Bill Harris | 18 Apr 17:21 2014

MCSim and mixture models

Does anyone have an example of the setup of a simple dynamic (ODE) mixture model in MCSim?  Without a predefined unit k-simplex distribution, I'm not quite sure where to start. 

Thanks,

Bill
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Bill Harris | 18 Apr 06:56 2014

MCSim and W7 success (mostly)

I only succeeded once in building MCSim on XP, and that was perhaps on
v5.2 or so.  I tried multiple times later, and it never worked.

I tried again today to install v. 5.5.0 on a 64-bit W7 system with
cygwin, and it mostly worked.  Configure reported no problems except
that it didn't work with spaces in the FQDN, but moving the directory
was easy.

make failed in building a texinfo file--something about not finding
/home/me/mcim5.5.0/doc/./mcsim.texinfo (from memory), and I never could
figure out how to point LaTeX to the correct file.  make check failed
for the same reason.

make install (as admin) worked, though, and some simple models compiled
and ran seemingly correctly.

That's _much_ easier than it was on XP but not quite as easy as it is on
Linux.  

FYI.

Bill
--

-- 
Bill Harris                  
Facilitated Systems
http://makingsense.facilitatedsystems.com/
Jana Václavíková | 17 Apr 11:40 2014
Picon

MCSIM Installation error

Hi,

Im student at Masaryk University in Czech Republic using yours MCSIM-SW for
PBPK Modelling. We find out some error during installation of 5.5.0 version
(during "make" - command):

janav <at> janavacl-Extensa-5635G:~/mcsim-5.5.0$ make check
Making check in mod
make[1]: Entering directory `/home/janav/mcsim-5.5.0/mod'
make[1]: Nothing to be done for `check'.
make[1]: Leaving directory `/home/janav/mcsim-5.5.0/mod'
Making check in sim
make[1]: Entering directory `/home/janav/mcsim-5.5.0/sim'
make[1]: Nothing to be done for `check'.
make[1]: Leaving directory `/home/janav/mcsim-5.5.0/sim'
Making check in doc
make[1]: Entering directory `/home/janav/mcsim-5.5.0/doc'
TEXINPUTS=".:$TEXINPUTS" \
	MAKEINFO='/bin/bash /home/janav/mcsim-5.5.0/missing makeinfo   -I .' \
	texi2dvi  --build-dir=mcsim.t2d -o mcsim.dvi  \
	mcsim.texinfo
/bin/bash: texi2dvi: command not found
make[1]: *** [mcsim.dvi] Error 127
make[1]: Leaving directory `/home/janav/mcsim-5.5.0/doc'
make: *** [check-recursive] Error 1

We havent find any possible solution. We will be grateful for any help or
advice.

Best regards,
Jana Václavíková

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Help-mcsim <at> gnu.org
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Arnon Chitsakhon | 22 Feb 15:41 2014
Picon

Re: Fwd: Bug installed and compiled Report GNU MCSim (5.5.0)

Hi Elizabeth,

Thank you for your reply and advice. Now, I have compiled package and tested it follow the User's manual GNU MCSim (perc.model).I get some error. Before that I have installed any package for compiled it include that your advice. but I get some error when I create model. 

I used "mod perc.model" command to create model.c.

root <at> arc-System-Product-Name:/usr/share/mcsim/samples/perc# mod perc.model

________________________________________

Mod v5.5.0 - Model Generator for MCSim

MCSim and associated software comes with ABSOLUTELY NO WARRANTY;
This is free software, and you are welcome to redistribute it
under certain conditions; see the GNU General Public License.

Using LibSBML.


* Created model file 'model.c'.


I used "dir" command to find the "model.c" created. The result is follow this.
The "model.c" have created.

root <at> arc-System-Product-Name:/usr/share/mcsim/samples/perc# dir
Makefile     mod.log          perc.mtc.in      perc.setpoint.dat
Makefile.in  perc.lsodes.in   perc.mtc.out     perc.setpoint.in
mcsim.log    perc.lsodes.out  perc.ndoses.in   perc.setpoint.out
model.c      perc.model       perc.ndoses.out  ref_model.c


And Then, I type "makemcsim perc.model" I don't get "mcsim.perc" same as follow User's manual GNU MCSim. but I get "mcsim.perc.model." instead.

root <at> arc-System-Product-Name:/usr/share/mcsim/samples/perc# makemcsim perc.modelCreating model.c file from perc.model ...

________________________________________

Mod v5.5.0 - Model Generator for MCSim

MCSim and associated software comes with ABSOLUTELY NO WARRANTY;
This is free software, and you are welcome to redistribute it
under certain conditions; see the GNU General Public License.

Using LibSBML.


* Created model file 'model.c'.


Compiling model ...
Cleaning up ...
Created executable mcsim.perc.model.


Finally, I type "mcsim.perc.model" to replace "mcsim.perc" in the terminal command. I get follow this.

root <at> arc-System-Product-Name:/usr/share/mcsim/samples/perc# mcsim.perc.model
mcsim.perc.model: command not found

And so I also type "mcsim.perc" I get it same.

I don't know how to fix this problem. Could you comment or suggest me about that?

Thanks a lot for follow my E-mail and advise me about MCSim.
I'm interested in and I select it for my work.


Best regard,
Arnon

On Sat, Feb 22, 2014 at 5:46 PM, <sunshinekisses <at> gmail.com> wrote:
Hi,

You need to install some other libraries/packages to compile & build xmcsim. Specifically, “
you need XWindows, Tcl/Tk and wish” per the documentation[1]. Gnuplot & makeinfo appear to be good packages for mcsim so you may want to add those too.

