads'
/usr/bin/install -c 'fix_map_ordering' '/home/ole/tophat/tophat-1.0.12/bin/fix_map_ordering'
/usr/bin/install -c 'library_stats' '/home/ole/tophat/tophat-1.0.12/bin/library_stats'
/usr/bin/install -c 'mask_sam' '/home/ole/tophat/tophat-1.0.12/bin/mask_sam'
/usr/bin/install -c 'wiggles' '/home/ole/tophat/tophat-1.0.12/bin/wiggles'
test -z "/home/ole/tophat/tophat-1.0.12/bin" || /bin/mkdir -p "/home/ole/tophat/tophat-1.0.12/bin"
/usr/bin/install -c 'contig_to_chr_coords.py' '/home/ole/tophat/tophat-1.0.12/bin/contig_to_chr_coords.py'
/usr/bin/install -c 'tophat.py' '/home/ole/tophat/tophat-1.0.12/bin/tophat.py'
/usr/bin/install -c 'bed_to_juncs.py' '/home/ole/tophat/tophat-1.0.12/bin/bed_to_juncs.py'
make install-exec-hook
make[3]: Entering directory `/home/ole/tophat/tophat-1.0.12/src'
configuring python 'contig_to_chr_coords'
configuring python 'tophat'
configuring python 'bed_to_juncs'
make[3]: Leaving directory `/home/ole/tophat/tophat-1.0.12/src'
make[2]: Nothing to be done for `install-data-am'.
make[2]: Leaving directory `/home/ole/tophat/tophat-1.0.12/src'
make[1]: Leaving directory `/home/ole/tophat/tophat-1.0.12/src'
make[1]: Entering directory `/home/ole/tophat/tophat-1.0.12'
make[2]: Entering directory `/home/ole/tophat/tophat-1.0.12'
make[2]: Nothing to be done for `install-exec-am'.
make[2]: Nothing to be done for `install-data-am'.
make[2]: Leaving directory `/home/ole/tophat/tophat-1.0.12'
make[1]: Leaving directory `/home/ole/tophat/tophat-1.0.12'

and finally the output running tophat on test data:
le@ole-desktop:~/tophat/tophat-1.0.11/test_data$ tophat -r 20 test_ref reads_1.fq reads_2.fq

[Wed Nov 11 22:34:39 2009] Beginning TopHat run (v1.0.12)
-----------------------------------------------
[Wed Nov 11 22:34:39 2009] Preparing output location ./tophat_out/
[Wed Nov 11 22:34:39 2009] Checking for Bowtie index files
[Wed Nov 11 22:34:39 2009] Checking for reference FASTA file
[Wed Nov 11 22:34:39 2009] Checking for Bowtie
Bowtie version: 0.11.3.0
[Wed Nov 11 22:34:39 2009] Checking reads
seed length: 75bp
format: fastq
quality scale: --phred33-quals
[Wed Nov 11 22:34:39 2009] Mapping reads against test_ref with Bowtie
[Wed Nov 11 22:34:39 2009] Joining segment hits
Splitting reads into 3 segments
[Wed Nov 11 22:34:39 2009] Mapping reads against test_ref with Bowtie
[Wed Nov 11 22:34:39 2009] Mapping reads against test_ref with Bowtie
[Wed Nov 11 22:34:39 2009] Mapping reads against test_ref with Bowtie
[Wed Nov 11 22:34:39 2009] Mapping reads against test_ref with Bowtie
[Wed Nov 11 22:34:39 2009] Joining segment hits
Splitting reads into 3 segments
[Wed Nov 11 22:34:39 2009] Mapping reads against test_ref with Bowtie
[Wed Nov 11 22:34:39 2009] Mapping reads against test_ref with Bowtie
[Wed Nov 11 22:34:39 2009] Mapping reads against test_ref with Bowtie
[Wed Nov 11 22:34:39 2009] Searching for junctions via segment mapping
[Wed Nov 11 22:34:39 2009] Retrieving sequences for splices
[Wed Nov 11 22:34:39 2009] Indexing splices
[Wed Nov 11 22:34:39 2009] Mapping reads against segment_juncs with Bowtie
[Wed Nov 11 22:34:39 2009] Mapping reads against segment_juncs with Bowtie
[Wed Nov 11 22:34:39 2009] Mapping reads against segment_juncs with Bowtie
[Wed Nov 11 22:34:39 2009] Joining segment hits
[Wed Nov 11 22:34:39 2009] Mapping reads against segment_juncs with Bowtie
[Wed Nov 11 22:34:39 2009] Mapping reads against segment_juncs with Bowtie
[Wed Nov 11 22:34:39 2009] Mapping reads against segment_juncs with Bowtie
[Wed Nov 11 22:34:39 2009] Joining segment hits
[Wed Nov 11 22:34:39 2009] Reporting output tracks
[FAILED]
Error: Report generation failed with err = 1
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Old 11-11-2009, 12:40 PM   #12
Cole Trapnell
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The warnings should be safely ignorable.

Several users have reported the failed run to me, and its resolvable by adding the tophat binaries and main script to the PATH environment variable. It also appears that in this failed run, the only thing that you should be missing is the coverage wigglegram, which you can manually generate with the "wiggles" binary included in the distribution. The bug will be fixed in the next release
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Old 11-11-2009, 12:53 PM   #13
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Hi Cole

Thanks for your swift reply. Everything is now running perfect.
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Old 12-13-2009, 03:16 PM   #14
Greg
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Hello, I added the #include <cstdio> to src/gff_juncs.cpp but the configure is still running into problems.

I'm on a x64 machine with ubuntu 9.10.

thanks!

greg@greg-desktop:~/Desktop/programs/tophat-1.0.12$ ./configure --prefix=/Desktop/programs/tophat-1.0.12
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++... no
checking for c++... no
checking for gpp... no
checking for aCC... no
checking for CC... no
checking for cxx... no
checking for cc++... no
checking for cl.exe... no
checking for FCC... no
checking for KCC... no
checking for RCC... no
checking for xlC_r... no
checking for xlC... no
checking whether we are using the GNU C++ compiler... no
checking whether g++ accepts -g... no
checking for gawk... no
checking for mawk... mawk
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... ${exec_prefix}/lib/python2.6/site-packages
checking if gcc accepts -m64... no
checking for gzread in -lz... no
checking how to run the C++ preprocessor... /lib/cpp
configure: error: in `/home/greg/Desktop/programs/tophat-1.0.12':
configure: error: C++ preprocessor "/lib/cpp" fails sanity check
See `config.log' for more details.
greg@greg-desktop:~/Desktop/programs/tophat-1.0.12$ make
make: *** No targets specified and no makefile found. Stop.
greg@greg-desktop:~/Desktop/programs/tophat-1.0.12$
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Old 12-14-2009, 01:13 AM   #15
jmarshall
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Quote:
Originally Posted by Greg View Post
checking for gcc... gcc
[...]
checking for g++... no
checking for c++... no
checking for gpp... no
checking for aCC... no
[...]
...and it can't find any other C++ compilers either. Perhaps you haven't installed one?
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Old 12-14-2009, 09:48 AM   #16
Greg
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Yes that was the problem, not sure how i missed that.

Now I still get the following complaints when compiling.
...
checking for _Bool... no
...
checking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... no
...

Not sure how to fix these ones.

Thanks again,
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