rohanmaddamsetti
commented
7 months ago just an update-- still haven't gotten themisto to install on my mac laptop, but I did get the themisto binary installed on our compute cluster. so will probably just work with that.
But here's the progress I made to get themisto working on my laptop--
changing rust versions didn't help, so I went back to nightly Rust as default: $ rustc --version rustc 1.79.0-nightly (88c2f4f5f 2024-04-02)
Then, I went into the ggcat directory, and ran the following to update rust dependencies: $ cargo update --recursive -v --color always
I then went into the build directory, and ran the following: cmake -DCMAKE_C_COMPILER=$(which gcc-13) -DCMAKE_CXX_COMPILER=$(which g++-13) -DMAX_KMER_LENGTH=31 ..
(I installed gcc with homebrew on mac-- gcc links to clang and g++ links to clang++, so to avoid breaking things, homebrew installs gcc as gcc-13 and g++ as g++-13, where 13 is the current version number)
I then ran make. I no longer get the "stdsimd" error, but get some other errors.
Here is the full output I get from running these steps-- my apologies if this is overwhelming and not helpful... it does look like I can get themisto working on our cluster, but it would be nice if I can get it working on my mac laptop too!
$ themisto % cd ggcat
$ ggcat % cargo update --recursive -v --color always
Updating crates.io index
Updating addr2line v0.20.0 -> v0.21.0
Updating ahash v0.8.3 -> v0.8.11
Updating aho-corasick v1.0.2 -> v1.1.3
Unchanged anes v0.1.6 (latest: v0.2.0)
Updating anstream v0.3.2 -> v0.6.13
Updating anstyle v1.0.1 -> v1.0.6
Updating anstyle-parse v0.2.1 -> v0.2.3
Updating anstyle-query v1.0.0 -> v1.0.2
Updating anstyle-wincon v1.0.1 -> v3.0.2
Updating anyhow v1.0.71 -> v1.0.81
Updating autocfg v1.1.0 -> v1.2.0
Updating backtrace v0.3.68 -> v0.3.71
Unchanged bigraph v2.1.1 (latest: v5.0.0)
Updating bio v1.3.1 -> v1.6.0
Updating bio-types v1.0.0 -> v1.0.1
Updating bitflags v2.3.3 -> v2.5.0
Unchanged bitflags v1.3.2 (latest: v2.5.0)
Updating bstr v1.5.0 -> v1.9.1
Updating bumpalo v3.13.0 -> v3.15.4
Updating bytecount v0.6.3 -> v0.6.7
Updating bytemuck v1.13.1 -> v1.15.0
Updating byteorder v1.4.3 -> v1.5.0
Updating bytesize v1.2.0 -> v1.3.0
Updating cc v1.0.79 -> v1.0.90
Updating chrono v0.4.26 -> v0.4.37
Updating ciborium v0.2.1 -> v0.2.2
Updating ciborium-io v0.2.1 -> v0.2.2
Updating ciborium-ll v0.2.1 -> v0.2.2
Updating clap v4.3.10 -> v4.5.4
Unchanged clap v2.34.0 (latest: v4.5.4)
Unchanged clap v3.2.25 (latest: v4.5.4)
Updating clap_builder v4.3.10 -> v4.5.2
Updating clap_derive v4.3.2 -> v4.5.4
Updating clap_lex v0.5.0 -> v0.7.0
Unchanged clap_lex v0.2.4 (latest: v0.7.0)
Updating cloudflare-zlib-sys v0.3.0 -> v0.3.3
Removing cmake v0.1.50
Unchanged compact-genome v1.3.1 (latest: v2.1.1)
Updating core-foundation v0.9.3 -> v0.9.4
Updating core-foundation-sys v0.8.4 -> v0.8.6
Unchanged core-graphics v0.22.3 (latest: v0.23.1)
Updating core-graphics-types v0.1.2 -> v0.1.3
Unchanged core-text v19.2.0 (latest: v20.1.0)
Updating crc32fast v1.3.2 -> v1.4.0
Unchanged criterion v0.4.0 (latest: v0.5.1)
Updating crossbeam v0.8.2 -> v0.8.4
Updating crossbeam-channel v0.5.8 -> v0.5.12
Updating crossbeam-deque v0.8.3 -> v0.8.5
Updating crossbeam-epoch v0.9.15 -> v0.9.18
Updating crossbeam-queue v0.3.8 -> v0.3.11
Updating crossbeam-utils v0.8.16 -> v0.8.19
Adding crunchy v0.2.2
Updating csv v1.2.2 -> v1.3.0
Updating csv-core v0.1.10 -> v0.1.11
Updating cxx v1.0.97 -> v1.0.120
Updating cxx-build v1.0.97 -> v1.0.120
