pcafrica · pcafrica · Apr 1, 2024 · Apr 1, 2024 · Apr 1, 2024 · Apr 1, 2024
diff --git a/Dockerfile b/Dockerfile
@@ -59,7 +59,7 @@ RUN tar czvf ${mkOutputBasename}-toolchain.tar.gz ${mkPrefix}
 SHELL ["/bin/bash", "-c"]
 
 RUN printf "\n# mk.\n\
-source /u/sw/etc/profile\n\
+source ${mkPrefix}/etc/profile\n\
 module load gcc-glibc\n" >> ${mkBashrc}
 
 

diff --git a/README.md b/README.md
@@ -20,3 +20,8 @@ Use `module avail` or `module spider` to check the available packages.
 A `Docker` image built upon [`Ubuntu`](https://hub.docker.com/_/ubuntu)
 (`x86-64` architecture) with `mk` installed is available
 [here](https://hub.docker.com/r/pcafrica/mk).
+
+### TODO
+
+Docker has deprecated and removed the `--squash` option.
+We should use [multi-stage builds](https://docs.docker.com/build/building/multi-stage/) instead.
diff --git a/base/automake/PKGBUILD b/base/automake/PKGBUILD
@@ -2,9 +2,9 @@
 
 pkgname=automake
 _pkgver=1.16
-pkgver=$_pkgver.3
-archive=$pkgname-$pkgver.tar.gz
-sum=b36e3877d961c1344351cc97b35b683a4dfadc0c
+pkgver=$_pkgver.5
+archive=$pkgname-$pkgver.tar.xz
+sum=32fb36e73568271ff506b60c55a6170b67681375
 
 dstdir=$mkToolchainBase
 
@@ -22,12 +22,18 @@ build() {
 }
 
 package() {
+  message "running package() in ${PWD}"	
   make -C $pkgname-$pkgver install
   rm -f "$dstdir"/bin/aclocal; ln -sf aclocal-$_pkgver "$dstdir"/bin/aclocal
   rm -f "$dstdir"/bin/automake; ln -sf automake-$_pkgver "$dstdir"/bin/automake
-  if [[ -d "$dstdir"/share/aclocal ]]; then
+  if [[ -d "$dstdir"/share/aclocal && ! -h "$dstdir"/share/aclocal ]]; then
     mv -v "$dstdir"/share/aclocal/* "$dstdir"/share/aclocal-$_pkgver/
     rmdir "$dstdir"/share/aclocal
+  elif [[ -h "$dstdir"/share/aclocal && ! "$dstdir"/share/aclocal -ef "$dstdir"/share/aclocal-$_pkgver ]]; then
+    mv -v "$dstdir"/share/aclocal/* "$dstdir"/share/aclocal-$_pkgver/
+    unlink "$dstdir"/share/aclocal	  
+  elif [[ -h "$dstdir"/share/aclocal && "$dstdir"/share/aclocal -ef "$dstdir"/share/aclocal-$_pkgver ]]; then
+    unlink "$dstdir"/share/aclocal
   fi
   ln -svf aclocal-$_pkgver "$dstdir"/share/aclocal
 }
diff --git a/base/cmake/PKGBUILD b/base/cmake/PKGBUILD
@@ -1,25 +1,26 @@
 #!/bin/bash
 
 pkgname=cmake
-pkgver=3.28.1
+pkgver=3.29.0
 archive=$pkgname-$pkgver.tar.gz
-sum=7e75b96ea2ca80cc70af6223e094495da3efc03c
+sum=eb0782641723651a19d337bb4301bc493e5efb33
 
 dstdir=$mkToolchainBase
 
 build() {
-  download https://www.cmake.org/files/v${pkgver%.*}/$archive
+  download https://github.com/Kitware/CMake/releases/download/v$pkgver/$pkgname-$pkgver.tar.gz
   check $archive $sum
   extract $archive
 
   pushd $pkgname-$pkgver
     message "Configuring $pkgname"
+    export VERBOSE=1
+    export LC_ALL=C
     ./configure --prefix="$dstdir" --parallel=$pkgJobs \
-                --mandir=/share/man --docdir=/share/doc/cmake \
-                --no-system-libs --no-qt-gui \
-                --sphinx-man
+                --mandir=share/man --docdir=share/doc/cmake \
+                --no-system-libs --no-qt-gui
     message "Compiling $pkgname"
-    make
+    LC_ALL=C make V=1 -j1
   popd
 }
 

diff --git a/base/emacs/PKGBUILD b/base/emacs/PKGBUILD
@@ -1,9 +1,9 @@
 #!/bin/bash
 
 pkgname=emacs
-pkgver=27.2
+pkgver=29.3
 archive=$pkgname-$pkgver.tar.xz
-sum=8d18e2bfb6e28cf060ce7587290954e9c582aa25
+sum=876fe639e4841c29550d94ed869f1d6754626002
 
