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picrust / picrust2

Code, unit tests, and tutorials for running PICRUSt2
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prerequisite installation issue #41

Closed swathipen closed 5 years ago

swathipen commented 5 years ago

I followed the pre-requisite installation instructions and received several errors while running the make commands :

cd epa-ng-0.2.1-beta-dev make

Running cmake CMake Warning (dev) at CMakeLists.txt:119: Syntax Warning in cmake code at column 71

Argument not separated from preceding token by whitespace. This warning is for project developers. Use -Wno-dev to suppress it.

-- The CXX compiler identification is GNU 4.8.5 -- The C compiler identification is GNU 4.8.5 -- Check for working CXX compiler: /usr/bin/c++ -- Check for working CXX compiler: /usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- Check for working C compiler: /usr/bin/cc -- Check for working C compiler: /usr/bin/cc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done CMake Error at CMakeLists.txt:39 (message): GNU compiler too old! Minimum required: 4.9.2

-- Configuring incomplete, errors occurred! See also "/users/spenumut/picrust2/placement_tools/epa-ng-0.2.1-beta-dev/build/CMakeFiles/CMakeOutput.log". make: *** [build/CMakeCache.txt] Error 1

cd gappa-0.0.0-dev make Running CMake... -- The CXX compiler identification is GNU 4.8.5 -- Check for working CXX compiler: /usr/bin/c++ -- Check for working CXX compiler: /usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - 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: /gpfs_home/spenumut/picrust2/placement_tools/gappa-0.0.0-dev/build/CLI11Download gmake[1]: Entering directory /gpfs_home/spenumut/picrust2/placement_tools/gappa-0.0.0-dev/build/CLI11Download' gmake[2]: Entering directory/gpfs_home/spenumut/picrust2/placement_tools/gappa-0.0.0-dev/build/CLI11Download' gmake[3]: Entering directory /gpfs_home/spenumut/picrust2/placement_tools/gappa-0.0.0-dev/build/CLI11Download' Scanning dependencies of target CLI11 gmake[3]: Leaving directory/gpfs_home/spenumut/picrust2/placement_tools/gappa-0.0.0-dev/build/CLI11Download' gmake[3]: Entering directory /gpfs_home/spenumut/picrust2/placement_tools/gappa-0.0.0-dev/build/CLI11Download' [ 11%] Creating directories for 'CLI11' [ 22%] Performing download step (download, verify and extract) for 'CLI11' -- Downloading... dst='/gpfs_home/spenumut/picrust2/placement_tools/gappa-0.0.0-dev/build/CLI11Download/CLI11-prefix/src/bd890e24a1f081d6db1a59a0cc372eccc64e9e52.zip' timeout='none' -- Using src='https://github.com/CLIUtils/CLI11/archive/bd890e24a1f081d6db1a59a0cc372eccc64e9e52.zip' -- Downloading... done -- extracting... src='/users/spenumut/picrust2/placement_tools/gappa-0.0.0-dev/build/CLI11Download/CLI11-prefix/src/bd890e24a1f081d6db1a59a0cc372eccc64e9e52.zip' dst='/users/spenumut/picrust2/placement_tools/gappa-0.0.0-dev/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%] Performing test step for 'CLI11' /bin/sh: DOWNLOAD_NO_PROGRESS 1: command not found gmake[3]: *** [CLI11-prefix/src/CLI11-stamp/CLI11-test] Error 127 gmake[3]: Leaving