[htslib, htscodecs] New ports

[teo-tsirpanis]

• Changes comply with the maintainer guide.
• The name of the port matches an existing name for this component on https://repology.org/ if possible, and/or is strongly associated with that component on search engines.
• Optional dependencies are resolved in exactly one way. For example, if the component is built with CMake, all find_package calls are REQUIRED, are satisfied by vcpkg.json's declared dependencies, or disabled with CMAKE_DISABLE_FIND_PACKAGE_Xxx.
• The versioning scheme in vcpkg.json matches what upstream says.
• The license declaration in vcpkg.json matches what upstream says.
• The installed as the "copyright" file matches what upstream says.
• The source code of the component installed comes from an authoritative source.
• The generated "usage text" is accurate. See adding-usage for context.
• The version database is fixed by rerunning ./vcpkg x-add-version --all and committing the result.
• Only one version is in the new port's versions file.
• Only one version is added to each modified port's versions file.

[dg0yt]

The has_${feature} variables are unused AFAICS.

[jimwang118]

@teo-tsirpanis Thanks for your PR, Is work still being done for this PR?

[teo-tsirpanis]

I will look at the Android failures later.

[teo-tsirpanis]

I can't download the artifacts to check the Android failures.

[dg0yt]

I can't download the artifacts to check the Android failures.

Can be downloaded as always.

ld.lld: error: unable to find library -lpthread
clang-17: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [Makefile:361: libhts.so] Error 1
make: *** Waiting for unfinished jobs....

This should probably be -pthread, for most modern systems.

[teo-tsirpanis]

Thanks @dg0yt! I finally found where the artifacts were located in AzDo.

[teo-tsirpanis]

CI is green.

[jimwang118]

All features passed with following triplet:

x64-linux

[dg0yt]

(Opinion)

[teo-tsirpanis]

Feedback addressed.

[JavierMatosD]

I was unable to install these ports. I'm using the a code spaces instance

% vcpkg install htslib htscodecs

CMake Error at scripts/cmake/vcpkg_execute_required_process.cmake:127 (message):
    Command failed: /usr/bin/bash -c "V=1 ./../src/1.20-30e933fbb9.clean/configure  \"--with-external-htscodecs\" \"--disable-libcurl\" \"--disable-gcs\" \"--disable-s3\" \"--disable-plugins\" \"--disable-bz2\" \"--disable-lzma\" \"--without-libdeflate\" \"--disable-silent-rules\" \"--verbose\" \"--disable-shared\" \"--enable-static\" \"--prefix=/workspaces/vcpkg/installed/x64-linux/debug\" \"--bindir=\\${prefix}/../tools/htslib/debug/bin\" \"--sbindir=\\${prefix}/../tools/htslib/debug/sbin\" \"--libdir=\\${prefix}/lib\" \"--includedir=\\${prefix}/../include\" \"--datarootdir=\\${prefix}/share/htslib\""
    Working Directory: /workspaces/vcpkg/buildtrees/htslib/x64-linux-dbg
    Error code: 1
    See logs for more information:
      /workspaces/vcpkg/buildtrees/htslib/config-x64-linux-dbg-config.log
      /workspaces/vcpkg/buildtrees/htslib/config-x64-linux-dbg-out.log
      /workspaces/vcpkg/buildtrees/htslib/config-x64-linux-dbg-err.log

Call Stack (most recent call first):
  scripts/cmake/vcpkg_configure_make.cmake:866 (vcpkg_execute_required_process)
  ports/htslib/portfile.cmake:32 (vcpkg_configure_make)
  scripts/ports.cmake:192 (include)

/workspaces/vcpkg/buildtrees/htslib/config-x64-linux-dbg-err.log

configure: WARNING: unrecognized options: --disable-silent-rules, --disable-shared, --enable-static
configure: error: libhtscodecs development files not found: missing library

You asked to use an external htscodecs library, but do not have the
required header / library files.  You either need to supply these and
if necessary set CPPFLAGS and LDFLAGS so the compiler can find them;
or configure using --without-external-htscodecs to build the required
functions from the htscodecs submodule.

It looks like it can't find:

• htscodecs/htscodecs.h
• libhtscodecs.so

[teo-tsirpanis]

Weird. Do these files exist? Did htscodecs build correctly? Can you try installing only htslib?

[teo-tsirpanis]

Apparently when trying to link to -lhtscodecs it fails because it does not find pthread. 🤔

[teo-tsirpanis]

After the latest patch, installing succeeds on a codespace.