 dstdir=$mkToolchainBase
 

diff --git a/base/htop/PKGBUILD b/base/htop/PKGBUILD
@@ -1,14 +1,14 @@
 #!/bin/bash
 
 pkgname=htop
-pkgver=3.0.5
-archive=$pkgver.tar.gz
-sum=de974e38e2c8d5900a4ab363111cb0544d391547
+pkgver=3.3.0
+archive=$pkgname-$pkgver.tar.xz
+sum=1b20a1aae696f0c00fa27be426121c38eae25146
 
 dstdir=$mkToolchainBase
 
 build() {
-  download https://github.com/$pkgname-dev/$pkgname/archive/$archive
+  download https://github.com/$pkgname-dev/htop/releases/download/$pkgver/$pkgname-$pkgver.tar.xz
   check $archive $sum
   extract $archive
 

diff --git a/base/libssh2/PKGBUILD b/base/libssh2/PKGBUILD
@@ -1,9 +1,9 @@
 #!/bin/bash
 
 pkgname=libssh2
-pkgver=1.9.0
+pkgver=1.11.0
 archive=$pkgname-$pkgver.tar.gz
-sum=21e98282b103307a16792e5e2d4c99beaf0b3b9c
+sum=fbdb4751a4bc93e895e9c3426f7f80b437d250fe
 
 dstdir=$mkToolchainBase
 
@@ -16,7 +16,8 @@ build() {
     message "Configuring $pkgname"
     ./configure --build=$TARGET --prefix="$dstdir" --disable-silent-rules \
                 --disable-static --disable-rpath --disable-examples-build \
-                --with-libz --with-crypto=openssl
+                --with-libz --with-crypto=openssl --disable-sshd-tests \
+		--disable-docker-tests
     message "Building $pkgname"
     make
   popd

diff --git a/base/libtool/PKGBUILD b/base/libtool/PKGBUILD
@@ -1,9 +1,9 @@
 #!/bin/bash
 
 pkgname=libtool
-pkgver=2.4.6
-archive=$pkgname-$pkgver.tar.gz
-sum=25b6931265230a06f0fc2146df64c04e5ae6ec33
+pkgver=2.4.7
+archive=$pkgname-$pkgver.tar.xz
+sum=0c90f1b046ea9cd7b32a4b5a6a9df4b46ddb637a
 
 dstdir=$mkToolchainBase
 

diff --git a/base/libxml2/PKGBUILD b/base/libxml2/PKGBUILD
@@ -1,23 +1,24 @@
 #!/bin/bash
 
 pkgname=libxml2
-pkgver=2.9.12
-archive=$pkgname-$pkgver.tar.gz
-sum=339fe5bb2a7d0c13f068c26d8f7cd194c13f9a2a
+pkgver=2.12
+pkgpatchlev=6
+archive=$pkgname-$pkgver.$pkgpatchlev.tar.xz
+sum=78f051918795f2885168cb4becde4e2c9f94c78c
 
 dstdir=$mkToolchainBase
 
 build() {
-  download http://xmlsoft.org/sources/$archive
+  download https://download.gnome.org/sources/libxml2/$pkgver/$archive
   check $archive $sum
   extract $archive
 
-  pushd $pkgname-$pkgver
+  pushd $pkgname-$pkgver.$pkgpatchlev
     # (2.9.10 with Python 3.9) https://bugzilla.redhat.com/show_bug.cgi?id=1808343
     sed -i "s|TRUE|true|g" encoding.c
-    if [[ -e "$srcdir"/$pkgname-$pkgver.patch ]]; then
+    if [[ -e "$srcdir"/$pkgname-$pkgver.$pkgpatchlev.patch ]]; then
       message "Applying patch to $pkgname"
-      patch -p1 -i "$srcdir"/$pkgname-$pkgver.patch
+      patch -p1 -i "$srcdir"/$pkgname-$pkgver.$pkgpatchlev.patch
     fi
 
     message "Configuring $pkgname"
@@ -29,8 +30,8 @@ build() {
 }
 
 package() {
-  make -C $pkgname-$pkgver install
-  pushd $pkgname-$pkgver/python
+  make -C $pkgname-$pkgver.$pkgpatchlev install
+  pushd $pkgname-$pkgver.$pkgpatchlev/python
     sed -i "s|\"/usr/include\",$||g" setup.py
     sed -i "s|\"/usr/local/include\",$||g" setup.py
     sed -i "s|\"/opt/include\",$||g" setup.py

diff --git a/base/mercurial/PKGBUILD b/base/mercurial/PKGBUILD
@@ -6,5 +6,5 @@ pkgver=5.8
 dstdir=$mkToolchainBase
 
