Some packages could not be installed.

[wxc...@gmail.com]

Hi Dr Satya,

This happens when i tried to install Spatiocyte in my Ubuntu 14.04 LTS:

Some packages could not be installed. This may mean that you have
requested an impossible situation or if you are using the unstable
distribution that some required packages have not yet been created
or been moved out of Incoming.
The following information may help to resolve the situation:

The following packages have unmet dependencies:
 libcheese-gtk23 : Depends: libclutter-gtk-1.0-0 (>= 0.91.8) but it is not going to be installed
                   Depends: libcogl15 (>= 1.15.8) but it is not going to be installed
 libcheese7 : Depends: libclutter-gst-2.0-0 (>= 0.10.0) but it is not going to be installed
              Depends: gstreamer1.0-clutter but it is not going to be installed
 libclutter-1.0-0 : Depends: libcogl-pango15 (>= 1.15.8) but it is not going to be installed
                    Depends: libcogl15 (>= 1.15.8) but it is not going to be installed
E: Error, pkgProblemResolver::Resolve generated breaks, this may be caused by held packages.
+ echo export PATH=.:$HOME/root/bin:$PATH
+ echo export LD_LIBRARY_PATH=$HOME/root/lib:$LD_LIBRARY_PATH:.
+ echo export PYTHONPATH=$HOME/root/lib/python2.7/site-packages:$PYTHONPATH
+ echo export ECELL3_DM_PATH=.
+ source /home/wxc/.bashrc
install-spatiocyte-ubuntu.sh: 7: install-spatiocyte-ubuntu.sh: source: not found
+ cd
+ mkdir wrk
mkdir: cannot create directory ‘wrk’: File exists
+ cd wrk
+ git clone git://github.com/ecell/spatiocyte
install-spatiocyte-ubuntu.sh: 11: install-spatiocyte-ubuntu.sh: git: not found
+ cd spatiocyte
install-spatiocyte-ubuntu.sh: 12: cd: can't cd to spatiocyte
+ ./autogen.sh
install-spatiocyte-ubuntu.sh: 13: install-spatiocyte-ubuntu.sh: ./autogen.sh: not found
+ ./configure --prefix=/home/wxc/root
install-spatiocyte-ubuntu.sh: 14: install-spatiocyte-ubuntu.sh: ./configure: not found
+ make -j4
make: *** No targets specified and no makefile found.  Stop.
+ make install
make: *** No rule to make target `install'.  Stop.
+ echo Close and reopen this terminal before proceeding
Close and reopen this terminal before proceeding

Any idea what went wrong?
Thanks.

Chew

[Satya Arjunan]

Hi Chew,

When you issue the following in the terminal, can you provide the full output messages? I would like to know which package gives the error.

sudo apt-get install git autoconf automake libtool g++ libgsl0-dev python-numpy python-ply python-gtk2 libboost-python-dev libgtkmm-2.4-dev libgtkglextmm-x11-1.2-dev libhdf5-dev libav-tools blender vlc python-numpy python-scipy python-matplotlib valgrind

Thanks.

satya

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[Satya Arjunan]

Please reply your messages to spatiocyte-users <spatiocy...@googlegroups.com> too, since it would help other users having similar problems in future. Thanks.

satya

On 30 March 2015 at 11:39, Satya Arjunan <satya....@gmail.com> wrote:

It seems it is a bug with your version of Ubuntu, not Spatiocyte. Here is a solution from http://answers.ros.org/question/203610/ubuntu-14042-unmet-dependencies/

sudo apt-get update

sudo apt-get install xserver-xorg-dev-lts-utopic mesa-common-dev-lts-utopic libxatracker-dev-lts-utopic libopenvg1-mesa-dev-lts-utopic libgles2-mesa-dev-lts-utopic libgles1-mesa-dev-lts-utopic libgl1-mesa-dev-lts-utopic libgbm-dev-lts-utopic libegl1-mesa-dev-lts-utopic

After running the above try again the following:

sudo apt-get install git autoconf automake libtool g++ libgsl0-dev python-numpy python-ply python-gtk2 libboost-python-dev libgtkmm-2.4-dev libgtkglextmm-x11-1.2-dev libhdf5-dev libav-tools blender vlc python-numpy python-scipy python-matplotlib valgrind

satya

On 30 March 2015 at 11:31, chew wx <wxc...@gmail.com> wrote:

Dear Dr Satya,

These are the output:

Reading package lists... Done
Building dependency tree      
Reading state information... Done
g++ is already the newest version.
g++ set to manually installed.
python-gtk2 is already the newest version.
python-gtk2 set to manually installed.

