configure: error: ./configure failed for ecell

[許翔傑Hsu, Hsiang-Chieh]

Dear Dr Satya:

I would like to install Spatiocyte on my laptop, and my system distribution is Ubuntu 20.04.6 LTS (inux version 5.15.0-88-generic (buildd@lcy02-amd64-011)).

I follow the instrument on the website (https://spatiocyte.org/):

$ wget https://raw.githubusercontent.com/ecell/spatiocyte/master/install-spatiocyte-ubuntu.sh 

$ sh -x install-spatiocyte-ubuntu.sh

I always has the problem in configure ecell and fain in makefile.

Part of the error message are as follows:

-----------------------------------------------------------------------------------------------------------

checking for python library location... -L/usr/lib -L/usr/lib/python2.7/config-x86_64-linux-gnu -L/usr/lib -lpython2.7 -lpthread -ldl  -lutil -lm  -Xlinker -export-dynamic -Wl,-O1 -Wl,-Bsymbolic-functions
checking boost/python.hpp usability... yes
checking boost/python.hpp presence... yes
checking for boost/python.hpp... yes
checking for Boost.Python runtime library availability... no
configure: error: could not find Boost.Python library
configure: error: ./configure failed for ecell
+ make -j4
make  all-recursive
make[1]: Entering directory '/home/hsiang-chieh/wrk/spatiocyte'
Making all in libltdl
make[2]: Entering directory '/home/hsiang-chieh/wrk/spatiocyte/libltdl'
make  all-am
make[3]: Entering directory '/home/hsiang-chieh/wrk/spatiocyte/libltdl'
/bin/sh ./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/sh ./libtool  --tag=CC   --mode=link gcc  -g -O2   -o libltdlc.la  ltdl.lo -ldl
libtool: link: ar cr .libs/libltdlc.a .libs/ltdl.o
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/hsiang-chieh/wrk/spatiocyte/libltdl'
make[2]: Leaving directory '/home/hsiang-chieh/wrk/spatiocyte/libltdl'
Making all in dmtool
make[2]: Entering directory '/home/hsiang-chieh/wrk/spatiocyte/dmtool'
make  all-am
make[3]: Entering directory '/home/hsiang-chieh/wrk/spatiocyte/dmtool'
make[3]: Leaving directory '/home/hsiang-chieh/wrk/spatiocyte/dmtool'
make[2]: Leaving directory '/home/hsiang-chieh/wrk/spatiocyte/dmtool'
Making all in ecell
make[2]: Entering directory '/home/hsiang-chieh/wrk/spatiocyte/ecell'
make[2]: *** No rule to make target 'all'.  Stop.
make[2]: Leaving directory '/home/hsiang-chieh/wrk/spatiocyte/ecell'
make[1]: *** [Makefile:413: all-recursive] Error 1
make[1]: Leaving directory '/home/hsiang-chieh/wrk/spatiocyte'
make: *** [Makefile:345: all] Error 2
+ make install
Making install in libltdl
make[1]: Entering directory '/home/hsiang-chieh/wrk/spatiocyte/libltdl'
make[2]: Entering directory '/home/hsiang-chieh/wrk/spatiocyte/libltdl'
make[2]: Leaving directory '/home/hsiang-chieh/wrk/spatiocyte/libltdl'
make[1]: Leaving directory '/home/hsiang-chieh/wrk/spatiocyte/libltdl'
Making install in dmtool
make[1]: Entering directory '/home/hsiang-chieh/wrk/spatiocyte/dmtool'
make[2]: Entering directory '/home/hsiang-chieh/wrk/spatiocyte/dmtool'
 /usr/bin/mkdir -p '/home/hsiang-chieh/root/bin'
 /usr/bin/install -c dmcompile '/home/hsiang-chieh/root/bin'
 /usr/bin/mkdir -p '/home/hsiang-chieh/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/hsiang-chieh/root/include/dmtool'
make[2]: Leaving directory '/home/hsiang-chieh/wrk/spatiocyte/dmtool'
make[1]: Leaving directory '/home/hsiang-chieh/wrk/spatiocyte/dmtool'
Making install in ecell
make[1]: Entering directory '/home/hsiang-chieh/wrk/spatiocyte/ecell'
make[1]: *** No rule to make target 'install'.  Stop.
make[1]: Leaving directory '/home/hsiang-chieh/wrk/spatiocyte/ecell'
make: *** [Makefile:413: install-recursive] Error 1
+ echo 'Close and reopen this terminal before proceeding'
Close and reopen this terminal before proceeding

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I guess the problem is the installation of boost.python, however, I have already installed them. I tried different method but still could not work. Do you have any idea? Thanks!

The attachment (error.log) shows the whole error message .

Best,

Hsiang-Chieh

[Satya Arjunan]

Hi Hsiang-Chieh,

I think the main problem is that the https://raw.githubusercontent.com/ecell/spatiocyte/master/install-spatiocyte-ubuntu.sh script has not been updated for the more recent versions of Ubuntu. The script is still using Python 2.7. Ubuntu 20.04.6 uses Python 3.6 or 3.8. So, you will need to update the script (-L/usr/lib/python2.7/config-x86_64-linux-gnu -L/usr/lib -lpython2.7) to support the new version of Python. I will try to update the script myself when I get the time.

Cheers,

Satya

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[許翔傑Hsu, Hsiang-Chieh]

Dear Dr.Satya:

Thanks for the immediate response. I am a little not familiar with the make process, to be honest. Where could I update the script (-L/usr/lib/python2.7/config-x86_64-linux-gnu -L/usr/lib -lpython2.7) ? 
I tried to edit the https://raw.githubusercontent.com/ecell/spatiocyte/master/install-spatiocyte-ubuntu.sh script here by replacing 

echo "export PYTHONPATH=\$HOME/root/lib/python2.7/site-packages:\$PYTHONPATH" >> ~/.bashrc

to

echo "export PYTHONPATH=\$HOME/root/lib/python3.8/site-packages:\$PYTHONPATH" >> ~/.bashrc

(before executing it again, I remove the lines that have been added inside previously.)

But it didn't work for me, and I got the same results. The error messages are same as before. I also notice the other parts in the log have also shown that they use the python2.7 version:

-----------------------------------------------------------------------------------------------------------

checking for a Python interpreter with version >= 2.2... python
checking for python... /usr/bin/python
checking for python version... 2.7
checking for python platform... linux2
checking for python script directory... ${prefix}/lib/python2.7/site-packages
checking for python extension module directory... ${exec_prefix}/lib/python2.7/site-packages

-----------------------------------------------------------------------------------------------------------

I also checked the autogen.sh and configure files, however, I still could not find where I could update them to Python 3. Sorry for my naive question. Could you give me some hints to solve it? Thanks!

Best,

Hsiang-Chieh

Satya Arjunan 在 2023年11月8日 星期三晚上8:58:12 [UTC+8] 的信中寫道：