warning: **** $EMB_ROOT not set
Searching EMBOSS libraries in -L/lib -lnucleus -lajax -lajaxg -leplplot 
Searching EMBOSS headers in 
warning: **** $EMB_VERSION not set in Makefile.PL
Checking if your kit is complete...
Looks good
Note (probably harmless): No library found for -lnucleus
Note (probably harmless): No library found for -lajax
Note (probably harmless): No library found for -lajaxg
Note (probably harmless): No library found for -leplplot
Writing Makefile for Bio::Emboss
cp Emboss.pm blib/lib/Bio/Emboss.pm
cp lib/Bio/Emboss/Methods.pm blib/lib/Bio/Emboss/Methods.pm
/home/cpanrun/ia64-lp64/build/5.8.2/bin/perl scripts/get_boot_for_modules.pl Emboss_acd.xs Emboss_align.xs Emboss_arr.xs Emboss_assert.xs Emboss_base.xs Emboss_call.xs Emboss_cod.xs Emboss_dan.xs Emboss_dmx.xs Emboss_domain.xs Emboss_feat.xs Emboss_file.xs Emboss_fmt.xs Emboss_graph.xs Emboss_hist.xs Emboss_index.xs Emboss_list.xs Emboss_math.xs Emboss_matrices.xs Emboss_mem.xs Emboss_mess.xs Emboss_nam.xs Emboss_nexus.xs Emboss_pdb.xs Emboss_pdbio.xs Emboss_phylo.xs Emboss_range.xs Emboss_reg.xs Emboss_report.xs Emboss_seq.xs Emboss_seqabi.xs Emboss_seqdb.xs Emboss_seqread.xs Emboss_seqtype.xs Emboss_seqwrite.xs Emboss_sort.xs Emboss_str.xs Emboss_sys.xs Emboss_table.xs Emboss_time.xs Emboss_translate.xs Emboss_tree.xs Emboss_util.xs Emboss_vector.xs Emboss_embcom.xs Emboss_embcons.xs Emboss_embdata.xs Emboss_embdbi.xs Emboss_embdmx.xs Emboss_embdomain.xs Emboss_embest.xs Emboss_embexit.xs Emboss_embgroup.xs Emboss_embiep.xs Emboss_embindex.xs Emboss_embinit.xs Emboss_embmat.xs Emboss_embmisc.xs Emboss_embmol.xs Emboss_embnmer.xs Emboss_embpatlist.xs Emboss_embpdb.xs Emboss_embprop.xs Emboss_embread.xs Emboss_embshow.xs Emboss_embword.xs deprecated_Emboss_acd.xs deprecated_Emboss_hist.xs deprecated_Emboss_list.xs deprecated_Emboss_seq.xs deprecated_Emboss_seqwrite.xs deprecated_Emboss_str.xs deprecated_Emboss_sys.xs deprecated_Emboss_table.xs deprecated_Emboss_time.xs deprecated_Emboss_util.xs
/home/cpanrun/ia64-lp64/build/5.8.2/bin/perl /home/cpanrun/ia64-lp64/build/5.8.2/lib/5.8.2/ExtUtils/xsubpp  -typemap /home/cpanrun/ia64-lp64/build/5.8.2/lib/5.8.2/ExtUtils/typemap -typemap typemap  Emboss.xs > Emboss.xsc && mv Emboss.xsc Emboss.c
cc -c  -I.  -D_POSIX_C_SOURCE=199506L -D_REENTRANT -Ae -D_HPUX_SOURCE -Wl,+vnocompatwarnings +DD64 -DNO_HASH_SEED -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -fast +DSitanium2 +Ofltacc=strict   -DVERSION=\"5.0.0.1\" -DXS_VERSION=\"5.0.0.1\" +Z "-I/home/cpanrun/ia64-lp64/build/5.8.2/lib/5.8.2/IA64.ARCHREV_0-thread-multi-LP64/CORE"   Emboss.c
Error 112: "emboss_perl.h", line 61 # Include file "emboss.h" not found.
    #include "emboss.h"
             ^^^^^^^^^^
make: *** [Emboss.o] Error 2