* CPV: sci-chemistry/validation-6.2 * REPO: gentoo * USE: elibc_glibc kernel_linux test userland_GNU x86 >>> Unpacking source... >>> Unpacking pdb-extract-v1.700-prod-src.tar.gz to /var/tmp/portage/sci-chemistry/validation-6.2/work * Applying respect-cflags-and-fix-install.patch ...  [ ok ] * Deleting redundant directories ...  [ ok ] >>> Source unpacked in /var/tmp/portage/sci-chemistry/validation-6.2/work >>> Compiling source in /var/tmp/portage/sci-chemistry/validation-6.2/work/pdb-extract-v1.700-prod-src ... make -j14 Using platform specific configuration for system: gnu4 Platform configuration done. ------------------------------------------------------------ **** Making validation-v6.2 **** ------------------------------------------------------------ make[1]: Entering directory `/var/tmp/portage/sci-chemistry/validation-6.2/work/pdb-extract-v1.700-prod-src/validation-v6.2' i686-pc-linux-gnu-g++ -O2 -pipe -ansi -Wall -Wno-deprecated -DHAVE_STRCASECMP -DINCL_TEMPLATE_SRC -DHAVE_PLACEMENT_NEW -DNO_RANGE_CHECK -I./include -I../include -I/usr/include/rcsb -c ./src/_validation.C -o obj/_validation.o i686-pc-linux-gnu-g++ -O2 -pipe -ansi -Wall -Wno-deprecated -DHAVE_STRCASECMP -DINCL_TEMPLATE_SRC -DHAVE_PLACEMENT_NEW -DNO_RANGE_CHECK -I./include -I../include -I/usr/include/rcsb -c ./src/align_standard.C -o obj/align_standard.o i686-pc-linux-gnu-g++ -O2 -pipe -ansi -Wall -Wno-deprecated -DHAVE_STRCASECMP -DINCL_TEMPLATE_SRC -DHAVE_PLACEMENT_NEW -DNO_RANGE_CHECK -I./include -I../include -I/usr/include/rcsb -c ./src/atom.C -o obj/atom.o i686-pc-linux-gnu-g++ -O2 -pipe -ansi -Wall -Wno-deprecated -DHAVE_STRCASECMP -DINCL_TEMPLATE_SRC -DHAVE_PLACEMENT_NEW -DNO_RANGE_CHECK -I./include -I../include -I/usr/include/rcsb -c ./src/atomlist.C -o obj/atomlist.o i686-pc-linux-gnu-g++ -O2 -pipe -ansi -Wall -Wno-deprecated -DHAVE_STRCASECMP -DINCL_TEMPLATE_SRC -DHAVE_PLACEMENT_NEW -DNO_RANGE_CHECK -I./include -I../include -I/usr/include/rcsb -c ./src/base_information.C -o obj/base_information.o i686-pc-linux-gnu-g++ -O2 -pipe -ansi -Wall -Wno-deprecated -DHAVE_STRCASECMP -DINCL_TEMPLATE_SRC -DHAVE_PLACEMENT_NEW -DNO_RANGE_CHECK -I./include -I../include -I/usr/include/rcsb -c ./src/bond_angle_torsion.C -o obj/bond_angle_torsion.o i686-pc-linux-gnu-g++ -O2 -pipe -ansi -Wall -Wno-deprecated -DHAVE_STRCASECMP -DINCL_TEMPLATE_SRC -DHAVE_PLACEMENT_NEW -DNO_RANGE_CHECK -I./include -I../include -I/usr/include/rcsb -c ./src/check.C -o obj/check.o i686-pc-linux-gnu-g++ -O2 -pipe -ansi -Wall -Wno-deprecated -DHAVE_STRCASECMP -DINCL_TEMPLATE_SRC -DHAVE_PLACEMENT_NEW -DNO_RANGE_CHECK -I./include -I../include -I/usr/include/rcsb -c ./src/color_util.C -o obj/color_util.o i686-pc-linux-gnu-g++ -O2 -pipe -ansi -Wall -Wno-deprecated -DHAVE_STRCASECMP -DINCL_TEMPLATE_SRC -DHAVE_PLACEMENT_NEW -DNO_RANGE_CHECK -I./include -I../include -I/usr/include/rcsb -c ./src/contact.C -o obj/contact.o i686-pc-linux-gnu-g++ -O2 -pipe -ansi -Wall -Wno-deprecated -DHAVE_STRCASECMP -DINCL_TEMPLATE_SRC -DHAVE_PLACEMENT_NEW -DNO_RANGE_CHECK -I./include -I../include -I/usr/include/rcsb -c ./src/datacheck.C -o obj/datacheck.o i686-pc-linux-gnu-g++ -O2 -pipe -ansi -Wall -Wno-deprecated -DHAVE_STRCASECMP -DINCL_TEMPLATE_SRC -DHAVE_PLACEMENT_NEW -DNO_RANGE_CHECK -I./include -I../include -I/usr/include/rcsb -c ./src/gridcell.C -o obj/gridcell.o i686-pc-linux-gnu-g++ -O2 -pipe -ansi -Wall -Wno-deprecated -DHAVE_STRCASECMP -DINCL_TEMPLATE_SRC -DHAVE_PLACEMENT_NEW -DNO_RANGE_CHECK -I./include -I../include -I/usr/include/rcsb -c ./src/misc_util.C -o obj/misc_util.o i686-pc-linux-gnu-g++ -O2 -pipe -ansi -Wall -Wno-deprecated -DHAVE_STRCASECMP -DINCL_TEMPLATE_SRC -DHAVE_PLACEMENT_NEW -DNO_RANGE_CHECK -I./include -I../include -I/usr/include/rcsb -c ./src/na_classification.C -o obj/na_classification.o i686-pc-linux-gnu-g++ -O2 -pipe -ansi -Wall -Wno-deprecated -DHAVE_STRCASECMP -DINCL_TEMPLATE_SRC -DHAVE_PLACEMENT_NEW -DNO_RANGE_CHECK -I./include -I../include -I/usr/include/rcsb -c ./src/ndb_atlas.C -o obj/ndb_atlas.o In file included from ./src/bond_angle_torsion.C:142: ./include/bond_angle_torsion.h:143:19: error: _atom.h: No such file or directory In file included from ./src/bond_angle_torsion.C:142: ./include/bond_angle_torsion.h:147: error: ISO C++ forbids declaration of ‘_ATOM’ with no type ./include/bond_angle_torsion.h:147: error: expected ‘;’ before ‘*’ token ./include/bond_angle_torsion.h:148: error: ISO C++ forbids declaration of ‘_ATOM’ with no type ./include/bond_angle_torsion.h:148: error: expected ‘;’ before ‘*’ token ./include/bond_angle_torsion.h:153: error: ISO C++ forbids declaration of ‘_ATOM’ with no type ./include/bond_angle_torsion.h:153: error: expected ‘;’ before ‘*’ token ./include/bond_angle_torsion.h:154: error: ISO C++ forbids declaration of ‘_ATOM’ with no type ./include/bond_angle_torsion.h:154: error: expected ‘;’ before ‘*’ token ./include/bond_angle_torsion.h:155: error: ISO C++ forbids declaration of ‘_ATOM’ with no type ./include/bond_angle_torsion.h:155: error: expected ‘;’ before ‘*’ token ./include/bond_angle_torsion.h:160: error: ISO C++ forbids declaration of ‘_ATOM’ with no type ./include/bond_angle_torsion.h:160: error: expected ‘;’ before ‘*’ token ./include/bond_angle_torsion.h:161: error: ISO C++ forbids declaration of ‘_ATOM’ with no type ./include/bond_angle_torsion.h:161: error: expected ‘;’ before ‘*’ token ./include/bond_angle_torsion.h:162: error: ISO C++ forbids declaration of ‘_ATOM’ with no type ./include/bond_angle_torsion.h:162: error: expected ‘;’ before ‘*’ token ./include/bond_angle_torsion.h:163: error: ISO C++ forbids declaration of ‘_ATOM’ with no type ./include/bond_angle_torsion.h:163: error: expected ‘;’ before ‘*’ token ./include/bond_angle_torsion.h:167: error: ISO C++ forbids declaration of ‘_ATOM’ with no type ./include/bond_angle_torsion.h:167: error: expected ‘;’ before ‘*’ token ./include/bond_angle_torsion.h:168: error: ISO C++ forbids declaration of ‘_ATOM’ with no type ./include/bond_angle_torsion.h:168: error: expected ‘;’ before ‘*’ token ./include/bond_angle_torsion.h:169: error: ISO C++ forbids declaration of ‘_ATOM’ with no type ./include/bond_angle_torsion.h:169: error: expected ‘;’ before ‘*’ token ./include/bond_angle_torsion.h:170: error: ISO C++ forbids declaration of ‘_ATOM’ with no type ./include/bond_angle_torsion.h:170: error: expected ‘;’ before ‘*’ token ./include/bond_angle_torsion.h:173: warning: ‘cal_angle’ initialized and declared ‘extern’ ./include/bond_angle_torsion.h:173: error: ‘_ATOM’ was not declared in this scope ./include/bond_angle_torsion.h:173: error: ‘atom1’ was not declared in this scope ./include/bond_angle_torsion.h:173: error: ‘_ATOM’ was not declared in this scope ./include/bond_angle_torsion.h:173: error: ‘atom2’ was not declared in this scope ./include/bond_angle_torsion.h:173: error: ‘_ATOM’ was not declared in this scope ./include/bond_angle_torsion.h:173: error: ‘atom3’ was not declared in this scope ./include/bond_angle_torsion.h:173: error: initializer expression list treated as compound expression ./include/bond_angle_torsion.h:174: warning: ‘cal_torsion’ initialized and declared ‘extern’ ./include/bond_angle_torsion.h:174: error: ‘_ATOM’ was not declared in this scope ./include/bond_angle_torsion.h:174: error: ‘atom1’ was not declared in this scope ./include/bond_angle_torsion.h:174: error: ‘_ATOM’ was not declared in this scope ./include/bond_angle_torsion.h:174: error: ‘atom2’ was not declared in this scope ./include/bond_angle_torsion.h:174: error: ‘_ATOM’ was not declared in this scope ./include/bond_angle_torsion.h:174: error: ‘atom3’ was not declared in this scope ./include/bond_angle_torsion.h:174: error: ‘_ATOM’ was not declared in this scope ./include/bond_angle_torsion.h:174: error: ‘atom4’ was not declared in this scope ./include/bond_angle_torsion.h:174: error: initializer expression list treated as compound expression ./include/bond_angle_torsion.h:175: warning: ‘calc_chiral_volume’ initialized and declared ‘extern’ ./include/bond_angle_torsion.h:175: error: ‘_ATOM’ was not declared in this scope ./include/bond_angle_torsion.h:175: error: ‘atom_ic’ was not declared in this scope ./include/bond_angle_torsion.h:175: error: ‘_ATOM’ was not declared in this scope ./include/bond_angle_torsion.h:175: error: ‘atom_iu’ was not declared in this scope ./include/bond_angle_torsion.h:176: error: ‘_ATOM’ was not declared in this scope ./include/bond_angle_torsion.h:176: error: ‘atom_iv’ was not declared in this scope ./include/bond_angle_torsion.h:176: error: ‘_ATOM’ was not declared in this scope ./include/bond_angle_torsion.h:176: error: ‘atom_iw’ was not declared in this scope ./include/bond_angle_torsion.h:176: error: expected primary-expression before ‘double’ ./include/bond_angle_torsion.h:176: error: initializer expression list treated as compound expression ./include/bond_angle_torsion.h:177: warning: ‘cal_bonds’ initialized and declared ‘extern’ ./include/bond_angle_torsion.h:177: error: ‘_ATOM’ was not declared in this scope ./include/bond_angle_torsion.h:177: error: ‘atom1’ was not declared in this scope ./include/bond_angle_torsion.h:177: error: expected primary-expression before ‘const’ ./include/bond_angle_torsion.h:177: error: ‘_ATOM’ was not declared in this scope ./include/bond_angle_torsion.h:177: error: ‘atom2’ was not declared in this scope ./include/bond_angle_torsion.h:177: error: expected primary-expression before ‘const’ ./include/bond_angle_torsion.h:177: error: initializer expression list treated as compound expression ./include/bond_angle_torsion.h:178: warning: ‘cal_angles’ initialized and declared ‘extern’ ./include/bond_angle_torsion.h:178: error: ‘_ATOM’ was not declared in this scope ./include/bond_angle_torsion.h:178: error: ‘atom1’ was not declared in this scope ./include/bond_angle_torsion.h:178: error: expected primary-expression before ‘const’ ./include/bond_angle_torsion.h:178: error: ‘_ATOM’ was not declared in this scope ./include/bond_angle_torsion.h:178: error: ‘atom2’ was not declared in this scope ./include/bond_angle_torsion.h:179: error: expected primary-expression before ‘const’ ./include/bond_angle_torsion.h:179: error: ‘_ATOM’ was not declared in this scope ./include/bond_angle_torsion.h:179: error: ‘atom3’ was not declared in this scope ./include/bond_angle_torsion.h:179: error: expected primary-expression before ‘const’ ./include/bond_angle_torsion.h:179: error: initializer expression list treated as compound expression ./include/bond_angle_torsion.h:180: error: ‘_ATOM’ has not been declared ./include/bond_angle_torsion.h:180: error: ‘_ATOM’ has not been declared ./include/bond_angle_torsion.h:181: error: ‘_ATOM’ has not been declared ./include/bond_angle_torsion.h:181: error: ‘_ATOM’ has not been declared ./include/bond_angle_torsion.h:182: error: ‘_ATOM’ has not been declared ./include/bond_angle_torsion.h:182: error: ‘_ATOM’ has not been declared ./include/bond_angle_torsion.h:183: error: ‘_ATOM’ has not been declared ./include/bond_angle_torsion.h:183: error: ‘_ATOM’ has not been declared ./src/bond_angle_torsion.C:149: error: redefinition of ‘double cal_angle’ ./include/bond_angle_torsion.h:173: error: ‘double cal_angle’ previously defined here ./src/bond_angle_torsion.C:149: error: ‘_ATOM’ was not declared in this scope ./src/bond_angle_torsion.C:149: error: ‘atom1’ was not declared in this scope ./src/bond_angle_torsion.C:149: error: ‘_ATOM’ was not declared in this scope ./src/bond_angle_torsion.C:149: error: ‘atom2’ was not declared in this scope ./src/bond_angle_torsion.C:149: error: ‘_ATOM’ was not declared in this scope ./src/bond_angle_torsion.C:149: error: ‘atom3’ was not declared in this scope ./src/bond_angle_torsion.C:176: error: redefinition of ‘double cal_torsion’ ./include/bond_angle_torsion.h:174: error: ‘double cal_torsion’ previously defined here ./src/bond_angle_torsion.C:176: error: ‘_ATOM’ was not declared in this scope ./src/bond_angle_torsion.C:176: error: ‘atom1’ was not declared in this scope ./src/bond_angle_torsion.C:176: error: ‘_ATOM’ was not declared in this scope ./src/bond_angle_torsion.C:176: error: ‘atom2’ was not declared in this scope ./src/bond_angle_torsion.C:176: error: ‘_ATOM’ was not declared in this scope ./src/bond_angle_torsion.C:176: error: ‘atom3’ was not declared in this scope ./src/bond_angle_torsion.C:176: error: ‘_ATOM’ was not declared in this scope ./src/bond_angle_torsion.C:176: error: ‘atom4’ was not declared in this scope ./src/bond_angle_torsion.C:144: warning: ‘double ndb_dihed_angle(double, double, double, double)’ declared ‘static’ but never defined ./src/bond_angle_torsion.C:145: warning: ‘void crossp3x(double, double, double, double, double, double, double&, double&, double&)’ declared ‘static’ but never defined make[1]: *** [obj/bond_angle_torsion.o] Error 1 make[1]: *** Waiting for unfinished jobs.... ./src/base_information.C:148:20: error: _index.h: No such file or directory ./src/base_information.C:149:22: error: BTreeObj.h: No such file or directory ./src/base_information.C:150:25: error: TblIndexObj.h: No such file or directory ./src/base_information.C:151:25: error: ndb_misclib.h: No such file or directory In file included from ./src/base_information.C:152: ./include/_validation.h:144:22: error: _fileobj.h: No such file or directory In file included from ./src/atomlist.C:141: ./include/atom.h:143:21: error: fstream.h: No such file or directory ./include/atom.h:144:22: error: iostream.h: No such file or directory In file included from ./src/atom.C:145: ./include/atom.h:143:21: error: fstream.h: No such file or directory ./include/atom.h:144:22: error: iostream.h: No such file or directory In file included from ./src/base_information.C:155: ./include/misc_util.h:143:19: error: _atom.h: No such file or directory In file included from ./src/base_information.C:156: ./include/xtal.h:143:21: error: fstream.h: No such file or directory In file included from ./include/xtal.h:145, from ./src/base_information.C:156: ./include/atom.h:144:22: error: iostream.h: No such file or directory In file included from ./src/base_information.C:156: ./include/xtal.h:149:23: error: _molecule.h: No such file or directory ./include/xtal.h:150:22: error: cry_util.h: No such file or directory In file included from ./src/base_information.C:157: /usr/include/rcsb/util.h:11:21: error: CifFile.h: No such file or directory /usr/include/rcsb/util.h:12:23: error: TableFile.h: No such file or directory ./src/datacheck.C:1:22: error: iostream.h: No such file or directory ./src/datacheck.C:2:21: error: fstream.h: No such file or directory In file included from ./src/_validation.C:142: ./include/_validation.h:144:22: error: _fileobj.h: No such file or directory In file included from ./src/atom.C:150: ./include/xtal.h:149:23: error: _molecule.h: No such file or directory ./include/xtal.h:150:22: error: cry_util.h: No such file or directory In file included from ./src/atomlist.C:144: ./include/xtal.h:149:23: error: _molecule.h: No such file or directory ./include/xtal.h:150:22: error: cry_util.h: No such file or directory ./src/_validation.C:143:22: error: erf_util.h: No such file or directory In file included from ./src/_validation.C:144: /usr/include/rcsb/util.h:11:21: error: CifFile.h: No such file or directory /usr/include/rcsb/util.h:12:23: error: TableFile.h: No such file or directory In file included from ./include/list.h:146, from ./include/atom.h:147, from ./src/atomlist.C:141: ./include/symop.h:153: error: ISO C++ forbids declaration of ‘ostream’ with no type ./include/symop.h:153: error: ‘ostream’ is neither function nor member function; cannot be declared friend ./include/symop.h:153: error: expected ‘;’ before ‘&’ token ./include/symop.h:158: error: expected ‘)’ before ‘&’ token ./src/align_standard.C:6:25: error: ndb_misclib.h: No such file or directory In file included from ./src/datacheck.C:7: ./include/datacheck.h:4:24: error: CifFileObj.h: No such file or directory ./include/datacheck.h:5:24: error: DICFileObj.h: No such file or directory ./src/datacheck.C:8:22: error: erf_util.h: No such file or directory In file included from ./include/_validation.h:148, from ./src/base_information.C:152: ./include/check.h:159: error: ‘MxStrLen’ was not declared in this scope In file included from ./src/base_information.C:152: ./include/_validation.h:207: error: ISO C++ forbids declaration of ‘_RESIDUE’ with no type ./include/_validation.h:207: error: expected ‘;’ before ‘*’ token ./include/_validation.h:213: error: ‘COORD’ does not name a type ./include/_validation.h:214: error: ‘COORD’ does not name a type ./include/_validation.h:215: error: ‘COORD’ does not name a type ./include/_validation.h:216: error: ‘COORD’ does not name a type ./include/_validation.h:217: error: ‘COORD’ does not name a type ./include/_validation.h:218: error: ‘COORD’ does not name a type In file included from ./src/check.C:146: ./include/_validation.h:144:22: error: _fileobj.h: No such file or directory ./include/_validation.h:232: error: ISO C++ forbids declaration of ‘_ATOM’ with no type ./include/_validation.h:232: error: expected ‘;’ before ‘*’ token ./include/_validation.h:233: error: ISO C++ forbids declaration of ‘_ATOM’ with no type ./include/_validation.h:233: error: expected ‘;’ before ‘*’ token ./include/_validation.h:234: error: ISO C++ forbids declaration of ‘_ATOM’ with no type ./include/_validation.h:234: error: expected ‘;’ before ‘*’ token ./include/_validation.h:266: error: ISO C++ forbids declaration of ‘_ATOM’ with no type ./include/_validation.h:266: error: expected ‘;’ before ‘*’ token ./include/_validation.h:267: error: ISO C++ forbids declaration of ‘_ATOM’ with no type ./include/_validation.h:267: error: expected ‘;’ before ‘*’ token ./include/_validation.h:268: error: ISO C++ forbids declaration of ‘_ATOM’ with no type ./include/_validation.h:268: error: expected ‘;’ before ‘*’ token ./include/_validation.h:269: error: ISO C++ forbids declaration of ‘_ATOM’ with no type ./include/_validation.h:269: error: expected ‘;’ before ‘*’ token ./include/_validation.h:305: error: ‘CifString’ does not name a type ./include/_validation.h:315: error: ‘CifString’ does not name a type ./include/_validation.h:327: error: ‘COORD’ does not name a type ./include/_validation.h:328: error: ‘COORD’ does not name a type ./include/_validation.h:329: error: ‘COORD’ does not name a type ./include/_validation.h:339: error: ‘COORD’ does not name a type ./include/_validation.h:344: error: ISO C++ forbids declaration of ‘_ATOM’ with no type ./include/_validation.h:344: error: expected ‘;’ before ‘*’ token ./include/_validation.h:348: error: expected class-name before ‘{’ token ./include/_validation.h:377: error: ‘_ATOM’ has not been declared ./include/_validation.h:377: error: ‘_ATOM’ has not been declared ./include/_validation.h:380: error: ‘_ATOM’ has not been declared ./include/_validation.h:380: error: ‘_ATOM’ has not been declared ./include/_validation.h:380: error: ‘_ATOM’ has not been declared ./include/_validation.h:382: error: ‘_ATOM’ has not been declared ./include/_validation.h:382: error: ‘_ATOM’ has not been declared ./include/_validation.h:382: error: ‘_ATOM’ has not been declared ./include/_validation.h:382: error: ‘_ATOM’ has not been declared ./src/check.C:148:22: error: BTreeObj.h: No such file or directory ./include/_validation.h:398: error: ‘CifString’ has not been declared ./include/_validation.h:421: error: ‘_RESIDUE’ has not been declared ./include/_validation.h:422: error: ‘_RESIDUE’ has not been declared ./include/_validation.h:422: error: ‘_RESIDUE’ has not been declared ./include/_validation.h:423: error: ‘_ATOM’ has not been declared ./include/_validation.h:423: error: ‘_ATOM’ has not been declared ./include/_validation.h:423: error: ‘_ATOM’ has not been declared ./include/_validation.h:423: error: ‘_ATOM’ has not been declared ./include/_validation.h:426: error: ‘CifString’ has not been declared ./include/_validation.h:426: error: ‘CifString’ has not been declared ./include/_validation.h:427: error: ‘CifString’ has not been declared ./include/_validation.h:433: error: ‘_MOLECULE’ has not been declared ./include/_validation.h:434: error: ‘_CHAIN’ has not been declared ./include/_validation.h:434: error: ‘COORD’ has not been declared ./include/_validation.h:434: error: ‘_RESIDUE’ has not been declared ./include/_validation.h:435: error: ‘_CHAIN’ has not been declared ./include/_validation.h:436: error: ‘_ATOM’ has not been declared ./include/_validation.h:436: error: ‘_ATOM’ has not been declared ./include/_validation.h:437: error: ‘_CHAIN’ has not been declared ./include/_validation.h:438: error: ‘COORD’ has not been declared ./include/_validation.h:438: error: ‘COORD’ has not been declared ./include/_validation.h:444: error: ‘ISTable’ has not been declared ./include/_validation.h:492: error: ‘TblIndexObj’ does not name a type In file included from ./src/check.C:150: ./include/datacheck.h:4:24: ./include/_validation.h:493: error: ‘TblIndexObj’ does not name a typeerror: CifFileObj.h: No such file or directory ./include/_validation.h:494: error: ‘TblIndexObj’ does not name a type ./include/_validation.h:495: error: ‘TblIndexObj’ does not name a type ./include/_validation.h:496: error: ‘TblIndexObj’ does not name a type ./include/_validation.h:497: error: ‘TblIndexObj’ does not name a type ./include/datacheck.h:5:24: error: ./include/_validation.h:498: error: ‘TblIndexObj’ does not name a type DICFileObj.h: No such file or directory ./include/_validation.h:500: error: ‘CifString’ does not name a type ./include/_validation.h:501: error: ‘CifString’ does not name a type ./include/_validation.h:502: error: ‘CifString’ does not name a type ./src/check.C:152:22: error: erf_util.h: No such file or directory In file included from ./src/check.C:153: /usr/include/rcsb/util.h:11:21: error: CifFile.h: No such file or directory /usr/include/rcsb/util.h:12:23: error: TableFile.h: No such file or directory ./include/_validation.h:507: warning: ‘get_residue_index’ initialized and declared ‘extern’ ./include/_validation.h:507: error: ‘_MOLECULE’ was not declared in this scope ./include/_validation.h:507: error: ‘mol’ was not declared in this scope ./include/_validation.h:507: error: ‘ISTable’ was not declared in this scope ./include/_validation.h:507: error: ‘Table’ was not declared in this scope ./include/_validation.h:507: error: expected primary-expression before ‘const’ ./include/_validation.h:508: error: expected primary-expression before ‘const’ ./include/_validation.h:508: error: expected primary-expression before ‘const’ ./include/_validation.h:508: error: expected primary-expression before ‘const’ ./include/_validation.h:509: error: expected primary-expression before ‘const’ ./include/_validation.h:509: error: expected primary-expression before ‘const’ ./include/_validation.h:509: error: expected primary-expression before ‘const’ ./include/_validation.h:510: error: expected primary-expression before ‘const’ ./include/_validation.h:510: error: expected primary-expression before ‘int’ ./include/_validation.h:510: error: expected primary-expression before ‘int’ ./include/_validation.h:510: error: ‘CifString’ was not declared in this scope ./include/_validation.h:510: error: ‘name’ was not declared in this scope ./include/_validation.h:510: error: initializer expression list treated as compound expression In file included from ./src/misc_util.C:145: ./include/misc_util.h:143:19: error: _atom.h: No such file or directory In file included from ./src/atomlist.C:144: ./include/xtal.h:166: error: ISO C++ forbids declaration of ‘NDBCELLCONST’ with no type ./include/xtal.h:166: error: expected ‘,’ or ‘...’ before ‘*’ token ./include/xtal.h:167: error: ‘COORD’ has not been declared ./include/xtal.h:167: error: ‘COORD’ has not been declared In file included from ./src/base_information.C:155: ./include/misc_util.h:155: error: variable or field ‘arb_rotation’ declared void ./include/misc_util.h:155: error: ‘COORD’ was not declared in this scope ./include/misc_util.h:155: error: ‘COORD’ was not declared in this scope ./include/misc_util.h:155: error: ‘va’ was not declared in this scope ./include/misc_util.h:155: error: expected primary-expression before ‘double’ ./include/misc_util.h:158: error: variable or field ‘get_vector’ declared void ./include/misc_util.h:158: error: ‘COORD’ was not declared in this scope ./include/misc_util.h:158: error: ‘va’ was not declared in this scope ./include/misc_util.h:158: error: ‘COORD’ was not declared in this scope ./include/misc_util.h:158: error: ‘vref’ was not declared in this scope ./include/misc_util.h:158: error: expected primary-expression before ‘double’ ./include/misc_util.h:158: error: ‘COORD’ was not declared in this scope ./include/misc_util.h:158: error: ‘vo’ was not declared in this scope ./include/misc_util.h:159: warning: ‘magang’ initialized and declared ‘extern’ ./include/misc_util.h:159: error: ‘COORD’ was not declared in this scope ./include/misc_util.h:159: error: ‘va’ was not declared in this scope ./include/misc_util.h:159: error: ‘COORD’ was not declared in this scope ./include/misc_util.h:159: error: ‘vb’ was not declared in this scope ./include/misc_util.h:159: error: initializer expression list treated as compound expression ./include/misc_util.h:161: error: variable or field ‘multi_matrix’ declared void ./include/misc_util.h:161: error: ‘COORD’ was not declared in this scope ./include/misc_util.h:161: error: expected primary-expression before ‘const’ ./include/misc_util.h:161: error: expected primary-expression before ‘const’ ./include/misc_util.h:163: error: variable or field ‘vector_init’ declared void ./include/misc_util.h:163: error: ‘COORD’ was not declared in this scope ./include/misc_util.h:163: error: ‘dest’ was not declared in this scope ./include/misc_util.h:163: error: expected primary-expression before ‘const’ ./include/misc_util.h:163: error: expected primary-expression before ‘const’ ./include/misc_util.h:163: error: expected primary-expression before ‘const’ ./include/misc_util.h:164: error: variable or field ‘vector_copy’ declared void ./include/misc_util.h:164: error: ‘COORD’ was not declared in this scope ./include/misc_util.h:164: error: ‘dest’ was not declared in this scope ./include/misc_util.h:164: error: expected primary-expression before ‘const’ ./include/misc_util.h:165: error: variable or field ‘vector_sum’ declared void ./include/misc_util.h:165: error: ‘COORD’ was not declared in this scope ./include/misc_util.h:165: error: ‘dest’ was not declared in this scope ./include/misc_util.h:165: error: expected primary-expression before ‘const’ ./include/misc_util.h:165: error: expected primary-expression before ‘const’ ./include/misc_util.h:166: error: variable or field ‘vector_difference’ declared void ./include/misc_util.h:166: error: ‘COORD’ was not declared in this scope ./include/misc_util.h:166: error: ‘dest’ was not declared in this scope ./include/misc_util.h:166: error: expected primary-expression before ‘const’ ./include/misc_util.h:166: error: expected primary-expression before ‘const’ ./include/misc_util.h:167: error: variable or field ‘vector_scaled’ declared void ./include/misc_util.h:167: error: ‘COORD’ was not declared in this scope ./include/misc_util.h:167: error: ‘dest’ was not declared in this scope ./include/misc_util.h:167: error: expected primary-expression before ‘const’ ./include/misc_util.h:167: error: expected primary-expression before ‘const’ ./include/misc_util.h:168: error: variable or field ‘vector_add’ declared void ./include/misc_util.h:168: error: ‘COORD’ was not declared in this scope ./include/misc_util.h:168: error: ‘dest’ was not declared in this scope ./include/misc_util.h:168: error: expected primary-expression before ‘const’ ./include/misc_util.h:169: error: variable or field ‘vector_subtract’ declared void ./include/misc_util.h:169: error: ‘COORD’ was not declared in this scope ./include/misc_util.h:169: error: ‘dest’ was not declared in this scope ./include/misc_util.h:169: error: expected primary-expression before ‘const’ ./include/misc_util.h:170: error: variable or field ‘vector_scale’ declared void ./include/misc_util.h:170: error: ‘COORD’ was not declared in this scope ./include/misc_util.h:170: error: ‘dest’ was not declared in this scope ./include/misc_util.h:170: error: expected primary-expression before ‘const’ ./include/misc_util.h:171: error: variable or field ‘vector_invert’ declared void ./include/misc_util.h:171: error: ‘COORD’ was not declared in this scope ./include/misc_util.h:171: error: ‘v’ was not declared in this scope ./include/misc_util.h:172: error: variable or field ‘vector_reverse’ declared void ./include/misc_util.h:172: error: ‘COORD’ was not declared in this scope ./include/misc_util.h:172: error: ‘v’ was not declared in this scope ./include/misc_util.h:173: error: variable or field ‘vector_sum_scaled’ declared void ./include/misc_util.h:173: error: ‘COORD’ was not declared in this scope ./include/misc_util.h:173: error: ‘dest’ was not declared in this scope ./include/misc_util.h:173: error: expected primary-expression before ‘const’ ./include/misc_util.h:173: error: expected primary-expression before ‘const’ ./include/misc_util.h:173: error: expected primary-expression before ‘const’ ./include/misc_util.h:174: error: variable or field ‘vector_add_scaled’ declared void ./include/misc_util.h:174: error: ‘COORD’ was not declared in this scope ./include/misc_util.h:174: error: ‘dest’ was not declared in this scope ./include/misc_util.h:174: error: expected primary-expression before ‘const’ ./include/misc_util.h:174: error: expected primary-expression before ‘const’ ./include/misc_util.h:175: error: ISO C++ forbids declaration of ‘COORD’ with no type ./include/misc_util.h:175: error: expected ‘,’ or ‘...’ before ‘v1’ ./include/misc_util.h:176: error: variable or field ‘vector_cross_product’ declared void ./include/misc_util.h:176: error: ‘COORD’ was not declared in this scope ./include/misc_util.h:176: error: ‘vz’ was not declared in this scope ./include/misc_util.h:176: error: expected primary-expression before ‘const’ ./include/misc_util.h:176: error: expected primary-expression before ‘const’ ./include/misc_util.h:177: error: variable or field ‘vector_normalize’ declared void ./include/misc_util.h:177: error: ‘COORD’ was not declared in this scope ./include/misc_util.h:177: error: ‘v’ was not declared in this scope ./include/misc_util.h:178: error: variable or field ‘vector_middle’ declared void ./include/misc_util.h:178: error: ‘COORD’ was not declared in this scope ./include/misc_util.h:178: error: ‘dest’ was not declared in this scope ./include/misc_util.h:178: error: expected primary-expression before ‘const’ ./include/misc_util.h:178: error: expected primary-expression before ‘const’ ./include/misc_util.h:179: error: ISO C++ forbids declaration of ‘COORD’ with no type ./include/misc_util.h:179: error: expected ‘,’ or ‘...’ before ‘v1’ ./include/misc_util.h:180: error: ISO C++ forbids declaration of ‘COORD’ with no type ./include/misc_util.h:180: error: expected ‘,’ or ‘...’ before ‘v’ ./include/misc_util.h:181: error: ISO C++ forbids declaration of ‘COORD’ with no type ./include/misc_util.h:181: error: expected ‘,’ or ‘...’ before ‘va’ ./include/misc_util.h:182: error: variable or field ‘vector_orthogonal’ declared void ./include/misc_util.h:182: error: ‘COORD’ was not declared in this scope ./include/misc_util.h:182: error: ‘va’ was not declared in this scope ./include/misc_util.h:182: error: ‘COORD’ was not declared in this scope ./include/misc_util.h:182: error: ‘vref’ was not declared in this scope ./include/misc_util.h:194: error: variable or field ‘matrix_transform’ declared void ./include/misc_util.h:194: error: ‘COORD’ was not declared in this scope ./include/misc_util.h:194: error: ‘v’ was not declared in this scope ./include/misc_util.h:194: error: expected primary-expression before ‘const’ ./include/misc_util.h:195: error: variable or field ‘matrix_rotate’ declared void ./include/misc_util.h:195: error: ‘COORD’ was not declared in this scope ./include/misc_util.h:195: error: ‘v’ was not declared in this scope ./include/misc_util.h:195: error: expected primary-expression before ‘const’ ./include/misc_util.h:196: error: variable or field ‘matrix_rotate_translate’ declared void ./include/misc_util.h:196: error: ‘COORD’ was not declared in this scope ./include/misc_util.h:196: error: ‘v’ was not declared in this scope ./include/misc_util.h:196: error: expected primary-expression before ‘const’ ./src/color_util.C:145:23: error: erf_iolib.h: No such file or directory ./src/color_util.C:146:25: error: ndb_misclib.h: No such file or directory In file included from ./include/list.h:146, from ./include/atom.h:147, from ./include/xtal.h:145, from ./src/base_information.C:156: ./include/symop.h:153: error: ISO C++ forbids declaration of ‘ostream’ with no type ./include/symop.h:153: error: ‘ostream’ is neither function nor member function; cannot be declared friend ./include/symop.h:153: error: expected ‘;’ before ‘&’ token ./include/symop.h:158: error: expected ‘)’ before ‘&’ token In file included from ./src/color_util.C:147: /usr/include/rcsb/util.h:11:21: error: CifFile.h: No such file or directory /usr/include/rcsb/util.h:12:23: error: TableFile.h: No such file or directory In file included from ./src/base_information.C:156: ./include/xtal.h:166: error: ISO C++ forbids declaration of ‘NDBCELLCONST’ with no type ./include/xtal.h:166: error: expected ‘,’ or ‘...’ before ‘*’ token ./include/xtal.h:167: error: ‘COORD’ has not been declared ./include/xtal.h:167: error: ‘COORD’ has not been declared In file included from ./src/base_information.C:157: /usr/include/rcsb/util.h:67: error: ‘CifFile’ was not declared in this scope /usr/include/rcsb/util.h:67: error: ‘fobj’ was not declared in this scope /usr/include/rcsb/util.h:67: error: expected primary-expression before ‘const’ /usr/include/rcsb/util.h:68: error: expected primary-expression before ‘const’ /usr/include/rcsb/util.h:68: error: expected primary-expression before ‘const’ /usr/include/rcsb/util.h:68: error: initializer expression list treated as compound expression /usr/include/rcsb/util.h:69: error: ‘CifFile’ was not declared in this scope /usr/include/rcsb/util.h:69: error: ‘fobj’ was not declared in this scope /usr/include/rcsb/util.h:69: error: expected primary-expression before ‘const’ /usr/include/rcsb/util.h:70: error: expected primary-expression before ‘const’ /usr/include/rcsb/util.h:70: error: expected primary-expression before ‘const’ /usr/include/rcsb/util.h:71: error: expected primary-expression before ‘long’ /usr/include/rcsb/util.h:71: error: initializer expression list treated as compound expression /usr/include/rcsb/util.h:74: error: ‘int check_category(const char*, char*, char*)’ redeclared as different kind of symbol ./include/check.h:191: error: previous declaration of ‘CHECK_CATEGORY check_category [6]’ ./src/base_information.C:160: error: ‘_RESIDUE’ was not declared in this scope ./src/base_information.C:160: error: ‘res’ was not declared in this scope ./src/base_information.C:160: error: expected primary-expression before ‘const’ ./src/base_information.C:160: error: expected primary-expression before ‘const’ ./src/base_information.C:161: error: expected primary-expression before ‘const’ ./src/base_information.C:161: error: expected primary-expression before ‘const’ ./src/base_information.C:161: error: expected primary-expression before ‘const’ ./src/base_information.C:161: error: initializer expression list treated as compound expression ./src/base_information.C:162: error: ‘_RESIDUE’ was not declared in this scope ./src/base_information.C:162: error: ‘residue’ was not declared in this scope ./src/base_information.C:162: error: expected primary-expression before ‘double’ ./src/base_information.C:162: error: expected primary-expression before ‘double’ ./src/base_information.C:163: error: expected primary-expression before ‘double’ ./src/base_information.C:163: error: expected primary-expression before ‘int’ ./src/base_information.C:163: error: initializer expression list treated as compound expression ./src/base_information.C:166: error: ISO C++ forbids declaration of ‘NDBCELLCONST’ with no type ./src/base_information.C:166: error: expected ‘,’ or ‘...’ before ‘*’ token ./src/base_information.C:168: error: ‘_ATOM’ was not declared in this scope ./src/base_information.C:168: error: ‘atom_a’ was not declared in this scope ./src/base_information.C:168: error: ‘_ATOM’ was not declared in this scope ./src/base_information.C:168: error: ‘atom_b’ was not declared in this scope ./src/base_information.C:168: error: expected primary-expression before ‘const’ ./src/base_information.C:169: error: expected primary-expression before ‘const’ ./src/base_information.C:169: error: expected primary-expression before ‘const’ ./src/base_information.C:169: error: expected primary-expression before ‘const’ ./src/base_information.C:169: error: expected primary-expression before ‘const’ ./src/base_information.C:169: error: initializer expression list treated as compound expression ./src/base_information.C:172: error: variable or field ‘bpstep_par’ declared void ./src/base_information.C:172: error: ‘COORD’ was not declared in this scope ./src/base_information.C:172: error: expected primary-expression before ‘const’ ./src/base_information.C:172: error: ‘COORD’ was not declared in this scope ./src/base_information.C:173: error: expected primary-expression before ‘const’ ./src/base_information.C:173: error: expected primary-expression before ‘double’ ./src/base_information.C:173: error: ‘COORD’ was not declared in this scope ./src/base_information.C:173: error: ‘COORD’ was not declared in this scope ./src/base_information.C:173: error: ‘mst_org’ was not declared in this scope ./src/base_information.C:174: error: variable or field ‘helical_par’ declared void ./src/base_information.C:174: error: ‘COORD’ was not declared in this scope ./src/base_information.C:174: error: expected primary-expression before ‘const’ ./src/base_information.C:174: error: ‘COORD’ was not declared in this scope ./src/base_information.C:175: error: expected primary-expression before ‘const’ ./src/base_information.C:175: error: expected primary-expression before ‘double’ ./src/base_information.C:175: error: ‘COORD’ was not declared in this scope ./src/base_information.C:175: error: ‘COORD’ was not declared in this scope ./src/base_information.C:175: error: ‘mst_org’ was not declared in this scope ./src/base_information.C:176: error: ISO C++ forbids declaration of ‘COORD’ with no type ./src/base_information.C:176: error: expected ‘,’ or ‘...’ before ‘P_1_i_plus_1’ ./src/base_information.C: In member function ‘void _VALIDATION::get_bspair_information()’: ./src/base_information.C:209: error: ‘_CHAIN’ was not declared in this scope ./src/base_information.C:209: error: ‘chain’ was not declared in this scope ./src/base_information.C:211: error: ‘BTreeObj’ was not declared in this scope ./src/base_information.C:211: error: ‘_SIndex’ was not declared in this scope ./src/base_information.C:211: error: ‘_SymmetryIndex’ was not declared in this scope ./src/base_information.C:212: error: expected ‘;’ before ‘index’ ./src/base_information.C:216: error: ‘_num_mol’ was not declared in this scope ./src/base_information.C:217: error: ‘_cell’ was not declared in this scope ./src/base_information.C:223: error: ‘_molecules’ was not declared in this scope ./src/base_information.C:225: error: ‘ATOMN_TOKEN’ was not declared in this scope ./src/base_information.C:227: error: ‘_RESIDUE’ was not declared in this scope ./src/base_information.C:227: error: ‘res’ was not declared in this scope ./src/base_information.C:233: error: ‘_cell’ was not declared in this scope ./src/base_information.C:233: error: ‘base_frame’ cannot be used as a function ./src/base_information.C:259: error: ‘_cell’ was not declared in this scope ./src/base_information.C:288: error: ‘index’ does not have class type ./src/base_information.C:292: error: ‘index’ does not have class type ./src/base_information.C:294: error: ‘index’ does not have class type ./src/base_information.C:322: error: ‘struct BASE_BASE_PARAMS’ has no member named ‘ChnID_I’ ./src/base_information.C:323: error: ‘struct BASE_BASE_PARAMS’ has no member named ‘ChnID_J’ ./src/base_information.C:333: error: ‘ATOMN_TOKEN’ was not declared in this scope ./src/base_information.C:335: error: ‘_RESIDUE’ was not declared in this scope ./src/base_information.C:335: error: ‘res’ was not declared in this scope ./src/base_information.C:337: error: ‘base_frame’ cannot be used as a function ./src/base_information.C:345: error: ‘base_frame’ cannot be used as a function ./src/base_information.C: In member function ‘int _VALIDATION::get_bspair_information(int, _BASE**, int*)’: ./src/base_information.C:379: error: ‘_cell’ was not declared in this scope ./src/base_information.C:379: error: ‘_molecules’ was not declared in this scope ./src/base_information.C: In member function ‘void _VALIDATION::insert_base_pairs(int, CONTACT**)’: ./src/base_information.C:481: error: ‘BTreeObj’ was not declared in this scope ./src/base_information.C:481: error: expected primary-expression before ‘>’ token ./src/base_information.C:481: error: ‘_BPIdx’ was not declared in this scope ./src/base_information.C:509: error: ‘res_name_cmp_na’ was not declared in this scope ./src/base_information.C:527: error: ‘res_name_cmp_na’ was not declared in this scope In file included from ./include/_validation.h:147, from ./src/_validation.C:142: ./include/plot.h: In member function ‘void _plot::set_x_axis_title(const char*)’: ./include/plot.h:199: error: ‘strcpy’ was not declared in this scope ./include/plot.h: In member function ‘void _plot::set_y_axis_title(const char*)’: ./include/plot.h:200: error: ‘strcpy’ was not declared in this scope ./include/plot.h: In member function ‘void _plot::set_picture_title(const char*)’: ./include/plot.h:201: error: ‘strcpy’ was not declared in this scope In file included from ./include/_validation.h:148, from ./src/_validation.C:142: ./include/check.h: At global scope: ./include/check.h:159: error: ‘MxStrLen’ was not declared in this scope ./src/base_information.C: In member function ‘void _VALIDATION::re_ordering(int, int*, _BASE**)’: ./src/base_information.C:552: error: ‘COORD’ was not declared in this scope ./src/base_information.C:552: error: expected ‘;’ before ‘zave’ In file included from ./src/_validation.C:142: ./include/_validation.h:207: error: ISO C++ forbids declaration of ‘_RESIDUE’ with no type ./src/base_information.C:556: error: ‘bp_xyz’ was not declared in this scope ./include/_validation.h:207: error: expected ‘;’ before ‘*’ token ./src/base_information.C:556: error: expected type-specifier before ‘COORD’ ./src/base_information.C:556: error: expected ‘;’ before ‘COORD’ ./include/_validation.h:213: error: ‘COORD’ does not name a type ./include/_validation.h:214: error: ‘COORD’ does not name a type ./src/base_information.C:560: error: ‘struct _BASE’ has no member named ‘org’ ./src/base_information.C:561: error: ‘struct _BASE’ has no member named ‘org’ ./src/base_information.C:561: error: ‘vector_middle’ was not declared in this scope ./src/base_information.C:573: error: ‘struct _BASE’ has no member named ‘orien’ ./include/_validation.h:215: error: ‘COORD’ does not name a type ./include/_validation.h:216: error: ‘COORD’ does not name a type ./include/_validation.h:217: error: ‘COORD’ does not name a type ./src/base_information.C:574: error: ‘struct _BASE’ has no member named ‘orien’ ./include/_validation.h:218: error: ‘COORD’ does not name a type ./src/base_information.C:576: error: ‘zave’ was not declared in this scope ./src/base_information.C:576: error: ‘struct _BASE’ has no member named ‘orien’ ./src/base_information.C:577: error: ‘struct _BASE’ has no member named ‘orien’./include/_validation.h:232: error: ISO C++ forbids declaration of ‘_ATOM’ with no type ./src/base_information.C:577: error: ‘vector_difference’ was not declared in this scope ./include/_validation.h:232: error: expected ‘;’ before ‘*’ token ./include/_validation.h:233: error: ISO C++ forbids declaration of ‘_ATOM’ with no type ./src/base_information.C:578: error: ‘zave’ was not declared in this scope ./include/_validation.h:233: error: expected ‘;’ before ‘*’ token ./src/base_information.C:578: error: ‘struct _BASE’ has no member named ‘orien’./include/_validation.h:234: error: ISO C++ forbids declaration of ‘_ATOM’ with no type ./include/_validation.h:234: error: expected ‘;’ before ‘*’ token ./src/base_information.C:579: error: ‘struct _BASE’ has no member named ‘orien’ ./src/base_information.C:579: error: ‘vector_sum’ was not declared in this scope ./src/base_information.C:582: error: ‘txyz’ was not declared in this scope ./src/base_information.C:582: error: ‘vector_difference’ was not declared in this scope ./include/_validation.h:266: error: ISO C++ forbids declaration of ‘_ATOM’ with no type ./include/_validation.h:266: error: expected ‘;’ before ‘*’ token ./include/_validation.h:267: error: ISO C++ forbids declaration of ‘_ATOM’ with no type ./include/_validation.h:267: error: expected ‘;’ before ‘*’ token ./include/_validation.h:268: error: ISO C++ forbids declaration of ‘_ATOM’ with no type ./include/_validation.h:268: error: expected ‘;’ before ‘*’ token ./include/_validation.h:269: error: ISO C++ forbids declaration of ‘_ATOM’ with no type ./include/_validation.h:269: error: expected ‘;’ before ‘*’ token ./src/base_information.C:605: error: ‘txyz’ was not declared in this scope ./src/base_information.C:605: error: ‘vector_difference’ was not declared in this scope ./src/base_information.C:606: error: ‘zave’ was not declared in this scope ./src/base_information.C:610: error: ‘txyz2’ was not declared in this scope ./include/_validation.h:305: error: ‘CifString’ does not name a type ./src/base_information.C:621: error: ‘txyz2’ was not declared in this scope ./include/_validation.h:315: error: ‘CifString’ does not name a type ./src/base_information.C:636: error: ‘txyz2’ was not declared in this scope ./include/_validation.h:327: error: ‘COORD’ does not name a type ./include/_validation.h:328: error: ‘COORD’ does not name a type ./include/_validation.h:329: error: ‘COORD’ does not name a type ./include/_validation.h:339: error: ‘COORD’ does not name a type ./include/_validation.h:344: error: ISO C++ forbids declaration of ‘_ATOM’ with no type ./include/_validation.h:344: error: expected ‘;’ before ‘*’ token ./include/_validation.h:348: error: expected class-name before ‘{’ token ./include/_validation.h:377: error: ‘_ATOM’ has not been declared ./include/_validation.h:377: error: ‘_ATOM’ has not been declared ./include/_validation.h:380: error: ‘_ATOM’ has not been declared ./include/_validation.h:380: error: ‘_ATOM’ has not been declared ./include/_validation.h:380: error: ‘_ATOM’ has not been declared ./include/_validation.h:382: error: ‘_ATOM’ has not been declared ./include/_validation.h:382: error: ‘_ATOM’ has not been declared ./include/_validation.h:382: error: ‘_ATOM’ has not been declared ./include/_validation.h:382: error: ‘_ATOM’ has not been declared ./src/base_information.C:729: error: type ‘’ argument given to ‘delete’, expected pointer ./include/_validation.h:398: error: ‘CifString’ has not been declared ./include/_validation.h:421: error: ‘_RESIDUE’ has not been declared ./include/_validation.h:422: error: ‘_RESIDUE’ has not been declared ./include/_validation.h:422: error: ‘_RESIDUE’ has not been declared ./include/_validation.h:423: error: ‘_ATOM’ has not been declared ./include/_validation.h:423: error: ‘_ATOM’ has not been declared ./include/_validation.h:423: error: ‘_ATOM’ has not been declared ./include/_validation.h:423: error: ‘_ATOM’ has not been declared ./include/_validation.h:426: error: ‘CifString’ has not been declared ./include/_validation.h:426: error: ‘CifString’ has not been declared ./include/_validation.h:427: error: ‘CifString’ has not been declared ./include/_validation.h:433: error: ‘_MOLECULE’ has not been declared ./include/_validation.h:434: error: ‘_CHAIN’ has not been declared ./include/_validation.h:434: error: ‘COORD’ has not been declared ./include/_validation.h:434: error: ‘_RESIDUE’ has not been declared ./include/_validation.h:435: error: ‘_CHAIN’ has not been declared ./include/_validation.h:436: error: ‘_ATOM’ has not been declared ./include/_validation.h:436: error: ‘_ATOM’ has not been declared ./include/_validation.h:437: error: ‘_CHAIN’ has not been declared ./include/_validation.h:438: error: ‘COORD’ has not been declared ./include/_validation.h:438: error: ‘COORD’ has not been declared ./src/base_information.C:790: error: ‘txyz’ was not declared in this scope ./src/base_information.C:790: error: ‘struct _BASE’ has no member named ‘orien’ ./src/base_information.C:790: error: ‘struct _BASE’ has no member named ‘orien’ ./src/base_information.C:790: error: ‘vector_sum’ was not declared in this scope ./src/base_information.C:791: error: ‘txyz2’ was not declared in this scope ./src/base_information.C:791: error: ‘struct _BASE’ has no member named ‘orien’ ./include/_validation.h:444: error: ‘ISTable’ has not been declared ./src/base_information.C:791: error: ‘struct _BASE’ has no member named ‘orien’ ./src/base_information.C:792: error: ‘magang’ cannot be used as a function ./src/base_information.C:797: error: ‘struct _BASE’ has no member named ‘orien’ ./src/base_information.C:798: error: ‘struct _BASE’ has no member named ‘orien’ ./src/base_information.C:798: error: ‘vector_difference’ was not declared in this scope ./src/base_information.C:799: error: ‘struct _BASE’ has no member named ‘orien’ ./src/base_information.C:800: error: ‘struct _BASE’ has no member named ‘orien’ ./src/base_information.C:801: error: ‘vector_normalize’ was not declared in this scope ./src/base_information.C:804: error: ‘struct _BASE’ has no member named ‘orien’ ./src/base_information.C:805: error: ‘struct _BASE’ has no member named ‘orien’ ./include/_validation.h:492: error: ‘TblIndexObj’ does not name a type ./include/_validation.h:493: error: ‘TblIndexObj’ does not name a type ./include/_validation.h:494: error: ‘TblIndexObj’ does not name a type ./include/_validation.h:495: error: ‘TblIndexObj’ does not name a type ./include/_validation.h:496: error: ‘TblIndexObj’ does not name a type ./include/_validation.h:497: error: ‘TblIndexObj’ does not name a type ./include/_validation.h:498: error: ‘TblIndexObj’ does not name a type ./include/_validation.h:500: error: ‘CifString’ does not name a type ./include/_validation.h:501: error: ‘CifString’ does not name a type ./include/_validation.h:502: error: ‘CifString’ does not name a type ./include/_validation.h:507: warning: ‘get_residue_index’ initialized and declared ‘extern’ ./include/_validation.h:507: error: ‘_MOLECULE’ was not declared in this scope ./include/_validation.h:507: error: ‘mol’ was not declared in this scope ./include/_validation.h:507: error: ‘ISTable’ was not declared in this scope ./include/_validation.h:507: error: ‘Table’ was not declared in this scope ./include/_validation.h:507: error: expected primary-expression before ‘const’ ./include/_validation.h:508: error: expected primary-expression before ‘const’ ./include/_validation.h:508: error: expected primary-expression before ‘const’ ./include/_validation.h:508: error: expected primary-expression before ‘const’ ./include/_validation.h:509: error: expected primary-expression before ‘const’ ./include/_validation.h:509: error: expected primary-expression before ‘const’ ./include/_validation.h:509: error: expected primary-expression before ‘const’ ./include/_validation.h:510: error: expected primary-expression before ‘const’ ./include/_validation.h:510: error: expected primary-expression before ‘int’ ./include/_validation.h:510: error: expected primary-expression before ‘int’ ./include/_validation.h:510: error: ‘CifString’ was not declared in this scope ./include/_validation.h:510: error: ‘name’ was not declared in this scope ./include/_validation.h:510: error: initializer expression list treated as compound expression In file included from ./src/_validation.C:144: /usr/include/rcsb/util.h:67: error: ‘CifFile’ was not declared in this scope /usr/include/rcsb/util.h:67: error: ‘fobj’ was not declared in this scope /usr/include/rcsb/util.h:67: error: expected primary-expression before ‘const’ /usr/include/rcsb/util.h:68: error: expected primary-expression before ‘const’ /usr/include/rcsb/util.h:68: error: expected primary-expression before ‘const’ /usr/include/rcsb/util.h:68: error: initializer expression list treated as compound expression /usr/include/rcsb/util.h:69: error: ‘CifFile’ was not declared in this scope /usr/include/rcsb/util.h:69: error: ‘fobj’ was not declared in this scope /usr/include/rcsb/util.h:69: error: expected primary-expression before ‘const’ /usr/include/rcsb/util.h:70: error: expected primary-expression before ‘const’ /usr/include/rcsb/util.h:70: error: expected primary-expression before ‘const’ /usr/include/rcsb/util.h:71: error: expected primary-expression before ‘long’ /usr/include/rcsb/util.h:71: error: initializer expression list treated as compound expression /usr/include/rcsb/util.h:74: error: ‘int check_category(const char*, char*, char*)’ redeclared as different kind of symbol ./src/base_information.C:926: error: type ‘’ argument given to ‘delete’, expected pointer In file included from ./src/misc_util.C:145: ./include/misc_util.h:155: error: variable or field ‘arb_rotation’ declared void ./include/misc_util.h:155: error: ‘COORD’ was not declared in this scope ./include/misc_util.h:155: error: ‘COORD’ was not declared in this scope ./include/misc_util.h:155: error: ‘va’ was not declared in this scope ./include/misc_util.h:155: error: expected primary-expression before ‘double’ ./include/misc_util.h:158: error: variable or field ‘get_vector’ declared void ./include/misc_util.h:158: error: ‘COORD’ was not declared in this scope ./include/misc_util.h:158: error: ‘va’ was not declared in this scope ./include/misc_util.h:158: error: ‘COORD’ was not declared in this scope ./include/misc_util.h:158: error: ‘vref’ was not declared in this scope ./include/misc_util.h:158: error: expected primary-expression before ‘double’ ./include/misc_util.h:158: error: ‘COORD’ was not declared in this scope ./include/misc_util.h:158: error: ‘vo’ was not declared in this scope ./include/misc_util.h:159: warning: ‘magang’ initialized and declared ‘extern’ ./include/misc_util.h:159: error: ‘COORD’ was not declared in this scope ./include/misc_util.h:159: error: ‘va’ was not declared in this scope ./include/misc_util.h:159: error: ‘COORD’ was not declared in this scope ./include/misc_util.h:159: error: ‘vb’ was not declared in this scope ./include/misc_util.h:159: error: initializer expression list treated as compound expression ./include/misc_util.h:161: error: variable or field ‘multi_matrix’ declared void ./include/misc_util.h:161: error: ‘COORD’ was not declared in this scope ./include/misc_util.h:161: error: expected primary-expression before ‘const’ ./include/misc_util.h:161: error: expected primary-expression before ‘const’ ./include/misc_util.h:163: error: variable or field ‘vector_init’ declared void ./include/misc_util.h:163: error: ‘COORD’ was not declared in this scope ./include/misc_util.h:163: error: ‘dest’ was not declared in this scope ./include/misc_util.h:163: error: expected primary-expression before ‘const’ ./include/misc_util.h:163: error: expected primary-expression before ‘const’ ./include/misc_util.h:163: error: expected primary-expression before ‘const’ ./include/misc_util.h:164: error: variable or field ‘vector_copy’ declared void ./include/misc_util.h:164: error: ‘COORD’ was not declared in this scope ./include/misc_util.h:164: error: ‘dest’ was not declared in this scope ./include/misc_util.h:164: error: expected primary-expression before ‘const’ ./include/misc_util.h:165: error: variable or field ‘vector_sum’ declared void ./include/misc_util.h:165: error: ‘COORD’ was not declared in this scope ./include/misc_util.h:165: error: ‘dest’ was not declared in this scope ./include/misc_util.h:165: error: expected primary-expression before ‘const’ ./include/misc_util.h:165: error: expected primary-expression before ‘const’ ./include/misc_util.h:166: error: variable or field ‘vector_difference’ declared void ./include/misc_util.h:166: error: ‘COORD’ was not declared in this scope ./include/misc_util.h:166: error: ‘dest’ was not declared in this scope ./include/misc_util.h:166: error: expected primary-expression before ‘const’ ./include/misc_util.h:166: error: expected primary-expression before ‘const’ ./include/misc_util.h:167: error: variable or field ‘vector_scaled’ declared void ./include/misc_util.h:167: error: ‘COORD’ was not declared in this scope ./include/misc_util.h:167: error: ‘dest’ was not declared in this scope ./include/misc_util.h:167: error: expected primary-expression before ‘const’ ./include/misc_util.h:167: error: expected primary-expression before ‘const’ ./include/misc_util.h:168: error: variable or field ‘vector_add’ declared void ./include/misc_util.h:168: error: ‘COORD’ was not declared in this scope ./include/misc_util.h:168: error: ‘dest’ was not declared in this scope ./include/misc_util.h:168: error: expected primary-expression before ‘const’ ./include/misc_util.h:169: error: variable or field ‘vector_subtract’ declared void ./include/misc_util.h:169: error: ‘COORD’ was not declared in this scope ./include/misc_util.h:169: error: ‘dest’ was not declared in this scope ./include/misc_util.h:169: error: expected primary-expression before ‘const’ ./include/misc_util.h:170: error: variable or field ‘vector_scale’ declared void ./include/misc_util.h:170: error: ‘COORD’ was not declared in this scope ./include/misc_util.h:170: error: ‘dest’ was not declared in this scope ./include/misc_util.h:170: error: expected primary-expression before ‘const’ ./include/misc_util.h:171: error: variable or field ‘vector_invert’ declared void ./include/misc_util.h:171: error: ‘COORD’ was not declared in this scope ./include/misc_util.h:171: error: ‘v’ was not declared in this scope ./include/misc_util.h:172: error: variable or field ‘vector_reverse’ declared void ./include/misc_util.h:172: error: ‘COORD’ was not declared in this scope ./include/misc_util.h:172: error: ‘v’ was not declared in this scope ./include/misc_util.h:173: error: variable or field ‘vector_sum_scaled’ declared void ./include/misc_util.h:173: error: ‘COORD’ was not declared in this scope ./include/misc_util.h:173: error: ‘dest’ was not declared in this scope ./include/misc_util.h:173: error: expected primary-expression before ‘const’ ./include/misc_util.h:173: error: expected primary-expression before ‘const’ ./include/misc_util.h:173: error: expected primary-expression before ‘const’ ./include/misc_util.h:174: error: variable or field ‘vector_add_scaled’ declared void ./include/misc_util.h:174: error: ‘COORD’ was not declared in this scope ./include/misc_util.h:174: error: ‘dest’ was not declared in this scope ./include/misc_util.h:174: error: expected primary-expression before ‘const’ ./include/misc_util.h:174: error: expected primary-expression before ‘const’ ./include/misc_util.h:175: error: ISO C++ forbids declaration of ‘COORD’ with no type ./include/misc_util.h:175: error: expected ‘,’ or ‘...’ before ‘v1’ ./include/misc_util.h:176: error: variable or field ‘vector_cross_product’ declared void ./include/misc_util.h:176: error: ‘COORD’ was not declared in this scope ./include/misc_util.h:176: error: ‘vz’ was not declared in this scope ./include/misc_util.h:176: error: expected primary-expression before ‘const’ ./include/misc_util.h:176: error: expected primary-expression before ‘const’ ./include/misc_util.h:177: error: variable or field ‘vector_normalize’ declared void ./include/misc_util.h:177: error: ‘COORD’ was not declared in this scope ./include/misc_util.h:177: error: ‘v’ was not declared in this scope ./include/misc_util.h:178: error: variable or field ‘vector_middle’ declared void ./include/misc_util.h:178: error: ‘COORD’ was not declared in this scope ./include/misc_util.h:178: error: ‘dest’ was not declared in this scope ./include/misc_util.h:178: error: expected primary-expression before ‘const’ ./include/misc_util.h:178: error: expected primary-expression before ‘const’ ./include/misc_util.h:179: error: ISO C++ forbids declaration of ‘COORD’ with no type ./include/misc_util.h:179: error: expected ‘,’ or ‘...’ before ‘v1’ ./include/misc_util.h:180: error: ISO C++ forbids declaration of ‘COORD’ with no type ./include/misc_util.h:180: error: expected ‘,’ or ‘...’ before ‘v’ ./include/misc_util.h:181: error: ISO C++ forbids declaration of ‘COORD’ with no type ./include/misc_util.h:181: error: expected ‘,’ or ‘...’ before ‘va’ ./include/misc_util.h:182: error: variable or field ‘vector_orthogonal’ declared void ./include/misc_util.h:182: error: ‘COORD’ was not declared in this scope ./include/misc_util.h:182: error: ‘va’ was not declared in this scope ./include/misc_util.h:182: error: ‘COORD’ was not declared in this scope ./include/misc_util.h:182: error: ‘vref’ was not declared in this scope ./include/misc_util.h:194: error: variable or field ‘matrix_transform’ declared void ./include/misc_util.h:194: error: ‘COORD’ was not declared in this scope ./include/misc_util.h:194: error: ‘v’ was not declared in this scope ./include/misc_util.h:194: error: expected primary-expression before ‘const’ ./include/misc_util.h:195: error: variable or field ‘matrix_rotate’ declared void ./include/misc_util.h:195: error: ‘COORD’ was not declared in this scope ./include/misc_util.h:195: error: ‘v’ was not declared in this scope ./include/misc_util.h:195: error: expected primary-expression before ‘const’ ./include/misc_util.h:196: error: variable or field ‘matrix_rotate_translate’ declared void ./include/misc_util.h:196: error: ‘COORD’ was not declared in this scope ./include/misc_util.h:196: error: ‘v’ was not declared in this scope ./include/misc_util.h:196: error: expected primary-expression before ‘const’ ./src/misc_util.C:148: error: variable or field ‘arb_rotation’ declared void ./src/misc_util.C:148: error: ‘COORD’ was not declared in this scope ./src/misc_util.C:148: error: ‘COORD’ was not declared in this scope ./src/misc_util.C:148: error: ‘va’ was not declared in this scope ./src/misc_util.C:148: error: expected primary-expression before ‘double’ make[1]: *** [obj/misc_util.o] Error 1 ./src/base_information.C: In member function ‘void _VALIDATION::get_parameters(int, int*, _BASE**)’: ./src/base_information.C:937: error: ‘COORD’ was not declared in this scope ./src/base_information.C:937: error: expected ‘;’ before ‘mfi’ ./src/base_information.C:938: error: expected ‘;’ before ‘mst_orien’ ./src/base_information.C:940: error: ‘_RESIDUE’ was not declared in this scope ./src/base_information.C:940: error: ‘res1’ was not declared in this scope ./src/base_information.C:940: error: ‘res2’ was not declared in this scope ./src/base_information.C:940: error: ‘res3’ was not declared in this scope ./src/base_information.C:940: error: ‘res4’ was not declared in this scope ./src/base_information.C:942: error: ‘mfoi_prev’ was not declared in this scope ./src/base_information.C:948: error: ‘struct _BASE’ has no member named ‘orien’ ./src/base_information.C:949: error: ‘struct _BASE’ has no member named ‘orien’ ./src/base_information.C:950: error: ‘struct _BASE’ has no member named ‘orien’ ./src/base_information.C:950: error: ‘vector_reverse’ was not declared in this scope ./src/base_information.C:951: error: ‘struct _BASE’ has no member named ‘orien’ ./src/base_information.C:959: error: ‘mst_org’ was not declared in this scope ./src/base_information.C:959: error: ‘struct _BASE’ has no member named ‘org’ ./src/base_information.C:960: error: ‘struct _BASE’ has no member named ‘org’ ./src/base_information.C:960: error: ‘vector_difference’ was not declared in this scope ./src/base_information.C:961: error: ‘mst_org’ was not declared in this scope ./src/base_information.C:962: error: ‘struct _BASE’ has no member named ‘orien’ ./src/base_information.C:968: error: ‘struct _BASE’ has no member named ‘orien’ ./src/base_information.C:968: error: ‘vector_reverse’ was not declared in this scope ./src/base_information.C:969: error: ‘struct _BASE’ has no member named ‘orien’ ./src/base_information.C:976: error: ‘aveS’ was not declared in this scope ./src/base_information.C:976: error: expected type-specifier before ‘COORD’ ./src/base_information.C:976: error: expected ‘;’ before ‘COORD’ ./src/base_information.C:977: error: ‘aveH’ was not declared in this scope ./src/base_information.C:977: error: expected type-specifier before ‘COORD’ ./src/base_information.C:977: error: expected ‘;’ before ‘COORD’ ./src/base_information.C:979: error: ‘vector_init’ was not declared in this scope ./src/base_information.C:983: error: ‘struct _BASE’ has no member named ‘orien’ ./src/base_information.C:983: error: ‘struct _BASE’ has no member named ‘org’ ./src/base_information.C:984: error: ‘struct _BASE’ has no member named ‘orien’ ./src/base_information.C:984: error: ‘struct _BASE’ has no member named ‘org’ ./src/base_information.C:985: error: ‘mfi’ was not declared in this scope ./src/base_information.C:985: error: ‘mfoi’ was not declared in this scope ./src/base_information.C:985: error: ‘bpstep_par’ was not declared in this scope ./src/base_information.C:987: error: ‘struct _BASE’ has no member named ‘res’ ./src/base_information.C:988: error: ‘struct _BASE’ has no member named ‘res’ ./src/base_information.C:1001: error: ‘struct BASE_BASE_PARAMS’ has no member named ‘ChnID_I’ ./src/base_information.C:1008: error: ‘struct BASE_BASE_PARAMS’ has no member named ‘ChnID_J’ ./src/base_information.C:1054: error: ‘mfi_prev’ was not declared in this scope ./src/base_information.C:1058: error: ‘mfi_prev’ was not declared in this scope ./src/base_information.C:1058: error: ‘mst_orien’ was not declared in this scope ./src/base_information.C:1058: error: ‘mst_org’ was not declared in this scope ./src/base_information.C:1059: error: ‘mst_orienH’ was not declared in this scope ./src/base_information.C:1059: error: ‘mst_orgH’ was not declared in this scope ./src/base_information.C:1059: error: ‘helical_par’ was not declared in this scope ./src/base_information.C:1066: error: ‘struct _BASE’ has no member named ‘P_xyz’ ./src/base_information.C:1067: error: ‘struct _BASE’ has no member named ‘P_xyz’ ./src/base_information.C:1069: error: ‘struct _BASE’ has no member named ‘P_xyz’ ./src/base_information.C:1070: error: ‘struct _BASE’ has no member named ‘P_xyz’ ./src/base_information.C:1077: error: ‘struct _BASE’ has no member named ‘res’ ./src/base_information.C:1078: error: ‘struct _BASE’ has no member named ‘res’ ./src/base_information.C:1090: error: ‘struct INTER_BASE_PARAMS’ has no member named ‘ChnID_I1’ ./src/base_information.C:1098: error: ‘struct INTER_BASE_PARAMS’ has no member named ‘ChnID_J1’ In file included from ./include/_validation.h:148, from ./src/check.C:146: ./include/check.h:159: error: ‘MxStrLen’ was not declared in this scope In file included from ./src/check.C:146: ./include/_validation.h:207: error: ISO C++ forbids declaration of ‘_RESIDUE’ with no type ./include/_validation.h:207: error: expected ‘;’ before ‘*’ token ./include/_validation.h:213: error: ‘COORD’ does not name a type ./include/_validation.h:214: error: ‘COORD’ does not name a type ./include/_validation.h:215: error: ‘COORD’ does not name a type ./include/_validation.h:216: error: ‘COORD’ does not name a type ./include/_validation.h:217: error: ‘COORD’ does not name a type ./include/_validation.h:218: error: ‘COORD’ does not name a type ./include/_validation.h:232: error: ISO C++ forbids declaration of ‘_ATOM’ with no type ./include/_validation.h:232: error: expected ‘;’ before ‘*’ token ./include/_validation.h:233: error: ISO C++ forbids declaration of ‘_ATOM’ with no type ./include/_validation.h:233: error: expected ‘;’ before ‘*’ token ./include/_validation.h:234: error: ISO C++ forbids declaration of ‘_ATOM’ with no type ./include/_validation.h:234: error: expected ‘;’ before ‘*’ token ./include/_validation.h:266: error: ISO C++ forbids declaration of ‘_ATOM’ with no type ./include/_validation.h:266: error: expected ‘;’ before ‘*’ token ./include/_validation.h:267: error: ISO C++ forbids declaration of ‘_ATOM’ with no type ./include/_validation.h:267: error: expected ‘;’ before ‘*’ token ./include/_validation.h:268: error: ISO C++ forbids declaration of ‘_ATOM’ with no type ./include/_validation.h:268: error: expected ‘;’ before ‘*’ token ./include/_validation.h:269: error: ISO C++ forbids declaration of ‘_ATOM’ with no type ./src/base_information.C:1113: error: ‘struct INTER_BASE_PARAMS’ has no member named ‘ChnID_I2’./include/_validation.h:269: error: expected ‘;’ before ‘*’ token ./src/base_information.C:1121: error: ‘struct INTER_BASE_PARAMS’ has no member named ‘ChnID_J2’ ./include/_validation.h:305: error: ‘CifString’ does not name a type ./include/_validation.h:315: error: ‘CifString’ does not name a type ./include/_validation.h:327: error: ‘COORD’ does not name a type ./include/_validation.h:328: error: ‘COORD’ does not name a type ./include/_validation.h:329: error: ‘COORD’ does not name a type ./include/_validation.h:339: error: ‘COORD’ does not name a type ./include/_validation.h:344: error: ISO C++ forbids declaration of ‘_ATOM’ with no type ./include/_validation.h:344: error: expected ‘;’ before ‘*’ token ./include/_validation.h:348: error: expected class-name before ‘{’ token ./src/base_information.C:1184: error: type ‘’ argument given to ‘delete’, expected pointer ./include/_validation.h:377: error: ‘_ATOM’ has not been declared./src/base_information.C:1185: error: type ‘’ argument given to ‘delete’, expected pointer ./include/_validation.h:377: error: ‘_ATOM’ has not been declared ./include/_validation.h:380: error: ‘_ATOM’ has not been declared ./include/_validation.h:380: error: ‘_ATOM’ has not been declared ./include/_validation.h:380: error: ‘_ATOM’ has not been declared ./include/_validation.h:382: error: ‘_ATOM’ has not been declared ./include/_validation.h:382: error: ‘_ATOM’ has not been declared ./include/_validation.h:382: error: ‘_ATOM’ has not been declared ./include/_validation.h:382: error: ‘_ATOM’ has not been declared ./include/check.h:191: error: previous declaration of ‘CHECK_CATEGORY check_category [6]’ ./include/_validation.h:398: error: ‘CifString’ has not been declared ./src/_validation.C:146: error: ‘_STBIOL’ has not been declared ./src/_validation.C:148: error: ‘_STBIOL’ has not been declared ./src/_validation.C:150: error: ‘_STBIOL’ has not been declared ./src/_validation.C: In constructor ‘_VALIDATION::_VALIDATION(int, int)’: ./src/_validation.C:153: error: class ‘_VALIDATION’ does not have any field named ‘_FileObj’ ./include/_validation.h:421: error: ‘_RESIDUE’ has not been declared ./include/_validation.h:422: error: ‘_RESIDUE’ has not been declared ./include/_validation.h:422: error: ‘_RESIDUE’ has not been declared ./include/_validation.h:423: error: ‘_ATOM’ has not been declared In file included from ./include/gridcell.h:144./include/_validation.h:423: error: ‘_ATOM’ has not been declared, from ./src/gridcell.C:142 : ./include/atom.h:143:21: ./include/_validation.h:423: error: ‘_ATOM’ has not been declarederror: fstream.h: No such file or directory ./include/atom.h:144:22:./include/_validation.h:423: error: ‘_ATOM’ has not been declared error: iostream.h: No such file or directory ./include/_validation.h:426: error: ‘CifString’ has not been declared ./include/_validation.h:426: error: ‘CifString’ has not been declared ./include/_validation.h:427: error: ‘CifString’ has not been declared ./include/_validation.h:433: error: ‘_MOLECULE’ has not been declared ./include/_validation.h:434: error: ‘_CHAIN’ has not been declared ./include/_validation.h:434: error: ‘COORD’ has not been declared ./include/_validation.h:434: error: ‘_RESIDUE’ has not been declared ./include/_validation.h:435: error: ‘_CHAIN’ has not been declared ./src/_validation.C:179: error: ‘_bondResIndex’ was not declared in this scope ./include/_validation.h:436: error: ‘_ATOM’ has not been declared ./src/_validation.C:180: error: ‘_bondNamIndex’ was not declared in this scope ./include/_validation.h:436: error: ‘_ATOM’ has not been declared ./src/_validation.C:181: error: ‘_bondComIndex’ was not declared in this scope ./src/_validation.C:182: error: ‘_angleResIndex’ was not declared in this scope./include/_validation.h:437: error: ‘_CHAIN’ has not been declared ./src/_validation.C:183: error: ‘_angleNamIndex’ was not declared in this scope ./src/_validation.C:184: error: ‘_angleComIndex’ was not declared in this scope ./src/_validation.C:185: error: ‘_torsionIndex’ was not declared in this scope ./include/_validation.h:438: error: ‘COORD’ has not been declared ./src/_validation.C:187: error: ‘_spell_check’ was not declared in this scope ./include/_validation.h:438: error: ‘COORD’ has not been declared ./src/_validation.C:188: error: ‘_large_cell’ was not declared in this scope ./src/_validation.C:189: error: ‘_date_error’ was not declared in this scope ./include/_validation.h:444: error: ‘ISTable’ has not been declared ./include/_validation.h:492: error: ‘TblIndexObj’ does not name a type ./include/_validation.h:493: error: ‘TblIndexObj’ does not name a type ./include/_validation.h:494: error: ‘TblIndexObj’ does not name a type ./include/_validation.h:495: error: ‘TblIndexObj’ does not name a type ./include/_validation.h:496: error: ‘TblIndexObj’ does