Updating cxxbridge-flags v1.0.97 -> v1.0.120
Updating cxxbridge-macro v1.0.97 -> v1.0.120
Updating dashmap v5.4.0 -> v5.5.3
Adding deranged v0.3.11
Unchanged derive-new v0.5.9 (latest: v0.6.0)
Updating either v1.8.1 -> v1.10.0
Updating enum-map v1.1.1 -> v2.7.3
Updating enum-map-derive v0.6.0 -> v0.17.0
Adding equivalent v1.0.1
Updating errno v0.3.1 -> v0.3.8
Removing errno-dragonfly v0.1.2
Updating fdeflate v0.3.0 -> v0.3.4
Unchanged fdlimit v0.2.1 (latest: v0.3.0)
Unchanged fixedbitset v0.4.2 (latest: v0.5.6)
Updating flate2 v1.0.26 -> v1.0.28
Unchanged float-ord v0.2.0 (latest: v0.3.2)
Unchanged font-kit v0.11.0 (latest: v0.13.0)
Unchanged foreign-types v0.3.2 (latest: v0.5.0)
Unchanged foreign-types-shared v0.1.1 (latest: v0.3.1)
Updating freetype v0.7.0 -> v0.7.1
Updating freetype-sys v0.13.1 -> v0.19.0 (latest: v0.20.0)
Updating futures-core v0.3.28 -> v0.3.30
Unchanged genome-graph v5.2.0 (latest: v8.0.0)
Updating getrandom v0.2.10 -> v0.2.12
Removing getset v0.1.2
Unchanged gif v0.12.0 (latest: v0.13.1)
Updating gimli v0.27.3 -> v0.28.1
Updating half v1.8.2 -> v2.4.0
Adding hashbrown v0.14.3
Unchanged hashbrown v0.12.3 (latest: v0.14.3)
Unchanged hashbrown v0.13.2 (latest: v0.14.3)
Adding heck v0.5.0
Unchanged heck v0.3.3 (latest: v0.5.0)
Unchanged heck v0.4.1 (latest: v0.5.0)
Updating hermit-abi v0.3.2 -> v0.3.9
Unchanged hermit-abi v0.1.19 (latest: v0.3.9)
Updating human_format v1.0.3 -> v1.1.0
Updating iana-time-zone v0.1.57 -> v0.1.60
Updating image v0.24.6 -> v0.24.9 (latest: v0.25.1)
Adding indexmap v2.2.6
Unchanged indexmap v1.9.3 (latest: v2.2.6)
Unchanged io-lifetimes v1.0.11 (latest: v2.0.3)
Removing is-terminal v0.4.8
Unchanged itertools v0.10.5 (latest: v0.12.1)
Unchanged itertools v0.11.0 (latest: v0.12.1)
Updating itoa v1.0.8 -> v1.0.11
Updating jpeg-decoder v0.3.0 -> v0.3.1
Updating js-sys v0.3.64 -> v0.3.69
Updating libc v0.2.147 -> v0.2.153
Updating libloading v0.8.0 -> v0.8.3
Updating libm v0.2.7 -> v0.2.8
Adding libredox v0.1.3
Removing linux-raw-sys v0.4.3
Unchanged linux-raw-sys v0.1.4 (latest: v0.6.4)
Updating lock_api v0.4.10 -> v0.4.11
Updating log v0.4.19 -> v0.4.21
Unchanged matchtigs v1.7.0 (latest: v2.1.6)
Updating matrixmultiply v0.3.7 -> v0.3.8
Updating memchr v2.5.0 -> v2.7.2
Removing memoffset v0.9.0
Updating miniz_oxide v0.7.1 -> v0.7.2
Updating multimap v0.8.3 -> v0.9.1 (latest: v0.10.0)
Unchanged nalgebra v0.29.0 (latest: v0.32.5)
Unchanged nalgebra-macros v0.1.0 (latest: v0.2.1)
Updating num-complex v0.4.3 -> v0.4.5
Adding num-conv v0.1.0
Updating num-integer v0.1.45 -> v0.1.46
Updating num-traits v0.2.15 -> v0.2.18
Updating num_threads v0.1.6 -> v0.1.7
Updating object v0.31.1 -> v0.32.2 (latest: v0.34.0)
Updating once_cell v1.18.0 -> v1.19.0
Updating ordered-float v3.7.0 -> v3.9.2 (latest: v4.2.0)
Updating os_str_bytes v6.5.1 -> v6.6.1 (latest: v7.0.0)
Updating parking_lot_core v0.9.8 -> v0.9.9
Updating paste v1.0.13 -> v1.0.14
Updating pathfinder_simd v0.5.1 -> v0.5.2
Removing pest v2.7.0
Updating petgraph v0.6.3 -> v0.6.4
Updating pin-project-lite v0.2.10 -> v0.2.14
Updating pkg-config v0.3.27 -> v0.3.30
Updating png v0.17.9 -> v0.17.13
Adding powerfmt v0.2.0
Updating proc-macro2 v1.0.63 -> v1.0.79
Unchanged proc-macro2 v0.4.30 (latest: v1.0.79)
Unchanged procfs v0.15.1 (latest: v0.16.0)
Updating quote v1.0.29 -> v1.0.35
Unchanged quote v0.6.13 (latest: v1.0.35)
Unchanged radium v0.7.0 (latest: v1.1.0)
Updating rayon v1.7.0 -> v1.10.0
Updating rayon-core v1.11.0 -> v1.12.1
Removing redox_syscall v0.2.16
Removing redox_syscall v0.3.5
