Error while compiling on MacOSX with -DUSE_LSD2=ON

[lguy]

Hi there,
First, thanks heaps for providing and maintaining IQTREE, it's one of the most useful and best working molecular evolution tool. It's been working flawless for me, to this day that is, where I'm trying a more experimental feature.
I'm trying to use LSD2 on my Mac. Apparently that feature is not included in the compiled version. I tried to install from source, but got an error.
I have a MacBook Pro with MacOSX 11.4 (20F71). I had to install Boost 1.76.0 and eigen 3.3.9 through brew to get to cmake to work. I cloned iqtree2 (3267aec) with submodules to get lsd2:

git clone --recurse-submodules --remote-submodules https://github.com/iqtree/iqtree2.git
cd iqtree2
mkdir build
cd build
cmake -DIQTREE_FLAGS=omp -DUSE_LSD2=ON ..

That works (see log below). Now trying to make:
% make -j

I'm getting the following errors:

[ 23%] Building CXX object main/CMakeFiles/main.dir/timetree.cpp.o
/Users/liogu139/bin/iqtree2/main/timetree.cpp:275:28: error: no matching constructor
      for initialization of 'lsd::InputOutputStream'
  ...io(tree_stream.str(), outgroup_stream.str(), date_stream.str(), "", "");
     ^  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/Users/liogu139/bin/iqtree2/lsd2/src/lsd.h:56:9: note: candidate constructor not
      viable: requires 6 arguments, but 5 were provided
        InputOutputStream(string tree, string outgroup, string date,string rate...
        ^
/Users/liogu139/bin/iqtree2/lsd2/src/lsd.h:15:11: note: candidate constructor (the
      implicit copy constructor) not viable: requires 1 argument, but 5 were provided
    class InputOutputStream {
          ^
/Users/liogu139/bin/iqtree2/lsd2/src/lsd.h:48:9: note: candidate constructor not
      viable: requires 0 arguments, but 5 were provided
        InputOutputStream();
        ^
1 error generated.

I've tried to make just lsd2 and that works and I can execute lsd2. My command of C is not good enough to go further, can you help me?

On a side note, I didn't have to install a newer version of Clang separately, the omp version compiled without problem.

Cheers,

Lionel

Log of CMake:

 CMake Deprecation Warning at CMakeLists.txt:58 (cmake_minimum_required):
  Compatibility with CMake < 2.8.12 will be removed from a future version of
  CMake.

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


-- The C compiler identification is AppleClang 11.0.3.11030032
-- The CXX compiler identification is AppleClang 11.0.3.11030032
-- 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 Boost: /usr/local/lib/cmake/Boost-1.76.0/BoostConfig.cmake (found version "1.76.0")
IQ-TREE flags : omp
Build mode   : Release
Target OS     : Mac OS X
Compiler      : Clang
Compiler version: 11.0.3.11030032
Target binary : 64-bit
OpenMP        : Yes
MPI           : NONE
Vectorization : SSE3/AVX/AVX2
C flags       :  -pthread  -O3 -ffunction-sections -fdata-sections
CXX flags     :  -std=c++11 -stdlib=libc++ -Xpreprocessor -fopenmp -pthread  -O3 -ffunction-sections -fdata-sections
LINKER flags  :  --target=x86_64-apple-macos10.7 -lomp  -Wl,-dead_strip
-- Looking for gettimeofday
-- Looking for gettimeofday - found
-- Looking for getrusage
-- Looking for getrusage - found
-- Looking for GlobalMemoryStatusEx
-- Looking for GlobalMemoryStatusEx - not found
-- Looking for strndup
-- Looking for strndup - found
-- Looking for strtok_r
-- Looking for strtok_r - found
-- Looking for backtrace
-- Looking for backtrace - found
-- backtrace facility detected in default set of libraries
-- Found Backtrace: /Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/usr/include
-- Found ZLIB: /Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/usr/lib/libz.tbd (found version "1.2.11")
Using system zlib
-- Performing Test FLAG_WEXTRA
-- Performing Test FLAG_WEXTRA - Success
-- clang-tidy not found.
-- Configuring done
-- Generating done
-- Build files have been written to: /Users/liogu139/bin/iqtree2/build

[thomaskf]

Hi Lionel,
Sorry for the late reply. Can you try the latest version and see whether the problem exists?

