printf ' ' | fink --no-use-binary-dist --yes --build-as-nobody rebuild rnamotif 2>&1 The package 'rnamotif' will be built without being installed. Reading build dependency for rnamotif-3.0.7-1... Reading dependency for rnamotif-3.0.7-1... Reading build conflict for rnamotif-3.0.7-1... The following package will be rebuilt: rnamotif curl --connect-timeout 30 -f -L -A 'fink/0.37.0' -O http://distfiles.master.finkmirrors.net/distfiles/rnamotif-3.0.7.tar.gz % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 0 899k 0 1206 0 0 2282 0 0:06:43 --:--:-- 0:06:43 2279 79 899k 79 711k 0 0 468k 0 0:00:01 0:00:01 --:--:-- 468k 100 899k 100 899k 0 0 540k 0 0:00:01 0:00:01 --:--:-- 540k Setting runtime build-lock... dpkg-deb -b /sw/build.build/root-fink-buildlock-rnamotif-3.0.7-1 /sw/build.build dpkg-deb: building package `fink-buildlock-rnamotif-3.0.7-1' in `/sw/build.build/fink-buildlock-rnamotif-3.0.7-1_2014.07.30-08.59.17_darwin-x86_64.deb'. Installing build-lock package... /sw/bin/dpkg-lockwait -i /sw/build.build/fink-buildlock-rnamotif-3.0.7-1_2014.07.30-08.59.17_darwin-x86_64.deb Selecting previously deselected package fink-buildlock-rnamotif-3.0.7-1. (Reading database ... 4296 files and directories currently installed.) Unpacking fink-buildlock-rnamotif-3.0.7-1 (from .../fink-buildlock-rnamotif-3.0.7-1_2014.07.30-08.59.17_darwin-x86_64.deb) ... Setting up fink-buildlock-rnamotif-3.0.7-1 (2014.07.30-08.59.17) ... sudo -u fink-bld [ENV] sh -c /tmp/fink.DgJP3 env LANG=C LC_ALL=C /sw/bin/tar --no-same-owner --no-same-permissions -xvf /sw/src/rnamotif-3.0.7.tar.gz rnamotif-3.0.7/README rnamotif-3.0.7/COPYING.GNU rnamotif-3.0.7/revision.history rnamotif-3.0.7/iupac.codes rnamotif-3.0.7/Makefile rnamotif-3.0.7/config.h rnamotif-3.0.7/doc/rnamotif.pdf rnamotif-3.0.7/src/ rnamotif-3.0.7/src/compile.c rnamotif-3.0.7/src/dbutil.c rnamotif-3.0.7/src/dbutil.h rnamotif-3.0.7/src/dump.c rnamotif-3.0.7/src/efn.c rnamotif-3.0.7/src/efn2.c rnamotif-3.0.7/src/efn2_drv.c rnamotif-3.0.7/src/efn_drv.c rnamotif-3.0.7/src/errormsg.c rnamotif-3.0.7/src/find_motif.c rnamotif-3.0.7/src/fmap.c rnamotif-3.0.7/src/fmap.h rnamotif-3.0.7/src/getargs.c rnamotif-3.0.7/src/Makefile rnamotif-3.0.7/src/Makefile.mrnamotif rnamotif-3.0.7/src/mk_dumpnode.h.sh rnamotif-3.0.7/src/mm_redriver.c rnamotif-3.0.7/src/mm_regexp.c rnamotif-3.0.7/src/mm_regexp.h rnamotif-3.0.7/src/mrnamotif.c rnamotif-3.0.7/src/node.c rnamotif-3.0.7/src/preprocessor.c rnamotif-3.0.7/src/regexp.c rnamotif-3.0.7/src/rm2ct.c rnamotif-3.0.7/src/rmdefs.h rnamotif-3.0.7/src/rmfmt.c rnamotif-3.0.7/src/rmgrm.y rnamotif-3.0.7/src/rmlex.l rnamotif-3.0.7/src/rmprune.c rnamotif-3.0.7/src/rnamot.c rnamotif-3.0.7/src/rnamot.h rnamotif-3.0.7/src/score.c rnamotif-3.0.7/src/split.c rnamotif-3.0.7/efndata/ rnamotif-3.0.7/efndata/asint1x2.dat rnamotif-3.0.7/efndata/coaxial.dat rnamotif-3.0.7/efndata/coaxstack.dat rnamotif-3.0.7/efndata/dangle.dat rnamotif-3.0.7/efndata/int11.dat rnamotif-3.0.7/efndata/int21.dat rnamotif-3.0.7/efndata/int22.dat rnamotif-3.0.7/efndata/loop.dat rnamotif-3.0.7/efndata/miscloop.dat rnamotif-3.0.7/efndata/README rnamotif-3.0.7/efndata/sint2.dat rnamotif-3.0.7/efndata/sint4.dat rnamotif-3.0.7/efndata/stack.dat rnamotif-3.0.7/efndata/tloop.dat rnamotif-3.0.7/efndata/triloop.dat rnamotif-3.0.7/efndata/tstack.dat rnamotif-3.0.7/efndata/tstackcoax.dat rnamotif-3.0.7/efndata/tstackh.dat rnamotif-3.0.7/efndata/tstacki.dat rnamotif-3.0.7/efndata/tstackm.dat rnamotif-3.0.7/test/ rnamotif-3.0.7/test/bulge.chk rnamotif-3.0.7/test/bulge.descr rnamotif-3.0.7/test/bulge.strict.chk rnamotif-3.0.7/test/bulge.strict.descr rnamotif-3.0.7/test/efn.chk rnamotif-3.0.7/test/efn.descr rnamotif-3.0.7/test/efn.strict.chk rnamotif-3.0.7/test/efn.strict.descr rnamotif-3.0.7/test/gbrna.111.0.fastn