=> Building biology/cdbfasta Started : Thursday, 30 AUG 2018 at 13:00:45 UTC Platform: 5.3-DEVELOPMENT DragonFly 5.3-DEVELOPMENT #140: Wed Aug 29 22:06:30 PDT 2018 root@test.backplane.com:/usr/obj/usr/src/sys/X86_64_GENERIC x86_64 -------------------------------------------------- -- Environment -------------------------------------------------- UNAME_r=5.3-SYNTH UNAME_m=x86_64 UNAME_p=x86_64 UNAME_v=DragonFly 5.3-SYNTH UNAME_s=DragonFly PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SSL_NO_VERIFY_PEER=1 TERM=dumb PKG_CACHEDIR=/var/cache/pkg8 PKG_DBDIR=/var/db/pkg8 PORTSDIR=/xports LANG=C HOME=/root USER=root -------------------------------------------------- -- Options -------------------------------------------------- -------------------------------------------------- -- CONFIGURE_ENV -------------------------------------------------- MAKE=gmake XDG_DATA_HOME=/construction/biology/cdbfasta XDG_CONFIG_HOME=/construction/biology/cdbfasta HOME=/construction/biology/cdbfasta TMPDIR="/tmp" PATH=/construction/biology/cdbfasta/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCVER=gcc50 -------------------------------------------------- -- CONFIGURE_ARGS -------------------------------------------------- -------------------------------------------------- -- MAKE_ENV -------------------------------------------------- XDG_DATA_HOME=/construction/biology/cdbfasta XDG_CONFIG_HOME=/construction/biology/cdbfasta HOME=/construction/biology/cdbfasta TMPDIR="/tmp" PATH=/construction/biology/cdbfasta/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin 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 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 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" -------------------------------------------------- -- MAKE_ARGS -------------------------------------------------- DESTDIR=/construction/biology/cdbfasta/stage -------------------------------------------------- -- PLIST_SUB -------------------------------------------------- PORTDOCS="" PORTEXAMPLES="" OSREL=5.3 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PROFILE="@comment " DOCSDIR="share/doc/cdbfasta" EXAMPLESDIR="share/examples/cdbfasta" DATADIR="share/cdbfasta" WWWDIR="www/cdbfasta" ETCDIR="etc/cdbfasta" -------------------------------------------------- -- SUB_LIST -------------------------------------------------- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/cdbfasta DOCSDIR=/usr/local/share/doc/cdbfasta EXAMPLESDIR=/usr/local/share/examples/cdbfasta WWWDIR=/usr/local/www/cdbfasta ETCDIR=/usr/local/etc/cdbfasta -------------------------------------------------- -- /etc/make.conf -------------------------------------------------- SYNTHPROFILE=LiveSystem USE_PACKAGE_DEPENDS_ONLY=yes PACKAGE_BUILDING=yes BATCH=yes PKG_CREATE_VERBOSE=yes PORTSDIR=/xports DISTDIR=/distfiles WRKDIRPREFIX=/construction PORT_DBDIR=/options PACKAGES=/packages MAKE_JOBS_NUMBER_LIMIT=12 _ALTCCVERSION_921dbbb2=none _OBJC_ALTCCVERSION_921dbbb2=none _SMP_CPUS=32 UID=0 ARCH=x86_64 OPSYS=DragonFly DFLYVERSION=500316 OSVERSION=9999999 OSREL=5.3 _OSRELEASE=5.3-SYNTH PYTHONBASE=/usr/local _PKG_CHECKED=1 -------------------------------------------------------------------------------- -- Phase: check-sanity -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: pkg-depends -------------------------------------------------------------------------------- ===> cdbfasta-2010.07.22 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.10.5_1.txz Installing pkg-1.10.5_1... Extracting pkg-1.10.5_1: .......... done ===> cdbfasta-2010.07.22 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of cdbfasta-2010.07.22 -------------------------------------------------------------------------------- -- Phase: fetch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: fetch -------------------------------------------------------------------------------- ===> Fetching all distfiles required by cdbfasta-2010.07.22 for building -------------------------------------------------------------------------------- -- Phase: