Installation issue: libxml2+python

[everythingfunctional]

Steps to reproduce the issue

$ spack spec -I libxml2+python
[+]  libxml2@2.15.3+pic+python+shared build_system=autotools platform=linux os=rocky9 target=x86_64_v3 %c=gcc@14.3.0
[+]      ^compiler-wrapper@1.1.0 build_system=generic platform=linux os=rocky9 target=x86_64_v3 
[+]      ^gcc@14.3.0+binutils+bootstrap~graphite+libsanitizer~mold~nvptx~piclibs~profiled~strip build_system=autotools build_type=RelWithDebInfo languages:='c,c++,fortran' patches:=8b79314 platform=linux os=rocky9 target=x86_64_v3 %c,cxx=gcc@11.5.0
[+]          ^binutils@2.46.1~debuginfod+gas~gprofng~headers~interwork+ld~libiberty~lto~nls~pgo+plugins build_system=autotools compress_debug_sections=zlib libs:=shared,static platform=linux os=rocky9 target=x86_64_v3 %c,cxx=gcc@11.5.0
[e]          ^diffutils@3.7 build_system=autotools platform=linux os=rocky9 target=x86_64 
[e]          ^gawk@5.1.0~nls build_system=autotools platform=linux os=rocky9 target=x86_64 
[e]          ^gcc@11.5.0+binutils+bootstrap~graphite+libsanitizer~nvptx~piclibs~profiled~strip build_system=autotools build_type=RelWithDebInfo languages:='c,c++,fortran' platform=linux os=rocky9 target=x86_64 
[+]          ^gcc-runtime@11.5.0 build_system=generic platform=linux os=rocky9 target=x86_64_v3 
[+]          ^gmp@6.3.0+cxx build_system=autotools libs:=shared,static platform=linux os=rocky9 target=x86_64_v3 %c,cxx=gcc@11.5.0
[e]              ^autoconf@2.69 build_system=autotools platform=linux os=rocky9 target=x86_64 
[e]              ^automake@1.16.2 build_system=autotools platform=linux os=rocky9 target=x86_64 
[e]              ^m4@1.4.19+sigsegv build_system=autotools platform=linux os=rocky9 target=x86_64 
[+]          ^libtool@2.5.4 build_system=autotools platform=linux os=rocky9 target=x86_64_v3 %c=gcc@11.5.0
[+]              ^file@5.46+static build_system=autotools platform=linux os=rocky9 target=x86_64_v3 %c=gcc@11.5.0
[+]                  ^xz@5.8.3~pic build_system=autotools libs:=shared,static platform=linux os=rocky9 target=x86_64_v3 %c=gcc@11.5.0
[e]              ^findutils@4.8.0 build_system=autotools platform=linux os=rocky9 target=x86_64 
[+]          ^mpc@1.4.1 build_system=autotools libs:=shared,static platform=linux os=rocky9 target=x86_64_v3 %c=gcc@11.5.0
[+]          ^mpfr@4.2.2 build_system=autotools libs:=shared,static platform=linux os=rocky9 target=x86_64_v3 %c=gcc@11.5.0
[+]              ^autoconf-archive@2024.10.16 build_system=autotools platform=linux os=rocky9 target=x86_64_v3 
[+]          ^perl@5.42.0+cpanm+opcode+open+shared+threads build_system=generic platform=linux os=rocky9 target=x86_64_v3 %c=gcc@11.5.0
[+]              ^berkeley-db@18.1.40+cxx~docs+stl build_system=autotools patches:=26090f4,b231fcc platform=linux os=rocky9 target=x86_64_v3 %c,cxx=gcc@11.5.0
[+]              ^bzip2@1.0.8~debug~pic+shared build_system=generic platform=linux os=rocky9 target=x86_64_v3 %c=gcc@11.5.0
[+]              ^gdbm@1.26 build_system=autotools platform=linux os=rocky9 target=x86_64_v3 %c=gcc@11.5.0
[+]              ^less@692 build_system=autotools platform=linux os=rocky9 target=x86_64_v3 %c=gcc@11.5.0
[+]          ^texinfo@7.2~xs build_system=autotools platform=linux os=rocky9 target=x86_64_v3 %c,cxx=gcc@11.5.0
[e]              ^gettext@0.21+bzip2+curses+git~libunistring+libxml2+pic+shared+tar+xz build_system=autotools platform=linux os=rocky9 target=x86_64 
[+]              ^ncurses@6.6~symlinks+termlib abi=none build_system=autotools patches:=7a351bc platform=linux os=rocky9 target=x86_64_v3 %c,cxx=gcc@11.5.0
[+]          ^zlib-ng@2.3.3+compat+new_strategies+opt+pic+shared build_system=autotools platform=linux os=rocky9 target=x86_64_v3 %c,cxx=gcc@11.5.0
[+]          ^zstd@1.5.7~programs build_system=makefile libs:=shared,static platform=linux os=rocky9 target=x86_64_v3 %c,cxx=gcc@11.5.0
