=> Building biology/cdbfasta Started : Thursday, 7 MAR 2019 at 18:08:50 UTC Platform: 5.5-DEVELOPMENT DragonFly v5.5.0.192.g15ae7f0-DEVELOPMENT #34: Tue Feb 19 09:07:07 PST 2019 root@pkgbox64.dragonflybsd.org:/usr/obj/usr/src/sys/X86_64_GENERIC x86_64 -------------------------------------------------- -- Environment -------------------------------------------------- UNAME_r=5.5-SYNTH UNAME_m=x86_64 UNAME_p=x86_64 UNAME_v=DragonFly 5.5-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=gcc80 -------------------------------------------------- -- 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=gcc80 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 -------------------------------------------------- OSREL=5.5 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=Release-BE 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=5 LICENSES_ACCEPTED= NONE HAVE_COMPAT_IA32_KERN= CONFIGURE_MAX_CMD_LEN=262144 _PERL5_FROM_BIN=5.26.2 _ALTCCVERSION_921dbbb2=none _OBJC_ALTCCVERSION_921dbbb2=none _SMP_CPUS=8 UID=0 ARCH=x86_64 OPSYS=DragonFly DFLYVERSION=500500 OSVERSION=9999999 OSREL=5.5 _OSRELEASE=5.5-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_5.txz Installing pkg-1.10.5_5... Extracting pkg-1.10.5_5: .......... 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_3.txz Installing gmake-4.2.1_3... `-- Installing gettext-runtime-0.19.8.1_2... | `-- Installing indexinfo-0.3.1... | `-- Extracting indexinfo-0.3.1: .... done `-- Extracting gettext-runtime-0.19.8.1_2: .......... done Extracting gmake-4.2.1_3: .......... 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 In file included from cdbfasta.cpp:5: ./gclib/GBase.h: In function 'void swap(bool&, bool&)': ./gclib/GBase.h:172:8: warning: operation on 'arg1' may be undefined [-Wsequence-point] { arg1 ^= arg2 ^= arg1 ^= arg2; } ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ In file included from ./gclib/gcdb.h:7, from gcdbz.h:6, from gcdbz.cpp:1: ./gclib/GBase.h: In function 'void swap(bool&, bool&)': ./gclib/GBase.h:172:8: warning: operation on 'arg1' may be undefined [-Wsequence-point] { arg1 ^= arg2 ^= arg1 ^= arg2; } ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ In file included from gclib/GStr.h:8, from gclib/GStr.cpp:2: gclib/GBase.h: In function 'void swap(bool&, bool&)': gclib/GBase.h:172:8: warning: operation on 'arg1' may be undefined [-Wsequence-point] { arg1 ^= arg2 ^= arg1 ^= arg2; } ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ 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 ^~~ In file included from gclib/GBase.cpp:3: gclib/GBase.h: In function 'void swap(bool&, bool&)': gclib/GBase.h:172:8: warning: operation on 'arg1' may be undefined [-Wsequence-point] { arg1 ^= arg2 ^= arg1 ^= arg2; } ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ In file included from gclib/gcdb.h:7, from gclib/gcdb.cpp:1: gclib/GBase.h: In function 'void swap(bool&, bool&)': gclib/GBase.h:172:8: warning: operation on 'arg1' may be undefined [-Wsequence-point] { arg1 ^= arg2 ^= arg1 ^= arg2; } ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ gclib/gcdb.cpp: In function 'unsigned int gcdb_strlen(const char*)': gclib/gcdb.cpp:102:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (!*t) return t - s; ++t; ^~ gclib/gcdb.cpp:102:28: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if (!*t) return t - s; ++t; ^~ gclib/gcdb.cpp:103:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (!*t) return t - s; ++t; ^~ gclib/gcdb.cpp:103:28: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if (!*t) return t - s; ++t; ^~ gclib/gcdb.cpp:104:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (!*t) return t - s; ++t; ^~ gclib/gcdb.cpp:104:28: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if (!*t) return t - s; ++t; ^~ gclib/gcdb.cpp:105:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (!*t) return t - s; ++t; ^~ gclib/gcdb.cpp:105:28: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if (!*t) return t - s; ++t; ^~ gclib/gcdb.cpp: In function 'int byte_diff(char*, unsigned int, char*)': gclib/gcdb.cpp:112:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (!n) return 0; if (*s != *t) break; ++s; ++t; --n; ^~ gclib/gcdb.cpp:112:23: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if (!n) return 0; if (*s != *t) break; ++s; ++t; --n; ^~ gclib/gcdb.cpp:113:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (!n) return 0; if (*s != *t) break; ++s; ++t; --n; ^~ gclib/gcdb.cpp:113:23: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if (!n) return 0; if (*s != *t) break; ++s; ++t; --n; ^~ gclib/gcdb.cpp:114:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (!n) return 0; if (*s != *t) break; ++s; ++t; --n; ^~ gclib/gcdb.cpp:114:23: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if (!n) return 0; if (*s != *t) break; ++s; ++t; --n; ^~ gclib/gcdb.cpp:115:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (!n) return 0; if (*s != *t) break; ++s; ++t; --n; ^~ gclib/gcdb.cpp:115:23: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if (!n) return 0; if (*s != *t) break; ++s; ++t; --n; ^~ gclib/gcdb.cpp: In function 'void