Comments (5)
from iqtree2.
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
from iqtree2.
from iqtree2.
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
from iqtree2.
@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!```
from iqtree2.
Related Issues (20)
- ERROR: phylotreepars.cpp:63: void PhyloTree
- segfault on large analysis HOT 3
- weird example file default installation path HOT 1
- taxon label length get shortened in output
- Unable to compile on macOS, ARM64 HOT 7
- Numerical underflow for non-rev lh-branch Noname HOT 2
- Possible error with -scfl option HOT 1
- Segfault/leak when analysing partitioned mixed data HOT 2
- Using model parameters from v2.1.2 in v2.2.2+ sCFL calculation?
- Please use only 1 MPI process! We are currently working on the MPI parallelization of model selection. HOT 2
- AliSim output phylip format contains error HOT 1
- [Enhancement] AliSim input/output without files HOT 4
- -bnni incompatibility with -wt & UFBoot2 estimation
- scflg HOT 1
- ModelFinder crash on simulated alignment (iqtree v2.2.3)
- Continue the program after filter out invariant sites HOT 2
- Failed to get a matrix of amino acid substitution model HOT 1
- ERROR: phylokernel.h:1576: void PhyloTree::computePartialParsimonyFastSIMD(PhyloNeighbor *, PhyloNode *) [VectorClass = Vec8ui]: Assertion `state < 23' failed. HOT 8
- '-mremove' option or alike?
- BUG: Identical sequences not added to tree at end when restarting analysis from checkpoint
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from iqtree2.