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Gentoo's Bugzilla – Attachment 212814 Details for
Bug 296651
sci-chemistry/validation fails to build
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Build log
validation-6.2:20091212-184723.log (text/plain), 204.63 KB, created by
Diego Elio Pettenò (RETIRED)
on 2009-12-12 19:17:49 UTC
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Description:
Build log
Filename:
MIME Type:
Creator:
Diego Elio Pettenò (RETIRED)
Created:
2009-12-12 19:17:49 UTC
Size:
204.63 KB
patch
obsolete
> [32;01m*[0m CPV: sci-chemistry/validation-6.2 > [32;01m*[0m REPO: gentoo > [32;01m*[0m 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 > [32;01m*[0m Applying respect-cflags-and-fix-install.patch ... >[A[72C [34;01m[ [32;01mok[34;01m ][0m > [32;01m*[0m Deleting redundant directories ... >[A[72C [34;01m[ [32;01mok[34;01m ][0m >>>> 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 â_ATOMâ with no type >./include/bond_angle_torsion.h:147: error: expected â;â before â*â token >./include/bond_angle_torsion.h:148: error: ISO C++ forbids declaration of â_ATOMâ with no type >./include/bond_angle_torsion.h:148: error: expected â;â before â*â token >./include/bond_angle_torsion.h:153: error: ISO C++ forbids declaration of â_ATOMâ with no type >./include/bond_angle_torsion.h:153: error: expected â;â before â*â token >./include/bond_angle_torsion.h:154: error: ISO C++ forbids declaration of â_ATOMâ with no type >./include/bond_angle_torsion.h:154: error: expected â;â before â*â token >./include/bond_angle_torsion.h:155: error: ISO C++ forbids declaration of â_ATOMâ with no type >./include/bond_angle_torsion.h:155: error: expected â;â before â*â token >./include/bond_angle_torsion.h:160: error: ISO C++ forbids declaration of â_ATOMâ with no type >./include/bond_angle_torsion.h:160: error: expected â;â before â*â token >./include/bond_angle_torsion.h:161: error: ISO C++ forbids declaration of â_ATOMâ with no type >./include/bond_angle_torsion.h:161: error: expected â;â before â*â token >./include/bond_angle_torsion.h:162: error: ISO C++ forbids declaration of â_ATOMâ with no type >./include/bond_angle_torsion.h:162: error: expected â;â before â*â token >./include/bond_angle_torsion.h:163: error: ISO C++ forbids declaration of â_ATOMâ with no type >./include/bond_angle_torsion.h:163: error: expected â;â before â*â token >./include/bond_angle_torsion.h:167: error: ISO C++ forbids declaration of â_ATOMâ with no type >./include/bond_angle_torsion.h:167: error: expected â;â before â*â token >./include/bond_angle_torsion.h:168: error: ISO C++ forbids declaration of â_ATOMâ with no type >./include/bond_angle_torsion.h:168: error: expected â;â before â*â token >./include/bond_angle_torsion.h:169: error: ISO C++ forbids declaration of â_ATOMâ with no type >./include/bond_angle_torsion.h:169: error: expected â;â before â*â token >./include/bond_angle_torsion.h:170: error: ISO C++ forbids declaration of â_ATOMâ with no type >./include/bond_angle_torsion.h:170: error: expected â;â before â*â token >./include/bond_angle_torsion.h:173: warning: âcal_angleâ initialized and declared âexternâ >./include/bond_angle_torsion.h:173: error: â_ATOMâ was not declared in this scope >./include/bond_angle_torsion.h:173: error: âatom1â was not declared in this scope >./include/bond_angle_torsion.h:173: error: â_ATOMâ was not declared in this scope >./include/bond_angle_torsion.h:173: error: âatom2â was not declared in this scope >./include/bond_angle_torsion.h:173: error: â_ATOMâ was not declared in this scope >./include/bond_angle_torsion.h:173: error: âatom3â 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: âcal_torsionâ initialized and declared âexternâ >./include/bond_angle_torsion.h:174: error: â_ATOMâ was not declared in this scope >./include/bond_angle_torsion.h:174: error: âatom1â was not declared in this scope >./include/bond_angle_torsion.h:174: error: â_ATOMâ was not declared in this scope >./include/bond_angle_torsion.h:174: error: âatom2â was not declared in this scope >./include/bond_angle_torsion.h:174: error: â_ATOMâ was not declared in this scope >./include/bond_angle_torsion.h:174: error: âatom3â was not declared in this scope >./include/bond_angle_torsion.h:174: error: â_ATOMâ was not declared in this scope >./include/bond_angle_torsion.h:174: error: âatom4â 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: âcalc_chiral_volumeâ initialized and declared âexternâ >./include/bond_angle_torsion.h:175: error: â_ATOMâ was not declared in this scope >./include/bond_angle_torsion.h:175: error: âatom_icâ was not declared in this scope >./include/bond_angle_torsion.h:175: error: â_ATOMâ was not declared in this scope >./include/bond_angle_torsion.h:175: error: âatom_iuâ was not declared in this scope >./include/bond_angle_torsion.h:176: error: â_ATOMâ was not declared in this scope >./include/bond_angle_torsion.h:176: error: âatom_ivâ was not declared in this scope >./include/bond_angle_torsion.h:176: error: â_ATOMâ was not declared in this scope >./include/bond_angle_torsion.h:176: error: âatom_iwâ was not declared in this scope >./include/bond_angle_torsion.h:176: error: expected primary-expression before âdoubleâ >./include/bond_angle_torsion.h:176: error: initializer expression list treated as compound expression >./include/bond_angle_torsion.h:177: warning: âcal_bondsâ initialized and declared âexternâ >./include/bond_angle_torsion.h:177: error: â_ATOMâ was not declared in this scope >./include/bond_angle_torsion.h:177: error: âatom1â was not declared in this scope >./include/bond_angle_torsion.h:177: error: expected primary-expression before âconstâ >./include/bond_angle_torsion.h:177: error: â_ATOMâ was not declared in this scope >./include/bond_angle_torsion.h:177: error: âatom2â was not declared in this scope >./include/bond_angle_torsion.h:177: error: expected primary-expression before âconstâ >./include/bond_angle_torsion.h:177: error: initializer expression list treated as compound expression >./include/bond_angle_torsion.h:178: warning: âcal_anglesâ initialized and declared âexternâ >./include/bond_angle_torsion.h:178: error: â_ATOMâ was not declared in this scope >./include/bond_angle_torsion.h:178: error: âatom1â was not declared in this scope >./include/bond_angle_torsion.h:178: error: expected primary-expression before âconstâ >./include/bond_angle_torsion.h:178: error: â_ATOMâ was not declared in this scope >./include/bond_angle_torsion.h:178: error: âatom2â was not declared in this scope >./include/bond_angle_torsion.h:179: error: expected primary-expression before âconstâ >./include/bond_angle_torsion.h:179: error: â_ATOMâ was not declared in this scope >./include/bond_angle_torsion.h:179: error: âatom3â was not declared in this scope >./include/bond_angle_torsion.h:179: error: expected primary-expression before âconstâ >./include/bond_angle_torsion.h:179: error: initializer expression list treated as compound expression >./include/bond_angle_torsion.h:180: error: â_ATOMâ has not been declared >./include/bond_angle_torsion.h:180: error: â_ATOMâ has not been declared >./include/bond_angle_torsion.h:181: error: â_ATOMâ has not been declared >./include/bond_angle_torsion.h:181: error: â_ATOMâ has not been declared >./include/bond_angle_torsion.h:182: error: â_ATOMâ has not been declared >./include/bond_angle_torsion.h:182: error: â_ATOMâ has not been declared >./include/bond_angle_torsion.h:183: error: â_ATOMâ has not been declared >./include/bond_angle_torsion.h:183: error: â_ATOMâ has not been declared >./src/bond_angle_torsion.C:149: error: redefinition of âdouble cal_angleâ >./include/bond_angle_torsion.h:173: error: âdouble cal_angleâ previously defined here >./src/bond_angle_torsion.C:149: error: â_ATOMâ was not declared in this scope >./src/bond_angle_torsion.C:149: error: âatom1â was not declared in this scope >./src/bond_angle_torsion.C:149: error: â_ATOMâ was not declared in this scope >./src/bond_angle_torsion.C:149: error: âatom2â was not declared in this scope >./src/bond_angle_torsion.C:149: error: â_ATOMâ was not declared in this scope >./src/bond_angle_torsion.C:149: error: âatom3â was not declared in this scope >./src/bond_angle_torsion.C:176: error: redefinition of âdouble cal_torsionâ >./include/bond_angle_torsion.h:174: error: âdouble cal_torsionâ previously defined here >./src/bond_angle_torsion.C:176: error: â_ATOMâ was not declared in this scope >./src/bond_angle_torsion.C:176: error: âatom1â was not declared in this scope >./src/bond_angle_torsion.C:176: error: â_ATOMâ was not declared in this scope >./src/bond_angle_torsion.C:176: error: âatom2â was not declared in this scope >./src/bond_angle_torsion.C:176: error: â_ATOMâ was not declared in this scope >./src/bond_angle_torsion.C:176: error: âatom3â was not declared in this scope >./src/bond_angle_torsion.C:176: error: â_ATOMâ was not declared in this scope >./src/bond_angle_torsion.C:176: error: âatom4â was not declared in this scope >./src/bond_angle_torsion.C:144: warning: âdouble ndb_dihed_angle(double, double, double, double)â declared âstaticâ but never defined >./src/bond_angle_torsion.C:145: warning: âvoid crossp3x(double, double, double, double, double, double, double&, double&, double&)â declared âstaticâ 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 âostreamâ with no type >./include/symop.h:153: error: âostreamâ is neither function nor member function; cannot be declared friend >./include/symop.h:153: error: expected â;â before â&â token >./include/symop.h:158: error: expected â)â before â&â 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: âMxStrLenâ 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 â_RESIDUEâ with no type >./include/_validation.h:207: error: expected â;â before â*â token >./include/_validation.h:213: error: âCOORDâ does not name a type >./include/_validation.h:214: error: âCOORDâ does not name a type >./include/_validation.h:215: error: âCOORDâ does not name a type >./include/_validation.h:216: error: âCOORDâ does not name a type >./include/_validation.h:217: error: âCOORDâ does not name a type >./include/_validation.h:218: error: âCOORDâ 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 â_ATOMâ with no type >./include/_validation.h:232: error: expected â;â before â*â token >./include/_validation.h:233: error: ISO C++ forbids declaration of â_ATOMâ with no type >./include/_validation.h:233: error: expected â;â before â*â token >./include/_validation.h:234: error: ISO C++ forbids declaration of â_ATOMâ with no type >./include/_validation.h:234: error: expected â;â before â*â token >./include/_validation.h:266: error: ISO C++ forbids declaration of â_ATOMâ with no type >./include/_validation.h:266: error: expected â;â before â*â token >./include/_validation.h:267: error: ISO C++ forbids declaration of â_ATOMâ with no type >./include/_validation.h:267: error: expected â;â before â*â token >./include/_validation.h:268: error: ISO C++ forbids declaration of â_ATOMâ with no type >./include/_validation.h:268: error: expected â;â before â*â token >./include/_validation.h:269: error: ISO C++ forbids declaration of â_ATOMâ with no type >./include/_validation.h:269: error: expected â;â before â*â token >./include/_validation.h:305: error: âCifStringâ does not name a type >./include/_validation.h:315: error: âCifStringâ does not name a type >./include/_validation.h:327: error: âCOORDâ does not name a type >./include/_validation.h:328: error: âCOORDâ does not name a type >./include/_validation.h:329: error: âCOORDâ does not name a type >./include/_validation.h:339: error: âCOORDâ does not name a type >./include/_validation.h:344: error: ISO C++ forbids declaration of â_ATOMâ with no type >./include/_validation.h:344: error: expected â;â before â*â token >./include/_validation.h:348: error: expected class-name before â{â token >./include/_validation.h:377: error: â_ATOMâ has not been declared >./include/_validation.h:377: error: â_ATOMâ has not been declared >./include/_validation.h:380: error: â_ATOMâ has not been declared >./include/_validation.h:380: error: â_ATOMâ has not been declared >./include/_validation.h:380: error: â_ATOMâ has not been declared >./include/_validation.h:382: error: â_ATOMâ has not been declared >./include/_validation.h:382: error: â_ATOMâ has not been declared >./include/_validation.h:382: error: â_ATOMâ has not been declared >./include/_validation.h:382: error: â_ATOMâ has not been declared >./src/check.C:148:22: error: BTreeObj.h: No such file or directory >./include/_validation.h:398: error: âCifStringâ has not been declared >./include/_validation.h:421: error: â_RESIDUEâ has not been declared >./include/_validation.h:422: error: â_RESIDUEâ has not been declared >./include/_validation.h:422: error: â_RESIDUEâ has not been declared >./include/_validation.h:423: error: â_ATOMâ has not been declared >./include/_validation.h:423: error: â_ATOMâ has not been declared >./include/_validation.h:423: error: â_ATOMâ has not been declared >./include/_validation.h:423: error: â_ATOMâ has not been declared >./include/_validation.h:426: error: âCifStringâ has not been declared >./include/_validation.h:426: error: âCifStringâ has not been declared >./include/_validation.h:427: error: âCifStringâ has not been declared >./include/_validation.h:433: error: â_MOLECULEâ has not been declared >./include/_validation.h:434: error: â_CHAINâ has not been declared >./include/_validation.h:434: error: âCOORDâ has not been declared >./include/_validation.h:434: error: â_RESIDUEâ has not been declared >./include/_validation.h:435: error: â_CHAINâ has not been declared >./include/_validation.h:436: error: â_ATOMâ has not been declared >./include/_validation.h:436: error: â_ATOMâ has not been declared >./include/_validation.h:437: error: â_CHAINâ has not been declared >./include/_validation.h:438: error: âCOORDâ has not been declared >./include/_validation.h:438: error: âCOORDâ has not been declared >./include/_validation.h:444: error: âISTableâ has not been declared >./include/_validation.h:492: error: âTblIndexObjâ does not name a type >In file included from ./src/check.C:150: >./include/datacheck.h:4:24: ./include/_validation.h:493: error: âTblIndexObjâ does not name a typeerror: >CifFileObj.h: No such file or directory >./include/_validation.h:494: error: âTblIndexObjâ does not name a type >./include/_validation.h:495: error: âTblIndexObjâ does not name a type >./include/_validation.h:496: error: âTblIndexObjâ does not name a type >./include/_validation.h:497: error: âTblIndexObjâ does not name a type >./include/datacheck.h:5:24: error: ./include/_validation.h:498: error: âTblIndexObjâ does not name a type >DICFileObj.h: No such file or directory >./include/_validation.h:500: error: âCifStringâ does not name a type >./include/_validation.h:501: error: âCifStringâ does not name a type >./include/_validation.h:502: error: âCifStringâ 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: âget_residue_indexâ initialized and declared âexternâ >./include/_validation.h:507: error: â_MOLECULEâ was not declared in this scope >./include/_validation.h:507: error: âmolâ was not declared in this scope >./include/_validation.h:507: error: âISTableâ was not declared in this scope >./include/_validation.h:507: error: âTableâ was not declared in this scope >./include/_validation.h:507: error: expected primary-expression before âconstâ >./include/_validation.h:508: error: expected primary-expression before âconstâ >./include/_validation.h:508: error: expected primary-expression before âconstâ >./include/_validation.h:508: error: expected primary-expression before âconstâ >./include/_validation.h:509: error: expected primary-expression before âconstâ >./include/_validation.h:509: error: expected primary-expression before âconstâ >./include/_validation.h:509: error: expected primary-expression before âconstâ >./include/_validation.h:510: error: expected primary-expression before âconstâ >./include/_validation.h:510: error: expected primary-expression before âintâ >./include/_validation.h:510: error: expected primary-expression before âintâ >./include/_validation.h:510: error: âCifStringâ was not declared in this scope >./include/_validation.h:510: error: ânameâ 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 âNDBCELLCONSTâ with no type >./include/xtal.h:166: error: expected â,â or â...â before â*â token >./include/xtal.h:167: error: âCOORDâ has not been declared >./include/xtal.h:167: error: âCOORDâ has not been declared >In file included from ./src/base_information.C:155: >./include/misc_util.h:155: error: variable or field âarb_rotationâ declared void >./include/misc_util.h:155: error: âCOORDâ was not declared in this scope >./include/misc_util.h:155: error: âCOORDâ was not declared in this scope >./include/misc_util.h:155: error: âvaâ was not declared in this scope >./include/misc_util.h:155: error: expected primary-expression before âdoubleâ >./include/misc_util.h:158: error: variable or field âget_vectorâ declared void >./include/misc_util.h:158: error: âCOORDâ was not declared in this scope >./include/misc_util.h:158: error: âvaâ was not declared in this scope >./include/misc_util.h:158: error: âCOORDâ was not declared in this scope >./include/misc_util.h:158: error: âvrefâ was not declared in this scope >./include/misc_util.h:158: error: expected primary-expression before âdoubleâ >./include/misc_util.h:158: error: âCOORDâ was not declared in this scope >./include/misc_util.h:158: error: âvoâ was not declared in this scope >./include/misc_util.h:159: warning: âmagangâ initialized and declared âexternâ >./include/misc_util.h:159: error: âCOORDâ was not declared in this scope >./include/misc_util.h:159: error: âvaâ was not declared in this scope >./include/misc_util.h:159: error: âCOORDâ was not declared in this scope >./include/misc_util.h:159: error: âvbâ 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 âmulti_matrixâ declared void >./include/misc_util.h:161: error: âCOORDâ was not declared in this scope >./include/misc_util.h:161: error: expected primary-expression before âconstâ >./include/misc_util.h:161: error: expected primary-expression before âconstâ >./include/misc_util.h:163: error: variable or field âvector_initâ declared void >./include/misc_util.h:163: error: âCOORDâ was not declared in this scope >./include/misc_util.h:163: error: âdestâ was not declared in this scope >./include/misc_util.h:163: error: expected primary-expression before âconstâ >./include/misc_util.h:163: error: expected primary-expression before âconstâ >./include/misc_util.h:163: error: expected primary-expression before âconstâ >./include/misc_util.h:164: error: variable or field âvector_copyâ declared void >./include/misc_util.h:164: error: âCOORDâ was not declared in this scope >./include/misc_util.h:164: error: âdestâ was not declared in this scope >./include/misc_util.h:164: error: expected primary-expression before âconstâ >./include/misc_util.h:165: error: variable or field âvector_sumâ declared void >./include/misc_util.h:165: error: âCOORDâ was not declared in this scope >./include/misc_util.h:165: error: âdestâ was not declared in this scope >./include/misc_util.h:165: error: expected primary-expression before âconstâ >./include/misc_util.h:165: error: expected primary-expression before âconstâ >./include/misc_util.h:166: error: variable or field âvector_differenceâ declared void >./include/misc_util.h:166: error: âCOORDâ was not declared in this scope >./include/misc_util.h:166: error: âdestâ was not declared in this scope >./include/misc_util.h:166: error: expected primary-expression before âconstâ >./include/misc_util.h:166: error: expected primary-expression before âconstâ >./include/misc_util.h:167: error: variable or field âvector_scaledâ declared void >./include/misc_util.h:167: error: âCOORDâ was not declared in this scope >./include/misc_util.h:167: error: âdestâ was not declared in this scope >./include/misc_util.h:167: error: expected primary-expression before âconstâ >./include/misc_util.h:167: error: expected primary-expression before âconstâ >./include/misc_util.h:168: error: variable or field âvector_addâ declared void >./include/misc_util.h:168: error: âCOORDâ was not declared in this scope >./include/misc_util.h:168: error: âdestâ was not declared in this scope >./include/misc_util.h:168: error: expected primary-expression before âconstâ >./include/misc_util.h:169: error: variable or field âvector_subtractâ declared void >./include/misc_util.h:169: error: âCOORDâ was not declared in this scope >./include/misc_util.h:169: error: âdestâ was not declared in this scope >./include/misc_util.h:169: error: expected primary-expression before âconstâ >./include/misc_util.h:170: error: variable or field âvector_scaleâ declared void >./include/misc_util.h:170: error: âCOORDâ was not declared in this scope >./include/misc_util.h:170: error: âdestâ was not declared in this scope >./include/misc_util.h:170: error: expected primary-expression before âconstâ >./include/misc_util.h:171: error: variable or field âvector_invertâ declared void >./include/misc_util.h:171: error: âCOORDâ was not declared in this scope >./include/misc_util.h:171: error: âvâ was not declared in this scope >./include/misc_util.h:172: error: variable or field âvector_reverseâ declared void >./include/misc_util.h:172: error: âCOORDâ was not declared in this scope >./include/misc_util.h:172: error: âvâ was not declared in this scope >./include/misc_util.h:173: error: variable or field âvector_sum_scaledâ declared void >./include/misc_util.h:173: error: âCOORDâ was not declared in this scope >./include/misc_util.h:173: error: âdestâ was not declared in this scope >./include/misc_util.h:173: error: expected primary-expression before âconstâ >./include/misc_util.h:173: error: expected primary-expression before âconstâ >./include/misc_util.h:173: error: expected primary-expression before âconstâ >./include/misc_util.h:174: error: variable or field âvector_add_scaledâ declared void >./include/misc_util.h:174: error: âCOORDâ was not declared in this scope >./include/misc_util.h:174: error: âdestâ was not declared in this scope >./include/misc_util.h:174: error: expected primary-expression before âconstâ >./include/misc_util.h:174: error: expected primary-expression before âconstâ >./include/misc_util.h:175: error: ISO C++ forbids declaration of âCOORDâ with no type >./include/misc_util.h:175: error: expected â,â or â...â before âv1â >./include/misc_util.h:176: error: variable or field âvector_cross_productâ declared void >./include/misc_util.h:176: error: âCOORDâ was not declared in this scope >./include/misc_util.h:176: error: âvzâ was not declared in this scope >./include/misc_util.h:176: error: expected primary-expression before âconstâ >./include/misc_util.h:176: error: expected primary-expression before âconstâ >./include/misc_util.h:177: error: variable or field âvector_normalizeâ declared void >./include/misc_util.h:177: error: âCOORDâ was not declared in this scope >./include/misc_util.h:177: error: âvâ was not declared in this scope >./include/misc_util.h:178: error: variable or field âvector_middleâ declared void >./include/misc_util.h:178: error: âCOORDâ was not declared in this scope >./include/misc_util.h:178: error: âdestâ was not declared in this scope >./include/misc_util.h:178: error: expected primary-expression before âconstâ >./include/misc_util.h:178: error: expected primary-expression before âconstâ >./include/misc_util.h:179: error: ISO C++ forbids declaration of âCOORDâ with no type >./include/misc_util.h:179: error: expected â,â or â...