=> Building biology/grappa build started at Tue Oct 4 23:36:57 PDT 2016 port directory: /usr/ports/biology/grappa building for: DragonFly pkgbox64.dragonflybsd.org 4.7-DEVELOPMENT DragonFly v4.7.0.78.g7d868-DEVELOPMENT #7: Mon Aug 1 22:25:32 PDT 2016 root@pkgbox64.dragonflybsd.org:/usr/obj/usr/src/sys/X86_64_GENERIC x86_64 maintained by: ports@FreeBSD.org ident warning: no id keywords in /build/boomdata/data/.m/bleeding-edge-default/ref/../04//usr/ports/biology/grappa/Makefile Makefile ident: Poudriere version: 3.1-pre Host OSVERSION: 400700 Jail OSVERSION: 400702 !!! Jail is newer than host. (Jail: 400702, Host: 400700) !!! !!! This is not supported. !!! !!! Host kernel must be same or newer than jail. !!! !!! Expect build failures. !!! ---Begin Environment--- STATUS=1 SAVED_TERM=screen MASTERMNT=/build/boomdata/data/.m/bleeding-edge-default/ref PATH=/usr/local/libexec/poudriere:/sbin:/bin:/usr/sbin:/usr/bin:/usr/pkg/bin:/usr/pkg/sbin:/usr/games:/usr/local/sbin:/usr/local/bin:/usr/pkg/xorg/bin:/usr/X11R6/bin:/root/bin:/sbin:/usr/sbin POUDRIERE_BUILD_TYPE=bulk PKGNAME=grappa-2.0 OLDPWD=/root/boom PWD=/build/boomdata/data/.m/bleeding-edge-default/ref/.p/pool MASTERNAME=bleeding-edge-default TERM=cons25 USER=root HOME=/root POUDRIERE_VERSION=3.1-pre LOCALBASE=/usr/local PACKAGE_BUILDING=yes ---End Environment--- ---Begin OPTIONS List--- ---End OPTIONS List--- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- MAKE=gmake XDG_DATA_HOME=/wrkdirs/biology/grappa XDG_CONFIG_HOME=/wrkdirs/biology/grappa HOME=/wrkdirs/biology/grappa TMPDIR="/tmp" SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCVER=gcc50 --End CONFIGURE_ENV-- --MAKE_ENV-- XDG_DATA_HOME=/wrkdirs/biology/grappa XDG_CONFIG_HOME=/wrkdirs/biology/grappa HOME=/wrkdirs/biology/grappa TMPDIR="/tmp" NO_PIE=yes MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES CCVER=gcc50 PREFIX=/usr/local LOCALBASE=/usr/local LIBDIR="/usr/lib" NOPROFILE=1 CC="cc" CFLAGS="-pipe -O2 -fno-strict-aliasing" CPP="cpp" CPPFLAGS="" LDFLAGS="" LIBS="" CXX="c++" CXXFLAGS=" -pipe -O2 -fno-strict-aliasing" MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 444" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" --End MAKE_ENV-- --PLIST_SUB-- OSREL=4.7 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local PORTDOCS="" PORTEXAMPLES="" LIB32DIR=lib PROFILE="@comment " DOCSDIR="share/doc/grappa" EXAMPLESDIR="share/examples/grappa" DATADIR="share/grappa" WWWDIR="www/grappa" ETCDIR="etc/grappa" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/grappa DOCSDIR=/usr/local/share/doc/grappa EXAMPLESDIR=/usr/local/share/examples/grappa WWWDIR=/usr/local/www/grappa ETCDIR=/usr/local/etc/grappa --End SUB_LIST-- ---Begin make.conf--- USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs NO_BACKUP=yes USE_PACKAGE_DEPENDS=yes PKG_CREATE_VERBOSE=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORT_DBDIR=/options PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles MAKE_JOBS_NUMBER=5 ---End make.conf--- =================================================== ===> NOTICE: The grappa port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://www.freebsd.org/doc/en/articles/contributing/ports-contributing.html#maintain-port ===> License GPLv2 accepted by the user =========================================================================== =================================================== ===> grappa-2.0 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.8.7_3.txz Installing pkg-1.8.7_3... Extracting pkg-1.8.7_3: .......... done ===> grappa-2.0 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of grappa-2.0 =========================================================================== =================================================== =========================================================================== =================================================== ===> NOTICE: The grappa port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://www.freebsd.org/doc/en/articles/contributing/ports-contributing.html#maintain-port ===> License GPLv2 accepted by the user ===> Fetching all distfiles required by grappa-2.0 for building =========================================================================== =================================================== ===> NOTICE: The grappa port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://www.freebsd.org/doc/en/articles/contributing/ports-contributing.html#maintain-port ===> License GPLv2 accepted by the user ===> Fetching all distfiles required by grappa-2.0 for building => SHA256 Checksum OK for GRAPPA20.tar.gz. =========================================================================== =================================================== =========================================================================== =================================================== ===> NOTICE: The grappa port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://www.freebsd.org/doc/en/articles/contributing/ports-contributing.html#maintain-port ===> License GPLv2 accepted by the user ===> Fetching all distfiles required by grappa-2.0 for building ===> Extracting for grappa-2.0 => SHA256 Checksum OK for GRAPPA20.tar.gz. =========================================================================== =================================================== =========================================================================== =================================================== ===> Patching for grappa-2.0 ===> Applying ports patches for grappa-2.0 =========================================================================== =================================================== ===> grappa-2.0 depends on executable: gmake - not found ===> Installing existing package /packages/All/gmake-4.2.1_1.txz Installing gmake-4.2.1_1... `-- Installing indexinfo-0.2.5... `-- Extracting indexinfo-0.2.5: .... done `-- Installing gettext-runtime-0.19.8.1... `-- Extracting gettext-runtime-0.19.8.1: .......... done Extracting gmake-4.2.1_1: .......... done ===> grappa-2.0 depends on executable: gmake - found ===> Returning to build of grappa-2.0 =========================================================================== =================================================== =========================================================================== =================================================== ===> Configuring for grappa-2.0 =========================================================================== =================================================== ===> Building for grappa-2.0 gmake[1]: Entering directory '/wrkdirs/biology/grappa/GRAPPA20' cc -pipe -O2 -fno-strict-aliasing -DDragonFly -DINIT -c convert.c -o convert.o cc -pipe -O2 -fno-strict-aliasing -DDragonFly -DINIT -c labeltree.c -o labeltree.o cc -pipe -O2 -fno-strict-aliasing -DDragonFly -DINIT -c main.c -o main.o cc -pipe -O2 -fno-strict-aliasing -DDragonFly -DINIT -c binencode.c -o binencode.o cc -pipe -O2 -fno-strict-aliasing -DDragonFly -DINIT -c gen_tree.c -o gen_tree.o cc -pipe -O2 -fno-strict-aliasing -DDragonFly -DINIT -c inittree.c -o inittree.o cc -pipe -O2 -fno-strict-aliasing -DDragonFly -DINIT -c circ_order.c -o circ_order.o cc -pipe -O2 -fno-strict-aliasing -DDragonFly -DINIT -c lk_main.c -o lk_main.o cc -pipe -O2 -fno-strict-aliasing -DDragonFly -DINIT -c bbtsp.c -o bbtsp.o cc -pipe -O2 -fno-strict-aliasing -DDragonFly -DINIT -c condense.c -o condense.o cc -pipe -O2 -fno-strict-aliasing -DDragonFly -DINIT -c const_tree.c -o const_tree.o cc -pipe -O2 -fno-strict-aliasing -DDragonFly -DINIT -c greedy_median.c -o greedy_median.o cc -pipe -O2 -fno-strict-aliasing -DDragonFly -DINIT -c invdist.c -o invdist.o cc -pipe -O2 -fno-strict-aliasing -DDragonFly -DINIT -c uf.c -o uf.o cc -pipe -O2 -fno-strict-aliasing -DDragonFly -DINIT -c neighborj.c -o neighborj.o cc -pipe -O2 -fno-strict-aliasing -DDragonFly -DINIT -c condense3.c -o condense3.o cc -pipe -O2 -fno-strict-aliasing -DDragonFly -DINIT -c getopt3.c -o getopt3.o cc -pipe -O2 -fno-strict-aliasing -DDragonFly -DINIT -c randomBSD.c -o randomBSD.o