Adding redox_syscall v0.4.1 (latest: v0.5.1)
Updating redox_users v0.4.3 -> v0.4.5
Updating ref-cast v1.0.18 -> v1.0.22
Updating ref-cast-impl v1.0.18 -> v1.0.22
Updating regex v1.8.4 -> v1.10.4
Updating regex-automata v0.1.10 -> v0.4.6
Updating regex-syntax v0.7.2 -> v0.8.3
Removing retain_mut v0.1.7
Updating roaring v0.10.1 -> v0.10.3
Updating rustc_version v0.3.3 -> v0.4.0
Unchanged rustc_version v0.1.7 (latest: v0.4.0)
Removing rustix v0.36.14
Removing rustix v0.38.2
Adding rustix v0.36.17 (latest: v0.38.32)
Updating rustversion v1.0.13 -> v1.0.14
Updating ryu v1.0.14 -> v1.0.17
Updating safe_arch v0.7.0 -> v0.7.1
Updating scopeguard v1.1.0 -> v1.2.0
Updating scratch v1.0.5 -> v1.0.7
Updating semver v0.11.0 -> v1.0.22
Unchanged semver v0.1.20 (latest: v1.0.22)
Removing semver-parser v0.10.2
Updating serde v1.0.166 -> v1.0.197
Updating serde_derive v1.0.166 -> v1.0.197
Updating serde_json v1.0.100 -> v1.0.115
Unchanged simba v0.6.0 (latest: v0.8.1)
Updating simd-adler32 v0.3.5 -> v0.3.7
Updating simplelog v0.12.1 -> v0.12.2
Updating siphasher v0.3.10 -> v0.3.11 (latest: v1.0.1)
Updating smallvec v1.10.0 -> v1.13.2
Updating strsim v0.10.0 -> v0.11.1
Unchanged strsim v0.8.0 (latest: v0.11.1)
Unchanged strum v0.25.0 (latest: v0.26.2)
Removing strum_macros v0.24.3
Removing strum_macros v0.25.1
Adding strum_macros v0.25.3 (latest: v0.26.2)
Updating syn v2.0.23 -> v2.0.58
Unchanged syn v0.15.44 (latest: v2.0.58)
Unchanged syn v1.0.109 (latest: v2.0.58)
Updating termcolor v1.1.3 -> v1.4.1
Updating textwrap v0.16.0 -> v0.16.1
Unchanged textwrap v0.11.0 (latest: v0.16.1)
Updating thiserror v1.0.41 -> v1.0.58
Updating thiserror-impl v1.0.41 -> v1.0.58
Updating thread_local v1.1.7 -> v1.1.8
Removing time v0.1.45
Removing time v0.3.22
Adding time v0.3.34
Updating time-core v0.1.1 -> v0.1.2
Updating time-macros v0.2.9 -> v0.2.17
Updating tokio v1.29.1 -> v1.37.0
Updating tokio-macros v2.1.0 -> v2.2.0
Updating tokio-stream v0.1.14 -> v0.1.15
Updating tracing v0.1.37 -> v0.1.40
Updating tracing-attributes v0.1.26 -> v0.1.27
Updating tracing-core v0.1.31 -> v0.1.32
Unchanged traitgraph v2.2.0 (latest: v5.0.0)
Unchanged traitgraph-algo v5.4.0 (latest: v8.1.0)
Unchanged traitsequence v1.1.0 (latest: v2.0.0)
Unchanged ttf-parser v0.17.1 (latest: v0.20.0)
Updating typenum v1.16.0 -> v1.17.0
Removing ucd-trie v0.1.5
Updating unicode-ident v1.0.10 -> v1.0.12
Updating unicode-segmentation v1.10.1 -> v1.11.0
Updating unicode-width v0.1.10 -> v0.1.11
Unchanged unicode-xid v0.1.0 (latest: v0.2.4)
Updating uuid v1.4.0 -> v1.8.0
Updating walkdir v2.3.3 -> v2.5.0
Removing wasi v0.10.0+wasi-snapshot-preview1
Unchanged wasi v0.11.0+wasi-snapshot-preview1 (latest: v0.13.0+wasi-0.2.0)
Updating wasm-bindgen v0.2.87 -> v0.2.92
Updating wasm-bindgen-backend v0.2.87 -> v0.2.92
Updating wasm-bindgen-macro v0.2.87 -> v0.2.92
Updating wasm-bindgen-macro-support v0.2.87 -> v0.2.92
Updating wasm-bindgen-shared v0.2.87 -> v0.2.92
Updating web-sys v0.3.64 -> v0.3.69
Updating weezl v0.1.7 -> v0.1.8
Updating wide v0.7.10 -> v0.7.15
Updating winapi-util v0.1.5 -> v0.1.6
Removing windows v0.48.0
Adding windows-core v0.52.0 (latest: v0.55.0)
Adding windows-sys v0.52.0
Unchanged windows-sys v0.45.0 (latest: v0.52.0)
Unchanged windows-sys v0.48.0 (latest: v0.52.0)
Removing windows-targets v0.48.1
Adding windows-targets v0.48.5 (latest: v0.52.4)
Adding windows-targets v0.52.4
Unchanged windows-targets v0.42.2 (latest: v0.52.4)
Removing windows_aarch64_gnullvm v0.48.0