â before âv1â >./include/misc_util.h:180: error: ISO C++ forbids declaration of âCOORDâ with no type >./include/misc_util.h:180: error: expected â,â or â...â before âvâ >./include/misc_util.h:181: error: ISO C++ forbids declaration of âCOORDâ with no type >./include/misc_util.h:181: error: expected â,â or â...â before âvaâ >./include/misc_util.h:182: error: variable or field âvector_orthogonalâ declared void >./include/misc_util.h:182: error: âCOORDâ was not declared in this scope >./include/misc_util.h:182: error: âvaâ was not declared in this scope >./include/misc_util.h:182: error: âCOORDâ was not declared in this scope >./include/misc_util.h:182: error: âvrefâ was not declared in this scope >./include/misc_util.h:194: error: variable or field âmatrix_transformâ declared void >./include/misc_util.h:194: error: âCOORDâ was not declared in this scope >./include/misc_util.h:194: error: âvâ was not declared in this scope >./include/misc_util.h:194: error: expected primary-expression before âconstâ >./include/misc_util.h:195: error: variable or field âmatrix_rotateâ declared void >./include/misc_util.h:195: error: âCOORDâ was not declared in this scope >./include/misc_util.h:195: error: âvâ was not declared in this scope >./include/misc_util.h:195: error: expected primary-expression before âconstâ >./include/misc_util.h:196: error: variable or field âmatrix_rotate_translateâ declared void >./include/misc_util.h:196: error: âCOORDâ was not declared in this scope >./include/misc_util.h:196: error: âvâ was not declared in this scope >./include/misc_util.h:196: error: expected primary-expression before âconstâ >./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 âostreamâ with no type >./include/symop.h:153: error: âostreamâ is neither function nor member function; cannot be declared friend >./include/symop.h:153: error: expected â;â before â&â token >./include/symop.h:158: error: expected â)â before â&â 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 âNDBCELLCONSTâ with no type >./include/xtal.h:166: error: expected â,â or â...â before â*â token >./include/xtal.h:167: error: âCOORDâ has not been declared >./include/xtal.h:167: error: âCOORDâ has not been declared >In file included from ./src/base_information.C:157: >/usr/include/rcsb/util.h:67: error: âCifFileâ was not declared in this scope >/usr/include/rcsb/util.h:67: error: âfobjâ was not declared in this scope >/usr/include/rcsb/util.h:67: error: expected primary-expression before âconstâ >/usr/include/rcsb/util.h:68: error: expected primary-expression before âconstâ >/usr/include/rcsb/util.h:68: error: expected primary-expression before âconstâ >/usr/include/rcsb/util.h:68: error: initializer expression list treated as compound expression >/usr/include/rcsb/util.h:69: error: âCifFileâ was not declared in this scope >/usr/include/rcsb/util.h:69: error: âfobjâ was not declared in this scope >/usr/include/rcsb/util.h:69: error: expected primary-expression before âconstâ >/usr/include/rcsb/util.h:70: error: expected primary-expression before âconstâ >/usr/include/rcsb/util.h:70: error: expected primary-expression before âconstâ >/usr/include/rcsb/util.h:71: error: expected primary-expression before âlongâ >/usr/include/rcsb/util.h:71: error: initializer expression list treated as compound expression >/usr/include/rcsb/util.h:74: error: âint check_category(const char*, char*, char*)â redeclared as different kind of symbol >./include/check.h:191: error: previous declaration of âCHECK_CATEGORY check_category [6]â >./src/base_information.C:160: error: â_RESIDUEâ was not declared in this scope >./src/base_information.C:160: error: âresâ was not declared in this scope >./src/base_information.C:160: error: expected primary-expression before âconstâ >./src/base_information.C:160: error: expected primary-expression before âconstâ >./src/base_information.C:161: error: expected primary-expression before âconstâ >./src/base_information.C:161: error: expected primary-expression before âconstâ >./src/base_information.C:161: error: expected primary-expression before âconstâ >./src/base_information.C:161: error: initializer expression list treated as compound expression >./src/base_information.C:162: error: â_RESIDUEâ was not declared in this scope >./src/base_information.C:162: error: âresidueâ was not declared in this scope >./src/base_information.C:162: error: expected primary-expression before âdoubleâ >./src/base_information.C:162: error: expected primary-expression before âdoubleâ >./src/base_information.C:163: error: expected primary-expression before âdoubleâ >./src/base_information.C:163: error: expected primary-expression before âintâ >./src/base_information.C:163: error: initializer expression list treated as compound expression >./src/base_information.C:166: error: ISO C++ forbids declaration of âNDBCELLCONSTâ with no type >./src/base_information.C:166: error: expected â,â or â...â before â*â token >./src/base_information.C:168: error: â_ATOMâ was not declared in this scope >./src/base_information.C:168: error: âatom_aâ was not declared in this scope >./src/base_information.C:168: error: â_ATOMâ was not declared in this scope >./src/base_information.C:168: error: âatom_bâ was not declared in this scope >./src/base_information.C:168: error: expected primary-expression before âconstâ >./src/base_information.C:169: error: expected primary-expression before âconstâ >./src/base_information.C:169: error: expected primary-expression before âconstâ >./src/base_information.C:169: error: expected primary-expression before âconstâ >./src/base_information.C:169: error: expected primary-expression before âconstâ >./src/base_information.C:169: error: initializer expression list treated as compound expression >./src/base_information.C:172: error: variable or field âbpstep_parâ declared void >./src/base_information.C:172: error: âCOORDâ was not declared in this scope >./src/base_information.C:172: error: expected primary-expression before âconstâ >./src/base_information.C:172: error: âCOORDâ was not declared in this scope >./src/base_information.C:173: error: expected primary-expression before âconstâ >./src/base_information.C:173: error: expected primary-expression before âdoubleâ >./src/base_information.C:173: error: âCOORDâ was not declared in this scope >./src/base_information.C:173: error: âCOORDâ was not declared in this scope >./src/base_information.C:173: error: âmst_orgâ was not declared in this scope >./src/base_information.C:174: error: variable or field âhelical_parâ declared void >./src/base_information.C:174: error: âCOORDâ was not declared in this scope >./src/base_information.C:174: error: expected primary-expression before âconstâ >./src/base_information.C:174: error: âCOORDâ was not declared in this scope >./src/base_information.C:175: error: expected primary-expression before âconstâ >./src/base_information.C:175: error: expected primary-expression before âdoubleâ >./src/base_information.C:175: error: âCOORDâ was not declared in this scope >./src/base_information.C:175: error: âCOORDâ was not declared in this scope >./src/base_information.C:175: error: âmst_orgâ was not declared in this scope >./src/base_information.C:176: error: ISO C++ forbids declaration of âCOORDâ with no type >./src/base_information.C:176: error: expected â,â or â...â before âP_1_i_plus_1â >./src/base_information.C: In member function âvoid _VALIDATION::get_bspair_information()â: >./src/base_information.C:209: error: â_CHAINâ was not declared in this scope >./src/base_information.C:209: error: âchainâ was not declared in this scope >./src/base_information.C:211: error: âBTreeObjâ was not declared in this scope >./src/base_information.C:211: error: â_SIndexâ was not declared in this scope >./src/base_information.C:211: error: â_SymmetryIndexâ was not declared in this scope >./src/base_information.C:212: error: expected â;â before âindexâ >./src/base_information.C:216: error: â_num_molâ was not declared in this scope >./src/base_information.C:217: error: â_cellâ was not declared in this scope >./src/base_information.C:223: error: â_moleculesâ was not declared in this scope >./src/base_information.C:225: error: âATOMN_TOKENâ was not declared in this scope >./src/base_information.C:227: error: â_RESIDUEâ was not declared in this scope >./src/base_information.C:227: error: âresâ was not declared in this scope >./src/base_information.C:233: error: â_cellâ was not declared in this scope >./src/base_information.C:233: error: âbase_frameâ cannot be used as a function >./src/base_information.C:259: error: â_cellâ was not declared in this scope >./src/base_information.C:288: error: âindexâ does not have class type >./src/base_information.C:292: error: âindexâ does not have class type >./src/base_information.C:294: error: âindexâ does not have class type >./src/base_information.C:322: error: âstruct BASE_BASE_PARAMSâ has no member named âChnID_Iâ >./src/base_information.C:323: error: âstruct BASE_BASE_PARAMSâ has no member named âChnID_Jâ >./src/base_information.C:333: error: âATOMN_TOKENâ was not declared in this scope >./src/base_information.C:335: error: â_RESIDUEâ was not declared in this scope >./src/base_information.C:335: error: âresâ was not declared in this scope >./src/base_information.C:337: error: âbase_frameâ cannot be used as a function >./src/base_information.C:345: error: âbase_frameâ cannot be used as a function >./src/base_information.C: In member function âint _VALIDATION::get_bspair_information(int, _BASE**, int*)â: >./src/base_information.C:379: error: â_cellâ was not declared in this scope >./src/base_information.C:379: error: â_moleculesâ was not declared in this scope >./src/base_information.C: In member function âvoid _VALIDATION::insert_base_pairs(int, CONTACT**)â: >./src/base_information.C:481: error: âBTreeObjâ was not declared in this scope >./src/base_information.C:481: error: expected primary-expression before â>â token >./src/base_information.C:481: error: â_BPIdxâ was not declared in this scope >./src/base_information.C:509: error: âres_name_cmp_naâ was not declared in this scope >./src/base_information.C:527: error: âres_name_cmp_naâ 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 âvoid _plot::set_x_axis_title(const char*)â: >./include/plot.h:199: error: âstrcpyâ was not declared in this scope >./include/plot.h: In member function âvoid _plot::set_y_axis_title(const char*)â: >./include/plot.h:200: error: âstrcpyâ was not declared in this scope >./include/plot.h: In member function âvoid _plot::set_picture_title(const char*)â: >./include/plot.h:201: error: âstrcpyâ 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: âMxStrLenâ was not declared in this scope >./src/base_information.C: In member function âvoid _VALIDATION::re_ordering(int, int*, _BASE**)â: >./src/base_information.C:552: error: âCOORDâ was not declared in this scope >./src/base_information.C:552: error: expected â;â before âzaveâ >In file included from ./src/_validation.C:142: >./include/_validation.h:207: error: ISO C++ forbids declaration of â_RESIDUEâ with no type >./src/base_information.C:556: error: âbp_xyzâ was not declared in this scope >./include/_validation.h:207: error: expected â;â before â*â token >./src/base_information.C:556: error: expected type-specifier before âCOORDâ >./src/base_information.C:556: error: expected â;â before âCOORDâ >./include/_validation.h:213: error: âCOORDâ does not name a type >./include/_validation.h:214: error: âCOORDâ does not name a type >./src/base_information.C:560: error: âstruct _BASEâ has no member named âorgâ >./src/base_information.C:561: error: âstruct _BASEâ has no member named âorgâ >./src/base_information.C:561: error: âvector_middleâ was not declared in this scope >./src/base_information.C:573: error: âstruct _BASEâ has no member named âorienâ >./include/_validation.h:215: error: âCOORDâ does not name a type >./include/_validation.h:216: error: âCOORDâ does not name a type >./include/_validation.h:217: error: âCOORDâ does not name a type >./src/base_information.C:574: error: âstruct _BASEâ has no member named âorienâ >./include/_validation.h:218: error: âCOORDâ does not name a type >./src/base_information.C:576: error: âzaveâ was not declared in this scope >./src/base_information.C:576: error: âstruct _BASEâ has no member named âorienâ >./src/base_information.C:577: error: âstruct _BASEâ has no member named âorienâ./include/_validation.h:232: error: ISO C++ forbids declaration of â_ATOMâ with no type > >./src/base_information.C:577: error: âvector_differenceâ was not declared in this scope >./include/_validation.h:232: error: expected â;â before â*â token >./include/_validation.h:233: error: ISO C++ forbids declaration of â_ATOMâ with no type >./src/base_information.C:578: error: âzaveâ was not declared in this scope >./include/_validation.h:233: error: expected â;â before â*â token >./src/base_information.C:578: error: âstruct _BASEâ has no member named âorienâ./include/_validation.h:234: error: ISO C++ forbids declaration of â_ATOMâ with no type > >./include/_validation.h:234: error: expected â;â before â*â token >./src/base_information.C:579: error: âstruct _BASEâ has no member named âorienâ >./src/base_information.C:579: error: âvector_sumâ was not declared in this scope >./src/base_information.C:582: error: âtxyzâ was not declared in this scope >./src/base_information.C:582: error: âvector_differenceâ was not declared in this scope >./include/_validation.h:266: error: ISO C++ forbids declaration of â_ATOMâ with no type >./include/_validation.h:266: error: expected â;â before â*â token >./include/_validation.h:267: error: ISO C++ forbids declaration of â_ATOMâ with no type >./include/_validation.h:267: error: expected â;â before â*â token >./include/_validation.h:268: error: ISO C++ forbids declaration of â_ATOMâ with no type >./include/_validation.h:268: error: expected â;â before â*â token >./include/_validation.h:269: error: ISO C++ forbids declaration of â_ATOMâ with no type >./include/_validation.h:269: error: expected â;â before â*â token >./src/base_information.C:605: error: âtxyzâ was not declared in this scope >./src/base_information.C:605: error: âvector_differenceâ was not declared in this scope >./src/base_information.C:606: error: âzaveâ was not declared in this scope >./src/base_information.C:610: error: âtxyz2â was not declared in this scope >./include/_validation.h:305: error: âCifStringâ does not name a type >./src/base_information.C:621: error: âtxyz2â was not declared in this scope >./include/_validation.h:315: error: âCifStringâ does not name a type >./src/base_information.C:636: error: âtxyz2â was not declared in this scope >./include/_validation.h:327: error: âCOORDâ does not name a type >./include/_validation.h:328: error: âCOORDâ does not name a type >./include/_validation.h:329: error: âCOORDâ does not name a type >./include/_validation.h:339: error: âCOORDâ does not name a type >./include/_validation.h:344: error: ISO C++ forbids declaration of â_ATOMâ with no type >./include/_validation.h:344: error: expected â;â before â*â token >./include/_validation.h:348: error: expected class-name before â{â token >./include/_validation.h:377: error: â_ATOMâ has not been declared >./include/_validation.h:377: error: â_ATOMâ has not been declared >./include/_validation.h:380: error: â_ATOMâ has not been declared >./include/_validation.h:380: error: â_ATOMâ has not been declared >./include/_validation.h:380: error: â_ATOMâ has not been declared >./include/_validation.h:382: error: â_ATOMâ has not been declared >./include/_validation.h:382: error: â_ATOMâ has not been declared >./include/_validation.h:382: error: â_ATOMâ has not been declared >./include/_validation.h:382: error: â_ATOMâ has not been declared >./src/base_information.C:729: error: type â<type error>â argument given to âdeleteâ, expected pointer >./include/_validation.h:398: error: âCifStringâ has not been declared >./include/_validation.h:421: error: â_RESIDUEâ has not been declared >./include/_validation.h:422: error: â_RESIDUEâ has not been declared >./include/_validation.h:422: error: â_RESIDUEâ has not been declared >./include/_validation.h:423: error: â_ATOMâ has not been declared >./include/_validation.h:423: error: â_ATOMâ has not been declared >./include/_validation.h:423: error: â_ATOMâ has not been declared >./include/_validation.h:423: error: â_ATOMâ has not been declared >./include/_validation.h:426: error: âCifStringâ has not been declared >./include/_validation.h:426: error: âCifStringâ has not been declared >./include/_validation.h:427: error: âCifStringâ has not been declared >./include/_validation.h:433: error: â_MOLECULEâ has not been declared >./include/_validation.h:434: error: â_CHAINâ has not been declared >./include/_validation.h:434: error: âCOORDâ has not been declared >./include/_validation.h:434: error: â_RESIDUEâ has not been declared >./include/_validation.h:435: error: â_CHAINâ has not been declared >./include/_validation.h:436: error: â_ATOMâ has not been declared >./include/_validation.h:436: error: â_ATOMâ has not been declared >./include/_validation.h:437: error: â_CHAINâ has not been declared >./include/_validation.h:438: error: âCOORDâ has not been declared >./include/_validation.h:438: error: âCOORDâ has not been declared >./src/base_information.C:790: error: âtxyzâ was not declared in this scope >./src/base_information.C:790: error: âstruct _BASEâ has no member named âorienâ >./src/base_information.C:790: error: âstruct _BASEâ has no member named âorienâ >./src/base_information.C:790: error: âvector_sumâ was not declared in this scope >./src/base_information.C:791: error: âtxyz2â was not declared in this scope >./src/base_information.C:791: error: âstruct _BASEâ has no member named âorienâ >./include/_validation.h:444: error: âISTableâ has not been declared >./src/base_information.C:791: error: âstruct _BASEâ has no member named âorienâ >./src/base_information.C:792: error: âmagangâ cannot be used as a function >./src/base_information.C:797: error: âstruct _BASEâ has no member named âorienâ >./src/base_information.C:798: error: âstruct _BASEâ has no member named âorienâ >./src/base_information.C:798: error: âvector_differenceâ was not declared in this scope >./src/base_information.C:799: error: âstruct _BASEâ has no member named âorienâ >./src/base_information.C:800: error: âstruct _BASEâ has no member named âorienâ >./src/base_information.C:801: error: âvector_normalizeâ was not declared in this scope >./src/base_information.C:804: error: âstruct _BASEâ has no member named âorienâ >./src/base_information.C:805: error: âstruct _BASEâ has no member named âorienâ >./include/_validation.h:492: error: âTblIndexObjâ does not name a type >./include/_validation.h:493: error: âTblIndexObjâ does not name a type >./include/_validation.h:494: error: âTblIndexObjâ does not name a type >./include/_validation.h:495: error: âTblIndexObjâ does not name a type >./include/_validation.h:496: error: âTblIndexObjâ does not name a type >./include/_validation.h:497: error: âTblIndexObjâ does not name a type >./include/_validation.h:498: error: âTblIndexObjâ does not name a type >./include/_validation.h:500: error: âCifStringâ does not name a type >./include/_validation.h:501: error: âCifStringâ does not name a type >./include/_validation.h:502: error: âCifStringâ does not name a type >./include/_validation.h:507: warning: âget_residue_indexâ initialized and declared âexternâ >./include/_validation.h:507: error: â_MOLECULEâ was not declared in this scope >./include/_validation.h:507: error: âmolâ was not declared in this scope >./include/_validation.h:507: error: âISTableâ was not declared in this scope >./include/_validation.h:507: error: âTableâ was not declared in this scope >./include/_validation.h:507: error: expected primary-expression before âconstâ >./include/_validation.h:508: error: expected primary-expression before âconstâ >./include/_validation.h:508: error: expected primary-expression before âconstâ >./include/_validation.h:508: error: expected primary-expression before âconstâ >./include/_validation.h:509: error: expected primary-expression before âconstâ >./include/_validation.h:509: error: expected primary-expression before âconstâ >./include/_validation.h:509: error: expected primary-expression before âconstâ >./include/_validation.h:510: error: expected primary-expression before âconstâ >./include/_validation.h:510: error: expected primary-expression before âintâ >./include/_validation.h:510: error: expected primary-expression before âintâ >./include/_validation.h:510: error: âCifStringâ was not declared in this scope >./include/_validation.h:510: error: ânameâ 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: âCifFileâ was not declared in this scope >/usr/include/rcsb/util.h:67: error: âfobjâ was not declared in this scope >/usr/include/rcsb/util.h:67: error: expected primary-expression before âconstâ >/usr/include/rcsb/util.h:68: error: expected primary-expression before âconstâ >/usr/include/rcsb/util.h:68: error: expected primary-expression before âconstâ >/usr/include/rcsb/util.h:68: error: initializer expression list treated as compound expression >/usr/include/rcsb/util.h:69: error: âCifFileâ was not declared in this scope >/usr/include/rcsb/util.h:69: error: âfobjâ was not declared in this scope >/usr/include/rcsb/util.h:69: error: expected primary-expression before âconstâ >/usr/include/rcsb/util.h:70: error: expected primary-expression before âconstâ >/usr/include/rcsb/util.h:70: error: expected primary-expression before âconstâ >/usr/include/rcsb/util.h:71: error: expected primary-expression before âlongâ >/usr/include/rcsb/util.h:71: error: initializer expression list treated as compound expression >/usr/include/rcsb/util.h:74: error: âint check_category(const char*, char*, char*)â redeclared as different kind of symbol >./src/base_information.C:926: error: type â<type error>â argument given to âdeleteâ, expected pointer >In file included from ./src/misc_util.C:145: >./include/misc_util.h:155: error: variable or field âarb_rotationâ declared void >./include/misc_util.h:155: error: âCOORDâ was not declared in this scope >./include/misc_util.h:155: error: âCOORDâ was not declared in this scope >./include/misc_util.h:155: error: âvaâ was not declared in this scope >./include/misc_util.h:155: error: expected primary-expression before âdoubleâ >./include/misc_util.h:158: error: variable or field âget_vectorâ declared void >./include/misc_util.h:158: error: âCOORDâ was not declared in this scope >./include/misc_util.h:158: error: âvaâ was not declared in this scope >./include/misc_util.h:158: error: âCOORDâ was not declared in this scope >./include/misc_util.h:158: error: âvrefâ was not declared in this scope >./include/misc_util.h:158: error: expected primary-expression before âdoubleâ >./include/misc_util.h:158: error: âCOORDâ was not declared in this scope >./include/misc_util.h:158: error: âvoâ was not declared in this scope >./include/misc_util.h:159: warning: âmagangâ initialized and declared âexternâ >./include/misc_util.h:159: error: âCOORDâ was not declared in this scope >./include/misc_util.h:159: error: âvaâ was not declared in this scope >./include/misc_util.h:159: error: âCOORDâ was not declared in this scope >./include/misc_util.h:159: error: âvbâ 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 âmulti_matrixâ declared void >./include/misc_util.h:161: error: âCOORDâ was not declared in this scope >./include/misc_util.h:161: error: expected primary-expression before âconstâ >./include/misc_util.h:161: error: expected primary-expression before âconstâ >./include/misc_util.h:163: error: variable or field âvector_initâ declared void >./include/misc_util.h:163: error: âCOORDâ was not declared in this scope >./include/misc_util.h:163: error: âdestâ was not declared in this scope >./include/misc_util.h:163: error: expected primary-expression before âconstâ >./include/misc_util.h:163: error: expected primary-expression before âconstâ >./include/misc_util.h:163: error: expected primary-expression before âconstâ >./include/misc_util.h:164: error: variable or field âvector_copyâ declared void >./include/misc_util.h:164: error: âCOORDâ was not declared in this scope >./include/misc_util.h:164: error: âdestâ was not declared in this scope >./include/misc_util.h:164: error: expected primary-expression before âconstâ >./include/misc_util.h:165: error: variable or field âvector_sumâ declared void >./include/misc_util.h:165: error: âCOORDâ was not declared in this scope >./include/misc_util.h:165: error: âdestâ was not declared in this scope >./include/misc_util.h:165: error: expected primary-expression before âconstâ >./include/misc_util.h:165: error: expected primary-expression before âconstâ >./include/misc_util.h:166: error: variable or field âvector_differenceâ declared void >./include/misc_util.h:166: error: âCOORDâ was not declared in this scope >./include/misc_util.h:166: error: âdestâ was not declared in this scope >./include/misc_util.h:166: error: expected primary-expression before âconstâ >./include/misc_util.h:166: error: expected primary-expression before âconstâ >./include/misc_util.h:167: error: variable or field âvector_scaledâ declared void >./include/misc_util.h:167: error: âCOORDâ was not declared in this scope >./include/misc_util.h:167: error: âdestâ was not declared in this scope >./include/misc_util.h:167: error: expected primary-expression before âconstâ >./include/misc_util.h:167: error: expected primary-expression before âconstâ >./include/misc_util.h:168: error: variable or field âvector_addâ declared void >./include/misc_util.h:168: error: âCOORDâ was not declared in this scope >./include/misc_util.h:168: error: âdestâ was not declared in this scope >./include/misc_util.h:168: error: expected primary-expression before âconstâ >./include/misc_util.h:169: error: variable or field âvector_subtractâ declared void >./include/misc_util.h:169: error: âCOORDâ was not declared in this scope >./include/misc_util.h:169: error: âdestâ was not declared in this scope >./include/misc_util.h:169: error: expected primary-expression before âconstâ >./include/misc_util.h:170: error: variable or field âvector_scaleâ declared void >./include/misc_util.h:170: error: âCOORDâ was not declared in this scope >./include/misc_util.h:170: error: âdestâ was not declared in this scope >./include/misc_util.h:170: error: expected primary-expression before âconstâ >./include/misc_util.h:171: error: variable or field âvector_invertâ declared void >./include/misc_util.h:171: error: âCOORDâ was not declared in this scope >./include/misc_util.h:171: error: âvâ was not declared in this scope >./include/misc_util.h:172: error: variable or field âvector_reverseâ declared void >./include/misc_util.h:172: error: âCOORDâ was not declared in this scope >./include/misc_util.h:172: error: âvâ was not declared in this scope >./include/misc_util.h:173: error: variable or field âvector_sum_scaledâ declared void >./include/misc_util.h:173: error: âCOORDâ was not declared in this scope >./include/misc_util.h:173: error: âdestâ was not declared in this scope >./include/misc_util.h:173: error: expected primary-expression before âconstâ >./include/misc_util.h:173: error: expected primary-expression before âconstâ >./include/misc_util.h:173: error: expected primary-expression before âconstâ >./include/misc_util.h:174: error: variable or field âvector_add_scaledâ declared void >./include/misc_util.h:174: error: âCOORDâ was not declared in this scope >./include/misc_util.h:174: error: âdestâ was not declared in this scope >./include/misc_util.h:174: error: expected primary-expression before âconstâ >./include/misc_util.h:174: error: expected primary-expression before âconstâ >./include/misc_util.h:175: error: ISO C++ forbids declaration of âCOORDâ with no type >./include/misc_util.h:175: error: expected â,â or â...â before âv1â >./include/misc_util.h:176: error: variable or field âvector_cross_productâ declared void >./include/misc_util.h:176: error: âCOORDâ was not declared in this scope >./include/misc_util.h:176: error: âvzâ was not declared in this scope >./include/misc_util.h:176: error: expected primary-expression before âconstâ >./include/misc_util.h:176: error: expected primary-expression before âconstâ >./include/misc_util.h:177: error: variable or field âvector_normalizeâ declared void >./include/misc_util.h:177: error: âCOORDâ was not declared in this scope >./include/misc_util.h:177: error: âvâ was not declared in this scope >./include/misc_util.h:178: error: variable or field âvector_middleâ declared void >./include/misc_util.h:178: error: âCOORDâ was not declared in this scope >./include/misc_util.h:178: error: âdestâ was not declared in this scope >./include/misc_util.h:178: error: expected primary-expression before âconstâ >./include/misc_util.h:178: error: expected primary-expression before âconstâ >./include/misc_util.h:179: error: ISO C++ forbids declaration of âCOORDâ with no type >./include/misc_util.h:179: error: expected â,â or â...â before âv1â >./include/misc_util.h:180: error: ISO C++ forbids declaration of âCOORDâ with no type >./include/misc_util.h:180: error: expected â,â or â...â before âvâ >./include/misc_util.h:181: error: ISO C++ forbids declaration of âCOORDâ with no type >./include/misc_util.h:181: error: expected â,â or â...â before âvaâ >./include/misc_util.h:182: error: variable or field âvector_orthogonalâ declared void >./include/misc_util.h:182: error: âCOORDâ was not declared in this scope >./include/misc_util.h:182: error: âvaâ was not declared in this scope >./include/misc_util.h:182: error: âCOORDâ was not declared in this scope >./include/misc_util.h:182: error: âvrefâ was not declared in this scope >./include/misc_util.h:194: error: variable or field âmatrix_transformâ declared void >./include/misc_util.h:194: error: âCOORDâ was not declared in this scope >./include/misc_util.h:194: error: âvâ was not declared in this scope >./include/misc_util.h:194: error: expected primary-expression before âconstâ >./include/misc_util.h:195: error: variable or field âmatrix_rotateâ declared void >./include/misc_util.h:195: error: âCOORDâ was not declared in this scope >./include/misc_util.h:195: error: âvâ was not declared in this scope >./include/misc_util.h:195: error: expected primary-expression before âconstâ >./include/misc_util.h:196: error: variable or field âmatrix_rotate_translateâ declared void >./include/misc_util.h:196: error: âCOORDâ was not declared in this scope >./include/misc_util.h:196: error: âvâ was not declared in this scope >./include/misc_util.h:196: error: expected primary-expression before âconstâ >./src/misc_util.C:148: error: variable or field âarb_rotationâ declared void >./src/misc_util.C:148: error: âCOORDâ was not declared in this scope >./src/misc_util.C:148: error: âCOORDâ was not declared in this scope >./src/misc_util.C:148: error: âvaâ was not declared in this scope >./src/misc_util.C:148: error: expected primary-expression before âdoubleâ >make[1]: *** [obj/misc_util.o] Error 1 >./src/base_information.C: In member function âvoid _VALIDATION::get_parameters(int, int*, _BASE**)â: >./src/base_information.C:937: error: âCOORDâ was not declared in this scope >./src/base_information.C:937: error: expected â;â before âmfiâ >./src/base_information.C:938: error: expected â;â before âmst_orienâ >./src/base_information.C:940: error: â_RESIDUEâ was not declared in this scope >./src/base_information.C:940: error: âres1â was not declared in this scope >./src/base_information.C:940: error: âres2â was not declared in this scope >./src/base_information.C:940: error: âres3â was not declared in this scope >./src/base_information.C:940: error: âres4â was not declared in this scope >./src/base_information.C:942: error: âmfoi_prevâ was not declared in this scope >./src/base_information.C:948: error: âstruct _BASEâ has no member named âorienâ >./src/base_information.C:949: error: âstruct _BASEâ has no member named âorienâ >./src/base_information.C:950: error: âstruct _BASEâ has no member named âorienâ >./src/base_information.C:950: error: âvector_reverseâ was not declared in this scope >./src/base_information.C:951: error: âstruct _BASEâ has no member named âorienâ >./src/base_information.C:959: error: âmst_orgâ was not declared in this scope >./src/base_information.C:959: error: âstruct _BASEâ has no member named âorgâ >./src/base_information.C:960: error: âstruct _BASEâ has no member named âorgâ >./src/base_information.C:960: error: âvector_differenceâ was not declared in this scope >./src/base_information.C:961: error: âmst_orgâ was not declared in this scope >./src/base_information.C:962: error: âstruct _BASEâ has no member named âorienâ >./src/base_information.C:968: error: âstruct _BASEâ has no member named âorienâ >./src/base_information.C:968: error: âvector_reverseâ was not declared in this scope >./src/base_information.C:969: error: âstruct _BASEâ has no member named âorienâ >./src/base_information.C:976: error: âaveSâ was not declared in this scope >./src/base_information.C:976: error: expected type-specifier before âCOORDâ >./src/base_information.C:976: error: expected â;â before âCOORDâ >./src/base_information.C:977: error: âaveHâ was not declared in this scope >./src/base_information.C:977: error: expected type-specifier before âCOORDâ >./src/base_information.C:977: error: expected â;â before âCOORDâ >./src/base_information.C:979: error: âvector_initâ was not declared in this scope >./src/base_information.C:983: error: âstruct _BASEâ has no member named âorienâ >./src/base_information.C:983: error: âstruct _BASEâ has no member named âorgâ >./src/base_information.C:984: error: âstruct _BASEâ has no member named âorienâ >./src/base_information.C:984: error: âstruct _BASEâ has no member named âorgâ >./src/base_information.C:985: error: âmfiâ was not declared in this scope >./src/base_information.C:985: error: âmfoiâ was not declared in this scope >./src/base_information.C:985: error: âbpstep_parâ was not declared in this scope >./src/base_information.C:987: error: âstruct _BASEâ has no member named âresâ >./src/base_information.C:988: error: âstruct _BASEâ has no member named âresâ >./src/base_information.C:1001: error: âstruct BASE_BASE_PARAMSâ has no member named âChnID_Iâ >./src/base_information.C:1008: error: âstruct BASE_BASE_PARAMSâ has no member named âChnID_Jâ >./src/base_information.C:1054: error: âmfi_prevâ was not declared in this scope >./src/base_information.C:1058: error: âmfi_prevâ was not declared in this scope >./src/base_information.C:1058: error: âmst_orienâ was not declared in this scope >./src/base_information.C:1058: error: âmst_orgâ was not declared in this scope >./src/base_information.C:1059: error: âmst_orienHâ was not declared in this scope >./src/base_information.C:1059: error: âmst_orgHâ was not declared in this scope >./src/base_information.C:1059: error: âhelical_parâ was not declared in this scope >./src/base_information.C:1066: error: âstruct _BASEâ has no member named âP_xyzâ >./src/base_information.C:1067: error: âstruct _BASEâ has no member named âP_xyzâ >./src/base_information.C:1069: error: âstruct _BASEâ has no member named âP_xyzâ >./src/base_information.C:1070: error: âstruct _BASEâ has no member named âP_xyzâ >./src/base_information.C:1077: error: âstruct _BASEâ has no member named âresâ >./src/base_information.C:1078: error: âstruct _BASEâ has no member named âresâ >./src/base_information.C:1090: error: âstruct INTER_BASE_PARAMSâ has no member named âChnID_I1â >./src/base_information.C:1098: error: âstruct INTER_BASE_PARAMSâ has no member named âChnID_J1â >In file included from ./include/_validation.h:148, > from ./src/check.C:146: >./include/check.h:159: error: âMxStrLenâ was not declared in this scope >In file included from ./src/check.C:146: >./include/_validation.h:207: error: ISO C++ forbids declaration of â_RESIDUEâ with no type >./include/_validation.h:207: error: expected â;â before â*â token >./include/_validation.h:213: error: âCOORDâ does not name a type >./include/_validation.h:214: error: âCOORDâ does not name a type >./include/_validation.h:215: error: âCOORDâ does not name a type >./include/_validation.h:216: error: âCOORDâ does not name a type >./include/_validation.h:217: error: âCOORDâ does not name a type >./include/_validation.h:218: error: âCOORDâ does not name a type >./include/_validation.h:232: error: ISO C++ forbids declaration of â_ATOMâ with no type >./include/_validation.h:232: error: expected â;â before â*â token >./include/_validation.h:233: error: ISO C++ forbids declaration of â_ATOMâ with no type >./include/_validation.h:233: error: expected â;â before â*â token >./include/_validation.h:234: error: ISO C++ forbids declaration of â_ATOMâ with no type >./include/_validation.h:234: error: expected â;â before â*â token >./include/_validation.h:266: error: ISO C++ forbids declaration of â_ATOMâ with no type >./include/_validation.h:266: error: expected â;â before â*â token >./include/_validation.h:267: error: ISO C++ forbids declaration of â_ATOMâ with no type >./include/_validation.h:267: error: expected â;â before â*â token >./include/_validation.h:268: error: ISO C++ forbids declaration of â_ATOMâ with no type >./include/_validation.h:268: error: expected â;â before â*â token >./include/_validation.h:269: error: ISO C++ forbids declaration of â_ATOMâ with no type >./src/base_information.C:1113: error: âstruct INTER_BASE_PARAMSâ has no member named âChnID_I2â./include/_validation.h:269: error: expected â;â before â*â token > >./src/base_information.C:1121: error: âstruct INTER_BASE_PARAMSâ has no member named âChnID_J2â >./include/_validation.h:305: error: âCifStringâ does not name a type >./include/_validation.h:315: error: âCifStringâ does not name a type >./include/_validation.h:327: error: âCOORDâ does not name a type >./include/_validation.h:328: error: âCOORDâ does not name a type >./include/_validation.h:329: error: âCOORDâ does not name a type >./include/_validation.h:339: error: âCOORDâ does not name a type >./include/_validation.h:344: error: ISO C++ forbids declaration of â_ATOMâ with no type >./include/_validation.h:344: error: expected â;â before â*â token >./include/_validation.h:348: error: expected class-name before â{â token >./src/base_information.C:1184: error: type â<type error>â argument given to âdeleteâ, expected pointer >./include/_validation.h:377: error: â_ATOMâ has not been declared./src/base_information.C:1185: error: type â<type error>â argument given to âdeleteâ, expected pointer > >./include/_validation.h:377: error: â_ATOMâ has not been declared >./include/_validation.h:380: error: â_ATOMâ has not been declared >./include/_validation.h:380: error: â_ATOMâ has not been declared >./include/_validation.h:380: error: â_ATOMâ has not been declared >./include/_validation.h:382: error: â_ATOMâ has not been declared >./include/_validation.h:382: error: â_ATOMâ has not been declared >./include/_validation.h:382: error: â_ATOMâ has not been declared >./include/_validation.h:382: error: â_ATOMâ has not been declared >./include/check.h:191: error: previous declaration of âCHECK_CATEGORY check_category [6]â >./include/_validation.h:398: error: âCifStringâ has not been declared >./src/_validation.C:146: error: â_STBIOLâ has not been declared >./src/_validation.C:148: error: â_STBIOLâ has not been declared >./src/_validation.C:150: error: â_STBIOLâ has not been declared >./src/_validation.C: In constructor â_VALIDATION::_VALIDATION(int, int)â: >./src/_validation.C:153: error: class â_VALIDATIONâ does not have any field named â_FileObjâ >./include/_validation.h:421: error: â_RESIDUEâ has not been declared >./include/_validation.h:422: error: â_RESIDUEâ has not been declared >./include/_validation.h:422: error: â_RESIDUEâ has not been declared >./include/_validation.h:423: error: â_ATOMâ has not been declared >In file included from ./include/gridcell.h:144./include/_validation.h:423: error: â_ATOMâ has not been declared, > from ./src/gridcell.C:142 >: >./include/atom.h:143:21: ./include/_validation.h:423: error: â_ATOMâ has not been declarederror: >fstream.h: No such file or directory >./include/atom.h:144:22:./include/_validation.h:423: error: â_ATOMâ has not been declared >error: iostream.h: No such file or directory >./include/_validation.h:426: error: âCifStringâ has not been declared >./include/_validation.h:426: error: âCifStringâ has not been declared >./include/_validation.h:427: error: âCifStringâ has not been declared >./include/_validation.h:433: error: â_MOLECULEâ has not been declared >./include/_validation.h:434: error: â_CHAINâ has not been declared >./include/_validation.h:434: error: âCOORDâ has not been declared >./include/_validation.h:434: error: â_RESIDUEâ has not been declared >./include/_validation.h:435: error: â_CHAINâ has not been declared >./src/_validation.C:179: error: â_bondResIndexâ was not declared in this scope >./include/_validation.h:436: error: â_ATOMâ has not been declared >./src/_validation.C:180: error: â_bondNamIndexâ was not declared in this scope >./include/_validation.h:436: error: â_ATOMâ has not been declared >./src/_validation.C:181: error: â_bondComIndexâ was not declared in this scope >./src/_validation.C:182: error: â_angleResIndexâ was not declared in this scope./include/_validation.h:437: error: â_CHAINâ has not been declared > >./src/_validation.C:183: error: â_angleNamIndexâ was not declared in this scope >./src/_validation.C:184: error: â_angleComIndexâ was not declared in this scope >./src/_validation.C:185: error: â_torsionIndexâ was not declared in this scope >./include/_validation.h:438: error: âCOORDâ has not been declared >./src/_validation.C:187: error: â_spell_checkâ was not declared in this scope >./include/_validation.h:438: error: âCOORDâ has not been declared >./src/_validation.C:188: error: â_large_cellâ was not declared in this scope >./src/_validation.C:189: error: â_date_errorâ was not declared in this scope >./include/_validation.h:444: error: âISTableâ has not been declared >./include/_validation.h:492: error: âTblIndexObjâ does not name a type >./include/_validation.h:493: error: âTblIndexObjâ does not name a type >./include/_validation.h:494: error: âTblIndexObjâ does not name a type >./include/_validation.h:495: error: âTblIndexObjâ does not name a type >./include/_validation.h:496: error: âTblIndexObjâ does not name a type >./include/_validation.h:497: error: âTblIndexObjâ does not name a type >./include/_validation.h:498: error: âTblIndexObjâ does not name a type >./include/_validation.h:500: error: âCifStringâ does not name a type >./include/_validation.h:501: error: âCifStringâ does not name a type >./include/_validation.h:502: error: âCifStringâ does not name a type >./include/_validation.h:507: warning: âget_residue_indexâ initialized and declared âexternâ >./include/_validation.h:507: error: â_MOLECULEâ was not declared in this scope >./include/_validation.h:507: error: âmolâ was not declared in this scope >./include/_validation.h:507: error: âISTableâ was not declared in this scope >./include/_validation.h:507: error: âTableâ was not declared in this scope >./include/_validation.h:507: error: expected primary-expression before âconstâ >./include/_validation.h:508: error: expected primary-expression before âconstâ >./include/_validation.h:508: error: expected primary-expression before âconstâ >./include/_validation.h:508: error: expected primary-expression before âconstâ >./include/_validation.h:509: error: expected primary-expression before âconstâ >./include/_validation.h:509: error: expected primary-expression before âconstâ >./include/_validation.h:509: error: expected primary-expression before âconstâ >./include/_validation.h:510: error: expected primary-expression before âconstâ >./include/_validation.h:510: error: expected primary-expression before âintâ >./include/_validation.h:510: error: expected primary-expression before âintâ >./include/_validation.h:510: error: âCifStringâ was not declared in this scope >./include/_validation.h:510: error: ânameâ 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 âcreate_blocksâ declared void >./src/base_information.C:1188: error: â_CHAINâ was not declared in this scope >./src/base_information.C:1188: error: âchainâ was not declared in this scope >./src/base_information.C:1188: error: expected primary-expression before âconstâ >./include/base_information.h:374: warning: â_base_typeâ defined but not used >./include/base_information.h:703: warning: âbase_hbond_typeâ defined but not used >./include/base_information.h:727: warning: âR_RingAtomâ defined but not used >./include/base_information.h:728: warning: âY_RingAtomâ defined but not used >./include/base_information.h:730: warning: âR_BLOCKâ defined but not used >./include/base_information.h:741: warning: âY_BLOCKâ defined but not used >./include/base_information.h:752: warning: âSTAND_Aâ defined but not used >./include/base_information.h:771: warning: âSTAND_Câ defined but not used >./include/base_information.h:790: warning: âSTAND_Gâ defined but not used >./include/base_information.h:809: warning: âSTAND_Pâ defined but not used >./include/base_information.h:829: warning: âSTAND_Tâ defined but not used >./include/base_information.h:849: warning: âSTAND_Uâ defined but not used >./src/base_information.C:159: warning: âvoid realloc_base(_BASE***, int, int&)â declared âstaticâ but never defined >./src/base_information.C:162: warning: âfind_matchâ defined but not used >./src/base_information.C:164: warning: â_BASE_PAIR* find_all_pairs(int, _BASE**)â declared âstaticâ but never defined >./src/base_information.C:165: warning: âCONTACT** find_real_base_pairs(int, _BASE**, _BASE_PAIR*, int&, int)â declared âstaticâ but never defined >./src/base_information.C:168: warning: âcal_distâ defined but not used >./src/base_information.C:170: warning: âint get_best_pair(_BASE_PAIR*, int&, int&, int&, int&, int*)â declared âstaticâ but never defined >./src/base_information.C:176: warning: âvoid project_xyzP(int)â declared âstaticâ but never defined >./src/base_information.C:178: warning: âdouble distance_ab(_BASE*, int, _BASE*, int)â declared