directory/gpfs_home/spenumut/picrust2/placement_tools/gappa-0.0.0-dev/build/CLI11Download' gmake[2]: [CMakeFiles/CLI11.dir/all] Error 2 gmake[2]: Leaving directory `/gpfs_home/spenumut/picrust2/placement_tools/gappa-0.0.0-dev/build/CLI11Download' gmake[1]: [all] Error 2 gmake[1]: Leaving directory /gpfs_home/spenumut/picrust2/placement_tools/gappa-0.0.0-dev/build/CLI11Download' -- Cannot build CLI11: 2 -- genesis not found -- Downloading genesis from https://github.com/lczech/genesis/archive/6e1aa0665614df91ec51400356d339ca88c7134b.zip -- Configuring done -- Generating done -- Build files have been written to: /gpfs_home/spenumut/picrust2/placement_tools/gappa-0.0.0-dev/build/genesisDownload gmake[1]: Entering directory/gpfs_home/spenumut/picrust2/placement_tools/gappa-0.0.0-dev/build/genesisDownload' gmake[2]: Entering directory /gpfs_home/spenumut/picrust2/placement_tools/gappa-0.0.0-dev/build/genesisDownload' gmake[3]: Entering directory/gpfs_home/spenumut/picrust2/placement_tools/gappa-0.0.0-dev/build/genesisDownload' Scanning dependencies of target genesis gmake[3]: Leaving directory /gpfs_home/spenumut/picrust2/placement_tools/gappa-0.0.0-dev/build/genesisDownload' gmake[3]: Entering directory/gpfs_home/spenumut/picrust2/placement_tools/gappa-0.0.0-dev/build/genesisDownload' [ 11%] Creating directories for 'genesis' [ 22%] Performing download step (download, verify and extract) for 'genesis' -- Downloading... dst='/gpfs_home/spenumut/picrust2/placement_tools/gappa-0.0.0-dev/build/genesisDownload/genesis-prefix/src/6e1aa0665614df91ec51400356d339ca88c7134b.zip' timeout='none' -- Using src='https://github.com/lczech/genesis/archive/6e1aa0665614df91ec51400356d339ca88c7134b.zip' -- Downloading... done -- extracting... src='/users/spenumut/picrust2/placement_tools/gappa-0.0.0-dev/build/genesisDownload/genesis-prefix/src/6e1aa0665614df91ec51400356d339ca88c7134b.zip' dst='/users/spenumut/picrust2/placement_tools/gappa-0.0.0-dev/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%] Performing test step for 'genesis' /bin/sh: DOWNLOAD_NO_PROGRESS 1: command not found gmake[3]: [genesis-prefix/src/genesis-stamp/genesis-test] Error 127 gmake[3]: Leaving directory /gpfs_home/spenumut/picrust2/placement_tools/gappa-0.0.0-dev/build/genesisDownload' gmake[2]: Leaving directory/gpfs_home/spenumut/picrust2/placement_tools/gappa-0.0.0-dev/build/genesisDownload' gmake[2]: [CMakeFiles/genesis.dir/all] Error 2 gmake[1]: [all] Error 2 gmake[1]: Leaving directory /gpfs_home/spenumut/picrust2/placement_tools/gappa-0.0.0-dev/build/genesisDownload' -- Cannot build genesis: 2 -- sparsepp not found -- Downloading sparsepp from https://github.com/greg7mdp/sparsepp/archive/6bfe3b4bdb364993e612d6bb729d680cf4c77649.zip -- Configuring done -- Generating done -- Build files have been written to: /gpfs_home/spenumut/picrust2/placement_tools/gappa-0.0.0-dev/build/sparseppDownload gmake[1]: Entering directory/gpfs_home/spenumut/picrust2/placement_tools/gappa-0.0.0-dev/build/sparseppDownload' gmake[2]: Entering directory /gpfs_home/spenumut/picrust2/placement_tools/gappa-0.0.0-dev/build/sparseppDownload' gmake[3]: Entering directory/gpfs_home/spenumut/picrust2/placement_tools/gappa-0.0.0-dev/build/sparseppDownload' Scanning