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From: Dave L. <dl...@ge...> - 2012-11-27 14:44:03
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Dear Liliana,
I will gladly help. It is difficult to make out precisely what the
trouble is from what you have mailed out. Is there additional error
messages after the message about the constructor? If so, could you send
them? Could you also let me know what operating system you are running
(Mac or Linux) and what distribution/version?
Thanks,
Dave
On 11/26/2012 10:48 AM, Liliana Greger wrote:
> Hello
> I have problems with installing pairoscope. After running make it just stopped:
> Scanning dependencies of target pairoscope
> [ 12%] Building CXX object CMakeFiles/pairoscope.dir/src/pairoscope.o
> [ 25%] Building CXX object CMakeFiles/pairoscope.dir/src/YAlignmentFetcher.o
> [ 37%] Building CXX object CMakeFiles/pairoscope.dir/src/YGeneView.o
> /ebi/microarray/home/lgreger/TOOLS/pairoscope-0.2/src/YGeneView.cpp: In constructor ‘YGeneView::YGeneView(cairo_t*, YRect, const char*, unsigned int, unsigned int, std::vector<YTranscript*, std::allocator<YTranscript*> >*, bool, double)’:
> where it stops
> Could you please identify the problem.
>
> Thank you very much
>
> Liliana
>
>
> Dr. Liliana Greger
> EMBL Outstation - Hinxton,
> European Bioinformatics Institute,
> Wellcome Trust Genome Campus,
> Hinxton,
> Cambridge, CB10 1SD
>
>
>
>
> ------------------------------------------------------------------------------
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> Pai...@li...
> https://lists.sourceforge.net/lists/listinfo/pairoscope-help
|
|
From: Liliana G. <lg...@eb...> - 2012-11-26 16:44:51
|
Hello I have problems with installing pairoscope. After running make it just stopped: Scanning dependencies of target pairoscope [ 12%] Building CXX object CMakeFiles/pairoscope.dir/src/pairoscope.o [ 25%] Building CXX object CMakeFiles/pairoscope.dir/src/YAlignmentFetcher.o [ 37%] Building CXX object CMakeFiles/pairoscope.dir/src/YGeneView.o /ebi/microarray/home/lgreger/TOOLS/pairoscope-0.2/src/YGeneView.cpp: In constructor ‘YGeneView::YGeneView(cairo_t*, YRect, const char*, unsigned int, unsigned int, std::vector<YTranscript*, std::allocator<YTranscript*> >*, bool, double)’: where it stops Could you please identify the problem. Thank you very much Liliana Dr. Liliana Greger EMBL Outstation - Hinxton, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD |
|
From: Powers, D. <Po...@do...> - 2012-07-29 03:42:37
|
Hi -
I wanted to share that I have built pairoscope on a RHEL 5.5 environment. I'm not sure if others have done this or not. Since I did not find any obvious installs on this platform through Google searching, I thought I would share how I did it, in case it might help others down the road.
( A ) Environment specifics
OS: Red Hat Enterprise Linux Server release 5.5 (Tikanga)
Kernel: Linux 2.6.18-194.el5 #1 SMP Tue Mar 16 21:52:39 EDT 2010 x86_64 x86_64 x86_64 GNU/Linux
gcc: 4.6.1
( B ) Steps to build pairoscope:
( 1 ) build pixman 0.10.0 library from source
( 2 ) build cairo 1.6.0 from source
( 3 ) build samtools 0.1.18 from source
( 4 ) build cmake 2.8.8 from source
( 5 ) build pairoscope 0.2 from source
( C) Pairoscope specific changes
After going through ccmake and configuring the environment and building the Makefile, you can execute "make" on the command line.
I found that when I executed the "make" command, there were a lot of "error: 'function' was not declared in this scope as shown below...
