1. Troubleshooting FAQ

1.1. Can you give me more info on GNU automake/autoconf/libtool?

The comprehensive info is read in a book GNU Autoconf, Automake, and Libtool. The book is on line.

Some web pages are useful: Simple examples are here and here. Bigger example is about writing Gnome application. here.

I created a directory which lists a project starting without autoconf but makefile and ended up with the full configured one. If you are inside MGH, then see /space/martinos/1/recon/tosa/autoconf directory. There is a steps.tar.gz file which contains every single step so that you can open it locally to see how it is done.

1.2. What are the dependencies of various files used in autoconf?

Here is the dependencies of various files:

Input files: /dev/acinclude.m4, /dev/,'s and /dev/config/*.
Output files: /dev/aclocal.m4, /dev/configure, /dev/, /dev/config.h,
    's, Makefile's

Usually you generate files in the following order:

aclocal   : acinclude.m4 and  --> aclocal.m4 (macro replacing definitions)
autoheader: aclocal.m4 and    -->
automake  : and's -->'s
autoconf  : and aclocal.m4    --> configure
configure :'s                  --> Makefile's
make      : Makefile's and config.h        --> project targets  

Now you know what to do if some files are missing or producing complaints.

1.3.,,, and configure are non-mergeable

In order to avoid CVS do a stupid merge,,,, and configure are set non-mergeable. This setting is done in dev/CVS_ROOT/cvswrappers. You checkout this file and edit and check it in. Actual lines are as follows: -m 'COPY' -m 'COPY' -m 'COPY'
   configure -m 'COPY'

You get the following message when CVS thinks merge being necessary:

   U utils/
   cvs server: nonmergeable file needs merge
   cvs server: revision 1.6 from repository is now in utils/
   cvs server: file from working directory is now in

Therefore, you do not lose your version of non-mergeable files.

1.4. How can I start configure from scratch?(I screwed up miserably)

If you screwed up configure so badly, then you may want to clean up and start from scratch. If you were able to create Makefile's, then you can try the following:

   $ cd $dev
   $ make distclean 

This will remove all the cached information on autoconf. If this fails, just remove the entire dev directory and resync again.

1.5. How can I resolve "required directory does not exist" ?

After cvs update . in dev, I tried to do make, but I get the following errors:

   $ make
   cd . && /bin/sh /home/tosa/dev/config/missing --run aclocal-1.6
   cd . && \
   /bin/sh /home/tosa/dev/config/missing --run automake-1.6 --gnu  Makefile required directory ./utilscpp does not exist
   make: *** [] Error 1

This occured because while you were working, new directory was added. The command "cvs update ." does not add a new directory. Therefore, you have to do

   $ cvs update -d utilscpp
   $ make
   cd . && /bin/sh /home/tosa/dev/config/missing --run autoconf
   /bin/sh ./config.status --recheck
   running /bin/sh ./configure  --prefix=/usr/local/freesurfer/alpha --with-mni-dir=/usr/local/mni/1.3  --no-create --no-recursion
   configure: Setting System ...
   checking build system type... i686-pc-linux-gnu
   checking host system type... i686-pc-linux-gnu

Note that autoconf automatically detected needing to run autoconf to recreate Makefile's.

1.6. How can I resolve "*** No rule to make target `all'" ?

When I did make, I get

   Making all in utilscpp
   make[2]: Entering directory `/home/tosa/dev/utilscpp'
   make[2]: *** No rule to make target `all'.  Stop.
   make[2]: Leaving directory `/home/tosa/dev/utilscpp'
   make[1]: *** [all-recursive] Error 1

This error usually means that there is no Makefile present in the directory it is making or Makefile is incompatible.

You can fix this by running config.status in dev directory:

   $ ./config.status
   config.status: creating utilscpp/Makefile

If the system is MacOSX Panther, then go to another section.

1.7. How can I resolve "cannot find input file"?

When I did config.status, I get

   config.status: error: cannot find input file: mri_make_density_map/

Usually this means that either 1) the directory is present but no files exist in the directory or 2) was not checked in by the developer who created this directory. In the fist case, you have to

   $ rm -rf mri_make_density_map
   $ cvs update -d mri_make_density_map
   cvs server: Updating mri_make_density_map
   U mri_make_density_map/
   U mri_make_density_map/
   U mri_make_density_map/mri_make_density_map.c
   $ config.status
   config.status: creating mri_make_density_map/Makefile

In the second case, you have to generate it by running automake.

