Error installing last version EPACTS

[gcpmendez]

Any solution?

[jonathonl]

This should be fixed in v3.4.2 (https://github.com/statgen/EPACTS/releases/tag/v3.4.2).

[gcpmendez]

I don't find the configure file in tar.gz

[jonathonl]

Newer versions use Cmake instead of Autotools. See build instructions in readme.

[gcpmendez]

Could you tell me the way to run cget?

[jonathonl]

Remove python -m. It should be cget install -DCMAKE_C_FLAGS="-fPIC" -DCMAKE_CXX_FLAGS="-fPIC" -f requirements.txt.

You may need to install cget beforehand with pip install cget.

[gcpmendez]

After install cget with pip3 install cget I can't use cget like a executable file, just inside python3 importing like package import cget
Any solution?

[jonathonl]

The bin path in which cget is installed probably isn't in your PATH environment variable. There's a good chance that it is located at ~/.local/bin/cget. If not, running pip3 uninstall cget <<<"n" should display the bin path.

[gcpmendez]

Now I obtain this error:

CMake Error at CMakeLists.txt:21 (find_package):
  By not providing "Findsavvy.cmake" in CMAKE_MODULE_PATH this project has
  asked CMake to find a package configuration file provided by "savvy", but
  CMake did not find one.

  Could not find a package configuration file provided by "savvy" with any of
  the following names:

    savvyConfig.cmake
    savvy-config.cmake

  Add the installation prefix of "savvy" to CMAKE_PREFIX_PATH or set
  "savvy_DIR" to a directory containing one of the above files.  If "savvy"
  provides a separate development package or SDK, be sure it has been
  installed.


-- Configuring incomplete, errors occurred!

[jonathonl]

You didn't correctly configure the toolchain file. If you haven't already created a build directory, create it. Otherwise, clear the directory (rm -r build/*). Then run cmake -DCMAKE_TOOLCHAIN_FILE=../cget/cget/cget.cmake -DCMAKE_BUILD_TYPE=Release .. from the build directory. The toolchain file tells cmake how to find savvy. If you want to install EPACTS to somewhere other than the default system location, you can add -DCMAKE_INSTALL_PREFIX=</path/to/install> to the cmake command (as shown in README).

[gcpmendez]

$ tar xvf v3.4.2
$ cd EPACTS-3.4.2/
$ mkdir build
$ /root/.local/bin/cget install -DCMAKE_C_FLAGS="-fPIC" -DCMAKE_CXX_FLAGS="-fPIC" -f requirements.txt.
$ cd build/
$ cmake -DCMAKE_INSTALL_PREFIX=/opt/envhpc/utils/rhel6/epacts/3.4.2/gcc-10.2.0 -DCMAKE_TOOLCHAIN_FILE=../cget/cget/cget.cmake -DCMAKE_BUILD_TYPE=Release ..

and I got that error .. any step more I forgot?

Readme steps:

git clone https://github.com/statgen/EPACTS.git
cd EPACTS
cget install -DCMAKE_C_FLAGS="-fPIC" -DCMAKE_CXX_FLAGS="-fPIC" -f requirements.txt
mkdir build; cd build
cmake -DCMAKE_INSTALL_PREFIX=</path/to/install> -DCMAKE_TOOLCHAIN_FILE=../cget/cget/cget.cmake -DCMAKE_BUILD_TYPE=Release ..
make
make install

[jonathonl]

You could verify that cget/share/savvy/savvy-config.cmake exists and manually set the prefix path (the toolchain file already does this) with -DCMAKE_PREFIX_PATH=$(pwd)/cget (i.e., set prefix path to absolute path of cget directory). If that doesn't work, send me your OS version and cmake version so that I can try to reproduce. Though I don't have access to a REHL6 system if that is the case. Also, if cget/share/savvy/savvy-config.cmake file doesn't exist, then there is likely a build error in one of the dependencies.

[gcpmendez]

This is the error ..

[jonathonl]

The downloads from Github are failing. This could be for many reasons. It could be at system level or at python level. There are many potential solutions for this error on the internet (e.g., https://stackoverflow.com/a/43855394/1034772). I don't know what is the correct solution for your system.

Ultimately, you need to install the dependencies for EPACTS. Cget is meant to automate the process, but if you can't download through python (i.e., fix the SSL cert verification error), you'll need an alternate route. Another automated way is through conda, but you'll need to install savvy v1.3.0 instead of v2.x for EPACTS v3.4.2.

[gcpmendez]

Maybe CentOS 6.5 is too old for this version.
Could you recommend me one?

[jonathonl]

It looks like your cmake binary was built either on a different system or in a different environment on the same system. At this point it would probably be easier to just fix the build errors in EPACTS v3.3.2 (the version you first tried). For the error messages in your original post, you just need to add the word constexpr after the word static for each line that produces that error.

For example, replace
static double const DEFAULT_MIN = 1e-6
with
static constexpr double DEFAULT_MIN = 1e-6