dependencies of target sparsepp gmake[3]: Leaving directory /gpfs_home/spenumut/picrust2/placement_tools/gappa-0.0.0-dev/build/sparseppDownload' gmake[3]: Entering directory/gpfs_home/spenumut/picrust2/placement_tools/gappa-0.0.0-dev/build/sparseppDownload' [ 11%] Creating directories for 'sparsepp' [ 22%] Performing download step (download, verify and extract) for 'sparsepp' -- Downloading... dst='/gpfs_home/spenumut/picrust2/placement_tools/gappa-0.0.0-dev/build/sparseppDownload/sparsepp-prefix/src/6bfe3b4bdb364993e612d6bb729d680cf4c77649.zip' timeout='none' -- Using src='https://github.com/greg7mdp/sparsepp/archive/6bfe3b4bdb364993e612d6bb729d680cf4c77649.zip' -- Downloading... done -- extracting... src='/users/spenumut/picrust2/placement_tools/gappa-0.0.0-dev/build/sparseppDownload/sparsepp-prefix/src/6bfe3b4bdb364993e612d6bb729d680cf4c77649.zip' dst='/users/spenumut/picrust2/placement_tools/gappa-0.0.0-dev/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%] Performing test step for 'sparsepp' /bin/sh: DOWNLOAD_NO_PROGRESS 1: command not found gmake[3]: [sparsepp-prefix/src/sparsepp-stamp/sparsepp-test] Error 127 gmake[3]: Leaving directory /gpfs_home/spenumut/picrust2/placement_tools/gappa-0.0.0-dev/build/sparseppDownload' gmake[2]: *** [CMakeFiles/sparsepp.dir/all] Error 2 gmake[2]: Leaving directory/gpfs_home/spenumut/picrust2/placement_tools/gappa-0.0.0-dev/build/sparseppDownload' gmake[1]: [all] Error 2 gmake[1]: Leaving directory `/gpfs_home/spenumut/picrust2/placement_tools/gappa-0.0.0-dev/build/sparseppDownload' -- Cannot build sparsepp: 2 -- Configuring Genesis -- CMake version 3.12.0 -- The C compiler identification is GNU 4.8.5 -- Check for working C compiler: /usr/bin/cc -- Check for working C compiler: /usr/bin/cc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Genesis version: v0.19.0 -- Building Genesis as a dependency -- Build type: RELEASE -- Unity build: FULL -- C++ compiler: GNU 4.8.5 at /usr/bin/c++ -- C compiler : GNU 4.8.5 at /usr/bin/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 pthread.h -- Looking for pthread.h - found -- Looking for pthread_create -- Looking for pthread_create - not found -- Check if compiler accepts -pthread -- Check if compiler accepts -pthread - yes -- Found Threads: TRUE
-- Found Threads: -pthread -- Using Threads -- Looking for OpenMP -- Found OpenMP_C: -fopenmp (found version "3.1") -- Found OpenMP_CXX: -fopenmp (found version "3.1") -- Found OpenMP: TRUE (found version "3.1")
-- Found OpenMP: -fopenmp -- Using OpenMP -- Building static lib -- Finished configuring Genesis -- CMAKE_EXE_LINKER_FLAGS
-- GENESIS_LINK_LIBRARIES -pthread;genesis_lib_static -- Configuring done -- Generating done -- Build files have been written to: /users/spenumut/picrust2/placement_tools/gappa-0.0.0-dev/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 [ 6%] Linking CXX static library ../../../../../libs/genesis/bin/libgenesis.a [ 6%] Built target genesis_lib_static Scanning dependencies of target gappa [ 9%] Building CXX object CMakeFiles/gappa.dir/src/commands/analyze/assign.cpp.o [ 12%] Building CXX object CMakeFiles/gappa.dir/src/commands/analyze/correlation.cpp.o [ 15%] Building CXX object