The commands are:

git clone --recursive https://github.com/iqtree/iqtree2
cd iqtree2
mkdir build
cd build
cmake -DUSE_LSD2=ON ..
make -j

Thomas

[lguy]

Dear Thomas, It worked like a charm! If that’s of interest to you, I’m now using MacOS Monterey 12.2.1 (21D62). Best regards, Lionel

…

On 23 Feb 2022, at 11:59, Thomas Wong ***@***.***> wrote: Hi Lionel, Sorry for the late reply. Can you try the latest version and see whether the problem exists? The commands are: git clone --recursive https://github.com/iqtree/iqtree2 cd iqtree2 mkdir build cd build cmake -DUSE_LSD2=ON .. make -j Thomas — Reply to this email directly, view it on GitHub, or unsubscribe. Triage notifications on the go with GitHub Mobile for iOS or Android. You are receiving this because you authored the thread.

-- Lionel Guy Department for Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden phone: +46 18 471 4246; mobile +46 73 976 0618; postal address: Box 582, SE-751 23 Uppsala; visiting address: BMC D7:308b, Husargatan 3, SE-752 37 Uppsala ***@***.*** När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy

[GianRos]

Hello,
maybe it's naive, but I just wanted to notify that this same solution worked well on a Linux Ubuntu 22.04.1 LTS.
Cheers,
Gianluigi

[JGLAHE]

@thomaskf
Hi Thomas, what is the cmake flag now? cmake -DUSE_LSD2=ON .. doesn't seem to work with 2.2.3?

iqtree2-2.2.3 $>mkdir build; cd build
build $>cmake -DUSE_LSD2=ON ..
CMake Deprecation Warning at CMakeLists.txt:58 (cmake_minimum_required):
  Compatibility with CMake < 3.5 will be removed from a future version of
  CMake.

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


-- The C compiler identification is GNU 11.4.0
-- The CXX compiler identification is GNU 11.4.0
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /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: /usr/bin/c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Found Boost: /usr/lib/x86_64-linux-gnu/cmake/Boost-1.74.0/BoostConfig.cmake (found version "1.74.0")
IQ-TREE flags :
Build mode   : Release
Target OS     : Unix
Compiler      : GNU Compiler (gcc)
Compiler version: 11.4.0
Target binary : 64-bit
OpenMP        : Yes
MPI           : NONE
Vectorization : SSE3/AVX/AVX2
C flags       :  -pthread  -O2 -g -ffunction-sections -fdata-sections
CXX flags     :  -std=c++11 -fopenmp -pthread  -O2 -g -ffunction-sections -fdata-sections
LINKER flags  :  -rdynamic  -Wl,--gc-sections
-- Looking for gettimeofday
-- Looking for gettimeofday - found
-- Looking for getrusage
-- Looking for getrusage - found
-- Looking for GlobalMemoryStatusEx
-- Looking for GlobalMemoryStatusEx - not found
-- Looking for strndup
-- Looking for strndup - found
-- Looking for strtok_r
-- Looking for strtok_r - found
-- Looking for backtrace
-- Looking for backtrace - found
-- backtrace facility detected in default set of libraries
-- Found Backtrace: /usr/include
-- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.2.11")
Using system zlib
CMake Deprecation Warning at yaml-cpp/CMakeLists.txt:5 (cmake_minimum_required):
  Compatibility with CMake < 3.5 will be removed from a future version of
  CMake.