Adding windows_aarch64_gnullvm v0.48.5 (latest: v0.52.4)
Adding windows_aarch64_gnullvm v0.52.4
Unchanged windows_aarch64_gnullvm v0.42.2 (latest: v0.52.4)
Removing windows_aarch64_msvc v0.48.0
Adding windows_aarch64_msvc v0.48.5 (latest: v0.52.4)
Adding windows_aarch64_msvc v0.52.4
Unchanged windows_aarch64_msvc v0.42.2 (latest: v0.52.4)
Removing windows_i686_gnu v0.48.0
Adding windows_i686_gnu v0.48.5 (latest: v0.52.4)
Adding windows_i686_gnu v0.52.4
Unchanged windows_i686_gnu v0.42.2 (latest: v0.52.4)
Removing windows_i686_msvc v0.48.0
Adding windows_i686_msvc v0.48.5 (latest: v0.52.4)
Adding windows_i686_msvc v0.52.4
Unchanged windows_i686_msvc v0.42.2 (latest: v0.52.4)
Removing windows_x86_64_gnu v0.48.0
Adding windows_x86_64_gnu v0.48.5 (latest: v0.52.4)
Adding windows_x86_64_gnu v0.52.4
Unchanged windows_x86_64_gnu v0.42.2 (latest: v0.52.4)
Removing windows_x86_64_gnullvm v0.48.0
Adding windows_x86_64_gnullvm v0.48.5 (latest: v0.52.4)
Adding windows_x86_64_gnullvm v0.52.4
Unchanged windows_x86_64_gnullvm v0.42.2 (latest: v0.52.4)
Removing windows_x86_64_msvc v0.48.0
Adding windows_x86_64_msvc v0.48.5 (latest: v0.52.4)
Adding windows_x86_64_msvc v0.52.4
Unchanged windows_x86_64_msvc v0.42.2 (latest: v0.52.4)
Unchanged wyz v0.5.1 (latest: v0.6.1)
Unchanged yeslogic-fontconfig-sys v3.2.0 (latest: v5.0.0)
Adding zerocopy v0.7.32
Adding zerocopy-derive v0.7.32
note: to see how you depend on a package, run cargo tree --invert --package <dep>@<ver>
$ ggcat % cd ..
$ themisto % ls
CMakeLists.txt LICENSE.txt build googletest src version.h.in
CMakeLists_zlib.txt.in README.md example_input include testcases zstr
Dockerfile SBWT ggcat integration_tests tests
(cobra) rohan@HAL9000 themisto % cd build
(cobra) rohan@HAL9000 build % cmake -DCMAKE_C_COMPILER=$(which gcc-13) -DCMAKE_CXX_COMPILER=$(which g++-13) -DMAX_KMER_LENGTH=31 ..
-- The C compiler identification is GNU 13.2.0
-- The CXX compiler identification is GNU 13.2.0
-- Checking whether C compiler has -isysroot
-- Checking whether C compiler has -isysroot - yes
-- Checking whether C compiler supports OSX deployment target flag
-- Checking whether C compiler supports OSX deployment target flag - yes
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /opt/homebrew/bin/gcc-13 - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Checking whether CXX compiler has -isysroot
-- Checking whether CXX compiler has -isysroot - yes
-- Checking whether CXX compiler supports OSX deployment target flag
-- Checking whether CXX compiler supports OSX deployment target flag - yes
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /opt/homebrew/bin/g++-13 - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Maximum k-mer length is: 31
-- To change the maximum k-mer length, use the option -DMAX_KMER_LENGTH=n
-- (n can be up to 255)
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success
-- Found Threads: TRUE
-- Found OpenMP_C: -fopenmp (found version "4.5")
-- Found OpenMP_CXX: -fopenmp (found version "4.5")
-- Found OpenMP: TRUE (found version "4.5")
-- Found Git: /usr/bin/git (found version "2.39.3 (Apple Git-145)")
-- Submodule update
-- Themisto version: v3.2.1-3-ge7e8a8c
-- Submodule update
-- SBWT version: v3.2.1-3-ge7e8a8c
-- Maximum k-mer length is: 31
-- To change the maximum k-mer length, use the option -DMAX_KMER_LENGTH=n
-- (n can be up to 255)
CMake Deprecation Warning at SBWT/sdsl-lite/CMakeLists.txt:1 (cmake_minimum_required):
Compatibility with CMake < 3.5 will be removed from a future version of
CMake.
