Using autoreconf without root rights on a prefix path results in a corrupted configure-script

I am trying to compile a package (libdrm-2.4.59) and to use sed and autoreconf to remove a dependency: sed -e "/pthread-stubs/d" -i configure.ac && autoreconf -fiv It produces the following output: autoreconf: Entering directory `.' autoreconf: configure.ac: not using Gettext autoreconf: running: aclocal -I /u/f0/students/estermad/tmp/share/aclocal --force -I m4 ${ACLOCAL_FLAGS} autoreconf: configure.ac: tracing autoreconf: running: libtoolize --install --copy --force libtoolize: putting auxiliary files in AC_CONFIG_AUX_DIR, 'build-aux'. libtoolize: copying file 'build-aux/config.guess' libtoolize: copying file 'build-aux/config.sub' libtoolize: copying file 'build-aux/install-sh' libtoolize: copying file 'build-aux/ltmain.sh' libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'm4'. libtoolize: copying file 'm4/libtool.m4' libtoolize: You should add the contents of 'm4/libtool.m4' to 'aclocal.m4'. libtoolize: copying file 'm4/ltoptions.m4' libtoolize: You should add the contents of 'm4/ltoptions.m4' to 'aclocal.m4'. libtoolize: copying file 'm4/ltsugar.m4' libtoolize: You should add the contents of 'm4/ltsugar.m4' to 'aclocal.m4'. libtoolize: copying file 'm4/ltversion.m4' libtoolize: copying file 'm4/lt~obsolete.m4' libtoolize: You should add the contents of 'm4/lt~obsolete.m4' to 'aclocal.m4'. autoreconf: running: /usr/bin/autoconf --force autoreconf: running: /usr/bin/autoheader --force autoreconf: running: automake --add-missing --copy --force-missing configure.ac:32: installing `build-aux/missing' exynos/Makefile.am: installing `build-aux/depcomp' autoreconf: Leaving directory `.' This looks fine so far but as I call configure the build stops with a strange error: ... checking for pkg-config... /u/f0/students/estermad/tmp/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for PCIACCESS... configure: error: in `/u/f0/students/estermad/xc/libdrm-2.4.59': configure: error: The pkg-config script could not be found or is too old. Make sure it is in your PATH or set the PKG_CONFIG environment variable to the full path to pkg-config. ... Here are some parts of the config.log which show the error, the corresponding compiler and linker flags which were set correctly and the values related to pkg-config which are not set: configure:12927: checking for PCIACCESS configure:12932: $PKG_CONFIG --exists --print-errors "pciaccess >= 0.10" configure:12935: $? = 0 configure:12945: $PKG_CONFIG --exists --print-errors "pciaccess >= 0.10" configure:12948: $? = 0 configure:12970: error: in `/u/f0/students/estermad/xc/libdrm-2.4.59': ... ac_cv_env_PCIACCESS_CFLAGS_set=set ac_cv_env_PCIACCESS_CFLAGS_value=-I/u/f0/students/estermad/tmp/include ac_cv_env_PCIACCESS_LIBS_set=set ac_cv_env_PCIACCESS_LIBS_value='-L/u/f0/students/estermad/tmp/lib -lpciaccess' ac_cv_env_PKG_CONFIG_set= ac_cv_env_PKG_CONFIG_value= The autoreconf uses libtoolize which was missing on my system so I had to build libtool myself. All builds I do on this system have a prefix. The prefix used to build dependencies of libdrm among other things. For libtool I ran following: $ cd libtool-2.4.5 $ ./configure --prefix=/u/f0/students/estermad/tmp && make && make install $ libtool --finish /u/f0/students/estermad/tmp/lib However the build and install of the libtool runs without any errors. I have no idea if the resulting configure-script is corrupted due to autoreconf (located in /usr/bin/autoreconf), libtoolize (located in /u/f0/students/estermad/tmp/bin), aclocal or something different. I tried to build libdrm without using autoreconf, commenting out pthread-stubs manually. The build ran fine. Hence the above stated issue reveals only after running autoreconf. I would really appreciate some useful hints.