CMake Deprecation Warning at 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 <min> value or use a ...<max> suffix to tell
  CMake that the project does not need compatibility with older versions.


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diamond-0.9.36/
diamond-0.9.36/.dockerignore
diamond-0.9.36/.gitattributes
diamond-0.9.36/.gitignore
diamond-0.9.36/.travis.yml
diamond-0.9.36/CMakeLists.txt
diamond-0.9.36/Dockerfile
diamond-0.9.36/LICENSE
diamond-0.9.36/README.md
diamond-0.9.36/build_simple.sh
diamond-0.9.36/src/
diamond-0.9.36/src/ChangeLog
diamond-0.9.36/src/align/
diamond-0.9.36/src/align/align.cpp
diamond-0.9.36/src/align/align.h
diamond-0.9.36/src/align/culling.cpp
diamond-0.9.36/src/align/extend.cpp
diamond-0.9.36/src/align/extend.h
diamond-0.9.36/src/align/gapped.cpp
diamond-0.9.36/src/align/gapped_filter.cpp
diamond-0.9.36/src/align/legacy/
diamond-0.9.36/src/align/legacy/banded_swipe_pipeline.cpp
diamond-0.9.36/src/align/legacy/query_mapper.cpp
diamond-0.9.36/src/align/legacy/query_mapper.h
diamond-0.9.36/src/align/legacy/swipe_pipeline.cpp
diamond-0.9.36/src/align/output.cpp
diamond-0.9.36/src/align/ranking.cpp
diamond-0.9.36/src/align/target.h
diamond-0.9.36/src/align/ungapped.cpp
diamond-0.9.36/src/basic/
diamond-0.9.36/src/basic/basic.cpp
diamond-0.9.36/src/basic/config.cpp
diamond-0.9.36/src/basic/config.h
diamond-0.9.36/src/basic/const.h
diamond-0.9.36/src/basic/diagonal_segment.h
diamond-0.9.36/src/basic/hssp.cpp
diamond-0.9.36/src/basic/masking.cpp
diamond-0.9.36/src/basic/masking.h
diamond-0.9.36/src/basic/match.h
diamond-0.9.36/src/basic/matrix_tables.cpp
diamond-0.9.36/src/basic/packed_loc.h
diamond-0.9.36/src/basic/packed_sequence.h
diamond-0.9.36/src/basic/packed_transcript.h
diamond-0.9.36/src/basic/parameters.h
diamond-0.9.36/src/basic/reduction.h
diamond-0.9.36/src/basic/score_matrix.cpp
diamond-0.9.36/src/basic/score_matrix.h
diamond-0.9.36/src/basic/seed.h
diamond-0.9.36/src/basic/seed_iterator.h
diamond-0.9.36/src/basic/sequence.h
diamond-0.9.36/src/basic/shape.h
diamond-0.9.36/src/basic/shape_config.h
diamond-0.9.36/src/basic/statistics.h
diamond-0.9.36/src/basic/translate.h
diamond-0.9.36/src/basic/translated_position.h
diamond-0.9.36/src/basic/value.cpp
diamond-0.9.36/src/basic/value.h
diamond-0.9.36/src/chaining/
diamond-0.9.36/src/chaining/chaining.h
diamond-0.9.36/src/chaining/greedy_align.cpp
diamond-0.9.36/src/chaining/smith_waterman.cpp
diamond-0.9.36/src/cluster/
diamond-0.9.36/src/cluster/cluster.h
diamond-0.9.36/src/cluster/cluster_registry.cpp
diamond-0.9.36/src/cluster/cluster_registry.h
diamond-0.9.36/src/cluster/disjoint_set.h
diamond-0.9.36/src/cluster/mcl.cpp
diamond-0.9.36/src/cluster/mcl.h
diamond-0.9.36/src/cluster/medoid.cpp
diamond-0.9.36/src/cluster/multi_step_cluster.cpp
diamond-0.9.36/src/cluster/multi_step_cluster.h
diamond-0.9.36/src/data/
diamond-0.9.36/src/data/frequent_seeds.cpp
diamond-0.9.36/src/data/frequent_seeds.h
diamond-0.9.36/src/data/index.h
diamond-0.9.36/src/data/load_seqs.h
diamond-0.9.36/src/data/metadata.h
diamond-0.9.36/src/data/queries.cpp
diamond-0.9.36/src/data/queries.h
diamond-0.9.36/src/data/ref_dictionary.cpp