This appears to be a simple compilation issue hence the reason I chirped in. I haven't used mcsim in a few years but still monitor the email lists.

Good luck!
Elizabeth
Bangkok

From: Arnon Chitsakhon
Sent: Saturday, February 22, 2014 11:49 AM
To: help-mcsim <at> gnu.org

---------- Forwarded message ----------
From: "Arnon Chitsakhon" <arnonrx17 <at> gmail.com>
Date: Feb 22, 2014 11:23 AM
Subject: Bug installed and compiled Report GNU MCSim (5.5.0)
To: <bug-mcsim <at> gnu.org>
Cc: "Manupat Lohitnavy" <manupatl <at> gmail.com>, "Brad Reisfeld" <brad.reisfeld <at> gmail.com>, "Kitza Kritsada" <kitza11317 <at> gmail.com>

Dear Sir,

My name is Arnon. I'm a student from Naresuan University in Thailand. I'm doing my work about PKPB modeling. I'm interested in your GNU MCSim program for my work.

I have attempted to install GNU MCSim (5.5.0) on Ubuntu version 12.10 but I found a few bugs when I installed and compiled.

I have used the command prompt follow this email install package.
($ represents the Ubuntu command prompt.)

I must to very apologize you for the very long E-mail to you first.
I hope that you help me about fix this problem .


The First, I have used  "./configure" command and result is follow.

--------------------------------------------------------------------------------------------
arc <at> arc-System-Product-Name:~/Documents/mcsim-5.5.0$ ./configure
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... no
checking for mawk... mawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking for style of include used by make... GNU
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking dependency style of gcc... gcc3
checking for ar... ar
checking the archiver (ar) interface... ar
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking how to print strings... printf
checking for a sed that does not truncate output... /bin/sed
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for fgrep... /bin/grep -F
checking for ld used by gcc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 1572864
checking whether the shell understands some XSI constructs... yes
checking whether the shell understands "+="... yes
checking how to convert x86_64-unknown-linux-gnu file names to x86_64-unknown-linux-gnu format... func_convert_file_noop
checking how to convert x86_64-unknown-linux-gnu file names to toolchain format... func_convert_file_noop
checking for /usr/bin/ld option to reload object files... -r
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for archiver <at> FILE support... <at>
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm -B output from gcc object... ok
checking for sysroot... no
checking for mt... mt
checking if mt is a manifest tool... no
checking how to run the C preprocessor... gcc -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for dlfcn.h... yes
checking for objdir... .libs
checking if gcc supports -fno-rtti -fno-exceptions... no
checking for gcc option to produce PIC... -fPIC -DPIC
checking if gcc PIC flag -fPIC -DPIC works... yes
checking if gcc static flag -static works... yes
checking if gcc supports -c -o file.o... yes
checking if gcc supports -c -o file.o... (cached) yes
checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... yes
checking for gcc... (cached) gcc
checking whether we are using the GNU C compiler... (cached) yes
checking whether gcc accepts -g... (cached) yes
checking for gcc option to accept ISO C89... (cached) none needed
checking dependency style of gcc... (cached) gcc3
checking for wish... no
checking for gnuplot... no
checking for info... yes
checking for install-info... yes
checking for makeinfo... no
checking for main in -lgslcblas... yes
checking for main in -lgsl... yes
checking for main in -lm... yes
checking for main in -lsbml... no
checking for ANSI C header files... (cached) yes
checking float.h usability... yes
checking float.h presence... yes
checking for float.h... yes
checking limits.h usability... yes
checking limits.h presence... yes
checking for limits.h... yes
checking for an ANSI C-conforming const... yes
checking whether struct tm is in sys/time.h or time.h... time.h
checking for stdlib.h... (cached) yes
checking for GNU libc compatible malloc... yes
checking for stdlib.h... (cached) yes
checking for GNU libc compatible realloc... yes
checking for floor... yes
checking for modf... yes
checking for pow... yes
checking for sqrt... yes
checking for strchr... yes
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating mod/Makefile
config.status: creating sim/Makefile
config.status: creating sim/makemcsim
config.status: creating sim/makemcsimd
config.status: creating sim/makemcsims
config.status: creating samples/perc/Makefile
config.status: creating doc/Makefile
config.status: creating config.h
config.status: executing depfiles commands
config.status: executing libtool commands





Second, I have used "make" command and result is follow.
So, when this step I found the Error.

