Building t_coffee-9.03_2.txz (origin /buildshare/ports/355755/biology/t_coffee) for powerpc-10-0 on XXX
slot2: created
x distfiles/
x distfiles/T-COFFEE_distribution_Version_9.03.r1318.tar.gz
x packages/
x packages/mpc-1.0.2.txz
x packages/pkg-1.2.7_2.txz
x packages/perl5-5.16.3_10.txz
x packages/gettext-0.18.3.1_1.txz
x packages/m4-1.4.17_1,1.txz
x packages/gcc-4.7.3_1.txz
x packages/clustalw-2.1_1.txz
x packages/mpfr-3.1.2_2.txz
x packages/bison-2.7.1,1.txz
x packages/binutils-2.24.txz
x packages/gmp-5.1.3_2.txz
x packages/gmake-3.82_1.txz
ELF ldconfig path: /lib /usr/lib /usr/lib/compat
Make depends
===>   t_coffee-9.03_2 depends on file: /usr/local/sbin/pkg - not found
===>    Verifying install for /usr/local/sbin/pkg in /buildshare/ports/355755/ports-mgmt/pkg
===>   Installing existing package /packages/pkg-1.2.7_2.txz
Installing pkg-1.2.7_2... done
If you are upgrading from the old package format, first run:

  # pkg2ng
===>   Returning to build of t_coffee-9.03_2
===>   t_coffee-9.03_2 depends on executable: gfortran47 - not found
===>    Verifying install for gfortran47 in /buildshare/ports/355755/lang/gcc
===>   Installing existing package /packages/gcc-4.7.3_1.txz
Installing gcc-4.7.3_1...Installing binutils-2.24...Installing gettext-0.18.3.1_1... done
 done
Installing gmp-5.1.3_2... done
Installing mpc-1.0.2...Installing mpfr-3.1.2_2... done
 done
 done
To ensure binaries built with this toolchain find appropriate versions
of the necessary run-time libraries, you may want to link using

  -Wl,-rpath=/usr/local/lib/gcc47

For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens
transparently.
===>   Returning to build of t_coffee-9.03_2
===>   t_coffee-9.03_2 depends on file: /usr/local/bin/as - found
===>   t_coffee-9.03_2 depends on executable: clustalw - not found
===>    Verifying install for clustalw in /buildshare/ports/355755/biology/clustalw
===>   Installing existing package /packages/clustalw-2.1_1.txz
Installing clustalw-2.1_1... done
===>   Returning to build of t_coffee-9.03_2
===>   t_coffee-9.03_2 depends on executable: gfortran47 - found
Make install
===>  License GPLv2 accepted by the user
===>   t_coffee-9.03_2 depends on file: /usr/local/sbin/pkg - found
===> Fetching all distfiles required by t_coffee-9.03_2 for building
===>  Extracting for t_coffee-9.03_2
=> SHA256 Checksum OK for T-COFFEE_distribution_Version_9.03.r1318.tar.gz.
===>  Patching for t_coffee-9.03_2
===>  Applying FreeBSD patches for t_coffee-9.03_2
===>   t_coffee-9.03_2 depends on executable: gfortran47 - found
===>   t_coffee-9.03_2 depends on file: /usr/local/bin/as - found
===>  Configuring for t_coffee-9.03_2
===>  Building for t_coffee-9.03_2
cc -O2 -pipe -Wno-return-type -fno-strict-aliasing  -c util_constraints_list.c
util_constraints_list.c: In function 'method_file_tag2value':
util_constraints_list.c:1122: warning: comparison is always true due to limited range of data type
cc -O2 -pipe -Wno-return-type -fno-strict-aliasing  -c util_job_handling.c
cc -O2 -pipe -Wno-return-type -fno-strict-aliasing  -c util_dps.c
cc -O2 -pipe -Wno-return-type -fno-strict-aliasing  -c util_domain_constraints_list.c
cc -O2 -pipe -Wno-return-type -fno-strict-aliasing  -c util_analyse_constraints_list.c
cc -O2 -pipe -Wno-return-type -fno-strict-aliasing  -c util_aln_analyze.c
cc -O2 -pipe -Wno-return-type -fno-strict-aliasing  -c aln_convertion_util.c
cc -O2 -pipe -Wno-return-type -fno-strict-aliasing  -c util_declare.c
cc -O2 -pipe -Wno-return-type -fno-strict-aliasing  -c hsearch.c
cc -O2 -pipe -Wno-return-type -fno-strict-aliasing  -c random.c