diamond-0.9.36/src/data/ref_dictionary.h
diamond-0.9.36/src/data/reference.cpp
diamond-0.9.36/src/data/reference.h
diamond-0.9.36/src/data/seed_array.cpp
diamond-0.9.36/src/data/seed_array.h
diamond-0.9.36/src/data/seed_histogram.cpp
diamond-0.9.36/src/data/seed_histogram.h
diamond-0.9.36/src/data/seed_set.cpp
diamond-0.9.36/src/data/seed_set.h
diamond-0.9.36/src/data/sequence_set.h
diamond-0.9.36/src/data/string_set.h
diamond-0.9.36/src/data/taxon_list.cpp
diamond-0.9.36/src/data/taxon_list.h
diamond-0.9.36/src/data/taxonomy.cpp
diamond-0.9.36/src/data/taxonomy.h
diamond-0.9.36/src/data/taxonomy_filter.cpp
diamond-0.9.36/src/data/taxonomy_nodes.cpp
diamond-0.9.36/src/data/taxonomy_nodes.h
diamond-0.9.36/src/dp/
diamond-0.9.36/src/dp/banded_sw.cpp
diamond-0.9.36/src/dp/comp_based_stats.cpp
diamond-0.9.36/src/dp/comp_based_stats.h
diamond-0.9.36/src/dp/dp.h
diamond-0.9.36/src/dp/hsp_traits.h
diamond-0.9.36/src/dp/needleman_wunsch.cpp
diamond-0.9.36/src/dp/scan_diags.cpp
diamond-0.9.36/src/dp/scan_diags.h
diamond-0.9.36/src/dp/score_profile.h
diamond-0.9.36/src/dp/score_vector.h
diamond-0.9.36/src/dp/score_vector_int16.h
diamond-0.9.36/src/dp/score_vector_int8.h
diamond-0.9.36/src/dp/sw_3frame.cpp
diamond-0.9.36/src/dp/swipe/
diamond-0.9.36/src/dp/swipe/banded_3frame_swipe.cpp
diamond-0.9.36/src/dp/swipe/banded_swipe.cpp
diamond-0.9.36/src/dp/swipe/swipe.cpp
diamond-0.9.36/src/dp/swipe/swipe.h
diamond-0.9.36/src/dp/swipe/swipe_wrapper.cpp
diamond-0.9.36/src/dp/swipe/target_iterator.h
diamond-0.9.36/src/dp/traceback.h
diamond-0.9.36/src/dp/ungapped.h
diamond-0.9.36/src/dp/ungapped_align.cpp
diamond-0.9.36/src/dp/ungapped_simd.cpp
diamond-0.9.36/src/dp/ungapped_simd.h
diamond-0.9.36/src/lib/
diamond-0.9.36/src/lib/Eigen/
diamond-0.9.36/src/lib/Eigen/CMakeLists.txt
diamond-0.9.36/src/lib/Eigen/Cholesky
diamond-0.9.36/src/lib/Eigen/CholmodSupport
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diamond-0.9.36/src/lib/Eigen/Dense
diamond-0.9.36/src/lib/Eigen/Eigen
diamond-0.9.36/src/lib/Eigen/Eigenvalues
diamond-0.9.36/src/lib/Eigen/Geometry
diamond-0.9.36/src/lib/Eigen/Householder
diamond-0.9.36/src/lib/Eigen/IterativeLinearSolvers
diamond-0.9.36/src/lib/Eigen/Jacobi
diamond-0.9.36/src/lib/Eigen/LU
diamond-0.9.36/src/lib/Eigen/MetisSupport
diamond-0.9.36/src/lib/Eigen/OrderingMethods
diamond-0.9.36/src/lib/Eigen/PaStiXSupport
diamond-0.9.36/src/lib/Eigen/PardisoSupport
diamond-0.9.36/src/lib/Eigen/QR
diamond-0.9.36/src/lib/Eigen/QtAlignedMalloc
diamond-0.9.36/src/lib/Eigen/SPQRSupport
diamond-0.9.36/src/lib/Eigen/SVD
diamond-0.9.36/src/lib/Eigen/Sparse
diamond-0.9.36/src/lib/Eigen/SparseCholesky
diamond-0.9.36/src/lib/Eigen/SparseCore
diamond-0.9.36/src/lib/Eigen/SparseLU
diamond-0.9.36/src/lib/Eigen/SparseQR
diamond-0.9.36/src/lib/Eigen/StdDeque
diamond-0.9.36/src/lib/Eigen/StdList
diamond-0.9.36/src/lib/Eigen/StdVector
diamond-0.9.36/src/lib/Eigen/SuperLUSupport
diamond-0.9.36/src/lib/Eigen/UmfPackSupport
diamond-0.9.36/src/lib/Eigen/src/
diamond-0.9.36/src/lib/Eigen/src/Cholesky/
diamond-0.9.36/src/lib/Eigen/src/Cholesky/LDLT.h
diamond-0.9.36/src/lib/Eigen/src/Cholesky/LLT.h
diamond-0.9.36/src/lib/Eigen/src/Cholesky/LLT_LAPACKE.h