-------------------------------------------------------------------------------------
arc <at> arc-System-Product-Name:~/Documents/mcsim-5.5.0$ make
make  all-recursive
make[1]: Entering directory `/home/arc/Documents/mcsim-5.5.0'
Making all in mod
make[2]: Entering directory `/home/arc/Documents/mcsim-5.5.0/mod'
gcc -DHAVE_CONFIG_H -I. -I..     -g -O2 -MT getopt.o -MD -MP -MF .deps/getopt.Tpo -c -o getopt.o getopt.c
mv -f .deps/getopt.Tpo .deps/getopt.Po
gcc -DHAVE_CONFIG_H -I. -I..     -g -O2 -MT lex.o -MD -MP -MF .deps/lex.Tpo -c -o lex.o lex.c
mv -f .deps/lex.Tpo .deps/lex.Po
gcc -DHAVE_CONFIG_H -I. -I..     -g -O2 -MT lexerr.o -MD -MP -MF .deps/lexerr.Tpo -c -o lexerr.o lexerr.c
mv -f .deps/lexerr.Tpo .deps/lexerr.Po
gcc -DHAVE_CONFIG_H -I. -I..     -g -O2 -MT lexfn.o -MD -MP -MF .deps/lexfn.Tpo -c -o lexfn.o lexfn.c
mv -f .deps/lexfn.Tpo .deps/lexfn.Po
gcc -DHAVE_CONFIG_H -I. -I..     -g -O2 -MT mod.o -MD -MP -MF .deps/mod.Tpo -c -o mod.o mod.c
mod.c: In function ‘PromptFilenames’:
mod.c:108:9: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
mod.c:117:11: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
mv -f .deps/mod.Tpo .deps/mod.Po
gcc -DHAVE_CONFIG_H -I. -I..     -g -O2 -MT modd.o -MD -MP -MF .deps/modd.Tpo -c -o modd.o modd.c
mv -f .deps/modd.Tpo .deps/modd.Po
gcc -DHAVE_CONFIG_H -I. -I..     -g -O2 -MT modi.o -MD -MP -MF .deps/modi.Tpo -c -o modi.o modi.c
mv -f .deps/modi.Tpo .deps/modi.Po
gcc -DHAVE_CONFIG_H -I. -I..     -g -O2 -MT modiSBML.o -MD -MP -MF .deps/modiSBML.Tpo -c -o modiSBML.o modiSBML.c
modiSBML.c: In function ‘CountLines’:
modiSBML.c:276:10: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
modiSBML.c:282:12: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
mv -f .deps/modiSBML.Tpo .deps/modiSBML.Po
gcc -DHAVE_CONFIG_H -I. -I..     -g -O2 -MT modiSBML2.o -MD -MP -MF .deps/modiSBML2.Tpo -c -o modiSBML2.o modiSBML2.c
mv -f .deps/modiSBML2.Tpo .deps/modiSBML2.Po
gcc -DHAVE_CONFIG_H -I. -I..     -g -O2 -MT modo.o -MD -MP -MF .deps/modo.Tpo -c -o modo.o modo.c
mv -f .deps/modo.Tpo .deps/modo.Po
gcc -DHAVE_CONFIG_H -I. -I..     -g -O2 -MT strutil.o -MD -MP -MF .deps/strutil.Tpo -c -o strutil.o strutil.c
mv -f .deps/strutil.Tpo .deps/strutil.Po
/bin/bash ../libtool  --tag=CC   --mode=link gcc  -g -O2   -o mod getopt.o lex.o lexerr.o lexfn.o mod.o modd.o modi.o modiSBML.o modiSBML2.o modo.o strutil.o  -lm -lgsl -lgslcblas
libtool: link: gcc -g -O2 -o mod getopt.o lex.o lexerr.o lexfn.o mod.o modd.o modi.o modiSBML.o modiSBML2.o modo.o strutil.o  -lm -lgsl -lgslcblas
make[2]: Leaving directory `/home/arc/Documents/mcsim-5.5.0/mod'
Making all in sim
make[2]: Entering directory `/home/arc/Documents/mcsim-5.5.0/sim'
/bin/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I..    -ffloat-store -g -O2 -MT libmodelu_la-modelu.lo -MD -MP -MF .deps/libmodelu_la-modelu.Tpo -c -o libmodelu_la-modelu.lo `test -f 'modelu.c' || echo './'`modelu.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -ffloat-store -g -O2 -MT libmodelu_la-modelu.lo -MD -MP -MF .deps/libmodelu_la-modelu.Tpo -c modelu.c  -fPIC -DPIC -o .libs/libmodelu_la-modelu.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -ffloat-store -g -O2 -MT libmodelu_la-modelu.lo -MD -MP -MF .deps/libmodelu_la-modelu.Tpo -c modelu.c -o libmodelu_la-modelu.o >/dev/null 2>&1
mv -f .deps/libmodelu_la-modelu.Tpo .deps/libmodelu_la-modelu.Plo
/bin/bash ../libtool  --tag=CC   --mode=link gcc -ffloat-store -g -O2   -o libmodelu.la -rpath /usr/local/lib libmodelu_la-modelu.lo  -lm -lgsl -lgslcblas
libtool: link: gcc -shared  -fPIC -DPIC  .libs/libmodelu_la-modelu.o   -lm -lgsl -lgslcblas  -O2   -Wl,-soname -Wl,libmodelu.so.0 -o .libs/libmodelu.so.0.0.0
libtool: link: (cd ".libs" && rm -f "libmodelu.so.0" && ln -s "libmodelu.so.0.0.0" "libmodelu.so.0")
libtool: link: (cd ".libs" && rm -f "libmodelu.so" && ln -s "libmodelu.so.0.0.0" "libmodelu.so")
libtool: link: ar cru .libs/libmodelu.a  libmodelu_la-modelu.o
libtool: link: ranlib .libs/libmodelu.a
libtool: link: ( cd ".libs" && rm -f "libmodelu.la" && ln -s "../libmodelu.la" "libmodelu.la" )
/bin/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I..     -g -O2 -MT getopt.lo -MD -MP -MF .deps/getopt.Tpo -c -o getopt.lo getopt.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -g -O2 -MT getopt.lo -MD -MP -MF .deps/getopt.Tpo -c getopt.c  -fPIC -DPIC -o .libs/getopt.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -g -O2 -MT getopt.lo -MD -MP -MF .deps/getopt.Tpo -c getopt.c -o getopt.o >/dev/null 2>&1
mv -f .deps/getopt.Tpo .deps/getopt.Plo
/bin/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I..     -g -O2 -MT lex.lo -MD -MP -MF .deps/lex.Tpo -c -o lex.lo lex.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -g -O2 -MT lex.lo -MD -MP -MF .deps/lex.Tpo -c lex.c  -fPIC -DPIC -o .libs/lex.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -g -O2 -MT lex.lo -MD -MP -MF .deps/lex.Tpo -c lex.c -o lex.o >/dev/null 2>&1
mv -f .deps/lex.Tpo .deps/lex.Plo
/bin/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I..     -g -O2 -MT lexerr.lo -MD -MP -MF .deps/lexerr.Tpo -c -o lexerr.lo lexerr.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -g -O2 -MT lexerr.lo -MD -MP -MF .deps/lexerr.Tpo -c lexerr.c  -fPIC -DPIC -o .libs/lexerr.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -g -O2 -MT lexerr.lo -MD -MP -MF .deps/lexerr.Tpo -c lexerr.c -o lexerr.o >/dev/null 2>&1
