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lczech / gappa

A toolkit for analyzing and visualizing phylogenetic (placement) data
GNU General Public License v3.0
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error: 'genesis::utils::KmeansClusteringInfo' has not been declared #2

Closed vmaffei closed 6 years ago

vmaffei commented 6 years ago

Hello! While building gappa, I'm running into the cmake errors below: 

Running CMake...
-- The CXX compiler identification is GNU 7.2.0
-- Check for working CXX compiler: /code/miniconda2/envs/epa/bin/x86_64-conda_cos6-linux-gnu-c++
-- Check for working CXX compiler: /code/miniconda2/envs/epa/bin/x86_64-conda_cos6-linux-gnu-c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Gappa build type: RELEASE
-- Static linking of system libraries: OFF
-- CLI11 not found
-- Downloading CLI11 from https://github.com/CLIUtils/CLI11/archive/bd890e24a1f081d6db1a59a0cc372eccc64e9e52.zip
-- Configuring done
-- Generating done
-- Build files have been written to: /code/gappa/build/CLI11Download
make[1]: Entering directory `/code/gappa/build/CLI11Download'
make[2]: Entering directory `/code/gappa/build/CLI11Download'
make[3]: Entering directory `/code/gappa/build/CLI11Download'
Scanning dependencies of target CLI11
make[3]: Leaving directory `/code/gappa/build/CLI11Download'
make[3]: Entering directory `/code/gappa/build/CLI11Download'
[ 11%] Creating directories for 'CLI11'
[ 22%] Performing download step (download, verify and extract) for 'CLI11'
-- downloading...
     src='https://github.com/CLIUtils/CLI11/archive/bd890e24a1f081d6db1a59a0cc372eccc64e9e52.zip'
     dst='/code/gappa/build/CLI11Download/CLI11-prefix/src/bd890e24a1f081d6db1a59a0cc372eccc64e9e52.zip'
     timeout='none'
-- [download 0% complete]
-- [download 1% complete]
[ truncated ]
-- [download 100% complete]
-- downloading... done
-- verifying file...
     file='/code/gappa/build/CLI11Download/CLI11-prefix/src/bd890e24a1f081d6db1a59a0cc372eccc64e9e52.zip'
-- verifying file... warning: did not verify file - no URL_HASH specified?
-- extracting...
     src='/code/gappa/build/CLI11Download/CLI11-prefix/src/bd890e24a1f081d6db1a59a0cc372eccc64e9e52.zip'
     dst='/code/gappa/libs/CLI11'
-- extracting... [tar xfz]
-- extracting... [analysis]
-- extracting... [rename]
-- extracting... [clean up]
-- extracting... done
[ 33%] No patch step for 'CLI11'
[ 44%] No update step for 'CLI11'
[ 55%] No configure step for 'CLI11'
[ 66%] No build step for 'CLI11'
[ 77%] No install step for 'CLI11'
[ 88%] No test step for 'CLI11'
[100%] Completed 'CLI11'
make[3]: Leaving directory `/code/gappa/build/CLI11Download'
[100%] Built target CLI11
make[2]: Leaving directory `/code/gappa/build/CLI11Download'
make[1]: Leaving directory `/code/gappa/build/CLI11Download'
-- Finished downloading CLI11
-- genesis not found
-- Downloading genesis from https://github.com/lczech/genesis/archive/a8244e4db206f96caac795e1d6953140a5611e69.zip
-- Configuring done
-- Generating done
-- Build files have been written to: /code/gappa/build/genesisDownload
make[1]: Entering directory `/code/gappa/build/genesisDownload'
make[2]: Entering directory `/code/gappa/build/genesisDownload'
make[3]: Entering directory `/code/gappa/build/genesisDownload'
Scanning dependencies of target genesis
make[3]: Leaving directory `/code/gappa/build/genesisDownload'
make[3]: Entering directory `/code/gappa/build/genesisDownload'
[ 11%] Creating directories for 'genesis'
[ 22%] Performing download step (download, verify and extract) for 'genesis'
-- downloading...
     src='https://github.com/lczech/genesis/archive/a8244e4db206f96caac795e1d6953140a5611e69.zip'
     dst='/code/gappa/build/genesisDownload/genesis-prefix/src/a8244e4db206f96caac795e1d6953140a5611e69.zip'
     timeout='none'
-- [download 0% complete]
[ truncated]
-- [download 99% complete]
-- [download 100% complete]
-- downloading... done
-- verifying file...
     file='/code/gappa/build/genesisDownload/genesis-prefix/src/a8244e4db206f96caac795e1d6953140a5611e69.zip'
-- verifying file... warning: did not verify file - no URL_HASH specified?
-- extracting...
     src='/code/gappa/build/genesisDownload/genesis-prefix/src/a8244e4db206f96caac795e1d6953140a5611e69.zip'