 package() {
-  pip install -I --prefix="$dstdir" "$pkgname==$pkgver"
+  pip install -I --prefix="$dstdir" "$pkgname"
 }
diff --git a/base/ninja/PKGBUILD b/base/ninja/PKGBUILD
@@ -1,9 +1,9 @@
 #!/bin/bash
 
 pkgname=ninja
-pkgver=1.10.2
+pkgver=1.11.1
 archive=v$pkgver.tar.gz
-sum=8d2e8c1c070c27fb9dc46b4a6345bbb1de7ccbaf
+sum=938723cdfc7a6f7c8f84c83b9a2cecdf1e5e1ad3
 
 dstdir=$mkToolchainBase
 

diff --git a/base/openmpi/PKGBUILD b/base/openmpi/PKGBUILD
@@ -1,9 +1,9 @@
 #!/bin/bash
 
 pkgname=openmpi
-pkgver=4.1.2
+pkgver=5.0.2
 archive=$pkgname-$pkgver.tar.bz2
-sum=193242d2e1684dd5310a797ebff85c2f
+sum=18b05755c842b2a0a87b1baa2a6ea34e8fd516c7
 dstdir=$mkToolchainBase
 
 install_ofed() {
@@ -131,7 +131,7 @@ package() {
                 --without-libltdl --disable-dlopen \
                 --enable-pretty-print-stacktrace \
                 $with_valgrind $with_ib $with_tm \
-                --with-hwloc="$mkToolchainBase"
+                --with-hwloc="$mkToolchainBase" --disable-sphinx
     message "Compiling $pkgname"
     make install
   popd

diff --git a/base/openssh/PKGBUILD b/base/openssh/PKGBUILD
@@ -1,9 +1,9 @@
 #!/bin/bash
 
 pkgname=openssh
-pkgver=8.6p1
+pkgver=9.7p1
 archive=$pkgname-$pkgver.tar.gz
-sum=8f9f0c94317baeb97747d6258f3997b4542762c0
+sum=ce8985ea0ea2f16a5917fd982ade0972848373cc
 
 dstdir=$mkToolchainBase
 

diff --git a/base/openssl/PKGBUILD b/base/openssl/PKGBUILD
@@ -1,18 +1,18 @@
 #!/bin/bash
 
 pkgname=openssl
-pkgver=1.1.1k
-archive=OpenSSL_${pkgver//./_}.tar.gz
-sum=95a5b6a0f9e866b1b131d71ec13b7f2b83a93da1
+pkgver=3.2.1
+archive=$pkgname-$pkgver.tar.gz
+sum=9668723d65d21a9d13e985203ce8c27ac5ecf3ae
 
 dstdir=$mkToolchainBase
 
 build() {
-  download https://github.com/openssl/openssl/archive/$archive
+  download https://github.com/openssl/openssl/releases/download/$pkgname-$pkgver/$archive
   check $archive $sum
   extract $archive
 
-  pushd $pkgname-OpenSSL_${pkgver//./_}
+  pushd $pkgname-$pkgver
     message "Configuring $pkgname"
     KERNEL_BITS=64 \
     ./config --prefix="$dstdir" --openssldir="$dstdir"/etc/ssl --libdir=lib \
@@ -24,7 +24,7 @@ build() {
 
 package() {
   # installing openssl
-  make -C $pkgname-OpenSSL_${pkgver//./_} MANDIR="$dstdir"/share/man MANSUFFIX=ssl install
+  make -C $pkgname-$pkgver MANDIR="$dstdir"/share/man MANSUFFIX=ssl install
   sed -i "1s:/usr/bin/perl:$(which perl):" "$dstdir"/bin/c_rehash
   sed -i "1s:/usr/bin/perl:$(which perl):" "$dstdir"/etc/ssl/misc/tsget
 
@@ -40,7 +40,8 @@ package() {
   sed -i "1s:/bin/bash:$(which bash):" "$dstdir"/libexec/ssl/make-ca
 
   "$dstdir"/libexec/ssl/make-ca -f -g
-
+
+  chmod u+w "$dstdir"/etc/ssl/certs
   ln -s "$dstdir"/etc/pki/tls/certs/ca-bundle.crt "$dstdir"/etc/ssl/certs/ca-bundle.crt
   ln -s "$dstdir"/etc/pki/tls/certs/ca-bundle.crt "$dstdir"/etc/ssl/certs/ca-certificates.crt
 }
diff --git a/base/packages.txt b/base/packages.txt
@@ -248,7 +248,7 @@ dependencies:
     Portable Hardware Locality is a portable abstraction of hierarchical
     architectures.
 
