unable to compile root digger using cmake

[Niv94]

Dear team member,

This is the same issue I posted last month. Sorry I could not reopen it. I downloaded the source code and built it using the 'cmake' command. But I am not sure what went wrong . I don't see rd file inside the 'bin'. Could you please help? Attached is the log after running cmake. Thanks in advance.

MacBook-Pro:root_digger nivi$ cmake /Users/nivi/root_digger/ -- The C compiler identification is AppleClang 13.1.6.13160021 -- The CXX compiler identification is AppleClang 13.1.6.13160021 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /Library/Developer/CommandLineTools/usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /Library/Developer/CommandLineTools/usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found Git: /usr/bin/git (found version "2.32.0 (Apple Git-132)") -- Could NOT find OpenMP_C (missing: OpenMP_C_FLAGS OpenMP_C_LIB_NAMES) -- Could NOT find OpenMP_CXX (missing: OpenMP_CXX_FLAGS OpenMP_CXX_LIB_NAMES) -- Could NOT find OpenMP (missing: OpenMP_C_FOUND OpenMP_CXX_FOUND) -- Could NOT find PkgConfig (missing: PKG_CONFIG_EXECUTABLE) -- Found GSL: /usr/local/include (found version "2.6") CMake Deprecation Warning at lib/pll-modules/CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 2.8.12 will be removed from a future version of CMake.

Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions.

-- pll-modules static build enabled CMake Deprecation Warning at lib/pll-modules/libs/libpll/CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 2.8.12 will be removed from a future version of CMake.

Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions.

-- Found BISON: /usr/bin/bison (found version "2.3") -- Found FLEX: /usr/bin/flex (found version "2.6.4") -- Disable sse simd, because not supported -- Disable avx simd, because not supported -- Disable avx2 simd, because not supported -- Libpll static build enabled -- pll_static CMake Deprecation Warning at lib/pll-modules/src/CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 2.8.12 will be removed from a future version of CMake.

Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions.

-- Will compile pll-module optimize -- Will compile pll-module algorithm -- Will compile pll-module binary -- Will compile pll-module msa -- Will compile pll-module tree -- Will compile pll-module util -- Configuring done -- Generating done -- Build files have been written to: /Users/nivi/root_digger

[computations]

Hey, thanks for following up.

This is just the configure step. You still need to run make wherever these files are stored. So in this case you should run

cd /Users/nivi/root_digger
make

Let me know if that works!

[Niv94]

Thank you so much. But now it gives an error. Can you please help?

Nivedithas-MacBook-Pro:root_digger nivi$ make make: /private/var/folders/xw/lny73q992td8sd5cr7259bh40000gn/T/AppTranslocation/D979807B-97F4-49A6-9A1A-EF230FC28242/d/CMake.app/Contents/bin/cmake: No such file or directory make: *** [cmake_check_build_system] Error 1

On Apr 19, 2022, at 12:02 AM, computations @.***> wrote:

Hey, thanks for following up.

This is just the configure step. You still need to run make wherever these files are stored. So in this case you should run

cd /Users/nivi/root_digger make Let me know if that works!

— Reply to this email directly, view it on GitHub https://github.com/computations/root_digger/issues/8#issuecomment-1102166591, or unsubscribe https://github.com/notifications/unsubscribe-auth/AKQOLVWUPYCBU4I2TSP4XC3VFZLBVANCNFSM5TXDFD7Q. You are receiving this because you authored the thread.

[computations]

Can you try removing the directory, using git to download it again, and then just running make again? I think there are some conflicts with what CMake did and some existing flies. Try this and see if it works.

[Niv94]

Hi,

I tried it and still doesn’t work . Please advise.

Nivedithas-MacBook-Pro:root_digger nivi$ make /bin/sh: cmake: command not found make: *** [release] Error 127

Nivedithas-MacBook-Pro:root_digger nivi$ make makefile make: Nothing to be done for `makefile'.

On Apr 19, 2022, at 8:50 AM, computations @.***> wrote:

Can you try removing the directory, using git to download it again, and then just running make again? I think there are some conflicts with what CMake did and some existing flies. Try this and see if it works.

— Reply to this email directly, view it on GitHub https://github.com/computations/root_digger/issues/8#issuecomment-1102815442, or unsubscribe https://github.com/notifications/unsubscribe-auth/AKQOLVSCTA2J2SKIZTIXMSLVF3I5LANCNFSM5TXDFD7Q. You are receiving this because you authored the thread.

[computations]

I guess this is a bit odd, because the cmake command worked earlier. Did something change? Possibly you need to either install it, or if you have it installed already then add it to your path.

[Niv94]

Sorry I added make to the path and now it is giving me an error towards the end. Please advise

make -- The C compiler identification is AppleClang 13.1.6.13160021 -- The CXX compiler identification is AppleClang 13.1.6.13160021 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /Library/Developer/CommandLineTools/usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /Library/Developer/CommandLineTools/usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found Git: /usr/bin/git (found version "2.32.0 (Apple Git-132)") -- Could NOT find OpenMP_C (missing: OpenMP_C_FLAGS OpenMP_C_LIB_NAMES) -- Could NOT find OpenMP_CXX (missing: OpenMP_CXX_FLAGS OpenMP_CXX_LIB_NAMES) -- Could NOT find OpenMP (missing: OpenMP_C_FOUND OpenMP_CXX_FOUND) -- Could NOT find PkgConfig (missing: PKG_CONFIG_EXECUTABLE) -- Found GSL: /usr/local/include (found version "2.6") CMake Deprecation Warning at lib/pll-modules/CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 2.8.12 will be removed from a future version of CMake.

Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions.

-- pll-modules static build enabled CMake Deprecation Warning at lib/pll-modules/libs/libpll/CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 2.8.12 will be removed from a future version of CMake.

Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions.

-- Found BISON: /usr/bin/bison (found version "2.3") -- Found FLEX: /usr/bin/flex (found version "2.6.4") -- Disable sse simd, because not supported -- Disable avx simd, because not supported -- Disable avx2 simd, because not supported -- Libpll static build enabled -- pll_static CMake Deprecation Warning at lib/pll-modules/src/CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 2.8.12 will be removed from a future version of CMake.

Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions.

-- Will compile pll-module optimize -- Will compile pll-module algorithm -- Will compile pll-module binary -- Will compile pll-module msa -- Will compile pll-module tree -- Will compile pll-module util -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project:

BENCHMARK_ENABLE_LTO

-- Build files have been written to: /Users/nivi/root_digger/build [ 1%] [BISON][parse_utree_t] Building parser with bison 2.3 [ 2%] [FLEX][lex_rtree_t] Building scanner with flex 2.6.4 [ 3%] [FLEX][lex_utree_t] Building scanner with flex 2.6.4 [ 4%] [BISON][parse_rtree_t] Building parser with bison 2.3 [ 5%] Building C object lib/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/compress.c.o clang: error: no such file or directory: 'NOTFOUND' make[3]: [lib/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/compress.c.o] Error 1 make[2]: [lib/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/all] Error 2 make[1]: [all] Error 2 make: [release] Error 2

On Apr 19, 2022, at 12:54 PM, computations @.***> wrote:

I guess this is a bit odd, because the cmake command worked earlier. Did something change? Possibly you need to either install it, or if you have it installed already then add it to your path.