[foo@bar]% make
Scanning dependencies of target pairoscope
[ 12%] Building CXX object CMakeFiles/pairoscope.dir/src/pairoscope.cpp.o
[ 25%] Building CXX object CMakeFiles/pairoscope.dir/src/YAlignmentFetcher.cpp.o
[ 37%] Building CXX object CMakeFiles/pairoscope.dir/src/YGeneView.cpp.o
In file included from /share/apps/pairoscope/src/YGeneView.h:16:0,
from /share/apps/pairoscope/src/YGeneView.cpp:8:
/share/apps/pairoscope/src/YTranscript.h: In constructor 'YTranscript::YTranscript()':
/share/apps/pairoscope/src/YTranscript.h:32:30: error: 'NULL' was not declared in this scope
/share/apps/pairoscope/src/YGeneView.cpp: In constructor 'YGeneView::YGeneView(cairo_t*, YRect, const char*, unsigned int, unsigned int, std::vector<YTranscript*>*, bool, double)':
/share/apps/pairoscope/src/YGeneView.cpp:13:32: error: 'strlen' was not declared in this scope
/share/apps/pairoscope/src/YGeneView.cpp:15:34: error: 'strcpy' was not declared in this scope
/share/apps/pairoscope/src/YGeneView.cpp: In member function 'virtual void YGeneView::draw()':
/share/apps/pairoscope/src/YGeneView.cpp:44:13: error: 'stderr' was not declared in this scope
/share/apps/pairoscope/src/YGeneView.cpp:44:53: error: 'fprintf' was not declared in this scope
/share/apps/pairoscope/src/YGeneView.cpp:117:100: error: 'snprintf' was not declared in this scope
/share/apps/pairoscope/src/YGeneView.cpp: In member function 'int YGeneView::transcriptStatusPriority(char*)':
/share/apps/pairoscope/src/YGeneView.cpp:208:31: error: 'strcmp' was not declared in this scope
/share/apps/pairoscope/src/YGeneView.cpp:211:32: error: 'strcmp' was not declared in this scope
/share/apps/pairoscope/src/YGeneView.cpp:214:34: error: 'strcmp' was not declared in this scope
/share/apps/pairoscope/src/YGeneView.cpp:217:32: error: 'strcmp' was not declared in this scope
/share/apps/pairoscope/src/YGeneView.cpp:220:28: error: 'strcmp' was not declared in this scope
/share/apps/pairoscope/src/YGeneView.cpp:223:31: error: 'strcmp' was not declared in this scope
make[2]: *** [CMakeFiles/pairoscope.dir/src/YGeneView.cpp.o] Error 1
make[1]: *** [CMakeFiles/pairoscope.dir/all] Error 2
make: *** [all] Error 2
When I fixed these first errors, there were more that followed from various files. Here is the list of five ".h" and ".cpp" files and simple changes that I made to the files to get them to compile successfully:
( 1 ) ../pairoscope/src/YTranscript.h
add the following:
#include <cstddef>
( 2 ) ../pairoscope/src/YGeneView.h
add the following:
#include <cstring>
#include <stdio.h>
( 3 ) ../pairoscope/src/YPairView.h
add the following:
#include <cstdlib>
( 4 ) ../pairoscope/src/YDepthView.h
add the following:
#include <stdio.h>
#include <cstring>
( 5 ) ../pairoscope/src/YPairView.cpp
add the following:
#include <cstring>
After I made these changes, I was able to successfully compile pairoscope as shown below:
[foo@bar]% make
[ 12%] Building CXX object CMakeFiles/pairoscope.dir/src/pairoscope.cpp.o
[ 25%] Building CXX object CMakeFiles/pairoscope.dir/src/YAlignmentFetcher.cpp.o
[ 37%] Building CXX object CMakeFiles/pairoscope.dir/src/YGeneView.cpp.o
[ 50%] Building CXX object CMakeFiles/pairoscope.dir/src/YPairView.cpp.o
[ 62%] Building CXX object CMakeFiles/pairoscope.dir/src/YView.cpp.o
[ 75%] Building CXX object CMakeFiles/pairoscope.dir/src/YDepthView.cpp.o
[ 87%] Building CXX object CMakeFiles/pairoscope.dir/src/YGenomeView.cpp.o
[100%] Building CXX object CMakeFiles/pairoscope.dir/src/YTranscriptFetcher.cpp.o
Linking CXX executable pairoscope
[100%] Built target pairoscope
[foo@bar]%
I hope this helps someone else!
Dave
|
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From: Dave L. <dl...@ge...> - 2012-06-05 13:23:44
|
Dear Yaping,
You are correct. It is possible to get grey lines if the
orientation is correct, but the aligner has marked it as not being a
proper pair. To answer your second question, if both mates are mapped
within the region then an arc is drawn between them. The long bars that
you see are a result of reads being mapped right next to (or
overlapping) with their mates. In this case, the arc appears as a
straight line due to the proximity of the two reads.
