gmane.comp.gnu.mcsim.bugs

Re: texi2dvi error in make

Robert J Goedman — 2013-05-13T15:26:17

Hi Frederic,

After taking out the '-o $< at >' in the build lines for .texinfo.dvi and .texinfo.pdf in Makefile.in in the docs subdirectory, the build completes without problems, including the mcsim.pdf & mcsim.dvi. i.e.:

make distclean
./configure CC=clang
make
make install


I added the 'CC=clang' to make sure the right compiler was selected.

make check fails, but manually perc.model works as per the documentation. Not sure about the Makefile in that directory, the Makefile in samples/1cpt might be a better starting point for me. The R/deSolve examples work great!

Regards,
Rob J. Goedman
goedman< at >icloud.com




On May 13, 2013, at 6:56 AM, Robert J Goedman <goedman< at >icloud.com> wrote:

Re: texi2dvi error in make

Robert J Goedman — 2013-05-13T13:56:16

Hi Frederic,

Thank you for the answer. I'll play around with it a bit more, but as you state, the error is not affecting the usage of the package.

Regards,
Rob J. Goedman
goedman< at >icloud.com




On May 13, 2013, at 1:29 AM, Frederic Bois <frederic.bois< at >utc.fr> wrote:

Re: texi2dvi error in make

Frederic Bois — 2013-05-13T08:29:12

Hi,

I don't know, I don't get it and I see nothing wrong with the command 
given.
Building the doc automatically is more problems that I imagined for 
automake...
In any case, the doc is made last; so if it fails it's no big deal. The 
compiled doc is in the distributed package
anyway and you don't even need to redo it. If you want the info file 
installed, the best is then to
do "install-info mcsim.info" yourself.

Sorry about that. Maybe I should remove the troubled makefile from the 
doc directory...

Frederic Bois



On 10/05/2013 19:21, Robert J Goedman wrote:

texi2dvi error in make

Robert J Goedman — 2013-05-10T17:21:00

Hi,

To install mcsim-5.5.0 I'm using texi2dvi (GNU Texinfo 4.8) 1.34 on Mac OSX 10.8 and get below error message.

I wonder if there is a workaround for that.

Rob J. Goedman
goedman< at >icloud.com


...
libtool: link: ranlib .libs/libmcsim.a
libtool: link: ( cd ".libs" && rm -f "libmcsim.la" && ln -s "../libmcsim.la" "libmcsim.la" )
Making all in doc
TEXINPUTS=".:$TEXINPUTS" \
MAKEINFO='/bin/sh /Users/rob/Projects/mcsim-5.5.0/missing makeinfo   -I .' \
texi2dvi  --build-dir=mcsim.t2d -o mcsim.dvi  \
mcsim.texinfo
/usr/bin/texi2dvi: Can't use option `--output' with more than one argument.
make[2]: *** [mcsim.dvi] Error 2
make[1]: *** [all-recursive] Error 1
make: *** [all] Error 2
robs-15inch-2:mcsim-5.5.0 rob$

problems with make check on linux in MCSim v 5.5.0

Setzer, Woodrow — 2013-03-18T17:27:03

I've run into a couple of problems with 'make check'.
1) $(MCSIMHOME)/samples/perc/Makefile needs to have the 'executable' attribute set (chmod +x $(MCSIMHOME)/samples/perc/Makefile).
2) On line 35 of $(MCSIMHOME)/samples/perc/Makefile (below, with line numbers and extra lines for context)

31 # perc.lsodes.in
32 echo
33 echo Testing Lsodes with perc.lsodes.in ...
34 TEST3=0
35 (mcsim.perc perc.lsodes.in sim.out &> mcsim.log) || TEST3=1
36 if test $TEST3 -eq 1;
37  then echo '-FAILED-'
38  else echo '-PASSED-'
39 fi;

(mcsim.perc needs to be (./mcsim.perc

Otherwise, great work!

Woody

MCSim version 5.5.0 released on March 17, 2013

Frederic Bois — 2013-03-17T14:34:11

Version 5.5.0 of MCsim is available at http://ftp.gnu.org/gnu/mcsim/
See the official web page at http://www.gnu.org/software/mcsim/

The latest version of the model generator "mod" can now
generate C code directly usable with the R package deSolve. Simply use 
the "-R" option for that.

Version 5.5.0 also fixes a potential security problem at the 
installation phase
(originating from automake).

mcsim 5.4.0 Mac OS X 10.82 Mountain Lion build errors

Christopher Ruark — 2013-02-17T21:02:18

I'm trying to build mcsim 5.4.0 on my Mac OS X 10.8.2 Mountain Lion.  I've also installed GNU gsl through MacPorts.  I run ./configure without a problem.  When I type make I get this error at the bottom:

ld: library not found for -lgsl
collect2: error: ld returned 1 exit status
make[2]: *** [libmcsim.la] Error 1
make[1]: *** [all-recursive] Error 1
make: *** [all] Error 2

When I install libsbml-5.7.0-libxml2-macosx-mountainlion.dmg and then rerun the ./configure and type make I receive this error:

modiSBML2.c:53:29: fatal error: sbml/SBMLReader.h: No such file or directory
compilation terminated.
make[2]: *** [modiSBML2.o] Error 1
make[1]: *** [all-recursive] Error 1
make: *** [all] Error 2

Suggestions?

