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  • Ms@New
    replied
    Hi everyone,

    I'm trying to install maqview, but I get the

    I have the same problem
    view_panel.o: In function `resetPickMatrixs':
    /home/athena/Desktop/TMP/runHMAQ/maqview-0.2.1/view_panel.c:270: undefined reference to `gluPickMatrix'
    collect2: ld returned 1 exit status
    make[1]: *** [maqview] Error 1


    changing it to GLLIBS = -lGL -lglut -lGLU -lm didn't help

    any idea?

    I'm new to all this, and I'm trying to install 0.2.1 version. and I'm using a 32 bit ubuntu

    Thanks, I'm stuck!
    ----
    later : Actually it did help!
    I was just running everything from scratch eachtime
    every time u run ./configure, it makes Makefile again,, so after running ./configure. change Makefile, and then run make, or I'm guessing change makefile.generic, so the new makefile would be the modified version
    Last edited by Ms@New; 07-21-2010, 08:53 PM.

    Leave a comment:


  • nshrine
    replied
    Originally posted by Lspoor View Post
    Iam also getting the following error when typing in the "make" command as the last step to install the latest version of MAQVIEW, does anyone know what it means?

    g++ -g -O2 -o maqview read_cache.o view_goto.o view_panel.o gl_gui.o MainFrame.o btree.o maqmap_index.o zrio.o stdhashc.o cns_cache.o const.o adler32.o compress.o crc32.o deflate.o gzio.o inffast.o inflate.o infback.o inftrees.o trees.o uncompr.o zutil.o -lGL -lglut -lm
    view_panel.o: In function `resetPickMatrixs':
    /usr/local/bin/maqview/view_panel.c:270: undefined reference to `gluPickMatrix'
    collect2: ld returned 1 exit status
    make[1]: *** [maqview] Error 1
    make[1]: Leaving directory `/usr/local/bin/maqview'
    make: *** [all] Error 2
    I found that you have to add "-lGLU" to get it to compile, change this line in the Makefile:
    GLLIBS = -lGL -lglut -lm

    to this:
    GLLIBS = -lGL -lglut -lGLU -lm

    Leave a comment:


  • Lspoor
    replied
    I have freeglut3-dev and assoc packages installed on the newest version of Ubuntu? Not sure if I need to try another type of GLUT-dev package?

    Leave a comment:


  • Torst
    replied
    Originally posted by Lspoor View Post
    g++ -g -O2 -o maqview read_cache.o view_goto.o view_panel.o gl_gui.o MainFrame.o btree.o maqmap_index.o zrio.o stdhashc.o cns_cache.o const.o adler32.o compress.o crc32.o deflate.o gzio.o inffast.o inflate.o infback.o inftrees.o trees.o uncompr.o zutil.o -lGL -lglut -lm
    view_panel.o: In function `resetPickMatrixs':
    /usr/local/bin/maqview/view_panel.c:270: undefined reference to 'gluPickMatrix'
    You probably don't have the "glut" libraries installed, or an old version of them. If you are on an RPM based system (Redhat/Suse/...) you may need to install the "mesa-libGLU-devel" package, or equivalent.

    Leave a comment:


  • Lspoor
    replied
    Thanks, I'll have a go!

    Leave a comment:


  • sigusn
    replied
    Hi
    You can upload your own genomes into the IGV. Just upload the exact same fasta file as you aligned to using MAQ.

    Leave a comment:


  • Lspoor
    replied
    integrative genome viewer

    Hi I had a look at this but from what I could see I could only choose from the listed genomes? Mine wasn't in there and I couldn't see a way of uploading your own genome in there?

    I'm aligning Illumina paired end reads for bacterial isolates against a related reference genome in MAQ, then trying to view the aligned reads against their reference genome, so that I can visually identify SNPs and the aligned reads. I was using a program called Tablet quite nicely until I updated to the latest version when I encountered problems with uploading my assembly.

    Does anyone know of a program that could do similar? I'm giving up on Maqview unless a miracle happens!

    Leave a comment:


  • sigusn
    replied
    Hi
    I gave up on using maqview. Use this free tool instead, The Integrative Genomics Viewer (IGV).

    Leave a comment:


  • Lspoor
    replied
    SImilar problem in Maqview installation

    Iam also getting the following error when typing in the "make" command as the last step to install the latest version of MAQVIEW, does anyone know what it means?

    g++ -g -O2 -o maqview read_cache.o view_goto.o view_panel.o gl_gui.o MainFrame.o btree.o maqmap_index.o zrio.o stdhashc.o cns_cache.o const.o adler32.o compress.o crc32.o deflate.o gzio.o inffast.o inflate.o infback.o inftrees.o trees.o uncompr.o zutil.o -lGL -lglut -lm
    view_panel.o: In function `resetPickMatrixs':
    /usr/local/bin/maqview/view_panel.c:270: undefined reference to `gluPickMatrix'
    collect2: ld returned 1 exit status
    make[1]: *** [maqview] Error 1
    make[1]: Leaving directory `/usr/local/bin/maqview'
    make: *** [all] Error 2

    Leave a comment:


  • Lspoor
    replied
    Same problem but still no joy following the answer to the thread

    Originally posted by Albert N View Post
    Heeeelp!