Update the VERSION argument
-- Compiler is recent enough to support C++14. -- Performing Test HAVE_GCC_STD=C14WALLWEXTRADNDEBUG -- Performing Test HAVE_GCC_STD=C14WALLWEXTRADNDEBUG - Success -- Performing Test HAVE_GCC_O3FFAST_MATH__FUNROLL_LOOPS -- Performing Test HAVE_GCC_O3FFAST_MATH__FUNROLL_LOOPS - Success -- Performing Test HAVE_CXA_DEMANGLE -- Performing Test HAVE_CXA_DEMANGLE - Success -- Compiler supports DEMANGLE. -- Performing Test HAVE_GCC_DHAVE_CXA_DEMANGLE -- Performing Test HAVE_GCC_DHAVE_CXA_DEMANGLE - Success git found: /usr/bin/git CMake Deprecation Warning at SBWT/sdsl-lite/external/libdivsufsort/CMakeLists.txt:2 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake.
Update the VERSION argument
CMake Warning (dev) at SBWT/sdsl-lite/external/libdivsufsort/CMakeLists.txt:7 (project): Policy CMP0048 is not set: project() command manages VERSION variables. Run "cmake --help-policy CMP0048" for policy details. Use the cmake_policy command to set the policy and suppress this warning.
The following variable(s) would be set to empty:
PROJECT_VERSION
PROJECT_VERSION_MAJOR
PROJECT_VERSION_MINOR
PROJECT_VERSION_PATCHThis warning is for project developers. Use -Wno-dev to suppress it.
-- Performing Test HAVE_GCC_WALL -- Performing Test HAVE_GCC_WALL - Success -- Performing Test HAVE_GCC_FOMIT_FRAME_POINTER -- Performing Test HAVE_GCC_FOMIT_FRAME_POINTER - Success -- Looking for inttypes.h -- Looking for inttypes.h - found -- Looking for memory.h -- Looking for memory.h - found -- Looking for stddef.h -- Looking for stddef.h - found -- Looking for stdint.h -- Looking for stdint.h - found -- Looking for stdlib.h -- Looking for stdlib.h - found -- Looking for string.h -- Looking for string.h - found -- Looking for strings.h -- Looking for strings.h - found -- Looking for sys/types.h -- Looking for sys/types.h - found -- Performing Test HAVE_INLINE -- Performing Test HAVE_INLINE - Success -- Performing Test HAVEINLINE -- Performing Test HAVEINLINE - Success -- Performing Test HAVE_INLINE_ -- Performing Test HAVEINLINE - Success -- Performing Test HAVE___DECLSPECDLLEXPORT -- Performing Test HAVE_DECLSPECDLLEXPORT - Failed -- Performing Test HAVE_DECLSPECDLLIMPORT -- Performing Test HAVE_DECLSPECDLLIMPORT - Failed -- Check size of uint8_t -- Check size of uint8_t - done -- Check size of int32_t -- Check size of int32_t - done -- Looking for PRId32 -- Looking for PRId32 - found -- Check size of int64_t -- Check size of int64_t - done -- Looking for PRId64 -- Looking for PRId64 - found -- Looking for C++ include cstdio -- Looking for C++ include cstdio - found -- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE) CMake Deprecation Warning at SBWT/KMC/CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake.
Update the VERSION argument
-- Submodule update -- Found ZLIB: /Library/Developer/CommandLineTools/SDKs/MacOSX14.2.sdk/usr/lib/libz.tbd (found version "1.2.12") CMake Deprecation Warning at build/_deps/roaring-src/CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake.
Update the VERSION argument
CMake Deprecation Warning at build/_deps/roaring-src/tools/cmake/FindCTargets.cmake:2 (cmake_policy): Compatibility with CMake < 3.5 will be removed from a future version of CMake.
Update the VERSION argument
| -- BENCHMARK_DATA_DIR: /Users/rohan/Bioinformatics/themisto/build/_deps/roaring-src/benchmarks/realdata/
-- TEST_DATA_DIR: /Users/rohan/Bioinformatics/themisto/build/_deps/roaring-src/tests/testdata/
-- Building a static library.
