"Failed to rebase" error when installing

[ahwanpandey]

HI Jeremiah,

I am getting this error when installing. Please help.

]$ cmake .. -DHTSLIB_DIR=/config/binaries/htslib/1.17/
-- The C compiler identification is GNU 8.3.0
-- The CXX compiler identification is GNU 8.3.0
-- Check for working C compiler: /config/binaries/gcc/8.3.0/bin/gcc
-- Check for working C compiler: /config/binaries/gcc/8.3.0/bin/gcc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /config/binaries/gcc/8.3.0/bin/g++
-- Check for working CXX compiler: /config/binaries/gcc/8.3.0/bin/g++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Looking for pthread.h
-- Looking for 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
-- Found ZLIB: /usr/lib64/libz.so (found version "1.2.7")
-- Found BZip2: /usr/lib64/libbz2.so (found version "1.0.6")
-- Looking for BZ2_bzCompressInit
-- Looking for BZ2_bzCompressInit - found
Scanning dependencies of target catch2-populate
[ 11%] Creating directories for 'catch2-populate'
[ 22%] Performing download step (git clone) for 'catch2-populate'
Cloning into 'catch2-src'...
Switched to a new branch 'v2.x'
Branch v2.x set up to track remote branch v2.x from origin.
[ 33%] No patch step for 'catch2-populate'
[ 44%] Performing update step for 'catch2-populate'
Cannot rebase: You have unstaged changes.
Please commit or stash them.
No rebase in progress?
error: Your local changes to the following files would be overwritten by merge:
        CMake/llvm-cov-wrapper
        projects/TestScripts/testRandomOrder.py
        scripts/approvalTests.py
        scripts/approve.py
        scripts/benchmarkCompile.py
        scripts/benchmarkRunner.py
        scripts/developBuild.py
        scripts/embedClara.py
        scripts/fixWhitespace.py
        scripts/generateSingleHeader.py
        scripts/majorRelease.py
        scripts/minorRelease.py
        scripts/patchRelease.py
        scripts/releaseNotes.py
        scripts/updateDocumentToC.py
Please, commit your changes or stash them before you can merge.
Aborting
Index was not unstashed.
CMake Error at /researchers/ahwan.pandey/Tools/omics_tools/SvABA/final_fix/svaba/build/_deps/catch2-subbuild/catch2-populate-prefix/tmp/catch2-populate-gitupdate.cmake:102 (message):


  Failed to rebase in:
  '/researchers/ahwan.pandey/Tools/omics_tools/SvABA/final_fix/svaba/build/_deps/catch2-src/'.


  You will have to resolve the conflicts manually


gmake[2]: *** [catch2-populate-prefix/src/catch2-populate-stamp/catch2-populate-update] Error 1
gmake[1]: *** [CMakeFiles/catch2-populate.dir/all] Error 2
gmake: *** [all] Error 2

CMake Error at /config/binaries/cmake/3.16.5/share/cmake-3.16/Modules/FetchContent.cmake:915 (message):
  Build step for catch2 failed: 2
Call Stack (most recent call first):
  /config/binaries/cmake/3.16.5/share/cmake-3.16/Modules/FetchContent.cmake:1006 (__FetchContent_directPopulate)
  /config/binaries/cmake/3.16.5/share/cmake-3.16/Modules/FetchContent.cmake:1047 (FetchContent_Populate)
  SeqLib/CMakeLists.txt:95 (FetchContent_MakeAvailable)


-- Configuring incomplete, errors occurred!
See also "/researchers/ahwan.pandey/Tools/omics_tools/SvABA/final_fix/svaba/build/CMakeFiles/CMakeOutput.log".
See also "/researchers/ahwan.pandey/Tools/omics_tools/SvABA/final_fix/svaba/build/CMakeFiles/CMakeError.log".

COMMANDS USED

git clone --recursive https://github.com/walaj/svaba
cd svaba
git submodule update --recursive --remote

module purge
module load gcc/8.3.0
module load htslib/1.17
module load cmake/3.16.5
module load xz/5.8.1

export CC=/config/binaries/gcc/8.3.0/bin/gcc
export CXX=/config/binaries/gcc/8.3.0/bin/g++

mkdir build
cd build

export LZMA_INCLUDE_DIR=/config/binaries/xz/5.8.1/include
export LZMA_LIBRARY=/config/binaries/xz/5.8.1/bin

cmake .. -DHTSLIB_DIR=/config/binaries/htslib/1.17/

Thanks,
Ahwan