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[Help-mcsim] Rép. : Re: Fwd: Bug installe d and compiled Report GNU MCS
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From: |
Frederic BOIS |
|
Subject: |
[Help-mcsim] Rép. : Re: Fwd: Bug installe d and compiled Report GNU MCSim (5.5.0) |
|
Date: |
Thu, 27 Feb 2014 11:33:32 +0100 |
Hello,
Sorry, the manual is not totally up to date with respect to the name of the
executable generated.
But it looks like you are almost there.
To run it try the command "./mcsim.perc.model". Because it simply looks like
you do not have the current
directory in your command path (you can change that by editing your PATH
variable)
F. Bois
>>> Arnon Chitsakhon <address@hidden> 22/02/2014 15:41 >>>
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.
address@hidden:/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.
address@hidden:/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.
address@hidden:/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.
address@hidden:/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, <address@hidden> 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
>
> [1]
> http://toxi.ineris.fr/activites/toxicologie_quantitative/mcsim/mcsim_distrib/manmcsim_8.php
>
> *From:* Arnon Chitsakhon <address@hidden>
> *Sent:* Saturday, February 22, 2014 11:49 AM
> *To:* address@hidden
>
> ---------- Forwarded message ----------
> From: "Arnon Chitsakhon" <address@hidden>
> Date: Feb 22, 2014 11:23 AM
> Subject: Bug installed and compiled Report GNU MCSim (5.5.0)
> To: <address@hidden>
> Cc: "Manupat Lohitnavy" <address@hidden>, "Brad Reisfeld" <
> address@hidden>, "Kitza Kritsada" <address@hidden>
>
> 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.
>
>
> --------------------------------------------------------------------------------------------
> address@hidden:~/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 @FILE support... @
> 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.
>
>
> -------------------------------------------------------------------------------------
> address@hidden:~/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=".:$TEXINPUTS" \
> MAKEINFO='/bin/bash /home/arc/Documents/mcsim-5.5.0/missing makeinfo
> -I .' \
> texi2dvi --build-dir=mcsim.t2d -o mcsim.dvi \
> mcsim.texinfo
> /bin/bash: texi2dvi: command not found
> make[2]: *** [mcsim.dvi] Error 127
> make[2]: Leaving directory `/home/arc/Documents/mcsim-5.5.0/doc'
> make[1]: *** [all-recursive] Error 1
> make[1]: Leaving directory `/home/arc/Documents/mcsim-5.5.0'
> make: *** [all] Error 2
>
>
>
>
>
> Third, I have uesd "make check" command and result is follow.
> So, I got error again.
>
>
> ---------------------------------------------------------------------------------------------------
> address@hidden:~/Documents/mcsim-5.5.0$ 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=".:$TEXINPUTS" \
> MAKEINFO='/bin/bash /home/arc/Documents/mcsim-5.5.0/missing makeinfo
> -I .' \
> texi2dvi --build-dir=mcsim.t2d -o mcsim.dvi \
> mcsim.texinfo
> /bin/bash: texi2dvi: command not found
> make[1]: *** [mcsim.dvi] Error 127
> make[1]: Leaving directory `/home/arc/Documents/mcsim-5.5.0/doc'
> make: *** [check-recursive] Error 1
>
>
>
>
>
> Then I have used "make install" command I got error.
>
>
> ----------------------------------------------------------------------------------------------------
> address@hidden:~/Documents/mcsim-5.5.0$ sudo su
> [sudo] password for arc:
> address@hidden:/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.
>
>
> ----------------------------------------------------------------------------------------------------
> address@hidden:/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.
>
>
> --------------------------------------------------------------------------------------------------
> address@hidden:/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.
> address@hidden:/home/arc/Documents/mcsim-5.5.0/samples/perc#
>
>
>
>
> Cloud you help me please ?
>
> Thank you so much.
>
> Arnon
>