mv -f .deps/lexerr.Tpo .deps/lexerr.Plo
/bin/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I..     -g -O2 -MT lexfn.lo -MD -MP -MF .deps/lexfn.Tpo -c -o lexfn.lo lexfn.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -g -O2 -MT lexfn.lo -MD -MP -MF .deps/lexfn.Tpo -c lexfn.c  -fPIC -DPIC -o .libs/lexfn.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -g -O2 -MT lexfn.lo -MD -MP -MF .deps/lexfn.Tpo -c lexfn.c -o lexfn.o >/dev/null 2>&1
mv -f .deps/lexfn.Tpo .deps/lexfn.Plo
/bin/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I..     -g -O2 -MT list.lo -MD -MP -MF .deps/list.Tpo -c -o list.lo list.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -g -O2 -MT list.lo -MD -MP -MF .deps/list.Tpo -c list.c  -fPIC -DPIC -o .libs/list.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -g -O2 -MT list.lo -MD -MP -MF .deps/list.Tpo -c list.c -o list.o >/dev/null 2>&1
mv -f .deps/list.Tpo .deps/list.Plo
/bin/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I..     -g -O2 -MT lsodes1.lo -MD -MP -MF .deps/lsodes1.Tpo -c -o lsodes1.lo lsodes1.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -g -O2 -MT lsodes1.lo -MD -MP -MF .deps/lsodes1.Tpo -c lsodes1.c  -fPIC -DPIC -o .libs/lsodes1.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -g -O2 -MT lsodes1.lo -MD -MP -MF .deps/lsodes1.Tpo -c lsodes1.c -o lsodes1.o >/dev/null 2>&1
mv -f .deps/lsodes1.Tpo .deps/lsodes1.Plo
/bin/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I..     -g -O2 -MT lsodes2.lo -MD -MP -MF .deps/lsodes2.Tpo -c -o lsodes2.lo lsodes2.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -g -O2 -MT lsodes2.lo -MD -MP -MF .deps/lsodes2.Tpo -c lsodes2.c  -fPIC -DPIC -o .libs/lsodes2.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -g -O2 -MT lsodes2.lo -MD -MP -MF .deps/lsodes2.Tpo -c lsodes2.c -o lsodes2.o >/dev/null 2>&1
mv -f .deps/lsodes2.Tpo .deps/lsodes2.Plo
/bin/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I..     -g -O2 -MT matutil.lo -MD -MP -MF .deps/matutil.Tpo -c -o matutil.lo matutil.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -g -O2 -MT matutil.lo -MD -MP -MF .deps/matutil.Tpo -c matutil.c  -fPIC -DPIC -o .libs/matutil.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -g -O2 -MT matutil.lo -MD -MP -MF .deps/matutil.Tpo -c matutil.c -o matutil.o >/dev/null 2>&1
mv -f .deps/matutil.Tpo .deps/matutil.Plo
/bin/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I..     -g -O2 -MT matutilo.lo -MD -MP -MF .deps/matutilo.Tpo -c -o matutilo.lo matutilo.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -g -O2 -MT matutilo.lo -MD -MP -MF .deps/matutilo.Tpo -c matutilo.c  -fPIC -DPIC -o .libs/matutilo.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -g -O2 -MT matutilo.lo -MD -MP -MF .deps/matutilo.Tpo -c matutilo.c -o matutilo.o >/dev/null 2>&1
mv -f .deps/matutilo.Tpo .deps/matutilo.Plo
/bin/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I..     -g -O2 -MT mh.lo -MD -MP -MF .deps/mh.Tpo -c -o mh.lo mh.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -g -O2 -MT mh.lo -MD -MP -MF .deps/mh.Tpo -c mh.c  -fPIC -DPIC -o .libs/mh.o
mh.c: In function 'ReadRestart2':
mh.c:1788:10: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
mh.c:1821:12: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
mh.c: In function 'ReadRestart':
mh.c:1721:10: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
mh.c:1743:12: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
mh.c: In function 'DoMarkov':
mh.c:534:12: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -g -O2 -MT mh.lo -MD -MP -MF .deps/mh.Tpo -c mh.c -o mh.o >/dev/null 2>&1
mv -f .deps/mh.Tpo .deps/mh.Plo
/bin/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I..     -g -O2 -MT optdsign.lo -MD -MP -MF .deps/optdsign.Tpo -c -o optdsign.lo optdsign.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -g -O2 -MT optdsign.lo -MD -MP -MF .deps/optdsign.Tpo -c optdsign.c  -fPIC -DPIC -o .libs/optdsign.o
optdsign.c: In function 'ReadAndSimulate':
optdsign.c:384:10: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
optdsign.c:395:14: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
optdsign.c:401:12: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -g -O2 -MT optdsign.lo -MD -MP -MF .deps/optdsign.Tpo -c optdsign.c -o optdsign.o >/dev/null 2>&1
mv -f .deps/optdsign.Tpo .deps/optdsign.Plo
/bin/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I..     -g -O2 -MT random.lo -MD -MP -MF .deps/random.Tpo -c -o random.lo random.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -g -O2 -MT random.lo -MD -MP -MF .deps/random.Tpo -c random.c  -fPIC -DPIC -o .libs/random.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -g -O2 -MT random.lo -MD -MP -MF .deps/random.Tpo -c random.c -o random.o >/dev/null 2>&1
mv -f .deps/random.Tpo .deps/random.Plo
/bin/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I..     -g -O2 -MT sim.lo -MD -MP -MF .deps/sim.Tpo -c -o sim.lo sim.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -g -O2 -MT sim.lo -MD -MP -MF .deps/sim.Tpo -c sim.c  -fPIC -DPIC -o .libs/sim.o
sim.c: In function 'PromptFilenames':