diamond-0.9.36/src/lib/Eigen/src/CholmodSupport/
diamond-0.9.36/src/lib/Eigen/src/CholmodSupport/CholmodSupport.h
diamond-0.9.36/src/lib/Eigen/src/Core/
diamond-0.9.36/src/lib/Eigen/src/Core/Array.h
diamond-0.9.36/src/lib/Eigen/src/Core/ArrayBase.h
diamond-0.9.36/src/lib/Eigen/src/Core/ArrayWrapper.h
diamond-0.9.36/src/lib/Eigen/src/Core/Assign.h
diamond-0.9.36/src/lib/Eigen/src/Core/AssignEvaluator.h
diamond-0.9.36/src/lib/Eigen/src/Core/Assign_MKL.h
diamond-0.9.36/src/lib/Eigen/src/Core/BandMatrix.h
diamond-0.9.36/src/lib/Eigen/src/Core/Block.h
diamond-0.9.36/src/lib/Eigen/src/Core/BooleanRedux.h
diamond-0.9.36/src/lib/Eigen/src/Core/CommaInitializer.h
diamond-0.9.36/src/lib/Eigen/src/Core/ConditionEstimator.h
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diamond-0.9.36/src/lib/Eigen/src/Core/DenseStorage.h
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diamond-0.9.36/src/lib/Eigen/src/Core/Fuzzy.h
diamond-0.9.36/src/lib/Eigen/src/Core/GeneralProduct.h
diamond-0.9.36/src/lib/Eigen/src/Core/GenericPacketMath.h
diamond-0.9.36/src/lib/Eigen/src/Core/GlobalFunctions.h
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diamond-0.9.36/src/lib/Eigen/src/Core/Matrix.h
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diamond-0.9.36/src/lib/Eigen/src/Core/PermutationMatrix.h
diamond-0.9.36/src/lib/Eigen/src/Core/PlainObjectBase.h
diamond-0.9.36/src/lib/Eigen/src/Core/Product.h
diamond-0.9.36/src/lib/Eigen/src/Core/ProductEvaluators.h
diamond-0.9.36/src/lib/Eigen/src/Core/Random.h
diamond-0.9.36/src/lib/Eigen/src/Core/Redux.h
diamond-0.9.36/src/lib/Eigen/src/Core/Ref.h
diamond-0.9.36/src/lib/Eigen/src/Core/Replicate.h
diamond-0.9.36/src/lib/Eigen/src/Core/ReturnByValue.h
diamond-0.9.36/src/lib/Eigen/src/Core/Reverse.h
diamond-0.9.36/src/lib/Eigen/src/Core/Select.h
diamond-0.9.36/src/lib/Eigen/src/Core/SelfAdjointView.h
diamond-0.9.36/src/lib/Eigen/src/Core/SelfCwiseBinaryOp.h
diamond-0.9.36/src/lib/Eigen/src/Core/Solve.h
diamond-0.9.36/src/lib/Eigen/src/Core/SolveTriangular.h
diamond-0.9.36/src/lib/Eigen/src/Core/SolverBase.h
diamond-0.9.36/src/lib/Eigen/src/Core/StableNorm.h
diamond-0.9.36/src/lib/Eigen/src/Core/Stride.h
diamond-0.9.36/src/lib/Eigen/src/Core/Swap.h
diamond-0.9.36/src/lib/Eigen/src/Core/Transpose.h
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diamond-0.9.36/src/lib/Eigen/src/Core/TriangularMatrix.h
diamond-0.9.36/src/lib/Eigen/src/Core/VectorBlock.h
diamond-0.9.36/src/lib/Eigen/src/Core/VectorwiseOp.h
diamond-0.9.36/src/lib/Eigen/src/Core/Visitor.h
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diamond-0.9.36/src/lib/Eigen/src/Core/arch/AVX/MathFunctions.h
diamond-0.9.36/src/lib/Eigen/src/Core/arch/AVX/PacketMath.h
diamond-0.9.36/src/lib/Eigen/src/Core/arch/AVX/TypeCasting.h
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diamond-0.9.36/src/lib/Eigen/src/Core/arch/AVX512/PacketMath.h
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diamond-0.9.36/src/lib/Eigen/src/Core/arch/CUDA/
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diamond-0.9.36/src/lib/Eigen/src/Core/functors/
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diamond-0.9.36/src/lib/Eigen/src/Core/products/