cc -pipe -O2 -fno-strict-aliasing -DDragonFly -DINIT -c cheaptsp.c -o cheaptsp.o cc -pipe -O2 -fno-strict-aliasing -DDragonFly -DINIT -c specialtsp.c -o specialtsp.o cc -pipe -O2 -fno-strict-aliasing -DDragonFly -DINIT -c specialinit.c -o specialinit.o cc -pipe -O2 -fno-strict-aliasing -DDragonFly -DINIT -c read_input.c -o read_input.o cc -pipe -O2 -fno-strict-aliasing -DDragonFly -DINIT -c circular_ordering.c -o circular_ordering.o cc -pipe -O2 -fno-strict-aliasing -DDragonFly -DINIT -c correction.c -o correction.o cc -pipe -O2 -fno-strict-aliasing -DDragonFly -DINIT -c inversion_median.c -o inversion_median.o cc -pipe -O2 -fno-strict-aliasing -DDragonFly -DINIT -c inversion_median_alberto.c -o inversion_median_alberto.o cc -pipe -O2 -fno-strict-aliasing -DDragonFly -DINIT -c priority_stack.c -o priority_stack.o cc -pipe -O2 -fno-strict-aliasing -DDragonFly -DINIT -c hashtable.c -o hashtable.o cc -pipe -O2 -fno-strict-aliasing -DDragonFly -DINIT -c med_util.c -o med_util.o cc -pipe -O2 -fno-strict-aliasing -DDragonFly -DINIT -c simpleio.c -o simpleio.o cc -pipe -O2 -fno-strict-aliasing -DDragonFly -DINIT -c vertex_factory.c -o vertex_factory.o cc -pipe -O2 -fno-strict-aliasing -DDragonFly -DINIT -c growTree.c -o growTree.o cc -pipe -O2 -fno-strict-aliasing -DDragonFly -DINIT -c bitvector.c -o bitvector.o bitvector.c: In function 'bitvector_get_positions_of_ones': bitvector.c:153:27: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] push ( l, ( void * ) idx ); ^ bitvector.c: In function 'bitvector_set_positions_of_ones': bitvector.c:168:15: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] pos = ( int ) list_get ( l, i ); ^ cc -pipe -O2 -fno-strict-aliasing -DDragonFly -DINIT -c lists.c -o lists.o cc -pipe -O2 -fno-strict-aliasing -DDragonFly -DINIT -c sorting_reversal_median.c -o sorting_reversal_median.o cc -pipe -O2 -fno-strict-aliasing -DDragonFly -DINIT -c mythread_rwlock.c -o mythread_rwlock.o cc -pipe -O2 -fno-strict-aliasing -DDragonFly -DINIT -c all_sorting_reversals.c -o all_sorting_reversals.o all_sorting_reversals.c: In function 'find_all_sorting_reversals': all_sorting_reversals.c:145:16: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] ( void * ) i ); ^ all_sorting_reversals.c:167:16: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] ( void * ) i ); ^ all_sorting_reversals.c:179:17: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] j = ( int ) list_get ( &mem->conn_comp[i].cyclelist, 0 ); ^ all_sorting_reversals.c:299:21: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] a = ( int ) list_get ( &mem->cyclelist[i], j ); ^ all_sorting_reversals.c:300:21: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] b = ( int ) list_get ( &mem->cyclelist[c + 1 + i], k ); ^ all_sorting_reversals.c:351:29: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] a = ( int ) list_get ( &mem-> ^ all_sorting_reversals.c:354:29: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] b = ( int ) list_get ( &mem-> ^ all_sorting_reversals.c:460:43: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] cyclelist[( int ) ^ all_sorting_reversals.c:465:43: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] cyclelist[( int ) ^ all_sorting_reversals.c:473:41: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] a = ( int ) list_get ( edges1, k ); ^ all_sorting_reversals.c:474:41: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] b = ( int ) list_get ( edges2, k2 ); ^ all_sorting_reversals.c:497:35: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] push ( mem->mhurdles, ( void * ) i ); ^ all_sorting_reversals.c:515:22: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] h1 = ( int ) list_get ( mem->mhurdles, i ); ^ all_sorting_reversals.c:516:22: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] h2 = ( int ) list_get ( mem->mhurdles, j ); ^ all_sorting_reversals.c:565:26: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] oc = ( int ) list_get ( &ocs[i], k ); ^ all_sorting_reversals.c:569:29: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] h = ( int ) list_get ( mem->mhurdles, j ); ^ all_sorting_reversals.c:618:34: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] int o1 = ( int ) list_get ( &ocs[i], k ); ^ all_sorting_reversals.c:621:38: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] int o2 = ( int ) list_get ( &ocs[j], k2 ); ^ all_sorting_reversals.c:644:52: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] push ( &non_separated_ocs, ( void * ) i ); ^ all_sorting_reversals.c:658:33: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] int h = ( int ) list_get ( mem->mhurdles, i ); ^ all_sorting_reversals.c:659:44: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] push ( &to_merge1, ( void * ) h ); ^ all_sorting_reversals.c:664:38: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] int oc = ( int ) list_get ( &ocs[lidx[h]], j ); ^ all_sorting_reversals.c:665:48: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] push ( &to_merge1, ( void * ) oc ); ^ all_sorting_reversals.c:672:36: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] ( void * ) mem->conn_comp[h].anchor ); ^ all_sorting_reversals.c:683:52: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] push ( &to_merge2, ( void * ) j ); ^ all_sorting_reversals.c:693:33: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] ( int ) list_get ( &non_separated_ocs, j ); ^ all_sorting_reversals.c:698:52: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] push ( &to_merge2, ( void * ) bc ); ^ all_sorting_reversals.c:703:38: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] int c1 = ( int ) list_get ( &to_merge1, j ); ^ all_sorting_reversals.c:706:42: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] int c2 = ( int ) list_get ( &to_merge2, k ); ^ all_sorting_reversals.c:730:36: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] int hrdl = ( int ) list_get ( mem->mhurdles, i ); ^ all_sorting_reversals.c:734:36: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] ( void * ) mem->conn_comp[hrdl].anchor ); ^ all_sorting_reversals.c:739:43: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] push ( &tmpl, ( void * ) hrdl ); ^ all_sorting_reversals.c:758:55: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] push ( &tmpl, ( void * ) j ); ^ all_sorting_reversals.c:766:55: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] push ( &tmpl, ( void * ) j ); ^ all_sorting_reversals.c:775:33: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] ( int ) list_get ( &non_separated_ocs, j ); ^ all_sorting_reversals.c:783:47: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] push ( &tmpl, ( void * ) bc ); ^ all_sorting_reversals.c:790:34: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] if ( ( int ) ^ all_sorting_reversals.c:797:37: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] ( int ) list_get ( &mem->conn_comp[hrdl]. ^ all_sorting_reversals.c:800:47: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] push ( &tmpl, ( void * ) partner ); ^ all_sorting_reversals.c:816:40: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] int comp = ( int ) list_get ( &tmpl, j ); ^ all_sorting_reversals.c:833:41: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] ( int ) list_get ( &ocs[lidx[hrdl]], ^ all_sorting_reversals.c:856:37: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] ( int ) list_get ( &ocs[lidx[hrdl]], k ); ^ all_sorting_reversals.c:862:41: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] ( int ) list_get ( &ocs[lidx[hrdl]], ^ all_sorting_reversals.c: In function 'find_connected_components': all_sorting_reversals.c:952:32: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] push ( mem->stack, ( void * ) mem->cc_e[i] ); ^ all_sorting_reversals.c:953:15: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] top = ( int ) peek_stack ( mem->stack ); ^ all_sorting_reversals.c:965:19: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] top = ( int ) peek_stack ( mem->stack ); ^ all_sorting_reversals.c: In function 