Hope that helps,
Dave
---------------------------------------------------------------------------
Human Genomics
The Genome Institute
Washington University School of Medicine
---------------------------------------------------------------------------
|
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From: Yaping L. <lyp...@gm...> - 2012-06-05 01:41:58
|
Hi guys, What is the meaning of the grey bar in the following plot? I know grey means "Forward-Reverse" which should mean normal pair, but I did not use -n option, so these grey should not be printed out. Could someone tell me why it comes out? (Insert size too large? so it has not proper paired flag?) And what is the longer bar mean? Does it mean that it have pair while shorter one do not have pair? Thanks! |
|
From: Jonathan K. <jk...@tg...> - 2010-09-17 21:29:31
|
Hi Dave, That did the trick I installed MacPorts and their version of cairo (v1.10) and removed the fink version of cairo (v1.8) I had installed two days ago. Then unpacked the pairoscope tarball again and rebuilt the application as per the instructions and now the error message is gone and the plots still look great. Thanks for the help. Jonathan On 9/17/10 12:54 PM, "Dave Larson" <dl...@ge...> wrote: > Hi Jonathan, > The file you sent me looks like the expected output to me. I did a > little searching and it seems that the error message you are seeing may > be a Cairo bug in version 1.8. It seems MacPorts has Cairo 1.9, and > while I haven't tried it, that may cause this issue to disappear. > > Dave |
|
From: Dave L. <dl...@ge...> - 2010-09-17 20:00:38
|
I should also mention that if you can put up with the error messages, I don't think any part of the program is affected. Dave On 09/17/2010 02:54 PM, Dave Larson wrote: > Hi Jonathan, > The file you sent me looks like the expected output to me. I did a > little searching and it seems that the error message you are seeing may > be a Cairo bug in version 1.8. It seems MacPorts has Cairo 1.9, and > while I haven't tried it, that may cause this issue to disappear. > > Dave > > ------------------------------------------------------------------------------ > Start uncovering the many advantages of virtual appliances > and start using them to simplify application deployment and > accelerate your shift to cloud computing. > http://p.sf.net/sfu/novell-sfdev2dev > _______________________________________________ > Pairoscope-help mailing list > Pai...@li... > https://lists.sourceforge.net/lists/listinfo/pairoscope-help -- --------------------------------------------------------------------------- GC Medical Genomics Washington University School of Medicine 4444 Forest Park Blvd, Box 8501 St. Louis, Missouri 63108 --------------------------------------------------------------------------- Office: 4113 Phone: +1 (314) 286-1814 Fax: +1 (314) 286-1810 --------------------------------------------------------------------------- |
|
From: Dave L. <dl...@ge...> - 2010-09-17 19:54:27
|
Hi Jonathan, The file you sent me looks like the expected output to me. I did a little searching and it seems that the error message you are seeing may be a Cairo bug in version 1.8. It seems MacPorts has Cairo 1.9, and while I haven't tried it, that may cause this issue to disappear. Dave |
|
From: Dave L. <dl...@ge...> - 2010-09-17 17:49:05
|
Hi Jonathan,
Thanks for christening the mailing list! I haven't done much
testing on the Mac at all and I'm thrilled to hear you have it working.
The error messages seem clear enough that I think I could look at the
code and get an idea of what is going on. Does this happen every time
you run the program or only on specific regions? I'm also wondering what
options you are using (ie what does your command look like) as that may
narrow it down a bit.