checksum -------------------------------------------------------------------------------- ===> Fetching all distfiles required by cdbfasta-2010.07.22 for building => SHA256 Checksum OK for cdbfasta-2010.07.22.tar.gz. -------------------------------------------------------------------------------- -- Phase: extract-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: extract -------------------------------------------------------------------------------- ===> Fetching all distfiles required by cdbfasta-2010.07.22 for building ===> Extracting for cdbfasta-2010.07.22 => SHA256 Checksum OK for cdbfasta-2010.07.22.tar.gz. -------------------------------------------------------------------------------- -- Phase: patch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: patch -------------------------------------------------------------------------------- ===> Patching for cdbfasta-2010.07.22 ===> Applying ports patches for cdbfasta-2010.07.22 ===> Applying dragonfly patches for cdbfasta-2010.07.22 -------------------------------------------------------------------------------- -- Phase: build-depends -------------------------------------------------------------------------------- ===> cdbfasta-2010.07.22 depends on executable: gmake - not found ===> Installing existing package /packages/All/gmake-4.2.1_2.txz Installing gmake-4.2.1_2... `-- Installing gettext-runtime-0.19.8.1_1... | `-- Installing indexinfo-0.3.1... | `-- Extracting indexinfo-0.3.1: .... done `-- Extracting gettext-runtime-0.19.8.1_1: .......... done Extracting gmake-4.2.1_2: .......... done ===> cdbfasta-2010.07.22 depends on executable: gmake - found ===> Returning to build of cdbfasta-2010.07.22 -------------------------------------------------------------------------------- -- Phase: lib-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: configure -------------------------------------------------------------------------------- ===> Configuring for cdbfasta-2010.07.22 -------------------------------------------------------------------------------- -- Phase: build -------------------------------------------------------------------------------- ===> Building for cdbfasta-2010.07.22 gmake[1]: Entering directory '/construction/biology/cdbfasta/cdbfasta' c++ -O2 -DNDEBUG -Wall -I../zlib -I. -I./gclib -DENABLE_COMPRESSION=0 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -fno-exceptions -fno-rtti -fno-strict-aliasing -D_REENTRANT -c cdbfasta.cpp -o cdbfasta.o c++ -O2 -DNDEBUG -Wall -I../zlib -I. -I./gclib -DENABLE_COMPRESSION=0 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -fno-exceptions -fno-rtti -fno-strict-aliasing -D_REENTRANT -c gcdbz.cpp -o gcdbz.o c++ -O2 -DNDEBUG -Wall -I../zlib -I. -I./gclib -DENABLE_COMPRESSION=0 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -fno-exceptions -fno-rtti -fno-strict-aliasing -D_REENTRANT -c gclib/gcdb.cpp -o gclib/gcdb.o c++ -O2 -DNDEBUG -Wall -I../zlib -I. -I./gclib -DENABLE_COMPRESSION=0 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -fno-exceptions -fno-rtti -fno-strict-aliasing -D_REENTRANT -c gclib/GBase.cpp -o gclib/GBase.o c++ -O2 -DNDEBUG -Wall -I../zlib -I. -I./gclib -DENABLE_COMPRESSION=0 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -fno-exceptions -fno-rtti -fno-strict-aliasing -D_REENTRANT -c gclib/GStr.cpp -o gclib/GStr.o c++ -O2 -DNDEBUG -Wall -I../zlib -I. -I./gclib -DENABLE_COMPRESSION=0 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -fno-exceptions -fno-rtti -fno-strict-aliasing -D_REENTRANT -c gclib/GArgs.cpp -o gclib/GArgs.o c++ -O2 -DNDEBUG -Wall -I../zlib -I. -I./gclib -DENABLE_COMPRESSION=0 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -fno-exceptions -fno-rtti -fno-strict-aliasing -D_REENTRANT -c cdbyank.cpp -o cdbyank.o gcdbz.cpp: In member function 'char* GCdbz::compress(GReadBuf*, char*)': gcdbz.cpp:122:7: warning: variable 'bol' set but not used [-Wunused-but-set-variable] bool bol=false; //beginning of line flag ^ cdbyank.cpp: In function 'int