------------------------------------------------------------------------------- -- Phase: setup ------------------------------------------------------------------------------- Installing /packages/All/indexinfo-0.3.1.txz Installing /packages/All/gettext-runtime-0.21.txz Installing /packages/All/gmake-4.3_2.txz SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: check-sanity ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: pkg-depends ------------------------------------------------------------------------------- ===> cdbfasta-2010.07.22 depends on file: /usr/local/sbin/pkg - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch ------------------------------------------------------------------------------- ===> cdbfasta-2010.07.22 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by cdbfasta-2010.07.22 for building SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: checksum ------------------------------------------------------------------------------- ===> cdbfasta-2010.07.22 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by cdbfasta-2010.07.22 for building => SHA256 Checksum OK for cdbfasta-2010.07.22.tar.gz. SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract ------------------------------------------------------------------------------- ===> cdbfasta-2010.07.22 depends on file: /usr/local/sbin/pkg - found ===> 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. Extracted Memory Use: 0.26M SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch ------------------------------------------------------------------------------- ===> Patching for cdbfasta-2010.07.22 ===> Applying ports patches for cdbfasta-2010.07.22 from /xports/biology/cdbfasta/files ===> Applying dragonfly patches for cdbfasta-2010.07.22 from /xports/biology/cdbfasta/dragonfly SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: build-depends ------------------------------------------------------------------------------- ===> cdbfasta-2010.07.22 depends on package: gmake>=4.3 - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: lib-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: configure ------------------------------------------------------------------------------- ===> cdbfasta-2010.07.22 depends on package: gmake>=4.3 - found ===> Configuring for cdbfasta-2010.07.22 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- 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 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; } ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ 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/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; } ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ 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/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; } ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ 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; } ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ 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:139:21: 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); ^~~~~~~~ ~~~~ 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; } ~~~~~^~~~~~~~~~~~~~~~~~~~~~~ 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/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) ^ 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); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~ 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); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ 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++ -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' SUCCEEDED 00:00:02 ------------------------------------------------------------------------------- -- Phase: run-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- 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) ====> Running Q/A tests (stage-qa) Warning: You have disabled the licenses framework with DISABLE_LICENSES, unable to run checks SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: check-plist ------------------------------------------------------------------------------- ====> Checking for pkg-plist issues (check-plist) ===> Parsing plist ===> Checking for items in STAGEDIR missing from pkg-plist ===> Checking for items in pkg-plist which are not in STAGEDIR ===> No pkg-plist issues found (check-plist) SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: package ------------------------------------------------------------------------------- ===> Building package for cdbfasta-2010.07.22 file sizes/checksums [2]: 0% file sizes/checksums [2]: 100% packing files [2]: 0% packing files [2]: 100% packing directories [0]: 0% packing directories [0]: 100% SUCCEEDED 00:00:01 TOTAL TIME 00:00:05