not name a type ./include/_validation.h:497: error: ‘TblIndexObj’ does not name a type ./include/_validation.h:498: error: ‘TblIndexObj’ does not name a type ./include/_validation.h:500: error: ‘CifString’ does not name a type ./include/_validation.h:501: error: ‘CifString’ does not name a type ./include/_validation.h:502: error: ‘CifString’ does not name a type ./include/_validation.h:507: warning: ‘get_residue_index’ initialized and declared ‘extern’ ./include/_validation.h:507: error: ‘_MOLECULE’ was not declared in this scope ./include/_validation.h:507: error: ‘mol’ was not declared in this scope ./include/_validation.h:507: error: ‘ISTable’ was not declared in this scope ./include/_validation.h:507: error: ‘Table’ was not declared in this scope ./include/_validation.h:507: error: expected primary-expression before ‘const’ ./include/_validation.h:508: error: expected primary-expression before ‘const’ ./include/_validation.h:508: error: expected primary-expression before ‘const’ ./include/_validation.h:508: error: expected primary-expression before ‘const’ ./include/_validation.h:509: error: expected primary-expression before ‘const’ ./include/_validation.h:509: error: expected primary-expression before ‘const’ ./include/_validation.h:509: error: expected primary-expression before ‘const’ ./include/_validation.h:510: error: expected primary-expression before ‘const’ ./include/_validation.h:510: error: expected primary-expression before ‘int’ ./include/_validation.h:510: error: expected primary-expression before ‘int’ ./include/_validation.h:510: error: ‘CifString’ was not declared in this scope ./include/_validation.h:510: error: ‘name’ was not declared in this scope ./include/_validation.h:510: error: initializer expression list treated as compound expression ./src/base_information.C: At global scope: ./src/base_information.C:1188: error: variable or field ‘create_blocks’ declared void ./src/base_information.C:1188: error: ‘_CHAIN’ was not declared in this scope ./src/base_information.C:1188: error: ‘chain’ was not declared in this scope ./src/base_information.C:1188: error: expected primary-expression before ‘const’ ./include/base_information.h:374: warning: ‘_base_type’ defined but not used ./include/base_information.h:703: warning: ‘base_hbond_type’ defined but not used ./include/base_information.h:727: warning: ‘R_RingAtom’ defined but not used ./include/base_information.h:728: warning: ‘Y_RingAtom’ defined but not used ./include/base_information.h:730: warning: ‘R_BLOCK’ defined but not used ./include/base_information.h:741: warning: ‘Y_BLOCK’ defined but not used ./include/base_information.h:752: warning: ‘STAND_A’ defined but not used ./include/base_information.h:771: warning: ‘STAND_C’ defined but not used ./include/base_information.h:790: warning: ‘STAND_G’ defined but not used ./include/base_information.h:809: warning: ‘STAND_P’ defined but not used ./include/base_information.h:829: warning: ‘STAND_T’ defined but not used ./include/base_information.h:849: warning: ‘STAND_U’ defined but not used ./src/base_information.C:159: warning: ‘void realloc_base(_BASE***, int, int&)’ declared ‘static’ but never defined ./src/base_information.C:162: warning: ‘find_match’ defined but not used ./src/base_information.C:164: warning: ‘_BASE_PAIR* find_all_pairs(int, _BASE**)’ declared ‘static’ but never defined ./src/base_information.C:165: warning: ‘CONTACT** find_real_base_pairs(int, _BASE**, _BASE_PAIR*, int&, int)’ declared ‘static’ but never defined ./src/base_information.C:168: warning: ‘cal_dist’ defined but not used ./src/base_information.C:170: warning: ‘int get_best_pair(_BASE_PAIR*, int&, int&, int&, int&, int*)’ declared ‘static’ but never defined ./src/base_information.C:176: warning: ‘void project_xyzP(int)’ declared ‘static’ but never defined ./src/base_information.C:178: warning: ‘double distance_ab(_BASE*, int, _BASE*, int)’ declared ‘static’ but never defined ./src/base_information.C:179: warning: ‘void get_ij(int, int, int*, int&, int&)’ declared ‘static’ but never defined ./src/base_information.C:180: warning: ‘void reverse(int, int, int*)’ declared ‘static’ but never defined ./src/base_information.C:181: warning: ‘int is_linked(_BASE*, _BASE*)’ declared ‘static’ but never defined ./src/base_information.C:182: warning: ‘int is_wc_geometry(_BASE*, _BASE*)’ declared ‘static’ but never defined ./src/base_information.C:183: warning: ‘int check_others(_BASE**, int, int, int, int)’ declared ‘static’ but never defined ./src/base_information.C:185: warning: ‘int check_direction(int*, int*, int*, int*, _BASE**, int*)’ declared ‘static’ but never defined ./src/base_information.C:187: warning: ‘int find_atom_index(int, _ATOMNAME*, const char*)’ declared ‘static’ but never defined ./src/base_information.C:193: warning: ‘int base_hbond_type_compare(const void*, const void*)’ declared ‘static’ but never defined ./src/base_information.C:194: warning: ‘int name_compare1(const void*, const void*)’ declared ‘static’ but never defined ./src/base_information.C:195: warning: ‘int base_type_compare(const void*, const void*)’ declared ‘static’ but never defined ./src/base_information.C:196: warning: ‘int atom_edge_compare(const void*, const void*)’ declared ‘static’ but never defined In file included from ./src/check.C:149: ./include/check_global.h:217: warning: missing braces around initializer for ‘ATOM_FIELD [4]’ ./include/check_global.h:217: warning: missing braces around initializer for ‘ATOM_FIELD’ ./include/check_global.h:217: error: braces around scalar initializer for type ‘int’ In file included from ./include/list.h:146, from ./include/atom.h:147, from ./src/atom.C:145: ./include/symop.h:153: error: ISO C++ forbids declaration of ‘ostream’ with no type ./include/symop.h:153: error: ‘ostream’ is neither function nor member function; cannot be declared friend ./include/symop.h:153: error: expected ‘;’ before ‘&’ token ./include/symop.h:158: error: expected ‘)’ before ‘&’ token make[1]: *** [obj/base_information.o] Error 1 ./include/check_global.h:217: warning: missing braces around initializer for ‘ATOM_FIELD [4]’ ./include/check_global.h:217: warning: missing braces around initializer for ‘ATOM_FIELD’ ./include/check_global.h:217: error: braces around scalar initializer for type ‘int’ ./include/check_global.h:217: warning: missing braces around initializer for ‘ATOM_FIELD [4]’ ./include/check_global.h:217: warning: missing braces around initializer for ‘ATOM_FIELD’ ./include/check_global.h:217: error: braces around scalar initializer for type ‘int’ ./include/check_global.h:217: warning: missing braces around initializer for ‘ATOM_FIELD [4]’ ./include/check_global.h:217: warning: missing braces around initializer for ‘ATOM_FIELD’ ./include/check_global.h:217: error: braces around scalar initializer for type ‘int’ ./include/check_global.h:217: warning: missing braces around initializer for ‘ATOM_FIELD [4]’ ./include/check_global.h:217: warning: missing braces around initializer for ‘ATOM_FIELD’ ./include/check_global.h:217: error: braces around scalar initializer for type ‘int’ ./include/check_global.h:217: warning: missing braces around initializer for ‘ATOM_FIELD [4]’ ./include/check_global.h:217: warning: missing braces around initializer for ‘ATOM_FIELD’ ./include/check_global.h:217: error: braces around scalar initializer for type ‘int’ ./include/check_global.h:217: warning: missing braces around initializer for ‘ATOM_FIELD [4]’ ./include/check_global.h:217: warning: missing braces around initializer for ‘ATOM_FIELD’ ./include/check_global.h:217: error: braces around scalar initializer for type ‘int’ ./include/check_global.h:217: warning: missing braces around initializer for ‘ATOM_FIELD [4]’ ./include/check_global.h:217: warning: missing braces around initializer for ‘ATOM_FIELD’ ./include/check_global.h:217: error: braces around scalar initializer for type ‘int’ ./include/check_global.h:217: warning: missing braces around initializer for ‘ATOM_FIELD [4]’ ./include/check_global.h:217: warning: missing braces around initializer for ‘ATOM_FIELD’ ./include/check_global.h:217: error: braces around scalar initializer for type ‘int’ ./include/check_global.h:217: warning: missing braces around initializer for ‘ATOM_FIELD [4]’ ./include/check_global.h:217: warning: missing braces around initializer for ‘ATOM_FIELD’ ./include/check_global.h:217: error: braces around scalar initializer for type ‘int’ ./include/check_global.h:217: warning: missing braces around initializer for ‘ATOM_FIELD [4]’ ./include/check_global.h:217: warning: missing braces around initializer for ‘ATOM_FIELD’ ./include/check_global.h:217: error: braces around scalar initializer for type ‘int’ ./include/check_global.h:217: warning: missing braces around initializer for ‘ATOM_FIELD [4]’ ./include/check_global.h:217: warning: missing braces around initializer for ‘ATOM_FIELD’ ./include/check_global.h:217: error: braces around scalar initializer for type ‘int’ ./include/check_global.h:217: error: invalid conversion from ‘const char*’ to ‘int’ ./include/check_global.h:217: error: invalid conversion from ‘const char*’ to ‘int’ ./include/check_global.h:217: error: invalid conversion from ‘const char*’ to ‘int’ ./include/check_global.h:217: error: invalid conversion from ‘const char*’ to ‘int’ ./include/check_global.h:217: error: invalid conversion from ‘const char*’ to ‘int’ ./include/check_global.h:217: error: invalid conversion from ‘const char*’ to ‘int’ ./include/check_global.h:217: error: invalid conversion from ‘const char*’ to ‘int’ ./include/check_global.h:217: error: invalid conversion from ‘const char*’ to ‘int’ ./include/check_global.h:217: error: invalid conversion from ‘const char*’ to ‘int’ ./include/check_global.h:217: error: invalid conversion from ‘const char*’ to ‘int’ ./include/check_global.h:217: error: invalid conversion from ‘const char*’ to ‘int’ ./include/check_global.h:217: error: invalid conversion from ‘const char*’ to ‘int’ In file included from ./src/check.C:150: ./include/datacheck.h:7: warning: ‘DictionaryDataChecking’ initialized and declared ‘extern’ ./include/datacheck.h:7: error: ‘CifFileObj’ was not declared in this scope ./include/datacheck.h:7: error: ‘in’ was not declared in this scope ./include/datacheck.h:7: error: ‘DICFileObj’ was not declared in this scope ./include/datacheck.h:7: error: ‘ref’ was not declared in this scope ./include/datacheck.h:7: error: expected primary-expression before ‘*’ token ./include/datacheck.h:7: error: ‘fp’ was not declared in this scope ./include/datacheck.h:8: error: expected primary-expression before ‘const’ ./include/datacheck.h:8: error: expected primary-expression before ‘int’ ./include/datacheck.h:8: error: ‘CifString’ was not declared in this scope ./include/datacheck.h:8: error: ‘date_error’ was not declared in this scope ./include/datacheck.h:8: error: initializer expression list treated as compound expression make[1]: *** [obj/atomlist.o] Error 1 In file included from ./src/check.C:153: /usr/include/rcsb/util.h:67: error: ‘CifFile’ was not declared in this scope /usr/include/rcsb/util.h:67: error: ‘fobj’ was not declared in this scope /usr/include/rcsb/util.h:67: error: expected primary-expression before ‘const’ /usr/include/rcsb/util.h:68: error: expected primary-expression before ‘const’ /usr/include/rcsb/util.h:68: error: expected primary-expression before ‘const’ /usr/include/rcsb/util.h:68: error: initializer expression list treated as compound expression /usr/include/rcsb/util.h:69: error: ‘CifFile’ was not declared in this scope /usr/include/rcsb/util.h:69: error: ‘fobj’ was not declared in this scope /usr/include/rcsb/util.h:69: error: expected primary-expression before ‘const’ /usr/include/rcsb/util.h:70: error: expected primary-expression before ‘const’ /usr/include/rcsb/util.h:70: error: expected primary-expression before ‘const’ /usr/include/rcsb/util.h:71: error: expected primary-expression before ‘long’ /usr/include/rcsb/util.h:71: error: initializer expression list treated as compound expression /usr/include/rcsb/util.h:74: error: ‘int check_category(const char*, char*, char*)’ redeclared as different kind of symbol ./include/check_global.h:219: error: previous declaration of ‘CHECK_CATEGORY check_category [6]’ ./src/check.C:188: error: ‘TblIndexObj’ does not name a type ./src/check.C:192: error: variable or field ‘check_tokens’ declared void ./src/check.C:192: error: ‘_MOLECULE’ was not declared in this scope ./src/check.C:192: error: ‘mol’ was not declared in this scope ./src/check.C:192: error: ‘Cards_Info_Format’ was not declared in this scope ./src/check.C:192: error: ‘CardInfo’ was not declared in this scope ./src/check.C:193: error: expected primary-expression before ‘const’ ./src/check.C:193: error: expected primary-expression before ‘*’ token ./src/check.C:194: error: expected primary-expression before ‘const’ ./src/check.C:194: error: expected primary-expression before ‘const’ ./src/check.C:194: error: expected primary-expression before ‘*’ token ./src/check.C:194: error: ‘fp’ was not declared in this scope ./src/check.C:195: error: variable or field ‘check_categorys’ declared void ./src/check.C:195: error: ‘_MOLECULE’ was not declared in this scope ./src/check.C:195: error: ‘mol’ was not declared in this scope ./src/check.C:195: error: ‘ISTable’ was not declared in this scope ./src/check.C:195: error: ‘Table’ was not declared in this scope ./src/check.C:195: error: expected primary-expression before ‘*’ token ./src/check.C:195: error: ‘category’ was not declared in this scope ./src/check.C:196: error: expected primary-expression before ‘*’ token ./src/check.C:196: error: ‘fp’ was not declared in this scope ./src/check.C:196: error: expected primary-expression before ‘const’ ./src/check.C:196: error: expected primary-expression before ‘int’ ./src/check.C:197: error: variable or field ‘check_categorys1’ declared void ./src/check.C:197: error: ‘_MOLECULE’ was not declared in this scope ./src/check.C:197: error: ‘mol’ was not declared in this scope ./src/check.C:197: error: ‘ISTable’ was not declared in this scope ./src/check.C:197: error: ‘Table’ was not declared in this scope ./src/check.C:197: error: expected primary-expression before ‘*’ token ./src/check.C:197: error: ‘category’ was not declared in this scope ./src/check.C:198: error: expected primary-expression before ‘*’ token ./src/check.C:198: error: ‘fp’ was not declared in this scope ./src/check.C:198: error: expected primary-expression before ‘const’ ./src/check.C:198: error: expected primary-expression before ‘int’ ./src/check.C:199: error: variable or field ‘check_seqnum_redundancy’ declared void ./src/check.C:199: error: ‘_MOLECULE’ was not declared in this scope ./src/check.C:199: error: ‘mol’ was not declared in this scope ./src/check.C:199: error: expected primary-expression before ‘const’ ./src/check.C:199: error: expected primary-expression before ‘*’ token ./src/check.C:199: error: ‘fp’ was not declared in this scope ./src/check.C:199: error: expected primary-expression before ‘int’ ./src/check.C: In function ‘void get_taxonomylist(int)’: ./src/check.C:207: error: ‘CifString’ was not declared in this scope ./src/check.C:207: error: expected ‘;’ before ‘cifstring’ ./src/check.C:211: error: ‘TaxnomyList’ was not declared in this scope ./src/check.C:213: error: ‘root_dir’ was not declared in this scope ./src/check.C:220: error: ‘cifstring’ was not declared in this scope ./src/check.C:217: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result ./src/check.C: In member function ‘void _VALIDATION::write_check_results(FILE*)’: ./src/check.C:230: error: ‘CifString’ was not declared in this scope ./src/check.C:230: error: expected ‘;’ before ‘annotator’ ./src/check.C:231: error: ‘ISTable’ was not declared in this scope ./src/check.C:231: error: ‘Table’ was not declared in this scope ./src/check.C:233: error: ‘annotator’ was not declared in this scope ./src/check.C:234: error: ‘_CifObj’ was not declared in this scope ./src/check.C:234: error: ‘_StructureId’ was not declared in this scope ./src/check.C:235: error: ‘is_empty_table’ was not declared in this scope ./src/check.C:237: error: ‘get_value’ was not declared in this scope ./src/check.C:239: error: ‘_StructureId’ was not declared in this scope ./src/check.C:241: error: ‘_Error_Check’ was not declared in this scope ./src/check.C:245: error: ‘_Error_Check’ was not declared in this scope ./src/check.C:249: error: ‘_Error_Check’ was not declared in this scope ./src/check.C:253: error: ‘_Error_Check’ was not declared in this scope ./src/check.C:257: error: ‘_Error_Check’ was not declared in this scope ./src/check.C:261: error: ‘_Error_Check’ was not declared in this scope ./src/check.C:265: error: ‘_Error_Check’ was not declared in this scope ./src/check.C:269: error: ‘_Error_Check’ was not declared in this scope ./src/check.C:273: error: ‘_Error_Check’ was not declared in this scope ./src/check.C:277: error: ‘_Error_Check’ was not declared in this scope ./src/check.C:282: error: ‘_Error_Check’ was not declared in this scope ./src/check.C:286: error: ‘_Error_Check’ was not declared in this scope ./src/check.C:290: error: ‘_Error_Check’ was not declared in this scope ./src/check.C:294: error: ‘_Error_Check’ was not declared in this scope ./src/check.C:298: error: ‘_Error_Check’ was not declared in this scope ./src/align_standard.C: In function ‘int check_target_sequence(FILE*, const char*, const char*, const char*, const char*)’: ./src/align_standard.C:24: error: ‘ndb_clean_string’ was not declared in this scope ./src/check.C:302: error: ‘_Error_Check’ was not declared in this scope ./src/align_standard.C:26: error: ‘NDB_MSG_ERR’ was not declared in this scope ./src/check.C:306: error: ‘_Error_Check’ was not declared in this scope ./src/align_standard.C:26: error: ‘ndb_log_message’ was not declared in this scope ./src/align_standard.C:27: error: ‘ndb_close_log’ was not declared in this scope ./src/check.C:310: error: ‘_Error_Check’ was not declared in this scope ./src/check.C:314: error: ‘_Error_Check’ was not declared in this scope ./src/check.C:318: error: ‘_Error_Check’ was not declared in this scope ./src/check.C:322: error: ‘_Error_Check’ was not declared in this scope ./src/check.C:326: error: ‘_Error_Check’ was not declared in this scope ./src/check.C:330: error: ‘_Error_Check’ was not declared in this scope ./src/check.C:345: error: ‘_Error_Check’ was not declared in this scope ./src/check.C:349: error: ‘_Error_Check’ was not declared in this scope ./src/contact.C:144:20: ./src/check.C:353: error: ‘_Error_Check’ was not declared in this scope error: _index.h: No such file or directory ./src/check.C:357: error: ‘_Error_Check’ was not declared in this scope ./src/check.C:361: error: ‘_Error_Check’ was not declared in this scope ./src/check.C:365: error: ‘_Error_Check’ was not declared in this scope ./src/check.C:366: error: ‘_date_error’ was not declared in this scope ./src/check.C:369: error: ‘_Error_Check’ was not declared in this scope In file included from ./src/contact.C:145./src/check.C:373: error: ‘_Error_Check’ was not declared in this scope: ./include/_validation.h:144:22: error: _fileobj.h: No such file or directory ./src/check.C:377: error: ‘_Error_Check’ was not declared in this scope ./src/check.C:381: error: ‘_Error_Check’ was not declared in this scope ./src/check.C:385: error: ‘_Error_Check’ was not declared in this scope ./src/check.C:386: error: ‘_large_cell’ was not declared in this scope ./src/check.C:389: error: ‘_Error_Check’ was not declared in this scope ./src/check.C:393: error: ‘_Error_Check’ was not declared in this scope ./src/check.C:397: error: ‘_Error_Check’ was not declared in this scope ./src/check.C:398: error: ‘_Error_Check_Message’ was not declared in this scope ./src/check.C:401: error: ‘_Error_Check’ was not declared in this scope ./src/check.C:405: error: ‘_Error_Check’ was not declared in this scope ./src/check.C:409: error: ‘_spell_check’ was not declared in this scope ./src/check.C:413: error: ‘_error_message’ was not declared in this scope ./src/check.C:424: error: ‘_unrecognized_residue’ was not declared in this scope ./src/check.C:428: error: ‘_Error_Check’ was not declared in this scope ./src/check.C:437: error: ‘_Error_Check’ was not declared in this scope ./src/align_standard.C:22: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result ./src/check.C:441: error: ‘_Error_Check’ was not declared in this scope ./src/check.C:445: error: ‘_Error_Check’ was not declared in this scope ./src/check.C:449: error: ‘_Error_Check’ was not declared in this scope ./src/check.C:453: error: ‘_Error_Check’ was not declared in this scope ./src/check.C: In member function ‘void _VALIDATION::ndb_check_file(FILE*, int, CHECK_TOKEN_FORMAT*, int, CHECK_CATEGORY*, int, int, const char*, FILE*)’: ./src/check.C:484: error: ‘BTreeObj’ was not declared in this scope ./src/check.C:484: error: ‘_SSIndex’ was not declared in this scope ./src/check.C:484: error: ‘_AsymIndex’ was not declared in this scope ./src/check.C:484: error: ‘_BiolUnit’ was not declared in this scope ./src/check.C:485: error: ‘_CHAIN’ was not declared in this scope ./src/check.C:485: error: ‘chain’ was not declared in this scope ./src/check.C:486: error: ‘CifString’ was not declared in this scope ./src/check.C:486: error: expected ‘;’ before ‘string’ ./src/check.C:487: error: ‘ConnectFormat’ was not declared in this scope ./src/check.C:487: error: ‘drug’ was not declared in this scope ./src/check.C:488: error: ‘DICFileObj’ was not declared in this scope ./src/check.C:488: error: ‘dict’ was not declared in this scope ./src/check.C:489: error: ‘ISTable’ was not declared in this scope ./src/check.C:489: error: ‘Table’ was not declared in this scope ./src/check.C:489: error: ‘Table1’ was not declared in this scope ./src/check.C:489: error: ‘Table2’ was not declared in this scope ./src/check.C:490: error: ‘One_Card_Info_Format’ was not declared in this scope ./src/check.C:490: error: ‘pCard’ was not declared in this scope ./src/check.C:491: error: ‘_RESIDUE’ was not declared in this scope ./src/check.C:491: error: ‘residue’ was not declared in this scope ./src/check.C:492: error: expected ‘;’ before ‘idx’ ./src/check.C:493: error: ‘TblIndexObj’ was not declared in this scope ./src/check.C:493: error: expected ‘;’ before ‘_UniIndex’ ./src/check.C:495: error: ‘_num_mol’ was not declared in this scope ./src/check.C:496: error: ‘_input_format’ was not declared in this scope ./src/check.C:496: error: ‘NDB_FILE_FORMAT_PDB’ was not declared in this scope ./src/check.C:497: error: ‘NDB_FILE_FORMAT_MMCIF’ was not declared in this scope ./src/check.C:499: error: ‘_cell’ was not declared in this scope In file included from ./include/gridcell.h:144, from ./src/contact.C:147: ./include/atom.h:143:21: error: fstream.h: No such file or directory ./include/atom.h:144:22: error: iostream.h: No such file or directory ./src/check.C:532: error: ‘_input_filename’ was not declared in this scope ./src/check.C:535: error: ‘_Error_Check’ was not declared in this scope ./src/check.C:538: error: ‘_input_filename’ was not declared in this scope ./src/check.C:548: error: ‘_large_cell’ was not declared in this scope ./src/check.C:552: error: ‘_large_cell’ was not declared in this scope ./src/check.C:556: error: ‘_large_cell’ was not declared in this scope ./src/check.C:558: error: ‘_Error_Check’ was not declared in this scope ./src/check.C:561: error: ‘_input_filename’ was not declared in this scope ./src/check.C:562: error: ‘_Error_Check’ was not declared in this scope ./src/check.C:566: error: ‘_error_message’ was not declared in this scope ./src/check.C:568: error: ‘_input_format’ was not declared in this scope ./src/check.C:568: error: ‘NDB_FILE_FORMAT_PDB’ was not declared in this scope ./src/check.C:569: error: ‘NDB_FILE_FORMAT_MMCIF’ was not declared in this scope ./src/check.C:570: error: ‘_file_status’ was not declared in this scope ./src/check.C:570: error: ‘FILE_STATUS_MMCIF_PLUS_MOL’ was not declared in this scope ./src/check.C:571: error: ‘_molecules’ was not declared in this scope ./src/check.C:571: error: ‘_rep_mol’ was not declared in this scope ./src/check.C:571: error: ‘_CardInfo’ was not declared in this scope ./src/check.C:572: error: ‘_input_filename’ was not declared in this scope ./src/check.C:572: error: ‘check_tokens’ was not declared in this scope ./src/check.C:575: error: ‘_CifObj’ was not declared in this scope ./src/check.C:575: error: ‘_StructureId’ was not declared in this scope ./src/contact.C:148:22: error: BTreeObj.h: No such file or directory ./src/check.C:576: error: ‘is_empty_table’ was not declared in this scope ./src/check.C:577: error: ‘_molecules’ was not declared in this scope ./src/check.C:577: error: ‘_rep_mol’ was not declared in this scope ./src/check.C:578: error: ‘_input_filename’ was not declared in this scope ./src/check.C:578: error: ‘_Error_Check’ was not declared in this scope ./src/check.C:578: error: ‘check_categorys’ was not declared in this scope In file included from ./src/contact.C:149: /usr/include/rcsb/util.h:11:21: error: CifFile.h: No such file or directory ./src/check.C:581: error: ‘_CifObj’ was not declared in this scope ./src/check.C:581: error: ‘_StructureId’ was not declared in this scope /usr/include/rcsb/util.h:12:23: error: TableFile.h: No such file or directory ./src/check.C:582: error: ‘is_empty_table’ was not declared in this scope ./src/check.C:583: error: ‘_molecules’ was not declared in this scope ./src/check.C:583: error: ‘_rep_mol’ was not declared in this scope ./src/check.C:584: error: ‘_input_filename’ was not declared in this scope ./src/check.C:584: error: ‘_Error_Check’ was not declared in this scope ./src/check.C:584: error: ‘check_categorys1’ was not declared in this scope ./src/check.C:588: error: ‘_num_mol’ was not declared in this scope ./src/check.C:589: error: ‘_molecules’ was not declared in this scope ./src/check.C:589: error: ‘_input_filename’ was not declared in this scope ./src/check.C:589: error: ‘_Error_Check’ was not declared in this scope ./src/check.C:589: error: ‘check_seqnum_redundancy’ was not declared in this scope ./src/check.C:592: error: ‘_input_format’ was not declared in this scope ./src/check.C:592: error: ‘NDB_FILE_FORMAT_PDB’ was not declared in this scope ./src/check.C:593: error: ‘NDB_FILE_FORMAT_NDB’ was not declared in this scope ./src/check.C:595: error: ‘find_card_id’ was not declared in this scope ./src/check.C:596: error: ‘_CardInfo’ was not declared in this scope ./src/check.C:598: error: ‘_Error_Check’ was not declared in this scope ./src/check.C:599: error: ‘_input_filename’ was not declared in this scope In file included from ./src/contact.C:150: ./include/xtal.h:149:23: error: _molecule.h: No such file or directory ./include/xtal.h:150:22: error: ./src/check.C:610: error: ‘_input_filename’ was not declared in this scopecry_util.h: No such file or directory ./src/check.C:611: error: ‘_Error_Check’ was not declared in this scope ./src/check.C:616: error: ‘_CifObj’ was not declared in this scope ./src/check.C:616: error: ‘_StructureId’ was not declared in this scope ./src/check.C:617: error: ‘is_empty_table’ was not declared in this scope ./src/check.C:621: error: ‘string’ was not declared in this scope ./src/check.C:622: error: ‘is_a_standard_residue’ was not declared in this scope ./src/check.C:638: error: ‘_CifObj’ was not declared in this scope ./src/check.C:638: error: ‘_StructureId’ was not declared in this scope ./src/check.C:639: error: ‘is_empty_table’ was not declared in this scope ./src/check.C:654: error: ‘find_card_id’ was not declared in this scope ./src/check.C:656: error: ‘string’ was not declared in this scope ./src/check.C:659: error: ‘_CardInfo’ was not declared in this scope ./src/check.C:659: error: ‘NdbToken’ was not declared in this scope ./src/check.C:712: error: ‘_CardInfo’ was not declared in this scope ./src/check.C:716: error: ‘print_general_cards’ was not declared in this scope ./src/check.C:720: error: ‘_CardInfo’ was not declared in this scope ./src/check.C:724: error: ‘string’ was not declared in this scope ./src/check.C:727: error: ‘NdbToken’ was not declared in this scope ./src/check.C:783: error: ‘print_general_cards’ was not declared in this scope ./src/check.C:795: error: ‘is_empty_table’ was not declared in this scope ./src/check.C:799: error: ‘string’ was not declared in this scope ./src/check.C:800: error: ‘string1’ was not declared in this scope ./src/check.C:801: error: ‘is_not_empty’ was not declared in this scope In file included from ./include/list.h:146, from ./include/atom.h:147, from ./include/gridcell.h:144, from ./src/gridcell.C:142: ./include/symop.h:153: error: ISO C++ forbids declaration of ‘ostream’ with no type ./include/symop.h:153: error: ‘ostream’ is neither function nor member function; cannot be declared friend ./include/symop.h:153: error: expected ‘;’ before ‘&’ token ./src/check.C:813: error: ‘_Error_Check’ was not declared in this scope./include/symop.h:158: error: expected ‘)’ before ‘&’ token ./src/check.C:818: error: ‘_experiment_type’ was not declared in this scope ./src/check.C:818: error: ‘EXPERIMENT_TYPE_XRAY’ was not declared in this scope ./src/check.C:822: error: ‘is_empty_table’ was not declared in this scope ./src/check.C:827: error: ‘string’ was not declared in this scope ./src/check.C:828: error: ‘is_not_empty’ was not declared in this scope ./src/check.C:841: error: ‘_experiment_type’ was not declared in this scope ./src/check.C:841: error: ‘EXPERIMENT_TYPE_NMR’ was not declared in this scope ./src/check.C:844: error: ‘is_empty_table’ was not declared in this scope ./src/check.C:853: error: ‘string’ was not declared in this scope ./src/check.C:856: error: ‘is_not_empty’ was not declared in this scope ./src/check.C:867: error: ‘is_empty_table’ was not declared in this scope ./src/check.C:870: error: ‘string’ was not declared in this scope ./src/check.C:871: error: ‘is_not_empty’ was not declared in this scope ./src/check.C:872: error: ‘_num_mol’ was not declared in this scope ./src/check.C:886: error: ‘is_empty_table’ was not declared in this scope ./src/check.C:890: error: ‘string’ was not declared in this scope ./src/check.C:891: error: ‘string1’ was not declared in this scope ./src/check.C:892: error: ‘is_not_empty’ was not declared in this scope ./src/_validation.C: In member function ‘void _VALIDATION::Get_Stbiol(int)’: ./src/_validation.C:354: error: ‘CifString’ was not declared in this scope ./src/_validation.C:354: error: expected ‘;’ before ‘string’ ./src/_validation.C:355: error: ‘ReVarCifArray’ was not declared in this scope ./src/_validation.C:355: error: ‘ColumnNames’ was not declared in this scope ./src/_validation.C:356: error: ‘ISTable’ was not declared in this scope ./src/_validation.C:356: error: ‘Table’ was not declared in this scope ./src/_validation.C:357: error: ‘One_Card_Info_Format’ was not declared in this scope ./src/_validation.C:357: error: ‘pCard’ was not declared in this scope ./src/_validation.C:357: error: ‘_CardInfo’ was not declared in this scope ./src/_validation.C:357: error: ‘STBIOL_TOKEN’ was not declared in this scope ./src/_validation.C:360: error: ‘_CifObj’ was not declared in this scope ./src/_validation.C:360: error: ‘_StructureId’ was not declared in this scope ./src/_validation.C:361: error: ‘is_empty_table’ was not declared in this scope ./src/_validation.C:364: error: ‘_exist_pdb_chain_id’ was not declared in this scope ./src/check.C:918: error: ‘is_empty_table’ was not declared in this scope ./src/_validation.C:366: error: ‘_exist_pdb_chain_id’ was not declared in this scope ./src/_validation.C:372: error: ‘_stbiol’ was not declared in this scope ./src/_validation.C:373: error: ‘_n_stbiol’ was not declared in this scope ./src/check.C:923: error: ‘string’ was not declared in this scope ./src/check.C:924: error: ‘string1’ was not declared in this scope ./src/_validation.C:374: error: type ‘’ argument given to ‘delete’, expected pointer ./src/check.C:925: error: ‘string2’ was not declared in this scope ./src/_validation.C:376: error: ‘_n_stbiol’ was not declared in this scope ./src/check.C:926: error: ‘is_not_empty’ was not declared in this scope ./src/_validation.C:377: error: ‘_stbiol’ was not declared in this scope ./src/_validation.C:377: error: expected type-specifier before ‘_STBIOL’ ./src/_validation.C:377: error: expected ‘;’ before ‘_STBIOL’ ./src/_validation.C:380: error: expected type-specifier before ‘_STBIOL’ ./src/_validation.C:380: error: expected ‘;’ before ‘_STBIOL’ ./src/_validation.C:388: error: ‘strcpy’ was not declared in this scope ./src/_validation.C:394: error: ‘string’ was not declared in this scope ./src/_validation.C:396: error: ‘strcmp’ was not declared in this scope ./src/_validation.C:397: error: ‘atoi’ was not declared in this scope ./src/_validation.C:407: error: ‘atoi’ was not declared in this scope ./src/check.C:967: error: ‘is_empty_table’ was not declared in this scope ./src/_validation.C:409: error: ‘atoi’ was not declared in this scope ./src/_validation.C:411: error: ‘atoi’ was not declared in this scope ./src/check.C:973: error: ‘string’ was not declared in this scope ./src/_validation.C:413: error: ‘atoi’ was not declared in this scope ./src/_validation.C:415: error: ‘atoi’ was not declared in this scope ./src/_validation.C:418: error: type ‘’ argument given to ‘delete’, expected pointer In file included from ./src/color_util.C:147: /usr/include/rcsb/util.h:67: error: ‘CifFile’ was not declared in this scope /usr/include/rcsb/util.h:67: error: ‘fobj’ was not declared in this scope ./src/_validation.C:421: error: ‘is_empty_table’ was not declared in this scope /usr/include/rcsb/util.h:67: error: expected primary-expression before ‘const’ /usr/include/rcsb/util.h:68: error: expected primary-expression before ‘const’ /usr/include/rcsb/util.h:68: error: expected primary-expression before ‘const’ /usr/include/rcsb/util.h:68: error: initializer expression list treated as compound expression ./src/check.C:993: error: ‘string’ was not declared in this scope /usr/include/rcsb/util.h:69: error: ‘CifFile’ was not declared in this scope./src/_validation.C:429: error: ‘strcmp’ was not declared in this scope /usr/include/rcsb/util.h:69: error: ‘fobj’ was not declared in this scope /usr/include/rcsb/util.h:69: error: expected primary-expression before ‘const’ /usr/include/rcsb/util.h:70: error: expected primary-expression before ‘const’ ./src/_validation.C:431: error: ‘string’ was not declared in this scope /usr/include/rcsb/util.h:70: error: expected primary-expression before ‘const’ /usr/include/rcsb/util.h:71: error: expected primary-expression before ‘long’ /usr/include/rcsb/util.h:71: error: initializer expression list treated as compound expression ./src/_validation.C:436: error: ‘strcpy’ was not declared in this scope ./src/check.C:1004: error: ‘_experiment_type’ was not declared in this scope ./src/check.C:1004: error: ‘EXPERIMENT_TYPE_NMR’ was not declared in this scope ./src/check.C:1006: error: ‘is_empty_table’ was not declared in this scope ./src/check.C:1010: error: ‘string1’ was not declared in this scope ./src/check.C:1011: error: ‘string2’ was not declared in this scope ./src/check.C:1013: error: ‘string’ was not declared in this scope ./src/check.C:1022: error: ‘_Error_Check’ was not declared in this scope ./src/check.C:1028: error: ‘is_empty_table’ was not declared in this scope ./src/_validation.C: In member function ‘void _VALIDATION::Input_Stbiol()’: ./src/_validation.C:448: error: ‘_CHAIN’ was not declared in this scope ./src/_validation.C:448: error: ‘chain’ was not declared in this scope ./src/_validation.C:449: error: ‘One_Card_Info_Format’ was not declared in this scope ./src/_validation.C:449: error: ‘pCard’ was not declared in this scope./src/check.C:1034: error: ‘string’ was not declared in this scope ./src/_validation.C:449: error: ‘_CardInfo’ was not declared in this scope ./src/_validation.C:449: error: ‘STBIOL_TOKEN’ was not declared in this scope ./src/check.C:1038: error: ‘_spell_check’ was not declared in this scope ./src/_validation.C:456: error: ‘_stbiol’ was not declared in this scope ./src/_validation.C:457: error: ‘_n_stbiol’ was not declared in this scope ./src/check.C:1039: error: ‘_spell_check’ was not declared in this scope ./src/_validation.C:458: error: type ‘’ argument given to ‘delete’, expected pointer ./src/check.C:1044: error: ‘string’ was not declared in this scope ./src/_validation.C:460: error: ‘_n_stbiol’ was not declared in this scope ./src/_validation.C:461: error: ‘_stbiol’ was not declared in this scope ./src/_validation.C:461: error: expected type-specifier before ‘_STBIOL’ ./src/check.C:1048: error: ‘_spell_check’ was not declared in this scope./src/_validation.C:461: error: expected ‘;’ before ‘_STBIOL’ ./src/check.C:1049: error: ‘_spell_check’ was not declared in this scope ./src/_validation.C:466: error: expected type-specifier before ‘_STBIOL’ ./src/_validation.C:466: error: expected ‘;’ before ‘_STBIOL’./src/check.C:1057: error: ‘is_empty_table’ was not declared in this scope ./src/_validation.C:467: error: ‘atoi’ was not declared in this scope ./src/_validation.C:468: error: ‘strcmp’ was not declared in this scope ./src/check.C:1062: error: ‘string’ was not declared in this scope ./src/_validation.C:474: error: ‘strcpy’ was not declared in this scope ./src/check.C:1066: error: ‘_spell_check’ was not declared in this scope ./src/_validation.C:477: error: ‘strcmp’ was not declared in this scope ./src/check.C:1067: error: ‘_spell_check’ was not declared in this scope ./src/_validation.C:479: error: ‘strcmp’ was not declared in this scope ./src/check.C:1075: error: ‘is_empty_table’ was not declared in this scope ./src/check.C:1077: error: ‘string’ was not declared in this scope./src/_validation.C:482: error: ‘strcmp’ was not declared in this scope ./src/_validation.C:485: error: ‘strcmp’ was not declared in this scope ./src/_validation.C:488: error: ‘strcmp’ was not declared in this scope ./src/check.C:1091: error: ‘is_empty_table’ was not declared in this scope ./src/check.C:1092: error: ‘_experiment_type’ was not declared in this scope ./src/check.C:1092: error: ‘EXPERIMENT_TYPE_XRAY’ was not declared in this scope ./src/_validation.C:498: error: ‘_num_mol’ was not declared in this scope ./src/_validation.C:500: error: ‘ATOMP_TOKEN’ was not declared in this scope ./src/check.C:1096: error: ‘_UniIndex’ was not declared in this scope ./src/_validation.C:500: error: ‘ATOMN_TOKEN’ was not declared in this scope ./src/_validation.C:500: error: ‘ATOMS_TOKEN’ was not declared in this scope ./src/check.C:1098: error: ‘string’ was not declared in this scope ./src/_validation.C:501: error: ‘HETAD_TOKEN’ was not declared in this scope ./src/_validation.C:501: error: ‘HETAI_TOKEN’ was not declared in this scope ./src/_validation.C:501: error: ‘HETIC_TOKEN’ was not declared in this scope ./src/_validation.C:502: error: ‘HETAC_TOKEN’ was not declared in this scope ./src/_validation.C:502: error: ‘HETAIN_TOKEN’ was not declared in this scope ./src/_validation.C:502: error: ‘HETAS_TOKEN’ was not declared in this scope ./src/check.C:1111: error: ‘_BiolIndex’ was not declared in this scope ./src/_validation.C:505: error: ‘_molecules’ was not declared in this scope ./src/check.C:1115: error: ‘string’ was not declared in this scope ./src/_validation.C:505: error: ‘_rep_mol’ was not declared in this scope ./src/check.C:1117: error: ‘string1’ was not declared in this scope ./src/check.C:1119: error: ‘string2’ was not declared in this scope ./src/check.C:1124: error: ‘idx’ was not declared in this scope ./src/_validation.C: In member function ‘void _VALIDATION::Reorder_Stbiol()’: ./src/_validation.C:523: error: ‘_STBIOL’ was not declared in this scope ./src/_validation.C:523: error: ‘tmp’ was not declared in this scope ./src/_validation.C:525: error: ‘_stbiol’ was not declared in this scope ./src/_validation.C:526: error: expected type-specifier before ‘_STBIOL’ ./src/check.C:1151: error: ‘string’ was not declared in this scope ./src/_validation.C:526: error: expected ‘;’ before ‘_STBIOL’ ./src/check.C:1153: error: ‘string1’ was not declared in this scope ./src/_validation.C:527: error: ‘_n_stbiol’ was not declared in this scope ./src/check.C:1156: error: ‘idx’ was not declared in this scope ./src/_validation.C:533: error: ‘_n_stbiol’ was not declared in this scope./src/check.C:1159: error: ‘idx1’ was not declared in this scope ./src/_validation.C:535: error: expected type-specifier before ‘_STBIOL’ ./src/_validation.C:535: error: expected ‘;’ before ‘_STBIOL’ ./src/check.C:1167: error: ‘pidx’ was not declared in this scope ./src/check.C:1168: error: ‘_cell’ was not declared in this scope ./src/_validation.C:540: error: ‘strcpy’ was not declared in this scope ./src/check.C:1168: error: ‘rcsb_get_symmetry_operation_name’ was not declared in this scope ./src/check.C:1169: error: ‘string2’ was not declared in this scope ./src/_validation.C:564: error: expected type-specifier before ‘_STBIOL’ ./src/_validation.C:564: error: expected ‘;’ before ‘_STBIOL’ ./src/check.C:1204: error: ‘idx’ was not declared in this scope ./src/_validation.C:591: error: ‘_n_stbiol’ was not declared in this scope ./src/_validation.C:592: error: type ‘’ argument given to ‘delete’, expected pointer ./src/_validation.C: In member function ‘void _VALIDATION::Input_Link()’: ./src/_validation.C:599: error: ‘_num_mol’ was not declared in this scope ./src/_validation.C:599: error: ‘_molecules’ was not declared in this scope ./src/_validation.C:601: error: ‘_MOLECULE’ was not declared in this scope ./src/color_util.C: In function ‘int ndb_get_color_index(int, const char*, int, int)’: ./src/color_util.C:310: error: ‘ndb_clean_string’ was not declared in this scope ./src/_validation.C:601: error: ‘mol’ was not declared in this scope ./src/_validation.C:601: error: ‘_molecules’ was not declared in this scope./src/color_util.C:311: error: ‘ndb_set_string_to_lower’ was not declared in this scope ./src/_validation.C:603: error: ‘One_Card_Info_Format’ was not declared in this scope ./src/_validation.C:603: error: ‘pCard’ was not declared in this scope ./src/_validation.C:603: error: ‘_CardInfo’ was not declared in this scope ./src/_validation.C:603: error: ‘LINK_TOKEN’ was not declared in this scope ./src/check.C:1257: error: ‘_UniIndex’ was not declared in this scope ./src/_validation.C:606: error: ‘atoi’ was not declared in this scope./src/color_util.C:320: error: ‘ATOMP_TOKEN’ was not declared in this scope ./src/check.C:1261: error: ‘is_empty_table’ was not declared in this scope ./src/check.C:1265: error: ‘string’ was not declared in this scope ./src/_validation.C: In member function ‘void _VALIDATION::update_residues_nomenclature(int)’: ./src/_validation.C:622: error: ‘_CHAIN’ was not declared in this scope./src/check.C:1272: error: ‘_Error_Check’ was not declared in this scope ./src/_validation.C:622: error: ‘chain’ was not declared in this scope ./src/_validation.C:623: error: ‘_num_mol’ was not declared in this scope ./src/_validation.C:623: error: ‘_molecules’ was not declared in this scope ./src/_validation.C:625: error: ‘_num_mol’ was not declared in this scope./src/check.C:1282: error: ‘is_empty_table’ was not declared in this scope ./src/_validation.C:626: error: ‘_molecules’ was not declared in this scope ./src/check.C:1286: error: ‘string’ was not declared in this scope ./src/check.C:1287: error: ‘string1’ was not declared in this scope ./src/check.C:1288: error: ‘is_not_empty’ was not declared in this scope ./src/_validation.C: In member function ‘void _VALIDATION::match_stbiol_with_molecules()’: ./src/_validation.C:639: error: ‘_STBIOL’ was not declared in this scope ./src/_validation.C:639: error: ‘tmp’ was not declared in this scope ./src/_validation.C:639: error: ‘tmp1’ was not declared in this scope ./src/check.C:1298: error: ‘is_empty_table’ was not declared in this scope./src/_validation.C:640: error: ‘_CHAIN’ was not declared in this scope ./src/_validation.C:640: error: ‘chain’ was not declared in this scope ./src/_validation.C:641: error: ‘One_Card_Info_Format’ was not declared in this scope ./src/check.C:1301: error: ‘string’ was not declared in this scope ./src/_validation.C:641: error: ‘pCard’ was not declared in this scope ./src/check.C:1302: error: ‘is_not_empty’ was not declared in this scope./src/_validation.C:643: error: ‘_num_mol’ was not declared in this scope ./src/_validation.C:643: error: ‘_molecules’ was not declared in this scope ./src/_validation.C:645: error: ‘_molecules’ was not declared in this scope ./src/_validation.C:645: error: ‘_rep_mol’ was not declared in this scope ./src/_validation.C:647: error: ‘_n_stbiol’ was not declared in this scope ./src/check.C:1310: error: ‘is_empty_table’ was not declared in this scope./src/_validation.C:648: error: ‘_stbiol’ was not declared in this scope ./src/_validation.C:649: error: ‘strcmp’ was not declared in this scope ./src/_validation.C:651: error: ‘_n_stbiol’ was not declared in this scope ./src/check.C:1315: error: ‘string’ was not declared in this scope ./src/check.C:1315: error: ‘get_value’ was not declared in this scope ./src/_validation.C:655: error: ‘_CardInfo’ was not declared in this scope ./src/_validation.C:655: error: ‘SEQIFO_TOKEN’ was not declared in this scope ./src/check.C:1319: error: ‘isalpha’ was not declared in this scope ./src/check.C:1319: error: ‘islower’ was not declared in this scope ./src/_validation.C:667: error: ‘NdbToken’ was not declared in this scope ./src/_validation.C:672: error: ‘ATOMN_TOKEN’ was not declared in this scope ./src/check.C:1324: error: ‘_Error_Check’ was not declared in this scope ./src/_validation.C:675: error: ‘ATOMP_TOKEN’ was not declared in this scope ./src/check.C:1331: error: ‘is_empty_table’ was not declared in this scope ./src/check.C:1334: error: ‘string’ was not declared in this scope ./src/_validation.C:687: error: ‘_stbiol’ was not declared in this scope ./src/check.C:1335: error: ‘is_not_empty’ was not declared in this scope ./src/_validation.C:687: error: ‘_n_stbiol’ was not declared in this scope ./src/_validation.C:690: error: ‘strcmp’ was not declared in this scope ./src/_validation.C:693: error: expected type-specifier before ‘_STBIOL’ ./src/_validation.C:693: error: expected ‘;’ before ‘_STBIOL’ ./src/check.C:1352: error: ‘is_empty_table’ was not declared in this scope ./src/_validation.C:704: error: ‘strcpy’ was not declared in this scope ./src/_validation.C:708: error: expected type-specifier before ‘_STBIOL’ ./src/_validation.C:708: error: expected ‘;’ before ‘_STBIOL’ ./src/check.C:1362: error: ‘string’ was not declared in this scope ./src/_validation.C:712: error: type ‘’ argument given to ‘delete’, expected pointer./src/check.C:1364: error: ‘str’ was not declared in this scope ./src/_validation.C:714: error: expected type-specifier before ‘_STBIOL’ ./src/_validation.C:714: error: expected ‘;’ before ‘_STBIOL’ ./src/_validation.C:738: error: expected type-specifier before ‘_STBIOL’ ./src/check.C:1376: error: ‘str’ was not declared in this scope ./src/_validation.C:738: error: expected ‘;’ before ‘_STBIOL’ ./src/check.C:1384: error: ‘is_empty_table’ was not declared in this scope ./src/_validation.C:742: error: type ‘’ argument given to ‘delete’, expected pointer ./src/_validation.C:744: error: expected type-specifier before ‘_STBIOL’ ./src/_validation.C:744: error: expected ‘;’ before ‘_STBIOL’ ./src/check.C:1389: error: ‘string’ was not declared in this scope ./src/check.C:1389: error: ‘get_value’ was not declared in this scope ./src/check.C:1394: error: ‘isdigit’ was not declared in this scope ./src/check.C:1397: error: ‘_Error_Check’ was not declared in this scope ./src/check.C:1407: error: ‘isdigit’ was not declared in this scope ./src/check.C:1410: error: ‘_Error_Check’ was not declared in this scope ./src/_validation.C:781: error: type ‘’ argument given to ‘delete’, expected pointer ./src/check.C:1419: error: ‘is_empty_table’ was not declared in this scope ./src/check.C:1421: error: ‘string’ was not declared in this scope ./src/check.C:1421: error: ‘get_value’ was not declared in this scope ./src/_validation.C:796: error: ‘_num_mol’ was not declared in this scope ./src/check.C:1426: error: ‘string1’ was not declared in this scope ./src/check.C:1428: error: ‘_Error_Check’ was not declared in this scope ./src/_validation.C:809: error: ‘_CardInfo’ was not declared in this scope ./src/_validation.C:809: error: ‘SEQIFO_TOKEN’ was not declared in this scope ./src/_validation.C:821: error: ‘NdbToken’ was not declared in this scope ./src/check.C:1437: error: ‘string1’ was not declared in this scope ./src/_validation.C:826: error: ‘ATOMN_TOKEN’ was not declared in this scope ./src/check.C:1440: error: ‘_Error_Check’ was not declared in this scope ./src/_validation.C:829: error: ‘ATOMP_TOKEN’ was not declared in this scope ./src/check.C:1444: error: ‘_Error_Check’ was not declared in this scope ./src/check.C:1454: error: ‘is_empty_table’ was not declared in this scope ./src/check.C:1455: error: ‘_Error_Check’ was not declared in this scope ./src/check.C:1456: error: ‘_input_filename’ was not declared in