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diamond-0.9.36/src/lib/Eigen/src/Core/products/Parallelizer.h
diamond-0.9.36/src/lib/Eigen/src/Core/products/SelfadjointMatrixMatrix.h
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diamond-0.9.36/src/lib/Eigen/src/Core/products/SelfadjointMatrixVector.h
diamond-0.9.36/src/lib/Eigen/src/Core/products/SelfadjointMatrixVector_BLAS.h
diamond-0.9.36/src/lib/Eigen/src/Core/products/SelfadjointProduct.h
diamond-0.9.36/src/lib/Eigen/src/Core/products/SelfadjointRank2Update.h
diamond-0.9.36/src/lib/Eigen/src/Core/products/TriangularMatrixMatrix.h
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diamond-0.9.36/src/lib/Eigen/src/Core/products/TriangularMatrixVector.h
diamond-0.9.36/src/lib/Eigen/src/Core/products/TriangularMatrixVector_BLAS.h
diamond-0.9.36/src/lib/Eigen/src/Core/products/TriangularSolverMatrix.h
diamond-0.9.36/src/lib/Eigen/src/Core/products/TriangularSolverMatrix_BLAS.h
diamond-0.9.36/src/lib/Eigen/src/Core/products/TriangularSolverVector.h
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diamond-0.9.36/src/lib/Eigen/src/Core/util/DisableStupidWarnings.h
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diamond-0.9.36/src/lib/Eigen/src/Core/util/Memory.h
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diamond-0.9.36/src/lib/Eigen/src/Core/util/NonMPL2.h
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diamond-0.9.36/src/lib/Eigen/src/Core/util/StaticAssert.h
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diamond-0.9.36/src/lib/Eigen/src/Eigenvalues/Tridiagonalization.h
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[ 26%] Building CXX object CMakeFiles/diamond.dir/src/run/main.cpp.o
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/usr/src/slapt-src/academic/diamond/diamond-0.9.36/src/data/reference.cpp: In static member function ‘static bool DatabaseFile::is_diamond_db(const string&)’:
/usr/src/slapt-src/academic/diamond/diamond-0.9.36/src/data/reference.cpp:459:16: warning: catching polymorphic type ‘struct EndOfStream’ by value [-Wcatch-value=]
  459 |         catch (EndOfStream) {}
      |                ^~~~~~~~~~~
At global scope:
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[ 30%] Building CXX object CMakeFiles/diamond.dir/src/data/seed_histogram.cpp.o
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/usr/src/slapt-src/academic/diamond/diamond-0.9.36/src/align/align.cpp: In member function ‘bool Align_fetcher::operator()(size_t)’:
/usr/src/slapt-src/academic/diamond/diamond-0.9.36/src/align/align.cpp:56:48: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
   56 |                 target_parallel = (end - begin > config.query_parallel_limit) && (config.frame_shift == 0 || (config.toppercent < 100 && config.query_range_culling));
      |                                    ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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/usr/src/slapt-src/academic/diamond/diamond-0.9.36/src/cluster/mcl.cpp: In member function ‘void Workflow::Cluster::MCL::get_exp(Eigen::MatrixXf*, Eigen::MatrixXf*, float)’:
/usr/src/slapt-src/academic/diamond/diamond-0.9.36/src/cluster/mcl.cpp:77:46: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘Eigen::Index’ {aka ‘int’} [-Wsign-compare]
   77 |                 for(uint32_t idiag = 0; idiag<d.rows(); idiag++){
      |                                         ~~~~~^~~~~~~~~
/usr/src/slapt-src/academic/diamond/diamond-0.9.36/src/cluster/mcl.cpp: In member function ‘void Workflow::Cluster::MCL::get_gamma(Eigen::SparseMatrix<float>*, Eigen::SparseMatrix<float>*, float)’:
/usr/src/slapt-src/academic/diamond/diamond-0.9.36/src/cluster/mcl.cpp:96:29: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘Eigen::Index’ {aka ‘int’} [-Wsign-compare]
   96 |         for (uint32_t k=0; k<in->outerSize(); ++k){
      |                            ~^~~~~~~~~~~~~~~~
/usr/src/slapt-src/academic/diamond/diamond-0.9.36/src/cluster/mcl.cpp: In member function ‘void Workflow::Cluster::MCL::get_gamma(Eigen::MatrixXf*, Eigen::MatrixXf*, float)’:
/usr/src/slapt-src/academic/diamond/diamond-0.9.36/src/cluster/mcl.cpp:117:35: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘Eigen::Index’ {aka ‘int’} [-Wsign-compare]
  117 |         for (uint32_t icol=0; icol<in->cols(); ++icol){
      |                               ~~~~^~~~~~~~~~~
/usr/src/slapt-src/academic/diamond/diamond-0.9.36/src/cluster/mcl.cpp:119:43: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘Eigen::Index’ {aka ‘int’} [-Wsign-compare]
  119 |                 for (uint32_t irow=0; irow<in->rows(); ++irow){
      |                                       ~~~~^~~~~~~~~~~
/usr/src/slapt-src/academic/diamond/diamond-0.9.36/src/cluster/mcl.cpp:122:43: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘Eigen::Index’ {aka ‘int’} [-Wsign-compare]
  122 |                 for (uint32_t irow=0; irow<in->rows(); ++irow){
      |                                       ~~~~^~~~~~~~~~~
/usr/src/slapt-src/academic/diamond/diamond-0.9.36/src/cluster/mcl.cpp: In member function ‘void Workflow::Cluster::MCL::markov_process(Eigen::SparseMatrix<float>*, float, float)’:
/usr/src/slapt-src/academic/diamond/diamond-0.9.36/src/cluster/mcl.cpp:165:37: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘Eigen::Index’ {aka ‘int’} [-Wsign-compare]
  165 |         for (uint32_t idiag=0; idiag<m->cols(); ++idiag){
      |                                ~~~~~^~~~~~~~~~
/usr/src/slapt-src/academic/diamond/diamond-0.9.36/src/cluster/mcl.cpp: In member function ‘void Workflow::Cluster::MCL::markov_process(Eigen::MatrixXf*, float, float)’:
/usr/src/slapt-src/academic/diamond/diamond-0.9.36/src/cluster/mcl.cpp:184:37: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘Eigen::Index’ {aka ‘int’} [-Wsign-compare]
  184 |         for (uint32_t idiag=0; idiag<m->cols(); ++idiag){
      |                                ~~~~~^~~~~~~~~~
/usr/src/slapt-src/academic/diamond/diamond-0.9.36/src/cluster/mcl.cpp: In lambda function:
/usr/src/slapt-src/academic/diamond/diamond-0.9.36/src/cluster/mcl.cpp:412:61: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘Eigen::Index’ {aka ‘int’} [-Wsign-compare]
  412 |                                         for (uint32_t k=0; k<m_sparse.outerSize(); ++k){