     dst='/code/gappa/libs/genesis'
-- extracting... [tar xfz]
-- extracting... [analysis]
-- extracting... [rename]
-- extracting... [clean up]
-- extracting... done
[ 33%] No patch step for 'genesis'
[ 44%] No update step for 'genesis'
[ 55%] No configure step for 'genesis'
[ 66%] No build step for 'genesis'
[ 77%] No install step for 'genesis'
[ 88%] No test step for 'genesis'
[100%] Completed 'genesis'
make[3]: Leaving directory `/code/gappa/build/genesisDownload'
[100%] Built target genesis
make[2]: Leaving directory `/code/gappa/build/genesisDownload'
make[1]: Leaving directory `/code/gappa/build/genesisDownload'
-- Finished downloading genesis
-- sparsepp not found
-- Downloading sparsepp from https://github.com/greg7mdp/sparsepp/archive/6bfe3b4bdb364993e612d6bb729d680cf4c77649.zip
-- Configuring done
-- Generating done
-- Build files have been written to: /code/gappa/build/sparseppDownload
make[1]: Entering directory `/code/gappa/build/sparseppDownload'
make[2]: Entering directory `/code/gappa/build/sparseppDownload'
make[3]: Entering directory `/code/gappa/build/sparseppDownload'
Scanning dependencies of target sparsepp
make[3]: Leaving directory `/code/gappa/build/sparseppDownload'
make[3]: Entering directory `/code/gappa/build/sparseppDownload'
[ 11%] Creating directories for 'sparsepp'
[ 22%] Performing download step (download, verify and extract) for 'sparsepp'
-- downloading...
     src='https://github.com/greg7mdp/sparsepp/archive/6bfe3b4bdb364993e612d6bb729d680cf4c77649.zip'
     dst='/code/gappa/build/sparseppDownload/sparsepp-prefix/src/6bfe3b4bdb364993e612d6bb729d680cf4c77649.zip'
     timeout='none'
-- [download 0% complete]
download 99% complete]
-- [download 100% complete]
-- downloading... done
-- verifying file...
     file='/code/gappa/build/sparseppDownload/sparsepp-prefix/src/6bfe3b4bdb364993e612d6bb729d680cf4c77649.zip'
-- verifying file... warning: did not verify file - no URL_HASH specified?
-- extracting...
     src='/code/gappa/build/sparseppDownload/sparsepp-prefix/src/6bfe3b4bdb364993e612d6bb729d680cf4c77649.zip'
     dst='/code/gappa/libs/sparsepp'
-- extracting... [tar xfz]
-- extracting... [analysis]
-- extracting... [rename]
-- extracting... [clean up]
-- extracting... done
[ 33%] No patch step for 'sparsepp'
[ 44%] No update step for 'sparsepp'
[ 55%] No configure step for 'sparsepp'
[ 66%] No build step for 'sparsepp'
[ 77%] No install step for 'sparsepp'
[ 88%] No test step for 'sparsepp'
[100%] Completed 'sparsepp'
make[3]: Leaving directory `/code/gappa/build/sparseppDownload'
[100%] Built target sparsepp
make[2]: Leaving directory `/code/gappa/build/sparseppDownload'
make[1]: Leaving directory `/code/gappa/build/sparseppDownload'
-- Finished downloading sparsepp
-- Configuring Genesis
-- CMake version 2.8.12.2
-- The C compiler identification is GNU 7.2.0
-- Check for working C compiler: /code/miniconda2/envs/epa/bin/x86_64-conda_cos6-linux-gnu-cc
-- Check for working C compiler: /code/miniconda2/envs/epa/bin/x86_64-conda_cos6-linux-gnu-cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Genesis version: v0.19.0
-- Building Genesis as a dependency
-- Build type: RELEASE
-- Unity build: FULL
-- C++ compiler: GNU 7.2.0 at /code/miniconda2/envs/epa/bin/x86_64-conda_cos6-linux-gnu-c++
-- C compiler  : GNU 7.2.0 at /code/miniconda2/envs/epa/bin/x86_64-conda_cos6-linux-gnu-cc
-- Check if the system is big endian
-- Searching 16 bit integer
-- Looking for sys/types.h
-- Looking for sys/types.h - found
-- Looking for stdint.h
-- Looking for stdint.h - found
-- Looking for stddef.h
-- Looking for stddef.h - found
-- Check size of unsigned short
-- Check size of unsigned short - done
-- Using unsigned short
-- Check if the system is big endian - little endian
-- Looking for Threads
-- Looking for include file pthread.h
-- Looking for include file 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
-- Found Threads: -lpthread
-- Using Threads
-- Looking for OpenMP
-- 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
-- Found OpenMP: -fopenmp
-- Using OpenMP
-- Building static lib
-- Finished configuring Genesis
-- CMAKE_EXE_LINKER_FLAGS  -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now