— Reply to this email directly, view it on GitHub https://github.com/computations/root_digger/issues/8#issuecomment-1103051932, or unsubscribe https://github.com/notifications/unsubscribe-auth/AKQOLVRGF2DSBGFD7ZEDT6LVF4FPHANCNFSM5TXDFD7Q. You are receiving this because you authored the thread.

[computations]

hmmm, maybe the submodules aren't checked out? Try

git submodule update --init --recursive

and then make again.

[Niv94]

Unfortunately its still throwing the same error . Thank you so much for your guidance

-- Could NOT find OpenMP_C (missing: OpenMP_C_FLAGS OpenMP_C_LIB_NAMES) -- Could NOT find OpenMP_CXX (missing: OpenMP_CXX_FLAGS OpenMP_CXX_LIB_NAMES) -- Could NOT find OpenMP (missing: OpenMP_C_FOUND OpenMP_CXX_FOUND) -- Could NOT find PkgConfig (missing: PKG_CONFIG_EXECUTABLE) CMake Deprecation Warning at lib/pll-modules/CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 2.8.12 will be removed from a future version of CMake.

Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions.

-- pll-modules static build enabled CMake Deprecation Warning at lib/pll-modules/libs/libpll/CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 2.8.12 will be removed from a future version of CMake.

Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions.

-- Disable sse simd, because not supported -- Disable avx simd, because not supported -- Disable avx2 simd, because not supported -- Libpll static build enabled -- pll_static;pll_static;pll_static CMake Deprecation Warning at lib/pll-modules/src/CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 2.8.12 will be removed from a future version of CMake.

Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions.

-- Will compile pll-module optimize -- Will compile pll-module algorithm -- Will compile pll-module binary -- Will compile pll-module msa -- Will compile pll-module tree -- Will compile pll-module util -- Configuring done -- Generating done -- Build files have been written to: /Users/nivi/root_digger/build [ 1%] Building C object lib/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/compress.c.o clang: error: no such file or directory: 'NOTFOUND' make[3]: [lib/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/compress.c.o] Error 1 make[2]: [lib/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/all] Error 2 make[1]: [all] Error 2 make: [release] Error 2

On Apr 21, 2022, at 2:16 PM, computations @.***> wrote:

hmmm, maybe the submodules aren't checked out? Try

git submodule update --init --recursive and then make again.

— Reply to this email directly, view it on GitHub https://github.com/computations/root_digger/issues/8#issuecomment-1105768914, or unsubscribe https://github.com/notifications/unsubscribe-auth/AKQOLVW6VUAUCYV3LCJLCA3VGHAUXANCNFSM5TXDFD7Q. You are receiving this because you authored the thread.

[computations]

Thank you so much for sticking with it. I have one more thing that I need then. Can you run

VERBOSE=1 make

and let me know the output? Thanks!

[Niv94]

Thank you for the support. Here you go

MacBook-Pro:root_digger nivi$ VERBOSE=1 make Re-run cmake no build system arguments -- Could NOT find OpenMP_C (missing: OpenMP_C_FLAGS OpenMP_C_LIB_NAMES) -- Could NOT find OpenMP_CXX (missing: OpenMP_CXX_FLAGS OpenMP_CXX_LIB_NAMES) -- Could NOT find OpenMP (missing: OpenMP_C_FOUND OpenMP_CXX_FOUND) -- Could NOT find PkgConfig (missing: PKG_CONFIG_EXECUTABLE) CMake Deprecation Warning at lib/pll-modules/CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 2.8.12 will be removed from a future version of CMake.

Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions.

-- pll-modules static build enabled CMake Deprecation Warning at lib/pll-modules/libs/libpll/CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 2.8.12 will be removed from a future version of CMake.

Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions.

-- Disable sse simd, because not supported -- Disable avx simd, because not supported -- Disable avx2 simd, because not supported -- Libpll static build enabled -- pll_static;pll_static;pll_static;pll_static CMake Deprecation Warning at lib/pll-modules/src/CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 2.8.12 will be removed from a future version of CMake.

Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions.

-- Will compile pll-module optimize -- Will compile pll-module algorithm -- Will compile pll-module binary -- Will compile pll-module msa -- Will compile pll-module tree -- Will compile pll-module util -- Configuring done -- Generating done -- Build files have been written to: /Users/nivi/root_digger/build /Applications/CMake.app/Contents/bin/cmake -S/Users/nivi/root_digger -B/Users/nivi/root_digger/build --check-build-system CMakeFiles/Makefile.cmake 0 /Applications/CMake.app/Contents/bin/cmake -E cmake_progress_start /Users/nivi/root_digger/build/CMakeFiles /Users/nivi/root_digger/build//CMakeFiles/progress.marks /Library/Developer/CommandLineTools/usr/bin/make -f CMakeFiles/Makefile2 all /Library/Developer/CommandLineTools/usr/bin/make -f lib/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/build.make lib/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/depend cd /Users/nivi/root_digger/build && /Applications/CMake.app/Contents/bin/cmake -E cmake_depends "Unix Makefiles" /Users/nivi/root_digger /Users/nivi/root_digger/lib/pll-modules/libs/libpll/src /Users/nivi/root_digger/build /Users/nivi/root_digger/build/lib/pll-modules/libs/libpll/src /Users/nivi/root_digger/build/lib/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/DependInfo.cmake --color= /Library/Developer/CommandLineTools/usr/bin/make -f lib/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/build.make lib/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/build [ 1%] Building C object lib/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/compress.c.o cd /Users/nivi/root_digger/build/lib/pll-modules/libs/libpll/src && /Library/Developer/CommandLineTools/usr/bin/cc -DHAVE_X86INTRIN_H -I/Users/nivi/root_digger/build/localdeps/include -I/Users/nivi/root_digger/lib/pll-modules/libs/libpll/src -I/Users/nivi/root_digger/build/lib/pll-modules/libs/libpll/src NOTFOUND -Wall -Wsign-compare -D_GNU_SOURCE -O3 -fPIC -O3 -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX12.3.sdk -mmacosx-version-min=12.1 -MD -MT lib/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/compress.c.o -MF CMakeFiles/pll_obj.dir/compress.c.o.d -o CMakeFiles/pll_obj.dir/compress.c.o -c /Users/nivi/root_digger/lib/pll-modules/libs/libpll/src/compress.c clang: error: no such file or directory: 'NOTFOUND' make[3]: [lib/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/compress.c.o] Error 1 make[2]: [lib/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/all] Error 2 make[1]: [all] Error 2 make: [release] Error 2

On Apr 22, 2022, at 12:23 AM, computations @.***> wrote:

Thank you so much for sticking with it. I have one more thing that I need then. Can you run

VERBOSE=1 make and let me know the output? Thanks!

— Reply to this email directly, view it on GitHub https://github.com/computations/root_digger/issues/8#issuecomment-1106100228, or unsubscribe https://github.com/notifications/unsubscribe-auth/AKQOLVWGVJFCVNNIKCDXTF3VGJHVTANCNFSM5TXDFD7Q. You are receiving this because you authored the thread.

[computations]

Thank you so much for your efforts! There was an error in the build configuration, where if OpenMP was not installed, the build would fail. I have pushed a change which makes OpenMP optional. Please try again with the new git version.