Some packages could not be installed. This may mean that you have
requested an impossible situation or if you are using the unstable
distribution that some required packages have not yet been created
or been moved out of Incoming.
The following information may help to resolve the situation:

The following packages have unmet dependencies:
 libcheese-gtk23 : Depends: libclutter-gtk-1.0-0 (>= 0.91.8) but it is not going to be installed
                   Depends: libcogl15 (>= 1.15.8) but it is not going to be installed
 libcheese7 : Depends: libclutter-gst-2.0-0 (>= 0.10.0) but it is not going to be installed
              Depends: gstreamer1.0-clutter but it is not going to be installed
 libclutter-1.0-0 : Depends: libcogl-pango15 (>= 1.15.8) but it is not going to be installed
                    Depends: libcogl15 (>= 1.15.8) but it is not going to be installed
E: Error, pkgProblemResolver::Resolve generated breaks, this may be caused by held packages.

Regards,

Chew

[wxc...@gmail.com]

These are the output:

Reading package lists... Done
Building dependency tree       
Reading state information... Done
g++ is already the newest version.
g++ set to manually installed.
python-gtk2 is already the newest version.
python-gtk2 set to manually installed.

Some packages could not be installed. This may mean that you have
requested an impossible situation or if you are using the unstable
distribution that some required packages have not yet been created
or been moved out of Incoming.
The following information may help to resolve the situation:

The following packages have unmet dependencies:
 libcheese-gtk23 : Depends: libclutter-gtk-1.0-0 (>= 0.91.8) but it is not going to be installed
                   Depends: libcogl15 (>= 1.15.8) but it is not going to be installed
 libcheese7 : Depends: libclutter-gst-2.0-0 (>= 0.10.0) but it is not going to be installed
              Depends: gstreamer1.0-clutter but it is not going to be installed
 libclutter-1.0-0 : Depends: libcogl-pango15 (>= 1.15.8) but it is not going to be installed
                    Depends: libcogl15 (>= 1.15.8) but it is not going to be installed
E: Error, pkgProblemResolver::Resolve generated breaks, this may be caused by held packages.

[braichenk...@gmail.com]

Dear Satya

I'm running Ubuntu 18.04 and there are some problems with installation. It was complaining about pygtk (the log is above), and I've installed it but it's still unable to locate it. Do you have any ideas how to solve it?

checking for python module xml... yes
checking for python module ply... yes
checking for python module pygtk... no
configure: error: could not find Python pygtk module
configure: error: ./configure failed for ecell
+ make -j4
make  all-recursive
make[1]: Entering directory '/home/sbraiche/wrk/spatiocyte'
Making all in libltdl
make[2]: Entering directory '/home/sbraiche/wrk/spatiocyte/libltdl'
make  all-am
make[3]: Entering directory '/home/sbraiche/wrk/spatiocyte/libltdl'
/bin/bash ./libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.     -g -O2 -c -o ltdl.lo ltdl.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -g -O2 -c ltdl.c  -fPIC -DPIC -o .libs/ltdl.o
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -g -O2 -c ltdl.c -o ltdl.o >/dev/null 2>&1
/bin/bash ./libtool  --tag=CC   --mode=link gcc  -g -O2   -o libltdlc.la  ltdl.lo -ldl
libtool: link: ar cru .libs/libltdlc.a .libs/ltdl.o
ar: `u' modifier ignored since `D' is the default (see `U')
libtool: link: ranlib .libs/libltdlc.a
libtool: link: ( cd ".libs" && rm -f "libltdlc.la" && ln -s "../libltdlc.la" "libltdlc.la" )
make[3]: Leaving directory '/home/sbraiche/wrk/spatiocyte/libltdl'
make[2]: Leaving directory '/home/sbraiche/wrk/spatiocyte/libltdl'
Making all in dmtool
make[2]: Entering directory '/home/sbraiche/wrk/spatiocyte/dmtool'
make  all-am
make[3]: Entering directory '/home/sbraiche/wrk/spatiocyte/dmtool'
make[3]: Leaving directory '/home/sbraiche/wrk/spatiocyte/dmtool'
make[2]: Leaving directory '/home/sbraiche/wrk/spatiocyte/dmtool'
Making all in ecell
make[2]: Entering directory '/home/sbraiche/wrk/spatiocyte/ecell'
make[2]: *** No rule to make target 'all'. Stop.
make[2]: Leaving directory '/home/sbraiche/wrk/spatiocyte/ecell'
Makefile:413: recipe for target 'all-recursive' failed
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory '/home/sbraiche/wrk/spatiocyte'
Makefile:345: recipe for target 'all' failed
make: *** [all] Error 2
+ make install
Making install in libltdl
make[1]: Entering directory '/home/sbraiche/wrk/spatiocyte/libltdl'
make[2]: Entering directory '/home/sbraiche/wrk/spatiocyte/libltdl'
make[2]: Leaving directory '/home/sbraiche/wrk/spatiocyte/libltdl'
make[1]: Leaving directory '/home/sbraiche/wrk/spatiocyte/libltdl'
Making install in dmtool
make[1]: Entering directory '/home/sbraiche/wrk/spatiocyte/dmtool'
make[2]: Entering directory '/home/sbraiche/wrk/spatiocyte/dmtool'
 /bin/mkdir -p '/home/sbraiche/root/bin'
 /usr/bin/install -c dmcompile '/home/sbraiche/root/bin'
 /bin/mkdir -p '/home/sbraiche/root/include/dmtool'
 /usr/bin/install -c -m 644 DynamicModule.hpp DynamicModuleInfo.hpp DynamicModuleDescriptor.hpp DMException.hpp ModuleMaker.hpp SharedDynamicModule.hpp SharedModuleMaker.hpp SharedModuleMakerInterface.hpp DMObject.hpp '/home/sbraiche/root/include/dmtool'
make[2]: Leaving directory '/home/sbraiche/wrk/spatiocyte/dmtool'
make[1]: Leaving directory '/home/sbraiche/wrk/spatiocyte/dmtool'
Making install in ecell
make[1]: Entering directory '/home/sbraiche/wrk/spatiocyte/ecell'
make[1]: *** No rule to make target 'install'. Stop.
make[1]: Leaving directory '/home/sbraiche/wrk/spatiocyte/ecell'
Makefile:413: recipe for target 'install-recursive' failed
make: *** [install-recursive] Error 1