'build_uoc_list': all_sorting_reversals.c:1027:30: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] push ( uoc_list, ( void * ) current ); ^ all_sorting_reversals.c: In function 'find_superhurdles': all_sorting_reversals.c:1050:15: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] prevlbl = ( int ) list_get ( uoc_list, list_size ( uoc_list ) - 1 ); ^ all_sorting_reversals.c:1058:22: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] currentlbl = ( int ) list_get ( uoc_list, i ); ^ all_sorting_reversals.c:1067:31: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] ( void * ) ( idx[currentlbl] ) ) ) ^ all_sorting_reversals.c:1073:45: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] push ( &adj_list[idx[prevlbl]], ( void * ) idx[currentlbl] ); ^ all_sorting_reversals.c:1074:48: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] push ( &adj_list[idx[currentlbl]], ( void * ) idx[prevlbl] ); ^ all_sorting_reversals.c:1093:13: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] v = ( int ) pop_stack ( &S ); ^ all_sorting_reversals.c:1100:21: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] n = ( int ) list_get ( &adj_list[v], i ); ^ all_sorting_reversals.c:1105:44: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] push ( &cycles[n], ( void * ) ncycles ); ^ all_sorting_reversals.c:1110:48: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] push ( &cycles[u], ( void * ) ncycles ); ^ all_sorting_reversals.c:1115:56: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] push ( &three_cycles_memb, ( void * ) v ); ^ all_sorting_reversals.c:1120:36: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] push ( &S, ( void * ) n ); ^ all_sorting_reversals.c:1165:21: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] n = ( int ) list_get ( &adj_list[i], 0 ); ^ all_sorting_reversals.c:1193:16: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] u[0] = ( int ) list_get ( &three_cycles_memb, i ); ^ all_sorting_reversals.c:1229:28: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] ( void * ) label[w] ); ^ all_sorting_reversals.c:1231:28: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] ( void * ) label[v] ); ^ all_sorting_reversals.c:1254:25: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] j = ( int ) list_get ( &adj_list[i], 0 ); ^ all_sorting_reversals.c:1283:40: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] x1 = label[( int ) list_get ( &adj_list[i], 0 )]; ^ all_sorting_reversals.c:1284:40: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] x2 = label[( int ) list_get ( &adj_list[j], 0 )]; ^ all_sorting_reversals.c:1296:40: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] int newj = ( int ) list_get ( &adj_list[j], 0 ); ^ all_sorting_reversals.c:1300:37: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] j = ( int ) list_get ( &adj_list[j], 1 ); ^ all_sorting_reversals.c: In function 'find_single_hurdle': all_sorting_reversals.c:1327:13: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] v = ( int ) list_get ( &adj_list[u], i ); ^ all_sorting_reversals.c:1345:16: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] next = ( int ) list_get ( &adj_list[v], 0 ) == prev ? ^ all_sorting_reversals.c:1346:13: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] ( int ) list_get ( &adj_list[v], 1 ) : ^ all_sorting_reversals.c:1347:13: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] ( int ) list_get ( &adj_list[v], 0 ); ^ all_sorting_reversals.c: In function 'count_hurdles_after_reversal': all_sorting_reversals.c:1687:17: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] label = ( int ) list_get ( V, i ); ^ all_sorting_reversals.c: In function 'new_nhurdles_plus_nfortresses_cc': all_sorting_reversals.c:1791:49: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] push ( &mem->comp_grey_edges[comp], ( void * ) mem->upi_cpy[i] ); ^ all_sorting_reversals.c: In function 'add_all_merging_reversals': all_sorting_reversals.c:1860:36: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] ( int ) list_get ( &c1->cyclelist, i )]; ^ all_sorting_reversals.c:1863:36: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] ( int ) list_get ( &c2->cyclelist, j )]; ^ all_sorting_reversals.c:1868:33: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] a = ( int ) list_get ( edges1, k ); ^ all_sorting_reversals.c:1869:33: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] b = ( int ) list_get ( edges2, k2 ); ^ all_sorting_reversals.c: In function 'add_all_cutting_reversals': all_sorting_reversals.c:1892:28: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] edges = &cyclelist[( int ) list_get ( &cc->cyclelist, j )]; ^ all_sorting_reversals.c:1897:21: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] a = ( int ) list_get ( edges, k ); ^ all_sorting_reversals.c:1898:21: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] b = ( int ) list_get ( edges, k2 ); ^ all_sorting_reversals.c: In function 'form_double_superhurdle': all_sorting_reversals.c:1940:12: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] ( int ) list_get ( &conn_comp[h1].double_superhurdle_partners, ^ all_sorting_reversals.c:1943:18: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] && ( int ) list_get ( &conn_comp[h1]. ^ all_sorting_reversals.c: In function 'find_separating_hurdles': all_sorting_reversals.c:2219:24: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] comp = ( int ) pop_stack ( &tmpl ); ^ all_sorting_reversals.c:2222:40: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] push ( &separated_ocs, ( void * ) comp ); ^ all_sorting_reversals.c:2223:45: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] push ( &separating_hurdles, ( void * ) currenth ); ^ all_sorting_reversals.c:2248:25: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] int c = ( int ) pop_stack ( &tmpl ); ^ all_sorting_reversals.c:2324:27: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] push ( &tmpl, ( void * ) comp ); ^ all_sorting_reversals.c:2347:18: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] oc = ( int ) list_get ( &separated_ocs, i ); ^ all_sorting_reversals.c:2349:17: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] h = ( int ) list_get ( &separating_hurdles, i ); ^ all_sorting_reversals.c:2357:34: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] push ( &( *ocs )[j], ( void * ) oc ); ^ cc -pipe -O2 -fno-strict-aliasing -DDragonFly -DINIT -o grappa convert.o labeltree.o main.o binencode.o gen_tree.o inittree.o circ_order.o lk_main.o bbtsp.o condense.o const_tree.o greedy_median.o invdist.o uf.o neighborj.o condense3.o getopt3.o randomBSD.o cheaptsp.o specialtsp.o specialinit.o read_input.o circular_ordering.o correction.o inversion_median.o inversion_median_alberto.o priority_stack.o hashtable.o med_util.o simpleio.o vertex_factory.o growTree.o bitvector.o lists.o sorting_reversal_median.o mythread_rwlock.o all_sorting_reversals.o -lm -pthread ln -s grappa invdist ln -s grappa distmat gmake[1]: Leaving directory '/wrkdirs/biology/grappa/GRAPPA20' =========================================================================== =================================================== =========================================================================== =================================================== ===> Staging for grappa-2.0 ===> Generating temporary packing list (cd /wrkdirs/biology/grappa/GRAPPA20 && install -s -m 555 grappa /wrkdirs/biology/grappa/stage/usr/local/bin) ln -sf grappa /wrkdirs/biology/grappa/stage/usr/local/bin/invdist ln -sf grappa /wrkdirs/biology/grappa/stage/usr/local/bin/distmat ====> Compressing man pages (compress-man) =========================================================================== =================================================== ===> Building package for grappa-2.0 file sizes/checksums [6]: . done packing files [6]: . done packing directories [0]: . done =========================================================================== => Cleaning up wrkdir ===> Cleaning for grappa-2.0 build of biology/grappa ended at Tue Oct 4 23:37:09 PDT 2016 build time: 00:00:12