[SOLVED] ProbABEL: Compile problem

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J.Ireland
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Joined: Tue Mar 22, 2011 4:53 pm

[SOLVED] ProbABEL: Compile problem

Postby J.Ireland » Wed Mar 23, 2011 12:57 pm

Compiling ProbABEL 0.1-9d under Scientific Linux SL release 5.5 produces a fvlib include error,

Code: Select all

$ make
g++ -I src/include -O2 -DLOGISTIC src/main.cpp src/fvlib/*.cpp -o bin/palogist
In file included from src/main.cpp:44:
src/data.h:11:27: error: fvlib/frerror.h: No such file or directory
src/data.h: In member function 'void gendata::get_var(int, float*)':
src/data.h:295: error: 'error' was not declared in this scope
src/data.h: In member function 'void gendata::re_gendata(std::string, int, int, int, int, short unsigned int*, std::string*)':
src/data.h:311: error: 'error' was not declared in this scope

The directory fvlib exists, but does not contain frerror.h,

Code: Select all

$ ls src/fvlib/
 AbstractMatrix.cpp  const.h           FileVector.h        frutil.h     Logger.h                ReusableFileHandle.h
 AbstractMatrix.h    convert_util.cpp  FilteredMatrix.cpp  frversion.h  RealHandlerWrapper.cpp  Transposer.cpp
 CastUtils.cpp       convert_util.h    FilteredMatrix.h    fvflib.uxf   RealHandlerWrapper.h    Transposer.h
 CastUtils.h         FileVector.cpp    frutil.cpp          Logger.cpp   ReusableFileHandle.cpp

Any ideas?
Last edited by J.Ireland on Mon Mar 28, 2011 12:01 pm, edited 2 times in total.

lckarssen
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Re: ProbABEL: Compile problem

Postby lckarssen » Thu Mar 24, 2011 11:43 am

Indeed. I've tried to compile the development version of ProbABEL and the file seems to be missing.

I'll look into it.
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Lennart Karssen
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yurii
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GenABEL developer
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Re: ProbABEL: Compile problem

Postby yurii » Thu Mar 24, 2011 9:00 pm

Interesting.

Where did you get the code from -- was that development version from RForge or stable from http://www.genabel.org/packages/ProbABEL ?
Note that (Gen)ABELs are dynamically developing; while this post is intended to provide full information at the time of posting, please read on further posts, if any, as the topic may be updated with novel solutions at a later stage.

best regards,
Yurii

lckarssen
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Re: ProbABEL: Compile problem

Postby lckarssen » Sun Mar 27, 2011 9:29 am

yurii wrote:Where did you get the code from -- was that development version from RForge or stable from http://www.genabel.org/packages/ProbABEL ?

The tar-ball from http://www.genabel.org/packages/ProbABEL gives the same error.


In the mean time I've also tried to revive the missing frerror.h and frerror.cpp files from the svn repository. These two files were last changed in rev. 311 and were deleted in rev.599. It seems that not all references to the functions in these files were removed in rev 599. I reported this as a bug, but in the mean time you can download the missing frerror files from https://r-forge.r-project.org/scm/viewv ... vision=311.

Thanks for reporting this!
Last edited by lckarssen on Sun Mar 27, 2011 9:37 am, edited 1 time in total.
Reason: Added link to the bug report.
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Lennart Karssen
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lckarssen
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Re: [SOLVED] ProbABEL: Compile problem

Postby lckarssen » Fri Apr 01, 2011 1:08 pm

This problem has been fixed in svn revision 705. New ProbABEL source packages will be available on the website soon.
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MariaG
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GenABEL specialist
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Re: [SOLVED] ProbABEL: Compile problem

Postby MariaG » Fri Apr 15, 2011 2:35 pm

Dear all,

so is the working version already available?
Today I downloaded the ProbABEL 0.1-9d and I couldn't compile on it Ubuntu because of the error discussed above...

I also tried to download frerror.h and frerror.cpp from r-forge.r-project.org, as it was suggested, hovewer during the compilation I've got errors for frerror.h and data.h ...

:(

Dick_Howard
Posts: 3
Joined: Tue Apr 05, 2011 6:47 pm

ProbABEL 0.1-9d compile error

Postby Dick_Howard » Wed Apr 20, 2011 7:49 pm

Greetings,

Thank you for helping develop ProbABEL.

I am not an C programmer, but find I am unable to
compile ProbABEL 0.1-9d, but can compile 0.1-9c
without issues.

0.1.9d shows the following error messages upon compile:

Code: Select all

# gmake
g++ -I src/include -O2 -DLOGISTIC src/main.cpp src/fvlib/*.cpp -o bin/palogist
In file included from src/main.cpp:44:
src/data.h:11:27: error: fvlib/frerror.h: No such file or directory
src/data.h: In member function 'void gendata::get_var(int, float*)':
src/data.h:295: error: 'error' was not declared in this scope
src/data.h: In member function 'void gendata::re_gendata(std::string, int, int, int,

int, short unsigned int*, std::string*)':
src/data.h:311: error: 'error' was not declared in this scope
src/data.h:312: error: 'error' was not declared in this scope
src/data.h:327: error: 'error' was not declared in this scope
src/data.h:334: error: 'error' was not declared in this scope
gmake: *** [bin/palogist] Error 1
#

Comparing 0.1-9c source with 0.1-9d, we see:


1) 0.1-9c contains these two files which are not included in 0.1-9d

frerror.cpp
frerror.h

2) many changes to:

src/fvlib/CastUtils.cpp

src/fvlib/FileVector.cpp
including removal of "#include "frerror.h"


3) "include ferror.h" has been removed from:

src/fvlib/Transposer.cpp

src/fvlib/frutil.h

I suspect ferror.h is not being used in 0.1-9d
but some source files still reference this header file.

Any help would be appreciated.

Code: Select all

#g++ --version
g++ (GCC) 4.1.2 20080704 (Red Hat 4.1.2-50)

# gmake --version
GNU Make 3.81

# rpm -q libstdc++
libstdc++-4.1.2-50.el5
libstdc++-4.1.2-50.el5


Thanks,
Dick Howard
Last edited by lckarssen on Sun May 15, 2011 9:43 pm, edited 1 time in total.
Reason: Reformatted code with the code tag.

MariaG
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Re: ProbABEL: Compile problem

Postby MariaG » Thu Apr 21, 2011 6:28 am

Hi :)

Where is it possible to download ProbABEL 0.1-9c ?

thanks

Dick_Howard
Posts: 3
Joined: Tue Apr 05, 2011 6:47 pm

Re: ProbABEL: Compile problem

Postby Dick_Howard » Thu Apr 21, 2011 11:55 pm

Hello,

We downloaded 0.1-9c in February,
from the earlier site provided before we began
using genable.org.

I am new to this, but notice this post
on R-Forge shows a fix:

https://r-forge.r-project.org/tracker/? ... l&aid=1339

It does not mention version 0.1-9d, but is
dated April 2011, so I wonder if this new
release needs to be posted to:
http://www.genabel.org/

Thanks,
Dick Howard

lckarssen
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Re: [SOLVED] ProbABEL: Compile problem

Postby lckarssen » Sun May 15, 2011 9:32 pm

lckarssen wrote:This problem has been fixed in svn revision 705. New ProbABEL source packages will be available on the website soon.

Well, not that soon apparently :oops:, but now the latest source (ProbABEL 0.1-9e) can be found here and on the GenABEL website.
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