[Niv94]

Thanks a lot for your support. But I am still having errors sorry

CoS-Biology-Lluvia-Flores-Renteria-iMac-78PG:root_digger lluviaadmin$ make

-- The C compiler identification is AppleClang 13.0.0.13000027

-- The CXX compiler identification is AppleClang 13.0.0.13000027

-- Detecting C compiler ABI info

-- Detecting C compiler ABI info - done

-- Check for working C compiler: /Library/Developer/CommandLineTools/usr/bin/cc - skipped

-- Detecting C compile features

-- Detecting C compile features - done

-- Detecting CXX compiler ABI info

-- Detecting CXX compiler ABI info - done

-- Check for working CXX compiler: /Library/Developer/CommandLineTools/usr/bin/c++ - skipped

-- Detecting CXX compile features

-- Detecting CXX compile features - done

-- Found Git: /usr/bin/git (found version "2.30.1 (Apple Git-130)")

-- Found PkgConfig: /usr/local/bin/pkg-config (found version "0.29.2")

-- Found GSL: /usr/local/Cellar/gsl/2.5/include (found version "2.5")

CMake Deprecation Warning at lib/pll-modules/CMakeLists.txt:1 (cmake_minimum_required):

Compatibility with CMake < 2.8.12 will be removed from a future version of

CMake.

Update the VERSION argument value or use a ... suffix to tell

CMake that the project does not need compatibility with older versions.

-- pll-modules static build enabled

CMake Deprecation Warning at lib/pll-modules/libs/libpll/CMakeLists.txt:1 (cmake_minimum_required):

Compatibility with CMake < 2.8.12 will be removed from a future version of

CMake.

Update the VERSION argument value or use a ... suffix to tell

CMake that the project does not need compatibility with older versions.

-- Found BISON: /usr/bin/bison (found version "2.3")

-- Found FLEX: /usr/bin/flex (found version "2.6.4")

-- SSE enabled. To disable it, run cmake with -DENABLE_SSE=false

-- AVX enabled. To disable it, run cmake with -DENABLE_AVX=false

-- AVX2 enabled. To disable it, run cmake with -DENABLE_AVX2=false

-- Libpll static build enabled

-- pll_static

CMake Deprecation Warning at lib/pll-modules/src/CMakeLists.txt:1 (cmake_minimum_required):

Compatibility with CMake < 2.8.12 will be removed from a future version of

CMake.

Update the VERSION argument value or use a ... suffix to tell

CMake that the project does not need compatibility with older versions.

-- Will compile pll-module optimize

-- Will compile pll-module algorithm

-- Will compile pll-module binary

-- Will compile pll-module msa

-- Will compile pll-module tree

-- Will compile pll-module util

-- Looking for pthread.h

-- Looking for pthread.h - found

-- Performing Test CMAKE_HAVE_LIBC_PTHREAD

-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success

-- Found Threads: TRUE

-- Could NOT find OpenMP_C (missing: OpenMP_C_FLAGS OpenMP_C_LIB_NAMES)

-- Could NOT find OpenMP_CXX (missing: OpenMP_CXX_FLAGS OpenMP_CXX_LIB_NAMES)

-- Could NOT find OpenMP (missing: OpenMP_C_FOUND OpenMP_CXX_FOUND)

-- Configuring done

CMake Error at src/CMakeLists.txt:6 (add_executable):

Target "rd" links to target "OpenMP::OpenMP_CXX" but the target was not

found. Perhaps a find_package() call is missing for an IMPORTED target, or

an ALIAS target is missing?

-- Generating done

CMake Warning:

Manually-specified variables were not used by the project:

BENCHMARK_ENABLE_LTO

CMake Generate step failed. Build files cannot be regenerated correctly.

make: *** [release] Error 1

On Fri, Apr 22, 2022 at 1:11 PM computations @.***> wrote:

Thank you so much for your efforts! There was an error in the build configuration, where if OpenMP was not installed, the build would fail. I have pushed a change which makes OpenMP optional. Please try again with the new git version.

— Reply to this email directly, view it on GitHub https://github.com/computations/root_digger/issues/8#issuecomment-1106824318, or unsubscribe https://github.com/notifications/unsubscribe-auth/AKQOLVXUBZJVIBVPIY2DGLLVGMBYBANCNFSM5TXDFD7Q . You are receiving this because you authored the thread.Message ID: @.***>

[computations]

I sent a reply through email, but I am not sure if it actually made it. Sorry for the delay. Regardless, I just pushed a change that will (hopefully) truly fix this. However, if it doesn't work, I would suggest just installing openmp, as it will make the program run faster anyways.

[Niv94]

Thank you! I tried installing Openmp and I am still getting some errors that I attached below. Thank you for your help.

CoS-Biology-Lluvia-Flores-Renteria-iMac-78PG:root_digger lluviaadmin$ make

-- The C compiler identification is AppleClang 13.0.0.13000027

-- The CXX compiler identification is AppleClang 13.0.0.13000027

-- Detecting C compiler ABI info

-- Detecting C compiler ABI info - done

-- Check for working C compiler: /Library/Developer/CommandLineTools/usr/bin/cc - skipped

-- Detecting C compile features

-- Detecting C compile features - done

-- Detecting CXX compiler ABI info

-- Detecting CXX compiler ABI info - done

-- Check for working CXX compiler: /Library/Developer/CommandLineTools/usr/bin/c++ - skipped

-- Detecting CXX compile features

-- Detecting CXX compile features - done

-- Found Git: /usr/bin/git (found version "2.30.1 (Apple Git-130)")

-- Found PkgConfig: /usr/local/bin/pkg-config (found version "0.29.2")

-- Found GSL: /usr/local/Cellar/gsl/2.5/include (found version "2.5")

CMake Deprecation Warning at lib/pll-modules/CMakeLists.txt:1 (cmake_minimum_required):

Compatibility with CMake < 2.8.12 will be removed from a future version of

CMake.

Update the VERSION argument value or use a ... suffix to tell

CMake that the project does not need compatibility with older versions.

-- pll-modules static build enabled

CMake Deprecation Warning at lib/pll-modules/libs/libpll/CMakeLists.txt:1 (cmake_minimum_required):

Compatibility with CMake < 2.8.12 will be removed from a future version of

CMake.

Update the VERSION argument value or use a ... suffix to tell

CMake that the project does not need compatibility with older versions.

-- Found BISON: /usr/bin/bison (found version "2.3")

-- Found FLEX: /usr/bin/flex (found version "2.6.4")

-- SSE enabled. To disable it, run cmake with -DENABLE_SSE=false

-- AVX enabled. To disable it, run cmake with -DENABLE_AVX=false

-- AVX2 enabled. To disable it, run cmake with -DENABLE_AVX2=false

-- Libpll static build enabled

-- pll_static

CMake Deprecation Warning at lib/pll-modules/src/CMakeLists.txt:1 (cmake_minimum_required):

Compatibility with CMake < 2.8.12 will be removed from a future version of

CMake.

Update the VERSION argument value or use a ... suffix to tell

CMake that the project does not need compatibility with older versions.