âstaticâ but never defined >./src/base_information.C:179: warning: âvoid get_ij(int, int, int*, int&, int&)â declared âstaticâ but never defined >./src/base_information.C:180: warning: âvoid reverse(int, int, int*)â declared âstaticâ but never defined >./src/base_information.C:181: warning: âint is_linked(_BASE*, _BASE*)â declared âstaticâ but never defined >./src/base_information.C:182: warning: âint is_wc_geometry(_BASE*, _BASE*)â declared âstaticâ but never defined >./src/base_information.C:183: warning: âint check_others(_BASE**, int, int, int, int)â declared âstaticâ but never defined >./src/base_information.C:185: warning: âint check_direction(int*, int*, int*, int*, _BASE**, int*)â declared âstaticâ but never defined >./src/base_information.C:187: warning: âint find_atom_index(int, _ATOMNAME*, const char*)â declared âstaticâ but never defined >./src/base_information.C:193: warning: âint base_hbond_type_compare(const void*, const void*)â declared âstaticâ but never defined >./src/base_information.C:194: warning: âint name_compare1(const void*, const void*)â declared âstaticâ but never defined >./src/base_information.C:195: warning: âint base_type_compare(const void*, const void*)â declared âstaticâ but never defined >./src/base_information.C:196: warning: âint atom_edge_compare(const void*, const void*)â declared âstaticâ but never defined >In file included from ./src/check.C:149: >./include/check_global.h:217: warning: missing braces around initializer for âATOM_FIELD [4]â >./include/check_global.h:217: warning: missing braces around initializer for âATOM_FIELDâ >./include/check_global.h:217: error: braces around scalar initializer for type âintâ >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 âostreamâ with no type >./include/symop.h:153: error: âostreamâ is neither function nor member function; cannot be declared friend >./include/symop.h:153: error: expected â;â before â&â token >./include/symop.h:158: error: expected â)â before â&â token >make[1]: *** [obj/base_information.o] Error 1 >./include/check_global.h:217: warning: missing braces around initializer for âATOM_FIELD [4]â >./include/check_global.h:217: warning: missing braces around initializer for âATOM_FIELDâ >./include/check_global.h:217: error: braces around scalar initializer for type âintâ >./include/check_global.h:217: warning: missing braces around initializer for âATOM_FIELD [4]â >./include/check_global.h:217: warning: missing braces around initializer for âATOM_FIELDâ >./include/check_global.h:217: error: braces around scalar initializer for type âintâ >./include/check_global.h:217: warning: missing braces around initializer for âATOM_FIELD [4]â >./include/check_global.h:217: warning: missing braces around initializer for âATOM_FIELDâ >./include/check_global.h:217: error: braces around scalar initializer for type âintâ >./include/check_global.h:217: warning: missing braces around initializer for âATOM_FIELD [4]â >./include/check_global.h:217: warning: missing braces around initializer for âATOM_FIELDâ >./include/check_global.h:217: error: braces around scalar initializer for type âintâ >./include/check_global.h:217: warning: missing braces around initializer for âATOM_FIELD [4]â >./include/check_global.h:217: warning: missing braces around initializer for âATOM_FIELDâ >./include/check_global.h:217: error: braces around scalar initializer for type âintâ >./include/check_global.h:217: warning: missing braces around initializer for âATOM_FIELD [4]â >./include/check_global.h:217: warning: missing braces around initializer for âATOM_FIELDâ >./include/check_global.h:217: error: braces around scalar initializer for type âintâ >./include/check_global.h:217: warning: missing braces around initializer for âATOM_FIELD [4]â >./include/check_global.h:217: warning: missing braces around initializer for âATOM_FIELDâ >./include/check_global.h:217: error: braces around scalar initializer for type âintâ >./include/check_global.h:217: warning: missing braces around initializer for âATOM_FIELD [4]â >./include/check_global.h:217: warning: missing braces around initializer for âATOM_FIELDâ >./include/check_global.h:217: error: braces around scalar initializer for type âintâ >./include/check_global.h:217: warning: missing braces around initializer for âATOM_FIELD [4]â >./include/check_global.h:217: warning: missing braces around initializer for âATOM_FIELDâ >./include/check_global.h:217: error: braces around scalar initializer for type âintâ >./include/check_global.h:217: warning: missing braces around initializer for âATOM_FIELD [4]â >./include/check_global.h:217: warning: missing braces around initializer for âATOM_FIELDâ >./include/check_global.h:217: error: braces around scalar initializer for type âintâ >./include/check_global.h:217: warning: missing braces around initializer for âATOM_FIELD [4]â >./include/check_global.h:217: warning: missing braces around initializer for âATOM_FIELDâ >./include/check_global.h:217: error: braces around scalar initializer for type âintâ >./include/check_global.h:217: error: invalid conversion from âconst char*â to âintâ >./include/check_global.h:217: error: invalid conversion from âconst char*â to âintâ >./include/check_global.h:217: error: invalid conversion from âconst char*â to âintâ >./include/check_global.h:217: error: invalid conversion from âconst char*â to âintâ >./include/check_global.h:217: error: invalid conversion from âconst char*â to âintâ >./include/check_global.h:217: error: invalid conversion from âconst char*â to âintâ >./include/check_global.h:217: error: invalid conversion from âconst char*â to âintâ >./include/check_global.h:217: error: invalid conversion from âconst char*â to âintâ >./include/check_global.h:217: error: invalid conversion from âconst char*â to âintâ >./include/check_global.h:217: error: invalid conversion from âconst char*â to âintâ >./include/check_global.h:217: error: invalid conversion from âconst char*â to âintâ >./include/check_global.h:217: error: invalid conversion from âconst char*â to âintâ >In file included from ./src/check.C:150: >./include/datacheck.h:7: warning: âDictionaryDataCheckingâ initialized and declared âexternâ >./include/datacheck.h:7: error: âCifFileObjâ was not declared in this scope >./include/datacheck.h:7: error: âinâ was not declared in this scope >./include/datacheck.h:7: error: âDICFileObjâ was not declared in this scope >./include/datacheck.h:7: error: ârefâ was not declared in this scope >./include/datacheck.h:7: error: expected primary-expression before â*â token >./include/datacheck.h:7: error: âfpâ was not declared in this scope >./include/datacheck.h:8: error: expected primary-expression before âconstâ >./include/datacheck.h:8: error: expected primary-expression before âintâ >./include/datacheck.h:8: error: âCifStringâ was not declared in this scope >./include/datacheck.h:8: error: âdate_errorâ 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: âCifFileâ was not declared in this scope >/usr/include/rcsb/util.h:67: error: âfobjâ was not declared in this scope >/usr/include/rcsb/util.h:67: error: expected primary-expression before âconstâ >/usr/include/rcsb/util.h:68: error: expected primary-expression before âconstâ >/usr/include/rcsb/util.h:68: error: expected primary-expression before âconstâ >/usr/include/rcsb/util.h:68: error: initializer expression list treated as compound expression >/usr/include/rcsb/util.h:69: error: âCifFileâ was not declared in this scope >/usr/include/rcsb/util.h:69: error: âfobjâ was not declared in this scope >/usr/include/rcsb/util.h:69: error: expected primary-expression before âconstâ >/usr/include/rcsb/util.h:70: error: expected primary-expression before âconstâ >/usr/include/rcsb/util.h:70: error: expected primary-expression before âconstâ >/usr/include/rcsb/util.h:71: error: expected primary-expression before âlongâ >/usr/include/rcsb/util.h:71: error: initializer expression list treated as compound expression >/usr/include/rcsb/util.h:74: error: âint check_category(const char*, char*, char*)â redeclared as different kind of symbol >./include/check_global.h:219: error: previous declaration of âCHECK_CATEGORY check_category [6]â >./src/check.C:188: error: âTblIndexObjâ does not name a type >./src/check.C:192: error: variable or field âcheck_tokensâ declared void >./src/check.C:192: error: â_MOLECULEâ was not declared in this scope >./src/check.C:192: error: âmolâ was not declared in this scope >./src/check.C:192: error: âCards_Info_Formatâ was not declared in this scope >./src/check.C:192: error: âCardInfoâ was not declared in this scope >./src/check.C:193: error: expected primary-expression before âconstâ >./src/check.C:193: error: expected primary-expression before â*â token >./src/check.C:194: error: expected primary-expression before âconstâ >./src/check.C:194: error: expected primary-expression before âconstâ >./src/check.C:194: error: expected primary-expression before â*â token >./src/check.C:194: error: âfpâ was not declared in this scope >./src/check.C:195: error: variable or field âcheck_categorysâ declared void >./src/check.C:195: error: â_MOLECULEâ was not declared in this scope >./src/check.C:195: error: âmolâ was not declared in this scope >./src/check.C:195: error: âISTableâ was not declared in this scope >./src/check.C:195: error: âTableâ was not declared in this scope >./src/check.C:195: error: expected primary-expression before â*â token >./src/check.C:195: error: âcategoryâ was not declared in this scope >./src/check.C:196: error: expected primary-expression before â*â token >./src/check.C:196: error: âfpâ was not declared in this scope >./src/check.C:196: error: expected primary-expression before âconstâ >./src/check.C:196: error: expected primary-expression before âintâ >./src/check.C:197: error: variable or field âcheck_categorys1â declared void >./src/check.C:197: error: â_MOLECULEâ was not declared in this scope >./src/check.C:197: error: âmolâ was not declared in this scope >./src/check.C:197: error: âISTableâ was not declared in this scope >./src/check.C:197: error: âTableâ was not declared in this scope >./src/check.C:197: error: expected primary-expression before â*â token >./src/check.C:197: error: âcategoryâ was not declared in this scope >./src/check.C:198: error: expected primary-expression before â*â token >./src/check.C:198: error: âfpâ was not declared in this scope >./src/check.C:198: error: expected primary-expression before âconstâ >./src/check.C:198: error: expected primary-expression before âintâ >./src/check.C:199: error: variable or field âcheck_seqnum_redundancyâ declared void >./src/check.C:199: error: â_MOLECULEâ was not declared in this scope >./src/check.C:199: error: âmolâ was not declared in this scope >./src/check.C:199: error: expected primary-expression before âconstâ >./src/check.C:199: error: expected primary-expression before â*â token >./src/check.C:199: error: âfpâ was not declared in this scope >./src/check.C:199: error: expected primary-expression before âintâ >./src/check.C: In function âvoid get_taxonomylist(int)â: >./src/check.C:207: error: âCifStringâ was not declared in this scope >./src/check.C:207: error: expected â;â before âcifstringâ >./src/check.C:211: error: âTaxnomyListâ was not declared in this scope >./src/check.C:213: error: âroot_dirâ was not declared in this scope >./src/check.C:220: error: âcifstringâ was not declared in this scope >./src/check.C:217: warning: ignoring return value of âchar* fgets(char*, int, FILE*)â, declared with attribute warn_unused_result >./src/check.C: In member function âvoid _VALIDATION::write_check_results(FILE*)â: >./src/check.C:230: error: âCifStringâ was not declared in this scope >./src/check.C:230: error: expected â;â before âannotatorâ >./src/check.C:231: error: âISTableâ was not declared in this scope >./src/check.C:231: error: âTableâ was not declared in this scope >./src/check.C:233: error: âannotatorâ was not declared in this scope >./src/check.C:234: error: â_CifObjâ was not declared in this scope >./src/check.C:234: error: â_StructureIdâ was not declared in this scope >./src/check.C:235: error: âis_empty_tableâ was not declared in this scope >./src/check.C:237: error: âget_valueâ was not declared in this scope >./src/check.C:239: error: â_StructureIdâ was not declared in this scope >./src/check.C:241: error: â_Error_Checkâ was not declared in this scope >./src/check.C:245: error: â_Error_Checkâ was not declared in this scope >./src/check.C:249: error: â_Error_Checkâ was not declared in this scope >./src/check.C:253: error: â_Error_Checkâ was not declared in this scope >./src/check.C:257: error: â_Error_Checkâ was not declared in this scope >./src/check.C:261: error: â_Error_Checkâ was not declared in this scope >./src/check.C:265: error: â_Error_Checkâ was not declared in this scope >./src/check.C:269: error: â_Error_Checkâ was not declared in this scope >./src/check.C:273: error: â_Error_Checkâ was not declared in this scope >./src/check.C:277: error: â_Error_Checkâ was not declared in this scope >./src/check.C:282: error: â_Error_Checkâ was not declared in this scope >./src/check.C:286: error: â_Error_Checkâ was not declared in this scope >./src/check.C:290: error: â_Error_Checkâ was not declared in this scope >./src/check.C:294: error: â_Error_Checkâ was not declared in this scope >./src/check.C:298: error: â_Error_Checkâ was not declared in this scope >./src/align_standard.C: In function âint check_target_sequence(FILE*, const char*, const char*, const char*, const char*)â: >./src/align_standard.C:24: error: ândb_clean_stringâ was not declared in this scope >./src/check.C:302: error: â_Error_Checkâ was not declared in this scope >./src/align_standard.C:26: error: âNDB_MSG_ERRâ was not declared in this scope >./src/check.C:306: error: â_Error_Checkâ was not declared in this scope >./src/align_standard.C:26: error: ândb_log_messageâ was not declared in this scope >./src/align_standard.C:27: error: ândb_close_logâ was not declared in this scope >./src/check.C:310: error: â_Error_Checkâ was not declared in this scope >./src/check.C:314: error: â_Error_Checkâ was not declared in this scope >./src/check.C:318: error: â_Error_Checkâ was not declared in this scope >./src/check.C:322: error: â_Error_Checkâ was not declared in this scope >./src/check.C:326: error: â_Error_Checkâ was not declared in this scope >./src/check.C:330: error: â_Error_Checkâ was not declared in this scope >./src/check.C:345: error: â_Error_Checkâ was not declared in this scope >./src/check.C:349: error: â_Error_Checkâ was not declared in this scope >./src/contact.C:144:20: ./src/check.C:353: error: â_Error_Checkâ was not declared in this scope >error: _index.h: No such file or directory >./src/check.C:357: error: â_Error_Checkâ was not declared in this scope >./src/check.C:361: error: â_Error_Checkâ was not declared in this scope >./src/check.C:365: error: â_Error_Checkâ was not declared in this scope >./src/check.C:366: error: â_date_errorâ was not declared in this scope >./src/check.C:369: error: â_Error_Checkâ was not declared in this scope >In file included from ./src/contact.C:145./src/check.C:373: error: â_Error_Checkâ was not declared in this scope: > >./include/_validation.h:144:22: error: _fileobj.h: No such file or directory >./src/check.C:377: error: â_Error_Checkâ was not declared in this scope >./src/check.C:381: error: â_Error_Checkâ was not declared in this scope >./src/check.C:385: error: â_Error_Checkâ was not declared in this scope >./src/check.C:386: error: â_large_cellâ was not declared in this scope >./src/check.C:389: error: â_Error_Checkâ was not declared in this scope >./src/check.C:393: error: â_Error_Checkâ was not declared in this scope >./src/check.C:397: error: â_Error_Checkâ was not declared in this scope >./src/check.C:398: error: â_Error_Check_Messageâ was not declared in this scope >./src/check.C:401: error: â_Error_Checkâ was not declared in this scope >./src/check.C:405: error: â_Error_Checkâ was not declared in this scope >./src/check.C:409: error: â_spell_checkâ was not declared in this scope >./src/check.C:413: error: â_error_messageâ was not declared in this scope >./src/check.C:424: error: â_unrecognized_residueâ was not declared in this scope >./src/check.C:428: error: â_Error_Checkâ was not declared in this scope >./src/check.C:437: error: â_Error_Checkâ was not declared in this scope >./src/align_standard.C:22: warning: ignoring return value of âchar* fgets(char*, int, FILE*)â, declared with attribute warn_unused_result >./src/check.C:441: error: â_Error_Checkâ was not declared in this scope >./src/check.C:445: error: â_Error_Checkâ was not declared in this scope >./src/check.C:449: error: â_Error_Checkâ was not declared in this scope >./src/check.C:453: error: â_Error_Checkâ was not declared in this scope >./src/check.C: In member function âvoid _VALIDATION::ndb_check_file(FILE*, int, CHECK_TOKEN_FORMAT*, int, CHECK_CATEGORY*, int, int, const char*, FILE*)â: >./src/check.C:484: error: âBTreeObjâ was not declared in this scope >./src/check.C:484: error: â_SSIndexâ was not declared in this scope >./src/check.C:484: error: â_AsymIndexâ was not declared in this scope >./src/check.C:484: error: â_BiolUnitâ was not declared in this scope >./src/check.C:485: error: â_CHAINâ was not declared in this scope >./src/check.C:485: error: âchainâ was not declared in this scope >./src/check.C:486: error: âCifStringâ was not declared in this scope >./src/check.C:486: error: expected â;â before âstringâ >./src/check.C:487: error: âConnectFormatâ was not declared in this scope >./src/check.C:487: error: âdrugâ was not declared in this scope >./src/check.C:488: error: âDICFileObjâ was not declared in this scope >./src/check.C:488: error: âdictâ was not declared in this scope >./src/check.C:489: error: âISTableâ was not declared in this scope >./src/check.C:489: error: âTableâ was not declared in this scope >./src/check.C:489: error: âTable1â was not declared in this scope >./src/check.C:489: error: âTable2â was not declared in this scope >./src/check.C:490: error: âOne_Card_Info_Formatâ was not declared in this scope >./src/check.C:490: error: âpCardâ was not declared in this scope >./src/check.C:491: error: â_RESIDUEâ was not declared in this scope >./src/check.C:491: error: âresidueâ was not declared in this scope >./src/check.C:492: error: expected â;â before âidxâ >./src/check.C:493: error: âTblIndexObjâ was not declared in this scope >./src/check.C:493: error: expected â;â before â_UniIndexâ >./src/check.C:495: error: â_num_molâ was not declared in this scope >./src/check.C:496: error: â_input_formatâ was not declared in this scope >./src/check.C:496: error: âNDB_FILE_FORMAT_PDBâ was not declared in this scope >./src/check.C:497: error: âNDB_FILE_FORMAT_MMCIFâ was not declared in this scope >./src/check.C:499: error: â_cellâ 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: â_input_filenameâ was not declared in this scope >./src/check.C:535: error: â_Error_Checkâ was not declared in this scope >./src/check.C:538: error: â_input_filenameâ was not declared in this scope >./src/check.C:548: error: â_large_cellâ was not declared in this scope >./src/check.C:552: error: â_large_cellâ was not declared in this scope >./src/check.C:556: error: â_large_cellâ was not declared in this scope >./src/check.C:558: error: â_Error_Checkâ was not declared in this scope >./src/check.C:561: error: â_input_filenameâ was not declared in this scope >./src/check.C:562: error: â_Error_Checkâ was not declared in this scope >./src/check.C:566: error: â_error_messageâ was not declared in this scope >./src/check.C:568: error: â_input_formatâ was not declared in this scope >./src/check.C:568: error: âNDB_FILE_FORMAT_PDBâ was not declared in this scope >./src/check.C:569: error: âNDB_FILE_FORMAT_MMCIFâ was not declared in this scope >./src/check.C:570: error: â_file_statusâ was not declared in this scope >./src/check.C:570: error: âFILE_STATUS_MMCIF_PLUS_MOLâ was not declared in this scope >./src/check.C:571: error: â_moleculesâ was not declared in this scope >./src/check.C:571: error: â_rep_molâ was not declared in this scope >./src/check.C:571: error: â_CardInfoâ was not declared in this scope >./src/check.C:572: error: â_input_filenameâ was not declared in this scope >./src/check.C:572: error: âcheck_tokensâ was not declared in this scope >./src/check.C:575: error: â_CifObjâ was not declared in this scope >./src/check.C:575: error: â_StructureIdâ was not declared in this scope >./src/contact.C:148:22: error: BTreeObj.h: No such file or directory >./src/check.C:576: error: âis_empty_tableâ was not declared in this scope >./src/check.C:577: error: â_moleculesâ was not declared in this scope >./src/check.C:577: error: â_rep_molâ was not declared in this scope >./src/check.C:578: error: â_input_filenameâ was not declared in this scope >./src/check.C:578: error: â_Error_Checkâ was not declared in this scope >./src/check.C:578: error: âcheck_categorysâ 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: â_CifObjâ was not declared in this scope >./src/check.C:581: error: â_StructureIdâ 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: âis_empty_tableâ was not declared in this scope >./src/check.C:583: error: â_moleculesâ was not declared in this scope >./src/check.C:583: error: â_rep_molâ was not declared in this scope >./src/check.C:584: error: â_input_filenameâ was not declared in this scope >./src/check.C:584: error: â_Error_Checkâ was not declared in this scope >./src/check.C:584: error: âcheck_categorys1â was not declared in this scope >./src/check.C:588: error: â_num_molâ was not declared in this scope >./src/check.C:589: error: â_moleculesâ was not declared in this scope >./src/check.C:589: error: â_input_filenameâ was not declared in this scope >./src/check.C:589: error: â_Error_Checkâ was not declared in this scope >./src/check.C:589: error: âcheck_seqnum_redundancyâ was not declared in this scope >./src/check.C:592: error: â_input_formatâ was not declared in this scope >./src/check.C:592: error: âNDB_FILE_FORMAT_PDBâ was not declared in this scope >./src/check.C:593: error: âNDB_FILE_FORMAT_NDBâ was not declared in this scope >./src/check.C:595: error: âfind_card_idâ was not declared in this scope >./src/check.C:596: error: â_CardInfoâ was not declared in this scope >./src/check.C:598: error: â_Error_Checkâ was not declared in this scope >./src/check.C:599: error: â_input_filenameâ 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: â_input_filenameâ was not declared in this scopecry_util.h: No such file or directory > >./src/check.C:611: error: â_Error_Checkâ was not declared in this scope >./src/check.C:616: error: â_CifObjâ was not declared in this scope >./src/check.C:616: error: â_StructureIdâ was not declared in this scope >./src/check.C:617: error: âis_empty_tableâ was not declared in this scope >./src/check.C:621: error: âstringâ was not declared in this scope >./src/check.C:622: error: âis_a_standard_residueâ was not declared in this scope >./src/check.C:638: error: â_CifObjâ was not declared in this scope >./src/check.C:638: error: â_StructureIdâ was not declared in this scope >./src/check.C:639: error: âis_empty_tableâ was not declared in this scope >./src/check.C:654: error: âfind_card_idâ was not declared in