sim.c:648:9: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
sim.c:660:11: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -g -O2 -MT sim.lo -MD -MP -MF .deps/sim.Tpo -c sim.c -o sim.o >/dev/null 2>&1
mv -f .deps/sim.Tpo .deps/sim.Plo
/bin/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I..     -g -O2 -MT simi.lo -MD -MP -MF .deps/simi.Tpo -c -o simi.lo simi.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -g -O2 -MT simi.lo -MD -MP -MF .deps/simi.Tpo -c simi.c  -fPIC -DPIC -o .libs/simi.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -g -O2 -MT simi.lo -MD -MP -MF .deps/simi.Tpo -c simi.c -o simi.o >/dev/null 2>&1
mv -f .deps/simi.Tpo .deps/simi.Plo
/bin/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I..     -g -O2 -MT siminit.lo -MD -MP -MF .deps/siminit.Tpo -c -o siminit.lo siminit.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -g -O2 -MT siminit.lo -MD -MP -MF .deps/siminit.Tpo -c siminit.c  -fPIC -DPIC -o .libs/siminit.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -g -O2 -MT siminit.lo -MD -MP -MF .deps/siminit.Tpo -c siminit.c -o siminit.o >/dev/null 2>&1
mv -f .deps/siminit.Tpo .deps/siminit.Plo
/bin/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I..     -g -O2 -MT simmonte.lo -MD -MP -MF .deps/simmonte.Tpo -c -o simmonte.lo simmonte.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -g -O2 -MT simmonte.lo -MD -MP -MF .deps/simmonte.Tpo -c simmonte.c  -fPIC -DPIC -o .libs/simmonte.o
simmonte.c: In function 'ReadSetPoints':
simmonte.c:302:9: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
simmonte.c:329:10: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
simmonte.c: In function 'InitSetPoints':
simmonte.c:275:10: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result]
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -g -O2 -MT simmonte.lo -MD -MP -MF .deps/simmonte.Tpo -c simmonte.c -o simmonte.o >/dev/null 2>&1
mv -f .deps/simmonte.Tpo .deps/simmonte.Plo
/bin/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I..     -g -O2 -MT simo.lo -MD -MP -MF .deps/simo.Tpo -c -o simo.lo simo.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -g -O2 -MT simo.lo -MD -MP -MF .deps/simo.Tpo -c simo.c  -fPIC -DPIC -o .libs/simo.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -g -O2 -MT simo.lo -MD -MP -MF .deps/simo.Tpo -c simo.c -o simo.o >/dev/null 2>&1
mv -f .deps/simo.Tpo .deps/simo.Plo
/bin/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I..     -g -O2 -MT strutil.lo -MD -MP -MF .deps/strutil.Tpo -c -o strutil.lo strutil.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -g -O2 -MT strutil.lo -MD -MP -MF .deps/strutil.Tpo -c strutil.c  -fPIC -DPIC -o .libs/strutil.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -g -O2 -MT strutil.lo -MD -MP -MF .deps/strutil.Tpo -c strutil.c -o strutil.o >/dev/null 2>&1
mv -f .deps/strutil.Tpo .deps/strutil.Plo
/bin/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I..     -g -O2 -MT yourcode.lo -MD -MP -MF .deps/yourcode.Tpo -c -o yourcode.lo yourcode.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -g -O2 -MT yourcode.lo -MD -MP -MF .deps/yourcode.Tpo -c yourcode.c  -fPIC -DPIC -o .libs/yourcode.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -g -O2 -MT yourcode.lo -MD -MP -MF .deps/yourcode.Tpo -c yourcode.c -o yourcode.o >/dev/null 2>&1
mv -f .deps/yourcode.Tpo .deps/yourcode.Plo
/bin/bash ../libtool  --tag=CC   --mode=link gcc  -g -O2   -o libmcsim.la -rpath /usr/local/lib getopt.lo lex.lo lexerr.lo lexfn.lo list.lo lsodes1.lo lsodes2.lo matutil.lo matutilo.lo mh.lo optdsign.lo random.lo sim.lo simi.lo siminit.lo simmonte.lo simo.lo strutil.lo yourcode.lo libmodelu.la -lm -lgsl -lgslcblas
libtool: link: gcc -shared  -fPIC -DPIC  .libs/getopt.o .libs/lex.o .libs/lexerr.o .libs/lexfn.o .libs/list.o .libs/lsodes1.o .libs/lsodes2.o .libs/matutil.o .libs/matutilo.o .libs/mh.o .libs/optdsign.o .libs/random.o .libs/sim.o .libs/simi.o .libs/siminit.o .libs/simmonte.o .libs/simo.o .libs/strutil.o .libs/yourcode.o   -Wl,-rpath -Wl,/home/arc/Documents/mcsim-5.5.0/sim/.libs ./.libs/libmodelu.so -lm -lgsl -lgslcblas  -O2   -Wl,-soname -Wl,libmcsim.so.0 -o .libs/libmcsim.so.0.0.0
libtool: link: (cd ".libs" && rm -f "libmcsim.so.0" && ln -s "libmcsim.so.0.0.0" "libmcsim.so.0")
libtool: link: (cd ".libs" && rm -f "libmcsim.so" && ln -s "libmcsim.so.0.0.0" "libmcsim.so")
libtool: link: ar cru .libs/libmcsim.a  getopt.o lex.o lexerr.o lexfn.o list.o lsodes1.o lsodes2.o matutil.o matutilo.o mh.o optdsign.o random.o sim.o simi.o siminit.o simmonte.o simo.o strutil.o yourcode.o
libtool: link: ranlib .libs/libmcsim.a
libtool: link: ( cd ".libs" && rm -f "libmcsim.la" && ln -s "../libmcsim.la" "libmcsim.la" )
make[2]: Leaving directory `/home/arc/Documents/mcsim-5.5.0/sim'
Making all in doc
make[2]: Entering directory `/home/arc/Documents/mcsim-5.5.0/doc'
TEXINPUTS=".:$TEXINPUTS" \
    MAKEINFO='/bin/bash /home/arc/Documents/mcsim-5.5.0/missing makeinfo   -I .' \
    texi2dvi  --build-dir=mcsim.t2d -o mcsim.dvi  \
    mcsim.texinfo
/bin/bash: texi2dvi: command not found
make[2]: *** [mcsim.dvi] Error 127
make[2]: Leaving directory `/home/arc/Documents/mcsim-5.5.0/doc'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home/arc/Documents/mcsim-5.5.0'
make: *** [all] Error 2