Thanks,
Dave
> Hi,
>
> Just wanted to thank you for the nice application. It seems to work fine
> but does toss out a couple of error messages during a run but the output PNG
> look correct to me. I¹m happy to see if I can debug this issue if you can
> suggest a starting point. Errors listed below:
>
> Fri Sep 17 09:07:18 jkeats-ML.local pairoscope[17607]<Error>:
> CGContextSetFont: invalid context 0x0
> Fri Sep 17 09:07:18 jkeats-ML.local pairoscope[17607]<Error>:
> CGContextSetFontSize: invalid context 0x0
> Fri Sep 17 09:07:18 jkeats-ML.local pairoscope[17607]<Error>:
> CGContextSetTextMatrix: invalid context 0x0
> Fri Sep 17 09:07:18 jkeats-ML.local pairoscope[17607]<Error>:
> CGContextClearRect: invalid context 0x0
> Fri Sep 17 09:07:18 jkeats-ML.local pairoscope[17607]<Error>:
> CGContextSetRGBFillColor: invalid context 0x0
> Fri Sep 17 09:07:18 jkeats-ML.local pairoscope[17607]<Error>:
> CGContextShowGlyphsAtPoint: invalid context 0x0
> Fri Sep 17 09:07:18 jkeats-ML.local pairoscope[17607]<Error>:
> CGContextSetFont: invalid context 0x0
> Fri Sep 17 09:07:18 jkeats-ML.local pairoscope[17607]<Error>:
> CGContextSetFontSize: invalid context 0x0
> Fri Sep 17 09:07:18 jkeats-ML.local pairoscope[17607]<Error>:
> CGContextSetTextMatrix: invalid context 0x0
> Fri Sep 17 09:07:18 jkeats-ML.local pairoscope[17607]<Error>:
> CGContextClearRect: invalid context 0x0
> Fri Sep 17 09:07:18 jkeats-ML.local pairoscope[17607]<Error>:
> CGContextSetRGBFillColor: invalid context 0x0
> Fri Sep 17 09:07:18 jkeats-ML.local pairoscope[17607]<Error>:
> CGContextShowGlyphsAtPoint: invalid context 0x0
>
> Thanks,
>
> Jonathan
>
> --
> Jonathan Keats
> Associate Investigator
> Translational Genomics Research Institute (TGen)
>
> Email jk...@tg... <mailto:jk...@tg...>
> Office 602-343-8690
> Mobile 480-543-0634
> Google Voice 623-252-6709
>
> 445 N. Fifth Avenue, Suite 423
> Phoenix, AZ 85004
>
|
|
From: Jonathan K. <jk...@tg...> - 2010-09-17 16:14:48
|
Hi, Just wanted to thank you for the nice application. It seems to work fine but does toss out a couple of error messages during a run but the output PNG look correct to me. I¹m happy to see if I can debug this issue if you can suggest a starting point. Errors listed below: Fri Sep 17 09:07:18 jkeats-ML.local pairoscope[17607] <Error>: CGContextSetFont: invalid context 0x0 Fri Sep 17 09:07:18 jkeats-ML.local pairoscope[17607] <Error>: CGContextSetFontSize: invalid context 0x0 Fri Sep 17 09:07:18 jkeats-ML.local pairoscope[17607] <Error>: CGContextSetTextMatrix: invalid context 0x0 Fri Sep 17 09:07:18 jkeats-ML.local pairoscope[17607] <Error>: CGContextClearRect: invalid context 0x0 Fri Sep 17 09:07:18 jkeats-ML.local pairoscope[17607] <Error>: CGContextSetRGBFillColor: invalid context 0x0 Fri Sep 17 09:07:18 jkeats-ML.local pairoscope[17607] <Error>: CGContextShowGlyphsAtPoint: invalid context 0x0 Fri Sep 17 09:07:18 jkeats-ML.local pairoscope[17607] <Error>: CGContextSetFont: invalid context 0x0 Fri Sep 17 09:07:18 jkeats-ML.local pairoscope[17607] <Error>: CGContextSetFontSize: invalid context 0x0 Fri Sep 17 09:07:18 jkeats-ML.local pairoscope[17607] <Error>: CGContextSetTextMatrix: invalid context 0x0 Fri Sep 17 09:07:18 jkeats-ML.local pairoscope[17607] <Error>: CGContextClearRect: invalid context 0x0 Fri Sep 17 09:07:18 jkeats-ML.local pairoscope[17607] <Error>: CGContextSetRGBFillColor: invalid context 0x0 Fri Sep 17 09:07:18 jkeats-ML.local pairoscope[17607] <Error>: CGContextShowGlyphsAtPoint: invalid context 0x0 Thanks, Jonathan -- Jonathan Keats Associate Investigator Translational Genomics Research Institute (TGen) Email jk...@tg... Office 602-343-8690 Mobile 480-543-0634 Google Voice 623-252-6709 445 N. Fifth Avenue, Suite 423 Phoenix, AZ 85004 |