-- Will compile pll-module optimize

-- Will compile pll-module algorithm

-- Will compile pll-module binary

-- Will compile pll-module msa

-- Will compile pll-module tree

-- Will compile pll-module util

-- Looking for pthread.h

-- Looking for pthread.h - found

-- Performing Test CMAKE_HAVE_LIBC_PTHREAD

-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success

-- Found Threads: TRUE

-- Found OpenMP_C: -Xclang -fopenmp (found version "5.0")

-- Found OpenMP_CXX: -Xclang -fopenmp (found version "5.0")

-- Found OpenMP: TRUE (found version "5.0")

-- Configuring done

-- Generating done

CMake Warning:

Manually-specified variables were not used by the project:

BENCHMARK_ENABLE_LTO

-- Build files have been written to: /Users/lluviaadmin/root_digger/build

[ 1%] [BISON][parse_utree_t] Building parser with bison 2.3

[ 2%] [FLEX][lex_rtree_t] Building scanner with flex 2.6.4

[ 3%] [FLEX][lex_utree_t] Building scanner with flex 2.6.4

[ 4%] [BISON][parse_rtree_t] Building parser with bison 2.3

[ 5%] Building C object lib/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/compress.c.o

[ 6%] Building C object lib/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/parse_utree.c.o

[ 7%] Building C object lib/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/lex_utree.c.o

[ 8%] Building C object lib/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/parse_rtree.c.o

[ 9%] Building C object lib/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/lex_rtree.c.o

[ 10%] Building C object lib/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/core_derivatives.c.o

[ 11%] Building C object lib/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/core_likelihood.c.o

[ 12%] Building C object lib/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/core_partials.c.o

[ 13%] Building C object lib/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/core_pmatrix.c.o

/Users/lluviaadmin/root_digger/lib/pll-modules/libs/libpll/src/core_pmatrix.c:23:10: fatal error: 'gsl/gsl_linalg.h' file not found

include <gsl/gsl_linalg.h>

     ^~~~~~~~~~~~~~~~~~

1 error generated.

make[3]: *** [lib/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/core_pmatrix.c.o] Error 1

make[2]: *** [lib/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/all] Error 2

make[1]: *** [all] Error 2

make: *** [release] Error 2

On Mon, Apr 25, 2022 at 2:47 AM computations @.***> wrote:

I sent a reply through email, but I am not sure if it actually made it. Sorry for the delay. Regardless, I just pushed a change that will (hopefully) truly fix this. However, if it doesn't work, I would suggest just installing openmp, as it will make the program run faster anyways.

— Reply to this email directly, view it on GitHub https://github.com/computations/root_digger/issues/8#issuecomment-1108339670, or unsubscribe https://github.com/notifications/unsubscribe-auth/AKQOLVT7CS4E7VFX2PJ54F3VGZSZXANCNFSM5TXDFD7Q . You are receiving this because you authored the thread.Message ID: @.***>

[computations]

Hmm, thats odd. The build process should download and install gsl. You can try make static-gsl and it should force the build script to download and build gsl.

[Niv94]

Thanks. I tried to force install gsl and it didn't work. sorry and thanks for your help

1 warning generated.

[ 85%] Building C object lib/pll-modules/src/util/CMakeFiles/pllmodutil_obj.dir/models_aa.c.o

[ 86%] Building C object lib/pll-modules/src/util/CMakeFiles/pllmodutil_obj.dir/models_dna.c.o

[ 86%] Building C object lib/pll-modules/src/util/CMakeFiles/pllmodutil_obj.dir/models_gt.c.o

[ 87%] Building C object lib/pll-modules/src/util/CMakeFiles/pllmodutil_obj.dir/models_mult.c.o

[ 87%] Built target pllmodutil_obj

[ 88%] Linking C static library ../../../../localdeps/lib/libpllmodutil.a

[ 88%] Built target pllmodutil_static

[ 89%] Building C object lib/lbfgsb/CMakeFiles/lbfgs_lib.dir/lbfgsb.c.o

[ 89%] Building C object lib/lbfgsb/CMakeFiles/lbfgs_lib.dir/linesearch.c.o

[ 90%] Building C object lib/lbfgsb/CMakeFiles/lbfgs_lib.dir/linpack.c.o

[ 91%] Building C object lib/lbfgsb/CMakeFiles/lbfgs_lib.dir/miniCBLAS.c.o

[ 92%] Building C object lib/lbfgsb/CMakeFiles/lbfgs_lib.dir/subalgorithms.c.o

[ 93%] Linking C static library ../../localdeps/lib/liblbfgs_lib.a

[ 93%] Built target lbfgs_lib

[ 94%] Building CXX object src/CMakeFiles/rd.dir/main.cpp.o

warning: unknown warning option '-Wtrampolines' [-Wunknown-warning-option]

In file included from /Users/lluviaadmin/root_digger/src/main.cpp:4:

/Users/lluviaadmin/root_digger/build/localdeps/include/libpll/pll.h:448:5: warning: anonymous types declared in an anonymous union are an extension [-Wnested-anon-types]

struct

^

/Users/lluviaadmin/root_digger/build/localdeps/include/libpll/pll.h:459:5: warning: anonymous types declared in an anonymous union are an extension [-Wnested-anon-types]

struct

^

In file included from /Users/lluviaadmin/root_digger/src/main.cpp:31:

/Users/lluviaadmin/root_digger/src/checkpoint.hpp:255:3: error: must use 'struct' tag to refer to type 'flock' in this scope

flock _file_lock;

^

struct

/Library/Developer/CommandLineTools/SDKs/MacOSX12.1.sdk/usr/include/sys/fcntl.h:577:9: note: struct 'flock' is hidden by a non-type declaration of 'flock' here

int flock(int, int);

    ^

/Users/lluviaadmin/root_digger/src/main.cpp:61:50: warning: format specifies type 'unsigned long' but the argument has type 'uint64_t' (aka 'unsigned long long') [-Wformat]

debug_print(EMIT_LEVEL_IMPORTANT, "Seed: %lu", seed);

                                       ~~~   ^~~~

                                       %llu

/Users/lluviaadmin/root_digger/src/debug.h:66:26: note: expanded from macro 'debug_print'

    printf(fmt "\n", __VA_ARGS__);
\

           ~~~       ^~~~~~~~~~~

4 warnings and 1 error generated.

make[3]: *** [src/CMakeFiles/rd.dir/main.cpp.o] Error 1

make[2]: *** [src/CMakeFiles/rd.dir/all] Error 2

make[1]: *** [all] Error 2

make: *** [static-gsl] Error 2

On Mon, Apr 25, 2022 at 1:47 PM computations @.***> wrote:

Hmm, thats odd. The build process should download and install gsl. You can try make static-gsl and it should force the build script to download and build gsl.

— Reply to this email directly, view it on GitHub https://github.com/computations/root_digger/issues/8#issuecomment-1109025459, or unsubscribe https://github.com/notifications/unsubscribe-auth/AKQOLVTEDORXHYS5MZMVAMDVG4AFZANCNFSM5TXDFD7Q . You are receiving this because you authored the thread.Message ID: @.***>

[computations]

I pushed a change which should fix this. Thanks again for your efforts!

[computations]

@Niv94 Are you still having trouble building RootDigger?

[Niv94]

Hi,

Unfortunately yes I still couldn’t

Sincerely, Nivi

On Jun 10, 2022, at 12:15 PM, computations @.***> wrote:

 @Niv94 Are you still having trouble building RootDigger?

— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you were mentioned.

[computations]

I'm sorry that you have had such trouble building RootDigger. I am still happy to help. What was the most recent error that you got?

[Niv94]

No worries and thank you for helping me out. This time it doesn’t give any errors but when I check the “bin” folder there is nothing inside. I am attaching a picture of the command line below. Please advise.

Thank you

Sincerely, Nivi

On Jun 10, 2022, at 12:27 PM, computations @.***> wrote:

 I'm sorry that you have had such trouble building RootDigger. I am still happy to help. What was the most recent error that you got?

— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you were mentioned.

[computations]

I'm not sure the attachment made it through github. I am using the github issue tracker, and it appears that the image you attached didn't make it onto the issue. Would it be possible to upload the image, or even just paste the text of the terminal into an email?

[Niv94]

Hi,

Sorry about that. Please check text below

admin$ cmake ~/root_digger/ -- The C compiler identification is AppleClang 13.0.0.13000027 -- The CXX compiler identification is AppleClang 13.0.0.13000027 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /Library/Developer/CommandLineTools/usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /Library/Developer/CommandLineTools/usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found Git: /usr/bin/git (found version "2.30.1 (Apple Git-130)") -- Found PkgConfig: /usr/local/bin/pkg-config (found version "0.29.2") -- Found GSL: /usr/local/Cellar/gsl/2.5/include (found version "2.5") CMake Deprecation Warning at lib/pll-modules/CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 2.8.12 will be removed from a future version of CMake.

Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions.

-- pll-modules static build enabled CMake Deprecation Warning at lib/pll-modules/libs/libpll/CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 2.8.12 will be removed from a future version of CMake.

Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions.

-- Found BISON: /usr/bin/bison (found version "2.3") -- Found FLEX: /usr/bin/flex (found version "2.6.4") -- SSE enabled. To disable it, run cmake with -DENABLE_SSE=false -- AVX enabled. To disable it, run cmake with -DENABLE_AVX=false -- AVX2 enabled. To disable it, run cmake with -DENABLE_AVX2=false -- Libpll static build enabled -- pll_static CMake Deprecation Warning at lib/pll-modules/src/CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 2.8.12 will be removed from a future version of CMake.

Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions.

-- Will compile pll-module optimize -- Will compile pll-module algorithm -- Will compile pll-module binary -- Will compile pll-module msa -- Will compile pll-module tree -- Will compile pll-module util -- Looking for pthread.h -- Looking for pthread.h - found -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE
-- Found OpenMP_C: -Xclang -fopenmp (found version "5.0") -- Found OpenMP_CXX: -Xclang -fopenmp (found version "5.0") -- Found OpenMP: TRUE (found version "5.0")
-- Configuring done -- Generating done -- Build files have been written to: /Users/lluviaadmin/root_digger CoS-Biology-Lluvia-Flores-Renteria-iMac-78PG:root_digger lluviaadmin$ ls CMakeCache.txt LICENSE cmake_install.cmake localdeps test CMakeFiles benchmark docs makefile CMakeLists.txt bin lib src CoS-Biology-Lluvia-Flores-Renteria-iMac-78PG:root_digger lluviaadmin$ cd bin CoS-Biology-Lluvia-Flores-Renteria-iMac-78PG:bin lluviaadmin$ ls CoS-Biology-Lluvia-Flores-Renteria-iMac-78PG:bin lluviaadmin$

On Jun 13, 2022, at 10:06 AM, computations @.***> wrote:

I'm not sure the attachment made it through github. I am using the github issue tracker, and it appears that the image you attached didn't make it onto the issue. Would it be possible to upload the image, or even just paste the text of the terminal into an email?

— Reply to this email directly, view it on GitHub https://github.com/computations/root_digger/issues/8#issuecomment-1154169890, or unsubscribe https://github.com/notifications/unsubscribe-auth/AKQOLVWXHLVLWQHANYNPVZDVO5TCHANCNFSM5TXDFD7Q. You are receiving this because you were mentioned.

[computations]

Ah, I see a problem. You ran cmake which only sets up the build. After that you can run make, which will actually build the software. I'm sorry, I know its dumb, but without running make the bin directory should be empty.

[Niv94]

No worries. Thank you. But now I am having another error attached below.

admin$ make [ 1%] [BISON][parse_utree_t] Building parser with bison 2.3 [ 2%] [FLEX][lex_rtree_t] Building scanner with flex 2.6.4 [ 3%] [FLEX][lex_utree_t] Building scanner with flex 2.6.4 [ 4%] [BISON][parse_rtree_t] Building parser with bison 2.3 [ 5%] Building C object lib/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/compress.c.o [ 6%] Building C object lib/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/parse_utree.c.o [ 7%] Building C object lib/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/lex_utree.c.o [ 8%] Building C object lib/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/parse_rtree.c.o [ 9%] Building C object lib/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/lex_rtree.c.o [ 10%] Building C object lib/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/core_derivatives.c.o [ 11%] Building C object lib/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/core_likelihood.c.o [ 12%] Building C object lib/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/core_partials.c.o [ 13%] Building C object lib/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/core_pmatrix.c.o /Users/lluviaadmin/root_digger/lib/pll-modules/libs/libpll/src/core_pmatrix.c:23:10: fatal error: 'gsl/gsl_linalg.h' file not found

include <gsl/gsl_linalg.h>

     ^~~~~~~~~~~~~~~~~~

1 error generated. make[2]: [lib/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/core_pmatrix.c.o] Error 1 make[1]: [lib/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/all] Error 2 make: *** [all] Error 2

On Jun 13, 2022, at 1:19 PM, computations @.***> wrote:

Ah, I see a problem. You ran cmake which only sets up the build. After that you can run make, which will actually build the software. I'm sorry, I know its dumb, but without running make the bin directory should be empty.

— Reply to this email directly, view it on GitHub https://github.com/computations/root_digger/issues/8#issuecomment-1154388671, or unsubscribe https://github.com/notifications/unsubscribe-auth/AKQOLVX4NMZW3KY6KM2BWBDVO6JU3ANCNFSM5TXDFD7Q. You are receiving this because you were mentioned.

[tylermccraney]

Hello, I received same error as above. I cloned the repo and then used 'make'. I attached the result below. I am excited to RootDigger and would greatly appreciate your advice here. Best, Tyler

(base) [tyler@linux root_digger]$ make -- The C compiler identification is GNU 5.5.0 -- The CXX compiler identification is GNU 5.5.0 -- Check for working C compiler: /home/tyler/.linuxbrew/bin/cc -- Check for working C compiler: /home/tyler/.linuxbrew/bin/cc -- 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: /home/tyler/.linuxbrew/bin/c++ -- Check for working CXX compiler: /home/tyler/.linuxbrew/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found Git: /home/tyler/.linuxbrew/bin/git (found version "2.23.0") -- Found PkgConfig: /home/tyler/.linuxbrew/bin/pkg-config (found version "0.29.2") -- Found GSL: /usr/include (found version "1.15") -- pll-modules static build enabled -- Found BISON: /usr/bin/bison (found version "3.0.4") -- Found FLEX: /usr/bin/flex (found version "2.5.37") -- SSE enabled. To disable it, run cmake with -DENABLE_SSE=false -- AVX enabled. To disable it, run cmake with -DENABLE_AVX=false -- AVX2 enabled. To disable it, run cmake with -DENABLE_AVX2=false -- Libpll static build enabled -- pll_static -- Will compile pll-module optimize -- Will compile pll-module algorithm -- Will compile pll-module binary -- Will compile pll-module msa -- Will compile pll-module tree -- Will compile pll-module util -- Looking for pthread.h -- Looking for pthread.h - found -- Looking for pthread_create -- Looking for pthread_create - not found -- 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
-- Try OpenMP C flag = [-fopenmp] -- Performing Test OpenMP_FLAG_DETECTED -- Performing Test OpenMP_FLAG_DETECTED - Success -- Try OpenMP CXX flag = [-fopenmp] -- Performing Test OpenMP_FLAG_DETECTED -- Performing Test OpenMP_FLAG_DETECTED - Success -- Found OpenMP: -fopenmp
-- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project:

BENCHMARK_ENABLE_LTO

-- Build files have been written to: /home/tyler/applications/root_digger/build make[1]: Entering directory /home/tyler/applications/root_digger/build' make[2]: Entering directory/home/tyler/applications/root_digger/build' make[3]: Entering directory /home/tyler/applications/root_digger/build' [ 1%] [FLEX][lex_rtree_t] Building scanner with flex 2.5.37 [ 2%] [BISON][parse_utree_t] Building parser with bison 3.0.4 [ 3%] [FLEX][lex_utree_t] Building scanner with flex 2.5.37 [ 4%] [BISON][parse_rtree_t] Building parser with bison 3.0.4 Scanning dependencies of target pll_obj make[3]: Leaving directory/home/tyler/applications/root_digger/build' make[3]: Entering directory /home/tyler/applications/root_digger/build' [ 5%] Building C object lib/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/compress.c.o [ 6%] Building C object lib/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/parse_utree.c.o [ 7%] Building C object lib/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/lex_utree.c.o [ 8%] Building C object lib/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/parse_rtree.c.o [ 9%] Building C object lib/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/lex_rtree.c.o [ 10%] Building C object lib/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/core_derivatives.c.o [ 11%] Building C object lib/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/core_likelihood.c.o [ 12%] Building C object lib/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/core_partials.c.o [ 13%] Building C object lib/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/core_pmatrix.c.o /home/tyler/applications/root_digger/lib/pll-modules/libs/libpll/src/core_pmatrix.c:23:28: fatal error: gsl/gsl_linalg.h: No such file or directory compilation terminated. make[3]: *** [lib/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/core_pmatrix.c.o] Error 1 make[3]: Leaving directory/home/tyler/applications/root_digger/build' make[2]: [lib/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/all] Error 2 make[2]: Leaving directory `/home/tyler/applications/root_digger/build' make[1]: [all] Error 2 make[1]: Leaving directory `/home/tyler/applications/root_digger/build' make: *** [release] Error 2

[computations]

Thanks for the report! I think I have a good handle of what is going on here, but I can't reproduce the issue on my machine. This means I am probably going to have to borrow a computer to solve this issue. The unfortunate upshot is that it will be some time before I will be able to fix this, sorry :(. I will post in in this issue when I think it is fixed.

[computations]

I just updated RootDigger to v1.8.0, which changes the libraries used for building. Specifically, RootDigger no longer requires GSL. Maybe this fixes the problems that people in this thread have been having?

[computations]

I'm closing this issue due to inactivity

[Niv94]

I then ran

MacBook-Pro:root_digger nivi$ make makefile

It went through but I still cannot find a ‘rd’ folder in bin

Please advise.

Thank you Nivi

On Apr 19, 2022, at 7:51 AM, Niveditha Ramdoss @.***> wrote:

Thank you so much. But now it gives an error. Can you please help?

Nivedithas-MacBook-Pro:root_digger nivi$ make make: /private/var/folders/xw/lny73q992td8sd5cr7259bh40000gn/T/AppTranslocation/D979807B-97F4-49A6-9A1A-EF230FC28242/d/CMake.app/Contents/bin/cmake: No such file or directory make: *** [cmake_check_build_system] Error 1

On Apr 19, 2022, at 12:02 AM, computations @. @.>> wrote:

Hey, thanks for following up.

This is just the configure step. You still need to run make wherever these files are stored. So in this case you should run

cd /Users/nivi/root_digger make Let me know if that works!

— Reply to this email directly, view it on GitHub https://github.com/computations/root_digger/issues/8#issuecomment-1102166591, or unsubscribe https://github.com/notifications/unsubscribe-auth/AKQOLVWUPYCBU4I2TSP4XC3VFZLBVANCNFSM5TXDFD7Q. You are receiving this because you authored the thread.

[computations]

Could you please send me the terminal output from the command make? It is a little hard to tell what is going wrong without that information.

[computations]

Hmmm, something else is going on. But a solution that might work is too install OpenMP. Let me know if that works for you. On Fri, Apr 22, 2022, 23:13 Niv94 @.***> wrote:

Thanks a lot for your support. But I am still having errors sorry

CoS-Biology-Lluvia-Flores-Renteria-iMac-78PG:root_digger lluviaadmin$ make

-- The C compiler identification is AppleClang 13.0.0.13000027

-- The CXX compiler identification is AppleClang 13.0.0.13000027

-- Detecting C compiler ABI info

-- Detecting C compiler ABI info - done

-- Check for working C compiler: /Library/Developer/CommandLineTools/usr/bin/cc - skipped

-- Detecting C compile features

-- Detecting C compile features - done

-- Detecting CXX compiler ABI info

-- Detecting CXX compiler ABI info - done

-- Check for working CXX compiler: /Library/Developer/CommandLineTools/usr/bin/c++ - skipped

-- Detecting CXX compile features

-- Detecting CXX compile features - done

-- Found Git: /usr/bin/git (found version "2.30.1 (Apple Git-130)")

-- Found PkgConfig: /usr/local/bin/pkg-config (found version "0.29.2")

-- Found GSL: /usr/local/Cellar/gsl/2.5/include (found version "2.5")

CMake Deprecation Warning at lib/pll-modules/CMakeLists.txt:1 (cmake_minimum_required):

Compatibility with CMake < 2.8.12 will be removed from a future version of

CMake.

Update the VERSION argument value or use a ... suffix to tell

CMake that the project does not need compatibility with older versions.

-- pll-modules static build enabled

CMake Deprecation Warning at lib/pll-modules/libs/libpll/CMakeLists.txt:1 (cmake_minimum_required):

Compatibility with CMake < 2.8.12 will be removed from a future version of

CMake.

Update the VERSION argument value or use a ... suffix to tell

CMake that the project does not need compatibility with older versions.

-- Found BISON: /usr/bin/bison (found version "2.3")

-- Found FLEX: /usr/bin/flex (found version "2.6.4")

-- SSE enabled. To disable it, run cmake with -DENABLE_SSE=false

-- AVX enabled. To disable it, run cmake with -DENABLE_AVX=false

-- AVX2 enabled. To disable it, run cmake with -DENABLE_AVX2=false

-- Libpll static build enabled

-- pll_static

CMake Deprecation Warning at lib/pll-modules/src/CMakeLists.txt:1 (cmake_minimum_required):

Compatibility with CMake < 2.8.12 will be removed from a future version of

CMake.

Update the VERSION argument value or use a ... suffix to tell

CMake that the project does not need compatibility with older versions.

-- Will compile pll-module optimize

-- Will compile pll-module algorithm

-- Will compile pll-module binary

-- Will compile pll-module msa

-- Will compile pll-module tree

-- Will compile pll-module util

-- Looking for pthread.h

-- Looking for pthread.h - found

-- Performing Test CMAKE_HAVE_LIBC_PTHREAD

-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success

-- Found Threads: TRUE

-- Could NOT find OpenMP_C (missing: OpenMP_C_FLAGS OpenMP_C_LIB_NAMES)

-- Could NOT find OpenMP_CXX (missing: OpenMP_CXX_FLAGS OpenMP_CXX_LIB_NAMES)

-- Could NOT find OpenMP (missing: OpenMP_C_FOUND OpenMP_CXX_FOUND)

-- Configuring done

CMake Error at src/CMakeLists.txt:6 (add_executable):

Target "rd" links to target "OpenMP::OpenMP_CXX" but the target was not

found. Perhaps a find_package() call is missing for an IMPORTED target, or

an ALIAS target is missing?

