make: *** [Makefile:84: all] Error 2

[vinitamehlawat]

Hi @frederic-mahe

I clone the repository for genesis and tried to install it but when I call make in the main directory it is giving this error:

make[2]: ** [lib/genesis/CMakeFiles/genesis_lib_shared.dir/build.make:63: lib/genesis/CMakeFiles/genesis_lib_shared.dir///genesis_unity_sources/lib/all.cpp.o] Error 1 make[1]: [CMakeFiles/Makefile2:144: lib/genesis/CMakeFiles/genesis_lib_shared.dir/all] Error 2 make: * [Makefile:84: all] Error 2

It would be very helpful if you could please suggest why this software is not installing

Thank you Vinita

[lczech]

Hi @vinitamehlawat,

I've seen that you also opened a similar issue at BenoitMorel/covid19_cme_analysis - are these two connected?

So, from the error message that you posted above, I cannot tell much. Could you please post the full output of the make/cmake step here?

Thanks Lucas

[vinitamehlawat]

Hi @lczech

Yes I have also posted this same error to https://github.com/BenoitMorel/covid19_cme_analysis/issues/1 because I am having sars-cov2 data and for that data I want to create a robust phylogenetic tree and for this I am using there scripts but as you can see my genesis software is giving error so for that I raised issue for this software at both places. I tried to call make in the bin as well as build directory.

Here I am attaching a screen-shot of the full error whic I got on my terminal:

[lczech]

Thanks, I see the issue now. Somehow, you ended up with a genesis version that is in between a change of a feature. How did you obtain the copy of genesis in your home directory ~/genesis? Is that from the covid19_cme_analysis project, or did you clone or copy a version of genesis directly into there?

Also, @Pbdas, @BenoitMorel, does covid19_cme_analysis specify a particular commit of genesis when downloading? If not, that might cause the issue here - not sure how, but it smells like it.

[vinitamehlawat]

For genesis I just install setup.sh of https://github.com/BenoitMorel/covid19_cme_analysis but on linux mint and mac this repo is not installing but when I tried on Ubuntu server this works and all softwares installed without any error massase but the bin/apps folder is also epmpty there. For standalone I clone genesis from http://doc.genesis-lib.org/setup.html link and realised that this genesis is not installed properly in my home directory as well.

[BenoitMorel]

Hi Vinita and Lucas,

we download the most recent version of genesis (which was not very wise :D):

  git clone --recursive https://github.com/lczech/genesis.git

@lczech can you tell me which commit we should target in the setup script? I can do the update.

Best, Benoit

[lczech]

I was able to reproduce the exact issue that @vinitamehlawat described above.

But I am not entirely sure which version of genesis I used back there. It compiles for me with this change in https://github.com/BenoitMorel/covid19_cme_analysis/blob/master/setup.sh

install_genesis() {
  git clone --recursive https://github.com/lczech/genesis.git
  cd genesis
  git checkout e71a89704a87634ea84c1d15e80bafac234e0824
  echo "Installing genesis..."
  cd apps
  ln -s ../../../scripts/*.cpp .
  cd ..
  make -j 8
  make update -j 8
  cd ..
}

Let me know if this works for you as well :-)

UPDATE: I'm currently travelling, and don't have access to my hard drive where I have the covid project files on. I'll check next week which genesis version we actually used back then - but until then, you can use the one above to get it work for now.

PS: I also found some other issues when compiling the current master branch of genesis, which I'll fix later. Thanks for reporting this :-)

[BenoitMorel]

I have updated the setup script in the covid project. @vinitamehlawat you can update it with the git pull command.

If you find any other error while installing the project, you can open an issue in our repository https://github.com/BenoitMorel/covid19_cme_analysis

[lczech]

Hi @vinitamehlawat,

I've fixed the error in the genesis master branch that you described above, thanks for that!

Also, as he wrote above, @BenoitMorel has updated the covid19 project, it seems that this is fixed now. Please let us know if that worked.

I'm going to close this issue now. Feel free to re-open it should you still have problems with genesis, and please feel free to post another issue in the covid19 repository should something there still not work out!

All the best Lucas

[vinitamehlawat]

Hi @lczech

Please accept my apologies for the delay in responding; I reinstalled the genesis and it worked properly for me without any errors.

Thank you Vinita

[lczech]

Thank you, glad to hear!