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  • 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

  • #2
    Can you tell me what version of gcc you are using?

    Comment


    • #3
      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

      Comment


      • #4
        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, 02:14 AM.

        Comment


        • #5
          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

          Comment


          • #6
            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.

            Comment


            • #7
              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.

              Comment


              • #8
                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

                Comment


                • #9
                  Thanks, jmarshall!

                  I wrote now #include <cstdio> into the gff_juncs.cpp. And it worked! So, thank you, jmarshall , that's great!

                  Comment


                  • #10
                    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

                    Comment


                    • #11
                      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:
                      [email protected]:~/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:
                      [email protected]:~/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:
                      [email protected]:~/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

                      Comment


                      • #12
                        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

                        Comment


                        • #13
                          Hi Cole

                          Thanks for your swift reply. Everything is now running perfect.

                          Comment


                          • #14
                            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!

                            [email protected]:~/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... ${exec_prefix}/lib/python2.6/site-packages
                            checking if gcc accepts -m64... no
                            checking for gzread in -lz... no
                            checking how to run the C++ preprocessor... /lib/cpp
                            configure: error: in `/home/greg/Desktop/programs/tophat-1.0.12':
                            configure: error: C++ preprocessor "/lib/cpp" fails sanity check
                            See `config.log' for more details.
                            [email protected]:~/Desktop/programs/tophat-1.0.12$ make
                            make: *** No targets specified and no makefile found. Stop.
                            [email protected]:~/Desktop/programs/tophat-1.0.12$

                            Comment


                            • #15
                              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?

                              Comment

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