+ echo Close and reopen this terminal before proceeding
Close and reopen this terminal before proceeding

Best,

Svitlana

[Satya Arjunan]

Dear Svitlana,

Thank you for your interest in Spatiocyte. The instructions on the spatiocyte.org website is for the experimental version of Spatiocyte. This version of Spatiocyte runs on Linux with the python-gtk module (https://packages.ubuntu.com/search?keywords=python-gtk). The error message says that this module has not been installed on your system.

As a beginner user, it would be more convenient and easier to run Spatiocyte if you install the E-Cell 4 package: https://github.com/ecell/ecell4_base#installation

Here is a tutorial on how to run the Spatiocyte simulator using the E-Cell 4 package:

https://ecell4.readthedocs.io/en/latest/tutorials/tutorial10.html

Feel free to send a message here if you have any issues with the installation or building/running a model.

If you would like to continue using the bleeding edge version, let me know too if error persists after you install the python-gtk module. I will be happy to help.

Cheers,

Satya

To view this discussion on the web visit https://groups.google.com/d/msgid/spatiocyte-users/7f432b27-fdf1-4ac0-8e96-7eb021959812%40googlegroups.com.

[Satya Arjunan]

I just realized that you mentioned that you have already installed pygtk. Did you try installing the development version of python-gtk (python-gtk2-dev)? 

Cheers,

Saya

[Satya Arjunan]

Unfortunately, I don't have access to a Linux machine right now, so I can't check this but you can also try the following:

pip install pygtk

pip3 install pygtk

Satya

[braichenk...@gmail.com]

Hi, thanks for your reply. Unfortunately none of those worked for me. I'll try E-Cell 4 package.

Best

Svitlana

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[Satya Arjunan]

Thanks for the update. Let me know if you have any issues with Spatiocyte in the E-Cell 4 package.

Cheers,

Satya

To view this discussion on the web visit https://groups.google.com/d/msgid/spatiocyte-users/79506c27-7b67-4ea3-b7f8-1ba8ed86129a%40googlegroups.com.

[Svitlana Braichenko]

Hi Satya,

After some deviations in my project, I decided to come back to using ecell4 package. I posted this question on the slack channel, but not sure if it's still maintained. I’m trying to model a simple reaction A+B -> C with Spatiocyte world in ecell 4 package. I would like to add external molecules (crowders) that don’t participate in the reaction but create volume exclusion effect.  According to your documentation, the size of the voxel should be preferably equal to the largest molecule in the system and it works the best if the molecules are of the same size. Can you suggest any alternatives within your package (avoiding bd because it's extremely computationally expensive) if I wanted to simulate different sizes of molecules, say reactants twice larger than the crowders?

Cheers

Svitlana

[Satya Arjunan]

Hi Kaizu-san and Nishida-san,

Svitlana is using E-Cell4 and would like to simulate molecules with different diameters (see her message below). Can you please help her? Thanks!

Cheers,

Satya

To view this discussion on the web visit https://groups.google.com/d/msgid/spatiocyte-users/78a12988-f607-47b9-9b41-6f7ee9eb5637n%40googlegroups.com.

[Nayana G B]

Hi Dr. Satya,

Myself Nayana, wanted clarification that, can we build the model for a Lac-operon of a single cell using pSpaciocyte. So that if it works fine. I can proceed with the work by installing it.

Thank you.

Regards,

Nayana G.Bhat