fetch_record(char*, char*, int, int, int)': cdbyank.cpp:139:35: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'off_t {aka long int}' [-Wformat=] fprintf(fout, "%lld\n", fpos); ^ cdbyank.cpp:139:35: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'off_t {aka long int}' [-Wformat=] cdbyank.cpp:147:35: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'off_t {aka long int}' [-Wformat=] fprintf(fout, "%lld\n", fpos); ^ cdbyank.cpp:147:35: warning: format '%lld' expects argument of type 'long long int', but argument 3 has type 'off_t {aka long int}' [-Wformat=] gclib/gcdb.cpp: In constructor 'GCdbRead::GCdbRead(int)': gclib/gcdb.cpp:711:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if (st.st_size <= MAX_UINT) { ^ gclib/gcdb.cpp:710:6: warning: suggest explicit braces to avoid ambiguous 'else' [-Wparentheses] if (fstat(fd,&st) == 0) ^ gclib/gcdb.cpp: In constructor 'GCdbRead::GCdbRead(char*)': gclib/gcdb.cpp:748:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if (st.st_size <= MAX_UINT) { ^ gclib/gcdb.cpp:747:6: warning: suggest explicit braces to avoid ambiguous 'else' [-Wparentheses] if (fstat(fd,&st) == 0) ^ cdbyank.cpp: In function 'int main(int, char**)': cdbyank.cpp:669:64: warning: format '%lld' expects argument of type 'long long int', but argument 2 has type 'off_t {aka long int}' [-Wformat=] printf("Database size: %lld bytes\n", dbstat.dbsize); ^ cdbyank.cpp:669:64: warning: format '%lld' expects argument of type 'long long int', but argument 2 has type 'off_t {aka long int}' [-Wformat=] cdbfasta.cpp: In function 'int main(int, char**)': cdbfasta.cpp:550:26: warning: suggest parentheses around '&&' within '||' [-Wparentheses] if (strlen(marker)==4 && marker[0]=='\\' || (marker[0]=='0' && (toupper(marker[1])=='X'))) { ^ gclib/GBase.cpp: In function 'char* Gstrdup(const char*)': gclib/GBase.cpp:98:19: warning: 'copy' may be used uninitialized in this function [-Wmaybe-uninitialized] strcpy(copy,str); ^ gclib/GBase.cpp: In function 'char* Gstrdup(const char*, const char*)': gclib/GBase.cpp:114:36: warning: 'copy' may be used uninitialized in this function [-Wmaybe-uninitialized] strncpy(copy, sfrom, sto-sfrom+1); ^ gclib/GBase.cpp: In function 'char* Gsubstr(const char*, char*, char*)': gclib/GBase.cpp:224:29: warning: 'subs' may be used uninitialized in this function [-Wmaybe-uninitialized] memcpy(subs, str, newlen-1); ^ gclib/GBase.cpp: In function 'char* upCase(const char*)': gclib/GBase.cpp:348:8: warning: 'upstr' may be used uninitialized in this function [-Wmaybe-uninitialized] char* upstr; ^ gclib/GBase.cpp: In function 'char* loCase(const char*)': gclib/GBase.cpp:358:8: warning: 'lostr' may be used uninitialized in this function [-Wmaybe-uninitialized] char* lostr; ^ c++ -o cdbyank cdbyank.o gcdbz.o gclib/gcdb.o gclib/GBase.o gclib/GStr.o gclib/GArgs.o -lz c++ -o cdbfasta cdbfasta.o gcdbz.o gclib/gcdb.o gclib/GBase.o gclib/GStr.o gclib/GArgs.o -lz gmake[1]: Leaving directory '/construction/biology/cdbfasta/cdbfasta' -------------------------------------------------------------------------------- -- Phase: run-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: stage -------------------------------------------------------------------------------- ===> Staging for cdbfasta-2010.07.22 ===> Generating temporary packing list install -s -m 555 /construction/biology/cdbfasta/cdbfasta/cdbfasta /construction/biology/cdbfasta/stage/usr/local/bin install -s -m 555 /construction/biology/cdbfasta/cdbfasta/cdbyank /construction/biology/cdbfasta/stage/usr/local/bin ====> Compressing man pages (compress-man) -------------------------------------------------------------------------------- -- Phase: package -------------------------------------------------------------------------------- ===> Building package for cdbfasta-2010.07.22 file sizes/checksums [2]: . done packing files [2]: . done packing directories [0]: . done -------------------------------------------------- -- Termination -------------------------------------------------- Finished: Thursday, 30 AUG 2018 at 13:00:54 UTC Duration: 00:00:08