[+]      ^gcc-runtime@14.3.0 build_system=generic platform=linux os=rocky9 target=x86_64_v3 
[e]      ^glibc@2.34 build_system=autotools platform=linux os=rocky9 target=x86_64 
[e]      ^gmake@4.3~guile build_system=generic platform=linux os=rocky9 target=x86_64 
[+]      ^libiconv@1.18 build_system=autotools libs:=shared,static platform=linux os=rocky9 target=x86_64_v3 %c=gcc@14.3.0
[e]      ^pkgconf@1.7.3 build_system=autotools platform=linux os=rocky9 target=x86_64 
[+]      ^python@3.14.5+bz2+ctypes+dbm~debug~freethreading~libxml2+lzma~optimizations+pic+pyexpat+pythoncmd+readline+shared+sqlite3+ssl~static~tests~tkinter+uuid+zlib+zstd build_system=generic platform=linux os=rocky9 target=x86_64_v3 %c,cxx=gcc@14.3.0
[+]          ^bzip2@1.0.8~debug~pic+shared build_system=generic platform=linux os=rocky9 target=x86_64_v3 %c=gcc@14.3.0
[+]          ^expat@2.8.1+libbsd build_system=autotools platform=linux os=rocky9 target=x86_64_v3 %c,cxx=gcc@14.3.0
[+]              ^libbsd@0.12.2 build_system=autotools platform=linux os=rocky9 target=x86_64_v3 %c=gcc@14.3.0
[+]                  ^libmd@1.1.0 build_system=autotools platform=linux os=rocky9 target=x86_64_v3 %c=gcc@14.3.0
[+]          ^gdbm@1.26 build_system=autotools platform=linux os=rocky9 target=x86_64_v3 %c=gcc@14.3.0
[+]          ^libffi@3.5.2 build_system=autotools platform=linux os=rocky9 target=x86_64_v3 %c,cxx=gcc@14.3.0
[+]          ^ncurses@6.6~symlinks+termlib abi=none build_system=autotools patches:=7a351bc platform=linux os=rocky9 target=x86_64_v3 %c,cxx=gcc@14.3.0
[+]          ^openssl@3.6.1~docs+shared build_system=generic certs=mozilla platform=linux os=rocky9 target=x86_64_v3 %c,cxx=gcc@14.3.0
[+]              ^ca-certificates-mozilla@2026-03-19 build_system=generic platform=linux os=rocky9 target=x86_64_v3 
[+]              ^perl@5.42.0+cpanm+opcode+open+shared+threads build_system=generic platform=linux os=rocky9 target=x86_64_v3 %c=gcc@14.3.0
[+]                  ^berkeley-db@18.1.40+cxx~docs+stl build_system=autotools patches:=26090f4,b231fcc platform=linux os=rocky9 target=x86_64_v3 %c,cxx=gcc@14.3.0
[+]                  ^less@692 build_system=autotools platform=linux os=rocky9 target=x86_64_v3 %c=gcc@14.3.0
[e]          ^readline@8.1 build_system=autotools platform=linux os=rocky9 target=x86_64 
[+]          ^sqlite@3.53.1+column_metadata+fts+rtree build_system=autotools platform=linux os=rocky9 target=x86_64_v3 %c=gcc@14.3.0
[e]          ^util-linux-uuid@2.32 build_system=autotools platform=linux os=rocky9 target=x86_64 
[+]          ^zstd@1.5.7~programs build_system=makefile libs:=shared,static platform=linux os=rocky9 target=x86_64_v3 %c,cxx=gcc@14.3.0
[+]      ^python-venv@1.0 build_system=generic platform=linux os=rocky9 target=x86_64_v3 
[+]      ^xz@5.8.3~pic build_system=autotools libs:=shared,static platform=linux os=rocky9 target=x86_64_v3 %c=gcc@14.3.0
[+]      ^zlib-ng@2.3.3+compat+new_strategies+opt+pic+shared build_system=autotools platform=linux os=rocky9 target=x86_64_v3 %c,cxx=gcc@14.3.0

Error message

The installation silently fails to install the python modules. There should exist a python3.* folder in <prefix>/lib, but this doesn't exist. On further investigation, in <prefix>/.spack/archived-files/spack-src/config.log I found configure:18316: WARNING: unrecognized options: --with-lzma, --with-python-install-dir.

Information on your system

• Spack: 1.2.2 (spack/spack@3e19345)
• Builtin repo: d4f7c71
• Python: 3.9.21
• Platform: linux-rocky9-broadwell

Additional information

@AlexanderRichert-NOAA

config.log

General information

• I have run spack debug report and reported the version of Spack/Python/Platform
• I have run spack maintainers <name-of-the-package> and @mentioned any maintainers
• I have uploaded the build log and environment files
• I have searched the issues of this repo and believe this is not a duplicate