-- ROARING_LIB_TYPE: STATIC
-- Library output directory (does not apply to Visual Studio): /Users/rohan/Bioinformatics/themisto/build
-- CMAKE_SYSTEM_PROCESSOR: arm64
-- CMAKE_BUILD_TYPE: Release
-- ROARING_DISABLE_X64: OFF
-- ROARING_DISABLE_AVX: ON
-- ROARING_DISABLE_NEON: OFF
-- ROARING_DISABLE_NATIVE: ON
-- ROARING_ARCH: native
-- ROARING_BUILD_STATIC: ON
-- ROARING_LINK_STATIC: OFF
-- ROARING_BUILD_LTO: OFF
-- ROARING_SANITIZE: OFF
-- CMAKE_C_COMPILER: /opt/homebrew/bin/gcc-13
-- CMAKE_C_FLAGS: -std=c11 -fPIC -DDISABLEAVX -Wall -Wextra -Wsign-compare -Wshadow -Wwrite-strings -Wpointer-arith -Winit-self -- CMAKE_C_FLAGS_DEBUG: -ggdb -- CMAKE_C_FLAGS_RELEASE: -O3 -- Configuring done (11.8s) -- Generating done (0.1s) -- Build files have been written to: /Users/rohan/Bioinformatics/themisto/build $ build % make [ 0%] Building C object _deps/roaring-build/src/CMakeFiles/roaring.dir/array_util.c.o [ 1%] Building C object _deps/roaring-build/src/CMakeFiles/roaring.dir/bitset_util.c.o [ 2%] Building C object _deps/roaring-build/src/CMakeFiles/roaring.dir/containers/array.c.o /Users/rohan/Bioinformatics/themisto/build/_deps/roaring-src/src/containers/array.c: In function 'array_container_shrink_to_fit': /Users/rohan/Bioinformatics/themisto/build/_deps/roaring-src/src/containers/array.c:90:31: warning: pointer 'oldarray' may be used after 'realloc' [-Wuse-after-free] 90 |
if (src->array == NULL) free(oldarray); // should never happen? | ^ |
(uint16_t )realloc(oldarray, src->capacity sizeof(uint16_t)); | ^ |
if (container->array == NULL) free(array); | ^ |
(uint16_t )realloc(array, new_capacity sizeof(uint16_t)); | ^ |
if (src->runs == NULL) free(oldruns); // should never happen? | ^ |
src->runs = (rle16_t )realloc(oldruns, src->capacity sizeof(rle16_t)); | ^ |
if (run->runs == NULL) free(oldruns); | ^ |
(rle16_t )realloc(oldruns, run->capacity sizeof(rle16_t)); | ^RwLockIterator is never constructed
--> libs-crates/parallel-processor-rs/src/memory_fs/file/internal.rs:43:8 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 43 | struct RwLockIterator<'a, A, B, I: Iterator |
|||||||||||||||
| ^^^^^^^^^^^^^^ | ||||||||||||||||
= note: #[warn(dead_code)] on by default
warning: call to .deref() on a reference in this situation does nothing
--> libs-crates/parallel-processor-rs/src/memory_fs/file/writer.rs:57:60 |
57 | ... file_read.get_underlying_file().deref() | ^^^^^^^^ |
|---|
= note: the type UnderlyingFile does not implement Deref, so calling deref on &UnderlyingFile copies the reference, which does not do anything and can be removed
= note: #[warn(noop_method_call)] on by default
help: remove this redundant call |
57 - file_read.get_underlying_file().deref() 57 + file_read.get_underlying_file() |
|---|
help: if you meant to clone UnderlyingFile, implement Clone for it
--> libs-crates/parallel-processor-rs/src/memory_fs/file/internal.rs:107:1 |
107+ #[derive(Clone)] 108 | pub enum UnderlyingFile { |
|---|
warning: call to .deref() on a reference in this situation does nothing
--> libs-crates/parallel-processor-rs/src/execution_manager/execution_context.rs:212:22 |
212 | .unwrap() | __^ 213 | .deref() | ____^ |
|---|
= note: the type `PacketsPoolStrategy<E>` does not implement `Deref`, so calling `deref` on `&PacketsPoolStrategy<E>` copies the reference, which does not do anything and can be removed| help: remove this redundant call | 212 - .unwrap() 213 - .deref() 212 + .unwrap() |
|---|
help: if you meant to clone PacketsPoolStrategy<E>, implement Clone for it |
27 + #[derive(Clone)] 28 | pub(crate) enum PacketsPoolStrategy |
|---|
Compiling approx v0.5.1
Compiling csv-core v0.1.11
Compiling dynamic-dispatch-proc-macro v0.4.2 (/Users/rohan/Bioinformatics/themisto/ggcat/libs-crates/dynamic-dispatch-rs/dynamic-dispatch-proc-macro)
Compiling ggcat_config v0.1.0 (/Users/rohan/Bioinformatics/themisto/ggcat/crates/config)
Compiling ggcat_utils v0.1.0 (/Users/rohan/Bioinformatics/themisto/ggcat/crates/utils)
Compiling traitsequence v1.1.0
Compiling radium v0.7.0
Compiling feature-probe v0.1.1
Compiling structopt v0.3.26
Compiling dynamic-dispatch v0.4.3 (/Users/rohan/Bioinformatics/themisto/ggcat/libs-crates/dynamic-dispatch-rs)
Compiling streaming-libdeflate-rs v0.1.5 (/Users/rohan/Bioinformatics/themisto/ggcat/libs-crates/streaming-libdeflate-rs)
Compiling ggcat_hashes v0.1.0 (/Users/rohan/Bioinformatics/themisto/ggcat/crates/hashes)
Compiling bv v0.11.1
Compiling simba v0.6.0
Compiling ggcat_structs v0.1.0 (/Users/rohan/Bioinformatics/themisto/ggcat/crates/structs)
Compiling csv v1.3.0
Compiling ggcat_io v0.1.0 (/Users/rohan/Bioinformatics/themisto/ggcat/crates/io)
warning: the item FromIterator is imported redundantly
--> crates/io/src/compressed_read.rs:5:5 |
5 | use std::iter::FromIterator; | ^^^^^^^^^^^^^^^^^^^^^^^ --> /rustc/88c2f4f5f50ace5ddc7655ea311435104d3659bd/library/std/src/prelude/mod.rs:148:13 |