this scope ./src/check.C:1460: error: ‘_input_filename’ was not declared in this scope ./src/check.C:1461: error: ‘_Error_Check’ was not declared in this scope ./src/check.C:1463: error: ‘string’ was not declared in this scope ./src/check.C:1465: error: ‘_Error_Check’ was not declared in this scope ./src/check.C:1466: error: ‘_input_filename’ was not declared in this scope ./src/check.C:1471: error: ‘is_empty_table’ was not declared in this scope ./src/check.C:1472: error: ‘_Error_Check’ was not declared in this scope ./src/check.C:1473: error: ‘_input_filename’ was not declared in this scope ./src/check.C:1477: error: ‘_input_filename’ was not declared in this scope ./src/check.C:1478: error: ‘_Error_Check’ was not declared in this scope ./src/check.C:1480: error: ‘string’ was not declared in this scope ./src/check.C:1482: error: ‘_Error_Check’ was not declared in this scope ./src/check.C:1483: error: ‘_input_filename’ was not declared in this scope ./src/check.C:1488: error: ‘is_empty_table’ was not declared in this scope ./src/check.C:1489: error: ‘_Error_Check’ was not declared in this scope./src/_validation.C: In member function ‘void _VALIDATION::Insert_a_Link(const char*, const char*, const char*, int, int, const char*, const char*, const char*, int, int, const char*, const char*, const char*)’: ./src/_validation.C:852: error: ‘strcmp’ was not declared in this scope ./src/check.C:1490: error: ‘_input_filename’ was not declared in this scope ./src/check.C:1495: error: ‘_Error_Check’ was not declared in this scope ./src/check.C:1497: error: ‘_input_filename’ was not declared in this scope ./src/check.C:1501: error: ‘res_high’ was not declared in this scope ./src/check.C:1501: error: ‘get_value’ was not declared in this scope ./src/check.C:1502: error: ‘res_low’ was not declared in this scope ./src/check.C:1506: error: ‘_Error_Check’ was not declared in this scope ./src/check.C:1508: error: ‘_input_filename’ was not declared in this scope ./src/check.C:1509: error: ‘res_low’ was not declared in this scope ./src/check.C:1510: error: ‘_Error_Check’ was not declared in this scope ./src/check.C:1512: error: ‘_input_filename’ was not declared in this scope ./src/check.C:1514: error: ‘get_date’ was not declared in this scope ./src/check.C:1517: error: ‘res_high’ was not declared in this scope ./src/check.C:1517: error: ‘get_value’ was not declared in this scope ./src/check.C:1518: error: ‘res_low’ was not declared in this scope ./src/check.C:1521: error: ‘_input_filename’ was not declared in this scope ./src/_validation.C:879: error: ‘strcpy’ was not declared in this scope ./src/check.C:1523: error: ‘_date_error’ was not declared in this scope ./src/check.C:1524: error: ‘_Error_Check’ was not declared in this scope make[1]: *** [obj/color_util.o] Error 1 ./src/_validation.C:891: error: ‘strlen’ was not declared in this scope ./src/check.C:1528: error: ‘_input_filename’ was not declared in this scope ./src/check.C:1530: error: ‘_date_error’ was not declared in this scope ./src/check.C:1531: error: ‘_Error_Check’ was not declared in this scope ./src/check.C:1535: error: ‘_input_filename’ was not declared in this scope ./src/check.C:1537: error: ‘_date_error’ was not declared in this scope ./src/check.C:1538: error: ‘_Error_Check’ was not declared in this scope ./src/check.C:1546: error: ‘is_empty_table’ was not declared in this scope ./src/check.C:1546: error: ‘get_pdb_id’ was not declared in this scope ./src/check.C:1549: error: ‘is_empty_table’ was not declared in this scope ./src/check.C:1552: error: ‘res_low’ was not declared in this scope ./src/check.C:1552: error: ‘get_value’ was not declared in this scope ./src/check.C:1556: error: ‘_Error_Check’ was not declared in this scope ./src/check.C:1563: error: ‘is_empty_table’ was not declared in this scope ./src/check.C:1565: error: ‘res_high’ was not declared in this scope ./src/check.C:1565: error: ‘get_value’ was not declared in this scope ./src/check.C:1573: error: ‘res_low’ was not declared in this scope ./src/check.C:1577: error: ‘_Error_Check’ was not declared in this scope ./src/_validation.C: In member function ‘void _VALIDATION::Insert_a_Mismat(const char*, int, int, const char*, int, int)’: ./src/_validation.C:905: error: ‘strcmp’ was not declared in this scope ./src/check.C:1585: error: ‘is_empty_table’ was not declared in this scope ./src/check.C:1587: error: ‘res_high’ was not declared in this scope ./src/check.C:1587: error: ‘get_value’ was not declared in this scope ./src/check.C:1592: error: ‘_date_error’ was not declared in this scope ./src/check.C:1593: error: ‘_Error_Check’ was not declared in this scope ./src/check.C:1599: error: ‘is_empty_table’ was not declared in this scope ./src/check.C:1599: error: ‘_cell’ was not declared in this scope ./src/_validation.C:919: error: ‘strcpy’ was not declared in this scope ./src/check.C:1611: error: ‘res_high’ was not declared in this scope ./src/check.C:1611: error: ‘get_value’ was not declared in this scope ./src/_validation.C: In member function ‘void _VALIDATION::Insert_a_Bspair(const char*, const char*, int, int, const char*, const char*, int, int, const char*, const char*)’: ./src/_validation.C:935: error: ‘strcmp’ was not declared in this scope ./src/_validation.C:955: error: ‘strcpy’ was not declared in this scope ./src/check.C:1680: error: ‘_Error_Check’ was not declared in this scope ./src/check.C:1689: error: ‘is_empty_table’ was not declared in this scope In file included from ./src/atom.C:150: ./include/xtal.h:166: error: ISO C++ forbids declaration of ‘NDBCELLCONST’ with no type ./include/xtal.h:166: error: expected ‘,’ or ‘...’ before ‘*’ token ./include/xtal.h:167: error: ‘COORD’ has not been declared ./src/check.C:1699: error: ‘res_low’ was not declared in this scope ./include/xtal.h:167: error: ‘COORD’ has not been declared ./src/check.C:1699: error: ‘get_value’ was not declared in this scope ./src/check.C:1701: error: ‘res_high’ was not declared in this scope ./src/check.C:1717: error: ‘buff’ was not declared in this scope ./src/check.C:1718: error: ‘CompareNoCase’ was not declared in this scope ./src/check.C:1719: error: ‘string’ was not declared in this scope ./src/check.C:1720: error: ‘string1’ was not declared in this scope ./src/check.C:1725: error: ‘_Error_Check’ was not declared in this scope ./src/_validation.C: In member function ‘void _VALIDATION::generate_symmetry_strands(int)’: ./src/_validation.C:972: error: ‘_num_mol’ was not declared in this scope ./src/_validation.C:972: error: ‘_molecules’ was not declared in this scope ./src/_validation.C:974: error: ‘_n_stbiol’ was not declared in this scope ./src/check.C:1730: error: ‘_Error_Check’ was not declared in this scope ./src/_validation.C:975: error: ‘_stbiol’ was not declared in this scope ./src/_validation.C:975: error: ‘NDB_BASE_SYMMETRY’ was not declared in this scope ./src/_validation.C:975: error: ‘strcmp’ was not declared in this scope ./src/check.C:1737: error: ‘_Error_Check’ was not declared in this scope ./src/_validation.C:977: error: ‘_n_stbiol’ was not declared in this scope ./src/_validation.C:979: error: ‘_molecules’ was not declared in this scope ./src/_validation.C:979: error: ‘_cell’ was not declared in this scope ./src/check.C:1742: error: ‘_Error_Check’ was not declared in this scope ./src/_validation.C:979: error: ‘NDB_TRANS_ORTHO_TO_FRAC’ was not declared in this scope ./src/_validation.C:980: error: ‘_n_stbiol’ was not declared in this scope ./src/_validation.C:981: error: ‘_stbiol’ was not declared in this scope ./src/_validation.C:982: error: ‘_stbiol’ was not declared in this scope ./src/check.C:1751: error: ‘buff’ was not declared in this scope ./src/_validation.C:982: error: ‘NDB_BASE_SYMMETRY’ was not declared in this scope ./src/_validation.C:982: error: ‘strcmp’ was not declared in this scope ./src/check.C:1752: error: ‘CompareNoCase’ was not declared in this scope ./src/_validation.C:983: error: ‘atoi’ was not declared in this scope ./src/check.C:1753: error: ‘string’ was not declared in this scope ./src/_validation.C:985: error: ‘strlen’ was not declared in this scope ./src/check.C:1758: error: ‘_Error_Check’ was not declared in this scope ./src/check.C:1765: error: ‘_Error_Check’ was not declared in this scope ./src/check.C:1769: error: ‘_Error_Check’ was not declared in this scope ./src/_validation.C:1002: error: ‘strcpy’ was not declared in this scope ./src/_validation.C:1005: error: ‘NDB_TRANS_FRAC_TO_ORTHO’ was not declared in this scope ./src/check.C:1778: error: ‘buff’ was not declared in this scope ./src/check.C:1779: error: ‘CompareNoCase’ was not declared in this scope ./src/check.C:1780: error: ‘string’ was not declared in this scope ./src/check.C:1785: error: ‘_Error_Check’ was not declared in this scope ./src/_validation.C: At global scope: ./src/_validation.C:1010: error: ‘_ATOM’ has not been declared ./src/_validation.C:1010: error: ‘_ATOM’ has not been declared ./src/check.C:1791: error: ‘_Error_Check’ was not declared in this scope ./src/check.C:1796: error: ‘_Error_Check’ was not declared in this scope ./src/check.C:1808: error: ‘is_empty_table’ was not declared in this scope ./src/check.C:1808: error: ‘_num_mol’ was not declared in this scope ./src/check.C:1814: error: ‘res_high’ was not declared in this scope ./src/check.C:1814: error: ‘get_value’ was not declared in this scope ./src/check.C:1815: error: ‘res_low’ was not declared in this scope ./src/check.C:1816: error: ‘_molecules’ was not declared in this scope ./src/check.C:1816: error: ‘_rep_mol’ was not declared in this scope ./src/check.C:1819: error: ‘ATOMP_TOKEN’ was not declared in this scope ./src/_validation.C: In member function ‘void _VALIDATION::insert_bond(const char*, const char*, int, const char*, const char*, const char*, double, double, double, int, int*, int*)’: ./src/_validation.C:1024: error: ‘strcpy’ was not declared in this scope ./src/check.C:1820: error: ‘ATOMN_TOKEN’ was not declared in this scope ./src/check.C:1822: error: ‘_Error_Check’ was not declared in this scope ./src/check.C:1832: error: ‘is_empty_table’ was not declared in this scope ./src/_validation.C:1033: error: ‘struct _BOND’ has no member named ‘fst’ ./src/check.C:1837: error: ‘res_high’ was not declared in this scope ./src/check.C:1837: error: ‘get_value’ was not declared in this scope ./src/_validation.C:1034: error: ‘struct _BOND’ has no member named ‘snd’ ./src/_validation.C:1037: error: ‘CifString’ was not declared in this scope ./src/_validation.C:1037: error: expected ‘;’ before ‘index’ ./src/_validation.C:1038: error: ‘_bondResIndex’ was not declared in this scope ./src/_validation.C:1038: error: ‘index’ was not declared in this scope ./src/check.C:1844: error: ‘_Error_Check’ was not declared in this scope ./src/_validation.C:1039: error: ‘index’ was not declared in this scope ./src/check.C:1852: error: ‘is_empty_table’ was not declared in this scope ./src/_validation.C:1040: error: ‘_bondComIndex’ was not declared in this scope ./src/_validation.C:1042: error: ‘_bondNamIndex’ was not declared in this scope ./src/check.C:1858: error: ‘is_empty_table’ was not declared in this scope ./src/check.C:1869: error: ‘res_high’ was not declared in this scope ./src/check.C:1869: error: ‘get_value’ was not declared in this scope ./src/check.C:1870: error: ‘res_low’ was not declared in this scope ./src/check.C:1872: error: ‘_Error_Check’ was not declared in this scope ./src/check.C:1877: error: ‘string’ was not declared in this scope ./src/check.C:1881: error: ‘_Error_Check’ was not declared in this scope ./src/check.C:1887: error: ‘_Error_Check’ was not declared in this scope ./src/_validation.C: At global scope: ./src/_validation.C:1047: error: ‘_ATOM’ has not been declared ./src/check.C:1893: error: ‘res_high’ was not declared in this scope ./src/_validation.C:1047: error: ‘_ATOM’ has not been declared ./src/check.C:1893: error: ‘get_value’ was not declared in this scope ./src/_validation.C:1048: error: ‘_ATOM’ has not been declared ./src/check.C:1896: error: ‘isalpha’ was not declared in this scope ./src/check.C:1899: error: ‘_Error_Check’ was not declared in this scope ./src/check.C:1907: error: ‘isalpha’ was not declared in this scope ./src/check.C:1910: error: ‘_Error_Check’ was not declared in this scope ./src/check.C:1919: error: ‘is_empty_table’ was not declared in this scope ./src/_validation.C: In member function ‘void _VALIDATION::insert_angle(const char*, const char*, int, const char*, const char*, const char*, double, double, double, int, int*, int*, int*)’: ./src/_validation.C:1062: error: ‘strcpy’ was not declared in this scope ./src/check.C:1929: error: ‘res_high’ was not declared in this scope ./src/check.C:1929: error: ‘get_value’ was not declared in this scope ./src/check.C:1930: error: ‘res_low’ was not declared in this scope ./src/check.C:1932: error: ‘_Error_Check’ was not declared in this scope ./src/_validation.C:1071: error: ‘struct _BOND’ has no member named ‘fst’ ./src/_validation.C:1072: error: ‘struct _BOND’ has no member named ‘snd’ ./src/check.C:1937: error: ‘string’ was not declared in this scope ./src/_validation.C:1073: error: ‘struct _BOND’ has no member named ‘trd’ ./src/check.C:1941: error: ‘_Error_Check’ was not declared in this scope ./src/_validation.C:1076: error: ‘CifString’ was not declared in this scope ./src/_validation.C:1076: error: expected ‘;’ before ‘index’ ./src/_validation.C:1077: error: ‘_angleResIndex’ was not declared in this scope ./src/_validation.C:1077: error: ‘index’ was not declared in this scope ./src/check.C:1947: error: ‘_Error_Check’ was not declared in this scope ./src/_validation.C:1078: error: ‘index’ was not declared in this scope ./src/_validation.C:1079: error: ‘_angleComIndex’ was not declared in this scope ./src/_validation.C:1081: error: ‘_angleNamIndex’ was not declared in this scope ./src/check.C:1953: error: ‘res_high’ was not declared in this scope ./src/check.C:1953: error: ‘get_value’ was not declared in this scope ./src/check.C:1956: error: ‘isalpha’ was not declared in this scope ./src/check.C:1959: error: ‘_Error_Check’ was not declared in this scope ./src/check.C:1968: error: ‘is_empty_table’ was not declared in this scope ./src/check.C:1973: error: ‘res_high’ was not declared in this scope ./src/check.C:1973: error: ‘get_value’ was not declared in this scope ./src/check.C:1974: error: ‘res_low’ was not declared in this scope ./src/check.C:1978: error: ‘_Error_Check’ was not declared in this scope ./src/check.C:1982: error: ‘_Error_Check’ was not declared in this scope ./src/check.C:1988: error: ‘is_empty_table’ was not declared in this scope ./src/check.C:1993: error: ‘_Error_Check’ was not declared in this scope ./src/check.C:1996: error: ‘res_high’ was not declared in this scope ./src/check.C:1996: error: ‘get_value’ was not declared in this scope ./src/check.C:1999: error: ‘_Error_Check’ was not declared in this scope ./src/check.C:2006: error: ‘is_empty_table’ was not declared in this scope ./src/check.C:2016: error: ‘string’ was not declared in this scope ./src/check.C:2028: error: ‘_Error_Check’ was not declared in this scope ./src/check.C:2036: error: ‘res_low’ was not declared in this scope ./src/check.C:2036: error: ‘get_value’ was not declared in this scope ./src/check.C:2039: error: ‘_Error_Check’ was not declared in this scope ./src/check.C:2043: error: ‘res_low’ was not declared in this scope ./src/check.C:2043: error: ‘get_value’ was not declared in this scope ./src/check.C:2044: error: ‘string1’ was not declared in this scope ./src/check.C:2045: error: ‘string2’ was not declared in this scope ./src/check.C:2061: error: ‘root_dir’ was not declared in this scope ./src/check.C:2063: error: ‘is_empty_table’ was not declared in this scope ./src/check.C:2072: error: ‘string’ was not declared in this scope ./src/check.C:2073: error: ‘string1’ was not declared in this scope ./src/check.C:2074: error: ‘string2’ was not declared in this scopemake[1]: *** [obj/gridcell.o] Error 1 ./src/check.C:2106: error: ‘_Error_Check’ was not declared in this scope ./src/_validation.C: At global scope: ./src/_validation.C:1086: error: ‘_ATOM’ has not been declared ./src/check.C:2117: error: ‘string’ was not declared in this scope ./src/_validation.C:1086: error: ‘_ATOM’ has not been declared ./src/check.C:2117: error: ‘get_value’ was not declared in this scope ./src/_validation.C:1086: error: ‘_ATOM’ has not been declared ./src/check.C:2118: error: ‘string1’ was not declared in this scope ./src/_validation.C:1086: error: ‘_ATOM’ has not been declared ./src/check.C:2119: error: ‘string2’ was not declared in this scope make[1]: *** [obj/align_standard.o] Error 1 ./src/check.C:2140: error: ‘find_drug’ was not declared in this scope ./src/check.C:2143: error: ‘get_oneletter_code’ was not declared in this scope ./src/_validation.C: In member function ‘void _VALIDATION::insert_torsion(const char*, const char*, int, const char*, const char*, const char*, double, int, int*, int*, int*, int*)’: ./src/_validation.C:1100: error: ‘strcpy’ was not declared in this scope ./src/check.C:2152: error: ‘ndb_set_string_to_upper’ was not declared in this scope ./src/check.C:2162: error: ‘ndb_clean_string’ was not declared in this scope ./src/_validation.C:1107: error: ‘struct _TORSION’ has no member named ‘fst’ ./src/_validation.C:1108: error: ‘struct _TORSION’ has no member named ‘snd’ ./src/_validation.C:1109: error: ‘struct _TORSION’ has no member named ‘trd’ ./src/_validation.C:1110: error: ‘struct _TORSION’ has no member named ‘fth’ ./src/_validation.C:1113: error: ‘CifString’ was not declared in this scope ./src/_validation.C:1113: error: expected ‘;’ before ‘index’ ./src/_validation.C:1114: error: ‘_torsionIndex’ was not declared in this scope ./src/_validation.C:1114: error: ‘index’ was not declared in this scope ./src/check.C:2180: error: ‘_Error_Check’ was not declared in this scope ./src/check.C:2188: error: ‘_Error_Check’ was not declared in this scope ./src/check.C:2193: error: ‘_Error_Check’ was not declared in this scope ./src/check.C:2202: error: ‘is_empty_table’ was not declared in this scope ./src/check.C:2205: error: ‘string’ was not declared in this scope ./src/check.C:2206: error: ‘string1’ was not declared in this scope ./src/check.C:2224: error: ‘_experiment_type’ was not declared in this scope ./src/check.C:2224: error: ‘EXPERIMENT_TYPE_NMR’ was not declared in this scope ./src/check.C:2225: error: ‘EXPERIMENT_TYPE_MODEL’ was not declared in this scope ./src/check.C:2233: error: expected type-specifier before ‘DICFileObj’./src/_validation.C: In member function ‘void _VALIDATION::insert_torsion_pair(const char*, const char*, int, const char*, double, double, int)’: ./src/_validation.C:1133: error: ‘strcpy’ was not declared in this scope ./src/check.C:2233: error: expected ‘;’ before ‘DICFileObj’ ./src/check.C:2236: error: ‘_Error_Check’ was not declared in this scope ./src/check.C:2236: error: ‘_date_error’ was not declared in this scope ./src/check.C:2236: error: ‘DictionaryDataChecking’ cannot be used as a function ./src/check.C:2237: error: type ‘’ argument given to ‘delete’, expected pointer ./src/check.C:2243: error: ‘string’ was not declared in this scope ./src/check.C:2244: error: ‘string1’ was not declared in this scope ./src/check.C:2245: error: ‘string2’ was not declared in this scope ./src/check.C:2246: error: ‘buff’ was not declared in this scope ./src/check.C:2247: error: ‘res_high’ was not declared in this scope ./src/check.C:2248: error: ‘_num_mol’ was not declared in this scope ./src/check.C:2249: error: ‘_molecules’ was not declared in this scope ./src/check.C:2250: error: ‘_molecules’ was not declared in this scope ./src/check.C:2256: error: ‘_experiment_type’ was not declared in this scope ./src/check.C:2256: error: ‘EXPERIMENT_TYPE_NMR’ was not declared in this scope ./src/check.C:2269: error: ‘_Error_Check’ was not declared in this scope ./src/check.C:2273: error: ‘_Error_Check’ was not declared in this scope ./src/check.C:2277: error: ‘_Error_Check’ was not declared in this scope ./src/check.C:2281: error: ‘_Error_Check’ was not declared in this scope ./src/check.C:2285: error: ‘_Error_Check’ was not declared in this scope In file included from ./src/datacheck.C:7: ./include/datacheck.h:7: warning: ‘DictionaryDataChecking’ initialized and declared ‘extern’ ./include/datacheck.h:7: error: ‘CifFileObj’ was not declared in this scope ./include/datacheck.h:7: error: ‘in’ was not declared in this scope ./include/datacheck.h:7: error: ‘DICFileObj’ was not declared in this scope ./include/datacheck.h:7: error: ‘ref’ was not declared in this scope ./include/datacheck.h:7: error: expected primary-expression before ‘*’ token ./include/datacheck.h:7: error: ‘fp’ was not declared in this scope ./include/datacheck.h:8: error: expected primary-expression before ‘const’ ./include/datacheck.h:8: error: expected primary-expression before ‘int’ ./include/datacheck.h:8: error: ‘CifString’ was not declared in this scope ./src/check.C: At global scope: ./src/check.C:2289: error: variable or field ‘check_tokens’ declared void ./src/check.C:2289: error: ‘_MOLECULE’ was not declared in this scope ./src/check.C:2289: error: ‘mol’ was not declared in this scope ./src/check.C:2289: error: ‘Cards_Info_Format’ was not declared in this scope ./src/check.C:2289: error: ‘CardInfo’ was not declared in this scope ./src/check.C:2290: error: expected primary-expression before ‘const’ ./src/check.C:2290: error: expected primary-expression before ‘*’ token ./src/check.C:2291: error: expected primary-expression before ‘const’ ./src/check.C:2291: error: expected primary-expression before ‘const’ ./src/check.C:2291: error: expected primary-expression before ‘*’ token ./src/check.C:2291: error: ‘fp’ was not declared in this scope ./src/check.C:200: warning: ‘int get_wavelength_list(const char*)’ declared ‘static’ but never defined ./src/check.C:201: warning: ‘int check_taxonomy(const char*)’ declared ‘static’ but never defined ./src/check.C:202: warning: ‘char* get_word1(char*, char*)’ declared ‘static’ but never defined ./src/_validation.C: At global scope: ./src/_validation.C:1256: error: variable or field ‘get_link_record’ declared void ./src/_validation.C:1256: error: ‘ISTable’ was not declared in this scope ./src/_validation.C:1256: error: ‘Table’ was not declared in this scope ./src/_validation.C:1256: error: expected primary-expression before ‘const’ ./src/_validation.C:146: warning: ‘int find_symmetry_related_chain(int, int**, int, int)’ declared ‘static’ but never defined ./src/_validation.C:148: warning: ‘int find_symmetry_related_chains(int, int**, int, char*)’ declared ‘static’ but never defined ./src/_validation.C:150: warning: ‘int find_asymmetric_chains(int, int**, int)’ declared ‘static’ but never defined ./include/datacheck.h:8: error: ‘date_error’ was not declared in this scope ./include/datacheck.h:8: error: initializer expression list treated as compound expression ./src/datacheck.C:15: error: ‘CifFileObj’ was not declared in this scope ./src/datacheck.C:15: error: ‘in’ was not declared in this scope ./src/datacheck.C:15: error: ‘DICFileObj’ was not declared in this scope ./src/datacheck.C:15: error: ‘ref’ was not declared in this scope ./src/datacheck.C:15: error: ‘ofstream’ was not declared in this scope ./src/datacheck.C:15: error: ‘log’ was not declared in this scope ./src/datacheck.C:15: error: expected primary-expression before ‘const’ ./src/datacheck.C:16: error: expected primary-expression before ‘int’ ./src/datacheck.C:16: error: ‘CifString’ was not declared in this scope ./src/datacheck.C:16: error: ‘date_error’ was not declared in this scope ./src/datacheck.C:16: error: initializer expression list treated as compound expression ./src/datacheck.C:21: error: variable or field ‘ConvertEscapedString’ declared void ./src/datacheck.C:21: error: ‘CifString’ was not declared in this scope ./src/datacheck.C:21: error: ‘inString’ was not declared in this scope ./src/datacheck.C:21: error: ‘CifString’ was not declared in this scope ./src/datacheck.C:21: error: ‘outString’ was not declared in this scope ./src/datacheck.C:24: error: redefinition of ‘int DictionaryDataChecking’ ./include/datacheck.h:7: error: ‘int DictionaryDataChecking’ previously defined here ./src/datacheck.C:24: error: ‘CifFileObj’ was not declared in this scope ./src/datacheck.C:24: error: ‘in’ was not declared in this scope ./src/datacheck.C:24: error: ‘DICFileObj’ was not declared in this scope ./src/datacheck.C:24: error: ‘ref’ was not declared in this scope ./src/datacheck.C:24: error: expected primary-expression