Third, I have uesd "make check" command and result is follow.
So, I got error again.

---------------------------------------------------------------------------------------------------
arc <at> arc-System-Product-Name:~/Documents/mcsim-5.5.0$ make check
Making check in mod
make[1]: Entering directory `/home/arc/Documents/mcsim-5.5.0/mod'
make[1]: Nothing to be done for `check'.
make[1]: Leaving directory `/home/arc/Documents/mcsim-5.5.0/mod'
Making check in sim
make[1]: Entering directory `/home/arc/Documents/mcsim-5.5.0/sim'
make[1]: Nothing to be done for `check'.
make[1]: Leaving directory `/home/arc/Documents/mcsim-5.5.0/sim'
Making check in doc
make[1]: Entering directory `/home/arc/Documents/mcsim-5.5.0/doc'
TEXINPUTS=".:$TEXINPUTS" \
    MAKEINFO='/bin/bash /home/arc/Documents/mcsim-5.5.0/missing makeinfo   -I .' \
    texi2dvi  --build-dir=mcsim.t2d -o mcsim.dvi  \
    mcsim.texinfo
/bin/bash: texi2dvi: command not found
make[1]: *** [mcsim.dvi] Error 127
make[1]: Leaving directory `/home/arc/Documents/mcsim-5.5.0/doc'
make: *** [check-recursive] Error 1