    I have some troubles triying to compile maqview-0.2.6 (sorry I'm a beginner).
    Install file says: "To compile it, just run"./autogen.sh; ./configure; make"......but when I type ./autogen this is the output:
    albert@mambara:~/maqview$ ./autogen.sh
    running: aclocal
    eval: 1: aclocal: not found
    error: while running 'aclocal'

    Somebody knows what am I doing wrong?
    I had the same problem as Albert N. I followed the instructions in the thread. MaqView is trying to install and the initial configuration seems to go ok but I get the following error messages after I type "make", but I'm not sure what they mean:
    g++ -g -O2 -o maqview read_cache.o view_goto.o view_panel.o gl_gui.o MainFrame.o btree.o maqmap_index.o zrio.o stdhashc.o cns_cache.o const.o adler32.o compress.o crc32.o deflate.o gzio.o inffast.o inflate.o infback.o inftrees.o trees.o uncompr.o zutil.o -lGL -lglut -lm
    view_panel.o: In function `resetPickMatrixs':
    /usr/local/bin/maqview/view_panel.c:270: undefined reference to `gluPickMatrix'
    collect2: ld returned 1 exit status
    make[1]: *** [maqview] Error 1
    make[1]: Leaving directory `/usr/local/bin/maqview'
    make: *** [all] Error 2

    Any ideas?

    Leave a comment:


  • Yu_Sun
    replied
    "bus error" in maqindex

    Hi everyone,

    I still have the "bus error" problem when I tried to use maqindex command "maqindex -i all.map" . The error message showed as below:

    -- Indexing the alignment file 'all.map' ... Bus error

    My maqview is the latest version 0.2.6. When I used the previous version 0.2.5, no such bug showed up in the index process. I successfully finished indexing the map file and run maqview. But when I did a few click in the maqview window, an error with Bus error showed up and end the maqview automatically.

    I use mac os x 10.5.8. Great thanks to any helpful comments!

    Leave a comment:


  • new2NW
    replied
    Installing maqview on cygwin on PC

    Hello all! I am hoping someone out there can help me. I use a PC, but needed to run Maq and Maqview, so I installed cygwin and got Maq installed and usable. However, I am running into problems with Maqview. Everything looks good until I get to the 'make' command and I get a long string of stuff that ends in an error (this is just the last part):

    /cygdrive/d/maqview/MainFrame.c:91: undefined reference to `_glutReshapeWindow'
    /cygdrive/d/maqview/MainFrame.c:94: undefined reference to `_glutSetWindow'
    MainFrame.o: In function `main':
    /cygdrive/d/maqview/MainFrame.c:190: undefined reference to `_glutInit'
    /cygdrive/d/maqview/MainFrame.c:204: undefined reference to `_glutInitDisplayMod
    e'
    /cygdrive/d/maqview/MainFrame.c:205: undefined reference to `_glutInitWindowSize
    '
    /cygdrive/d/maqview/MainFrame.c:206: undefined reference to `_glutInitWindowPosi
    tion'
    /cygdrive/d/maqview/MainFrame.c:207: undefined reference to `_glutCreateWindow'
    /cygdrive/d/maqview/MainFrame.c:225: undefined reference to `_glutSetWindow'
    /cygdrive/d/maqview/MainFrame.c:226: undefined reference to `_glutReshapeFunc'
    /cygdrive/d/maqview/MainFrame.c:227: undefined reference to `_glutDisplayFunc'
    /cygdrive/d/maqview/MainFrame.c:228: undefined reference to `_glutKeyboardFunc'
    /cygdrive/d/maqview/MainFrame.c:229: undefined reference to `_glutSpecialFunc'
    /cygdrive/d/maqview/MainFrame.c:240: undefined reference to `_glutMainLoop'
    MainFrame.o: In function `main_display':
    /cygdrive/d/maqview/MainFrame.c:72: undefined reference to `_glutSwapBuffers'
    MainFrame.o: In function `main_reshape':
    /cygdrive/d/maqview/MainFrame.c:95: undefined reference to `_glutPostRedisplay'
    /cygdrive/d/maqview/MainFrame.c:95: undefined reference to `_glutPostRedisplay'
    collect2: ld returned 1 exit status
    make[1]: *** [maqview.exe] Error 1
    make[1]: Leaving directory `/cygdrive/d/maqview'
    make: *** [all] Error 2

    Gah!!!!! Help!