CMakeFiles/gappa.dir/src/commands/analyze/dispersion.cpp.o [ 18%] Building CXX object CMakeFiles/gappa.dir/src/commands/analyze/edgepca.cpp.o [ 21%] Building CXX object CMakeFiles/gappa.dir/src/commands/analyze/graft.cpp.o [ 24%] Building CXX object CMakeFiles/gappa.dir/src/commands/analyze/kmeans.cpp.o [ 27%] Building CXX object CMakeFiles/gappa.dir/src/commands/analyze/kmeans_imbalance.cpp.o [ 30%] Building CXX object CMakeFiles/gappa.dir/src/commands/analyze/kmeans_phylogenetic.cpp.o [ 33%] Building CXX object CMakeFiles/gappa.dir/src/commands/analyze/krd.cpp.o [ 36%] Building CXX object CMakeFiles/gappa.dir/src/commands/analyze/nhd.cpp.o [ 39%] Building CXX object CMakeFiles/gappa.dir/src/commands/analyze/squash.cpp.o [ 42%] Building CXX object CMakeFiles/gappa.dir/src/commands/analyze/visualize_color.cpp.o [ 45%] Building CXX object CMakeFiles/gappa.dir/src/commands/prepare/chunkify.cpp.o [ 48%] Building CXX object CMakeFiles/gappa.dir/src/commands/prepare/extract.cpp.o [ 51%] Building CXX object CMakeFiles/gappa.dir/src/commands/prepare/phat.cpp.o [ 54%] Building CXX object CMakeFiles/gappa.dir/src/commands/prepare/unchunkify.cpp.o [ 57%] Building CXX object CMakeFiles/gappa.dir/src/main.cpp.o [ 60%] Building CXX object CMakeFiles/gappa.dir/src/options/color/color_map.cpp.o [ 63%] Building CXX object CMakeFiles/gappa.dir/src/options/color/color_norm.cpp.o [ 66%] Building CXX object CMakeFiles/gappa.dir/src/options/color/single_color.cpp.o [ 69%] Building CXX object CMakeFiles/gappa.dir/src/options/file_input.cpp.o [ 72%] Building CXX object CMakeFiles/gappa.dir/src/options/file_output.cpp.o [ 75%] Building CXX object CMakeFiles/gappa.dir/src/options/global.cpp.o [ 78%] Building CXX object CMakeFiles/gappa.dir/src/options/jplace_input.cpp.o [ 81%] Building CXX object CMakeFiles/gappa.dir/src/options/matrix_output.cpp.o In file included from /users/spenumut/picrust2/placement_tools/gappa-0.0.0-dev/src/options/matrix_output.hpp:32:0, from /users/spenumut/picrust2/placement_tools/gappa-0.0.0-dev/src/options/matrix_output.cpp:24: /users/spenumut/picrust2/placement_tools/gappa-0.0.0-dev/libs/genesis/lib/genesis/utils/containers/matrix/writer.hpp: In constructor ‘genesis::utils::MatrixWriter::MatrixWriter() [with T = double]’: /users/spenumut/picrust2/placement_tools/gappa-0.0.0-dev/libs/genesis/lib/genesis/utils/containers/matrix/writer.hpp:72:5: error: conversion from ‘const char [2]’ to non-scalar type ‘std::string {aka std::basic_string}’ requested MatrixWriter() = default; ^ /users/spenumut/picrust2/placement_tools/gappa-0.0.0-dev/src/options/matrix_output.cpp: In member function ‘void MatrixOutputOptions::write_matrix(const genesis::utils::Matrix&, const std::vector<std::basic_string >&, const std::vector<std::basic_string >&, const string&) const’: /users/spenumut/picrust2/placement_tools/gappa-0.0.0-dev/src/options/matrix_output.cpp:99:40: note: synthesized method ‘genesis::utils::MatrixWriter::MatrixWriter() [with T = double]’ first required here auto writer = MatrixWriter(); ^ make[3]: [CMakeFiles/gappa.dir/src/options/matrix_output.cpp.o] Error 1 make[2]: [CMakeFiles/gappa.dir/all] Error 2 make[1]: [all] Error 2 make: *** [build] Error 2