Then I have used "make install" command I got error.

----------------------------------------------------------------------------------------------------
arc <at> arc-System-Product-Name:~/Documents/mcsim-5.5.0$ sudo su
[sudo] password for arc:
root <at> arc-System-Product-Name:/home/arc/Documents/mcsim-5.5.0# make install
Making install in mod
make[1]: Entering directory `/home/arc/Documents/mcsim-5.5.0/mod'
make[2]: Entering directory `/home/arc/Documents/mcsim-5.5.0/mod'
 /bin/mkdir -p '/usr/local/bin'
  /bin/bash ../libtool   --mode=install /usr/bin/install -c mod '/usr/local/bin'
libtool: install: /usr/bin/install -c mod /usr/local/bin/mod
 /bin/mkdir -p '/usr/local/share/mcsim/mod'
 /usr/bin/install -c -m 644 getopt.c getopt.h hungtype.h lex.c lex.h lexerr.c lexerr.h lexfn.c lexfn.h mod.c mod.h modd.c modd.h modi.c modi.h modiface.h modiSBML.c modiSBML2.c modiSBML.h modo.c modo.h strutil.c strutil.h '/usr/local/share/mcsim/mod'
make[2]: Leaving directory `/home/arc/Documents/mcsim-5.5.0/mod'
make[1]: Leaving directory `/home/arc/Documents/mcsim-5.5.0/mod'
Making install in sim
make[1]: Entering directory `/home/arc/Documents/mcsim-5.5.0/sim'
make[2]: Entering directory `/home/arc/Documents/mcsim-5.5.0/sim'
 /bin/mkdir -p '/usr/local/bin'
 /usr/bin/install -c makemcsim makemcsims makemcsimd '/usr/local/bin'
 /bin/mkdir -p '/usr/local/lib'
 /bin/bash ../libtool   --mode=install /usr/bin/install -c   libmodelu.la libmcsim.la '/usr/local/lib'
libtool: install: /usr/bin/install -c .libs/libmodelu.so.0.0.0 /usr/local/lib/libmodelu.so.0.0.0
libtool: install: (cd /usr/local/lib && { ln -s -f libmodelu.so.0.0.0 libmodelu.so.0 || { rm -f libmodelu.so.0 && ln -s libmodelu.so.0.0.0 libmodelu.so.0; }; })
libtool: install: (cd /usr/local/lib && { ln -s -f libmodelu.so.0.0.0 libmodelu.so || { rm -f libmodelu.so && ln -s libmodelu.so.0.0.0 libmodelu.so; }; })
libtool: install: /usr/bin/install -c .libs/libmodelu.lai /usr/local/lib/libmodelu.la
libtool: install: warning: relinking `libmcsim.la'
libtool: install: (cd /home/arc/Documents/mcsim-5.5.0/sim; /bin/bash /home/arc/Documents/mcsim-5.5.0/libtool  --tag CC --mode=relink gcc -g -O2 -o libmcsim.la -rpath /usr/local/lib getopt.lo lex.lo lexerr.lo lexfn.lo list.lo lsodes1.lo lsodes2.lo matutil.lo matutilo.lo mh.lo optdsign.lo random.lo sim.lo simi.lo siminit.lo simmonte.lo simo.lo strutil.lo yourcode.lo libmodelu.la -lm -lgsl -lgslcblas )
libtool: relink: gcc -shared  -fPIC -DPIC  .libs/getopt.o .libs/lex.o .libs/lexerr.o .libs/lexfn.o .libs/list.o .libs/lsodes1.o .libs/lsodes2.o .libs/matutil.o .libs/matutilo.o .libs/mh.o .libs/optdsign.o .libs/random.o .libs/sim.o .libs/simi.o .libs/siminit.o .libs/simmonte.o .libs/simo.o .libs/strutil.o .libs/yourcode.o   -L/usr/local/lib -lmodelu -lm -lgsl -lgslcblas  -O2   -Wl,-soname -Wl,libmcsim.so.0 -o .libs/libmcsim.so.0.0.0
libtool: install: /usr/bin/install -c .libs/libmcsim.so.0.0.0T /usr/local/lib/libmcsim.so.0.0.0
libtool: install: (cd /usr/local/lib && { ln -s -f libmcsim.so.0.0.0 libmcsim.so.0 || { rm -f libmcsim.so.0 && ln -s libmcsim.so.0.0.0 libmcsim.so.0; }; })
libtool: install: (cd /usr/local/lib && { ln -s -f libmcsim.so.0.0.0 libmcsim.so || { rm -f libmcsim.so && ln -s libmcsim.so.0.0.0 libmcsim.so; }; })
libtool: install: /usr/bin/install -c .libs/libmcsim.lai /usr/local/lib/libmcsim.la
libtool: install: /usr/bin/install -c .libs/libmodelu.a /usr/local/lib/libmodelu.a
libtool: install: chmod 644 /usr/local/lib/libmodelu.a
libtool: install: ranlib /usr/local/lib/libmodelu.a
libtool: install: /usr/bin/install -c .libs/libmcsim.a /usr/local/lib/libmcsim.a
libtool: install: chmod 644 /usr/local/lib/libmcsim.a
libtool: install: ranlib /usr/local/lib/libmcsim.a
libtool: finish: PATH="/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/sbin" ldconfig -n /usr/local/lib
----------------------------------------------------------------------
Libraries have been installed in:
   /usr/local/lib

If you ever happen to want to link against installed libraries
in a given directory, LIBDIR, you must either use libtool, and
specify the full pathname of the library, or use the `-LLIBDIR'
flag during linking and do at least one of the following:
   - add LIBDIR to the `LD_LIBRARY_PATH' environment variable
     during execution
   - add LIBDIR to the `LD_RUN_PATH' environment variable
     during linking
   - use the `-Wl,-rpath -Wl,LIBDIR' linker flag
   - have your system administrator add LIBDIR to `/etc/ld.so.conf'

See any operating system documentation about shared libraries for
more information, such as the ld(1) and ld.so(8) manual pages.
----------------------------------------------------------------------
 /bin/mkdir -p '/usr/local/include'
 /usr/bin/install -c -m 644 matutil.h list.h lex.h sim.h lexfn.h hungtype.h modiface.h modelu.h random.h yourcode.h '/usr/local/include'
 /bin/mkdir -p '/usr/local/share/mcsim/sim'
 /usr/bin/install -c -m 644 getopt.c getopt.h hungtype.h lex.c lex.h lexerr.c lexerr.h lexfn.c lexfn.h list.c list.h lsodes.h lsodes1.c lsodes2.c matutil.c matutil.h matutilo.c matutilo.h mh.c mh.h modiface.h optdsign.c optdsign.h random.c random.h sim.c sim.h simi.c simi.h siminit.c siminit.h simmonte.c simmonte.h simo.c simo.h strutil.c strutil.h yourcode.c yourcode.h modelu.c '/usr/local/share/mcsim/sim'
 /usr/bin/install -c -m 644 modelu.h '/usr/local/share/mcsim/sim'
make[2]: Leaving directory `/home/arc/Documents/mcsim-5.5.0/sim'
make[1]: Leaving directory `/home/arc/Documents/mcsim-5.5.0/sim'
Making install in doc
make[1]: Entering directory `/home/arc/Documents/mcsim-5.5.0/doc'
TEXINPUTS=".:$TEXINPUTS" \
    MAKEINFO='/bin/bash /home/arc/Documents/mcsim-5.5.0/missing makeinfo   -I .' \
    texi2dvi  --build-dir=mcsim.t2d -o mcsim.dvi  \
    mcsim.texinfo
/bin/bash: texi2dvi: command not found
make[1]: *** [mcsim.dvi] Error 127
make[1]: Leaving directory `/home/arc/Documents/mcsim-5.5.0/doc'
make: *** [install-recursive] Error 1