cc -O2 -pipe -Wno-return-type -fno-strict-aliasing  -c util_make_tree.c
cc -O2 -pipe -Wno-return-type -fno-strict-aliasing  -c util.c
util.c: In function 'remove_charset_from_file':
util.c:3040: warning: comparison is always true due to limited range of data type
util.c: In function 'get_first_non_white_char':
util.c:5101: warning: comparison is always true due to limited range of data type
util.c: In function 'dump_tcoffee':
util.c:5533: warning: comparison is always true due to limited range of data type
util.c:5546: warning: comparison is always true due to limited range of data type
util.c: In function 'dump_error_file':
util.c:5609: warning: comparison is always true due to limited range of data type
util.c: In function 'display_output_filename':
util.c:7301: warning: comparison is always true due to limited range of data type
cc -O2 -pipe -Wno-return-type -fno-strict-aliasing  -c reformat_struc.c
reformat_struc.c: In function 'struclist2nb':
reformat_struc.c:888: warning: comparison is always true due to limited range of data type
cc -O2 -pipe -Wno-return-type -fno-strict-aliasing  -c reformat.c
reformat.c: In function 'back_translate_dna_codon':
reformat.c:9983: warning: comparison is always true due to limited range of data type
cc -O2 -pipe -Wno-return-type -fno-strict-aliasing  -c aln_compare.c
cc -O2 -pipe -Wno-return-type -fno-strict-aliasing  -c io_func.c
cc -O2 -pipe -Wno-return-type -fno-strict-aliasing  -c pb_util_read_sequence.c
cc -O2 -pipe -Wno-return-type -fno-strict-aliasing  -c pb_util_read_seq_util.c
cc -O2 -pipe -Wno-return-type -fno-strict-aliasing  -c tree_util.c
tree_util.c: In function 'print_split':
tree_util.c:4560: warning: comparison is always true due to limited range of data type
cc -O2 -pipe -Wno-return-type -fno-strict-aliasing  -c util_graph_maln.c
cc -O2 -pipe -Wno-return-type -fno-strict-aliasing  -c util_dp_clean_maln.c
cc -O2 -pipe -Wno-return-type -fno-strict-aliasing  -c util_dp_ssec_pwaln.c
cc -O2 -pipe -Wno-return-type -fno-strict-aliasing  -c util_dp_sim.c
cc -O2 -pipe -Wno-return-type -fno-strict-aliasing  -c util_dp_mm_nw.c
cc -O2 -pipe -Wno-return-type -fno-strict-aliasing  -c util_dp_gotoh_nw.c
cc -O2 -pipe -Wno-return-type -fno-strict-aliasing  -c util_dp_suboptimal_nw.c
cc -O2 -pipe -Wno-return-type -fno-strict-aliasing  -c util_dp_cdna_fasta_nw.c
cc -O2 -pipe -Wno-return-type -fno-strict-aliasing  -c util_dp_generic_fasta_nw.c
cc -O2 -pipe -Wno-return-type -fno-strict-aliasing  -c util_dp_fasta_nw.c
cc -O2 -pipe -Wno-return-type -fno-strict-aliasing  -c util_dp_fasta_sw.c
cc -O2 -pipe -Wno-return-type -fno-strict-aliasing  -c util_dp_gotoh_sw.c
cc -O2 -pipe -Wno-return-type -fno-strict-aliasing  -c util_dp_est.c
cc -O2 -pipe -Wno-return-type -fno-strict-aliasing  -c util_domain_dp_drivers.c
cc -O2 -pipe -Wno-return-type -fno-strict-aliasing  -c util_dp_drivers.c
cc -O2 -pipe -Wno-return-type -fno-strict-aliasing  -c util_domain_dp.c
cc -O2 -pipe -Wno-return-type -fno-strict-aliasing  -c CUSTOM_evaluate_for_struc.c
cc -O2 -pipe -Wno-return-type -fno-strict-aliasing  -c evaluate_for_struc.c
cc -O2 -pipe -Wno-return-type -fno-strict-aliasing  -c evaluate_for_domain.c
cc -O2 -pipe -Wno-return-type -fno-strict-aliasing  -c evaluate_dirichlet.c
cc -O2 -pipe -Wno-return-type -fno-strict-aliasing  -c evaluate.c
cc -O2 -pipe -Wno-return-type -fno-strict-aliasing  -c showpair.c
cc -O2 -pipe -Wno-return-type -fno-strict-aliasing  -c fsa_dp.c
cc -O2 -pipe -Wno-return-type -fno-strict-aliasing  -c pavie_dp.c
cc -O2 -pipe -Wno-return-type -fno-strict-aliasing  -c dev1.c