Thanks!

Chris

Rép. : mcsim make check error

Frederic BOIS — 2012-03-05T08:33:20

Dear Sushil,

There is a problem with that check in particular and I did not find time to fix it. At this point you should bypass the
"make check" step and run the example by hand (you can manually compare the output with the reference files).
There might be some small rounding differences.
Honestly, as long as the programs compile OK (and you went up to compile the mcsim.perc step) I have never found a problem afterward (well, there might still be some bugs lingering, but the core code is pretty stable, the new additions - SBML, R compatibility - are more "beta" in a sense).

Frederic Bois
 

Hi mcsim,

    I am installing mcsim on my mac and I got the following error when I try to 'make check'.
    I dint get any output file called sim.out. Please help me with this error.

Thanks,
Sushil.


sh-3.2# make check
Making check in mod
make[1]: Nothing to be done for `check'.
Making check in sim
make[1]: Nothing to be done for `check'.
Making check in doc
make[1]: Nothing to be done for `check'.
make  check-TESTS

mcsim make check error

Amirisetty, Sushil — 2012-03-02T20:16:36

Hi mcsim,

    I am installing mcsim on my mac and I got the following error when I try to 'make check'.
    I dint get any output file called sim.out. Please help me with this error.

Thanks,
Sushil.


sh-3.2# make check
Making check in mod
make[1]: Nothing to be done for `check'.
Making check in sim
make[1]: Nothing to be done for `check'.
Making check in doc
make[1]: Nothing to be done for `check'.
make  check-TESTS

Testing directory is ./samples/perc

Testing mod on perc.model
-PASSED-

Testing makemcsim on perc.model
Compiling mcsim.perc...
-PASSED-

Testing Lsodes with perc.lsodes.in ...
./samples/perc/Makefile.in: line 44: mcsim.perc: command not found
-FAILED-

Please check that file samples/perc/sim.out contains reasonable output

FAIL: samples/perc/Makefile.in
==================================
1 of 1 test failed
Please report to bug-mcsim< at >gnu.org
==================================
make[2]: *** [check-TESTS] Error 1
make[1]: *** [check-am] Error 2
make: *** [check-recursive] Error 1

GNU MCSim and R

Frederic Bois — 2012-02-22T08:43:32

The latest version (available from savannah) of the model generator 
"mod" can now generate C code directly usable with the R package 
deSolve. Simply use the "-R" option for that. You just need to have R 
and its deSolve package installed...

Frederic Bois

fixed an SBML model processing bug in modiSBML2.c

Frederic Bois — 2012-01-22T14:21:36

Inline statements in templates were ill processed (e.g. blank spaces 
were removed) when coupled to an SBML model.
That is now fixed. Inline () statements are transcribed "as is".
The latest version of the file is available on
http://cvs.savannah.gnu.org/viewvc/mcsim/mod/?root=mcsim

F. Bois

fixed a printing bug in mh.c

Frederic Bois — 2012-01-22T10:12:25

When printing a fit check after MCMC simulations, the model prediction 
and data values were printed wrong
and mismatched if the Print and Data statements did follow the same 
order in the simulation input file. That did not affect
the results of MCMC simulations at all, but would eventually mess up the 
fit check.
That is now fixed (the latest version of the file is available on

http://cvs.savannah.gnu.org/viewvc/mcsim/sim/?root=mcsim)

F. Bois

fixed a small bug in mh.c

Frederic Bois — 2011-11-11T12:27:11

A stray line code at the end of mh.c caused a systematic crash when  
exiting MCMC simulations. That is now fixed (the latest version of the  
file is available on
http://cvs.savannah.gnu.org/viewvc/mcsim/sim/?root=mcsim)

F. Bois

GNU MCSim version 5.4.0 is available

Frederic Bois — 2011-01-18T22:25:24

Check the http://www.gnu.org/software/mcsim/ to access it.
It is now under FSF GPL v3

Frederic Bois

MCSim mod improvements

Frederic Bois — 2011-01-15T17:05:57

The latest "mod" code on 
http://cvs.savannah.gnu.org/viewvc/mcsim/mcsim/mod/ fixes a bug in SBML 
processing. You can also specify the name of the default (external) 
compartment in SBML files.
If you want to read in SBML files, we strongly recommend that you 
install libSBML prior to compiling mod (compilation with _HAS_SBML_LIB 
defined). SBML parsing without libSBML will not be maintained.
A new distribution should come out soon.

Frederic Bois

SBML parsing with PK template: Bug fixed

Frederic Bois — 2011-01-15T16:59:28

A bug preventing the proper merging of SBML files with a transport 
equations template has been fixed.
It occurred when using libSBML code. The native code, used if libSBML 
was not installed, did not suffer from it.

Frederic Bois.