-- Generating done

CMake Warning:

Manually-specified variables were not used by the project:

BENCHMARK_ENABLE_LTO

CMake Generate step failed. Build files cannot be regenerated correctly.

make: *** [release] Error 1

On Fri, Apr 22, 2022 at 1:11 PM computations @.***> wrote:

Thank you so much for your efforts! There was an error in the build configuration, where if OpenMP was not installed, the build would fail. I have pushed a change which makes OpenMP optional. Please try again with the new git version.

— Reply to this email directly, view it on GitHub < https://github.com/computations/root_digger/issues/8#issuecomment-1106824318 , or unsubscribe < https://github.com/notifications/unsubscribe-auth/AKQOLVXUBZJVIBVPIY2DGLLVGMBYBANCNFSM5TXDFD7Q

. You are receiving this because you authored the thread.Message ID: @.***>

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[KatherinOtalora]

Hello

How are you?

I have the same mistake. Could you help me?

(base) katherin_otalora@Katherin-Otaloras-MacBook-Pro Rootdigger % cd root_digger
(base) katherin_otalora@Katherin-Otaloras-MacBook-Pro root_digger % ls CMakeLists.txt benchmark lib src LICENSE docs makefile test (base) katherin_otalora@Katherin-Otaloras-MacBook-Pro root_digger % make makefile make: Nothing to be done for `makefile'. (base) katherin_otalora@Katherin-Otaloras-MacBook-Pro root_digger % make -- The C compiler identification is AppleClang 13.0.0.13000029 -- The CXX compiler identification is AppleClang 13.0.0.13000029 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /Library/Developer/CommandLineTools/usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /Library/Developer/CommandLineTools/usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found Git: /usr/bin/git (found version "2.30.1 (Apple Git-130)") -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE
-- Could NOT find OpenMP_C (missing: OpenMP_C_FLAGS OpenMP_C_LIB_NAMES) -- Could NOT find OpenMP_CXX (missing: OpenMP_CXX_FLAGS OpenMP_CXX_LIB_NAMES) -- Could NOT find OpenMP (missing: OpenMP_C_FOUND OpenMP_CXX_FOUND) -- Disable SSE simd, because not supported -- Disable AVX simd, because not supported -- Disable AVX2 simd, because not supported Non-rev enabled -- coraxlib libraries: corax_static -- Configuring done (1.1s) -- Generating done (0.0s) CMake Warning: Manually-specified variables were not used by the project:

BENCHMARK_ENABLE_LTO

-- Build files have been written to: /Users/katherin_otalora/Documents/Rootdigger/root_digger/build [ 1%] Building C object lib/lbfgsb/CMakeFiles/lbfgs_lib.dir/lbfgsb.c.o [ 2%] Building C object lib/lbfgsb/CMakeFiles/lbfgs_lib.dir/linesearch.c.o [ 3%] Building C object lib/lbfgsb/CMakeFiles/lbfgs_lib.dir/linpack.c.o [ 5%] Building C object lib/lbfgsb/CMakeFiles/lbfgs_lib.dir/miniCBLAS.c.o [ 6%] Building C object lib/lbfgsb/CMakeFiles/lbfgs_lib.dir/subalgorithms.c.o [ 7%] Linking C static library liblbfgs_lib.a [ 7%] Built target lbfgs_lib [ 7%] Building C object lib/coraxlib/src/corax/CMakeFiles/corax_obj.dir/core/common.c.o [ 9%] Building C object lib/coraxlib/src/corax/CMakeFiles/corax_obj.dir/core/parsimony.c.o [ 10%] Building C object lib/coraxlib/src/corax/CMakeFiles/corax_obj.dir/core/partition.c.o [ 11%] Building C object lib/coraxlib/src/corax/CMakeFiles/corax_obj.dir/core/repeats.c.o [ 13%] Building C object lib/coraxlib/src/corax/CMakeFiles/corax_obj.dir/io/binary.c.o [ 14%] Building C object lib/coraxlib/src/corax/CMakeFiles/corax_obj.dir/io/binary_io_operations.c.o [ 15%] Building C object lib/coraxlib/src/corax/CMakeFiles/corax_obj.dir/io/fasta.c.o [ 17%] Building C object lib/coraxlib/src/corax/CMakeFiles/corax_obj.dir/io/maps.c.o [ 18%] Building C object lib/coraxlib/src/corax/CMakeFiles/corax_obj.dir/io/output.c.o [ 19%] Building C object lib/coraxlib/src/corax/CMakeFiles/corax_obj.dir/io/phylip.c.o [ 21%] Building C object lib/coraxlib/src/corax/CMakeFiles/corax_obj.dir/io/utree_ascii.c.o [ 22%] Building C object lib/coraxlib/src/corax/CMakeFiles/corax_obj.dir/io/utree_newick.c.o [ 23%] Building C object lib/coraxlib/src/corax/CMakeFiles/corax_obj.dir/io/utree_svg.c.o [ 25%] Building CXX object lib/coraxlib/src/corax/CMakeFiles/corax_obj.dir/io/newick.cpp.o [ 26%] Building C object lib/coraxlib/src/corax/CMakeFiles/corax_obj.dir/kernel/generic/core_derivatives.c.o /Users/katherin_otalora/Documents/Rootdigger/root_digger/lib/coraxlib/src/corax/kernel/generic/core_derivatives.c:61:16: warning: unused variable 'use_bclv' [-Wunused-variable] unsigned int use_bclv = (bclv_buffer && (parent_sites < (sites 2) / 3)); ^ 1 warning generated. [ 27%] Building C object lib/coraxlib/src/corax/CMakeFiles/corax_obj.dir/kernel/generic/core_likelihood.c.o /Users/katherin_otalora/Documents/Rootdigger/root_digger/lib/coraxlib/src/corax/kernel/generic/core_likelihood.c:956:16: warning: unused variable 'use_bclv' [-Wunused-variable] unsigned int use_bclv = bclv && (child_sites < (sites 2) / 3); ^ 1 warning generated. [ 28%] Building C object lib/coraxlib/src/corax/CMakeFiles/corax_obj.dir/kernel/generic/core_clv.c.o [ 30%] **Building C object lib/coraxlib/src/corax/CMakeFiles/corax_obj.dir/kernel/generic/core_pmatrix.c.o /Users/katherin_otalora/Documents/Rootdigger/root_digger/lib/coraxlib/src/corax/kernel/generic/core_pmatrix.c:25:10: fatal error: 'cblas.h' file not found

include

     ^~~~~~~~~**

1 error generated. make[3]: [lib/coraxlib/src/corax/CMakeFiles/corax_obj.dir/kernel/generic/core_pmatrix.c.o] Error 1 make[2]: [lib/coraxlib/src/corax/CMakeFiles/corax_obj.dir/all] Error 2 make[1]: [all] Error 2 make: [release] Error 2 (base) katherin_otalora@Katherin-Otaloras-MacBook-Pro root_digger %

Thanks,

[computations]

It looks like you are missing the cblas dependency. You should be able to install it via brew, if you have that set up already. Also, if you are missing the cblas library, you are probably missing the lapacke library too, so make sure to install that as well.