this scope >./src/check.C:656: error: âstringâ was not declared in this scope >./src/check.C:659: error: â_CardInfoâ was not declared in this scope >./src/check.C:659: error: âNdbTokenâ was not declared in this scope >./src/check.C:712: error: â_CardInfoâ was not declared in this scope >./src/check.C:716: error: âprint_general_cardsâ was not declared in this scope >./src/check.C:720: error: â_CardInfoâ was not declared in this scope >./src/check.C:724: error: âstringâ was not declared in this scope >./src/check.C:727: error: âNdbTokenâ was not declared in this scope >./src/check.C:783: error: âprint_general_cardsâ was not declared in this scope >./src/check.C:795: error: âis_empty_tableâ was not declared in this scope >./src/check.C:799: error: âstringâ was not declared in this scope >./src/check.C:800: error: âstring1â was not declared in this scope >./src/check.C:801: error: âis_not_emptyâ 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 âostreamâ with no type >./include/symop.h:153: error: âostreamâ is neither function nor member function; cannot be declared friend >./include/symop.h:153: error: expected â;â before â&â token >./src/check.C:813: error: â_Error_Checkâ was not declared in this scope./include/symop.h:158: error: expected â)â before â&â token > >./src/check.C:818: error: â_experiment_typeâ was not declared in this scope >./src/check.C:818: error: âEXPERIMENT_TYPE_XRAYâ was not declared in this scope >./src/check.C:822: error: âis_empty_tableâ was not declared in this scope >./src/check.C:827: error: âstringâ was not declared in this scope >./src/check.C:828: error: âis_not_emptyâ was not declared in this scope >./src/check.C:841: error: â_experiment_typeâ was not declared in this scope >./src/check.C:841: error: âEXPERIMENT_TYPE_NMRâ was not declared in this scope >./src/check.C:844: error: âis_empty_tableâ was not declared in this scope >./src/check.C:853: error: âstringâ was not declared in this scope >./src/check.C:856: error: âis_not_emptyâ was not declared in this scope >./src/check.C:867: error: âis_empty_tableâ was not declared in this scope >./src/check.C:870: error: âstringâ was not declared in this scope >./src/check.C:871: error: âis_not_emptyâ was not declared in this scope >./src/check.C:872: error: â_num_molâ was not declared in this scope >./src/check.C:886: error: âis_empty_tableâ was not declared in this scope >./src/check.C:890: error: âstringâ was not declared in this scope >./src/check.C:891: error: âstring1â was not declared in this scope >./src/check.C:892: error: âis_not_emptyâ was not declared in this scope >./src/_validation.C: In member function âvoid _VALIDATION::Get_Stbiol(int)â: >./src/_validation.C:354: error: âCifStringâ was not declared in this scope >./src/_validation.C:354: error: expected â;â before âstringâ >./src/_validation.C:355: error: âReVarCifArrayâ was not declared in this scope >./src/_validation.C:355: error: âColumnNamesâ was not declared in this scope >./src/_validation.C:356: error: âISTableâ was not declared in this scope >./src/_validation.C:356: error: âTableâ was not declared in this scope >./src/_validation.C:357: error: âOne_Card_Info_Formatâ was not declared in this scope >./src/_validation.C:357: error: âpCardâ was not declared in this scope >./src/_validation.C:357: error: â_CardInfoâ was not declared in this scope >./src/_validation.C:357: error: âSTBIOL_TOKENâ was not declared in this scope >./src/_validation.C:360: error: â_CifObjâ was not declared in this scope >./src/_validation.C:360: error: â_StructureIdâ was not declared in this scope >./src/_validation.C:361: error: âis_empty_tableâ was not declared in this scope >./src/_validation.C:364: error: â_exist_pdb_chain_idâ was not declared in this scope >./src/check.C:918: error: âis_empty_tableâ was not declared in this scope >./src/_validation.C:366: error: â_exist_pdb_chain_idâ was not declared in this scope >./src/_validation.C:372: error: â_stbiolâ was not declared in this scope >./src/_validation.C:373: error: â_n_stbiolâ was not declared in this scope >./src/check.C:923: error: âstringâ was not declared in this scope >./src/check.C:924: error: âstring1â was not declared in this scope >./src/_validation.C:374: error: type â<type error>â argument given to âdeleteâ, expected pointer >./src/check.C:925: error: âstring2â was not declared in this scope >./src/_validation.C:376: error: â_n_stbiolâ was not declared in this scope >./src/check.C:926: error: âis_not_emptyâ was not declared in this scope >./src/_validation.C:377: error: â_stbiolâ was not declared in this scope >./src/_validation.C:377: error: expected type-specifier before â_STBIOLâ >./src/_validation.C:377: error: expected â;â before â_STBIOLâ >./src/_validation.C:380: error: expected type-specifier before â_STBIOLâ >./src/_validation.C:380: error: expected â;â before â_STBIOLâ >./src/_validation.C:388: error: âstrcpyâ was not declared in this scope >./src/_validation.C:394: error: âstringâ was not declared in this scope >./src/_validation.C:396: error: âstrcmpâ was not declared in this scope >./src/_validation.C:397: error: âatoiâ was not declared in this scope >./src/_validation.C:407: error: âatoiâ was not declared in this scope >./src/check.C:967: error: âis_empty_tableâ was not declared in this scope >./src/_validation.C:409: error: âatoiâ was not declared in this scope >./src/_validation.C:411: error: âatoiâ was not declared in this scope >./src/check.C:973: error: âstringâ was not declared in this scope >./src/_validation.C:413: error: âatoiâ was not declared in this scope >./src/_validation.C:415: error: âatoiâ was not declared in this scope >./src/_validation.C:418: error: type â<type error>â argument given to âdeleteâ, expected pointer >In file included from ./src/color_util.C:147: >/usr/include/rcsb/util.h:67: error: âCifFileâ was not declared in this scope >/usr/include/rcsb/util.h:67: error: âfobjâ was not declared in this scope >./src/_validation.C:421: error: âis_empty_tableâ was not declared in this scope >/usr/include/rcsb/util.h:67: error: expected primary-expression before âconstâ >/usr/include/rcsb/util.h:68: error: expected primary-expression before âconstâ >/usr/include/rcsb/util.h:68: error: expected primary-expression before âconstâ >/usr/include/rcsb/util.h:68: error: initializer expression list treated as compound expression >./src/check.C:993: error: âstringâ was not declared in this scope >/usr/include/rcsb/util.h:69: error: âCifFileâ was not declared in this scope./src/_validation.C:429: error: âstrcmpâ was not declared in this scope > >/usr/include/rcsb/util.h:69: error: âfobjâ was not declared in this scope >/usr/include/rcsb/util.h:69: error: expected primary-expression before âconstâ >/usr/include/rcsb/util.h:70: error: expected primary-expression before âconstâ >./src/_validation.C:431: error: âstringâ was not declared in this scope >/usr/include/rcsb/util.h:70: error: expected primary-expression before âconstâ >/usr/include/rcsb/util.h:71: error: expected primary-expression before âlongâ >/usr/include/rcsb/util.h:71: error: initializer expression list treated as compound expression >./src/_validation.C:436: error: âstrcpyâ was not declared in this scope >./src/check.C:1004: error: â_experiment_typeâ was not declared in this scope >./src/check.C:1004: error: âEXPERIMENT_TYPE_NMRâ was not declared in this scope >./src/check.C:1006: error: âis_empty_tableâ was not declared in this scope >./src/check.C:1010: error: âstring1â was not declared in this scope >./src/check.C:1011: error: âstring2â was not declared in this scope >./src/check.C:1013: error: âstringâ was not declared in this scope >./src/check.C:1022: error: â_Error_Checkâ was not declared in this scope >./src/check.C:1028: error: âis_empty_tableâ was not declared in this scope >./src/_validation.C: In member function âvoid _VALIDATION::Input_Stbiol()â: >./src/_validation.C:448: error: â_CHAINâ was not declared in this scope >./src/_validation.C:448: error: âchainâ was not declared in this scope >./src/_validation.C:449: error: âOne_Card_Info_Formatâ was not declared in this scope >./src/_validation.C:449: error: âpCardâ was not declared in this scope./src/check.C:1034: error: âstringâ was not declared in this scope > >./src/_validation.C:449: error: â_CardInfoâ was not declared in this scope >./src/_validation.C:449: error: âSTBIOL_TOKENâ was not declared in this scope >./src/check.C:1038: error: â_spell_checkâ was not declared in this scope >./src/_validation.C:456: error: â_stbiolâ was not declared in this scope >./src/_validation.C:457: error: â_n_stbiolâ was not declared in this scope >./src/check.C:1039: error: â_spell_checkâ was not declared in this scope >./src/_validation.C:458: error: type â<type error>â argument given to âdeleteâ, expected pointer >./src/check.C:1044: error: âstringâ was not declared in this scope >./src/_validation.C:460: error: â_n_stbiolâ was not declared in this scope >./src/_validation.C:461: error: â_stbiolâ was not declared in this scope >./src/_validation.C:461: error: expected type-specifier before â_STBIOLâ >./src/check.C:1048: error: â_spell_checkâ was not declared in this scope./src/_validation.C:461: error: expected â;â before â_STBIOLâ > >./src/check.C:1049: error: â_spell_checkâ was not declared in this scope >./src/_validation.C:466: error: expected type-specifier before â_STBIOLâ >./src/_validation.C:466: error: expected â;â before â_STBIOLâ./src/check.C:1057: error: âis_empty_tableâ was not declared in this scope > >./src/_validation.C:467: error: âatoiâ was not declared in this scope >./src/_validation.C:468: error: âstrcmpâ was not declared in this scope >./src/check.C:1062: error: âstringâ was not declared in this scope >./src/_validation.C:474: error: âstrcpyâ was not declared in this scope >./src/check.C:1066: error: â_spell_checkâ was not declared in this scope >./src/_validation.C:477: error: âstrcmpâ was not declared in this scope >./src/check.C:1067: error: â_spell_checkâ was not declared in this scope >./src/_validation.C:479: error: âstrcmpâ was not declared in this scope >./src/check.C:1075: error: âis_empty_tableâ was not declared in this scope >./src/check.C:1077: error: âstringâ was not declared in this scope./src/_validation.C:482: error: âstrcmpâ was not declared in this scope > >./src/_validation.C:485: error: âstrcmpâ was not declared in this scope >./src/_validation.C:488: error: âstrcmpâ was not declared in this scope >./src/check.C:1091: error: âis_empty_tableâ was not declared in this scope >./src/check.C:1092: error: â_experiment_typeâ was not declared in this scope >./src/check.C:1092: error: âEXPERIMENT_TYPE_XRAYâ was not declared in this scope >./src/_validation.C:498: error: â_num_molâ was not declared in this scope >./src/_validation.C:500: error: âATOMP_TOKENâ was not declared in this scope >./src/check.C:1096: error: â_UniIndexâ was not declared in this scope >./src/_validation.C:500: error: âATOMN_TOKENâ was not declared in this scope >./src/_validation.C:500: error: âATOMS_TOKENâ was not declared in this scope >./src/check.C:1098: error: âstringâ was not declared in this scope >./src/_validation.C:501: error: âHETAD_TOKENâ was not declared in this scope >./src/_validation.C:501: error: âHETAI_TOKENâ was not declared in this scope >./src/_validation.C:501: error: âHETIC_TOKENâ was not declared in this scope >./src/_validation.C:502: error: âHETAC_TOKENâ was not declared in this scope >./src/_validation.C:502: error: âHETAIN_TOKENâ was not declared in this scope >./src/_validation.C:502: error: âHETAS_TOKENâ was not declared in this scope >./src/check.C:1111: error: â_BiolIndexâ was not declared in this scope >./src/_validation.C:505: error: â_moleculesâ was not declared in this scope >./src/check.C:1115: error: âstringâ was not declared in this scope >./src/_validation.C:505: error: â_rep_molâ was not declared in this scope >./src/check.C:1117: error: âstring1â was not declared in this scope >./src/check.C:1119: error: âstring2â was not declared in this scope >./src/check.C:1124: error: âidxâ was not declared in this scope >./src/_validation.C: In member function âvoid _VALIDATION::Reorder_Stbiol()â: >./src/_validation.C:523: error: â_STBIOLâ was not declared in this scope >./src/_validation.C:523: error: âtmpâ was not declared in this scope >./src/_validation.C:525: error: â_stbiolâ was not declared in this scope >./src/_validation.C:526: error: expected type-specifier before â_STBIOLâ >./src/check.C:1151: error: âstringâ was not declared in this scope >./src/_validation.C:526: error: expected â;â before â_STBIOLâ >./src/check.C:1153: error: âstring1â was not declared in this scope >./src/_validation.C:527: error: â_n_stbiolâ was not declared in this scope >./src/check.C:1156: error: âidxâ was not declared in this scope >./src/_validation.C:533: error: â_n_stbiolâ was not declared in this scope./src/check.C:1159: error: âidx1â was not declared in this scope > >./src/_validation.C:535: error: expected type-specifier before â_STBIOLâ >./src/_validation.C:535: error: expected â;â before â_STBIOLâ >./src/check.C:1167: error: âpidxâ was not declared in this scope >./src/check.C:1168: error: â_cellâ was not declared in this scope >./src/_validation.C:540: error: âstrcpyâ was not declared in this scope >./src/check.C:1168: error: ârcsb_get_symmetry_operation_nameâ was not declared in this scope >./src/check.C:1169: error: âstring2â was not declared in this scope >./src/_validation.C:564: error: expected type-specifier before â_STBIOLâ >./src/_validation.C:564: error: expected â;â before â_STBIOLâ >./src/check.C:1204: error: âidxâ was not declared in this scope >./src/_validation.C:591: error: â_n_stbiolâ was not declared in this scope >./src/_validation.C:592: error: type â<type error>â argument given to âdeleteâ, expected pointer >./src/_validation.C: In member function âvoid _VALIDATION::Input_Link()â: >./src/_validation.C:599: error: â_num_molâ was not declared in this scope >./src/_validation.C:599: error: â_moleculesâ was not declared in this scope >./src/_validation.C:601: error: â_MOLECULEâ was not declared in this scope >./src/color_util.C: In function âint ndb_get_color_index(int, const char*, int, int)â: >./src/color_util.C:310: error: ândb_clean_stringâ was not declared in this scope >./src/_validation.C:601: error: âmolâ was not declared in this scope >./src/_validation.C:601: error: â_moleculesâ was not declared in this scope./src/color_util.C:311: error: ândb_set_string_to_lowerâ was not declared in this scope > >./src/_validation.C:603: error: âOne_Card_Info_Formatâ was not declared in this scope >./src/_validation.C:603: error: âpCardâ was not declared in this scope >./src/_validation.C:603: error: â_CardInfoâ was not declared in this scope >./src/_validation.C:603: error: âLINK_TOKENâ was not declared in this scope >./src/check.C:1257: error: â_UniIndexâ was not declared in this scope >./src/_validation.C:606: error: âatoiâ was not declared in this scope./src/color_util.C:320: error: âATOMP_TOKENâ was not declared in this scope > >./src/check.C:1261: error: âis_empty_tableâ was not declared in this scope >./src/check.C:1265: error: âstringâ was not declared in this scope >./src/_validation.C: In member function âvoid _VALIDATION::update_residues_nomenclature(int)â: >./src/_validation.C:622: error: â_CHAINâ was not declared in this scope./src/check.C:1272: error: â_Error_Checkâ was not declared in this scope > >./src/_validation.C:622: error: âchainâ was not declared in this scope >./src/_validation.C:623: error: â_num_molâ was not declared in this scope >./src/_validation.C:623: error: â_moleculesâ was not declared in this scope >./src/_validation.C:625: error: â_num_molâ was not declared in this scope./src/check.C:1282: error: âis_empty_tableâ was not declared in this scope > >./src/_validation.C:626: error: â_moleculesâ was not declared in this scope >./src/check.C:1286: error: âstringâ was not declared in this scope >./src/check.C:1287: error: âstring1â was not declared in this scope >./src/check.C:1288: error: âis_not_emptyâ was not declared in this scope >./src/_validation.C: In member function âvoid _VALIDATION::match_stbiol_with_molecules()â: >./src/_validation.C:639: error: â_STBIOLâ was not declared in this scope >./src/_validation.C:639: error: âtmpâ was not declared in this scope >./src/_validation.C:639: error: âtmp1â was not declared in this scope >./src/check.C:1298: error: âis_empty_tableâ was not declared in this scope./src/_validation.C:640: error: â_CHAINâ was not declared in this scope > >./src/_validation.C:640: error: âchainâ was not declared in this scope >./src/_validation.C:641: error: âOne_Card_Info_Formatâ was not declared in this scope >./src/check.C:1301: error: âstringâ was not declared in this scope >./src/_validation.C:641: error: âpCardâ was not declared in this scope >./src/check.C:1302: error: âis_not_emptyâ was not declared in this scope./src/_validation.C:643: error: â_num_molâ was not declared in this scope > >./src/_validation.C:643: error: â_moleculesâ was not declared in this scope >./src/_validation.C:645: error: â_moleculesâ was not declared in this scope >./src/_validation.C:645: error: â_rep_molâ was not declared in this scope >./src/_validation.C:647: error: â_n_stbiolâ was not declared in this scope >./src/check.C:1310: error: âis_empty_tableâ was not declared in this scope./src/_validation.C:648: error: â_stbiolâ was not declared in this scope > >./src/_validation.C:649: error: âstrcmpâ was not declared in this scope >./src/_validation.C:651: error: â_n_stbiolâ was not declared in this scope >./src/check.C:1315: error: âstringâ was not declared in this scope >./src/check.C:1315: error: âget_valueâ was not declared in this scope >./src/_validation.C:655: error: â_CardInfoâ was not declared in this scope >./src/_validation.C:655: error: âSEQIFO_TOKENâ was not declared in this scope >./src/check.C:1319: error: âisalphaâ was not declared in this scope >./src/check.C:1319: error: âislowerâ was not declared in this scope >./src/_validation.C:667: error: âNdbTokenâ was not declared in this scope >./src/_validation.C:672: error: âATOMN_TOKENâ was not declared in this scope >./src/check.C:1324: error: â_Error_Checkâ was not declared in this scope >./src/_validation.C:675: error: âATOMP_TOKENâ was not declared in this scope >./src/check.C:1331: error: âis_empty_tableâ was not declared in this scope >./src/check.C:1334: error: âstringâ was not declared in this scope >./src/_validation.C:687: error: â_stbiolâ was not declared in this scope >./src/check.C:1335: error: âis_not_emptyâ was not declared in this scope >./src/_validation.C:687: error: â_n_stbiolâ was not declared in this scope >./src/_validation.C:690: error: âstrcmpâ was not declared in this scope >./src/_validation.C:693: error: expected type-specifier before â_STBIOLâ >./src/_validation.C:693: error: expected â;â before â_STBIOLâ >./src/check.C:1352: error: âis_empty_tableâ was not declared in this scope >./src/_validation.C:704: error: âstrcpyâ was not declared in this scope >./src/_validation.C:708: error: expected type-specifier before â_STBIOLâ >./src/_validation.C:708: error: expected â;â before â_STBIOLâ >./src/check.C:1362: error: âstringâ was not declared in this scope >./src/_validation.C:712: error: type â<type error>â argument given to âdeleteâ, expected pointer./src/check.C:1364: error: âstrâ was not declared in this scope > >./src/_validation.C:714: error: expected type-specifier before â_STBIOLâ >./src/_validation.C:714: error: expected â;â before â_STBIOLâ >./src/_validation.C:738: error: expected type-specifier before â_STBIOLâ >./src/check.C:1376: error: âstrâ was not declared in this scope >./src/_validation.C:738: error: expected â;â before â_STBIOLâ >./src/check.C:1384: error: âis_empty_tableâ was not declared in this scope >./src/_validation.C:742: error: type â<type error>â argument given to âdeleteâ, expected pointer >./src/_validation.C:744: error: expected type-specifier before â_STBIOLâ >./src/_validation.C:744: error: expected â;â before â_STBIOLâ >./src/check.C:1389: error: âstringâ was not declared in this scope >./src/check.C:1389: error: âget_valueâ was not declared in this scope >./src/check.C:1394: error: âisdigitâ was not declared in this scope >./src/check.C:1397: error: â_Error_Checkâ was not declared in this scope >./src/check.C:1407: error: âisdigitâ was not declared in this scope >./src/check.C:1410: error: â_Error_Checkâ was not declared in this scope >./src/_validation.C:781: error: type â<type error>â argument given to âdeleteâ, expected pointer >./src/check.C:1419: error: âis_empty_tableâ was not declared in this scope >./src/check.C:1421: error: âstringâ was not declared in this scope >./src/check.C:1421: error: âget_valueâ was not declared in this scope >./src/_validation.C:796: error: â_num_molâ was not declared in this scope >./src/check.C:1426: error: âstring1â was not declared in this scope >./src/check.C:1428: error: â_Error_Checkâ was not declared in this scope >./src/_validation.C:809: error: â_CardInfoâ was not declared in this scope >./src/_validation.C:809: error: âSEQIFO_TOKENâ was not declared in this scope >./src/_validation.C:821: error: âNdbTokenâ was not declared in this scope >./src/check.C:1437: error: âstring1â was not declared in this scope >./src/_validation.C:826: error: âATOMN_TOKENâ was not declared in this scope >./src/check.C:1440: error: â_Error_Checkâ was not declared in this scope >./src/_validation.C:829: error: âATOMP_TOKENâ was not declared in this scope >./src/check.C:1444: error: â_Error_Checkâ was not declared in this scope >./src/check.C:1454: error: âis_empty_tableâ was not declared in this scope >./src/check.C:1455: error: â_Error_Checkâ was not declared in this scope >./src/check.C:1456: error: â_input_filenameâ was not declared in this scope >./src/check.C:1460: error: â_input_filenameâ was not declared in this scope >./src/check.C:1461: error: â_Error_Checkâ was not declared in this scope >./src/check.C:1463: error: âstringâ was not declared in this scope >./src/check.C:1465: error: â_Error_Checkâ was not declared in this scope >./src/check.C:1466: error: â_input_filenameâ was not declared in this scope >./src/check.C:1471: error: âis_empty_tableâ was not declared in this scope >./src/check.C:1472: error: â_Error_Checkâ was not declared in this scope >./src/check.C:1473: error: â_input_filenameâ was not declared in this scope >./src/check.C:1477: error: â_input_filenameâ was not declared in this scope >./src/check.C:1478: error: â_Error_Checkâ was not declared in this scope >./src/check.C:1480: error: âstringâ was not declared in this scope >./src/check.C:1482: error: â_Error_Checkâ was not declared in this scope >./src/check.C:1483: error: â_input_filenameâ was not declared in this scope >./src/check.C:1488: error: âis_empty_tableâ was not declared in this scope >./src/check.C:1489: error: â_Error_Checkâ was not declared in this scope./src/_validation.C: In member function âvoid _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*)â: >./src/_validation.C:852: error: âstrcmpâ was not declared in this scope > >./src/check.C:1490: error: â_input_filenameâ was not declared in this scope >./src/check.C:1495: error: â_Error_Checkâ was not declared in this scope >./src/check.C:1497: error: â_input_filenameâ was not declared in this scope >./src/check.C:1501: error: âres_highâ was not declared in this scope >./src/check.C:1501: error: âget_valueâ was not declared in this scope >./src/check.C:1502: error: âres_lowâ was not declared in this scope >./src/check.C:1506: error: â_Error_Checkâ was not declared in this scope >./src/check.C:1508: error: â_input_filenameâ was not declared in this scope >./src/check.C:1509: error: âres_lowâ was not declared in this scope >./src/check.C:1510: error: â_Error_Checkâ was not declared in this scope >./src/check.C:1512: error: â_input_filenameâ was not declared in this scope >./src/check.C:1514: error: âget_dateâ was not declared in this scope >./src/check.C:1517: error: âres_highâ was not declared in this scope >./src/check.C:1517: error: âget_valueâ was not declared in this scope >./src/check.C:1518: error: âres_lowâ was not declared in this scope >./src/check.C:1521: error: â_input_filenameâ was not declared in this scope >./src/_validation.C:879: error: âstrcpyâ was not declared in this scope >./src/check.C:1523: error: â_date_errorâ was not declared in this scope >./src/check.C:1524: error: â_Error_Checkâ was not declared in this scope >make[1]: *** [obj/color_util.o] Error 1 >./src/_validation.C:891: error: âstrlenâ was not declared in this scope >./src/check.C:1528: error: â_input_filenameâ was not declared in this scope >./src/check.C:1530: error: â_date_errorâ was not declared in this scope >./src/check.C:1531: error: â_Error_Checkâ was not declared in this scope >./src/check.C:1535: error: â_input_filenameâ was not declared in this scope >./src/check.C:1537: error: â_date_errorâ was not declared in this scope >./src/check.C:1538: error: â_Error_Checkâ was not declared in this scope >./src/check.C:1546: error: âis_empty_tableâ was not declared in this scope >./src/check.C:1546: error: âget_pdb_idâ was not declared in this scope >./src/check.C:1549: error: âis_empty_tableâ was not declared in this scope >./src/check.C:1552: error: âres_lowâ was not declared in this scope >./src/check.C:1552: error: âget_valueâ was not declared in this scope >./src/check.C:1556: error: â_Error_Checkâ was not declared in this scope >./src/check.C:1563: error: âis_empty_tableâ was not declared in this scope >./src/check.C:1565: error: âres_highâ was not declared in this scope >./src/check.C:1565: error: âget_valueâ was not declared in this scope >./src/check.C:1573: error: âres_lowâ was not declared in this scope >./src/check.C:1577: error: â_Error_Checkâ was not declared in this scope >./src/_validation.C: In member function âvoid _VALIDATION::Insert_a_Mismat(const char*, int, int, const char*, int, int)â: >./src/_validation.C:905: error: âstrcmpâ was not declared in this scope >./src/check.C:1585: error: âis_empty_tableâ was not declared in this scope >./src/check.C:1587: error: âres_highâ was not declared in this scope >./src/check.C:1587: error: âget_valueâ was not declared in this scope >./src/check.C:1592: error: â_date_errorâ was not declared in this scope >./src/check.C:1593: error: â_Error_Checkâ was not declared in this scope >./src/check.C:1599: error: âis_empty_tableâ was not declared in this scope >./src/check.C:1599: error: â_cellâ was not declared in this scope >./src/_validation.C:919: error: âstrcpyâ was not declared in this scope >./src/check.C:1611: error: âres_highâ was not declared in this scope >./src/check.C:1611: error: âget_valueâ was not declared in this scope >./src/_validation.C: In member function âvoid _VALIDATION::Insert_a_Bspair(const char*, const char*, int, int, const char*, const char*, int, int, const char*, const char*)â: >./src/_validation.C:935: error: âstrcmpâ was not declared in this scope >./src/_validation.C:955: error: âstrcpyâ was not declared in this scope >./src/check.C:1680: error: â_Error_Checkâ was not declared in this scope >./src/check.C:1689: error: âis_empty_tableâ was not declared in this scope >In file included from ./src/atom.C:150: >./include/xtal.h:166: error: ISO C++ forbids declaration of âNDBCELLCONSTâ with no type >./include/xtal.h:166: error: expected â,â or â...â before â*â token >./include/xtal.h:167: error: âCOORDâ has not been declared >./src/check.C:1699: error: âres_lowâ was not declared in this scope >./include/xtal.h:167: error: âCOORDâ has not been declared >./src/check.C:1699: error: âget_valueâ was not declared in this scope >./src/check.C:1701: error: âres_highâ was not declared in this scope >./src/check.C:1717: error: âbuffâ was not declared in this scope >./src/check.C:1718: error: âCompareNoCaseâ was not declared in this scope >./src/check.C:1719: error: âstringâ was not declared in this scope >./src/check.C:1720: error: âstring1â was not declared in this scope >./src/check.C:1725: error: â_Error_Checkâ was not declared in this scope >./src/_validation.C: In member function âvoid _VALIDATION::generate_symmetry_strands(int)â: >./src/_validation.C:972: error: â_num_molâ was not declared in this scope >./src/_validation.C:972: error: â_moleculesâ was not declared in this scope >./src/_validation.C:974: error: â_n_stbiolâ was not declared in this scope >./src/check.C:1730: error: â_Error_Checkâ was not declared in this scope >./src/_validation.C:975: error: â_stbiolâ was not declared in this scope >./src/_validation.C:975: error: âNDB_BASE_SYMMETRYâ was not declared in this scope >./src/_validation.C:975: error: âstrcmpâ was not declared in this scope >./src/check.C:1737: error: â_Error_Checkâ was not declared in this scope >./src/_validation.C:977: error: â_n_stbiolâ was not declared in this scope >./src/_validation.C:979: error: â_moleculesâ was not declared in this scope >./src/_validation.C:979: error: â_cellâ was not declared in this scope >./src/check.C:1742: error: â_Error_Checkâ was not declared in this scope >./src/_validation.C:979: error: âNDB_TRANS_ORTHO_TO_FRACâ was not declared in this scope >./src/_validation.C:980: error: â_n_stbiolâ was not declared in this scope >./src/_validation.C:981: error: â_stbiolâ was not declared in this scope >./src/_validation.C:982: error: â_stbiolâ was not declared in this scope >./src/check.C:1751: error: âbuffâ was not declared in this scope >./src/_validation.C:982: error: âNDB_BASE_SYMMETRYâ was not declared in this scope >./src/_validation.C:982: error: âstrcmpâ was not declared in this scope >./src/check.C:1752: error: âCompareNoCaseâ was not declared in this scope >./src/_validation.C:983: error: âatoiâ was not declared in this scope >./src/check.C:1753: error: âstringâ was not declared in this scope >./src/_validation.C:985: error: âstrlenâ was not declared in this scope >./src/check.C:1758: error: â_Error_Checkâ was not declared in this scope >./src/check.C:1765: error: â_Error_Checkâ was not declared in this scope >./src/check.C:1769: error: â_Error_Checkâ was not declared in this scope >./src/_validation.C:1002: error: âstrcpyâ was not declared in this scope >./src/_validation.C:1005: error: âNDB_TRANS_FRAC_TO_ORTHOâ was not declared in this scope >./src/check.C:1778: error: âbuffâ was not declared in this scope >./src/check.C:1779: error: âCompareNoCaseâ was not declared in this scope >./src/check.C:1780: error: âstringâ was not declared in this scope >./src/check.C:1785: error: â_Error_Checkâ was not declared in this scope >./src/_validation.C: At global scope: >./src/_validation.C:1010: error: â_ATOMâ has not been declared >./src/_validation.C:1010: error: â_ATOMâ has not been declared >./src/check.C:1791: error: â_Error_Checkâ was not declared in this scope >./src/check.C:1796: error: â_Error_Checkâ was not declared in this scope >./src/check.C:1808: error: âis_empty_tableâ was not declared in this scope >./src/check.C:1808: error: â_num_molâ was not declared in this scope >./src/check.C:1814: error: âres_highâ was not declared in this scope >./src/check.C:1814: error: âget_valueâ was not declared in this scope >./src/check.C:1815: error: âres_lowâ was not declared in this scope >./src/check.C:1816: error: â_moleculesâ was not declared in this scope >./src/check.C:1816: error: â_rep_molâ was not declared in this scope >./src/check.C:1819: error: âATOMP_TOKENâ was not declared in this scope >./src/_validation.C: In member function âvoid _VALIDATION::insert_bond(const char*, const char*, int, const char*, const char*, const char*, double, double, double, int, int*, int*)â: >./src/_validation.C:1024: error: âstrcpyâ was not declared in this scope >./src/check.C:1820: error: âATOMN_TOKENâ was not declared in this scope >./src/check.C:1822: error: â_Error_Checkâ was not declared in this scope >./src/check.C:1832: error: âis_empty_tableâ was not declared in this scope >./src/_validation.C:1033: error: âstruct _BONDâ has no member named âfstâ >./src/check.C:1837: error: âres_highâ was not declared in this scope >./src/check.C:1837: error: âget_valueâ was not declared in this scope >./src/_validation.C:1034: error: âstruct _BONDâ has no member named âsndâ >./src/_validation.C:1037: error: âCifStringâ was not declared in this scope >./src/_validation.C:1037: error: expected â;â before âindexâ >./src/_validation.C:1038: error: â_bondResIndexâ was not declared in this scope >./src/_validation.C:1038: error: âindexâ was not declared in this scope >./src/check.C:1844: error: â_Error_Checkâ was not declared in this scope >./src/_validation.C:1039: error: âindexâ was not declared in this scope >./src/check.C:1852: error: âis_empty_tableâ was not declared in this scope >./src/_validation.C:1040: error: â_bondComIndexâ was not declared in this scope >./src/_validation.C:1042: error: â_bondNamIndexâ was not declared in this scope >./src/check.C:1858: error: âis_empty_tableâ was not declared in this scope >./src/check.C:1869: error: âres_highâ was not declared in this scope >./src/check.C:1869: error: âget_valueâ was not declared in this scope >./src/check.C:1870: error: âres_lowâ was not declared in this scope >./src/check.C:1872: error: â_Error_Checkâ was not declared in this scope >./src/check.C:1877: error: âstringâ was not declared in this scope >./src/check.C:1881: error: â_Error_Checkâ was not declared in this scope >./src/check.C:1887: error: â_Error_Checkâ was not declared in this scope >./src/_validation.C: At global scope: >./src/_validation.C:1047: error: â_ATOMâ has not been declared >./src/check.C:1893: error: âres_highâ was not declared in this scope >./src/_validation.C:1047: error: â_ATOMâ has not been declared >./src/check.C:1893: error: âget_valueâ was not declared in this scope >./src/_validation.C:1048: error: â_ATOMâ has not been declared >./src/check.C:1896: error: âisalphaâ was not declared in this scope >./src/check.C:1899: error: â_Error_Checkâ was not declared in this scope >./src/check.C:1907: error: âisalphaâ was not declared in this scope >./src/check.C:1910: error: â_Error_Checkâ was not declared in this scope >./src/check.C:1919: error: âis_empty_tableâ was not declared in this scope >./src/_validation.C: In member function âvoid _VALIDATION::insert_angle(const char*, const char*, int, const char*, const char*, const char*, double, double, double, int, int*, int*, int*)â: >./src/_validation.C:1062: error: âstrcpyâ was not declared in this scope >./src/check.C:1929: error: âres_highâ was not declared in this scope >./src/check.C:1929: error: âget_valueâ was not declared in this scope >./src/check.C:1930: error: âres_lowâ was not declared in this scope >./src/check.C:1932: error: â_Error_Checkâ was not declared in this scope >./src/_validation.C:1071: error: âstruct _BONDâ has no member named âfstâ >./src/_validation.C:1072: error: âstruct _BONDâ has no member named âsndâ >./src/check.C:1937: error: âstringâ was not declared in this scope >./src/_validation.C:1073: error: âstruct _BONDâ has no member named âtrdâ >./src/check.C:1941: error: â_Error_Checkâ was not declared in this scope >./src/_validation.C:1076: error: âCifStringâ was not declared in this scope >./src/_validation.C:1076: error: expected â;â before âindexâ >./src/_validation.C:1077: error: â_angleResIndexâ was not declared in this scope >./src/_validation.C:1077: error: âindexâ was not declared in this scope >./src/check.C:1947: error: â_Error_Checkâ was not declared in this scope >./src/_validation.C:1078: error: âindexâ was not declared in this scope >./src/_validation.C:1079: error: â_angleComIndexâ was not declared in this scope >./src/_validation.C:1081: error: â_angleNamIndexâ was not declared in this scope >./src/check.C:1953: error: âres_highâ was not declared in this scope >./src/check.C:1953: error: âget_valueâ was not declared in this scope >./src/check.C:1956: error: âisalphaâ was not declared in this scope >./src/check.C:1959: error: â_Error_Checkâ was not declared in this scope >./src/check.C:1968: error: âis_empty_tableâ was not declared in this scope >./src/check.C:1973: error: âres_highâ was not declared in this scope >./src/check.C:1973: error: âget_valueâ was not declared in this scope >./src/check.C:1974: error: âres_lowâ was not declared in this scope >./src/check.C:1978: error: â_Error_Checkâ was not declared in this scope >./src/check.C:1982: error: â_Error_Checkâ was not declared in this scope >./src/check.C:1988: error: âis_empty_tableâ was not declared in this scope >./src/check.C:1993: error: â_Error_Checkâ was not declared in this scope >./src/check.C:1996: error: âres_highâ was not declared in this scope >./src/check.C:1996: error: âget_valueâ was not declared in this scope >./src/check.C:1999: error: â_Error_Checkâ was not declared in this scope >./src/check.C:2006: error: âis_empty_tableâ was not declared in this scope >./src/check.C:2016: error: âstringâ was not declared in this scope >./src/check.C:2028: error: â_Error_Checkâ was not declared in this scope >./src/check.C:2036: error: âres_lowâ was not declared in this scope >./src/check.C:2036: error: âget_valueâ was not declared in this scope >./src/check.C:2039: error: â_Error_Checkâ was not declared in this scope >./src/check.C:2043: error: âres_lowâ was not declared in this scope >./src/check.C:2043: error: âget_valueâ was not declared in this scope >./src/check.C:2044: error: âstring1â was not declared in this scope >./src/check.C:2045: error: âstring2â was not declared in this scope >./src/check.C:2061: error: âroot_dirâ was not declared in this scope >./src/check.C:2063: error: âis_empty_tableâ was not declared in this scope >./src/check.C:2072: error: âstringâ was not declared in this scope >./src/check.C:2073: error: âstring1â was not declared in this scope >./src/check.C:2074: error: âstring2â was not declared in this scopemake[1]: *** [obj/gridcell.o] Error 1 > >./src/check.C:2106: error: â_Error_Checkâ was not declared in this scope >./src/_validation.C: At global scope: >./src/_validation.C:1086: error: â_ATOMâ has not been declared >./src/check.C:2117: error: âstringâ was not declared in this scope >./src/_validation.C:1086: error: â_ATOMâ has not been declared >./src/check.C:2117: error: âget_valueâ was not declared in this scope >./src/_validation.C:1086: error: â_ATOMâ has not been declared >./src/check.C:2118: error: âstring1â was not declared in this scope >./src/_validation.C:1086: error: â_ATOMâ has not been declared >./src/check.C:2119: error: âstring2â was not declared in this scope >make[1]: *** [obj/align_standard.o] Error 1 >./src/check.C:2140: error: âfind_drugâ was not declared in this scope >./src/check.C:2143: error: âget_oneletter_codeâ was not declared in this scope >./src/_validation.C: In member function âvoid _VALIDATION::insert_torsion(const char*, const char*, int, const char*, const char*, const char*, double, int, int*, int*, int*, int*)â: >./src/_validation.C:1100: error: âstrcpyâ was not declared in this scope >./src/check.C:2152: error: ândb_set_string_to_upperâ was not declared in this scope >./src/check.C:2162: error: ândb_clean_stringâ was not declared in this scope >./src/_validation.C:1107: error: âstruct _TORSIONâ has no member named âfstâ >./src/_validation.C:1108: error: âstruct _TORSIONâ has no member named âsndâ >./src/_validation.C:1109: error: âstruct _TORSIONâ has no member named âtrdâ >./src/_validation.C:1110: error: âstruct _TORSIONâ has no member named âfthâ >./src/_validation.C:1113: error: âCifStringâ was not declared in this scope >./src/_validation.C:1113: error: expected â;â before âindexâ >./src/_validation.C:1114: error: â_torsionIndexâ was not declared in this scope >./src/_validation.C:1114: error: âindexâ was not declared in this scope >./src/check.C:2180: error: â_Error_Checkâ was not declared in this scope >./src/check.C:2188: error: â_Error_Checkâ was not declared in this scope >./src/check.C:2193: error: â_Error_Checkâ was not declared in this scope >./src/check.C:2202: error: âis_empty_tableâ was not declared in this scope >./src/check.C:2205: error: âstringâ was not declared in this scope >./src/check.C:2206: error: âstring1â was not declared in this scope >./src/check.C:2224: error: â_experiment_typeâ was not declared in this scope >./src/check.C:2224: error: âEXPERIMENT_TYPE_NMRâ was not declared in this scope >./src/check.C:2225: error: âEXPERIMENT_TYPE_MODELâ was not declared in this scope >./src/check.C:2233: error: expected type-specifier before âDICFileObjâ./src/_validation.C: In member function âvoid _VALIDATION::insert_torsion_pair(const char*, const char*, int, const char*, double, double, int)â: >./src/_validation.C:1133: error: âstrcpyâ was not declared in this scope > >./src/check.C:2233: error: expected â;â before âDICFileObjâ >./src/check.C:2236: error: â_Error_Checkâ was not declared in this scope >./src/check.C:2236: error: â_date_errorâ was not declared in this scope >./src/check.C:2236: error: âDictionaryDataCheckingâ cannot be used as a function >./src/check.C:2237: error: type â<type error>â argument given to âdeleteâ, expected pointer >./src/check.C:2243: error: âstringâ was not declared in this scope >./src/check.C:2244: error: âstring1â was not declared in this scope >./src/check.C:2245: error: âstring2â was not declared in this scope >./src/check.C:2246: error: âbuffâ was not declared in this scope >./src/check.C:2247: error: âres_highâ was not declared in this scope >./src/check.C:2248: error: â_num_molâ was not declared in this scope >./src/check.C:2249: error: â_moleculesâ was not declared in this scope >./src/check.C:2250: error: â_moleculesâ was not declared in this scope >./src/check.C:2256: error: â_experiment_typeâ was not declared in this scope >./src/check.C:2256: error: âEXPERIMENT_TYPE_NMRâ was not declared in this scope >./src/check.C:2269: error: â_Error_Checkâ was not declared in this scope >./src/check.C:2273: error: â_Error_Checkâ was not declared in this scope >./src/check.C:2277: error: â_Error_Checkâ was not declared in this scope >./src/check.C:2281: error: â_Error_Checkâ was not declared in this scope >./src/check.C:2285: error: â_Error_Checkâ was not declared in this scope >In file included from ./src/datacheck.C:7: >./include/datacheck.h:7: warning: âDictionaryDataCheckingâ initialized and declared âexternâ >./include/datacheck.h:7: error: âCifFileObjâ was not declared in this scope >./include/datacheck.h:7: error: âinâ was not declared in this scope >./include/datacheck.h:7: error: âDICFileObjâ was not declared in this scope >./include/datacheck.h:7: error: ârefâ was not declared in this scope >./include/datacheck.h:7: error: expected primary-expression before â*â token >./include/datacheck.h:7: error: âfpâ was not declared in this scope >./include/datacheck.h:8: error: expected primary-expression before âconstâ >./include/datacheck.h:8: error: expected primary-expression before âintâ >./include/datacheck.h:8: error: âCifStringâ was not declared in this scope >./src/check.C: At global scope: >./src/check.C:2289: error: variable or field âcheck_tokensâ declared void >./src/check.C:2289: error: â_MOLECULEâ was not declared in this scope >./src/check.C:2289: error: âmolâ was not declared in this scope >./src/check.C:2289: error: âCards_Info_Formatâ was not declared in this scope >./src/check.C:2289: error: âCardInfoâ was not declared in this scope >./src/check.C:2290: error: expected primary-expression before âconstâ >./src/check.C:2290: error: expected primary-expression before â*â token >./src/check.C:2291: error: expected primary-expression before âconstâ >./src/check.C:2291: error: expected primary-expression before âconstâ >./src/check.C:2291: error: expected primary-expression before â*â token >./src/check.C:2291: error: âfpâ was not declared in this scope >./src/check.C:200: warning: âint get_wavelength_list(const char*)â declared âstaticâ but never defined >./src/check.C:201: warning: âint check_taxonomy(const char*)â declared âstaticâ but never defined >./src/check.C:202: warning: âchar* get_word1(char*, char*)â declared âstaticâ but never defined >./src/_validation.C: At global scope: >./src/_validation.C:1256: error: variable or field âget_link_recordâ declared void >./src/_validation.C:1256: error: âISTableâ was not declared in this scope >./src/_validation.C:1256: error: âTableâ was not declared in this scope >./src/_validation.C:1256: error: expected primary-expression before âconstâ >./src/_validation.C:146: warning: âint find_symmetry_related_chain(int, int**, int, int)â declared âstaticâ but never defined >./src/_validation.C:148: warning: âint find_symmetry_related_chains(int, int**, int, char*)â declared âstaticâ but never defined >./src/_validation.C:150: warning: âint find_asymmetric_chains(int, int**, int)â declared âstaticâ but never defined >./include/datacheck.h:8: error: âdate_errorâ was not declared in this scope >./include/datacheck.h:8: error: initializer expression list treated as compound expression >./src/datacheck.C:15: error: âCifFileObjâ was not declared in this scope >./src/datacheck.C:15: error: âinâ was not declared in this scope >./src/datacheck.C:15: error: âDICFileObjâ was not declared in this scope >./src/datacheck.C:15: error: ârefâ was not declared in this scope >./src/datacheck.C:15: error: âofstreamâ was not declared in this scope >./src/datacheck.C:15: error: âlogâ was not declared in this scope >./src/datacheck.C:15: error: expected primary-expression before âconstâ >./src/datacheck.C:16: error: expected primary-expression before âintâ >./src/datacheck.C:16: error: âCifStringâ was not declared in this scope >./src/datacheck.C:16: error: âdate_errorâ 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 âConvertEscapedStringâ declared void >./src/datacheck.C:21: error: âCifStringâ was not declared in this scope >./src/datacheck.C:21: error: âinStringâ was not declared in this scope >./src/datacheck.C:21: error: âCifStringâ was not declared in this scope >./src/datacheck.C:21: error: âoutStringâ was not declared in this scope >./src/datacheck.C:24: error: redefinition of âint DictionaryDataCheckingâ >./include/datacheck.h:7: error: âint DictionaryDataCheckingâ previously defined here >./src/datacheck.C:24: error: âCifFileObjâ was not declared in this scope >./src/datacheck.C:24: error: âinâ was not declared in this scope >./src/datacheck.C:24: error: âDICFileObjâ was not declared in this scope >./src/datacheck.C:24: error: ârefâ was not declared in this scope >./src/datacheck.C:24: error: expected primary-expression before â*â token >./src/datacheck.C:24: error: âfpâ was not declared in this scope >./src/datacheck.C:24: error: expected primary-expression before âconstâ >./src/datacheck.C:25: error: expected primary-expression before âintâ >./src/datacheck.C:25: error: âCifStringâ was not declared in this scope >./src/datacheck.C:25: error: âdate_errorâ was not declared in this scope >./src/datacheck.C:15: warning: âItemsCheckingâ defined but not used >./src/datacheck.C:17: warning: âvoid GetKeywordFromItemName(char*, const char*)â declared âstaticâ but never defined >./src/datacheck.C:22: warning: âint is_wrong_date(const char*)â declared âstaticâ 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 âvoid _plot::set_x_axis_title(const char*)â: >./include/plot.h:199: error: âstrcpyâ was not declared in this scope >./include/plot.h: In member function âvoid _plot::set_y_axis_title(const char*)â: >./include/plot.h:200: error: âstrcpyâ was not declared in this scope >./include/plot.h: In member function âvoid _plot::set_picture_title(const char*)â: >./include/plot.h:201: error: âstrcpyâ 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: âMxStrLenâ was not declared in this scope >In file included from ./src/contact.C:145: >./include/_validation.h:207: error: ISO C++ forbids declaration of â_RESIDUEâ with no type >./include/_validation.h:207: error: expected â;â before â*â token >./include/_validation.h:213: error: âCOORDâ does not name a type >./include/_validation.h:214: error: âCOORDâ does not name a type >./include/_validation.h:215: error: âCOORDâ does not name a type >./include/_validation.h:216: error: âCOORDâ does not name a type >./include/_validation.h:217: error: âCOORDâ does not name a type >./include/_validation.h:218: error: âCOORDâ does not name a type >./include/_validation.h:232: error: ISO C++ forbids declaration of â_ATOMâ with no type >./include/_validation.h:232: error: expected â;â before â*â token >./include/_validation.h:233: error: ISO C++ forbids declaration of â_ATOMâ with no type >./include/_validation.h:233: error: expected â;â before â*â token >./include/_validation.h:234: error: ISO C++ forbids declaration of â_ATOMâ with no type >./include/_validation.h:234: error: expected â;â before â*â token >./include/_validation.h:266: error: ISO C++ forbids declaration of â_ATOMâ with no type >./include/_validation.h:266: error: expected â;â before â*â token >./include/_validation.h:267: error: ISO C++ forbids declaration of â_ATOMâ with no type >./include/_validation.h:267: error: expected â;â before â*â token >./include/_validation.h:268: error: ISO C++ forbids declaration of â_ATOMâ with no type >./include/_validation.h:268: error: expected â;â before â*â token >./include/_validation.h:269: error: ISO C++ forbids declaration of â_ATOMâ with no type >./include/_validation.h:269: error: expected â;â before â*â token >./include/_validation.h:305: error: âCifStringâ does not name a type >./include/_validation.h:315: error: âCifStringâ does not name a type >./include/_validation.h:327: error: âCOORDâ does not name a type >./include/_validation.h:328: error: âCOORDâ does not name a type >./include/_validation.h:329: error: âCOORDâ does not name a type >./include/_validation.h:339: error: âCOORDâ does not name a type >./include/_validation.h:344: error: ISO C++ forbids declaration of â_ATOMâ with no type >./include/_validation.h:344: error: expected â;â before â*â token >./include/_validation.h:348: error: expected class-name before â{â token >./include/_validation.h:377: error: â_ATOMâ has not been declared >./include/_validation.h:377: error: â_ATOMâ has not been declared >./include/_validation.h:380: error: â_ATOMâ has not been declared >./include/_validation.h:380: error: â_ATOMâ has not been declared >./include/_validation.h:380: error: â_ATOMâ has not been declared >./include/_validation.h:382: error: â_ATOMâ has not been declared >./include/_validation.h:382: error: â_ATOMâ has not been declared >./include/_validation.h:382: error: â_ATOMâ has not been declared >./include/_validation.h:382: error: â_ATOMâ has not been declared >./include/_validation.h:398: error: âCifStringâ has not been declared >./include/_validation.h:421: error: â_RESIDUEâ has not been declared >./include/_validation.h:422: error: â_RESIDUEâ has not been declared >./include/_validation.h:422: error: â_RESIDUEâ has not been declared >./include/_validation.h:423: error: â_ATOMâ has not been declared >./include/_validation.h:423: error: â_ATOMâ has not been declared >./include/_validation.h:423: error: â_ATOMâ has not been declared >./include/_validation.h:423: error: â_ATOMâ has not been declared >./include/_validation.h:426: error: âCifStringâ has not been declared >./include/_validation.h:426: error: âCifStringâ has not been declared >./include/_validation.h:427: error: âCifStringâ has not been declared >./include/_validation.h:433: error: â_MOLECULEâ has not been declared >./include/_validation.h:434: error: â_CHAINâ has not been declared >./include/_validation.h:434: error: âCOORDâ has not been declared >./include/_validation.h:434: error: â_RESIDUEâ has not been declared >./include/_validation.h:435: error: â_CHAINâ has not been declared >./include/_validation.h:436: error: â_ATOMâ has not been declared >./include/_validation.h:436: error: â_ATOMâ has not been declared >./include/_validation.h:437: error: â_CHAINâ has not been declared >./include/_validation.h:438: error: âCOORDâ has not been declared >./include/_validation.h:438: error: âCOORDâ has not been declared >./include/_validation.h:444: error: âISTableâ has not been declared >./include/_validation.h:492: error: âTblIndexObjâ does not name a type >./include/_validation.h:493: error: âTblIndexObjâ does not name a type >./include/_validation.h:494: error: âTblIndexObjâ does not name a type >./include/_validation.h:495: error: âTblIndexObjâ does not name a type >./include/_validation.h:496: error: âTblIndexObjâ does not name a type >./include/_validation.h:497: error: âTblIndexObjâ does not name a type >./include/_validation.h:498: error: âTblIndexObjâ does not name a type >./include/_validation.h:500: error: âCifStringâ does not name a type >./include/_validation.h:501: error: âCifStringâ does not name a type >./include/_validation.h:502: error: âCifStringâ does not name a type >./include/_validation.h:507: warning: âget_residue_indexâ initialized and declared âexternâ >./include/_validation.h:507: error: â_MOLECULEâ was not declared in this scope >./include/_validation.h:507: error: âmolâ was not declared in this scope >./include/_validation.h:507: error: âISTableâ was not declared in this scope >./include/_validation.h:507: error: âTableâ was not declared in this scope >./include/_validation.h:507: error: expected primary-expression before âconstâ >./include/_validation.h:508: error: expected primary-expression before âconstâ >./include/_validation.h:508: error: expected primary-expression before âconstâ >./include/_validation.h:508: error: expected primary-expression before âconstâ >./include/_validation.h:509: error: expected primary-expression before âconstâ >./include/_validation.h:509: error: expected primary-expression before âconstâ >./include/_validation.h:509: error: expected primary-expression before âconstâ >./include/_validation.h:510: error: expected primary-expression before âconstâ >./include/_validation.h:510: error: expected primary-expression before âintâ >./include/_validation.h:510: error: expected primary-expression before âintâ >./include/_validation.h:510: error: âCifStringâ was not declared in this scope >./include/_validation.h:510: error: ânameâ 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 âostreamâ with no type >./include/symop.h:153: error: âostreamâ is neither function nor member function; cannot be declared friend >./include/symop.h:153: error: expected â;â before â&â token >./include/symop.h:158: error: expected â)â before â&â token >In file included from ./src/contact.C:149: >/usr/include/rcsb/util.h:67: error: âCifFileâ was not declared in this scope >/usr/include/rcsb/util.h:67: error: âfobjâ was not declared in this scope >/usr/include/rcsb/util.h:67: error: expected primary-expression before âconstâ >/usr/include/rcsb/util.h:68: error: expected primary-expression before âconstâ >/usr/include/rcsb/util.h:68: error: expected primary-expression before âconstâ >/usr/include/rcsb/util.h:68: error: initializer expression list treated as compound expression >/usr/include/rcsb/util.h:69: error: âCifFileâ was not declared in this scope >/usr/include/rcsb/util.h:69: error: âfobjâ was not declared in this scope >/usr/include/rcsb/util.h:69: error: expected primary-expression before âconstâ >/usr/include/rcsb/util.h:70: error: expected primary-expression before âconstâ >/usr/include/rcsb/util.h:70: error: expected primary-expression before âconstâ >/usr/include/rcsb/util.h:71: error: expected primary-expression before âlongâ >/usr/include/rcsb/util.h:71: error: initializer expression list treated as compound expression >/usr/include/rcsb/util.h:74: error: âint check_category(const char*, char*, char*)â redeclared as different kind of symbol >./include/check.h:191: error: previous declaration of âCHECK_CATEGORY check_category [6]â >In file included from ./src/contact.C:150: >./include/xtal.h:166: error: ISO C++ forbids declaration of âNDBCELLCONSTâ with no type >./include/xtal.h:166: error: expected â,â or â...â before â*â token >./include/xtal.h:167: error: âCOORDâ has not been declared >./include/xtal.h:167: error: âCOORDâ has not been declared >./src/contact.C:152: error: variable or field âget_all_shell_atomsâ declared void >./src/contact.C:152: error: âBTreeObjâ was not declared in this scope >./src/contact.C:152: error: â_ISIndexâ was not declared in this scope >./src/contact.C:152: error: â_AllWatersâ was not declared in this scope >./src/contact.C:152: error: expected primary-expression before âconstâ >./src/contact.C:153: error: expected primary-expression before â*â token >./src/contact.C:153: error: âcontactâ was not declared in this scope >./src/contact.C: In member function âvoid _VALIDATION::find_all_links()â: >./src/contact.C:164: error: â_ATOMâ was not declared in this scope >./src/contact.C:164: error: âatom_O3â was not declared in this scope >./src/contact.C:164: error: âatom_Pâ was not declared in this scope >./src/contact.C:165: error: â_RESIDUEâ was not declared in this scope >./src/contact.C:165: error: âFstâ was not declared in this scope >./src/contact.C:165: error: âSndâ was not declared in this scope >./src/contact.C:166: error: â_CHAINâ was not declared in this scope >./src/contact.C:166: error: âchn1â was not declared in this scope >./src/contact.C:166: error: âchn2â was not declared in this scope >./src/contact.C:168: error: â_num_molâ was not declared in this scope >./src/contact.C:170: error: â_moleculesâ was not declared in this scope >./src/contact.C:172: error: âATOMN_TOKENâ was not declared in this scope >./src/contact.C:172: error: âATOMN_TYPE_TRNAâ was not declared in this scope >./src/contact.C:182: error: âis_a_nonstandard_trnaâ was not declared in this scope >./src/contact.C:189: error: âstrcmpâ was not declared in this scope >./src/contact.C:192: error: âis_a_bondâ was not declared in this scope >./src/contact.C:200: error: type â<type error>â argument given to âdeleteâ, expected pointer >./src/contact.C:201: error: type â<type error>â argument given to âdeleteâ, expected pointer >./src/contact.C:209: error: â_cellâ was not declared in this scope >./src/contact.C:212: error: â_cellâ was not declared in this scope >./src/contact.C:222: error: âstrcmpâ was not declared in this scope >./src/contact.C:238: error: âATOMP_TOKENâ was not declared in this scope >./src/contact.C:239: error: âATOMS_TOKENâ was not declared in this scope >./src/contact.C:240: error: âstrcmpâ was not declared in this scope >make[1]: *** [obj/atom.o] Error 1 >./src/contact.C: In member function âvoid _VALIDATION::calculate_contact_for_nmr()â: >./src/contact.C:292: error: â_num_molâ was not declared in this scope >./src/contact.C:295: error: â_cellâ was not declared in this scope >./src/contact.C:295: error: â_moleculesâ was not declared in this scope >./src/contact.C: In member function âCONTACT** _VALIDATION::calculate_all_contacts(int&, double, double)â: >./src/contact.C:332: error: â_num_molâ was not declared in this scope >./src/contact.C:335: error: â_cellâ was not declared in this scope >./src/contact.C:335: error: â_moleculesâ was not declared in this scope >./src/contact.C: In member function âvoid _VALIDATION::calculate_all_contact(double, int)â: >./src/contact.C:370: error: â_ATOMâ was not declared in this scope >./src/contact.C:370: error: expected primary-expression before â=â token >./src/contact.C:371: error: â_RESIDUEâ was not declared in this scope >./src/contact.C:371: error: âresidueâ was not declared in this scope >./src/contact.C:372: error: â_CHAINâ was not declared in this scope >./src/contact.C:372: error: âchainâ was not declared in this scope >./src/contact.C:374: error: âBTreeObjâ was not declared in this scope >./src/contact.C:374: error: expected primary-expression before â>â token >./src/contact.C:374: error: â_CIndexâ was not declared in this scope >./src/contact.C:375: error: â_ISIndexâ was not declared in this scope >./src/contact.C:375: error: expected â;â before âindexâ >./src/contact.C:376: error: â_AllWatersâ was not declared in this scope >./src/contact.C:378: error: â_num_molâ was not declared in this scope >./src/contact.C:379: error: â_cellâ was not declared in this scope >./src/contact.C:382: error: â_experiment_typeâ was not declared in this scope >./src/contact.C:382: error: âEXPERIMENT_TYPE_NMRâ was not declared in this scope >./src/contact.C:388: error: â_cellâ was not declared in this scope >./src/contact.C:388: error: â_moleculesâ was not declared in this scope >./src/contact.C:412: error: âstrcmpâ was not declared in this scope >./src/contact.C:470: error: â_moleculesâ was not declared in this scope >./src/contact.C:472: error: âHETAS_TOKENâ was not declared in this scope >./src/contact.C:474: error: âstrcmpâ was not declared in this scope >./src/contact.C:502: error: âstrcpyâ was not declared in this scope >./src/contact.C:533: error: âHETAS_TOKENâ was not declared in this scope >./src/contact.C:539: error: âstrcmpâ was not declared in this scope >./src/contact.C:544: error: expected unqualified-id before â=â token >./src/contact.C:545: error: expected primary-expression before â)â token >./src/contact.C:546: error: expected primary-expression before â->â token >./src/contact.C:546: error: âstrcmpâ was not declared in this scope >./src/contact.C:558: error: expected primary-expression before â->â token >./src/contact.C:558: error: âstrcpyâ was not declared in this scope >./src/contact.C:559: error: expected primary-expression before â->â token >./src/contact.C:560: error: expected primary-expression before â->â token >./src/contact.C:561: error: expected primary-expression before â->â token >./src/contact.C:562: error: expected primary-expression before â->â token >./src/contact.C:563: error: expected primary-expression before â->â token >./src/contact.C:570: error: âindexâ was not declared in this scope >./src/contact.C:570: error: expected primary-expression before â->â token >./src/contact.C:571: error: expected primary-expression before â->â token >./src/contact.C:577: error: expected unqualified-id before â=â token >./src/contact.C:585: error: âstrcmpâ was not declared in this scope >./src/contact.C:589: error: âstrcpyâ was not declared in this scope >./src/contact.C:620: error: âstrcmpâ was not declared in this scope >./src/contact.C:622: error: âindexâ was not declared in this scope >./src/contact.C:659: error: âget_all_shell_atomsâ was not declared in this scope >./src/contact.C:665: error: âindexâ was not declared in this scope >./src/contact.C:680: error: âindexâ was not declared in this scope >./src/contact.C:705: error: âstrcpyâ was not declared in this scope >./src/contact.C: In member function âint _VALIDATION::find_a_link(CONTACT*)â: >./src/contact.C:764: error: â_MOLECULEâ was not declared in this scope >./src/contact.C:764: error: âmolâ was not declared in this scope >./src/contact.C:764: error: â_moleculesâ was not declared in this scope >./src/contact.C:770: error: âstrcmpâ was not declared in this scope >./src/contact.C: In function âCONTACT** get_contact(xtal&, int&, double, double, const char*, const char*, const char*, int)â: >./src/contact.C:792: error: âBTreeObjâ was not declared in this scope >./src/contact.C:792: error: expected primary-expression before â>â token >./src/contact.C:792: error: â_CIndexâ 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: âstrcmpâ was not declared in this scope >./src/contact.C:839: error: âstrncmpâ was not declared in this scope >./src/contact.C:846: error: âstrcmpâ 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 â&&â within â||â >./src/contact.C:911: error: âstrcpyâ was not declared in this scope >./src/contact.C:972: error: âstrcpyâ was not declared in this scope >./src/contact.C: At global scope: >./src/contact.C:1038: error: variable or field âget_all_shell_atomsâ declared void >./src/contact.C:1038: error: âBTreeObjâ was not declared in this scope >./src/contact.C:1038: error: â_ISIndexâ was not declared in this scope >./src/contact.C:1038: error: â_AllWatersâ was not declared in this scope >./src/contact.C:1038: error: expected primary-expression before âconstâ >./src/contact.C:1039: error: expected primary-expression before â*â token >./src/contact.C:1039: error: âcontactâ 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: âMxStrLenâ 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 â_RESIDUEâ with no type >./include/_validation.h:207: error: expected â;â before â*â token >./include/_validation.h:213: error: âCOORDâ does not name a type >./include/_validation.h:214: error: âCOORDâ does not name a type >./include/_validation.h:215: error: âCOORDâ does not name a type >./include/_validation.h:216: error: âCOORDâ does not name a type >./include/_validation.h:217: error: âCOORDâ does not name a type >./include/_validation.h:218: error: âCOORDâ does not name a type >./include/_validation.h:232: error: ISO C++ forbids declaration of â_ATOMâ with no type >./include/_validation.h:232: error: expected â;â before â*â token >./include/_validation.h:233: error: ISO C++ forbids declaration of â_ATOMâ with no type >./include/_validation.h:233: error: expected â;â before â*â token >./include/_validation.h:234: error: ISO C++ forbids declaration of â_ATOMâ with no type >./include/_validation.h:234: error: expected â;â before â*â token >./include/_validation.h:266: error: ISO C++ forbids declaration of â_ATOMâ with no type >./include/_validation.h:266: error: expected â;â before â*â token >./include/_validation.h:267: error: ISO C++ forbids declaration of â_ATOMâ with no type >./include/_validation.h:267: error: expected â;â before â*â token >./include/_validation.h:268: error: ISO C++ forbids declaration of â_ATOMâ with no type >./include/_validation.h:268: error: expected â;â before â*â token >./include/_validation.h:269: error: ISO C++ forbids declaration of â_ATOMâ with no type >./include/_validation.h:269: error: expected â;â before â*â token >./include/_validation.h:305: error: âCifStringâ does not name a type >./include/_validation.h:315: error: âCifStringâ does not name a type >./include/_validation.h:327: error: âCOORDâ does not name a type >./include/_validation.h:328: error: âCOORDâ does not name a type >./include/_validation.h:329: error: âCOORDâ does not name a type >./include/_validation.h:339: error: âCOORDâ does not name a type >./include/_validation.h:344: error: ISO C++ forbids declaration of â_ATOMâ with no type >./include/_validation.h:344: error: expected â;â before â*â token >./include/_validation.h:348: error: expected class-name before â{â token >./include/_validation.h:377: error: â_ATOMâ has not been declared >./include/_validation.h:377: error: â_ATOMâ has not been declared >./include/_validation.h:380: error: â_ATOMâ has not been declared >./include/_validation.h:380: error: â_ATOMâ has not been declared >./include/_validation.h:380: error: â_ATOMâ has not been declared >./include/_validation.h:382: error: â_ATOMâ has not been declared >./include/_validation.h:382: error: â_ATOMâ has not been declared >./include/_validation.h:382: error: â_ATOMâ has not been declared >./include/_validation.h:382: error: â_ATOMâ has not been declared >./include/_validation.h:398: error: âCifStringâ has not been declared >./include/_validation.h:421: error: â_RESIDUEâ has not been declared >./include/_validation.h:422: error: â_RESIDUEâ has not been declared >./include/_validation.h:422: error: â_RESIDUEâ has not been declared >./include/_validation.h:423: error: â_ATOMâ has not been declared >./include/_validation.h:423: error: â_ATOMâ has not been declared >./include/_validation.h:423: error: â_ATOMâ has not been declared >./include/_validation.h:423: error: â_ATOMâ has not been declared >./include/_validation.h:426: error: âCifStringâ has not been declared >./include/_validation.h:426: error: âCifStringâ has not been declared >./include/_validation.h:427: error: âCifStringâ has not been declared >./include/_validation.h:433: error: â_MOLECULEâ has not been declared >./include/_validation.h:434: error: â_CHAINâ has not been declared >./include/_validation.h:434: error: âCOORDâ has not been declared >./include/_validation.h:434: error: â_RESIDUEâ has not been declared >./include/_validation.h:435: error: â_CHAINâ has not been declared >./include/_validation.h:436: error: â_ATOMâ has not been declared >./include/_validation.h:436: error: â_ATOMâ has not been declared >./include/_validation.h:437: error: â_CHAINâ has not been declared >./include/_validation.h:438: error: âCOORDâ has not been declared >./include/_validation.h:438: error: âCOORDâ has not been declared >./include/_validation.h:444: error: âISTableâ has not been declared >./include/_validation.h:492: error: âTblIndexObjâ does not name a type >./include/_validation.h:493: error: âTblIndexObjâ does not name a type >./include/_validation.h:494: error: âTblIndexObjâ does not name a type >./include/_validation.h:495: error: âTblIndexObjâ does not name a type >./include/_validation.h:496: error: âTblIndexObjâ does not name a type >./include/_validation.h:497: error: âTblIndexObjâ does not name a type >./include/_validation.h:498: error: âTblIndexObjâ does not name a type >./include/_validation.h:500: error: âCifStringâ does not name a type >./include/_validation.h:501: error: âCifStringâ does not name a type >./include/_validation.h:502: error: âCifStringâ does not name a type >./include/_validation.h:507: warning: âget_residue_indexâ initialized and declared âexternâ >./include/_validation.h:507: error: â_MOLECULEâ was not declared in this scope >./include/_validation.h:507: error: âmolâ was not declared in this scope >./include/_validation.h:507: error: âISTableâ was not declared in this scope >./include/_validation.h:507: error: âTableâ was not declared in this scope >./include/_validation.h:507: error: expected primary-expression before âconstâ >./include/_validation.h:508: error: expected primary-expression before âconstâ >./include/_validation.h:508: error: expected primary-expression before âconstâ >./include/_validation.h:508: error: expected primary-expression before âconstâ >./include/_validation.h:509: error: expected primary-expression before âconstâ >./include/_validation.h:509: error: expected primary-expression before âconstâ >./include/_validation.h:509: error: expected primary-expression before âconstâ >./include/_validation.h:510: error: expected primary-expression before âconstâ >./include/_validation.h:510: error: expected primary-expression before âintâ >./include/_validation.h:510: error: expected primary-expression before âintâ >./include/_validation.h:510: error: âCifStringâ was not declared in this scope >./include/_validation.h:510: error: ânameâ 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: âCifFileâ was not declared in this scope >/usr/include/rcsb/util.h:67: error: âfobjâ was not declared in this scope >/usr/include/rcsb/util.h:67: error: expected primary-expression before âconstâ >/usr/include/rcsb/util.h:68: error: expected primary-expression before âconstâ >/usr/include/rcsb/util.h:68: error: expected primary-expression before âconstâ >/usr/include/rcsb/util.h:68: error: initializer expression list treated as compound expression >/usr/include/rcsb/util.h:69: error: âCifFileâ was not declared in this scope >/usr/include/rcsb/util.h:69: error: âfobjâ was not declared in this scope >/usr/include/rcsb/util.h:69: error: expected primary-expression before âconstâ >/usr/include/rcsb/util.h:70: error: expected primary-expression before âconstâ >/usr/include/rcsb/util.h:70: error: expected primary-expression before âconstâ >/usr/include/rcsb/util.h:71: error: expected primary-expression before âlongâ >/usr/include/rcsb/util.h:71: error: initializer expression list treated as compound expression >/usr/include/rcsb/util.h:74: error: âint check_category(const char*, char*, char*)â redeclared as different kind of symbol >./include/check.h:191: error: previous declaration of âCHECK_CATEGORY check_category [6]â >./src/na_classification.C: In member function âvoid _VALIDATION::na_classification()â: >./src/na_classification.C:210: error: âCifStringâ was not declared in this scope >./src/na_classification.C:210: error: expected â;â before âindexâ >./src/na_classification.C:211: error: âTblIndexObjâ was not declared in this scope >./src/na_classification.C:211: error: expected â;â before â_BaseIndexâ >./src/na_classification.C:214: error: â_CHAINâ was not declared in this scope >./src/na_classification.C:214: error: âchainâ was not declared in this scope >./src/na_classification.C:217: error: âISTableâ was not declared in this scope >./src/na_classification.C:217: error: âTableâ was not declared in this scope >./src/na_classification.C:223: error: âindexâ 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: â_BaseIndexâ was not declared in this scope >./src/na_classification.C:248: error: â_MOLECULEâ was not declared in this scope >./src/na_classification.C:248: error: âmolâ was not declared in this scope >./src/na_classification.C:248: error: â_moleculesâ was not declared in this scope >./src/na_classification.C:336: warning: suggest parentheses around â&&â within â||â >./src/na_classification.C:381: error: âget_parent_nameâ was not declared in this scope >./src/na_classification.C:458: error: â_CifObjâ was not declared in this scope >./src/na_classification.C:459: error: â_StructureIdâ was not declared in this scope >./src/na_classification.C:460: error: âis_empty_tableâ was not declared in this scope >./src/na_classification.C:464: error: expected type-specifier before âISTableâ >./src/na_classification.C:464: error: expected â;â before âISTableâ >./src/na_classification.C:468: error: âentry_idâ was not declared in this scope >./src/na_classification.C:471: error: âfeatureâ was not declared in this scope >./src/na_classification.C:478: error: âfeatureâ was not declared in this scope >./src/na_classification.C:485: error: âfeatureâ was not declared in this scope >./src/na_classification.C:492: error: âfeatureâ was not declared in this scope >./src/na_classification.C:499: error: âfeatureâ was not declared in this scope >./src/na_classification.C:506: error: âfeatureâ was not declared in this scope >./src/na_classification.C:513: error: âfeatureâ was not declared in this scope >./src/na_classification.C:520: error: âfeatureâ was not declared in this scope >./src/na_classification.C:527: error: âfeatureâ was not declared in this scope >./src/na_classification.C:534: error: âfeatureâ was not declared in this scope >./src/na_classification.C:541: error: âfeatureâ was not declared in this scope >./src/na_classification.C:548: error: âfeatureâ was not declared in this scope >./src/na_classification.C:555: error: âfeatureâ was not declared in this scope >./src/na_classification.C:562: error: âfeatureâ 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: âMxStrLenâ 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 â_RESIDUEâ with no type >./include/_validation.h:207: error: expected â;â before â*â token >./include/_validation.h:213: error: âCOORDâ does not name a type >./include/_validation.h:214: error: âCOORDâ does not name a type >./include/_validation.h:215: error: âCOORDâ does not name a type >./include/_validation.h:216: error: âCOORDâ does not name a type >./include/_validation.h:217: error: âCOORDâ does not name a type >./include/_validation.h:218: error: âCOORDâ does not name a type >./include/_validation.h:232: error: ISO C++ forbids declaration of â_ATOMâ with no type >./include/_validation.h:232: error: expected â;â before â*â token >./include/_validation.h:233: error: ISO C++ forbids declaration of â_ATOMâ with no type >./include/_validation.h:233: error: expected â;â before â*â token >./include/_validation.h:234: error: ISO C++ forbids declaration of â_ATOMâ with no type >./include/_validation.h:234: error: expected â;â before â*â token >./include/_validation.h:266: error: ISO C++ forbids declaration of â_ATOMâ with no type >./include/_validation.h:266: error: expected â;â before â*â token >./include/_validation.h:267: error: ISO C++ forbids declaration of â_ATOMâ with no type >./include/_validation.h:267: error: expected â;â before â*â token >./include/_validation.h:268: error: ISO C++ forbids declaration of â_ATOMâ with no type >./include/_validation.h:268: error: expected â;â before â*â token >./include/_validation.h:269: error: ISO C++ forbids declaration of â_ATOMâ with no type >./include/_validation.h:269: error: expected â;â before â*â token >./include/_validation.h:305: error: âCifStringâ does not name a type >./include/_validation.h:315: error: âCifStringâ does not name a type >./include/_validation.h:327: error: âCOORDâ does not name a type >./include/_validation.h:328: error: âCOORDâ does not name a type >./include/_validation.h:329: error: âCOORDâ does not name a type >./include/_validation.h:339: error: âCOORDâ does not name a type >./include/_validation.h:344: error: ISO C++ forbids declaration of â_ATOMâ with no type >./include/_validation.h:344: error: expected â;â before â*â token >./include/_validation.h:348: error: expected class-name before â{â token >./include/_validation.h:377: error: â_ATOMâ has not been declared >./include/_validation.h:377: error: â_ATOMâ has not been declared >./include/_validation.h:380: error: â_ATOMâ has not been declared >./include/_validation.h:380: error: â_ATOMâ has not been declared >./include/_validation.h:380: error: â_ATOMâ has not been declared >./include/_validation.h:382: error: â_ATOMâ has not been declared >./include/_validation.h:382: error: â_ATOMâ has not been declared >./include/_validation.h:382: error: â_ATOMâ has not been declared >./include/_validation.h:382: error: â_ATOMâ has not been declared >./include/_validation.h:398: error: âCifStringâ has not been declared >./include/_validation.h:421: error: â_RESIDUEâ has not been declared >./include/_validation.h:422: error: â_RESIDUEâ has not been declared >./include/_validation.h:422: error: â_RESIDUEâ has not been declared >./include/_validation.h:423: error: â_ATOMâ has not been declared >./include/_validation.h:423: error: â_ATOMâ has not been declared >./include/_validation.h:423: error: â_ATOMâ has not been declared >./include/_validation.h:423: error: â_ATOMâ has not been declared >./include/_validation.h:426: error: âCifStringâ has not been declared >./include/_validation.h:426: error: âCifStringâ has not been declared >./include/_validation.h:427: error: âCifStringâ has not been declared >./include/_validation.h:433: error: â_MOLECULEâ has not been declared >./include/_validation.h:434: error: â_CHAINâ has not been declared >./include/_validation.h:434: error: âCOORDâ has not been declared >./include/_validation.h:434: error: â_RESIDUEâ has not been declared >./include/_validation.h:435: error: â_CHAINâ has not been declared >./include/_validation.h:436: error: â_ATOMâ has not been declared >./include/_validation.h:436: error: â_ATOMâ has not been declared >./include/_validation.h:437: error: â_CHAINâ has not been declared >./include/_validation.h:438: error: âCOORDâ has not been declared >./include/_validation.h:438: error: âCOORDâ has not been declared >./src/na_classification.C: In function âint non_watson_crick_pair(char, char)â: >./src/na_classification.C:1022: warning: suggest parentheses around â&&â within â||â >./include/_validation.h:444: error: âISTableâ has not been declared >./include/_validation.h:492: error: âTblIndexObjâ does not name a type >./include/_validation.h:493: error: âTblIndexObjâ does not name a type >./include/_validation.h:494: error: âTblIndexObjâ does not name a type >./include/_validation.h:495: error: âTblIndexObjâ does not name a type >./include/_validation.h:496: error: âTblIndexObjâ does not name a type >./include/_validation.h:497: error: âTblIndexObjâ does not name a type >./include/_validation.h:498: error: âTblIndexObjâ does not name a type >./include/_validation.h:500: error: âCifStringâ does not name a type >./include/_validation.h:501: error: âCifStringâ does not name a type >./include/_validation.h:502: error: âCifStringâ does not name a type >./include/_validation.h:507: warning: âget_residue_indexâ initialized and declared âexternâ >./include/_validation.h:507: error: â_MOLECULEâ was not declared in this scope >./include/_validation.h:507: error: âmolâ was not declared in this scope >./include/_validation.h:507: error: âISTableâ was not declared in this scope >./include/_validation.h:507: error: âTableâ was not declared in this scope >./include/_validation.h:507: error: expected primary-expression before âconstâ >./include/_validation.h:508: error: expected primary-expression before âconstâ >./include/_validation.h:508: error: expected primary-expression before âconstâ >./include/_validation.h:508: error: expected primary-expression before âconstâ >./include/_validation.h:509: error: expected primary-expression before âconstâ >./include/_validation.h:509: error: expected primary-expression before âconstâ >./include/_validation.h:509: error: expected primary-expression before âconstâ >./include/_validation.h:510: error: expected primary-expression before âconstâ >./include/_validation.h:510: error: expected primary-expression before âintâ >./include/_validation.h:510: error: expected primary-expression before âintâ >./include/_validation.h:510: error: âCifStringâ was not declared in this scope >./include/_validation.h:510: error: ânameâ 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: âCifFileâ was not declared in this scope >/usr/include/rcsb/util.h:67: error: âfobjâ was not declared in this scope >/usr/include/rcsb/util.h:67: error: expected primary-expression before âconstâ >/usr/include/rcsb/util.h:68: error: expected primary-expression before âconstâ >/usr/include/rcsb/util.h:68: error: expected primary-expression before âconstâ >/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: âCifFileâ was not declared in this scope >/usr/include/rcsb/util.h:69: error: âfobjâ was not declared in this scope >/usr/include/rcsb/util.h:69: error: expected primary-expression before âconstâ >/usr/include/rcsb/util.h:70: error: expected primary-expression before âconstâ >/usr/include/rcsb/util.h:70: error: expected primary-expression before âconstâ >/usr/include/rcsb/util.h:71: error: expected primary-expression before âlongâ >/usr/include/rcsb/util.h:71: error: initializer expression list treated as compound expression >/usr/include/rcsb/util.h:74: error: âint check_category(const char*, char*, char*)â redeclared as different kind of symbol >./include/check.h:191: error: previous declaration of âCHECK_CATEGORY check_category [6]â >./src/ndb_atlas.C:155: error: variable or field âget_citation_valâ declared void >./src/ndb_atlas.C:155: error: âCifStringâ was not declared in this scope >./src/ndb_atlas.C:155: error: âbuffâ was not declared in this scope >./src/ndb_atlas.C:155: error: âOne_Card_Info_Formatâ was not declared in this scope >./src/ndb_atlas.C:155: error: âHeadâ was not declared in this scope >./src/ndb_atlas.C:156: error: expected primary-expression before âconstâ >./src/ndb_atlas.C:156: error: expected primary-expression before âconstâ >./src/ndb_atlas.C:157: error: âOne_Card_Info_Formatâ was not declared in this scope >./src/ndb_atlas.C:157: error: âHeadâ was not declared in this scope >./src/ndb_atlas.C:157: error: expected primary-expression before âconstâ >./src/ndb_atlas.C:158: error: expected primary-expression before âconstâ >./src/ndb_atlas.C:158: error: expected primary-expression before âconstâ >./src/ndb_atlas.C:158: error: âCifStringâ was not declared in this scope >./src/ndb_atlas.C:158: error: âresâ 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: âCifStringâ was not declared in this scope >./src/ndb_atlas.C:161: error: âauthorsâ was not declared in this scope >./src/ndb_atlas.C:161: error: âCifStringâ was not declared in this scope >./src/ndb_atlas.C:161: error: âtitleâ was not declared in this scope >./src/ndb_atlas.C:161: error: âCifStringâ was not declared in this scope >./src/ndb_atlas.C:161: error: âjrnlâ was not declared in this scope >./src/ndb_atlas.C:162: error: âCifStringâ was not declared in this scope >./src/ndb_atlas.C:162: error: âvolumeâ was not declared in this scope >./src/ndb_atlas.C:162: error: âCifStringâ was not declared in this scope >./src/ndb_atlas.C:162: error: âfirst_pageâ was not declared in this scope >./src/ndb_atlas.C:162: error: âCifStringâ was not declared in this scope >./src/ndb_atlas.C:162: error: âlast_pageâ was not declared in this scope >./src/ndb_atlas.C:163: error: âCifStringâ was not declared in this scope >./src/ndb_atlas.C:163: error: âyearâ 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: âCifStringâ was not declared in this scope >./src/ndb_atlas.C:164: error: âmethodâ was not declared in this scope >./src/ndb_atlas.C:164: error: âCifStringâ was not declared in this scope >./src/ndb_atlas.C:164: error: âdropâ was not declared in this scope >./src/ndb_atlas.C:165: error: âCifStringâ was not declared in this scope >./src/ndb_atlas.C:165: error: âreservoirâ was not declared in this scope >./src/ndb_atlas.C:165: error: âCifStringâ was not declared in this scope >./src/ndb_atlas.C:165: error: âsoakingâ 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 âvoid _VALIDATION::ndb_write_atlas_entries(char*, int)â: >./src/ndb_atlas.C:172: error: â_StructureIdâ was not declared in this scope >./src/ndb_atlas.C:173: error: ândb_clean_stringâ was not declared in this scope >./src/ndb_atlas.C:178: error: â_CardInfoâ was not declared in this scope >./src/ndb_atlas.C:178: error: âPDBFIL_TOKENâ was not declared in this scope >./src/ndb_atlas.C:189: error: â_experiment_typeâ was not declared in this scope >./src/ndb_atlas.C: In member function âATLAS_TEXT* _VALIDATION::get_atlas_text(const char*, const char*)â: >./src/ndb_atlas.C:218: error: âCifStringâ was not declared in this scope >./src/ndb_atlas.C:218: error: expected â;â before âbuffâ >./src/ndb_atlas.C:219: error: expected â;â before âlast_pageâ >./src/ndb_atlas.C:221: error: âOne_Card_Info_Formatâ was not declared in this scope >./src/ndb_atlas.C:221: error: âpJrnlCardâ was not declared in this scope >./src/ndb_atlas.C:222: error: âISTableâ was not declared in this scope >./src/ndb_atlas.C:222: error: âTableâ was not declared in this scope >./src/ndb_atlas.C:240: error: âbuffâ was not declared in this scope >./src/ndb_atlas.C:246: error: âtmp_buffâ was not declared in this scope >./src/ndb_atlas.C:261: error: â_Num_Seqsâ was not declared in this scope >./src/ndb_atlas.C:267: error: â_Seqsâ was not declared in this scope >./src/ndb_atlas.C:273: error: âget_oneletter_codeâ was not declared in this scope >./src/ndb_atlas.C:304: error: âfind_jrnl_idâ was not declared in this scope >./src/ndb_atlas.C:305: error: â_JrnlCardInfoâ was not declared in this scope >./src/ndb_atlas.C:309: error: âatoiâ was not declared in this scope >./src/ndb_atlas.C:315: error: âauthorsâ was not declared in this scope >./src/ndb_atlas.C:315: error: âtitleâ was not declared in this scope >./src/ndb_atlas.C:315: error: âjrnlâ was not declared in this scope >./src/ndb_atlas.C:315: error: âvolumeâ was not declared in this scope >./src/ndb_atlas.C:316: error: âfirst_pageâ was not declared in this scope >./src/ndb_atlas.C:316: error: âlast_pageâ was not declared in this scope >./src/ndb_atlas.C:316: error: âyearâ was not declared in this scope >./src/ndb_atlas.C:319: error: âget_citation_valâ was not declared in this scope >./src/ndb_atlas.C:328: error: â_input_formatâ was not declared in this scope >./src/ndb_atlas.C:328: error: âNDB_FILE_FORMAT_MIXâ was not declared in this scope >./src/ndb_atlas.C:329: error: âNDB_FILE_FORMAT_MMCIFâ was not declared in this scope >./src/ndb_atlas.C:330: error: â_CifObjâ was not declared in this scope >./src/ndb_atlas.C:330: error: â_StructureIdâ was not declared in this scope >./src/ndb_atlas.C:331: error: âis_empty_tableâ was not declared in this scope >./src/ndb_atlas.C:333: error: âget_valueâ was not declared in this scope >./src/ndb_atlas.C:360: error: ândb_name_conversion_first_lastâ was not declared in this scope >./src/ndb_atlas.C:367: error: âget_refnâ cannot be used as a function >./src/ndb_atlas.C:369: error: â_cellâ was not declared in this scope >./src/ndb_atlas.C:382: error: â_CardInfoâ was not declared in this scope >./src/ndb_atlas.C:382: error: âCRMETH_TOKENâ was not declared in this scope >./src/ndb_atlas.C:382: error: âCRSOLU_TOKENâ was not declared in this scope >./src/ndb_atlas.C:386: error: ândb_set_string_to_mixedâ was not declared in this scope >./src/ndb_atlas.C:391: error: âget_multiple_rowsâ cannot be used as a function >./src/ndb_atlas.C:392: error: âget_multiple_rowsâ cannot be used as a function >./src/ndb_atlas.C:393: error: âget_multiple_rowsâ cannot be used as a function >./src/ndb_atlas.C:395: error: â_input_formatâ was not declared in this scope >./src/ndb_atlas.C:395: error: âNDB_FILE_FORMAT_MIXâ was not declared in this scope >./src/ndb_atlas.C:396: error: âNDB_FILE_FORMAT_MMCIFâ was not declared in this scope >./src/ndb_atlas.C:397: error: â_CifObjâ was not declared in this scope >./src/ndb_atlas.C:397: error: â_StructureIdâ was not declared in this scope >./src/ndb_atlas.C:398: error: âis_empty_tableâ was not declared in this scope >./src/ndb_atlas.C:400: error: âget_valueâ was not declared in this scope >./src/ndb_atlas.C:403: error: ândb_set_string_to_mixedâ was not declared in this scope >./src/ndb_atlas.C:408: error: âis_empty_tableâ was not declared in this scope >./src/ndb_atlas.C:413: error: âget_valueâ was not declared in this scope >./src/ndb_atlas.C:448: error: âget_crysâ cannot be used as a function >./src/ndb_atlas.C:450: error: â_experiment_typeâ was not declared in this scope >./src/ndb_atlas.C:450: error: âEXPERIMENT_TYPE_NMRâ was not declared in this scope >./src/ndb_atlas.C:451: error: âprogramâ was not declared in this scope >./src/ndb_atlas.C:451: error: ârvalueâ was not declared in this scope >./src/ndb_atlas.C:451: error: âreflectionsâ was not declared in this scope >./src/ndb_atlas.C:452: error: âhighâ was not declared in this scope >./src/ndb_atlas.C:452: error: âlowâ was not declared in this scope >./src/ndb_atlas.C:452: error: âsigmaFâ was not declared in this scope >./src/ndb_atlas.C:453: error: â_input_formatâ was not declared in this scope >./src/ndb_atlas.C:453: error: âNDB_FILE_FORMAT_MIXâ was not declared in this scope >./src/ndb_atlas.C:454: error: âNDB_FILE_FORMAT_MMCIFâ was not declared in this scope >./src/ndb_atlas.C:455: error: â_CifObjâ was not declared in this scope >./src/ndb_atlas.C:455: error: â_StructureIdâ was not declared in this scope >./src/ndb_atlas.C:456: error: âis_empty_tableâ was not declared in this scope >./src/ndb_atlas.C:458: error: âget_valueâ was not declared in this scope >./src/ndb_atlas.C:468: error: âatofâ was not declared in this scope >./src/ndb_atlas.C:487: error: âis_empty_tableâ was not declared in this scope >./src/ndb_atlas.C:489: error: âget_valueâ was not declared in this scope >./src/ndb_atlas.C:492: error: â_CardInfoâ was not declared in this scope >./src/ndb_atlas.C:492: error: âREFMET_TOKENâ was not declared in this scope >./src/ndb_atlas.C:496: error: â_CardInfoâ was not declared in this scope >./src/ndb_atlas.C:496: error: âRFACTR_TOKENâ was not declared in this scope >./src/ndb_atlas.C: At global scope: >./src/ndb_atlas.C:566: error: variable or field âget_name_stâ declared void >./src/ndb_atlas.C:566: error: âCifStringâ was not declared in this scope >./src/ndb_atlas.C:566: error: ânameâ was not declared in this scope >./src/ndb_atlas.C:566: error: âCifStringâ was not declared in this scope >./src/ndb_atlas.C:566: error: âmodifier_stâ was not declared in this scope >./src/ndb_atlas.C:153: warning: âvoid write_text_part(FILE*, ATLAS_TEXT*, int, int)â declared âstaticâ but never defined >./src/ndb_atlas.C:159: warning: âvoid add_superscripts(char*, char*, int)â declared âstaticâ but never defined >./src/ndb_atlas.C:160: warning: âvoid correct_string(char*)â declared âstaticâ 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 > [31;01m*[0m ERROR: sci-chemistry/validation-6.2 failed: > [31;01m*[0m emake failed > [31;01m*[0m > [31;01m*[0m Call stack: > [31;01m*[0m ebuild.sh, line 61: Called src_compile > [31;01m*[0m environment, line 2455: Called _eapi0_src_compile > [31;01m*[0m ebuild.sh, line 619: Called _eapi2_src_compile > [31;01m*[0m ebuild.sh, line 653: Called die > [31;01m*[0m The specific snippet of code: > [31;01m*[0m emake || die "emake failed" > [31;01m*[0m > [31;01m*[0m If you need support, post the output of 'emerge --info =sci-chemistry/validation-6.2', > [31;01m*[0m the complete build log and the output of 'emerge -pqv =sci-chemistry/validation-6.2'. > [31;01m*[0m The complete build log is located at '/var/log/portage/build/sci-chemistry/validation-6.2:20091212-184723.log'. > [31;01m*[0m The ebuild environment file is located at '/var/tmp/portage/sci-chemistry/validation-6.2/temp/environment'. > [31;01m*[0m S: '/var/tmp/portage/sci-chemistry/validation-6.2/work/pdb-extract-v1.700-prod-src'
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bug 296651
: 212814