tiledb: update to version 2.26.0 #25731

teo-tsirpanis · 2024-09-13T10:22:02Z

Description

This PR updates TileDB to version 2.26.0, and removes some no longer applicable patches and workarounds.

Type(s)

bugfix
enhancement
security fix

Tested on

CI on my fork

Verification

Have you

followed our Commit Message Guidelines?
squashed and minimized your commits?
checked that there aren't other open pull requests for the same change?
referenced existing tickets on Trac with full URL in commit message?
checked your Portfile with port lint --nitpick?
tried existing tests with sudo port test?
tried a full install with sudo port -vst install?
tested basic functionality of all binary files?
checked that the Portfile's most important variants haven't been broken?

macportsbot · 2024-09-13T10:22:05Z

Notifying maintainers:
@barracuda156 for port tiledb.

barracuda156

We need to:

Sort out dependencies, following changes in TileDB.
Fix patches which fail to apply now (this I will do).

barracuda156 · 2024-09-13T10:29:15Z

databases/tiledb/Portfile

-# Patch TileDB to find lz4 manually, because the lz4 package does not provide CMake configs.
-# Updating the lz4 port is blocked on lz4 releasing a new version, with some official
-# linkage-agnostic targets.
-patchfiles-append   lz4_fix.diff


Aside from the issue which I pointed out in the ticket, there are extra changes needed here, since now patches do not apply. We also need to add a dependency on libmagic from looks of things, and libpng (?).

I have already fixed patches, I will make a commit and you can pick that.

Libmagic is being obtained through the dependency on the file port, and libpng is optionally needed for some tests and there is a dependency to it in the test variant (see line 138 in the new portfile).

Ok, then only fixing the second patch is left. (libatomic one, not libmagic.)

barracuda156 · 2024-09-13T10:36:57Z

@teo-tsirpanis Please modify libmagic part however needed for it to use MacPorts one. (Notice, that is not the only required change, there are some purely technical.)

00eaf7d

teo-tsirpanis · 2024-09-13T10:53:27Z

I don't think any patches to FindLibMagic.cmake are needed anymore. I removed patching this file from patch-linking.diff.

barracuda156 · 2024-09-13T11:13:17Z

I don't think any patches to FindLibMagic.cmake are needed anymore. I removed patching this file from patch-linking.diff.

Does it find MacPorts libmagic? We rather not use vcpkg here.

P. S. databases/tiledb/files/patch-libatomic-32-bit.diff patch should be updated as well (just copy from my commit).

teo-tsirpanis · 2024-09-13T14:20:26Z

Does it find MacPorts libmagic? We rather not use vcpkg here.

Yes, vcpkg is not being used at all since #24239.

P. S. databases/tiledb/files/patch-libatomic-32-bit.diff patch should be updated as well (just copy from my commit).

Done.

barracuda156 · 2024-09-13T17:54:39Z

This should also be removed from the portfile, since that patch is gone:

    post-patch {
        reinplace "s,@PREFIX@,${prefix},g" ${worksrcpath}/cmake/Modules/FindMagic_EP.cmake
    }

UPD. @teo-tsirpanis You could just borrow this 570da65

barracuda156 · 2024-09-13T17:59:25Z

Configuring from your update, I still get all these not found during configure:

--->  Configuring tiledb
        (using ccache)
Executing:  cd "/opt/local/var/macports/build/_opt_PPCSnowLeopardPorts_databases_tiledb/tiledb/work/build" && /opt/local/bin/cmake -G "CodeBlocks - Unix Makefiles" -DCMAKE_BUILD_TYPE=MacPorts -DCMAKE_INSTALL_PREFIX="/opt/local" -DCMAKE_INSTALL_NAME_DIR="/opt/local/lib" -DCMAKE_SYSTEM_PREFIX_PATH="/opt/local;/usr" -DCMAKE_C_COMPILER_LAUNCHER=/opt/local/bin/ccache -DCMAKE_CXX_COMPILER_LAUNCHER=/opt/local/bin/ccache -DCMAKE_Fortran_COMPILER_LAUNCHER=/opt/local/bin/ccache -DCMAKE_OBJC_COMPILER_LAUNCHER=/opt/local/bin/ccache -DCMAKE_OBJCXX_COMPILER_LAUNCHER=/opt/local/bin/ccache -DCMAKE_ISPC_COMPILER_LAUNCHER=/opt/local/bin/ccache -DCMAKE_C_COMPILER="$CC" -DCMAKE_CXX_COMPILER="$CXX" -DCMAKE_OBJC_COMPILER="$CC" -DCMAKE_OBJCXX_COMPILER="$CXX" -DCMAKE_POLICY_DEFAULT_CMP0025=NEW -DCMAKE_POLICY_DEFAULT_CMP0060=NEW -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_COLOR_MAKEFILE=ON -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_EXPORT_COMPILE_COMMANDS=ON -DCMAKE_MAKE_PROGRAM=/usr/bin/make -DCMAKE_MODULE_PATH="/opt/local/share/cmake/Modules;/opt/local/lib/libfmt10/cmake" -DCMAKE_PREFIX_PATH="/opt/local/share/cmake/Modules;/opt/local/lib/libfmt10/cmake" -DCMAKE_BUILD_WITH_INSTALL_RPATH:BOOL=ON -DCMAKE_INSTALL_RPATH="/opt/local/lib" -Wno-dev -DCATCH_INCLUDE_DIR:STRING=/opt/local/include -DTILEDB_ASSERIONS=OFF -DTILEDB_AZURE=OFF -DTILEDB_CPP_API=ON -DTILEDB_EXPERIMENTAL_FEATURES=OFF -DTILEDB_GCS=OFF -DTILEDB_HDFS=OFF -DTILEDB_SERIALIZATION=OFF -DTILEDB_TESTS=OFF -DTILEDB_TOOLS=OFF -DTILEDB_VERBOSE=ON -DTILEDB_WEBP=OFF -DTILEDB_WERROR=OFF -DCOMPILER_SUPPORTS_AVX2=OFF -DOPENSSL_ROOT_DIR=/opt/local/libexec/openssl3 -DOPENSSL_INCLUDE_DIR=/opt/local/libexec/openssl3/include -DWITH_SSL=/opt/local/libexec/openssl3 -DCMAKE_OSX_ARCHITECTURES="ppc" -DCMAKE_OSX_DEPLOYMENT_TARGET="10.6" -DCMAKE_OSX_SYSROOT="/" /opt/local/var/macports/build/_opt_PPCSnowLeopardPorts_databases_tiledb/tiledb/work/TileDB-2.26.0 
Using vcpkg features: 
-- Found Doxygen: /opt/local/bin/doxygen (found version "1.12.0") found components: doxygen dot
-- Not found clang-tidy
-- Not found clang-format
-- was unable to find clang-format
-- The C compiler identification is GNU 14.2.0
-- The CXX compiler identification is GNU 14.2.0
-- 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/local/bin/gcc-mp-14 - 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/local/bin/g++-mp-14 - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Starting TileDB regular build.
--   CMake version: 3.30.3
AVX2 compiler support disabled by COMPILER_SUPPORTS_AVX2=OFF
-- Using vendored cpp17::pmr for polymorphic allocators because of macOS deployment target 10.6 < 14
-- Building with cpp17::pmr
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success
-- Found Threads: TRUE
-- Found BZip2: /opt/local/lib/libbz2.dylib (found version "1.0.8")
-- Looking for BZ2_bzCompressInit
-- Looking for BZ2_bzCompressInit - found
-- Could NOT find lz4 (missing: lz4_DIR)
-- Found LZ4: /opt/local/lib/liblz4.dylib
-- Found ZLIB: /opt/local/lib/libz.dylib (found version "1.3.1")
-- Found OpenSSL: /opt/local/libexec/openssl3/lib/libcrypto.dylib (found version "3.3.2")
-- Could NOT find unofficial-libmagic (missing: unofficial-libmagic_DIR)
-- Found libmagic: /opt/local/include
-- The TileDB library is compiled with verbosity.
-- The TileDB library is compiled with stats enabled.
-- Could NOT find lz4 (missing: lz4_DIR)
-- Could NOT find unofficial-libmagic (missing: unofficial-libmagic_DIR)
-- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY
-- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY - Success
-- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY
-- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY - Success
-- Performing Test COMPILER_HAS_DEPRECATED_ATTR
-- Performing Test COMPILER_HAS_DEPRECATED_ATTR - Success
-- Found PNG: /opt/local/lib/libpng.dylib (found version "1.6.43")
-- Configuring done (20.6s)
-- Generating done (8.4s)

This is confusing when the last info messages repeat not found after dependencies were already found above. This looks like a bug, even if it is harmless to the build as such.

It is probably worth getting rid of all these unofficial tags. MacPorts does not use that.

barracuda156 · 2024-09-13T18:36:26Z

A couple of questions:

I see that the build uses bundled blosc: -I/opt/local/var/macports/build/_opt_PPCSnowLeopardPorts_databases_tiledb/tiledb/work/TileDB-2.26.0/external/blosc/include. Is it possible to use MacPorts' blosc instead? This does not have to be addressed now, but if it is a matter of a configure flag, it would be nice.
Do we still need to keep blacklist of macports-clang-18? Related issue: 2.24.2 fails at linking on macOS 13 (only there): Undefined symbols for architecture x86_64: "std::exception_ptr::__from_native_exception_pointer(void*) TileDB-Inc/TileDB#5164

tiledb: update to 2.26.0

90be787

macportsbot added type: update maintainer: open Affects an openmaintainer port labels Sep 13, 2024

teo-tsirpanis mentioned this pull request Sep 13, 2024

Please fix finding libmagic and lz4 TileDB-Inc/TileDB#5307

Open

barracuda156 suggested changes Sep 13, 2024

View reviewed changes

Remove outdated patch of FindMagic_EP.cmake.

7309ec9

Update patches.

b9cac0e

teo-tsirpanis force-pushed the update-2.26 branch from ce3bc26 to b9cac0e Compare September 13, 2024 14:18

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tiledb: update to version 2.26.0 #25731

tiledb: update to version 2.26.0 #25731

teo-tsirpanis commented Sep 13, 2024

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tiledb: update to version 2.26.0 #25731

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tiledb: update to version 2.26.0 #25731

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teo-tsirpanis commented Sep 13, 2024

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