[KMC] New build for KMC v3.2.2 (#6655)

* [KMC] New build for KMC v3.2.2

* Build and install shared library from static library

* Link to libz to fix shared lib build on windows and macos

* Add expand_cxxstring_abis, try to fix linking issue on macos

* Fix wrong bash syntax

Co-authored-by: Mosè Giordano <[email protected]>

* Fix expand_cxxstring_abis call

Co-authored-by: Mosè Giordano <[email protected]>

* Simplify logic

Co-authored-by: Mosè Giordano <[email protected]>

* Use the real license

Co-authored-by: Mosè Giordano <[email protected]>

* Fixup

Co-authored-by: Mosè Giordano <[email protected]>

* Use -fPIC, ensure g++ is used for linking

* Install header files

* Simplify linking shared lib step

* Fix linking shared lib on macos

* Link to libz, fix linking on windows

* Build on aarch64, needs gcc-11, gcc 8-10 fail

* fix windows build, gcc-11 on windows adds .exe to binaries automagically

* disable on aarch64-apple-darwin, update comments

---------

Co-authored-by: Mosè Giordano <[email protected]>

K/KMC/build_tarballs.jl

@@ -0,0 +1,91 @@
+using BinaryBuilder, Pkg
+
+name = "KMC"
+version = v"3.2.2"
+
+# url = "https://github.com/refresh-bio/KMC"
+# description = "Fast and frugal disk based k-mer counter"
+
+# NOTES
+# - the code assumes that is either compiled on aarch64 or x86_64
+# - we use gcc/g++ on macos/freebsd, as the code uses GNU extensions
+#   (#include <ext/algorithm>)
+
+# Build issues
+#
+# - aarch64-apple-darwin: build fails
+#   [23:42:49] ld: warning: building for macOS, but linking in object file (/opt/aarch64-apple-darwin20/bin/../lib/gcc/aarch64-apple-darwin20/12.0.1/../../../../aarch64-apple-darwin20/lib/libstdc++.a(cp-demangle.o)) built for iOS
+#   [23:42:49] Undefined symbols for architecture arm64:
+#   [23:42:49]   "__ZN10RadulsSort17RadixSortMSD_NEONI5CKmerILj1EEEEvPT_S4_yjjP11CMemoryPool", referenced from:
+#   [23:42:49]       __ZN4CKMCILj1EE18ProcessStage2_implEv in libkmc_core.a(kmc_runner.o)
+#
+# - x86_64-apple-darwin: linker warnings (many about visibility)
+#   [23:36:43] ld: warning: direct access in function 'std::basic_ios<char, std::char_traits<char> >::copyfmt(std::basic_ios<char, std::char_traits<char> > const&)' from file '/opt/x86_64-apple-darwin14/bin/../lib/gcc/x86_64-apple-darwin14/7.1.0/../../../../x86_64-apple-darwin14/lib/libstdc++.a(ios-inst.o)' to global weak symbol 'std::ctype<char>::do_widen(char) const' from file 'kmc_tools/parameters_parser.o' means the weak symbol cannot be overridden at runtime. This was likely caused by different translation units being compiled with different visibility settings.
+
+sources = [
+    GitSource("https://github.com/refresh-bio/KMC",
+              "25d29e62bc5f6d8f171d846c19aedfdd4a3b799e"),
+    DirectorySource("./bundled"),
+]
+
+script = raw"""
+cd $WORKSPACE/srcdir/KMC*/
+
+atomic_patch -p1 ../patches/fix-missing-includes.patch
+
+# the Makefile expects zlib.h,libz.a in the 3rd_party/cloudflare/ dir
+ln -s "${includedir}/zlib.h" 3rd_party/cloudflare/zlib.h
+# we have to use ${prefix}/lib, as ${libdir} is ${prefix}/bin on windows
+ln -s "${prefix}/lib/libz.a" 3rd_party/cloudflare/libz.a
+
+# use gcc/g++ on macOS and FreeBSD
+if [[ "${target}" == *-freebsd* ]] || [[ "${target}" == *-apple-* ]]; then
+    CC=gcc
+    CXX=g++
+fi
+
+# Notes
+# - the Makefile expects ${CC} to be a C++ compiler
+make -j${nproc} CC="${CXX}" CXX="${CXX}" CPU_FLAGS= STATIC_CFLAGS="-fPIC -pthread" STATIC_LFLAGS="-lpthread" \
+    kmc kmc_dump kmc_tools
+
+# no `make install`
+for prg in kmc kmc_dump kmc_tools; do
+    install -Dvm 755 "./bin/${prg}${exeext}" "${bindir}/${prg}${exeext}"
+done
+# install header files
+for hdr in include/*; do
+    install -Dvm 644 "${hdr}" "${prefix}/include/$(basename "${hdr}")"
+done
+
+# build and install shared library
+if [[ "${target}" == *-apple-* ]]; then
+    # Avoid linker error on macos, can't find file ' '
+    # I think it's because -Wl,$(flagon --no-whole-archive) expands to -Wl, (with a space at the end?)
+    link_libs="-Wl,$(flagon --whole-archive) ./bin/libkmc_core.a -lz"
+else
+    link_libs="-Wl,$(flagon --whole-archive) ./bin/libkmc_core.a -Wl,$(flagon --no-whole-archive) -lz"
+fi
+"${CXX}" -O3 -shared -o "${libdir}/libkmc_core.${dlext}" $link_libs
+
+# no explicit license file, the README says KMC is licensed under the GNU GPL 3
+install_license /usr/share/licenses/GPL-3.0+
+"""
+
+platforms = supported_platforms(; exclude = p -> arch(p) ∉ ("x86_64", "aarch64")
+                                              || (Sys.isapple(p) && arch(p) == "aarch64"))
+platforms = expand_cxxstring_abis(platforms; skip=Returns(false))
+
+products = [
+    ExecutableProduct("kmc", :kmc),
+    ExecutableProduct("kmc_dump", :kmc_dump),
+    ExecutableProduct("kmc_tools", :kmc_tools),
+    LibraryProduct("libkmc_core", :libkmc_core),
+]
+
+dependencies = [
+    Dependency("Zlib_jll"),
+]
+
+build_tarballs(ARGS, name, version, sources, script, platforms, products, dependencies;
+               julia_compat="1.6", preferred_gcc_version = v"11")

K/KMC/bundled/patches/fix-missing-includes.patch

@@ -0,0 +1,24 @@
+diff --git a/kmc_api/kmer_api.h b/kmc_api/kmer_api.h
+index fb98980..f47df35 100644
+--- a/kmc_api/kmer_api.h
++++ b/kmc_api/kmer_api.h
+@@ -14,6 +14,7 @@ Date   : 2023-03-10
+
+ #include "kmer_defs.h"
+ #include <string>
++#include <cstring>
+ #include <iostream>
+ #include <vector>
+ #include "mmer.h"
+diff --git a/kmc_core/queues.h b/kmc_core/queues.h
+index 99fccb9..20198f6 100644
+--- a/kmc_core/queues.h
++++ b/kmc_core/queues.h
+@@ -25,6 +25,7 @@
+ #include <cassert>
+ #include <thread>
+ #include <mutex>
++#include <algorithm>
+
+ using namespace std;
+