autogen.sh fails to honor --prefix

[Lyude]

It seems that even when specifying an installation prefix to the autogen.sh script in the root directory, the make files generated don't always honor the --prefix. For example

make[4]: Leaving directory `/home/lyudess/Projects/MATE/local/mate-panel/mate-panel'
make[3]: Leaving directory `/home/lyudess/Projects/MATE/local/mate-panel/mate-panel'
make[2]: Leaving directory `/home/lyudess/Projects/MATE/local/mate-panel/mate-panel'
make[1]: Leaving directory `/home/lyudess/Projects/MATE/local/mate-panel/mate-panel'
Making install in libmate-panel-applet
make[1]: Entering directory `/home/lyudess/Projects/MATE/local/mate-panel/libmate-panel-applet'
make  install-am
make[2]: Entering directory `/home/lyudess/Projects/MATE/local/mate-panel/libmate-panel-applet'
make[3]: Entering directory `/home/lyudess/Projects/MATE/local/mate-panel/libmate-panel-applet'
 /bin/mkdir -p '/usr/share/gir-1.0'
 /bin/mkdir -p '/home/lyudess/Projects/MATE/local/prefix/lib'
 /bin/sh ../libtool   --mode=install /usr/bin/install -c   libmate-panel-applet-4.la '/home/lyudess/Projects/MATE/local/prefix/lib'
 /bin/mkdir -p '/home/lyudess/Projects/MATE/local/prefix/lib/pkgconfig'
 /bin/mkdir -p '/home/lyudess/Projects/MATE/local/prefix/include/mate-panel-4.0/libmate-panel-applet'
 /usr/bin/install -c -m 644 mate-panel-applet.h mate-panel-applet-gsettings.h mate-panel-applet-enums.h '/home/lyudess/Projects/MATE/local/prefix/include/mate-panel-4.0/libmate-panel-applet'
 /usr/bin/install -c -m 644 libmatepanelapplet-4.0.pc '/home/lyudess/Projects/MATE/local/prefix/lib/pkgconfig'
 /usr/bin/install -c -m 644 MatePanelApplet-4.0.gir '/usr/share/gir-1.0'
/usr/bin/install: cannot create regular file ‘/usr/share/gir-1.0/MatePanelApplet-4.0.gir’: Permission denied
make[3]: *** [install-girDATA] Error 1
make[3]: *** Waiting for unfinished jobs....
 /bin/mkdir -p '/usr/lib64/girepository-1.0'
 /usr/bin/install -c -m 644 MatePanelApplet-4.0.typelib '/usr/lib64/girepository-1.0'
/usr/bin/install: cannot create regular file ‘/usr/lib64/girepository-1.0/MatePanelApplet-4.0.typelib’: Permission denied
make[3]: *** [install-typelibDATA] Error 1
libtool: install: /usr/bin/install -c .libs/libmate-panel-applet-4.so.1.0.1 /home/lyudess/Projects/MATE/local/prefix/lib/libmate-panel-applet-4.so.1.0.1
libtool: install: (cd /home/lyudess/Projects/MATE/local/prefix/lib && { ln -s -f libmate-panel-applet-4.so.1.0.1 libmate-panel-applet-4.so.1 || { rm -f libmate-panel-applet-4.so.1 && ln -s libmate-panel-applet-4.so.1.0.1 libmate-panel-applet-4.so.1; }; })
libtool: install: (cd /home/lyudess/Projects/MATE/local/prefix/lib && { ln -s -f libmate-panel-applet-4.so.1.0.1 libmate-panel-applet-4.so || { rm -f libmate-panel-applet-4.so && ln -s libmate-panel-applet-4.so.1.0.1 libmate-panel-applet-4.so; }; })
libtool: install: /usr/bin/install -c .libs/libmate-panel-applet-4.lai /home/lyudess/Projects/MATE/local/prefix/lib/libmate-panel-applet-4.la
libtool: install: /usr/bin/install -c .libs/libmate-panel-applet-4.a /home/lyudess/Projects/MATE/local/prefix/lib/libmate-panel-applet-4.a
libtool: install: chmod 644 /home/lyudess/Projects/MATE/local/prefix/lib/libmate-panel-applet-4.a
libtool: install: ranlib /home/lyudess/Projects/MATE/local/prefix/lib/libmate-panel-applet-4.a
libtool: finish: PATH="/usr/local/bin:/usr/bin:/bin:/opt/bin:/usr/x86_64-pc-linux-gnu/gcc-bin/4.6.3:/usr/x86_64-pc-linux-gnu/arm-unknown-linux-uclibc/gcc-bin/4.7.2:/opt/sgpp-lite-arm-eabi-bin-2010.09.51/bin:/opt/android-ndk:/opt/android-ndk/toolchains/arm-linux-androideabi-4.4.3/prebuilt/linux-x86/bin/:/opt/android-ndk/toolchains/arm-linux-androideabi-4.6/prebuilt/linux-x86/bin/:/opt/android-ndk/toolchains/mipsel-linux-android-4.4.3/prebuilt/linux-x86/bin/:/opt/android-ndk/toolchains/mipsel-linux-android-4.6/prebuilt/linux-x86/bin/:/opt/android-ndk/toolchains/x86-4.4.3/prebuilt/linux-x86/bin/:/opt/android-ndk/toolchains/x86-4.6/prebuilt/linux-x86/bin/:/opt/android-sdk-update-manager/tools:/opt/android-sdk-update-manager/platform-tools:/usr/lib64/subversion/bin:/usr/games/bin:/sbin" ldconfig -n /home/lyudess/Projects/MATE/local/prefix/lib
----------------------------------------------------------------------
Libraries have been installed in:
   /home/lyudess/Projects/MATE/local/prefix/lib

If you ever happen to want to link against installed libraries
in a given directory, LIBDIR, you must either use libtool, and
specify the full pathname of the library, or use the `-LLIBDIR'
flag during linking and do at least one of the following:
   - add LIBDIR to the `LD_LIBRARY_PATH' environment variable
     during execution
   - add LIBDIR to the `LD_RUN_PATH' environment variable
     during linking
   - use the `-Wl,-rpath -Wl,LIBDIR' linker flag
   - have your system administrator add LIBDIR to `/etc/ld.so.conf'

See any operating system documentation about shared libraries for
more information, such as the ld(1) and ld.so(8) manual pages.
----------------------------------------------------------------------
make[3]: Leaving directory `/home/lyudess/Projects/MATE/local/mate-panel/libmate-panel-applet'
make[2]: *** [install-am] Error 2
make[2]: Leaving directory `/home/lyudess/Projects/MATE/local/mate-panel/libmate-panel-applet'
make[1]: *** [install] Error 2
make[1]: Leaving directory `/home/lyudess/Projects/MATE/local/mate-panel/libmate-panel-applet'
make: *** [install-recursive] Error 1

This is the result after trying to use make install when running autoconf with --prefix set to /home/lyudess/Projects/MATE/local/prefix. This also seems to occur with a few other packages (I'll go through them and add their respective bug reports). This was tested using the latest version of the git repository as of this posting.

[Lyude]

Never mind, it looks like this simply results from not having gobject-introspection in the prefix. Can't believe it took me this long to figure that out. closing this issue.