* Package: sci-libs/cifparse-obj-7.025-r1 * Repository: gentoo * Maintainer: sci-chemistry@gentoo.org * USE: abi_x86_64 amd64 elibc_glibc kernel_linux userland_GNU * FEATURES: preserve-libs sandbox userpriv usersandbox >>> Unpacking source... >>> Unpacking cifparse-obj-v7.025-prod-src.tar.gz to /var/tmp/portage/sci-libs/cifparse-obj-7.025-r1/work >>> Source unpacked in /var/tmp/portage/sci-libs/cifparse-obj-7.025-r1/work >>> Preparing source in /var/tmp/portage/sci-libs/cifparse-obj-7.025-r1/work/cifparse-obj-v7.025-prod-src ... * Applying cifparse-obj-7.025-makefile.patch ... [ ok ] * Applying cifparse-obj-7.025-gcc4.3.patch ... [ ok ] * Applying cifparse-obj-7.025-gcc4.7.patch ... [ ok ] * Applying cifparse-obj-7.025-gcc5.patch ... [ ok ] >>> Source prepared. >>> Configuring source in /var/tmp/portage/sci-libs/cifparse-obj-7.025-r1/work/cifparse-obj-v7.025-prod-src ... >>> Source configured. >>> Compiling source in /var/tmp/portage/sci-libs/cifparse-obj-7.025-r1/work/cifparse-obj-v7.025-prod-src ... make -j1 -j1 Using platform specific configuration for system: gnu2 Platform configuration done. ------------------------------------------------------------ **** Making common-v4.5 **** ------------------------------------------------------------ make[1]: Entering directory '/var/tmp/portage/sci-libs/cifparse-obj-7.025-r1/work/cifparse-obj-v7.025-prod-src/common-v4.5' g++ -ansi -DINCL_TEMPLATE_SRC -Wall -I./include -I../include -c src/BlockIO.C -o ./obj/BlockIO.o g++ -ansi -DINCL_TEMPLATE_SRC -Wall -I./include -I../include -c src/Serializer.C -o ./obj/Serializer.o g++ -ansi -DINCL_TEMPLATE_SRC -Wall -I./include -I../include -c src/GenString.C -o ./obj/GenString.o g++ -ansi -DINCL_TEMPLATE_SRC -Wall -I./include -I../include -c src/CifString.C -o ./obj/CifString.o src/CifString.C: In static member function ‘static void CifString::rcsb_clean_string(std::__cxx11::string&)’: src/CifString.C:266:70: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] if ((!isalnum(inString[i-1]) || !isalnum(inString[i+1])) && ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ (inString[i] == '\n' || inString[i] == '\t') || ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -ansi -DINCL_TEMPLATE_SRC -Wall -I./include -I../include -c src/Exceptions.C -o ./obj/Exceptions.o g++ -ansi -DINCL_TEMPLATE_SRC -Wall -I./include -I../include -c src/mapped_vector.C -o ./obj/mapped_vector.o g++ -ansi -DINCL_TEMPLATE_SRC -Wall -I./include -I../include -c src/mapped_ptr_vector.C -o ./obj/mapped_ptr_vector.o a - BlockIO.o a - Serializer.o a - GenString.o a - CifString.o a - Exceptions.o a - mapped_vector.o a - mapped_ptr_vector.o true lib/common.a lib/common.a is up to date. ../etc/cifinstall -m 0444 ./lib/common.a ../lib x - BlockIO.o x - Serializer.o x - GenString.o x - CifString.o x - Exceptions.o x - mapped_vector.o x - mapped_ptr_vector.o x - BlockIO.o x - Serializer.o x - GenString.o x - CifString.o x - Exceptions.o x - mapped_vector.o x - mapped_ptr_vector.o a - BlockIO.o a - CifString.o a - Exceptions.o a - GenString.o a - mapped_ptr_vector.o a - mapped_vector.o a - Serializer.o ../etc/cifinstall -m 0444 ./lib/all.a ../lib make[1]: Leaving directory '/var/tmp/portage/sci-libs/cifparse-obj-7.025-r1/work/cifparse-obj-v7.025-prod-src/common-v4.5' ------------------------------------------------------------ **** Making tables-v8.0 **** ------------------------------------------------------------ make[1]: Entering directory '/var/tmp/portage/sci-libs/cifparse-obj-7.025-r1/work/cifparse-obj-v7.025-prod-src/tables-v8.0' g++ -ansi -DINCL_TEMPLATE_SRC -Wall -I./include -I../include -c src/TTable.C -o ./obj/TTable.o g++ -ansi -DINCL_TEMPLATE_SRC -Wall -I./include -I../include -c src/ITTable.C -o ./obj/ITTable.o g++ -ansi -DINCL_TEMPLATE_SRC -Wall -I./include -I../include -c src/ISTable.C -o ./obj/ISTable.o g++ -ansi -DINCL_TEMPLATE_SRC -Wall -I./include -I../include -c src/TableFile.C -o ./obj/TableFile.o a - TTable.o a - ITTable.o a - ISTable.o a - TableFile.o true lib/tables.a lib/tables.a is up to date. ../etc/cifinstall -m 0444 ./lib/tables.a ../lib x - BlockIO.o x - CifString.o x - Exceptions.o x - GenString.o x - mapped_ptr_vector.o x - mapped_vector.o x - Serializer.o x - TTable.o x - ITTable.o x - ISTable.o x - TableFile.o a - BlockIO.o a - CifString.o a - Exceptions.o a - GenString.o a - ISTable.o a - ITTable.o a - mapped_ptr_vector.o a - mapped_vector.o a - Serializer.o a - TableFile.o a - TTable.o ../etc/cifinstall -m 0444 ./lib/all.a ../lib make[1]: Leaving directory '/var/tmp/portage/sci-libs/cifparse-obj-7.025-r1/work/cifparse-obj-v7.025-prod-src/tables-v8.0' ------------------------------------------------------------ **** Making regex-v2.2 **** ------------------------------------------------------------ make[1]: Entering directory '/var/tmp/portage/sci-libs/cifparse-obj-7.025-r1/work/cifparse-obj-v7.025-prod-src/regex-v2.2' gcc -Wall -I./include -I../include -DPOSIX_MISTAKE -c src/regcomp.c -o ./obj/regcomp.o src/regcomp.c: In function ‘p_ere’: src/regcomp.c:54:30: warning: value computed is not used [-Wunused-value] #define REQUIRE(co, e) ((co) || SETERROR(e)) ^ src/regcomp.c:205:3: note: in expansion of macro ‘REQUIRE’ REQUIRE(HERE() != conc, REG_EMPTY); /* require nonempty */ ^~~~~~~ src/regcomp.c: In function ‘p_ere_exp’: src/regcomp.c:54:30: warning: value computed is not used [-Wunused-value] #define REQUIRE(co, e) ((co) || SETERROR(e)) ^ src/regcomp.c:252:3: note: in expansion of macro ‘REQUIRE’ REQUIRE(MORE(), REG_EPAREN); ^~~~~~~ src/regcomp.c:54:30: warning: value computed is not used [-Wunused-value] #define REQUIRE(co, e) ((co) || SETERROR(e)) ^ src/regcomp.c:56:24: note: in expansion of macro ‘REQUIRE’ #define MUSTEAT(c, e) (REQUIRE(MORE() && GETNEXT() == (c), e)) ^~~~~~~ src/regcomp.c:265:3: note: in expansion of macro ‘MUSTEAT’ MUSTEAT(')', REG_EPAREN); ^~~~~~~ src/regcomp.c:54:30: warning: value computed is not used [-Wunused-value] #define REQUIRE(co, e) ((co) || SETERROR(e)) ^ src/regcomp.c:308:3: note: in expansion of macro ‘REQUIRE’ REQUIRE(MORE(), REG_EESCAPE); ^~~~~~~ src/regcomp.c:54:30: warning: value computed is not used [-Wunused-value] #define REQUIRE(co, e) ((co) || SETERROR(e)) ^ src/regcomp.c:313:3: note: in expansion of macro ‘REQUIRE’ REQUIRE(!MORE() || !isdigit(PEEK()), REG_BADRPT); ^~~~~~~ src/regcomp.c:54:30: warning: value computed is not used [-Wunused-value] #define REQUIRE(co, e) ((co) || SETERROR(e)) ^ src/regcomp.c:329:2: note: in expansion of macro ‘REQUIRE’ REQUIRE(!wascaret, REG_BADRPT); ^~~~~~~ src/regcomp.c:54:30: warning: value computed is not used [-Wunused-value] #define REQUIRE(co, e) ((co) || SETERROR(e)) ^ src/regcomp.c:356:5: note: in expansion of macro ‘REQUIRE’ REQUIRE(count <= count2, REG_BADBR); ^~~~~~~ src/regcomp.c:54:30: warning: value computed is not used [-Wunused-value] #define REQUIRE(co, e) ((co) || SETERROR(e)) ^ src/regcomp.c:365:4: note: in expansion of macro ‘REQUIRE’ REQUIRE(MORE(), REG_EBRACE); ^~~~~~~ src/regcomp.c: In function ‘p_str’: src/regcomp.c:54:30: warning: value computed is not used [-Wunused-value] #define REQUIRE(co, e) ((co) || SETERROR(e)) ^ src/regcomp.c:388:2: note: in expansion of macro ‘REQUIRE’ REQUIRE(MORE(), REG_EMPTY); ^~~~~~~ src/regcomp.c: In function ‘p_bre’: src/regcomp.c:54:30: warning: value computed is not used [-Wunused-value] #define REQUIRE(co, e) ((co) || SETERROR(e)) ^ src/regcomp.c:431:2: note: in expansion of macro ‘REQUIRE’ REQUIRE(HERE() != start, REG_EMPTY); /* require nonempty */ ^~~~~~~ src/regcomp.c: In function ‘p_simp_re’: src/regcomp.c:54:30: warning: value computed is not used [-Wunused-value] #define REQUIRE(co, e) ((co) || SETERROR(e)) ^ src/regcomp.c:456:3: note: in expansion of macro ‘REQUIRE’ REQUIRE(MORE(), REG_EESCAPE); ^~~~~~~ src/regcomp.c:54:30: warning: value computed is not used [-Wunused-value] #define REQUIRE(co, e) ((co) || SETERROR(e)) ^ src/regcomp.c:486:3: note: in expansion of macro ‘REQUIRE’ REQUIRE(EATTWO('\\', ')'), REG_EPAREN); ^~~~~~~ src/regcomp.c:54:30: warning: value computed is not used [-Wunused-value] #define REQUIRE(co, e) ((co) || SETERROR(e)) ^ src/regcomp.c:516:3: note: in expansion of macro ‘REQUIRE’ REQUIRE(starordinary, REG_BADRPT); ^~~~~~~ src/regcomp.c:54:30: warning: value computed is not used [-Wunused-value] #define REQUIRE(co, e) ((co) || SETERROR(e)) ^ src/regcomp.c:534:5: note: in expansion of macro ‘REQUIRE’ REQUIRE(count <= count2, REG_BADBR); ^~~~~~~ src/regcomp.c:54:30: warning: value computed is not used [-Wunused-value] #define REQUIRE(co, e) ((co) || SETERROR(e)) ^ src/regcomp.c:543:4: note: in expansion of macro ‘REQUIRE’ REQUIRE(MORE(), REG_EBRACE); ^~~~~~~ src/regcomp.c: In function ‘p_count’: src/regcomp.c:54:30: warning: value computed is not used [-Wunused-value] #define REQUIRE(co, e) ((co) || SETERROR(e)) ^ src/regcomp.c:568:2: note: in expansion of macro ‘REQUIRE’ REQUIRE(ndigits > 0 && count <= DUPMAX, REG_BADBR); ^~~~~~~ src/regcomp.c: In function ‘p_bracket’: src/regcomp.c:54:30: warning: value computed is not used [-Wunused-value] #define REQUIRE(co, e) ((co) || SETERROR(e)) ^ src/regcomp.c:56:24: note: in expansion of macro ‘REQUIRE’ #define MUSTEAT(c, e) (REQUIRE(MORE() && GETNEXT() == (c), e)) ^~~~~~~ src/regcomp.c:608:2: note: in expansion of macro ‘MUSTEAT’ MUSTEAT(']', REG_EBRACK); ^~~~~~~ src/regcomp.c: In function ‘p_b_term’: src/regcomp.c:54:30: warning: value computed is not used [-Wunused-value] #define REQUIRE(co, e) ((co) || SETERROR(e)) ^ src/regcomp.c:679:3: note: in expansion of macro ‘REQUIRE’ REQUIRE(MORE(), REG_EBRACK); ^~~~~~~ src/regcomp.c:54:30: warning: value computed is not used [-Wunused-value] #define REQUIRE(co, e) ((co) || SETERROR(e)) ^ src/regcomp.c:681:3: note: in expansion of macro ‘REQUIRE’ REQUIRE(c != '-' && c != ']', REG_ECTYPE); ^~~~~~~ src/regcomp.c:54:30: warning: value computed is not used [-Wunused-value] #define REQUIRE(co, e) ((co) || SETERROR(e)) ^ src/regcomp.c:683:3: note: in expansion of macro ‘REQUIRE’ REQUIRE(MORE(), REG_EBRACK); ^~~~~~~ src/regcomp.c:54:30: warning: value computed is not used [-Wunused-value] #define REQUIRE(co, e) ((co) || SETERROR(e)) ^ src/regcomp.c:684:3: note: in expansion of macro ‘REQUIRE’ REQUIRE(EATTWO(':', ']'), REG_ECTYPE); ^~~~~~~ src/regcomp.c:54:30: warning: value computed is not used [-Wunused-value] #define REQUIRE(co, e) ((co) || SETERROR(e)) ^ src/regcomp.c:688:3: note: in expansion of macro ‘REQUIRE’ REQUIRE(MORE(), REG_EBRACK); ^~~~~~~ src/regcomp.c:54:30: warning: value computed is not used [-Wunused-value] #define REQUIRE(co, e) ((co) || SETERROR(e)) ^ src/regcomp.c:690:3: note: in expansion of macro ‘REQUIRE’ REQUIRE(c != '-' && c != ']', REG_ECOLLATE); ^~~~~~~ src/regcomp.c:54:30: warning: value computed is not used [-Wunused-value] #define REQUIRE(co, e) ((co) || SETERROR(e)) ^ src/regcomp.c:692:3: note: in expansion of macro ‘REQUIRE’ REQUIRE(MORE(), REG_EBRACK); ^~~~~~~ src/regcomp.c:54:30: warning: value computed is not used [-Wunused-value] #define REQUIRE(co, e) ((co) || SETERROR(e)) ^ src/regcomp.c:693:3: note: in expansion of macro ‘REQUIRE’ REQUIRE(EATTWO('=', ']'), REG_ECOLLATE); ^~~~~~~ src/regcomp.c:54:30: warning: value computed is not used [-Wunused-value] #define REQUIRE(co, e) ((co) || SETERROR(e)) ^ src/regcomp.c:708:3: note: in expansion of macro ‘REQUIRE’ REQUIRE(start <= finish, REG_ERANGE); ^~~~~~~ src/regcomp.c: In function ‘p_b_symbol’: src/regcomp.c:54:30: warning: value computed is not used [-Wunused-value] #define REQUIRE(co, e) ((co) || SETERROR(e)) ^ src/regcomp.c:776:2: note: in expansion of macro ‘REQUIRE’ REQUIRE(MORE(), REG_EBRACK); ^~~~~~~ src/regcomp.c:54:30: warning: value computed is not used [-Wunused-value] #define REQUIRE(co, e) ((co) || SETERROR(e)) ^ src/regcomp.c:782:2: note: in expansion of macro ‘REQUIRE’ REQUIRE(EATTWO('.', ']'), REG_ECOLLATE); ^~~~~~~ gcc -Wall -I./include -I../include -DPOSIX_MISTAKE -c src/regexec.c -o ./obj/regexec.o In file included from src/regexec.c:46:0: src/engine.c: In function ‘sdissect’: src/engine.c:251:17: warning: variable ‘dp’ set but not used [-Wunused-but-set-variable] register char *dp; ^~ In file included from src/regexec.c:95:0: src/engine.c: In function ‘ldissect’: src/engine.c:251:17: warning: variable ‘dp’ set but not used [-Wunused-but-set-variable] register char *dp; ^~ gcc -Wall -I./include -I../include -DPOSIX_MISTAKE -c src/regerror.c -o ./obj/regerror.o gcc -Wall -I./include -I../include -DPOSIX_MISTAKE -c src/regfree.c -o ./obj/regfree.o a - regcomp.o a - regexec.o a - regerror.o a - regfree.o true lib/regex.a lib/regex.a is up to date. ../etc/cifinstall -m 0444 ./lib/regex.a ../lib x - BlockIO.o x - CifString.o x - Exceptions.o x - GenString.o x - ISTable.o x - ITTable.o x - mapped_ptr_vector.o x - mapped_vector.o x - Serializer.o x - TableFile.o x - TTable.o x - regcomp.o x - regexec.o x - regerror.o x - regfree.o a - BlockIO.o a - CifString.o a - Exceptions.o a - GenString.o a - ISTable.o a - ITTable.o a - mapped_ptr_vector.o a - mapped_vector.o a - regcomp.o a - regerror.o a - regexec.o a - regfree.o a - Serializer.o a - TableFile.o a - TTable.o ../etc/cifinstall -m 0444 ./lib/all.a ../lib make[1]: Leaving directory '/var/tmp/portage/sci-libs/cifparse-obj-7.025-r1/work/cifparse-obj-v7.025-prod-src/regex-v2.2' ------------------------------------------------------------ **** Making cif-file-v1.0 **** ------------------------------------------------------------ make[1]: Entering directory '/var/tmp/portage/sci-libs/cifparse-obj-7.025-r1/work/cifparse-obj-v7.025-prod-src/cif-file-v1.0' g++ -ansi -DINCL_TEMPLATE_SRC -Wall -I./include -I../include -c src/CifFile.C -o ./obj/CifFile.o src/CifFile.C: In member function ‘int CifFile::_PrintItemValue(std::ostream&, const string&, unsigned int&, CifFile::eIdentType, unsigned int)’: src/CifFile.C:554:13: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] if (linePos + width - N < _maxCifLineLength) ^~ src/CifFile.C:557:17: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the ‘if’ linePos += width - N; ^~~~~~~ src/CifFile.C:567:17: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] if (linePos + width - N < _maxCifLineLength) ^~ src/CifFile.C:570:21: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the ‘if’ linePos += width - N; ^~~~~~~ src/CifFile.C:665:13: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] if (linePos + width - N < _maxCifLineLength) ^~ src/CifFile.C:668:17: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the ‘if’ linePos += width - N; ^~~~~~~ src/CifFile.C:696:13: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] if (linePos + width - (N - 1) < _maxCifLineLength) ^~ src/CifFile.C:699:17: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the ‘if’ linePos += width - (N - 1); ^~~~~~~ src/CifFile.C: In member function ‘int CifFile::_PrintItemNameInHeader(std::ostream&, const string&, unsigned int&, CifFile::eIdentType, unsigned int)’: src/CifFile.C:752:13: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] if (linePos + width - N < _maxCifLineLength) ^~ src/CifFile.C:755:17: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the ‘if’ linePos += width - N; ^~~~~~~ src/CifFile.C:765:17: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] if (linePos + width - N < _maxCifLineLength) ^~ src/CifFile.C:768:21: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the ‘if’ linePos += width - N; ^~~~~~~ src/CifFile.C:862:13: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] if (linePos + width - N < _maxCifLineLength) ^~ src/CifFile.C:865:17: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the ‘if’ linePos += width - N; ^~~~~~~ src/CifFile.C:893:13: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] if (linePos + width - (N - 1) < _maxCifLineLength) ^~ src/CifFile.C:896:17: note: ...this statement, but the latter is misleadingly indented as if it is guarded by the ‘if’ linePos += width - (N - 1); ^~~~~~~ g++ -ansi -DINCL_TEMPLATE_SRC -Wall -I./include -I../include -c src/DdlFile.C -o ./obj/DdlFile.o g++ -ansi -DINCL_TEMPLATE_SRC -Wall -I./include -I../include -c src/DicFile.C -o ./obj/DicFile.o a - CifFile.o a - DdlFile.o a - DicFile.o true lib/cif-file.a lib/cif-file.a is up to date. ../etc/cifinstall -m 0444 ./lib/cif-file.a ../lib x - BlockIO.o x - CifString.o x - Exceptions.o x - GenString.o x - ISTable.o x - ITTable.o x - mapped_ptr_vector.o x - mapped_vector.o x - regcomp.o x - regerror.o x - regexec.o x - regfree.o x - Serializer.o x - TableFile.o x - TTable.o x - CifFile.o x - DdlFile.o x - DicFile.o a - BlockIO.o a - CifFile.o a - CifString.o a - DdlFile.o a - DicFile.o a - Exceptions.o a - GenString.o a - ISTable.o a - ITTable.o a - mapped_ptr_vector.o a - mapped_vector.o a - regcomp.o a - regerror.o a - regexec.o a - regfree.o a - Serializer.o a - TableFile.o a - TTable.o ../etc/cifinstall -m 0444 ./lib/all.a ../lib make[1]: Leaving directory '/var/tmp/portage/sci-libs/cifparse-obj-7.025-r1/work/cifparse-obj-v7.025-prod-src/cif-file-v1.0' ------------------------------------------------------------ **** Making misclib-v2.2 **** ------------------------------------------------------------ make[1]: Entering directory '/var/tmp/portage/sci-libs/cifparse-obj-7.025-r1/work/cifparse-obj-v7.025-prod-src/misclib-v2.2' In file included from src/ndb_misclib.C:150:0: ./include/ndb_misclib.h:172:5: error: conflicting declaration of C function ‘int strncasecmp(const char*, const char*, unsigned int)’ int strncasecmp (const char *s1, const char *s2, unsigned int n); ^~~~~~~~~~~ In file included from src/ndb_misclib.C:146:0: /usr/include/string.h:533:12: note: previous declaration ‘int strncasecmp(const char*, const char*, size_t)’ extern int strncasecmp (const char *__s1, const char *__s2, size_t __n) ^~~~~~~~~~~ make[1]: *** [Makefile:138: ndb_misclib.o] Error 1 make[1]: Leaving directory '/var/tmp/portage/sci-libs/cifparse-obj-7.025-r1/work/cifparse-obj-v7.025-prod-src/misclib-v2.2' make: *** [Makefile:60: compile] Error 1 * ERROR: sci-libs/cifparse-obj-7.025-r1::gentoo failed (compile phase): * emake failed * * If you need support, post the output of `emerge --info '=sci-libs/cifparse-obj-7.025-r1::gentoo'`, * the complete build log and the output of `emerge -pqv '=sci-libs/cifparse-obj-7.025-r1::gentoo'`. * The complete build log is located at '/var/log/portage/sci-libs:cifparse-obj-7.025-r1:20160917-022820.log'. * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-libs/cifparse-obj-7.025-r1/temp/build.log'. * The ebuild environment file is located at '/var/tmp/portage/sci-libs/cifparse-obj-7.025-r1/temp/environment'. * Working directory: '/var/tmp/portage/sci-libs/cifparse-obj-7.025-r1/work/cifparse-obj-v7.025-prod-src' * S: '/var/tmp/portage/sci-libs/cifparse-obj-7.025-r1/work/cifparse-obj-v7.025-prod-src'