  $ cd dev
  $ automake -v 
  $ config.status

Make sure that you see mris_make_density_map/Makefile is generated in this case at automake line. Make sure that config.status should generate Makefile in mris_make_density_map directory in this case.

1.8. How can I resolve 'can't locate object method "path" via package "Request"'?

The exact error message is the following:

Can't locate object method "path" via package "Request" at 
/usr/share/autoconf/Autom4te/ line 69, <GEN1> line 214.
aclocal: autom4te failed with exit status: 1

It is really weird error message. It turned out that this is telling the fact that the cached one in $project/autom4te.cache is out of sync. What you should do is to remove autom4te.cache directory.

1.9. How can I resolve "WARNING: `aclocal-1.6' is missing on your system" ?

When I tried make on SuSE 9.1 system, I get the following message:

$ make
cd . && /bin/sh /space/birn/12/users/tosa/jupiter/dev/config/missing --run aclocal-1.6
/space/birn/12/users/tosa/jupiter/dev/config/missing: line 46: aclocal-1.6: command not found
WARNING: `aclocal-1.6' is missing on your system.  You should only need it if
         you modified `acinclude.m4' or `'.  You might want
         to install the `Automake' and `Perl' packages.  Grab them from
         any GNU archive site.

This is because SuSE 9.1 has a newer version of aclocal. This can be fixed by generating a new aclocal.m4 and use it to generate all the files:

  $ aclocal 
  $ autoheader
  $ automake
  $ autoconf
  $ config.status

1.10. How can I resolve "version mismatch. This is automake 1.8.3 ..."

Here is the error emitted on jupiter (SuSE 9.1):

jupiter/dev> automake version mismatch.  This is Automake 1.8.3, but the definition used by this AM_INIT_AUTOMAKE comes from Automake 1.6.3.  You should recreate aclocal.m4 with aclocal and run automake again.
/usr/share/automake-1.8/am/ am__fastdepCC does not appear in AM_CONDITIONAL
/usr/share/automake-1.8/am/ am__fastdepCC does not appear in AM_CONDITIONAL
/usr/share/automake-1.8/am/ am__fastdepCC does not appear in AM_CONDITIONAL

SuSE9.1 has new version of automake (not autmake 1.6.3). Thus you have to recreate new aclocal.m4 (which consists of m4 macros for this particular system but not the one checked in). Therefore you need to do

  $ aclocal
  $ automake
  $ autoconf
  $ configure ...

1.11. How can I resolve "make[3]: AR@: Command not found"?

I got the following error:

make[3]: Entering directory `/autofs/space/lyon_001/fsdev/work/tosa/dev/utils'
Unmatched `.
/home/tosa/dev/utils>rm -f libutils.a
/home/tosa/dev/utils>make[3]: AR@: Command not found
make[3]:: Too many arguments.

This is due to the fact that the bad (where @AR@ was not substituded) was checked in. Autoconf can recreate the correct by doing the following:

  $ cd utils
  $ rm
  $ make
  cd .. && \
  /bin/sh /space/lyon/1/fsdev/work/tosa/dev/config/missing --run automake-1.6 --gnu  utils/Makefile
  cd .. && /bin/sh ./config.status utils/Makefile
  config.status: creating utils/Makefile

Please check in the corrected

1.12. How can I resolve "make[2]: RANLIB@: Command not found"? (MacOSX)

This happens on MacOSX Panther, because fink version of configuration binaries, aclocal, automake, etc. are not compatible with freesurfer build. Start your shell without syncing /sw/bin/init.csh. Panther version of aclocal, automake, etc lives in /usr/bin.

1.13. How can I resolve "Makefile:...: *** missing separator. Stop."?

Here is the actual error message I got:

Make[3]: Entering directory `/autofs/space/tensor_004/users/fischl/dev/utils/test'
Makefile:561: *** missing separator.  Stop.

