automake after adding local code

[Derek Gatherer]

I have installed 2.7.1 on a Tru64 into a directory EMBOSS.  I have added 
locally written code to the EMBOSS/emboss/ directory.  Then I modified 
EMBOSS/emboss/Makefile.am as described on 
http://www.hgmp.mrc.ac.uk/Software/EMBOSS/Doc/Develop/program.html section 3.

I then ran automake from the EMBOSS directory.  The message "required file: 
./ltconfig not found" appeared, but Makefile.in seemed to be created in the 
right place.  I then ran ./configure as usual, which was fine, various 
Makefiles were produced, and ./make.

This produced a rapid crash with the output given below.

Obviously I'm doing something wrong here. Am I running automake 
inappropriately?  From the automake GNU documentation, it would appear that 
it only needs to be run once as there is only a single configure.in file.

Output from ./make

#make
No suffix list.
Making all in plplot
Making all in lib
No suffix list.
cd ../..  && CONFIG_FILES=plplot/lib/Makefile CONFIG_HEADERS= /bin/ksh 
./config.status
config.status: creating plplot/lib/Makefile
config.status: executing depfiles commands
cd ..  && CONFIG_FILES=plplot/Makefile CONFIG_HEADERS= /bin/ksh ./config.status
config.status: creating plplot/Makefile
config.status: executing depfiles commands
/bin/ksh ../libtool --mode=compile cc -DPACKAGE_NAME=\"\" 
-DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" 
-DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"EMBOSS\" -DVERSION=\"2.7.1\" 
-DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 
-DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 
-DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DHAVE_DIRENT_H=1 -DSTDC_HEADERS=1 
-DHAVE_UNISTD_H=1 -DGETPGRP_VOID=1 -DHAVE_STRFTIME=1 -DHAVE_UNISTD_H=1 
-DHAVE_FORK=1 -DHAVE_VFORK=1 -DHAVE_WORKING_VFORK=1 -DHAVE_WORKING_FORK=1 
-DHAVE_VPRINTF=1 -DHAVE_DOPRNT=1 -DHAVE_MEMMOVE=1 -DHAVE_LIBM=1  -I. 
-I.   -I./ -I/usr/include/gd  -DNO_AUTH  -g -ieee -c
sh: .deps/pdfutils.pp: cannot create
*** Exit 1
Stop.
*** Exit 1
Stop.
*** Exit 1
Stop.