    Leave a comment:


  • hoyusnd
    replied
    Hi everyone I'm trying to install maqview but I think I have a problem.
    Now I'm using cygwin, maq-0.7.1, maqview-0.2.5.

    A part of the error message when I typed './autogen.sh' is below.

    ---

    $ ./autogen.sh
    running: aclocal
    3 [main] perl 1184 C:\cygwin\bin\perl.exe: *** fatal error - unable to remap C:\cygwin\lib\perl5\5.10\i686-cygwin\auto\File\Glob\Glob.dll to same address
    as parent(0x12B0000) != 0x1E10000
    3 [main] perl 1184 C:\cygwin\bin\perl.exe: *** fatal error - unable to remap C:\cygwin\lib\perl5\5.10\i686-cygwin\auto\File\Glob\Glob.dll to same address
    as parent(0x12B0000) != 0x1E10000
    3 [main] perl 2196 fork: child 1184 - died waiting for dll loading, errno 11
    3 [main] perl 2196 fork: child 1184 - died waiting for dll loading, errno 11
    5405969 [main] perl 2396 C:\cygwin\bin\perl.exe: *** fatal error - unable to remap C:\cygwin\lib\perl5\5.10\i686-cygwin\auto\File\Glob\Glob.dll to same address
    as parent(0x12B0000) != 0x1E10000
    5405969 [main] perl 2396 C:\cygwin\bin\perl.exe: *** fatal error - unable to remap C:\cygwin\lib\perl5\5.10\i686-cygwin\auto\File\Glob\Glob.dll to same address
    as parent(0x12B0000) != 0x1E10000
    5425460 [main] perl 2196 fork: child 2396 - died waiting for dll loading, errno 11
    5425460 [main] perl 2196 fork: child 2396 - died waiting for dll loading, errno 11
    11015791 [main] perl 3648 C:\cygwin\bin\perl.exe: *** fatal error - unable to remap C:\cygwin\lib\perl5\5.10\i686-cygwin\auto\File\Glob\Glob.dll to same address
    as parent(0x12B0000) != 0x1E10000
    11015791 [main] perl 3648 C:\cygwin\bin\perl.exe: *** fatal error - unable to remap C:\cygwin\lib\perl5\5.10\i686-cygwin\auto\File\Glob\Glob.dll to same address
    as parent(0x12B0000) != 0x1E10000
    11037204 [main] perl 2196 fork: child 3648 - died waiting for dll loading, errno 11
    11037204 [main] perl 2196 fork: child 3648 - died waiting for dll loading, errno 11
    16251520 [main] perl 848 C:\cygwin\bin\perl.exe: *** fatal error - unable to remap C:\cygwin\lib\perl5\5.10\i686-cygwin\auto\File\Glob\Glob.dll to same address
    as parent(0x12B0000) != 0x1E10000
    16251520 [main] perl 848 C:\cygwin\bin\perl.exe: *** fatal error - unable to remap C:\cygwin\lib\perl5\5.10\i686-cygwin\auto\File\Glob\Glob.dll to same address
    as parent(0x12B0000) != 0x1E10000
    16272947 [main] perl 2196 fork: child 848 - died waiting for dll loading, errno 11
    16272947 [main] perl 2196 fork: child 848 - died waiting for dll loading, errno 11

    Is there anybody who knows about this problem??

    Leave a comment:


  • olus
    replied
    Originally posted by xuer View Post
    I got a "Segmentation fault" error when i tried
    ./maqindex -v input.map chrI:1-200

    or ./maqindex -i input.map.


    Is there anybody could help me?
    I was having segmentation fault both with maqview-0.2.5 and maqview-0.2.6.
    I resolved installing 0.2.3.
    Not sure it works also for you....

    Cheers

    Leave a comment:


  • olus
    replied
    Originally posted by olus View Post
    Thanks every body for this community.

    I had experienced "segmentation fault" with maqindex 2.5 when trying to index .map files (1 solexa lane, 14,853,012 sequences, pair end, 36 bp).
    The reference genome is Sc288 (Yeast 12Mbp).

    I tried with mapview-2.6, commented out line 11 of const.h, and compiled.
    Everithing goes fine

    But when I did the following:
    $ maqindex -c s_8.consensus.cns -i s_8.map
    I had this:
    -- Indexing the alignment file 's_8.map' ... -- Found error seqid is too large 1549491744 >= 17 in notify -- maqmap_index.c:123 --
    Segmentation fault

    Can you help me to interpret this error?

    My Best.
    G.
    Sorry for the doubled posting...

    By the way, I solved my problem installing maqview-0.2.3.

    maqindex -i -c s_1.consensus.cns s_1.map
    -- Indexing the alignment file 's_1.map' ... DONE!
    -- Indexing the consensus file 's_1.consensus.cns' ... DONE!

    Thanks

    Leave a comment:

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