-- GENESIS_LINK_LIBRARIES -lpthread;genesis_lib_static
-- Configuring done
-- Generating done
-- Build files have been written to: /code/gappa/build
Running make...
make -s -C build
Scanning dependencies of target genesis_lib_static
[  3%] Building CXX object libs/genesis/lib/genesis/CMakeFiles/genesis_lib_static.dir/__/__/__/__/genesis_unity_sources/lib/all.cpp.o
Linking CXX static library ../../../../../libs/genesis/bin/libgenesis.a
[  3%] Built target genesis_lib_static
Scanning dependencies of target gappa
[  6%] Building CXX object CMakeFiles/gappa.dir/src/commands/analyze/assign.cpp.o
[ 10%] Building CXX object CMakeFiles/gappa.dir/src/commands/analyze/correlation.cpp.o
[ 13%] Building CXX object CMakeFiles/gappa.dir/src/commands/analyze/dispersion.cpp.o
[ 16%] Building CXX object CMakeFiles/gappa.dir/src/commands/analyze/graft.cpp.o
[ 20%] Building CXX object CMakeFiles/gappa.dir/src/commands/analyze/ikmeans.cpp.o
In file included from /code/gappa/src/commands/analyze/ikmeans.hpp:29:0,
                 from /code/gappa/src/commands/analyze/ikmeans.cpp:24:
/code/gappa/src/commands/common/kmeans.hpp:66:21: error: 'genesis::utils::KmeansClusteringInfo' has not been declared
     genesis::utils::KmeansClusteringInfo const& cluster_info,
                     ^~~~~~~~~~~~~~~~~~~~
/code/gappa/src/commands/common/kmeans.hpp:73:21: error: 'genesis::utils::KmeansClusteringInfo' has not been declared
     genesis::utils::KmeansClusteringInfo const& cluster_info,
                     ^~~~~~~~~~~~~~~~~~~~
/code/gappa/src/commands/analyze/ikmeans.cpp: In function 'void run_ikmeans(const IkmeansOptions&)':
/code/gappa/src/commands/analyze/ikmeans.cpp:185:13: error: 'class genesis::utils::EuclideanKmeans' has no member named 'report_iteration'; did you mean 'max_iterations'?
     ikmeans.report_iteration = [&]( size_t iteration ){
             ^~~~~~~~~~~~~~~~
             max_iterations
/code/gappa/src/commands/analyze/ikmeans.cpp:202:78: error: invalid initialization of reference of type 'const int&' from expression of type 'const genesis::utils::Kmeans<std::vector<double> >::ClusteringInfo'
         write_assignment_file( options, ikmeans.assignments(), clust_info, k );
                                                                              ^
In file included from /code/gappa/src/commands/analyze/ikmeans.hpp:29:0,
                 from /code/gappa/src/commands/analyze/ikmeans.cpp:24:
/code/gappa/src/commands/common/kmeans.hpp:63:6: note: in passing argument 3 of 'void write_assignment_file(const KmeansOptions&, const std::vector<long unsigned int>&, const int&, size_t)'
 void write_assignment_file(
      ^~~~~~~~~~~~~~~~~~~~~
/code/gappa/src/commands/analyze/ikmeans.cpp:203:75: error: invalid initialization of reference of type 'const int&' from expression of type 'const genesis::utils::Kmeans<std::vector<double> >::ClusteringInfo'
         write_cluster_info( options, ikmeans.assignments(), clust_info, k );
                                                                           ^
In file included from /code/gappa/src/commands/analyze/ikmeans.hpp:29:0,
                 from /code/gappa/src/commands/analyze/ikmeans.cpp:24:
/code/gappa/src/commands/common/kmeans.hpp:70:6: note: in passing argument 3 of 'void write_cluster_info(const KmeansOptions&, const std::vector<long unsigned int>&, const int&, size_t)'
 void write_cluster_info(
      ^~~~~~~~~~~~~~~~~~
make[3]: *** [CMakeFiles/gappa.dir/src/commands/analyze/ikmeans.cpp.o] Error 1
make[2]: *** [CMakeFiles/gappa.dir/all] Error 2
make[1]: *** [all] Error 2
make: *** [build] Error 2

Any guidance on how to troubleshoot? Thanks in advance for your time!

vmaffei commented 6 years ago

version info: gcc (crosstool-NG fa8859cb) version 7.2.0 cmake version 2.8.12.2 GNU Make 3.81

lczech commented 6 years ago

Oooops, I see what happened there. I did some changes yesterday and forgot to push one of them... Please download gappa again and try again to compile. It should work now!

vmaffei commented 6 years ago

No worries at all! Compiled 100%...thanks for the quick reply!!

lczech commented 6 years ago

Nice, glad to hear! Let me know if you have any other trouble!