Let me know if that fixes your problem.

[KatherinOtalora]

Thank you

I have performed what you said but it still doesn`t work.

(base) katherin_otalora@Katherin-Otaloras-MacBook-Pro root_digger % brew install lapack
Warning: lapack 3.11 is already installed and up-to-date. To reinstall 3.11, run: brew reinstall lapack (base) katherin_otalora@Katherin-Otaloras-MacBook-Pro root_digger % brew install openblas Warning: openblas 0.3.21 is already installed and up-to-date. To reinstall 0.3.21, run: brew reinstall openblas (base) katherin_otalora@Katherin-Otaloras-MacBook-Pro root_digger % brew install clblas
Warning: clblas 2.12_1 is already installed and up-to-date. To reinstall 2.12_1, run: brew reinstall clblas (base) katherin_otalora@Katherin-Otaloras-MacBook-Pro root_digger % make
-- Could NOT find OpenMP_C (missing: OpenMP_C_FLAGS OpenMP_C_LIB_NAMES) -- Could NOT find OpenMP_CXX (missing: OpenMP_CXX_FLAGS OpenMP_CXX_LIB_NAMES) -- Could NOT find OpenMP (missing: OpenMP_C_FOUND OpenMP_CXX_FOUND) -- Disable SSE simd, because not supported -- Disable AVX simd, because not supported -- Disable AVX2 simd, because not supported Non-rev enabled -- coraxlib libraries: corax_static -- Configuring done (0.5s) -- Generating done (0.1s) -- Build files have been written to: /Users/katherin_otalora/Documents/Rootdigger/root_digger/build [ 7%] Built target lbfgs_lib [ 9%] Building C object lib/coraxlib/src/corax/CMakeFiles/corax_obj.dir/kernel/generic/core_pmatrix.c.o /Users/katherin_otalora/Documents/Rootdigger/root_digger/lib/coraxlib/src/corax/kernel/generic/core_pmatrix.c:25:10: fatal error: 'cblas.h' file not found

include

     ^~~~~~~~~

1 error generated. make[3]: [lib/coraxlib/src/corax/CMakeFiles/corax_obj.dir/kernel/generic/core_pmatrix.c.o] Error 1 make[2]: [lib/coraxlib/src/corax/CMakeFiles/corax_obj.dir/all] Error 2 make[1]: [all] Error 2 make: [release] Error 2

Thank you very much for your help

[computations]

Hmm, that is curious. I want to spend some time fixing the dependency checks in CMake. But in the meantime there are some things to point out:

• clblas is different than cblas. clblas is a GPU based version of blas, where cblas is the a BLAS implementation in C.
• lapack is different than lapacke. The former is a FORTRAN implementation, and the latter is a C implementation.
• OpenBLAS doesn't provide either cblas or lapacke.

The naming around linear algebra libraries is a disaster, I'm super sorry for the confusion. Maybe try cblas and lapacke and check if those work?

[KatherinOtalora]

Yes, from the beginning I was trying those two options, but I share with you the results:

(base) katherin_otalora@Katherin-Otaloras-MacBook-Pro root_digger % brew install cblas Warning: No available formula with the name "cblas". Did you mean clblas, clash, blast or clblast? ==> Searching for similarly named formulae and casks... ==> Formulae clblas ✔ clash blast ✔ clblast ✔

To install clblas ✔, run: brew install clblas ✔

==> Casks clashx

To install clashx, run: brew install --cask clashx (base) katherin_otalora@Katherin-Otaloras-MacBook-Pro root_digger % brew install lapacke Warning: No available formula with the name "lapacke". Did you mean lapack? ==> Searching for similarly named formulae and casks... ==> Formulae lapack ✔

To install lapack ✔, run: brew install lapack ✔

==> Casks lapce

To install lapce, run: brew install --cask lapce

Thank you very much for your help

[computations]

Ok, thanks for trying that out. Sorry it didn't work, I know this library stuff can be frustrating (at least, I find it annoying). I have updated RootDigger and the library that it depends on to do better dependency management, but I don't really expect that to help in this case. Additionally, there is a bit of extra documentation now at the coraxlib repository on what is actually required.

As for your specific problem, I'm at a bit of a loss. I can't seem to find a way to install lapacke or cblas on MacOS. OpenBLAS sometimes has lapacke and cblas, depending on the package manager.

If you want to try again with the updated changes, you will need to run git submodule update --recursive after git pull. Again, I don't expect it to fix the problem, so I am going to try to prepare a docker container, which hopefully will work better.

[computations]

Alright, there is now a docker file as part of the repository. It works for me, but I haven't tested it extensively.

[KatherinOtalora]

Thank you very much for your support.

I did it all over again and I get the error about the packages.

(base) katherin_otalora@Katherin-Otaloras-MacBook-Pro root_digger % make -- Could NOT find OpenMP_C (missing: OpenMP_C_FLAGS OpenMP_C_LIB_NAMES) -- Could NOT find OpenMP_CXX (missing: OpenMP_CXX_FLAGS OpenMP_CXX_LIB_NAMES) -- Could NOT find OpenMP (missing: OpenMP_C_FOUND OpenMP_CXX_FOUND) -- SSE SIMD not supported -> disabling -- AVX SIMD not supported -> disabling -- AVX2 SIMD not supported -> disabling -- Build type: Release -- Building coraxlib as a static library. -- Building documentation: OFF -- Building tests: OFF -- Building benchmarks: OFF -- Building difficutly prediction: OFF -- Enable SSE SIMD kernels: Off -- Enable AVX SIMD kernels: Off -- Enable AVX2 SIMD kernels: Off Non-rev enabled -- A cache variable, namely LAPACKE_DIR, has been set to specify the install directory of LAPACKE -- Looking for LAPACKE_dgeqrf -- Looking for LAPACKE_dgeqrf - not found -- Looking for lapacke : test with lapack fails -- Looking for lapacke -- lapacke.h not found -- Looking for lapacke -- lib lapacke not found CMake Error at /Applications/CMake.app/Contents/share/cmake-3.26/Modules/FindPackageHandleStandardArgs.cmake:230 (message): Could NOT find LAPACKE (missing: LAPACKE_LIBRARIES LAPACKE_WORKS) Call Stack (most recent call first): /Applications/CMake.app/Contents/share/cmake-3.26/Modules/FindPackageHandleStandardArgs.cmake:600 (_FPHSA_FAILURE_MESSAGE) lib/coraxlib/cmake/FindLAPACKE.cmake:410 (find_package_handle_standard_args) lib/coraxlib/src/corax/CMakeLists.txt:57 (find_package)

-- Configuring incomplete, errors occurred!

I will try OpenBLAS to see if there is a solution.

Thank you very much for your help

[computations]

Just checking in and seeing if there is an update with your issue. Did you manage to get it working?

[KatherinOtalora]

No, I tried again with Openblas installed but unfortunately it didnt work.

Thank you very much for your help

[computations]

I'm sorry that is hasn't worked so far. At this point I can only suggest that you try to build the docker version. Alternatively, you can wait until I remove the lapacke dependency. I plan to get this done sometime in the next couple of months, but I am a bit busy for it at the moment. Sorry

[computations]

Closing this issue as there has been no traffic for some time