cc -O2 -pipe -Wno-return-type -fno-strict-aliasing  -c dev2.c
cc -O2 -pipe -Wno-return-type -fno-strict-aliasing  -c dev3.c
cc -O2 -pipe -Wno-return-type -fno-strict-aliasing  -c dev4.c
cc -O2 -pipe -Wno-return-type -fno-strict-aliasing  -c fastal.c
cc -O2 -pipe -Wno-return-type -fno-strict-aliasing  -c parttree.c
cc -O2 -pipe -Wno-return-type -fno-strict-aliasing  -c tree.c
cc -O2 -pipe -Wno-return-type -fno-strict-aliasing  -c diagonal.c
cc -O2 -pipe -Wno-return-type -fno-strict-aliasing  -c fastal_opt_parsing.c
cc -O2 -pipe -Wno-return-type -fno-strict-aliasing  -c scoring.c
cc -O2 -pipe -Wno-return-type -fno-strict-aliasing  -c iteration.c
cc -O2 -pipe -Wno-return-type -fno-strict-aliasing  -c Stack.c
cc -O2 -pipe -Wno-return-type -fno-strict-aliasing  -c Vector.c
cc -O2 -pipe -Wno-return-type -fno-strict-aliasing  -c classes.c
cc -O2 -pipe -Wno-return-type -fno-strict-aliasing  -c km_util.c
cc -O2 -pipe -Wno-return-type -fno-strict-aliasing  -c kmeans.c
cc -O2 -pipe -Wno-return-type -fno-strict-aliasing  -c km_coffee.c
cc -O2 -pipe -Wno-return-type -fno-strict-aliasing  -c t_coffee.c
cc -O2 -pipe -Wno-return-type -fno-strict-aliasing  -o t_coffee util_constraints_list.o util_job_handling.o util_dps.o util_domain_constraints_list.o util_analyse_constraints_list.o util_aln_analyze.o aln_convertion_util.o util_declare.o hsearch.o random.o util_make_tree.o util.o reformat_struc.o reformat.o aln_compare.o io_func.o pb_util_read_sequence.o pb_util_read_seq_util.o tree_util.o util_graph_maln.o util_dp_clean_maln.o util_dp_ssec_pwaln.o util_dp_sim.o util_dp_mm_nw.o util_dp_gotoh_nw.o util_dp_suboptimal_nw.o util_dp_cdna_fasta_nw.o util_dp_generic_fasta_nw.o util_dp_fasta_nw.o util_dp_fasta_sw.o util_dp_gotoh_sw.o util_dp_est.o util_domain_dp_drivers.o util_dp_drivers.o util_domain_dp.o CUSTOM_evaluate_for_struc.o evaluate_for_struc.o evaluate_for_domain.o evaluate_dirichlet.o evaluate.o showpair.o fsa_dp.o pavie_dp.o dev1.o dev2.o dev3.o dev4.o fastal.o parttree.o tree.o diagonal.o fastal_opt_parsing.o scoring.o iteration.o Stack.o Vector.o classes.o km_util.o kmeans.o km_coffee.o t_coffee.o  -lm
util.o: In function `get_os':
util.c:(.text+0xbc34): warning: warning: tmpnam() possibly used unsafely; consider using mkstemp()
gfortran47 -O -Wl,-rpath=/usr/local/lib/gcc47 TMalign.f -o TMalign
===>  Staging for t_coffee-9.03_2
===>   t_coffee-9.03_2 depends on executable: clustalw - found
===>   t_coffee-9.03_2 depends on executable: gfortran47 - found
===>   Generating temporary packing list
(cd /obj/buildshare/ports/355755/biology/t_coffee/work/T-COFFEE_distribution_Version_9.03.r1318/t_coffee_source  && install  -s -o root -g wheel -m 555 TMalign t_coffee /obj/buildshare/ports/355755/biology/t_coffee/work/stage/usr/local/bin)
/bin/mkdir -p /obj/buildshare/ports/355755/biology/t_coffee/work/stage/usr/local/share/examples/t_coffee
(cd /obj/buildshare/ports/355755/biology/t_coffee/work/T-COFFEE_distribution_Version_9.03.r1318/example && /bin/sh -c '(/usr/bin/find -d $0 $2 | /usr/bin/cpio -dumpl $1 >/dev/null  2>&1) &&  /usr/sbin/chown -Rh root:wheel $1 &&  /usr/bin/find -d $0 $2 -type d -exec chmod 755 $1/{} \; &&  /usr/bin/find -d $0 $2 -type f -exec chmod 444 $1/{} \;' -- . /obj/buildshare/ports/355755/biology/t_coffee/work/stage/usr/local/share/examples/t_coffee)
====> Compressing man pages (compress-man)
===>  Installing for t_coffee-9.03_2
===>  Checking if biology/t_coffee already installed
===>   Registering installation for t_coffee-9.03_2
Installing t_coffee-9.03_2... done
Make package
===>  Building package for t_coffee-9.03_2
slot2: removed