gavinmdouglas commented 5 years ago

Hey there,

The key error is: "GNU compiler too old! Minimum required: 4.9.2”. You’ll need to update your version of gcc to get EPA-NG working. Please note that I just released a QIIME2 plugin of PICRUSt2 that can be used with the q2-fragment-insertion QIIME2 plugin instead of using EPA-NG and GAPPA. There are less options with this plugin, but it should be much easier to install. See here for details: https://github.com/picrust/picrust2/wiki/q2-picrust2-Tutorial https://github.com/picrust/picrust2/wiki/q2-picrust2-Tutorial

Gavin

On Oct 18, 2018, at 12:31 AM, Swathi Penumutchu notifications@github.com wrote:

I followed the pre-requisite installation instructions and received several errors while running the make commands :

cd epa-ng-0.2.1-beta-dev make

Running cmake CMake Warning (dev) at CMakeLists.txt:119: Syntax Warning in cmake code at column 71

Argument not separated from preceding token by whitespace. This warning is for project developers. Use -Wno-dev to suppress it.

-- The CXX compiler identification is GNU 4.8.5 -- The C compiler identification is GNU 4.8.5 -- Check for working CXX compiler: /usr/bin/c++ -- Check for working CXX compiler: /usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- Check for working C compiler: /usr/bin/cc -- Check for working C compiler: /usr/bin/cc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done CMake Error at CMakeLists.txt:39 (message): GNU compiler too old! Minimum required: 4.9.2

-- Configuring incomplete, errors occurred! See also "/users/spenumut/picrust2/placement_tools/epa-ng-0.2.1-beta-dev/build/CMakeFiles/CMakeOutput.log". make: *** [build/CMakeCache.txt] Error 1

