Installing EPACTS: [Makefile:599: pEmmax.o] Error 1

[adrtin]

Installing EPACTS in CentOS Linux release 7.9.2009.

The Make step has the following error messages: make[2]: [Makefile:599: pEmmax.o] Error 1 make[2]: Leaving directory '/users/atin/bin/EPACTS_3.2.6/EPACTS-3.2.6/src' make[1]: [Makefile:321: all-recursive] Error 1 make[1]: Leaving directory '/users/atin/bin/EPACTS_3.2.6/EPACTS-3.2.6' make: *** [Makefile:252: all] Error 2

Please advise a solution.

Thank you

[adrtin]

I tried both git clone https://github.com/statgen/EPACTS.git and EPACTS-3.2.6 The previous post has error messages from EPACTS-3.2.6.

The error messages from the git clone version are similar: make[2]: [Makefile:762: pEmmax.o] Error 1 make[2]: Leaving directory '/users/atin/bin/EPACTS/src' make[1]: [Makefile:408: all-recursive] Error 1 make[1]: Leaving directory '/users/atin/bin/EPACTS' make: *** [Makefile:339: all] Error 2

Please advise a solution. Thank you.

[Lvyxiao]

I also met the same problem, is there any good solution?

[jonathonl]

Please attach the full build log. The snippets above do not include the compiler error message.

[Lvyxiao]

https://gist.github.com/Lvyxiao/7c47b3a9f74c90f7b5700e57e87daf9d I don't know which part of the display will help fix the error, this is all the screen shows, please help me, this is my first time using make to install software! thank

[jonathonl]

I would try using https://github.com/statgen/EPACTS/releases/tag/v3.4.2 instead of the v3.2.6 (Note: it has different build instructions).

Alternatively, you will need to use an older compiler (not the conda version of gcc) to build v3.2.6.

[Lvyxiao]

I installed 3.4.2 and went to./configure --prefix but it showed./configure: No such file or directory

[jonathonl]

As I noted, the build instructions for this version are different (see https://github.com/statgen/EPACTS/blob/v3.4.2/README.md?plain=1#L11-L19). It uses CMake instead of autotools. You will also use cget, which can be installed with pip3 install cget.

[Lvyxiao]

I started installing EPACTS-3.4.2 with cget already installed, and when I run this command: get install -DCMAKE_C_FLAGS="-fPIC" -DCMAKE_CXX_FLAGS="-fPIC" -f requirements.txt,it says: Downloading https://github.com/statgen/savvy/archive/863c4a31e80024c75137fee8bc9e213a4c3a0eb3.tar.gz Unexpected error: <type 'exceptions.IOError'> ('http protocol error', 0, 'got a bad status line', None) Failed to build package statgen/savvy

[Lvyxiao]

I installed savvy using conda and then did the next steps. I got an error when make: make[3]: *** [/share/home/wangyuzhe/miniconda3/envs/locuzoom/lib/R/etc/Makeconf:177: epacts.o] Error 1 ERROR: compilation failed for package ‘epactsR’

• removing ‘/share/home/wangyuzhe/tools/locuzoom/EPACTS-3.4.2/build/epactsR’ make[2]: [CMakeFiles/epactsR-install.dir/build.make:71: CMakeFiles/epactsR-install] Error 1 make[1]: [CMakeFiles/Makefile2:131: CMakeFiles/epactsR-install.dir/all] Error 2 make: *** [Makefile:156: all] Error 2

[jonathonl]

I'm not sure about the "http protocol error". It could be that cget needs to be reinstalled/upgraded.

The second error you are presenting should have more details earlier in the log output. Also, there are multiple versions of Savvy on conda an EPACTS is tied to a specific version. It definitely won't work with savvy v2.x.x.

[Lvyxiao]

I still get errors: 1. When I install epacts3.2 series with different versions of gcc, I still get errors when I execute ‘make’ command: 2. When I install epacts3.4.2 and update cget, I still get errors: Downloading https://github.com/statgen/savvy/archive/863c4a31e80024c75137fee8bc9e213a4c3a0eb3.tar.gz Unexpected error: <type 'exceptions.IOError'> ('http protocol error', 0, 'got a bad status line', None) Failed to build package statgen/savvy , I can only consider trying to install the savvy package I downloaded, but I found that some of the commands in it still need to use cget, so there will still be errors. I am still checking how to use cget successfully. I'm wondering if it's my Linux server, because I can't use git cloud to download software on GitHub, so I can just download the installation package and decompress it myself

[Lvyxiao]

I got some ideas after reading this answer： https://github.com/statgen/EPACTS/issues/32 because I installed epacts to use locuszoom, my server's environment is Python2.7, and I used some other environment, which is Python3, with the conda command： conda install -c genomedk epacts and it was successfully installed, I still need to test whether it can be successfully used. Thank you very much for your answer. This is my first attempt to install the software!