-  openmpi: hwloc, libnl, libtool, valgrind
+  openmpi: hwloc, libnl, libtool, valgrind, sphinx
     The Open MPI Project is an open source Message Passing Interface
     implementation that is developed and maintained by a consortium of
     academic, research, and industry partners.

diff --git a/base/perl/PKGBUILD b/base/perl/PKGBUILD
@@ -29,7 +29,8 @@ build() {
                 -Dman1dir="$dstdir/share/man/man1" -Dman1ext=1perl \
                 -Dman3dir="$dstdir/share/man/man3" -Dman3ext=3perl \
                 -Dlocincpth="${mkToolchainPrefix}/include ${mkToolchainBase}/include" \
-                -Dloclibpth="${mkToolchainPrefix}/lib ${mkToolchainBase}/lib"
+                -Dloclibpth="${mkToolchainPrefix}/lib ${mkToolchainBase}/lib" \
+		-Dlibswanted="pthread db gdbm dl ld m"
 
     message "Compiling $pkgname"
     make

diff --git a/base/python/PKGBUILD b/base/python/PKGBUILD
@@ -1,9 +1,9 @@
 #!/bin/bash
 
 pkgname=python
-pkgver=3.9.6
+pkgver=3.12.2
 archive=Python-$pkgver.tar.xz
-sum=05826c93a178872958f6685094ee3514e53ba653
+sum=040eac171c17062253042f7faafea830b03bf07b
 
 dstdir=$mkToolchainBase
 
@@ -20,19 +20,23 @@ build() {
     # ensure to use system libraries
     rm -rf Modules/{expat,zlib,_ctypes/{darwin,libffi}*}
     # fixing the system paths
-    sed -i "s:/usr/include:$mkToolchainBase/include:g" setup.py
-    sed -i "s:/usr/lib:$mkToolchainBase/lib:g" setup.py
+    if [[ -r setup.py ]]; then
+      sed -i "s:/usr/include:$mkToolchainBase/include:g" setup.py
+      sed -i "s:/usr/lib:$mkToolchainBase/lib:g" setup.py
+    fi
     message "Configuring $pkgname"
     # --with-dbmliborder=bdb:gdbm
     #   Use this switch if you want to build Python DBM Module against Berkeley
     #   DB instead of GDBM
     # --enable-optimizations
     #   A release build with all optimizations active
+    message "TARGET is ${TARGET}"
     ./configure --build=$TARGET --prefix="$dstdir" --enable-shared \
                 --with-openssl=$mkToolchainBase --enable-ipv6 \
-                --with-system-expat --with-system-ffi --without-ensurepip \
+                --with-system-expat --without-ensurepip \
                 --with-dbmliborder=bdb:gdbm:ndbm \
-                --enable-optimizations
+                --enable-optimizations LIBFFI_CFLAGS="-I${mkToolchainBase}/include" \
+		LIBFFI_CFLAGS="-L${mkToolchainBase}/lib -lffi"
     message "Compiling $pkgname"
     make
   popd
@@ -41,6 +45,7 @@ build() {
 package() {
   make -C Python-$pkgver install
   ln -svf python3 "$dstdir"/bin/python
+  ln -svf python3-config "$dstdir"/bin/python-config
 
   # linker cache is not updated
   export LD_LIBRARY_PATH="$dstdir"/lib

diff --git a/base/sphinx/PKGBUILD b/base/sphinx/PKGBUILD
@@ -6,6 +6,6 @@ pkgver=5.0.0
 dstdir=$mkToolchainBase
 
 package() {
-  pip install -I --prefix="$dstdir" "$pkgname==$pkgver"
+  pip install -I --prefix="$dstdir" "$pkgname"
 }
 
diff --git a/base/vim/PKGBUILD b/base/vim/PKGBUILD
@@ -1,14 +1,14 @@
 #!/bin/bash
 
 pkgname=vim
-pkgver=8.2
+pkgver=9.0
 archive=$pkgname-$pkgver.tar.bz2
-sum=463c71ce8289923810ee594751a9f38200ad82e2
+sum=ff061751df99a5baff557c60a2ab5344f9f9e70d
 
 dstdir=$mkToolchainBase
 
 build() {
-  download ftp://ftp.vim.org/pub/vim/unix/$archive
+  download http://ftp.vim.org/pub/vim/unix/$archive
   check $archive $sum
   extract $archive
 

diff --git a/mk.config.in b/mk.config.in
@@ -10,7 +10,7 @@ BUGURL=https://github.com/pcafrica/mk/issues
 # Compiler flags
 # Compiler flags for the native cpu architecture can be retrieved with the
 # command gcc -march=native -Q --help=target (look for march).
-CFLAGS="-O2 -DNDEBUG -pipe -mtune=generic"
+CFLAGS="-O2 -DNDEBUG -pipe -mtune=native"
 CXXFLAGS=$CFLAGS
 FCFLAGS=$CFLAGS