rnamotif-3.0.7/test/getbest.chk rnamotif-3.0.7/test/getbest.descr rnamotif-3.0.7/test/getbest.strict.chk rnamotif-3.0.7/test/getbest.strict.descr rnamotif-3.0.7/test/ire.1.descr rnamotif-3.0.7/test/ire.1.strict.descr rnamotif-3.0.7/test/ire.chk rnamotif-3.0.7/test/ire.descr rnamotif-3.0.7/test/ire.strict.descr rnamotif-3.0.7/test/Makefile rnamotif-3.0.7/test/mp.ends.chk rnamotif-3.0.7/test/mp.ends.descr rnamotif-3.0.7/test/mp.ends.strict.chk rnamotif-3.0.7/test/mp.ends.strict.descr rnamotif-3.0.7/test/nanlin.chk rnamotif-3.0.7/test/nanlin.descr rnamotif-3.0.7/test/nanlin.strict.chk rnamotif-3.0.7/test/nanlin.strict.descr rnamotif-3.0.7/test/pk1.chk rnamotif-3.0.7/test/pk1.descr rnamotif-3.0.7/test/pk1.strict.chk rnamotif-3.0.7/test/pk1.strict.descr rnamotif-3.0.7/test/qu+tr.chk rnamotif-3.0.7/test/qu+tr.descr rnamotif-3.0.7/test/qu+tr.strict.chk rnamotif-3.0.7/test/qu+tr.strict.descr rnamotif-3.0.7/test/rs.bad.descr rnamotif-3.0.7/test/rs.bad.out rnamotif-3.0.7/test/rs.bad.seq rnamotif-3.0.7/test/score.1.chk rnamotif-3.0.7/test/score.1.descr rnamotif-3.0.7/test/score.1.strict.chk rnamotif-3.0.7/test/score.1.strict.descr rnamotif-3.0.7/test/score.2.chk rnamotif-3.0.7/test/score.2.descr rnamotif-3.0.7/test/score.2.strict.chk rnamotif-3.0.7/test/score.2.strict.descr rnamotif-3.0.7/test/sprintf.chk rnamotif-3.0.7/test/sprintf.descr rnamotif-3.0.7/test/sprintf.strict.chk rnamotif-3.0.7/test/sprintf.strict.descr rnamotif-3.0.7/test/trna.chk rnamotif-3.0.7/test/trna.descr rnamotif-3.0.7/test/trna.strict.chk rnamotif-3.0.7/test/trna.strict.descr sudo -u fink-bld [ENV] sh -c /tmp/fink.ynpKW perl -pi -e 's|/usr/local|/sw|g' config.h perl -pi -e 's|/sw/bin/bison|/usr/bin/bison|g' config.h perl -pi -e 's|#include ||g' src/*.c make cd src; make gcc -O2 -Wall -I/sw/include -c -o rnamot.o rnamot.c flex rmlex.l gcc -O2 -Wall -I/sw/include -c -o dbutil.o dbutil.c gcc -O2 -Wall -I/sw/include -c -o efn.o efn.c gcc -O2 -Wall -I/sw/include -c -o efn2.o efn2.c gcc -O2 -Wall -I/sw/include -c -o errormsg.o errormsg.c gcc -O2 -Wall -I/sw/include -c -o getargs.o getargs.c gcc -O2 -Wall -I/sw/include -c -o mm_regexp.o mm_regexp.c gcc -O2 -Wall -I/sw/include -c -o preprocessor.o preprocessor.c dbutil.c:84:30: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] for( cnt = 1, *dp++ = c; c = getc( fp ); ){ ~~^~~~~~~~~~~~ dbutil.c:84:30: note: place parentheses around the assignment to silence this warning for( cnt = 1, *dp++ = c; c = getc( fp ); ){ ^ ( ) dbutil.c:84:30: note: use '==' to turn this assignment into an equality comparison for( cnt = 1, *dp++ = c; c = getc( fp ); ){ ^ == dbutil.c:184:29: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] for( cnt = 1, *dp++ = c; c = getc( fp ); ){ ~~^~~~~~~~~~~~ dbutil.c:184:29: note: place parentheses around the assignment to silence this warning for( cnt = 1, *dp++ = c; c = getc( fp ); ){ ^ ( ) dbutil.c:184:29: note: use '==' to turn this assignment into an equality comparison for( cnt = 1, *dp++ = c; c = getc( fp ); ){ ^ == dbutil.c:287:9: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] if( dp = strchr( acc, '.' ) ) ~~~^~~~~~~~~~~~~~~~~~~~ dbutil.c:287:9: note: place parentheses around the assignment to silence this warning if( dp = strchr( acc, '.' ) ) ^ ( ) dbutil.c:287:9: note: use '==' to turn this assignment into an equality comparison if( dp = strchr( acc, '.' ) ) ^ == 3 warnings generated. gcc -O2 -Wall -I/sw/include -c -o regexp.o regexp.c preprocessor.c:70:13: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] for( ; dfp = RM_getline( line, sizeof( line ), dfp ); ){ ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ preprocessor.c:70:13: note: place parentheses around the assignment to silence this warning for( ; dfp = RM_getline( line, sizeof( line ), dfp ); ){ ^ ( ) preprocessor.c:70:13: note: use '==' to turn this assignment into an equality comparison for( ; dfp = RM_getline( line, sizeof( line ), dfp ); ){ ^ == preprocessor.c:77:16: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] }else if( dp = isdescr( line ) ){ ~~~^~~~~~~~~~~~~~~~~ preprocessor.c:77:16: note: place parentheses around the assignment to silence this warning }else if( dp = isdescr( line ) ){ ^ ( ) preprocessor.c:77:16: note: use '==' to turn this assignment into an equality comparison }else if( dp = isdescr( line ) ){ ^ == rnamot.c:35:1: warning: type specifier missing, defaults to 'int' [-Wimplicit-int] main( int argc, char *argv[] ) ^~~~ rnamot.c:52:3: warning: implicit declaration of function 'RM_dump' is invalid in C99 [-Wimplicit-function-declaration] RM_dump( stderr, 2, 0, 0, 0 ); ^ rnamot.c:69:6: warning: implicit declaration of function 'yyparse' is invalid in C99 [-Wimplicit-function-declaration] if( yyparse() ){ ^ rnamot.c:74:3: warning: implicit declaration of function 'unlink' is invalid in C99 [-Wimplicit-function-declaration] unlink( rm_args->a_xdfname ); ^ rnamot.c:118:12: warning: implicitly declaring library function 'strcmp' with type 'int (const char *, const char *)' else if( !strcmp( rm_args->a_dbfmt, DT_FASTN ) ) ^ preprocessor.c:207:11:rnamot.c:118:12: note: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] please include the header or explicitly provide a declaration for 'strcmp' if( fp = pushfile( path ) ) ~~~^~~~~~~~~~~~~~~~~~ preprocessor.c:207:11: note: place parentheses around the assignment to silence this warning if( fp = pushfile( path ) ) ^ ( ) preprocessor.c:207:11: note: use '==' to turn this assignment into an equality comparison if( fp = pushfile( path ) ) ^ == preprocessor.c:178:11: warning: variable 'c' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized] else if( *sp == '\'' ) ^~~~~~~~~~~ preprocessor.c:186:26: note: uninitialized use occurs here if( ( sp1 = strchr( sp, c ) ) == NULL ){ ^ preprocessor.c:178:7: note: remove the 'if' if its condition is always true else if( *sp == '\'' ) ^~~~~~~~~~~~~~~~~ preprocessor.c:161:7: note: initialize the variable 'c' to silence this warning int c; ^ = 0 preprocessor.c:241:13: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] }while( fp = popfile() ); ~~~^~~~~~~~~~~ preprocessor.c:241:13: note: place parentheses around the assignment to silence this warning }while( fp = popfile() ); ^ ( ) preprocessor.c:241:13: note: use '==' to turn this assignment into an equality comparison }while( fp = popfile() ); ^ == preprocessor.c:221:13: warning: unused function 'dumpfstk' [-Wunused-function] static void dumpfstk( FILE *fp, char msg[] ) ^ regexp.c:398:10: warning: implicit declaration of function 'advance' is invalid in C99 [-Wimplicit-function-declaration] return(advance(p1, p2)); ^ rnamot.c:126:15: warning: format specifies type 'int' but the argument has type 'char *' [-Wformat] argv[ 0 ], rm_args->a_dbfmt ); ^~~~~~~~~~~~~~~~ regexp.c:422:1: warning: type specifier missing, defaults to 'int' [-Wimplicit-int] advance(lp, ep) ^~~~~~~ gcc -O2 -Wall -I/sw/include -c -o split.o split.c regexp.c:474:12: warning: array subscript is of type 'char' [-Wchar-subscripts] braslist[*ep++] = lp; ^~~~~~ regexp.c:478:12: warning: array subscript is of type 'char' [-Wchar-subscripts] braelist[*ep++] = lp; ^~~~~~ regexp.c:550:19: warning: array subscript is of type 'char' [-Wchar-subscripts] bbeg = braslist[*ep]; ^~~~ regexp.c:551:17: warning: array subscript is of type 'char' [-Wchar-subscripts] ct = braelist[*ep++] - bbeg; ^~~~~~ regexp.c:553:7: warning: implicitly declaring library function 'strncmp' with type 'int (const char *, const char *, unsigned long)' if(ecmp(bbeg, lp, ct)) { ^ regexp.c:91:27: note: expanded from macro 'ecmp' #define ecmp(s1, s2, n) (!strncmp(s1, s2, n)) ^ regexp.c:553:7: note: please include the header or explicitly provide a declaration for 'strncmp' regexp.c:91:27: note: expanded from macro 'ecmp' #define ecmp(s1, s2, n) (!strncmp(s1, s2, n)) ^ regexp.c:560:19: warning: array subscript is of type 'char' [-Wchar-subscripts] bbeg = braslist[*ep]; ^~~~ regexp.c:561:17: warning: array subscript is of type 'char' [-Wchar-subscripts] ct = braelist[*ep++] - bbeg; ^~~~~~ regexp.c:620:19: warning: array subscript is of type 'char' [-Wchar-subscripts] c = *(braslist[ep[1]]); ^~~~~~ efn.c:247:6: warning: variable 't' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized] if( skipto( fp, "---", sizeof( line ), line ) ){ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ efn.c:260:6: note: uninitialized use occurs here if( t > MAXTLOOPS ){ ^ efn.c:247:2: note: remove the 'if' if its condition is always true if( skipto( fp, "---", sizeof( line ), line ) ){ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ efn.c:237:7: note: initialize the variable 't' to silence this warning int t, rval; ^ = 0 efn.c:289:6: warning: variable 't' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized] if( skipto( fp, "---", sizeof( line ), line ) ){ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ efn.c:301:6: note: uninitialized use occurs here if( t > MAXTRILOOPS ){ ^ efn.c:289:2: note: remove the 'if' if its condition is always true if( skipto( fp, "---", sizeof( line ), line ) ){ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ efn.c:279:7: note: initialize the variable 't' to silence this warning int t, rval; ^ = 0 rnamot.c:203:13: warning: array subscript is of type 'char' [-Wchar-subscripts] c = wc_cmp[ *sp ]; ^ ~~~ rnamot.c:204:15: warning: array subscript is of type 'char' [-Wchar-subscripts] *sp = wc_cmp[ *cp ]; ^ ~~~ efn2.c:408:15: warning: implicit declaration of function 'split' is invalid in C99 [-Wimplicit-function-declaration] n_fields = split( line, fields, " \t\n" ); ^ efn.c:533:15: warning: implicit declaration of function 'split' is invalid in C99 [-Wimplicit-function-declaration] n_fields = split( line, fields, " \t\n" ); ^ efn2.c:726:6: warning: variable 't' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized] if( skipto( fp, "---", sizeof( line ), line ) ){ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ efn2.c:741:6: note: uninitialized use occurs here if( t > EFN2_MAXTLOOP ){ ^ efn2.c:726:2: note: remove the 'if' if its condition is always true if( skipto( fp, "---", sizeof( line ), line ) ){ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ efn2.c:715:7: note: initialize the variable 't' to silence this warning int t; ^ = 0 efn2.c:770:6: warning: variable 't' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized] if( skipto( fp, "---", sizeof( line ), line ) ){ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ efn2.c:785:6: note: uninitialized use occurs here if( t > EFN2_MAXTRILOOP ){ ^ efn2.c:770:2: note: remove the 'if' if its condition is always true if( skipto( fp, "---", sizeof( line ), line ) ){ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ efn2.c:760:7: note: initialize the variable 't' to silence this warning int t, rval; ^ = 0 efn2.c:1234:20: warning: '&&' within '||' [-Wlogical-op-parentheses] if( h1 == 0 && helix[h1][1]-helix[n_helix-1][0] > 1 || ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~ efn2.c:1234:20: note: place parentheses around the '&&' expression to silence this warning if( h1 == 0 && helix[h1][1]-helix[n_helix-1][0] > 1 || ^ ( ) efn2.c:1235:17: warning: '&&' within '||' [-Wlogical-op-parentheses] h1 != 0 && helix[h1][1]-helix[h1-1][0] > 1 ) ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ efn2.c:1235:17: note: place parentheses