After that I go to the "usr/local/bin" directory I didn't find "xmcsim" in that path.
and the "usr/local/share" directory I didn't find "xmcsim" too.

then, I go to the "mcsim/samples/perc" directory I started to type "mod perc.model" I got follow this.

----------------------------------------------------------------------------------------------------
root <at> arc-System-Product-Name:/home/arc/Documents/mcsim-5.5.0/samples/perc# mod perc.model

________________________________________

Mod v5.5.0 - Model Generator for MCSim

MCSim and associated software comes with ABSOLUTELY NO WARRANTY;
This is free software, and you are welcome to redistribute it
under certain conditions; see the GNU General Public License.


* Created C model file 'model.c'.




After that, I have used "makemcsim perc.model" but mcsim.perc wasn't created. and I got follow this.

--------------------------------------------------------------------------------------------------
root <at> arc-System-Product-Name:/home/arc/Documents/mcsim-5.5.0/samples/perc# makemcsim perc.model
Creating model.c file from perc.model ...

________________________________________

Mod v5.5.0 - Model Generator for MCSim

MCSim and associated software comes with ABSOLUTELY NO WARRANTY;
This is free software, and you are welcome to redistribute it
under certain conditions; see the GNU General Public License.


* Created C model file 'model.c'.


Compiling model ...
model.c:75:15: fatal error: R.h: No such file or directory
compilation terminated.
root <at> arc-System-Product-Name:/home/arc/Documents/mcsim-5.5.0/samples/perc#



Cloud you help me please ?

Thank you so much.

Arnon

_______________________________________________
Help-mcsim mailing list
Help-mcsim <at> gnu.org
https://lists.gnu.org/mailman/listinfo/help-mcsim
Frederic Bois | 17 Mar 15:34 2013
Picon

MCSim version 5.5.0 released on March 17, 2013

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).

Lisa Lowe | 8 Jun 16:16 2012
Picon

mcsim.perc: command not found

I can "configure" and "make" mcsim, but the "make check" masses the first two tests and fails the next:
        Testing Lsodes with perc.lsodes.in ...
        ./samples/perc/Makefile.in: line 44: mcsim.perc: command not found
        -FAILED-
Anyone know how to fix this problem?  Thanks in advance.
_______________________________________________
Help-mcsim mailing list
Help-mcsim <at> gnu.org
https://lists.gnu.org/mailman/listinfo/help-mcsim
Lisa Lowe | 7 Jun 22:13 2012
Picon

gsl problems

Hi,

It says on the website that gsl is not required with the latest mcsim,
but I get the following error when doing "make check":
  -Testing mod on perc.model
  --PASSED-
  -Testing makemcsim on perc.model
  -Compiling mcsim.perc...
  -/usr/bin/ld: cannot find -lgsl
  -collect2: ld returned 1 exit status
  --FAILED-

Also, gsl is installed on the cluster where I am working, and I added
its path to LD_LIBRARY_PATH (/usr/local/gsl/lib).  The compiler still
doesn't find it.  As per the archived emails about this problem, I
tried the command : /sbin/ldconfig -p | grep gsl, and it comes up with
nothing.  Are there other system variables I should be setting so it
can find this library?  Should the latest version need the gsl library
to do the samples?

Thanks!
Lisa
Bill Harris | 25 Feb 17:39 2012

Debian package availability

In case anyone else here runs Debian, I created a Debian package that
may be of help.  It's the first time I have shared one, so there may be
all sorts of problems.

I created it using ./configure, make, checkinstall on a Debian Squeeze
(6.0.3) amd64 architecture system.  libsbml 5.4.0 had been installed
previously.  I presume (and Frederic seems to agree) that the
./configure is general enough so that specifics besides being a 64-bit
system may not be an issue.

While I think I'm trustworthy, use it at your own risk.  It's not much
easier to use this than to build it locally, but it does save a few
minutes.

While I don't have much spare time, I do welcome your feedback.  If I
did something strange that's preventing it from being useful, perhaps I
can learn and then improve it to make it more generally useful.

You can find the download on the main MCSim page at
http://www.gnu.org/software/mcsim/.  

Bill

PS: If anyone has a foolproof installation for Windows (in particular,
for XP Pro or XP 64), I'm still interested.  I did that once years ago
with an earlier version of MCSim, but my recent attempts have failed.
An msi or the like would be great, if anyone is _really_ dedicated. :-)
--

-- 
Bill Harris                  
Facilitated Systems
http://makingsense.facilitatedsystems.com/
Frederic Bois | 22 Feb 09:43 2012
Picon

GNU MCSim and R

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

Frederic Bois | 22 Jan 15:21 2012
Picon

fixed an SBML model processing bug in modiSBML2.c

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

Frederic Bois | 22 Jan 11:12 2012
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fixed a printing bug in mh.c

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


Gmane