      |                                                            ~^~~~~~~~~~~~~~~~~~~~~
/usr/src/slapt-src/academic/diamond/diamond-0.9.36/src/cluster/mcl.cpp:440:67: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘Eigen::Index’ {aka ‘int’} [-Wsign-compare]
  440 |                                         for (uint32_t icol=0; icol<m_dense.cols(); ++icol){
      |                                                               ~~~~^~~~~~~~~~~~~~~
/usr/src/slapt-src/academic/diamond/diamond-0.9.36/src/cluster/mcl.cpp:441:75: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘Eigen::Index’ {aka ‘int’} [-Wsign-compare]
  441 |                                                 for (uint32_t irow=0; irow<m_dense.rows(); ++irow){
      |                                                                       ~~~~^~~~~~~~~~~~~~~
At global scope:
cc1plus: note: unrecognized command-line option ‘-Wno-unknown-warning-option’ may have been intended to silence earlier diagnostics
[ 91%] Building CXX object CMakeFiles/diamond.dir/src/align/output.cpp.o
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[100%] Linking CXX executable diamond
[100%] Built target diamond
Consolidate compiler generated dependencies of target arch_avx2
[  8%] Built target arch_avx2
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[ 17%] Built target arch_generic
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[ 25%] Built target arch_sse4_1
Consolidate compiler generated dependencies of target diamond
[100%] Built target diamond
Install the project...
-- Install configuration: "Release"
-- Installing: /usr/src/slapt-src/academic/diamond/package-diamond/usr/bin/diamond

Slackware package maker, version 3.14159265.

Searching for symbolic links:

No symbolic links were found, so we won't make an installation script.
You can make your own later in ./install/doinst.sh and rebuild the
package if you like.

This next step is optional - you can set the directories in your package
to some sane permissions. If any of the directories in your package have
special permissions, then DO NOT reset them here!

Would you like to reset all directory permissions to 755 (drwxr-xr-x) and
directory ownerships to root.root ([y]es, [n]o)? n

Creating Slackware package:  /usr/src/slapt-src/academic/diamond/diamond-0.9.36-i586-1salix15.0.txz

./
install/
install/slack-desc
usr/
usr/bin/
usr/bin/diamond
usr/doc/
usr/doc/diamond-0.9.36/
usr/doc/diamond-0.9.36/ChangeLog
usr/doc/diamond-0.9.36/LICENSE
usr/doc/diamond-0.9.36/README.md
usr/doc/diamond-0.9.36/References
usr/doc/diamond-0.9.36/diamond.SlackBuild

Slackware package /usr/src/slapt-src/academic/diamond/diamond-0.9.36-i586-1salix15.0.txz created.

Installing package diamond-0.9.36-i586-1salix15.0...
| diamond (A sequence aligner for protein and translated DNA)
| 
| DIAMOND is a sequence aligner for protein and translated DNA
| searches, designed for high performance analysis of big sequence
| data. The key features are:
| 
| 1) 500x-20,000x speed of BLAST
| 2) Frameshift alignments for long read analysis.
| 3) Low resource requirements
| 4) Various output formats
| 
| 
|