cd gappa-0.0.0-dev make Running CMake... -- The CXX compiler identification is GNU 4.8.5 -- Check for working CXX compiler: /usr/bin/c++ -- Check for working CXX compiler: /usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - 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 https://github.com/CLIUtils/CLI11/archive/bd890e24a1f081d6db1a59a0cc372eccc64e9e52.zip -- Configuring done -- Generating done -- Build files have been written to: /gpfs_home/spenumut/picrust2/placement_tools/gappa-0.0.0-dev/build/CLI11Download gmake[1]: Entering directory /gpfs_home/spenumut/picrust2/placement_tools/gappa-0.0.0-dev/build/CLI11Download' gmake[2]: Entering directory/gpfs_home/spenumut/picrust2/placement_tools/gappa-0.0.0-dev/build/CLI11Download' gmake[3]: Entering directory /gpfs_home/spenumut/picrust2/placement_tools/gappa-0.0.0-dev/build/CLI11Download' Scanning dependencies of target CLI11 gmake[3]: Leaving directory/gpfs_home/spenumut/picrust2/placement_tools/gappa-0.0.0-dev/build/CLI11Download' gmake[3]: Entering directory /gpfs_home/spenumut/picrust2/placement_tools/gappa-0.0.0-dev/build/CLI11Download' [ 11%] Creating directories for 'CLI11' [ 22%] Performing download step (download, verify and extract) for 'CLI11' -- Downloading... dst='/gpfs_home/spenumut/picrust2/placement_tools/gappa-0.0.0-dev/build/CLI11Download/CLI11-prefix/src/bd890e24a1f081d6db1a59a0cc372eccc64e9e52.zip' timeout='none' -- Using src='https://github.com/CLIUtils/CLI11/archive/bd890e24a1f081d6db1a59a0cc372eccc64e9e52.zip' -- Downloading... done -- extracting... src='/users/spenumut/picrust2/placement_tools/gappa-0.0.0-dev/build/CLI11Download/CLI11-prefix/src/bd890e24a1f081d6db1a59a0cc372eccc64e9e52.zip' dst='/users/spenumut/picrust2/placement_tools/gappa-0.0.0-dev/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%] Performing test step for 'CLI11' /bin/sh: DOWNLOAD_NO_PROGRESS 1: command not found gmake[3]: [CLI11-prefix/src/CLI11-stamp/CLI11-test] Error 127 gmake[3]: Leaving directory/gpfs_home/spenumut/picrust2/placement_tools/gappa-0.0.0-dev/build/CLI11Download' gmake[2]: [CMakeFiles/CLI11.dir/all] Error 2 gmake[2]: Leaving directory /gpfs_home/spenumut/picrust2/placement_tools/gappa-0.0.0-dev/build/CLI11Download' gmake[1]: [all] Error 2 gmake[1]: Leaving directory/gpfs_home/spenumut/picrust2/placement_tools/gappa-0.0.0-dev/build/CLI11Download' -- Cannot build CLI11: 2 -- genesis not found -- Downloading genesis from https://github.com/lczech/genesis/archive/6e1aa0665614df91ec51400356d339ca88c7134b.zip https://github.com/lczech/genesis/archive/6e1aa0665614df91ec51400356d339ca88c7134b.zip -- Configuring done -- Generating done -- Build files have been written to: /gpfs_home/spenumut/picrust2/placement_tools/gappa-0.0.0-dev/build/genesisDownload gmake[1]: Entering directory /gpfs_home/spenumut/picrust2/placement_tools/gappa-0.0.0-dev/build/genesisDownload' gmake[2]: Entering directory/gpfs_home/spenumut/picrust2/placement_tools/gappa-0.0.0-dev/build/genesisDownload' gmake[3]: Entering directory /gpfs_home/spenumut/picrust2/placement_tools/gappa-0.0.0-dev/build/genesisDownload' Scanning dependencies of target genesis gmake[3]: Leaving directory/gpfs_home/spenumut/picrust2/placement_tools/gappa-0.0.0-dev/build/genesisDownload' gmake[3]: Entering directory /gpfs_home/spenumut/picrust2/placement_tools/gappa-0.0.0-dev/build/genesisDownload' [ 11%] Creating directories for 'genesis' [ 22%] Performing download step (download, verify and extract) for 'genesis' -- Downloading... dst='/gpfs_home/spenumut/picrust2/placement_tools/gappa-0.0.0-dev/build/genesisDownload/genesis-prefix/src/6e1aa0665614df91ec51400356d339ca88c7134b.zip' timeout='none' -- Using src='https://github.com/lczech/genesis/archive/6e1aa0665614df91ec51400356d339ca88c7134b.zip' -- Downloading... done -- extracting... src='/users/spenumut/picrust2/placement_tools/gappa-0.0.0-dev/build/genesisDownload/genesis-prefix/src/6e1aa0665614df91ec51400356d339ca88c7134b.zip' dst='/users/spenumut/picrust2/placement_tools/gappa-0.0.0-dev/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%] Performing test step for 'genesis' /bin/sh: DOWNLOAD_NO_PROGRESS 1: command not found gmake[3]: [genesis-prefix/src/genesis-stamp/genesis-test] Error 127 gmake[3]: Leaving directory/gpfs_home/spenumut/picrust2/placement_tools/gappa-0.0.0-dev/build/genesisDownload' gmake[2]: Leaving directory /gpfs_home/spenumut/picrust2/placement_tools/gappa-0.0.0-dev/build/genesisDownload' gmake[2]: [CMakeFiles/genesis.dir/all] Error 2 gmake[1]: [all] Error 2 gmake[1]: Leaving directory/gpfs_home/spenumut/picrust2/placement_tools/gappa-0.0.0-dev/build/genesisDownload' -- Cannot build genesis: 2 -- sparsepp not found -- Downloading sparsepp from https://github.com/greg7mdp/sparsepp/archive/6bfe3b4bdb364993e612d6bb729d680cf4c77649.zip https://github.com/greg7mdp/sparsepp/archive/6bfe3b4bdb364993e612d6bb729d680cf4c77649.zip -- Configuring done -- Generating done -- Build files have been written to: /gpfs_home/spenumut/picrust2/placement_tools/gappa-0.0.0-dev/build/sparseppDownload gmake[1]: Entering directory /gpfs_home/spenumut/picrust2/placement_tools/gappa-0.0.0-dev/build/sparseppDownload' gmake[2]: Entering directory/gpfs_home/spenumut/picrust2/placement_tools/gappa-0.0.0-dev/build/sparseppDownload' gmake[3]: Entering directory /gpfs_home/spenumut/picrust2/placement_tools/gappa-0.0.0-dev/build/sparseppDownload' Scanning dependencies of target sparsepp gmake[3]: Leaving directory/gpfs_home/spenumut/picrust2/placement_tools/gappa-0.0.0-dev/build/sparseppDownload' gmake[3]: Entering directory /gpfs_home/spenumut/picrust2/placement_tools/gappa-0.0.0-dev/build/sparseppDownload' [ 11%] Creating directories for 'sparsepp' [ 22%] Performing download step (download, verify and extract) for 'sparsepp' -- Downloading... dst='/gpfs_home/spenumut/picrust2/placement_tools/gappa-0.0.0-dev/build/sparseppDownload/sparsepp-prefix/src/6bfe3b4bdb364993e612d6bb729d680cf4c77649.zip' timeout='none' -- Using src='https://github.com/greg7mdp/sparsepp/archive/6bfe3b4bdb364993e612d6bb729d680cf4c77649.zip' -- Downloading... done -- extracting... src='/users/spenumut/picrust2/placement_tools/gappa-0.0.0-dev/build/sparseppDownload/sparsepp-prefix/src/6bfe3b4bdb364993e612d6bb729d680cf4c77649.zip' dst='/users/spenumut/picrust2/placement_tools/gappa-0.0.0-dev/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%] Performing test step for 'sparsepp' /bin/sh: DOWNLOAD_NO_PROGRESS 1: command not found gmake[3]: [sparsepp-prefix/src/sparsepp-stamp/sparsepp-test] Error 127 gmake[3]: Leaving directory/gpfs_home/spenumut/picrust2/placement_tools/gappa-0.0.0-dev/build/sparseppDownload' gmake[2]: [CMakeFiles/sparsepp.dir/all] Error 2 gmake[2]: Leaving directory /gpfs_home/spenumut/picrust2/placement_tools/gappa-0.0.0-dev/build/sparseppDownload' gmake[1]: [all] Error 2 gmake[1]: Leaving directory/gpfs_home/spenumut/picrust2/placement_tools/gappa-0.0.0-dev/build/sparseppDownload' -- Cannot build sparsepp: 2 -- Configuring Genesis -- CMake version 3.12.0 -- The C compiler identification is GNU 4.8.5 -- Check for working C compiler: /usr/bin/cc -- Check for working C compiler: /usr/bin/cc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Genesis version: v0.19.0 -- Building Genesis as a dependency -- Build type: RELEASE -- Unity build: FULL -- C++ compiler: GNU 4.8.5 at /usr/bin/c++ -- C compiler : GNU 4.8.5 at /usr/bin/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 pthread.h -- Looking for pthread.h - found -- Looking for pthread_create -- Looking for pthread_create - not found -- Check if compiler accepts -pthread -- Check if compiler accepts -pthread - yes -- Found Threads: TRUE -- Found Threads: -pthread -- Using Threads -- Looking for OpenMP -- Found OpenMP_C: -fopenmp (found version "3.1") -- Found OpenMP_CXX: -fopenmp (found version "3.1") -- Found OpenMP: TRUE (found version "3.1") -- Found OpenMP: -fopenmp -- Using OpenMP -- Building static lib -- Finished configuring Genesis -- CMAKE_EXE_LINKER_FLAGS -- GENESIS_LINK_LIBRARIES -pthread;genesis_lib_static -- Configuring done -- Generating done -- Build files have been written to: /users/spenumut/picrust2/placement_tools/gappa-0.0.0-dev/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 [ 6%] Linking CXX static library ../../../../../libs/genesis/bin/libgenesis.a [ 6%] Built target genesis_lib_static Scanning dependencies of target gappa [ 9%] Building CXX object CMakeFiles/gappa.dir/src/commands/analyze/assign.cpp.o [ 12%] Building CXX object CMakeFiles/gappa.dir/src/commands/analyze/correlation.cpp.o [ 15%] Building CXX object CMakeFiles/gappa.dir/src/commands/analyze/dispersion.cpp.o [ 18%] Building CXX object CMakeFiles/gappa.dir/src/commands/analyze/edgepca.cpp.o [ 21%] Building CXX object CMakeFiles/gappa.dir/src/commands/analyze/graft.cpp.o [ 24%] Building CXX object CMakeFiles/gappa.dir/src/commands/analyze/kmeans.cpp.o [ 27%] Building CXX object CMakeFiles/gappa.dir/src/commands/analyze/kmeans_imbalance.cpp.o [ 30%] Building CXX object CMakeFiles/gappa.dir/src/commands/analyze/kmeans_phylogenetic.cpp.o [ 33%] Building CXX object CMakeFiles/gappa.dir/src/commands/analyze/krd.cpp.o [ 36%] Building CXX object CMakeFiles/gappa.dir/src/commands/analyze/nhd.cpp.o [ 39%] Building CXX object CMakeFiles/gappa.dir/src/commands/analyze/squash.cpp.o [ 42%] Building CXX object CMakeFiles/gappa.dir/src/commands/analyze/visualize_color.cpp.o [ 45%] Building CXX object CMakeFiles/gappa.dir/src/commands/prepare/chunkify.cpp.o [ 48%] Building CXX object CMakeFiles/gappa.dir/src/commands/prepare/extract.cpp.o [ 51%] Building CXX object CMakeFiles/gappa.dir/src/commands/prepare/phat.cpp.o [ 54%] Building CXX object CMakeFiles/gappa.dir/src/commands/prepare/unchunkify.cpp.o [ 57%] Building CXX object CMakeFiles/gappa.dir/src/main.cpp.o [ 60%] Building CXX object CMakeFiles/gappa.dir/src/options/color/color_map.cpp.o [ 63%] Building CXX object CMakeFiles/gappa.dir/src/options/color/color_norm.cpp.o [ 66%] Building CXX object CMakeFiles/gappa.dir/src/options/color/single_color.cpp.o [ 69%] Building CXX object CMakeFiles/gappa.dir/src/options/file_input.cpp.o [ 72%] Building CXX object CMakeFiles/gappa.dir/src/options/file_output.cpp.o [ 75%] Building CXX object CMakeFiles/gappa.dir/src/options/global.cpp.o [ 78%] Building CXX object CMakeFiles/gappa.dir/src/options/jplace_input.cpp.o [ 81%] Building CXX object CMakeFiles/gappa.dir/src/options/matrix_output.cpp.o In file included from /users/spenumut/picrust2/placement_tools/gappa-0.0.0-dev/src/options/matrix_output.hpp:32:0, from /users/spenumut/picrust2/placement_tools/gappa-0.0.0-dev/src/options/matrix_output.cpp:24: /users/spenumut/picrust2/placement_tools/gappa-0.0.0-dev/libs/genesis/lib/genesis/utils/containers/matrix/writer.hpp: In constructor ‘genesis::utils::MatrixWriter::MatrixWriter() [with T = double]’: /users/spenumut/picrust2/placement_tools/gappa-0.0.0-dev/libs/genesis/lib/genesis/utils/containers/matrix/writer.hpp:72:5: error: conversion from ‘const char [2]’ to non-scalar type ‘std::string {aka std::basic_string}’ requested MatrixWriter() = default; ^ /users/spenumut/picrust2/placement_tools/gappa-0.0.0-dev/src/options/matrix_output.cpp: In member function ‘void MatrixOutputOptions::write_matrix(const genesis::utils::Matrix&, const std::vector&, const std::vector&, const string&) const’: /users/spenumut/picrust2/placement_tools/gappa-0.0.0-dev/src/options/matrix_output.cpp:99:40: note: synthesized method ‘genesis::utils::MatrixWriter::MatrixWriter() [with T = double]’ first required here auto writer = MatrixWriter(); ^ make[3]: [CMakeFiles/gappa.dir/src/options/matrix_output.cpp.o] Error 1 make[2]: [CMakeFiles/gappa.dir/all] Error 2 make[1]: [all] Error 2 make: *** [build] Error 2

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