|---|
= note: the item FromIterator is already defined here
|
= note: #[warn(unused_imports)] on by default
Compiling newtype_derive v0.1.6
Compiling roaring v0.10.3
Compiling ggcat_minimizer_bucketing v0.1.0 (/Users/rohan/Bioinformatics/themisto/ggcat/crates/minimizer_bucketing)
Compiling nalgebra-macros v0.1.0
Compiling rand_distr v0.4.3
warning: ggcat_io (lib) generated 1 warning
Compiling atoi v2.0.0
Compiling thread_local v1.1.8
Compiling anyhow v1.0.81
Compiling tap v1.0.1
Compiling bitvector v0.1.5
Compiling siphasher v0.3.11
Compiling ref-cast v1.0.22
Compiling heck v0.4.1
Compiling utf8parse v0.2.1
Compiling instrumenter-proc-macro v0.1.1 (/Users/rohan/Bioinformatics/themisto/ggcat/libs-crates/instrumenter-rs/instrumenter-proc-macro-rs)
Compiling anstyle-parse v0.2.3
Compiling strum_macros v0.25.3
Compiling instrumenter v0.1.2 (/Users/rohan/Bioinformatics/themisto/ggcat/libs-crates/instrumenter-rs)
Compiling ggcat_colors v0.1.0 (/Users/rohan/Bioinformatics/themisto/ggcat/crates/colors)
Compiling traitgraph v2.2.0
warning: creating a mutable reference to mutable static is discouraged
--> crates/colors/src/storage/run_length.rs:135:52 |
135 | ColorIndexSerializer::serialize_colors(&mut TEMP_COLOR_BUFFER, colors); | ^^^^^^^^^^^^^^^^^^^^^^ mutable reference to mutable static |
|---|
= note: for more information, see issue #114447 <https://github.com/rust-lang/rust/issues/114447>
= note: this will be a hard error in the 2024 edition
= note: this mutable reference has lifetime `'static`, but if the static gets accessed (read or written) by any other means, or any other reference is created, then any further use of this mutable reference is Undefined Behavior
= note: `#[warn(static_mut_refs)]` on by defaulthelp: use addr_of_mut! instead to create a raw pointer
|
135 | ColorIndexSerializer::serialize_colors(addr_of_mut!(TEMP_COLOR_BUFFER), colors);
| ~~~~~~~
Compiling wyz v0.5.1
Compiling enum-map-derive v0.17.0
Compiling ref-cast-impl v1.0.22
Compiling derive-new v0.5.9
Compiling error-chain v0.12.4
Compiling anstyle v1.0.6
Compiling powerfmt v0.2.0
Compiling colorchoice v1.0.0
Compiling time-core v0.1.2
Compiling anstyle-query v1.0.2
Compiling num-conv v0.1.0
Compiling bit-vec v0.6.3
Compiling funty v2.0.0
Compiling time-macros v0.2.17
Compiling bit-set v0.5.3
Compiling anstream v0.6.13
Compiling bitvec v1.0.1
Compiling nalgebra v0.29.0
Compiling deranged v0.3.11
Compiling bio-types v1.0.1
Compiling enum-map v2.7.3
warning: ggcat_colors (lib) generated 1 warning
Compiling traitgraph-algo v5.4.0
Compiling ggcat_kmers_transform v0.1.0 (/Users/rohan/Bioinformatics/themisto/ggcat/crates/kmers_transform)
Compiling ndarray v0.15.6
warning: parallel-processor (lib) generated 3 warnings (run cargo fix --lib -p parallel-processor to apply 2 suggestions)
Compiling multimap v0.9.1
Compiling fxhash v0.2.1
Compiling itertools-num v0.1.3
Compiling ordered-float v3.9.2
Compiling num_threads v0.1.7
Compiling itertools v0.11.0
Compiling link-cplusplus v1.0.9
Compiling strsim v0.11.1
Compiling editdistancek v1.0.2
Compiling scratch v1.0.7
Compiling log v0.4.21
Compiling custom_derive v0.1.7
Compiling strum v0.25.0
Compiling heck v0.5.0
Compiling bytecount v0.6.7
Compiling triple_accel v0.4.0
Compiling clap_lex v0.7.0
Compiling clap_derive v4.5.4
Compiling time v0.3.34
Compiling clap_builder v4.5.2
Compiling compact-genome v1.3.1
Compiling bigraph v2.1.1
Compiling termcolor v1.4.1
Compiling cxxbridge-flags v1.0.120
Compiling disjoint-sets v0.4.2
Compiling codespan-reporting v0.11.1
Compiling simplelog v0.12.2
Compiling cxx v1.0.120
Compiling ggcat_assembler_minimizer_bucketing v0.1.0 (/Users/rohan/Bioinformatics/themisto/ggcat/crates/assembler_minimizer_bucketing)
Compiling memory-stats v1.1.0
Compiling permutation v0.4.1
Compiling atomic-counter v1.0.1
Compiling cxx-build v1.0.120
Compiling ggcat_assembler_kmers_merge v0.1.0 (/Users/rohan/Bioinformatics/themisto/ggcat/crates/assembler_kmers_merge)
Compiling clap v4.5.4
Compiling fs_extra v1.3.0
Compiling ggcat_dumper v0.1.1 (/Users/rohan/Bioinformatics/themisto/ggcat/crates/dumper)
warning: the feature slice_group_by has been stable since 1.77.0 and no longer requires an attribute to enable
--> crates/dumper/src/lib.rs:1:12 |
1 | #![feature(slice_group_by)] | ^^^^^^^^^^^^^^ |
|---|
= note: #[warn(stable_features)] on by default
Compiling ggcat_querier v0.1.1 (/Users/rohan/Bioinformatics/themisto/ggcat/crates/querier)
error[E0599]: no method named group_by_mut found for struct Vec<(CompressedReadIndipendent, DumperKmersReferenceData<u32>)> in the current scope
--> crates/dumper/src/pipeline/dumper_colormap_reading.rs:99:48
|
99 | for unitigs_by_color in temp_sequences.group_by_mut(|a, b| a.1 == b.1) {
| ^^^^^^^^^^^^ method not found in Vec<(CompressedReadIndipendent, DumperKmersReferenceData<u32>)>
For more information about this error, try rustc --explain E0599.
