[Ms@New]

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

[nshrine]

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

[Lspoor]

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?

[Torst]

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.

[Lspoor]

Thanks, I'll have a go!

[sigusn]

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

[Lspoor]

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!

[sigusn]

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

http://www.broadinstitute.org/igv/

[Lspoor]

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

[Lspoor]

Same problem but still no joy following the answer to the thread

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?

[Yu_Sun]

"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!

[new2NW]

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!

[hoyusnd]

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??

[olus]

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

[olus]

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