Thérèse Godefroy | 11 May 11:35 2016
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[MCSim] Proposed upgrade of the home page

Hello,

I am a member of the gnu.org French translation team [0], and also try
to update obsolete features in web pages to make future style
improvement easier. The home page of MCSim [1] has a translation list
below the navigation bar; I propose to upgrade it to boilerplate 1.79
[2]. This would give the opportunity to fix a few XHTML errors. A diff
is attached.

Best regards,
Therese

[0] https://www.gnu.org/server/standards/README.translations.html#teams
[1] https://www.gnu.org/software/mcsim/index.html
[2]
http://web.cvs.savannah.gnu.org/viewvc/*checkout*/www/server/standards/boilerplate.html?root=www&content-type=text%2Fplain

Attachment (mcsim.diff.tar.gz): application/gzip, 3970 bytes
fredomatic | 27 Feb 16:44 2016
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GNU MCSim version 5.6.5 release

Announcing the latest version (5.6.5) of the GNU MCSim simulation 
software (see http://www.gnu.org/software/mcsim for info):

GNU MCSim is a simulation package which allows you to design your own
models (eventually dynamic, via ODEs) and to perform simple
simulations, Monte Carlo stochastic simulations, or Bayesian inference
through Markov Chain Monte Carlo simulations.

Version 5.6.5 fixes a bug that got the code stuck sometimes when using
the PerDose() or PerExp() input functions.

GNU MCSim is GNU software. You can redistribute it and/or modify it 
under the terms of the GNU General Public License as published by the 
Free Software Foundation; either version 3 of the License, or (at your
option) any later version.

The source code (tar.gz archive) is available on
http://ftp.gnu.org/gnu/mcsim/ or
ftp://ftp.gnu.org/gnu/mcsim/

Best regards

Frederic Bois
fbois <at> member.fsf.org

fredomatic | 27 Feb 12:05 2016
Picon

PerDose input function bug fixed

I just fixed a float comparison bug that popped up out of the blue in 
the latest release. It was affecting PerDose and PerExp inputs (getting 
stuck). The revised modelu.c is on savannah. I will make a new release 
soon I you can wait for that.

F. Bois

Frederic Yves Bois | 11 Feb 16:49 2016
Picon

[bug #47121] problem with PerDose in v5.6.4

URL:
  <http://savannah.gnu.org/bugs/?47121>

                 Summary: problem with PerDose in v5.6.4
                 Project: MCSim simulation sofware
            Submitted by: fredomatic
            Submitted on: Thu 11 Feb 2016 04:49:42 PM CET
                Category: None
                Severity: 3 - Normal
              Item Group: None
                  Status: Confirmed
                 Privacy: Public
             Assigned to: fredomatic
             Open/Closed: Open
         Discussion Lock: Any

    _______________________________________________________

Details:

The input function PerDose has a bug in that version. The integrator can get
stuck at a time discontinuity. 
If you get this problem use the NDoses input function instead.

    _______________________________________________________

Reply to this item at:

  <http://savannah.gnu.org/bugs/?47121>

(Continue reading)

Jannick | 3 Jan 13:48 2016
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Picon

[v5.6.3] Installation documentation: enhancements

Hi.

 

A tiny edit to the installation documentation (http://www.gnu.org/software/mcsim/mcsim.html - Installation, 3.3.2, second paragraph; same chapter in pdf, v5.6.3) for your consideration:

 

·       ‘delays.c’ missing in list of source files

·       Compilation requiring reference to ‘config.h’ sitting in the main folder one level above. Thus -I.. makes the compiler aware of config.h. Alternatively it could be copied into the sim folder to make the package complete (apart of model.c).

 

I bumped into that trying to compile a model on a Win10 machine ‘by hand’. With the above everything works like a charm.

 

Merci à tous,

J.

fredomatic | 6 Aug 11:02 2015
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all bugs fixed by now...

As far as I can tell.

F. Bois

Frederic Bois | 25 Sep 12:06 2014
Picon

problem with some of the latest code on savannah

Please do not use the following MCSim/mod files / versions on savannah:
mod.c 	 1.25 	  remove graph sampling stuff
mod.h 	 1.30 	  increase ID table size

There is a nasty bug I need to fix in there.

Apologies.

F. Bois

Arnon Chitsakhon | 22 Feb 05:23 2014
Picon

Bug installed and compiled Report GNU MCSim (5.5.0)

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
Robert J Goedman | 10 May 19:21 2013

texi2dvi error in make

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=".:$TEXINPUTS" \
	MAKEINFO='/bin/sh /Users/rob/Projects/mcsim-5.5.0/missing makeinfo   -I .' \
	texi2dvi  --build-dir=mcsim.t2d -o mcsim.dvi  \
	mcsim.texinfo
/usr/bin/texi2dvi: Can't use option `--output' with more than one argument.
make[2]: *** [mcsim.dvi] Error 2
make[1]: *** [all-recursive] Error 1
make: *** [all] Error 2
robs-15inch-2:mcsim-5.5.0 rob$ 

Setzer, Woodrow | 18 Mar 18:27 2013
Picon

problems with make check on linux in MCSim v 5.5.0

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
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).


Gmane