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


-- Performing Test FLAG_WEXTRA
-- Performing Test FLAG_WEXTRA - Success
CMake Deprecation Warning at terraphast/CMakeLists.txt:3 (cmake_minimum_required):
  Compatibility with CMake < 3.5 will be removed from a future version of
  CMake.

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


-- clang-tidy not found.
CMake Error at CMakeLists.txt:701 (add_subdirectory):
  The source directory

    /PATH/iqtree2-2.2.3/lsd2

  does not contain a CMakeLists.txt file.


CMake Error at CMakeLists.txt:739 (set_target_properties):
  set_target_properties Can not find target to add properties to: lsd2


-- Configuring incomplete, errors occurred!```

[thomaskf]

Hi, For the version 2.2.3, the flag USE_LSD2 by default is ON. So, you don't need to specify this when you use cmake. After checking your message, the folder lsd2 is empty. The lsd2 folder from the source code file enclosed in the release is empty, because lsd2 is from another repository in Github. You may download the folder lsd2 manually from https://github.com/tothuhien/lsd2, or use the following command to get the complete set of source codes:

git clone --recursive https://github.com/iqtree/iqtree2

Then you can use cmake. I hope this helps. Thomas

…

On Fri, Aug 25, 2023 at 10:44 PM lLLHMM ***@***.***> wrote: @thomaskf <https://github.com/thomaskf> Hi Thomas, what is the cmake flag now? cmake -DUSE_LSD2=ON .. doesn't seem to work with 2.2.3? iqtree2-2.2.3 $>mkdir build; cd build build $>cmake -DUSE_LSD2=ON .. CMake Deprecation Warning at CMakeLists.txt:58 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument <min> value or use a ...<max> suffix to tell CMake that the project does not need compatibility with older versions. -- The C compiler identification is GNU 11.4.0 -- The CXX compiler identification is GNU 11.4.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /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: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found Boost: /usr/lib/x86_64-linux-gnu/cmake/Boost-1.74.0/BoostConfig.cmake (found version "1.74.0") IQ-TREE flags : Build mode : Release Target OS : Unix Compiler : GNU Compiler (gcc) Compiler version: 11.4.0 Target binary : 64-bit OpenMP : Yes MPI : NONE Vectorization : SSE3/AVX/AVX2 C flags : -pthread -O2 -g -ffunction-sections -fdata-sections CXX flags : -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections LINKER flags : -rdynamic -Wl,--gc-sections -- Looking for gettimeofday -- Looking for gettimeofday - found -- Looking for getrusage -- Looking for getrusage - found -- Looking for GlobalMemoryStatusEx -- Looking for GlobalMemoryStatusEx - not found -- Looking for strndup -- Looking for strndup - found -- Looking for strtok_r -- Looking for strtok_r - found -- Looking for backtrace -- Looking for backtrace - found -- backtrace facility detected in default set of libraries -- Found Backtrace: /usr/include -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.2.11") Using system zlib CMake Deprecation Warning at yaml-cpp/CMakeLists.txt:5 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument <min> value or use a ...<max> suffix to tell CMake that the project does not need compatibility with older versions. -- Performing Test FLAG_WEXTRA -- Performing Test FLAG_WEXTRA - Success CMake Deprecation Warning at terraphast/CMakeLists.txt:3 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument <min> value or use a ...<max> suffix to tell CMake that the project does not need compatibility with older versions. -- clang-tidy not found. CMake Error at CMakeLists.txt:701 (add_subdirectory): The source directory /PATH/iqtree2-2.2.3/lsd2 does not contain a CMakeLists.txt file. CMake Error at CMakeLists.txt:739 (set_target_properties): set_target_properties Can not find target to add properties to: lsd2 -- Configuring incomplete, errors occurred!``` — Reply to this email directly, view it on GitHub <#31 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AENQCRTOAH5IPJ4MKE4VPSTXXCM3PANCNFSM45UK3ZYQ> . You are receiving this because you were mentioned.Message ID: ***@***.***>