### ### Mon Jun 7 08:22:33 EST 2004: ### /usr/pkg/bin/bmake bulk-package for gp-0.26 ### Current pkg count: 3 installed packages: digest-20021220 patch-2.5.4nb2 xpkgwedge-1.10 ### BULK> Full rebuild in progress... BULK> Cleaning package and its depends ===> Cleaning for gp-0.26 ===> Cleaning for patch-2.5.4nb2 BULK> Removing installed packages which are not needed to build gp-0.26 BULK> Keeping BULK_PREREQ: digest-20021220 (pkgtools/digest) BULK> gp-0.26 requires installed package patch-2.5.4nb2 (devel/patch) to build. /usr/pkg/sbin/pkg_delete -K /var/db/pkg -r xpkgwedge-1.10 pkg_delete: package 'xpkgwedge-1.10' doesn't have a prefix pkg_delete: package 'xpkgwedge-1.10' doesn't have a prefix BULK> Installing packages which are required to build gp-0.26. BULK> Required package patch-2.5.4nb2 (devel/patch) is already installed BULK> Required package digest-20021220 (pkgtools/digest) is already installed /usr/pkg/bin/bmake package (gp-0.26) ===> Checking for vulnerabilities in gp-0.26 => Checksum OK for gp-0.26.tgz. work -> /work/pkgbuild/biology/gp/work ===> Extracting for gp-0.26 ===> Required installed package patch>=2.2: patch-2.5.4nb2 found ===> Patching for gp-0.26 ===> Applying pkgsrc patches for gp-0.26 ===> Overriding tools for gp-0.26 ===> Buildlinking for gp-0.26 ===> Configuring for gp-0.26 ===> Building for gp-0.26 cd src ; make PROGRAMS="gp_acc gp_cusage gp_digest gp_dimer gp_findorf gp_gc gp_getseq gp_matrix gp_mkmtx gp_pars gp_pattern gp_qs gp_randseq gp_scan gp_seq2prot gp_shift gp_slen gp_tm gp_trimer gp_primer gp_adjust gp_cdndev" GDPROGRAMS="" CC=gcc LIBS=" -lm" CFLAGS="-pedantic -O3 -Wall -g" ; gcc -pedantic -O3 -Wall -g -c genpak.c Creating gp_acc gcc -pedantic -O3 -Wall -g -o gp_acc genpak.o gp_acc.c -lm Creating gp_cusage gcc -pedantic -O3 -Wall -g -o gp_cusage genpak.o gp_cusage.c -lm Creating gp_digest gcc -pedantic -O3 -Wall -g -o gp_digest genpak.o gp_digest.c -lm "gp_digest.c", line 211: warning: implicit function declaration: Compare Creating gp_dimer gcc -pedantic -O3 -Wall -g -o gp_dimer genpak.o gp_dimer.c -lm "gp_dimer.c", line 109: warning: implicit function declaration: PrintHeader Creating gp_findorf gcc -pedantic -O3 -Wall -g -o gp_findorf genpak.o gp_findorf.c -lm Creating gp_gc gcc -pedantic -O3 -Wall -g -o gp_gc genpak.o gp_gc.c -lm "gp_gc.c", line 194: warning: implicit function declaration: strlen Creating gp_getseq gcc -pedantic -O3 -Wall -g -o gp_getseq genpak.o gp_getseq.c -lm "gp_getseq.c", line 80: warning: implicit function declaration: strlen Creating gp_matrix gcc -pedantic -O3 -Wall -g -o gp_matrix genpak.o gp_matrix.c -lm "gp_matrix.c", line 606: warning: implicit function declaration: strcpy "gp_matrix.c", line 1034: warning: implicit function declaration: strlen Creating gp_mkmtx gcc -pedantic -O3 -Wall -g -o gp_mkmtx genpak.o gp_mkmtx.c -lm Creating gp_pars gcc -pedantic -O3 -Wall -g -o gp_pars genpak.o gp_pars.c -lm Creating gp_pattern gcc -pedantic -O3 -Wall -g -o gp_pattern genpak.o gp_pattern.c -lm "gp_pattern.c", line 128: warning: implicit function declaration: PrintHead "gp_pattern.c", line 133: warning: implicit function declaration: GetFreq "gp_pattern.c", line 134: warning: implicit function declaration: PrintFreq Creating gp_qs gcc -pedantic -O3 -Wall -g -o gp_qs genpak.o gp_qs.c -lm "gp_qs.c", line 121: warning: implicit function declaration: strlen "gp_qs.c", line 122: warning: implicit function declaration: strcpy "gp_qs.c", line 218: warning: implicit function declaration: strcat "gp_qs.c", line 241: warning: implicit function declaration: Compare Creating gp_randseq gcc -pedantic -O3 -Wall -g -o gp_randseq genpak.o gp_randseq.c -lm "gp_randseq.c", line 133: warning: implicit function declaration: strlen Creating gp_scan gcc -pedantic -O3 -Wall -g -o gp_scan genpak.o gp_scan.c -lm "gp_scan.c", line 203: warning: implicit function declaration: strlen Creating gp_seq2prot gcc -pedantic -O3 -Wall -g -o gp_seq2prot genpak.o gp_seq2prot.c -lm Creating gp_shift gcc -pedantic -O3 -Wall -g -o gp_shift genpak.o gp_shift.c -lm "gp_shift.c", line 118: warning: implicit function declaration: shift_positions Creating gp_slen gcc -pedantic -O3 -Wall -g -o gp_slen genpak.o gp_slen.c -lm Creating gp_tm gcc -pedantic -O3 -Wall -g -o gp_tm genpak.o gp_tm.c -lm Creating gp_trimer gcc -pedantic -O3 -Wall -g -o gp_trimer genpak.o gp_trimer.c -lm "gp_trimer.c", line 101: warning: implicit function declaration: PrintHeader Creating gp_primer gcc -pedantic -O3 -Wall -g -o gp_primer genpak.o gp_primer.c -lm "gp_primer.c", line 215: warning: implicit function declaration: Compare "gp_primer.c", line 233: warning: implicit function declaration: dimer_print "gp_primer.c", line 314: warning: implicit function declaration: stem_print Creating gp_adjust gcc -pedantic -O3 -Wall -g -o gp_adjust genpak.o gp_adjust.c -lm Creating gp_cdndev gcc -pedantic -O3 -Wall -g -o gp_cdndev genpak.o gp_cdndev.c -lm -e All programs compiled. Type 'make install' to install all programs. => Fixing buildlink references in files-to-be-installed. ===> Installing for gp-0.26 cd src ; make PROGRAMS="gp_acc gp_cusage gp_digest gp_dimer gp_findorf gp_gc gp_getseq gp_matrix gp_mkmtx gp_pars gp_pattern gp_qs gp_randseq gp_scan gp_seq2prot gp_shift gp_slen gp_tm gp_trimer gp_primer gp_adjust gp_cdndev" GDPROGRAMS="" CC=gcc LIBS=" -lm" CFLAGS="-pedantic -O3 -Wall -g" ; -e All programs compiled. Type 'make install' to install all programs. /bin/sh: test: argument expected *** Error code 1 Stop. bmake: stopped in /work/pkgbuild/biology/gp/work/gp-0.26 *** Error code 1 Stop. bmake: stopped in /usr/pkgsrc/biology/gp *** Error code 1 Stop. bmake: stopped in /usr/pkgsrc/biology/gp *** Error code 1 Stop. bmake: stopped in /usr/pkgsrc/biology/gp *** Error code 1 Stop. bmake: stopped in /usr/pkgsrc/biology/gp BULK> gp-0.26 was marked as broken: -rw-r--r-- 1 root other 5874 Jun 7 08:24 .broken.html /usr/pkg/bin/bmake deinstall ===> Deinstalling for gp BULK> Marking all packages which depend upon gp-0.26 as broken: BULK> Build for gp-0.26 was not successful, aborting.