warning: ggcat_dumper (lib) generated 1 warning
error: could not compile ggcat_dumper (lib) due to 1 previous error; 1 warning emitted
warning: build failed, waiting for other jobs to finish...
warning: the feature slice_group_by has been stable since 1.77.0 and no longer requires an attribute to enable
--> crates/querier/src/lib.rs:1:12 |
1 | #![feature(slice_group_by)] | ^^^^^^^^^^^^^^ |
|---|
= note: #[warn(stable_features)] on by default
error[E0599]: no method named group_by found for struct Vec<(u32, u64)> in the current scope
--> crates/querier/src/pipeline/colored_query_output.rs:213:53
|
213 | for (i, qc) in temp_colors_list.group_by(|a, b| a.0 == b.0).enumerate() {
| ^^^^^^^^ method not found in Vec<(u32, u64)>
error[E0599]: no method named group_by_mut found for struct Vec<(CounterEntry<u32>, u32)> in the current scope
--> crates/querier/src/pipeline/colormap_reading.rs:104:46
|
104 | for queries_by_color in counters_vec.group_by_mut(|a, b| a.1 == b.1) {
| ^^^^^^^^^^^^ method not found in Vec<(CounterEntry<u32>, u32)>
error[E0609]: no field query_index on type &_
--> crates/querier/src/pipeline/colormap_reading.rs:135:64
|
135 | temp_queries_buffer.sort_unstable_by_key(|c| c.query_index);
| ^^^^^^^^^^^ unknown field
error[E0599]: no method named group_by_mut found for struct Vec<(CounterEntry<<CX as ColorsManager>::SingleKmerColorDataType>, <CX as ColorsManager>::SingleKmerColorDataType)> in the current scope
--> crates/querier/src/pipeline/counters_sorting.rs:193:43
|
193 | for query_results in counters_vec.group_by_mut(|a, b| a.0.query_index == b.0.query_index) {
| ^^^^^^^^^^^^ method not found in Vec<(CounterEntry<<CX as ColorsManager>::SingleKmerColorDataType>, <CX as ColorsManager>::SingleKmerColorDataType)>
Some errors have detailed explanations: E0599, E0609.
For more information about an error, try rustc --explain E0599.
warning: ggcat_querier (lib) generated 1 warning
error: could not compile ggcat_querier (lib) due to 4 previous errors; 1 warning emitted
make[3]: [lib/libggcat_cpp_bindings.a] Error 101
make[2]: [CMakeFiles/ggcat_cpp_api] Error 2
make[1]: [CMakeFiles/ggcat_cpp_api.dir/all] Error 2
make: [all] Error 2
jnalanko
tmaklin
iosfwd
Hello,
When I run "make" to install themisto on my mac laptop, I get the following error:
error[E0635]: unknown feature
stdsimd--> /Users/rohan/.cargo/registry/src/index.crates.io-6f17d22bba15001f/ahash-0.8.3/src/lib.rs:99:42 | 99 | #![cfg_attr(feature = "stdsimd", feature(stdsimd))] | ^^^^^^^For more information about this error, try
rustc --explain E0635. error: could not compileahash(lib) due to 1 previous error warning: build failed, waiting for other jobs to finish... make[3]: [lib/libggcat_cpp_bindings.a] Error 101 make[2]: [CMakeFiles/ggcat_cpp_api] Error 2 make[1]: [CMakeFiles/ggcat_cpp_api.dir/all] Error 2 make: [all] Error 2Based on these links, it looks like the stdsimd feature was removed from Rust on February, breaking the themisto installation: https://users.rust-lang.org/t/error-e0635-unknown-feature-stdsimd/106445 https://github.com/tkaitchuck/aHash/issues/200
following some of these discussions, hoping to find a workaround by installing a Rust version dated February 4.