No patch for step for 'abseil'

[alanmejiamaza]

Hi,

I am trying to install ExpansionHunter into a conda environment . I have installed all dependencies but I am getting an error when using "make". The problem appears to be related to 'abseil' package but I haven't been able to solve it.

I tried installing abseil but It didn't solve the issue. Could you please help me here? Thanks

This is the output I get :

Scanning dependencies of target abseil [ 2%] Creating directories for 'abseil' [ 4%] Performing download step (git clone) for 'abseil' Initialized empty Git repository in /data/wheeler_lab/ALAN/HD/ExpansionHunter/build/abseil-prefix/src/abseil/.git/ Checking out files: 100% (1312/1312), done. Note: checking out '20210324.2'.

You are in 'detached HEAD' state. You can look around, make experimental changes and commit them, and you can discard any commits you make in this state without impacting any branches by performing another checkout.

If you want to create a new branch to retain commits you create, you may do so (now or later) by using -b with the checkout command again. Example:

git checkout -b new_branch_name

HEAD is now at 278e0a0... Abseil LTS 20210324, Patch 2 [ 6%] No patch step for 'abseil' [ 8%] No update step for 'abseil' [ 10%] Performing configure step for 'abseil' -- The CXX compiler identification is GNU 4.4.7 -- Check for working CXX compiler: /usr/bin/c++ -- Check for working CXX compiler: /usr/bin/c++ - works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- Looking for C++ include pthread.h -- Looking for C++ include pthread.h - found -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed -- Looking for pthread_create in pthreads -- Looking for pthread_create in pthreads - not found -- Looking for pthread_create in pthread -- Looking for pthread_create in pthread - found -- Found Threads: TRUE
-- Configuring done -- Generating done -- Build files have been written to: /data/wheeler_lab/ALAN/HD/ExpansionHunter/build/abseil-prefix/src/abseil-build [ 12%] Performing build step for 'abseil' Scanning dependencies of target strerror [ 1%] Building CXX object absl/base/CMakeFiles/strerror.dir/internal/strerror.cc.o cc1plus: error: unrecognized command line option "-Wconversion-null" cc1plus: error: unrecognized command line option "-Wunused-local-typedefs" cc1plus: error: unrecognized command line option "-Wunused-result" cc1plus: error: unrecognized command line option "-Wvarargs" make[5]: [absl/base/CMakeFiles/strerror.dir/internal/strerror.cc.o] Error 1 make[4]: [absl/base/CMakeFiles/strerror.dir/all] Error 2 make[3]: [all] Error 2 make[2]: [abseil-prefix/src/abseil-stamp/abseil-build] Error 2 make[1]: [CMakeFiles/abseil.dir/all] Error 2 make: [all] Error 2

[ctsa]

@alanmejiamaza, I believe this is an issue with the gcc version. The lowest gcc version known to compile the current version of EH is 5.1.

[alanmejiamaza]

Thanks for replying. I have gcc 11.2, so it's update. Any other thought? I'd much appreciate it.

[ctsa]

From the log snipper, it looks like cmake is finding gcc 4.4, likely the system compiler:

The CXX compiler identification is GNU 4.4.7

One way to build EH and configure the gcc version for cmake is:

$ cd ExpansionHunter
$ mkdir build
$ cd build
$ CC=/path/to/gcc CXX=/path/to/c++ cmake ..
$ make