before ‘*’ token ./src/datacheck.C:24: error: ‘fp’ was not declared in this scope ./src/datacheck.C:24: error: expected primary-expression before ‘const’ ./src/datacheck.C:25: error: expected primary-expression before ‘int’ ./src/datacheck.C:25: error: ‘CifString’ was not declared in this scope ./src/datacheck.C:25: error: ‘date_error’ was not declared in this scope ./src/datacheck.C:15: warning: ‘ItemsChecking’ defined but not used ./src/datacheck.C:17: warning: ‘void GetKeywordFromItemName(char*, const char*)’ declared ‘static’ but never defined ./src/datacheck.C:22: warning: ‘int is_wrong_date(const char*)’ declared ‘static’ but never defined make[1]: *** [obj/check.o] Error 1 make[1]: *** [obj/_validation.o] Error 1 make[1]: *** [obj/datacheck.o] Error 1 In file included from ./include/_validation.h:147, from ./src/contact.C:145: ./include/plot.h: In member function ‘void _plot::set_x_axis_title(const char*)’: ./include/plot.h:199: error: ‘strcpy’ was not declared in this scope ./include/plot.h: In member function ‘void _plot::set_y_axis_title(const char*)’: ./include/plot.h:200: error: ‘strcpy’ was not declared in this scope ./include/plot.h: In member function ‘void _plot::set_picture_title(const char*)’: ./include/plot.h:201: error: ‘strcpy’ was not declared in this scope In file included from ./include/_validation.h:148, from ./src/contact.C:145: ./include/check.h: At global scope: ./include/check.h:159: error: ‘MxStrLen’ was not declared in this scope In file included from ./src/contact.C:145: ./include/_validation.h:207: error: ISO C++ forbids declaration of ‘_RESIDUE’ with no type ./include/_validation.h:207: error: expected ‘;’ before ‘*’ token ./include/_validation.h:213: error: ‘COORD’ does not name a type ./include/_validation.h:214: error: ‘COORD’ does not name a type ./include/_validation.h:215: error: ‘COORD’ does not name a type ./include/_validation.h:216: error: ‘COORD’ does not name a type ./include/_validation.h:217: error: ‘COORD’ does not name a type ./include/_validation.h:218: error: ‘COORD’ does not name a type ./include/_validation.h:232: error: ISO C++ forbids declaration of ‘_ATOM’ with no type ./include/_validation.h:232: error: expected ‘;’ before ‘*’ token ./include/_validation.h:233: error: ISO C++ forbids declaration of ‘_ATOM’ with no type ./include/_validation.h:233: error: expected ‘;’ before ‘*’ token ./include/_validation.h:234: error: ISO C++ forbids declaration of ‘_ATOM’ with no type ./include/_validation.h:234: error: expected ‘;’ before ‘*’ token ./include/_validation.h:266: error: ISO C++ forbids declaration of ‘_ATOM’ with no type ./include/_validation.h:266: error: expected ‘;’ before ‘*’ token ./include/_validation.h:267: error: ISO C++ forbids declaration of ‘_ATOM’ with no type ./include/_validation.h:267: error: expected ‘;’ before ‘*’ token ./include/_validation.h:268: error: ISO C++ forbids declaration of ‘_ATOM’ with no type ./include/_validation.h:268: error: expected ‘;’ before ‘*’ token ./include/_validation.h:269: error: ISO C++ forbids declaration of ‘_ATOM’ with no type ./include/_validation.h:269: error: expected ‘;’ before ‘*’ token ./include/_validation.h:305: error: ‘CifString’ does not name a type ./include/_validation.h:315: error: ‘CifString’ does not name a type ./include/_validation.h:327: error: ‘COORD’ does not name a type ./include/_validation.h:328: error: ‘COORD’ does not name a type ./include/_validation.h:329: error: ‘COORD’ does not name a type ./include/_validation.h:339: error: ‘COORD’ does not name a type ./include/_validation.h:344: error: ISO C++ forbids declaration of ‘_ATOM’ with no type ./include/_validation.h:344: error: expected ‘;’ before ‘*’ token ./include/_validation.h:348: error: expected class-name before ‘{’ token ./include/_validation.h:377: error: ‘_ATOM’ has not been declared ./include/_validation.h:377: error: ‘_ATOM’ has not been declared ./include/_validation.h:380: error: ‘_ATOM’ has not been declared ./include/_validation.h:380: error: ‘_ATOM’ has not been declared ./include/_validation.h:380: error: ‘_ATOM’ has not been declared ./include/_validation.h:382: error: ‘_ATOM’ has not been declared ./include/_validation.h:382: error: ‘_ATOM’ has not been declared ./include/_validation.h:382: error: ‘_ATOM’ has not been declared ./include/_validation.h:382: error: ‘_ATOM’ has not been declared ./include/_validation.h:398: error: ‘CifString’ has not been declared ./include/_validation.h:421: error: ‘_RESIDUE’ has not been declared ./include/_validation.h:422: error: ‘_RESIDUE’ has not been declared ./include/_validation.h:422: error: ‘_RESIDUE’ has not been declared ./include/_validation.h:423: error: ‘_ATOM’ has not been declared ./include/_validation.h:423: error: ‘_ATOM’ has not been declared ./include/_validation.h:423: error: ‘_ATOM’ has not been declared ./include/_validation.h:423: error: ‘_ATOM’ has not been declared ./include/_validation.h:426: error: ‘CifString’ has not been declared ./include/_validation.h:426: error: ‘CifString’ has not been declared ./include/_validation.h:427: error: ‘CifString’ has not been declared ./include/_validation.h:433: error: ‘_MOLECULE’ has not been declared ./include/_validation.h:434: error: ‘_CHAIN’ has not been declared ./include/_validation.h:434: error: ‘COORD’ has not been declared ./include/_validation.h:434: error: ‘_RESIDUE’ has not been declared ./include/_validation.h:435: error: ‘_CHAIN’ has not been declared ./include/_validation.h:436: error: ‘_ATOM’ has not been declared ./include/_validation.h:436: error: ‘_ATOM’ has not been declared ./include/_validation.h:437: error: ‘_CHAIN’ has not been declared ./include/_validation.h:438: error: ‘COORD’ has not been declared ./include/_validation.h:438: error: ‘COORD’ has not been declared ./include/_validation.h:444: error: ‘ISTable’ has not been declared ./include/_validation.h:492: error: ‘TblIndexObj’ does not name a type ./include/_validation.h:493: error: ‘TblIndexObj’ does not name a type ./include/_validation.h:494: error: ‘TblIndexObj’ does not name a type ./include/_validation.h:495: error: ‘TblIndexObj’ does not name a type ./include/_validation.h:496: error: ‘TblIndexObj’ does not name a type ./include/_validation.h:497: error: ‘TblIndexObj’ does not name a type ./include/_validation.h:498: error: ‘TblIndexObj’ does not name a type ./include/_validation.h:500: error: ‘CifString’ does not name a type ./include/_validation.h:501: error: ‘CifString’ does not name a type ./include/_validation.h:502: error: ‘CifString’ does not name a type ./include/_validation.h:507: warning: ‘get_residue_index’ initialized and declared ‘extern’ ./include/_validation.h:507: error: ‘_MOLECULE’ was not declared in this scope ./include/_validation.h:507: error: ‘mol’ was not declared in this scope ./include/_validation.h:507: error: ‘ISTable’ was not declared in this scope ./include/_validation.h:507: error: ‘Table’ was not declared in this scope ./include/_validation.h:507: error: expected primary-expression before ‘const’ ./include/_validation.h:508: error: expected primary-expression before ‘const’ ./include/_validation.h:508: error: expected primary-expression before ‘const’ ./include/_validation.h:508: error: expected primary-expression before ‘const’ ./include/_validation.h:509: error: expected primary-expression before ‘const’ ./include/_validation.h:509: error: expected primary-expression before ‘const’ ./include/_validation.h:509: error: expected primary-expression before ‘const’ ./include/_validation.h:510: error: expected primary-expression before ‘const’ ./include/_validation.h:510: error: expected primary-expression before ‘int’ ./include/_validation.h:510: error: expected primary-expression before ‘int’ ./include/_validation.h:510: error: ‘CifString’ was not declared in this scope ./include/_validation.h:510: error: ‘name’ was not declared in this scope ./include/_validation.h:510: error: initializer expression list treated as compound expression In file included from ./include/list.h:146, from ./include/atom.h:147, from ./include/gridcell.h:144, from ./src/contact.C:147: ./include/symop.h:153: error: ISO C++ forbids declaration of ‘ostream’ with no type ./include/symop.h:153: error: ‘ostream’ is neither function nor member function; cannot be declared friend ./include/symop.h:153: error: expected ‘;’ before ‘&’ token ./include/symop.h:158: error: expected ‘)’ before ‘&’ token In file included from ./src/contact.C:149: /usr/include/rcsb/util.h:67: error: ‘CifFile’ was not declared in this scope /usr/include/rcsb/util.h:67: error: ‘fobj’ was not declared in this scope /usr/include/rcsb/util.h:67: error: expected primary-expression before ‘const’ /usr/include/rcsb/util.h:68: error: expected primary-expression before ‘const’ /usr/include/rcsb/util.h:68: error: expected primary-expression before ‘const’ /usr/include/rcsb/util.h:68: error: initializer expression list treated as compound expression /usr/include/rcsb/util.h:69: error: ‘CifFile’ was not declared in this scope /usr/include/rcsb/util.h:69: error: ‘fobj’ was not declared in this scope /usr/include/rcsb/util.h:69: error: expected primary-expression before ‘const’ /usr/include/rcsb/util.h:70: error: expected primary-expression before ‘const’ /usr/include/rcsb/util.h:70: error: expected primary-expression before ‘const’ /usr/include/rcsb/util.h:71: error: expected primary-expression before ‘long’ /usr/include/rcsb/util.h:71: error: initializer expression list treated as compound expression /usr/include/rcsb/util.h:74: error: ‘int check_category(const char*, char*, char*)’ redeclared as different kind of symbol ./include/check.h:191: error: previous declaration of ‘CHECK_CATEGORY check_category [6]’ In file included from ./src/contact.C:150: ./include/xtal.h:166: error: ISO C++ forbids declaration of ‘NDBCELLCONST’ with no type ./include/xtal.h:166: error: expected ‘,’ or ‘...’ before ‘*’ token ./include/xtal.h:167: error: ‘COORD’ has not been declared ./include/xtal.h:167: error: ‘COORD’ has not been declared ./src/contact.C:152: error: variable or field ‘get_all_shell_atoms’ declared void ./src/contact.C:152: error: ‘BTreeObj’ was not declared in this scope ./src/contact.C:152: error: ‘_ISIndex’ was not declared in this scope ./src/contact.C:152: error: ‘_AllWaters’ was not declared in this scope ./src/contact.C:152: error: expected primary-expression before ‘const’ ./src/contact.C:153: error: expected primary-expression before ‘*’ token ./src/contact.C:153: error: ‘contact’ was not declared in this scope ./src/contact.C: In member function ‘void _VALIDATION::find_all_links()’: ./src/contact.C:164: error: ‘_ATOM’ was not declared in this scope ./src/contact.C:164: error: ‘atom_O3’ was not declared in this scope ./src/contact.C:164: error: ‘atom_P’ was not declared in this scope ./src/contact.C:165: error: ‘_RESIDUE’ was not declared in this scope ./src/contact.C:165: error: ‘Fst’ was not declared in this scope ./src/contact.C:165: error: ‘Snd’ was not declared in this scope ./src/contact.C:166: error: ‘_CHAIN’ was not declared in this scope ./src/contact.C:166: error: ‘chn1’ was not declared in this scope ./src/contact.C:166: error: ‘chn2’ was not declared in this scope ./src/contact.C:168: error: ‘_num_mol’ was not declared in this scope ./src/contact.C:170: error: ‘_molecules’ was not declared in this scope ./src/contact.C:172: error: ‘ATOMN_TOKEN’ was not declared in this scope ./src/contact.C:172: error: ‘ATOMN_TYPE_TRNA’ was not declared in this scope ./src/contact.C:182: error: ‘is_a_nonstandard_trna’ was not declared in this scope ./src/contact.C:189: error: ‘strcmp’ was not declared in this scope ./src/contact.C:192: error: ‘is_a_bond’ was not declared in this scope ./src/contact.C:200: error: type ‘’ argument given to ‘delete’, expected pointer ./src/contact.C:201: error: type ‘’ argument given to ‘delete’, expected pointer ./src/contact.C:209: error: ‘_cell’ was not declared in this scope ./src/contact.C:212: error: ‘_cell’ was not declared in this scope ./src/contact.C:222: error: ‘strcmp’ was not declared in this scope ./src/contact.C:238: error: ‘ATOMP_TOKEN’ was not declared in this scope ./src/contact.C:239: error: ‘ATOMS_TOKEN’ was not declared in this scope ./src/contact.C:240: error: ‘strcmp’ was not declared in this scope make[1]: *** [obj/atom.o] Error 1 ./src/contact.C: In member function ‘void _VALIDATION::calculate_contact_for_nmr()’: ./src/contact.C:292: error: ‘_num_mol’ was not declared in this scope ./src/contact.C:295: error: ‘_cell’ was not declared in this scope ./src/contact.C:295: error: ‘_molecules’ was not declared in this scope ./src/contact.C: In member function ‘CONTACT** _VALIDATION::calculate_all_contacts(int&, double, double)’: ./src/contact.C:332: error: ‘_num_mol’ was not declared in this scope ./src/contact.C:335: error: ‘_cell’ was not declared in this scope ./src/contact.C:335: error: ‘_molecules’ was not declared in this scope ./src/contact.C: In member function ‘void _VALIDATION::calculate_all_contact(double, int)’: ./src/contact.C:370: error: ‘_ATOM’ was not declared in this scope ./src/contact.C:370: error: expected primary-expression before ‘=’ token ./src/contact.C:371: error: ‘_RESIDUE’ was not declared in this scope ./src/contact.C:371: error: ‘residue’ was not declared in this scope ./src/contact.C:372: error: ‘_CHAIN’ was not declared in this scope ./src/contact.C:372: error: ‘chain’ was not declared in this scope ./src/contact.C:374: error: ‘BTreeObj’ was not declared in this scope ./src/contact.C:374: error: expected primary-expression before ‘>’ token ./src/contact.C:374: error: ‘_CIndex’ was not declared in this scope ./src/contact.C:375: error: ‘_ISIndex’ was not declared in this scope ./src/contact.C:375: error: expected ‘;’ before ‘index’ ./src/contact.C:376: error: ‘_AllWaters’ was not declared in this scope ./src/contact.C:378: error: ‘_num_mol’ was not declared in this scope ./src/contact.C:379: error: ‘_cell’ was not declared in this scope ./src/contact.C:382: error: ‘_experiment_type’ was not declared in this scope ./src/contact.C:382: error: ‘EXPERIMENT_TYPE_NMR’ was not declared in this scope ./src/contact.C:388: error: ‘_cell’ was not declared in this scope ./src/contact.C:388: error: ‘_molecules’ was not declared in this scope ./src/contact.C:412: error: ‘strcmp’ was not declared in this scope ./src/contact.C:470: error: ‘_molecules’ was not declared in this scope ./src/contact.C:472: error: ‘HETAS_TOKEN’ was not declared in this scope ./src/contact.C:474: error: ‘strcmp’ was not declared in this scope ./src/contact.C:502: error: ‘strcpy’ was not declared in this scope ./src/contact.C:533: error: ‘HETAS_TOKEN’ was not declared in this scope ./src/contact.C:539: error: ‘strcmp’ was not declared in this scope ./src/contact.C:544: error: expected unqualified-id before ‘=’ token ./src/contact.C:545: error: expected primary-expression before ‘)’ token ./src/contact.C:546: error: expected primary-expression before ‘->’ token ./src/contact.C:546: error: ‘strcmp’ was not declared in this scope ./src/contact.C:558: error: expected primary-expression before ‘->’ token ./src/contact.C:558: error: ‘strcpy’ was not declared in this scope ./src/contact.C:559: error: expected primary-expression before ‘->’ token ./src/contact.C:560: error: expected primary-expression before ‘->’ token ./src/contact.C:561: error: expected primary-expression before ‘->’ token ./src/contact.C:562: error: expected primary-expression before ‘->’ token ./src/contact.C:563: error: expected primary-expression before ‘->’ token ./src/contact.C:570: error: ‘index’ was not declared in this scope ./src/contact.C:570: error: expected primary-expression before ‘->’ token ./src/contact.C:571: error: expected primary-expression before ‘->’ token ./src/contact.C:577: error: expected unqualified-id before ‘=’ token ./src/contact.C:585: error: ‘strcmp’ was not declared in this scope ./src/contact.C:589: error: ‘strcpy’ was not declared in this scope ./src/contact.C:620: error: ‘strcmp’ was not declared in this scope ./src/contact.C:622: error: ‘index’ was not declared in this scope ./src/contact.C:659: error: ‘get_all_shell_atoms’ was not declared in this scope ./src/contact.C:665: error: ‘index’ was not declared in this scope ./src/contact.C:680: error: ‘index’ was not declared in this scope ./src/contact.C:705: error: ‘strcpy’ was not declared in this scope ./src/contact.C: In member function ‘int _VALIDATION::find_a_link(CONTACT*)’: ./src/contact.C:764: error: ‘_MOLECULE’ was not declared in this scope ./src/contact.C:764: error: ‘mol’ was not declared in this scope ./src/contact.C:764: error: ‘_molecules’ was not declared in this scope ./src/contact.C:770: error: ‘strcmp’ was not declared in this scope ./src/contact.C: In function ‘CONTACT** get_contact(xtal&, int&, double, double, const char*, const char*, const char*, int)’: ./src/contact.C:792: error: ‘BTreeObj’ was not declared in this scope ./src/contact.C:792: error: expected primary-expression before ‘>’ token ./src/contact.C:792: error: ‘_CIndex’ was not declared in this scope In file included from ./src/na_classification.C:145: ./include/_validation.h:144:22: error: _fileobj.h: No such file or directory ./src/contact.C:810: error: ‘strcmp’ was not declared in this scope ./src/contact.C:839: error: ‘strncmp’ was not declared in this scope ./src/contact.C:846: error: ‘strcmp’ was not declared in this scope ./src/na_classification.C:146:22: error: erf_util.h: No such file or directory In file included from ./src/na_classification.C:147: /usr/include/rcsb/util.h:11:21: error: CifFile.h: No such file or directory /usr/include/rcsb/util.h:12:23: error: TableFile.h: No such file or directory ./src/contact.C:909: warning: suggest parentheses around ‘&&’ within ‘||’ ./src/contact.C:911: error: ‘strcpy’ was not declared in this scope ./src/contact.C:972: error: ‘strcpy’ was not declared in this scope ./src/contact.C: At global scope: ./src/contact.C:1038: error: variable or field ‘get_all_shell_atoms’ declared void ./src/contact.C:1038: error: ‘BTreeObj’ was not declared in this scope ./src/contact.C:1038: error: ‘_ISIndex’ was not declared in this scope ./src/contact.C:1038: error: ‘_AllWaters’ was not declared in this scope ./src/contact.C:1038: error: expected primary-expression before ‘const’ ./src/contact.C:1039: error: expected primary-expression before ‘*’ token ./src/contact.C:1039: error: ‘contact’ was not declared in this scope make[1]: *** [obj/contact.o] Error 1 In file included from ./src/ndb_atlas.C:147: ./include/_validation.h:144:22: error: _fileobj.h: No such file or directory ./src/ndb_atlas.C:148:22: error: erf_util.h: No such file or directory In file included from ./src/ndb_atlas.C:149: /usr/include/rcsb/util.h:11:21: error: CifFile.h: No such file or directory /usr/include/rcsb/util.h:12:23: error: TableFile.h: No such file or directory ./src/ndb_atlas.C:151:25: error: ndb_misclib.h: No such file or directory In file included from ./include/_validation.h:148, from ./src/na_classification.C:145: ./include/check.h:159: error: ‘MxStrLen’ was not declared in this scope In file included from ./src/na_classification.C:145: ./include/_validation.h:207: error: ISO C++ forbids declaration of ‘_RESIDUE’ with no type ./include/_validation.h:207: error: expected ‘;’ before ‘*’ token ./include/_validation.h:213: error: ‘COORD’ does not name a type ./include/_validation.h:214: error: ‘COORD’ does not name a type ./include/_validation.h:215: error: ‘COORD’ does not name a type ./include/_validation.h:216: error: ‘COORD’ does not name a type ./include/_validation.h:217: error: ‘COORD’ does not name a type ./include/_validation.h:218: error: ‘COORD’ does not name a type ./include/_validation.h:232: error: ISO C++ forbids declaration of ‘_ATOM’ with no type ./include/_validation.h:232: error: expected ‘;’ before ‘*’ token ./include/_validation.h:233: error: ISO C++ forbids declaration of ‘_ATOM’ with no type ./include/_validation.h:233: error: expected ‘;’ before ‘*’ token ./include/_validation.h:234: error: ISO C++ forbids declaration of ‘_ATOM’ with no type ./include/_validation.h:234: error: expected ‘;’ before ‘*’ token ./include/_validation.h:266: error: ISO C++ forbids declaration of ‘_ATOM’ with no type ./include/_validation.h:266: error: expected ‘;’ before ‘*’ token ./include/_validation.h:267: error: ISO C++ forbids declaration of ‘_ATOM’ with no type ./include/_validation.h:267: error: expected ‘;’ before ‘*’ token ./include/_validation.h:268: error: ISO C++ forbids declaration of ‘_ATOM’ with no type ./include/_validation.h:268: error: expected ‘;’ before ‘*’ token ./include/_validation.h:269: error: ISO C++ forbids declaration of ‘_ATOM’ with no type ./include/_validation.h:269: error: expected ‘;’ before ‘*’ token ./include/_validation.h:305: error: ‘CifString’ does not name a type ./include/_validation.h:315: error: ‘CifString’ does not name a type ./include/_validation.h:327: error: ‘COORD’ does not name a type ./include/_validation.h:328: error: ‘COORD’ does not name a type ./include/_validation.h:329: error: ‘COORD’ does not name a type ./include/_validation.h:339: error: ‘COORD’ does not name a type ./include/_validation.h:344: error: ISO C++ forbids declaration of ‘_ATOM’ with no type ./include/_validation.h:344: error: expected ‘;’ before ‘*’ token ./include/_validation.h:348: error: expected class-name before ‘{’ token ./include/_validation.h:377: error: ‘_ATOM’ has not been declared ./include/_validation.h:377: error: ‘_ATOM’ has not been declared ./include/_validation.h:380: error: ‘_ATOM’ has not been declared ./include/_validation.h:380: error: ‘_ATOM’ has not been declared ./include/_validation.h:380: error: ‘_ATOM’ has not been declared ./include/_validation.h:382: error: ‘_ATOM’ has not been declared ./include/_validation.h:382: error: ‘_ATOM’ has not been declared ./include/_validation.h:382: error: ‘_ATOM’ has not been declared ./include/_validation.h:382: error: ‘_ATOM’ has not been declared ./include/_validation.h:398: error: ‘CifString’ has not been declared ./include/_validation.h:421: error: ‘_RESIDUE’ has not been declared ./include/_validation.h:422: error: ‘_RESIDUE’ has not been declared ./include/_validation.h:422: error: ‘_RESIDUE’ has not been declared ./include/_validation.h:423: error: ‘_ATOM’ has not been declared ./include/_validation.h:423: error: ‘_ATOM’ has not been declared ./include/_validation.h:423: error: ‘_ATOM’ has not been declared ./include/_validation.h:423: error: ‘_ATOM’ has not been declared ./include/_validation.h:426: error: ‘CifString’ has not been declared ./include/_validation.h:426: error: ‘CifString’ has not been declared ./include/_validation.h:427: error: ‘CifString’ has not been declared ./include/_validation.h:433: error: ‘_MOLECULE’ has not been declared ./include/_validation.h:434: error: ‘_CHAIN’ has not been declared ./include/_validation.h:434: error: ‘COORD’ has not been declared ./include/_validation.h:434: error: ‘_RESIDUE’ has not been declared ./include/_validation.h:435: error: ‘_CHAIN’ has not been declared ./include/_validation.h:436: error: ‘_ATOM’ has not been declared ./include/_validation.h:436: error: ‘_ATOM’ has not been declared ./include/_validation.h:437: error: ‘_CHAIN’ has not been declared ./include/_validation.h:438: error: ‘COORD’ has not been declared ./include/_validation.h:438: error: ‘COORD’ has not been declared ./include/_validation.h:444: error: ‘ISTable’ has not been declared ./include/_validation.h:492: error: ‘TblIndexObj’ does not name a type ./include/_validation.h:493: error: ‘TblIndexObj’ does not name a type ./include/_validation.h:494: error: ‘TblIndexObj’ does not name a type ./include/_validation.h:495: error: ‘TblIndexObj’ does not name a type ./include/_validation.h:496: error: ‘TblIndexObj’ does not name a type ./include/_validation.h:497: error: ‘TblIndexObj’ does not name a type ./include/_validation.h:498: error: ‘TblIndexObj’ does not name a type ./include/_validation.h:500: error: ‘CifString’ does not name a type ./include/_validation.h:501: error: ‘CifString’ does not name a type ./include/_validation.h:502: error: ‘CifString’ does not name a type ./include/_validation.h:507: warning: ‘get_residue_index’ initialized and declared ‘extern’ ./include/_validation.h:507: error: ‘_MOLECULE’ was not declared in this scope ./include/_validation.h:507: error: ‘mol’ was not declared in this scope ./include/_validation.h:507: error: ‘ISTable’ was not declared in this scope ./include/_validation.h:507: error: ‘Table’ was not declared in this scope ./include/_validation.h:507: error: expected