gcdb_byte_copy(char*, unsigned int, char*)': gclib/gcdb.cpp:123:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (!n) return; *to++ = *from++; --n; ^~ gclib/gcdb.cpp:123:21: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if (!n) return; *to++ = *from++; --n; ^ gclib/gcdb.cpp:124:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (!n) return; *to++ = *from++; --n; ^~ gclib/gcdb.cpp:124:21: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if (!n) return; *to++ = *from++; --n; ^ gclib/gcdb.cpp:125:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (!n) return; *to++ = *from++; --n; ^~ gclib/gcdb.cpp:125:21: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if (!n) return; *to++ = *from++; --n; ^ gclib/gcdb.cpp:126:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (!n) return; *to++ = *from++; --n; ^~ gclib/gcdb.cpp:126:21: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if (!n) return; *to++ = *from++; --n; ^ gclib/gcdb.cpp: In function 'void gcdb_byte_copyr(char*, unsigned int, char*)': gclib/gcdb.cpp:134:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (!n) return; *--to = *--from; --n; ^~ gclib/gcdb.cpp:134:21: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if (!n) return; *--to = *--from; --n; ^ gclib/gcdb.cpp:135:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (!n) return; *--to = *--from; --n; ^~ gclib/gcdb.cpp:135:21: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if (!n) return; *--to = *--from; --n; ^ gclib/gcdb.cpp:136:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (!n) return; *--to = *--from; --n; ^~ gclib/gcdb.cpp:136:21: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if (!n) return; *--to = *--from; --n; ^ gclib/gcdb.cpp:137:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (!n) return; *--to = *--from; --n; ^~ gclib/gcdb.cpp:137:21: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if (!n) return; *--to = *--from; --n; ^ gclib/gcdb.cpp: In constructor 'GCdbRead::GCdbRead(int)': gclib/gcdb.cpp:711:20: warning: comparison of integer expressions of different signedness: 'off_t' {aka 'long int'} and 'long unsigned int' [-Wsign-compare] if (st.st_size <= MAX_UINT) { gclib/gcdb.cpp:710:6: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else] if (fstat(fd,&st) == 0) ^ gclib/gcdb.cpp: In constructor 'GCdbRead::GCdbRead(char*)': gclib/gcdb.cpp:748:20: warning: comparison of integer expressions of different signedness: 'off_t' {aka 'long int'} and 'long unsigned int' [-Wsign-compare] if (st.st_size <= MAX_UINT) { gclib/gcdb.cpp:747:6: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else] if (fstat(fd,&st) == 0) ^ gclib/GBase.cpp: In function 'char* Gstrdup(const char*, const char*)': gclib/GBase.cpp:114:10: warning: 'copy' may be used uninitialized in this function [-Wmaybe-uninitialized] strncpy(copy, sfrom, sto-sfrom+1); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ 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* Gsubstr(const char*, char*, char*)': gclib/GBase.cpp:224:8: warning: 'subs' may be used uninitialized in this function [-Wmaybe-uninitialized] memcpy(subs, str, newlen-1); ~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from gclib/GBase.cpp:3: gclib/GBase.h: In function 'char* upCase(const char*)': gclib/GBase.h:108:28: warning: 'upstr' may be used uninitialized in this function [-Wmaybe-uninitialized] #define GMALLOC(ptr,size) if (!GMalloc((pointer*)(&ptr),size)) \ ^~ gclib/GBase.cpp:348:8: note: 'upstr' was declared here char* upstr; ^~~~~ In file included from gclib/GBase.cpp:3: gclib/GBase.h: In function 'char* loCase(const char*)': gclib/GBase.h:108:28: warning: 'lostr' may be used uninitialized in this function [-Wmaybe-uninitialized] #define GMALLOC(ptr,size) if (!GMalloc((pointer*)(&ptr),size)) \ ^~ gclib/GBase.cpp:358:8: note: 'lostr' was declared here char* lostr; ^~~~~ 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 In file included from gclib/GArgs.cpp:8: gclib/GBase.h: In function 'void swap(bool&, bool&)': gclib/GBase.h:172:8: warning: operation on 'arg1' may be undefined [-Wsequence-point] { arg1 ^= arg2 ^= arg1 ^= arg2; } ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ 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 In file included from ./gclib/gcdb.h:7, from cdbyank.cpp:1: ./gclib/GBase.h: In function 'void swap(bool&, bool&)': ./gclib/GBase.h:172:8: warning: operation on 'arg1' may be undefined [-Wsequence-point] { arg1 ^= arg2 ^= arg1 ^= arg2; } ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ cdbyank.cpp: In function 'int fetch_record(char*, char*, int, int, int)': cdbyank.cpp:139:21: 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:147:21: 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: In function 'int main(int, char**)': cdbyank.cpp:669:20: 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); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ c++ -o cdbfasta cdbfasta.o gcdbz.o gclib/gcdb.o gclib/GBase.o gclib/GStr.o gclib/GArgs.o -lz c++ -o cdbyank cdbyank.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, 7 MAR 2019 at 18:09:03 UTC Duration: 00:00:12