around the '&&' expression to silence this warning h1 != 0 && helix[h1][1]-helix[h1-1][0] > 1 ) ^ ( ) efn.c:1401:19: warning: '&&' within '||' [-Wlogical-op-parentheses] if( i<=rm_l_base && ip>rm_l_base || jp<=rm_l_base && j>rm_l_base ) ~~~~~~~~~~~~~^~~~~~~~~~~~~~~ ~~ efn.c:1401:19: note: place parentheses around the '&&' expression to silence this warning if( i<=rm_l_base && ip>rm_l_base || jp<=rm_l_base && j>rm_l_base ) ^ ( ) efn.c:1401:52: warning: '&&' within '||' [-Wlogical-op-parentheses] if( i<=rm_l_base && ip>rm_l_base || jp<=rm_l_base && j>rm_l_base ) ~~ ~~~~~~~~~~~~~~^~~~~~~~~~~~~~ efn.c:1401:52: note: place parentheses around the '&&' expression to silence this warning if( i<=rm_l_base && ip>rm_l_base || jp<=rm_l_base && j>rm_l_base ) ^ ( ) efn.c:1657:13: warning: unused function 'push' [-Wunused-function] static void push( int a, int b, int c ) ^ efn.c:1670:12: warning: unused function 'pull' [-Wunused-function] static int pull( int *a, int *b, int *c ) ^ 8 warnings generated. gcc -O2 -Wall -I/sw/include -c -o rmprune.o rmprune.c gcc -O2 -Wall -I/sw/include -c -o rm2ct.o rm2ct.c split.c:30:12: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] if( efp = strpbrk( fp, fsep ) ){ ~~~~^~~~~~~~~~~~~~~~~~~~~ split.c:30:12: note: place parentheses around the assignment to silence this warning if( efp = strpbrk( fp, fsep ) ){ ^ ( ) split.c:30:12: note: use '==' to turn this assignment into an equality comparison if( efp = strpbrk( fp, fsep ) ){ ^ == split.c:50:11: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] if( fp = strchr( sp, *fsep ) ){ ~~~^~~~~~~~~~~~~~~~~~~~~ split.c:50:11: note: place parentheses around the assignment to silence this warning if( fp = strchr( sp, *fsep ) ){ ^ ( ) split.c:50:11: note: use '==' to turn this assignment into an equality comparison if( fp = strchr( sp, *fsep ) ){ ^ == rmprune.c:107:1: warning: type specifier missing, defaults to 'int' [-Wimplicit-int] main( int argc, char *argv[] ) ^~~~ rmprune.c:141:14: warning: implicit declaration of function 'split' is invalid in C99 [-Wimplicit-function-declaration] n_fields = split( line, fields, " \t\n" ); ^ rmprune.c:257:10: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] if( tp = strchr( fields[ d + dfield1 ], '(' ) ){ ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ rmprune.c:257:10: note: place parentheses around the assignment to silence this warning if( tp = strchr( fields[ d + dfield1 ], '(' ) ){ ^ ( ) rmprune.c:257:10: note: use '==' to turn this assignment into an equality comparison if( tp = strchr( fields[ d + dfield1 ], '(' ) ){ ^ == rmprune.c:262:12: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] if( tp1=strchr( fields[ d1 + dfield1 ], '(' ) ){ ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2rmprune.c:262:12: note: place parentheses around the assignment to silence this warning warnings generated. if( tp1=strchr( fields[ d1 + dfield1 ], '(' ) ){ 6 warnings generated. ^ ( ) rmprune.c:262:12: note: use '==' to turn this assignment into an equality comparison if( tp1=strchr( fields[ d1 + dfield1 ], '(' ) ){ ^ == gcc -O2 -Wall -I/sw/include -c -o rmfmt.o rmfmt.c gcc -O2 -Wall -I/sw/include -c -o efn_drv.o efn_drv.c gcc -O2 -Wall -I/sw/include -c -o efn2_drv.o efn2_drv.c rm2ct.c:91:1: warning: type specifier missing, defaults to 'int' [-Wimplicit-int] main( int argc, char *argv[] ) ^~~~ rm2ct.c:150:14: warning: implicit declaration of function 'split' is invalid in C99 [-Wimplicit-function-declaration] n_fields = split( line, fields, " \t\n" ); ^ rmprune.c:441:12: warning: unused function 'find_0_bulge' [-Wunused-function] static int find_0_bulge( int n_block, BLOCK_T block[] ) ^ rm2ct.c:266:10: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] if( tp = strchr( fields[ d + dfield1 ], '(' ) ){ ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ rm2ct.c:266:10: note: place parentheses around the assignment to silence this warning if( tp = strchr( fields[ d + dfield1 ], '(' ) ){ ^ ( ) rm2ct.c:266:10: note: use '==' to turn this assignment into an equality comparison if( tp = strchr( fields[ d + dfield1 ], '(' ) ){ ^ == rm2ct.c:271:12: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] if( tp1=strchr( fields[ d1 + dfield1 ], '(' ) ){ ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ rm2ct.c:271:12: note: place parentheses around the assignment to silence this warning if( tp1=strchr( fields[ d1 + dfield1 ], '(' ) ){ ^ ( ) rm2ct.c:271:12: note: use '==' to turn this assignment into an equality comparison if( tp1=strchr( fields[ d1 + dfield1 ], '(' ) ){ ^ == 10 warnings generated. bison -y -d -v -t rmgrm.y efn2_drv.c:29:1: warning: type specifier missing, defaults to 'int' [-Wimplicit-int] main( int argc, char* argv[] ) ^~~~ efn2_drv.c:68:37: warning: implicit declaration of function 'CT_read' is invalid in C99 [-Wimplicit-function-declaration] for( n_struct = 0; ( efn2_nbases = CT_read( cfp ) ) != 0; n_struct++ ){ ^ efn2_drv.c:129:34: warning: implicit declaration of function 'isspace' is invalid in C99 [-Wimplicit-function-declaration] for( --hp; hp >= efn2_header && isspace( *hp ); hp-- ) ^ efn2_drv.c:146:1: warning: unused label 'CLEAN_UP' [-Wunused-label] CLEAN_UP : ; ^~~~~~~~~~~ efn_drv.c:46:1: warning: type specifier missing, defaults to 'int' [-Wimplicit-int] main( argc, argv ) ^~~~ 1 warning generated. 4 warnings generated. gcc -O2 -Wall -o rm2ct rm2ct.o split.o rmfmt.c:47:1: warning: type specifier missing, defaults to 'int' [-Wimplicit-int] main( int argc, char *argv[] ) ^~~~ rmfmt.c:122:14: warning: implicit declaration of function 'split' is invalid in C99 [-Wimplicit-function-declaration] n_fields = split( line, fields, " \t\n" ); ^ rmfmt.c:352:3: warning: implicit declaration of function 'unlink' is invalid in C99 [-Wimplicit-function-declaration] unlink( tfnp2 ); ^ rmgrm.y:344.19-347.61: warning: unused value: $4 conflicts: 1 shift/reduce 4 warnings generated. 5 warnings generated. gcc -O2 -Wall -o rmprune rmprune.o split.o 3 warnings generated. gcc -O2 -Wall -o rmfmt rmfmt.o split.o gcc -O2 -Wall -I/sw/include -c -o compile.o compile.c gcc -O2 -Wall -I/sw/include -c -o dump.o dump.c gcc -O2 -Wall -I/sw/include -c -o find_motif.o find_motif.c find_motif.c:212:7: warning: implicit declaration of function 'step' is invalid in C99 [-Wimplicit-function-declaration] if( step( &fm_sbuf[ fm_opt_pos ], rm_o_expbuf ) ){ ^ find_motif.c:223:12: warning: implicit declaration of function 'mm_step' is invalid in C99 [-Wimplicit-function-declaration] }else if( mm_step( &fm_sbuf[ fm_opt_pos ], rm_o_expbuf, l_mm, &n_mm ) ){ ^ find_motif.c:425:9: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] if(n_h3=match_wchlx(stp,stp3,szero,sdollar,s3lim,h3,hlen,n_mpr )){ ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ find_motif.c:425:9: note: place parentheses around the assignment to silence this warning if(n_h3=match_wchlx(stp,stp3,szero,sdollar,s3lim,h3,hlen,n_mpr )){ ^ ( ) find_motif.c:425:9: note: use '==' to turn this assignment into an equality comparison if(n_h3=match_wchlx(stp,stp3,szero,sdollar,s3lim,h3,hlen,n_mpr )){ ^ == compile.c:1402:7: warning: inequality comparison result unused [-Wunused-comparison] err != chk_1_strel_parms( rm_lctx ); ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ compile.c:1402:7: note: use '|=' to turn this inequality comparison into an or-assignment err != chk_1_strel_parms( rm_lctx ); ^~ |= compile.c:1407:7: warning: inequality comparison result unused [-Wunused-comparison] err != chk_1_strel_parms( rm_rctx ); ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ compile.c:1407:7: note: use '|=' to turn this inequality comparison into an or-assignment err != chk_1_strel_parms( rm_rctx ); ^~ |= find_motif.c:566:11: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] if( n_h3=match_wchlx( stp5,stp3,s5,s3,s3lim,h3,hlen,n_mpr )){ ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ find_motif.c:566:11: note: place parentheses around the assignment to silence this warning if( n_h3=match_wchlx( stp5,stp3,s5,s3,s3lim,h3,hlen,n_mpr )){ ^ ( ) find_motif.c:566:11: note: use '==' to turn this assignment into an equality comparison if( n_h3=match_wchlx( stp5,stp3,s5,s3,s3lim,h3,hlen,n_mpr )){ ^ == compile.c:1681:4: warning: implicit declaration of function 'compile' is invalid in C99 [-Wimplicit-function-declaration] compile( stp->s_seq, stp->s_expbuf, ^ compile.c:1734:12: warning: variable 'maxl' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized] else if( x_maxl == i_maxl ) ^~~~~~~~~~~~~~~~ compile.c:1753:13: note: uninitialized use occurs here if( minl > maxl ){ ^~~~ compile.c:1734:8: note: remove the 'if' if its condition is always true else if( x_maxl == i_maxl ) ^~~~~~~~~~~~~~~~~~~~~~ compile.c:1634:16: note: initialize the variable 'maxl' to silence this warning int minl, maxl; ^ = 0 find_motif.c:832:9: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] if(n_h3=match_wchlx(stp,stp3,szero,sdollar,s3lim,h3,hlen,n_mpr)){ ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ find_motif.c:832:9: note: place parentheses around the assignment to silence this warning if(n_h3=match_wchlx(stp,stp3,szero,sdollar,s3lim,h3,hlen,n_mpr)){ ^ ( ) find_motif.c:832:9: note: use '==' to turn this assignment into an equality comparison if(n_h3=match_wchlx(stp,stp3,szero,sdollar,s3lim,h3,hlen,n_mpr)){ ^ == compile.c:2335:8: warning: variable 'ps' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized] if( open_pairset != NULL ) ^~~~~~~~~~~~~~~~~~~~ compile.c:2346:40: note: uninitialized use occurs here vp->v_value.v_pval = pairop( "copy", ps, NULL ); ^~ compile.c:2335:4: note: remove the 'if' if its condition is always true if( open_pairset != NULL ) ^~~~~~~~~~~~~~~~~~~~~~~~~~ compile.c:2294:15: note: initialize the variable 'ps' to silence this warning PAIRSET_T *ps ; ^ = NULL find_motif.c:1742:12: warning: variable 'rv' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized] }else if( sip->s_n_pos == 4 ){ ^~~~~~~~~~~~~~~~~ find_motif.c:1745:10: note: uninitialized use occurs here return( rv ); ^~ find_motif.c:1742:8: note: remove the 'if' if its condition is always true }else if( sip->s_n_pos == 4 ){ ^~~~~~~~~~~~~~~~~~~~~~~ find_motif.c:1715:8: note: initialize the variable 'rv' to silence this warning int rv; ^ = 0 find_motif.c:1327:12: warning: unused function 'chk_wchlx0' [-Wunused-function] static int chk_wchlx0( SEARCH_T *srp, int s5, int s3 ) ^ 5 warnings generated. compile.c:2627:17: warning: array subscript is of type 'char' [-Wchar-subscripts] bi1 = rm_b2bc[ pp->p_bases[ 0 ] ]; ^ ~~~~~~~~~~~~~~~~ compile.c:2628:17: warning: array subscript is of type 'char' [-Wchar-subscripts] bi2 = rm_b2bc[ pp->p_bases[ 1 ] ]; ^ ~~~~~~~~~~~~~~~~ 7 warnings generated. compile.c:2638:17: warning: array subscript is of type 'char' [-Wchar-subscripts] bi1 = rm_b2bc[ pp->p_bases[ 0 ] ]; ^ ~~~~~~~~~~~~~~~~ compile.c:2639:17: warning: array subscript is of type 'char' [-Wchar-subscripts] bi2 = rm_b2bc[ pp->p_bases[ 1 ] ]; ^ ~~~~~~~~~~~~~~~~ compile.c:2640:17: warning: array subscript is of type 'char' [-Wchar-subscripts] bi3 = rm_b2bc[ pp->p_bases[ 2 ] ]; ^ ~~~~~~~~~~~~~~~~ compile.c:2650:17: warning: array subscript is of type 'char' [-Wchar-subscripts] bi1 = rm_b2bc[ pp->p_bases[ 0 ] ]; ^ ~~~~~~~~~~~~~~~~ compile.c:2651:17: warning: array subscript is of type 