primary-expression before ‘const’ ./include/_validation.h:508: error: expected primary-expression before ‘const’ ./include/_validation.h:508: error: expected primary-expression before ‘const’ ./include/_validation.h:508: error: expected primary-expression before ‘const’ ./include/_validation.h:509: error: expected primary-expression before ‘const’ ./include/_validation.h:509: error: expected primary-expression before ‘const’ ./include/_validation.h:509: error: expected primary-expression before ‘const’ ./include/_validation.h:510: error: expected primary-expression before ‘const’ ./include/_validation.h:510: error: expected primary-expression before ‘int’ ./include/_validation.h:510: error: expected primary-expression before ‘int’ ./include/_validation.h:510: error: ‘CifString’ was not declared in this scope ./include/_validation.h:510: error: ‘name’ was not declared in this scope ./include/_validation.h:510: error: initializer expression list treated as compound expression In file included from ./src/na_classification.C:147: /usr/include/rcsb/util.h:67: error: ‘CifFile’ was not declared in this scope /usr/include/rcsb/util.h:67: error: ‘fobj’ was not declared in this scope /usr/include/rcsb/util.h:67: error: expected primary-expression before ‘const’ /usr/include/rcsb/util.h:68: error: expected primary-expression before ‘const’ /usr/include/rcsb/util.h:68: error: expected primary-expression before ‘const’ /usr/include/rcsb/util.h:68: error: initializer expression list treated as compound expression /usr/include/rcsb/util.h:69: error: ‘CifFile’ was not declared in this scope /usr/include/rcsb/util.h:69: error: ‘fobj’ was not declared in this scope /usr/include/rcsb/util.h:69: error: expected primary-expression before ‘const’ /usr/include/rcsb/util.h:70: error: expected primary-expression before ‘const’ /usr/include/rcsb/util.h:70: error: expected primary-expression before ‘const’ /usr/include/rcsb/util.h:71: error: expected primary-expression before ‘long’ /usr/include/rcsb/util.h:71: error: initializer expression list treated as compound expression /usr/include/rcsb/util.h:74: error: ‘int check_category(const char*, char*, char*)’ redeclared as different kind of symbol ./include/check.h:191: error: previous declaration of ‘CHECK_CATEGORY check_category [6]’ ./src/na_classification.C: In member function ‘void _VALIDATION::na_classification()’: ./src/na_classification.C:210: error: ‘CifString’ was not declared in this scope ./src/na_classification.C:210: error: expected ‘;’ before ‘index’ ./src/na_classification.C:211: error: ‘TblIndexObj’ was not declared in this scope ./src/na_classification.C:211: error: expected ‘;’ before ‘_BaseIndex’ ./src/na_classification.C:214: error: ‘_CHAIN’ was not declared in this scope ./src/na_classification.C:214: error: ‘chain’ was not declared in this scope ./src/na_classification.C:217: error: ‘ISTable’ was not declared in this scope ./src/na_classification.C:217: error: ‘Table’ was not declared in this scope ./src/na_classification.C:223: error: ‘index’ does not have class type ./src/na_classification.C:224: error: overloaded function with no contextual type information ./src/na_classification.C:225: error: overloaded function with no contextual type information ./src/na_classification.C:226: error: overloaded function with no contextual type information ./src/na_classification.C:227: error: overloaded function with no contextual type information ./src/na_classification.C:228: error: overloaded function with no contextual type information ./src/na_classification.C:229: error: overloaded function with no contextual type information ./src/na_classification.C:230: error: overloaded function with no contextual type information ./src/na_classification.C:231: error: overloaded function with no contextual type information ./src/na_classification.C:232: error: ‘_BaseIndex’ was not declared in this scope ./src/na_classification.C:248: error: ‘_MOLECULE’ was not declared in this scope ./src/na_classification.C:248: error: ‘mol’ was not declared in this scope ./src/na_classification.C:248: error: ‘_molecules’ was not declared in this scope ./src/na_classification.C:336: warning: suggest parentheses around ‘&&’ within ‘||’ ./src/na_classification.C:381: error: ‘get_parent_name’ was not declared in this scope ./src/na_classification.C:458: error: ‘_CifObj’ was not declared in this scope ./src/na_classification.C:459: error: ‘_StructureId’ was not declared in this scope ./src/na_classification.C:460: error: ‘is_empty_table’ was not declared in this scope ./src/na_classification.C:464: error: expected type-specifier before ‘ISTable’ ./src/na_classification.C:464: error: expected ‘;’ before ‘ISTable’ ./src/na_classification.C:468: error: ‘entry_id’ was not declared in this scope ./src/na_classification.C:471: error: ‘feature’ was not declared in this scope ./src/na_classification.C:478: error: ‘feature’ was not declared in this scope ./src/na_classification.C:485: error: ‘feature’ was not declared in this scope ./src/na_classification.C:492: error: ‘feature’ was not declared in this scope ./src/na_classification.C:499: error: ‘feature’ was not declared in this scope ./src/na_classification.C:506: error: ‘feature’ was not declared in this scope ./src/na_classification.C:513: error: ‘feature’ was not declared in this scope ./src/na_classification.C:520: error: ‘feature’ was not declared in this scope ./src/na_classification.C:527: error: ‘feature’ was not declared in this scope ./src/na_classification.C:534: error: ‘feature’ was not declared in this scope ./src/na_classification.C:541: error: ‘feature’ was not declared in this scope ./src/na_classification.C:548: error: ‘feature’ was not declared in this scope ./src/na_classification.C:555: error: ‘feature’ was not declared in this scope ./src/na_classification.C:562: error: ‘feature’ was not declared in this scope In file included from ./include/_validation.h:148, from ./src/ndb_atlas.C:147: ./include/check.h:159: error: ‘MxStrLen’ was not declared in this scope In file included from ./src/ndb_atlas.C:147: ./include/_validation.h:207: error: ISO C++ forbids declaration of ‘_RESIDUE’ with no type ./include/_validation.h:207: error: expected ‘;’ before ‘*’ token ./include/_validation.h:213: error: ‘COORD’ does not name a type ./include/_validation.h:214: error: ‘COORD’ does not name a type ./include/_validation.h:215: error: ‘COORD’ does not name a type ./include/_validation.h:216: error: ‘COORD’ does not name a type ./include/_validation.h:217: error: ‘COORD’ does not name a type ./include/_validation.h:218: error: ‘COORD’ does not name a type ./include/_validation.h:232: error: ISO C++ forbids declaration of ‘_ATOM’ with no type ./include/_validation.h:232: error: expected ‘;’ before ‘*’ token ./include/_validation.h:233: error: ISO C++ forbids declaration of ‘_ATOM’ with no type ./include/_validation.h:233: error: expected ‘;’ before ‘*’ token ./include/_validation.h:234: error: ISO C++ forbids declaration of ‘_ATOM’ with no type ./include/_validation.h:234: error: expected ‘;’ before ‘*’ token ./include/_validation.h:266: error: ISO C++ forbids declaration of ‘_ATOM’ with no type ./include/_validation.h:266: error: expected ‘;’ before ‘*’ token ./include/_validation.h:267: error: ISO C++ forbids declaration of ‘_ATOM’ with no type ./include/_validation.h:267: error: expected ‘;’ before ‘*’ token ./include/_validation.h:268: error: ISO C++ forbids declaration of ‘_ATOM’ with no type ./include/_validation.h:268: error: expected ‘;’ before ‘*’ token ./include/_validation.h:269: error: ISO C++ forbids declaration of ‘_ATOM’ with no type ./include/_validation.h:269: error: expected ‘;’ before ‘*’ token ./include/_validation.h:305: error: ‘CifString’ does not name a type ./include/_validation.h:315: error: ‘CifString’ does not name a type ./include/_validation.h:327: error: ‘COORD’ does not name a type ./include/_validation.h:328: error: ‘COORD’ does not name a type ./include/_validation.h:329: error: ‘COORD’ does not name a type ./include/_validation.h:339: error: ‘COORD’ does not name a type ./include/_validation.h:344: error: ISO C++ forbids declaration of ‘_ATOM’ with no type ./include/_validation.h:344: error: expected ‘;’ before ‘*’ token ./include/_validation.h:348: error: expected class-name before ‘{’ token ./include/_validation.h:377: error: ‘_ATOM’ has not been declared ./include/_validation.h:377: error: ‘_ATOM’ has not been declared ./include/_validation.h:380: error: ‘_ATOM’ has not been declared ./include/_validation.h:380: error: ‘_ATOM’ has not been declared ./include/_validation.h:380: error: ‘_ATOM’ has not been declared ./include/_validation.h:382: error: ‘_ATOM’ has not been declared ./include/_validation.h:382: error: ‘_ATOM’ has not been declared ./include/_validation.h:382: error: ‘_ATOM’ has not been declared ./include/_validation.h:382: error: ‘_ATOM’ has not been declared ./include/_validation.h:398: error: ‘CifString’ has not been declared ./include/_validation.h:421: error: ‘_RESIDUE’ has not been declared ./include/_validation.h:422: error: ‘_RESIDUE’ has not been declared ./include/_validation.h:422: error: ‘_RESIDUE’ has not been declared ./include/_validation.h:423: error: ‘_ATOM’ has not been declared ./include/_validation.h:423: error: ‘_ATOM’ has not been declared ./include/_validation.h:423: error: ‘_ATOM’ has not been declared ./include/_validation.h:423: error: ‘_ATOM’ has not been declared ./include/_validation.h:426: error: ‘CifString’ has not been declared ./include/_validation.h:426: error: ‘CifString’ has not been declared ./include/_validation.h:427: error: ‘CifString’ has not been declared ./include/_validation.h:433: error: ‘_MOLECULE’ has not been declared ./include/_validation.h:434: error: ‘_CHAIN’ has not been declared ./include/_validation.h:434: error: ‘COORD’ has not been declared ./include/_validation.h:434: error: ‘_RESIDUE’ has not been declared ./include/_validation.h:435: error: ‘_CHAIN’ has not been declared ./include/_validation.h:436: error: ‘_ATOM’ has not been declared ./include/_validation.h:436: error: ‘_ATOM’ has not been declared ./include/_validation.h:437: error: ‘_CHAIN’ has not been declared ./include/_validation.h:438: error: ‘COORD’ has not been declared ./include/_validation.h:438: error: ‘COORD’ has not been declared ./src/na_classification.C: In function ‘int non_watson_crick_pair(char, char)’: ./src/na_classification.C:1022: warning: suggest parentheses around ‘&&’ within ‘||’ ./include/_validation.h:444: error: ‘ISTable’ has not been declared ./include/_validation.h:492: error: ‘TblIndexObj’ does not name a type ./include/_validation.h:493: error: ‘TblIndexObj’ does not name a type ./include/_validation.h:494: error: ‘TblIndexObj’ does not name a type ./include/_validation.h:495: error: ‘TblIndexObj’ does not name a type ./include/_validation.h:496: error: ‘TblIndexObj’ does not name a type ./include/_validation.h:497: error: ‘TblIndexObj’ does not name a type ./include/_validation.h:498: error: ‘TblIndexObj’ does not name a type ./include/_validation.h:500: error: ‘CifString’ does not name a type ./include/_validation.h:501: error: ‘CifString’ does not name a type ./include/_validation.h:502: error: ‘CifString’ does not name a type ./include/_validation.h:507: warning: ‘get_residue_index’ initialized and declared ‘extern’ ./include/_validation.h:507: error: ‘_MOLECULE’ was not declared in this scope ./include/_validation.h:507: error: ‘mol’ was not declared in this scope ./include/_validation.h:507: error: ‘ISTable’ was not declared in this scope ./include/_validation.h:507: error: ‘Table’ was not declared in this scope ./include/_validation.h:507: error: expected primary-expression before ‘const’ ./include/_validation.h:508: error: expected primary-expression before ‘const’ ./include/_validation.h:508: error: expected primary-expression before ‘const’ ./include/_validation.h:508: error: expected primary-expression before ‘const’ ./include/_validation.h:509: error: expected primary-expression before ‘const’ ./include/_validation.h:509: error: expected primary-expression before ‘const’ ./include/_validation.h:509: error: expected primary-expression before ‘const’ ./include/_validation.h:510: error: expected primary-expression before ‘const’ ./include/_validation.h:510: error: expected primary-expression before ‘int’ ./include/_validation.h:510: error: expected primary-expression before ‘int’ ./include/_validation.h:510: error: ‘CifString’ was not declared in this scope ./include/_validation.h:510: error: ‘name’ was not declared in this scope ./include/_validation.h:510: error: initializer expression list treated as compound expression In file included from ./src/ndb_atlas.C:149: /usr/include/rcsb/util.h:67: error: ‘CifFile’ was not declared in this scope /usr/include/rcsb/util.h:67: error: ‘fobj’ was not declared in this scope /usr/include/rcsb/util.h:67: error: expected primary-expression before ‘const’ /usr/include/rcsb/util.h:68: error: expected primary-expression before ‘const’ /usr/include/rcsb/util.h:68: error: expected primary-expression before ‘const’ /usr/include/rcsb/util.h:68: error: initializer expression list treated as compound expression make[1]: *** [obj/na_classification.o] Error 1 /usr/include/rcsb/util.h:69: error: ‘CifFile’ was not declared in this scope /usr/include/rcsb/util.h:69: error: ‘fobj’ was not declared in this scope /usr/include/rcsb/util.h:69: error: expected primary-expression before ‘const’ /usr/include/rcsb/util.h:70: error: expected primary-expression before ‘const’ /usr/include/rcsb/util.h:70: error: expected primary-expression before ‘const’ /usr/include/rcsb/util.h:71: error: expected primary-expression before ‘long’ /usr/include/rcsb/util.h:71: error: initializer expression list treated as compound expression /usr/include/rcsb/util.h:74: error: ‘int check_category(const char*, char*, char*)’ redeclared as different kind of symbol ./include/check.h:191: error: previous declaration of ‘CHECK_CATEGORY check_category [6]’ ./src/ndb_atlas.C:155: error: variable or field ‘get_citation_val’ declared void ./src/ndb_atlas.C:155: error: ‘CifString’ was not declared in this scope ./src/ndb_atlas.C:155: error: ‘buff’ was not declared in this scope ./src/ndb_atlas.C:155: error: ‘One_Card_Info_Format’ was not declared in this scope ./src/ndb_atlas.C:155: error: ‘Head’ was not declared in this scope ./src/ndb_atlas.C:156: error: expected primary-expression before ‘const’ ./src/ndb_atlas.C:156: error: expected primary-expression before ‘const’ ./src/ndb_atlas.C:157: error: ‘One_Card_Info_Format’ was not declared in this scope ./src/ndb_atlas.C:157: error: ‘Head’ was not declared in this scope ./src/ndb_atlas.C:157: error: expected primary-expression before ‘const’ ./src/ndb_atlas.C:158: error: expected primary-expression before ‘const’ ./src/ndb_atlas.C:158: error: expected primary-expression before ‘const’ ./src/ndb_atlas.C:158: error: ‘CifString’ was not declared in this scope ./src/ndb_atlas.C:158: error: ‘res’ was not declared in this scope ./src/ndb_atlas.C:158: error: initializer expression list treated as compound expression ./src/ndb_atlas.C:161: error: ‘CifString’ was not declared in this scope ./src/ndb_atlas.C:161: error: ‘authors’ was not declared in this scope ./src/ndb_atlas.C:161: error: ‘CifString’ was not declared in this scope ./src/ndb_atlas.C:161: error: ‘title’ was not declared in this scope ./src/ndb_atlas.C:161: error: ‘CifString’ was not declared in this scope ./src/ndb_atlas.C:161: error: ‘jrnl’ was not declared in this scope ./src/ndb_atlas.C:162: error: ‘CifString’ was not declared in this scope ./src/ndb_atlas.C:162: error: ‘volume’ was not declared in this scope ./src/ndb_atlas.C:162: error: ‘CifString’ was not declared in this scope ./src/ndb_atlas.C:162: error: ‘first_page’ was not declared in this scope ./src/ndb_atlas.C:162: error: ‘CifString’ was not declared in this scope ./src/ndb_atlas.C:162: error: ‘last_page’ was not declared in this scope ./src/ndb_atlas.C:163: error: ‘CifString’ was not declared in this scope ./src/ndb_atlas.C:163: error: ‘year’ was not declared in this scope ./src/ndb_atlas.C:163: error: initializer expression list treated as compound expression ./src/ndb_atlas.C:164: error: ‘CifString’ was not declared in this scope ./src/ndb_atlas.C:164: error: ‘method’ was not declared in this scope ./src/ndb_atlas.C:164: error: ‘CifString’ was not declared in this scope ./src/ndb_atlas.C:164: error: ‘drop’ was not declared in this scope ./src/ndb_atlas.C:165: error: ‘CifString’ was not declared in this scope ./src/ndb_atlas.C:165: error: ‘reservoir’ was not declared in this scope ./src/ndb_atlas.C:165: error: ‘CifString’ was not declared in this scope ./src/ndb_atlas.C:165: error: ‘soaking’ was not declared in this scope ./src/ndb_atlas.C:165: error: initializer expression list treated as compound expression ./src/ndb_atlas.C: In member function ‘void _VALIDATION::ndb_write_atlas_entries(char*, int)’: ./src/ndb_atlas.C:172: error: ‘_StructureId’ was not declared in this scope ./src/ndb_atlas.C:173: error: ‘ndb_clean_string’ was not declared in this scope ./src/ndb_atlas.C:178: error: ‘_CardInfo’ was not declared in this scope ./src/ndb_atlas.C:178: error: ‘PDBFIL_TOKEN’ was not declared in this scope ./src/ndb_atlas.C:189: error: ‘_experiment_type’ was not declared in this scope ./src/ndb_atlas.C: In member function ‘ATLAS_TEXT* _VALIDATION::get_atlas_text(const char*, const char*)’: ./src/ndb_atlas.C:218: error: ‘CifString’ was not declared in this scope ./src/ndb_atlas.C:218: error: expected ‘;’ before ‘buff’ ./src/ndb_atlas.C:219: error: expected ‘;’ before ‘last_page’ ./src/ndb_atlas.C:221: error: ‘One_Card_Info_Format’ was not declared in this scope ./src/ndb_atlas.C:221: error: ‘pJrnlCard’ was not declared in this scope ./src/ndb_atlas.C:222: error: ‘ISTable’ was not declared in this scope ./src/ndb_atlas.C:222: error: ‘Table’ was not declared in this scope ./src/ndb_atlas.C:240: error: ‘buff’ was not declared in this scope ./src/ndb_atlas.C:246: error: ‘tmp_buff’ was not declared in this scope ./src/ndb_atlas.C:261: error: ‘_Num_Seqs’ was not declared in this scope ./src/ndb_atlas.C:267: error: ‘_Seqs’ was not declared in this scope ./src/ndb_atlas.C:273: error: ‘get_oneletter_code’ was not declared in this scope ./src/ndb_atlas.C:304: error: ‘find_jrnl_id’ was not declared in this scope ./src/ndb_atlas.C:305: error: ‘_JrnlCardInfo’ was not declared in this scope ./src/ndb_atlas.C:309: error: ‘atoi’ was not declared in this scope ./src/ndb_atlas.C:315: error: ‘authors’ was not declared in this scope ./src/ndb_atlas.C:315: error: ‘title’ was not declared in this scope ./src/ndb_atlas.C:315: error: ‘jrnl’ was not declared in this scope ./src/ndb_atlas.C:315: error: ‘volume’ was not declared in this scope ./src/ndb_atlas.C:316: error: ‘first_page’ was not declared in this scope ./src/ndb_atlas.C:316: error: ‘last_page’ was not declared in this scope ./src/ndb_atlas.C:316: error: ‘year’ was not declared in this scope ./src/ndb_atlas.C:319: error: ‘get_citation_val’ was not declared in this scope ./src/ndb_atlas.C:328: error: ‘_input_format’ was not declared in this scope ./src/ndb_atlas.C:328: error: ‘NDB_FILE_FORMAT_MIX’ was not declared in this scope ./src/ndb_atlas.C:329: error: ‘NDB_FILE_FORMAT_MMCIF’ was not declared in this scope ./src/ndb_atlas.C:330: error: ‘_CifObj’ was not declared in this scope ./src/ndb_atlas.C:330: error: ‘_StructureId’ was not declared in this scope ./src/ndb_atlas.C:331: error: ‘is_empty_table’ was not declared in this scope ./src/ndb_atlas.C:333: error: ‘get_value’ was not declared in this scope ./src/ndb_atlas.C:360: error: ‘ndb_name_conversion_first_last’ was not declared in this scope ./src/ndb_atlas.C:367: error: ‘get_refn’ cannot be used as a function ./src/ndb_atlas.C:369: error: ‘_cell’ was not declared in this scope ./src/ndb_atlas.C:382: error: ‘_CardInfo’ was not declared in this scope ./src/ndb_atlas.C:382: error: ‘CRMETH_TOKEN’ was not declared in this scope ./src/ndb_atlas.C:382: error: ‘CRSOLU_TOKEN’ was not declared in this scope ./src/ndb_atlas.C:386: error: ‘ndb_set_string_to_mixed’ was not declared in this scope ./src/ndb_atlas.C:391: error: ‘get_multiple_rows’ cannot be used as a function ./src/ndb_atlas.C:392: error: ‘get_multiple_rows’ cannot be used as a function ./src/ndb_atlas.C:393: error: ‘get_multiple_rows’ cannot be used as a function ./src/ndb_atlas.C:395: error: ‘_input_format’ was not declared in this scope ./src/ndb_atlas.C:395: error: ‘NDB_FILE_FORMAT_MIX’ was not declared in this scope ./src/ndb_atlas.C:396: error: ‘NDB_FILE_FORMAT_MMCIF’ was not declared in this scope ./src/ndb_atlas.C:397: error: ‘_CifObj’ was not declared in this scope ./src/ndb_atlas.C:397: error: ‘_StructureId’ was not declared in this scope ./src/ndb_atlas.C:398: error: ‘is_empty_table’ was not declared in this scope ./src/ndb_atlas.C:400: error: ‘get_value’ was not declared in this scope ./src/ndb_atlas.C:403: error: ‘ndb_set_string_to_mixed’ was not declared in this scope ./src/ndb_atlas.C:408: error: ‘is_empty_table’ was not declared in this scope ./src/ndb_atlas.C:413: error: ‘get_value’ was not declared in this scope ./src/ndb_atlas.C:448: error: ‘get_crys’ cannot be used as a function ./src/ndb_atlas.C:450: error: ‘_experiment_type’ was not declared in this scope ./src/ndb_atlas.C:450: error: ‘EXPERIMENT_TYPE_NMR’ was not declared in this scope ./src/ndb_atlas.C:451: error: ‘program’ was not declared in this scope ./src/ndb_atlas.C:451: error: ‘rvalue’ was not declared in this scope ./src/ndb_atlas.C:451: error: ‘reflections’ was not declared in this scope ./src/ndb_atlas.C:452: error: ‘high’ was not declared in this scope ./src/ndb_atlas.C:452: error: ‘low’ was not declared in this scope ./src/ndb_atlas.C:452: error: ‘sigmaF’ was not declared in this scope ./src/ndb_atlas.C:453: error: ‘_input_format’ was not declared in this scope ./src/ndb_atlas.C:453: error: ‘NDB_FILE_FORMAT_MIX’ was not declared in this scope ./src/ndb_atlas.C:454: error: ‘NDB_FILE_FORMAT_MMCIF’ was not declared in this scope ./src/ndb_atlas.C:455: error: ‘_CifObj’ was not declared in this scope ./src/ndb_atlas.C:455: error: ‘_StructureId’ was not declared in this scope ./src/ndb_atlas.C:456: error: ‘is_empty_table’ was not declared in this scope ./src/ndb_atlas.C:458: error: ‘get_value’ was not declared in this scope ./src/ndb_atlas.C:468: error: ‘atof’ was not declared in this scope ./src/ndb_atlas.C:487: error: ‘is_empty_table’ was not declared in this scope ./src/ndb_atlas.C:489: error: ‘get_value’ was not declared in this scope ./src/ndb_atlas.C:492: error: ‘_CardInfo’ was not declared in this scope ./src/ndb_atlas.C:492: error: ‘REFMET_TOKEN’ was not declared in this scope ./src/ndb_atlas.C:496: error: ‘_CardInfo’ was not declared in this scope ./src/ndb_atlas.C:496: error: ‘RFACTR_TOKEN’ was not declared in this scope ./src/ndb_atlas.C: At global scope: ./src/ndb_atlas.C:566: error: variable or field ‘get_name_st’ declared void ./src/ndb_atlas.C:566: error: ‘CifString’ was not declared in this scope ./src/ndb_atlas.C:566: error: ‘name’ was not declared in this scope ./src/ndb_atlas.C:566: error: ‘CifString’ was not declared in this scope ./src/ndb_atlas.C:566: error: ‘modifier_st’ was not declared in this scope ./src/ndb_atlas.C:153: warning: ‘void write_text_part(FILE*, ATLAS_TEXT*, int, int)’ declared ‘static’ but never defined ./src/ndb_atlas.C:159: warning: ‘void add_superscripts(char*, char*, int)’ declared ‘static’ but never defined ./src/ndb_atlas.C:160: warning: ‘void correct_string(char*)’ declared ‘static’ but never defined make[1]: *** [obj/ndb_atlas.o] Error 1 make[1]: Leaving directory `/var/tmp/portage/sci-chemistry/validation-6.2/work/pdb-extract-v1.700-prod-src/validation-v6.2' make: *** [compile] Error 1 * ERROR: sci-chemistry/validation-6.2 failed: * emake failed * * Call stack: * ebuild.sh, line 61: Called src_compile * environment, line 2455: Called _eapi0_src_compile * ebuild.sh, line 619: Called _eapi2_src_compile * ebuild.sh, line 653: Called die * The specific snippet of code: * emake || die "emake failed" * * If you need support, post the output of 'emerge --info =sci-chemistry/validation-6.2', * the complete build log and the output of 'emerge -pqv =sci-chemistry/validation-6.2'. * The complete build log is located at '/var/log/portage/build/sci-chemistry/validation-6.2:20091212-184723.log'. * The ebuild environment file is located at '/var/tmp/portage/sci-chemistry/validation-6.2/temp/environment'. * S: '/var/tmp/portage/sci-chemistry/validation-6.2/work/pdb-extract-v1.700-prod-src'