If I look at the offending Makefile, I find

@am__fastdepCC_TRUE@    if $(COMPILE) -MT $@ -MD -MP -MF "$(DEPDIR)/$*.Tpo" -c -o $@ $<; \
@am__fastdepCC_TRUE@    then mv -f "$(DEPDIR)/$*.Tpo" "$(DEPDIR)/$*.Po"; else rm -f "$(DEPDIR)/$*.Tpo"; exit 1; fi
@am__fastdepCC_FALSE@   source='$<' object='$@' libtool=no \
@am__fastdepCC_FALSE@   depfile='$(DEPDIR)/$*.Po' tmpdepfile='$(DEPDIR)/$*.TPo' \
@am__fastdepCC_FALSE@   $(CCDEPMODE) $(depcomp) \
@am__fastdepCC_FALSE@   $(COMPILE) -c $<

These lines should have been substituded (using the value of am_fastdepCC_TRUE and am_fastdepCC_FALSE) as

   source='$<' object='$@' libtool=no \
   depfile='$(DEPDIR)/$*.Po' tmpdepfile='$(DEPDIR)/$*.TPo' \
   $(CCDEPMODE) $(depcomp) \
   $(COMPILE) -c `test -f '$<' || echo '$(srcdir)/'`$<

Note that the variable is am__fastdepCC_TRUE, which implies that automake did not do the substitution. Since automake is the one creates, this is most likely produced by a bad check-in. Since Makefile is broken, you have to remove bad Makefile and Then, you recreate and Makefile assuming that is correct.

  $ cd 
  $ rm Makefile
  $ rm
  $ cd $(topsrc_dir)
  $ automake               <---- in order to create
  $ config.status          <---- in order to create Makefile from new

If still not working, is a suspect. Make sure that the content is correct.

1.14. How can I resolve " possibly undefined macro: AC_PROG_LIBTOOL" ? (MacOSX)

This occurs on MacOSX Panther. It turned out that Fink does not install libtool package. The easiest is not to source /sw/init.tcsh and start a new shell window. Make sure that your aclocal is coming from /usr/bin, not from /sw/bin. After aclocal to recreate aclocal.m4, you should edit aclocal.m4 described in the next item.

1.15. How can I resolve "Makefile not present in util direcotry"? (MacOSX)

This happens on MacOSX due to aclocal incompatibility.

  1. edit aclocal.m4
     comment out the following line
       AC_CHECK_TOOL(AR, ar, false)
       # AC_CHECK_TOOL(AR, ar, false)
  2. automake, autoconf, config.status

1.16. How can I resolve "Can't locate object method "path" via package "Autom4te..."?

This is a really weird message, but it is saying that /dev/autom4te.cache directory is bad. Please remove /dev/autom4te.cache directory. Then do automake, autoconf, config.status.

1.17. How can I create binary RPMs without source codes?

Usually you have to be root to create RPMs, since the default directory is /usr/src/redhat etc. You can avoid becoming root by adding a single file called .rpmmacros in your home directory. Here is the content of the file:

%packager       Yasunari Tosa
%vendor         Mass General Hospital NMR Center
%_topdir        /home/tosa/rust/

where _topdir specfies the directory where the RPM creation occurs. Under this directory, you create SPECS (where spec files are kept), SOURCES (where .tar.gz files are kept), BUILD (where build occurs), RPMS (built rpms are saved), and SRPMS (built source rpms are saved). Once you have this file, then source rpm installs go into this directory. Note that RPM install still go to the appropriate directory.

In order to create a binary only RPMs, you have to write a spec file which contains empty %build and %install section contains only creating directories for install and copying. However, if you have many files, this is really a pain to write all these. Fortunately, there is a package called rust which does this for you. Unfortunately, the package is out-of-date and it contained a few bugs in

I modified it to make it work on RH9, RHEL3, or Fedora and you can find the src rpm and the RH9 binary version. I communicated to the author, but he has not done the fixing at site. Once it created the source rpm, you may want to install it to edit the spec file to be more suitable content. You rebuild it by rpmbuild -ba (specfile).

1.18. Can you give me more info on RPM?

The official web side is The latest book on RPM is RedHat RPM Guide by E. Foster-Johnson (2003, Wiley Publishing) ISBN 0-7645-4965-0 $50. The older one (slightly outdated) but free: Maximum RPM by E.C. Bailey. Currently install rpm is separated from build rpm (rpmbuild). The web page has the pdf version link and its updated CVS version.