'char' [-Wchar-subscripts] bi2 = rm_b2bc[ pp->p_bases[ 1 ] ]; ^ ~~~~~~~~~~~~~~~~ compile.c:2652:17: warning: array subscript is of type 'char' [-Wchar-subscripts] bi3 = rm_b2bc[ pp->p_bases[ 2 ] ]; ^ ~~~~~~~~~~~~~~~~ compile.c:2653:17: warning: array subscript is of type 'char' [-Wchar-subscripts] bi4 = rm_b2bc[ pp->p_bases[ 3 ] ]; ^ ~~~~~~~~~~~~~~~~ compile.c:2643:12: warning: variable 'bmatp' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized] }else if( nb == 4 ){ ^~~~~~~ compile.c:2657:10: note: uninitialized use occurs here return( bmatp ); ^~~~~ compile.c:2643:8: note: remove the 'if' if its condition is always true }else if( nb == 4 ){ ^~~~~~~~~~~~~ compile.c:2613:13: note: initialize the variable 'bmatp' to silence this warning void *bmatp; ^ = NULL ./mk_dumpnode.h.sh y.tab.h > dumpnode.h gcc -O2 -Wall -I/sw/include -c -o score.o score.c compile.c:2773:11: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] if( s3 = rm_iupac[ c ] ){ ~~~^~~~~~~~~~~~~~~ compile.c:2773:11: note: place parentheses around the assignment to silence this warning if( s3 = rm_iupac[ c ] ){ ^ ( ) compile.c:2773:11: note: use '==' to turn this assignment into an equality comparison if( s3 = rm_iupac[ c ] ){ ^ == compile.c:1118:13: warning: unused function 'find_pknots0' [-Wunused-function] static void find_pknots0( STREL_T *stp, int n_descr, STREL_T descr[] ) ^ compile.c:1200:13: warning: unused function 'find_pknots1' [-Wunused-function] static void find_pknots1( STREL_T *stp, int n_descr, STREL_T descr[] ) ^ compile.c:3478:13: warning: unused function 'dump_bestpat' [-Wunused-function] static void dump_bestpat( FILE *fp, STREL_T *stp ) ^ gcc -O2 -Wall -I/sw/include -c -o y.tab.o y.tab.c y.tab.c:1702:16: warning: implicit declaration of function 'yylex' is invalid in C99 [-Wimplicit-function-declaration] yychar = YYLEX; ^ y.tab.c:1058:16: note: expanded from macro 'YYLEX' # define YYLEX yylex () ^ rmgrm.y:330:7: warning: implicit declaration of function 'RM_hold' is invalid in C99 [-Wimplicit-function-declaration] { RM_hold( (yyvsp[(2) - (3)].npval) ); } ^ rmgrm.y:342:7: warning: implicit declaration of function 'RM_release' is invalid in C99 [-Wimplicit-function-declaration] { RM_release( (yyvsp[(2) - (3)].npval) ); } ^ y.tab.c:2576:7: warning: implicit declaration of function 'yyerror' is invalid in C99 [-Wimplicit-function-declaration] yyerror (YY_("syntax error")); ^ gcc -O2 -Wall -o efn_drv efn_drv.o efn.o errormsg.o split.o -lm score.c:912:22: warning: '&&' within '||' [-Wlogical-op-parentheses] if( n_index == NULL && n_tag == NULL || ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ ~~ score.c:912:22: note: place parentheses around the '&&' expression to silence this warning if( n_index == NULL && n_tag == NULL || ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ score.c:913:19: warning: '&&' within '||' [-Wlogical-op-parentheses] n_index != NULL && n_tag != NULL ) ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ score.c:913:19: note: place parentheses around the '&&' expression to silence this warning n_index != NULL && n_tag != NULL ) ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ score.c:1042:7: warning: variable 'np3' is used uninitialized whenever 'if' condition is true [-Wsometimes-uninitialized] if( np1->n_sym != SYM_KW_STREF && np1->n_sym != SYM_IX_STREF ){ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ score.c:1064:3: note: uninitialized use occurs here np3->n_right = np2; ^~~ score.c:1042:3: note: remove the 'if' if its condition is always false if( np1->n_sym != SYM_KW_STREF && np1->n_sym != SYM_IX_STREF ){ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ score.c:1008:25: note: initialize the variable 'np3' to silence this warning NODE_T *np1, *np2, *np3; ^ = NULL score.c:1295:3: warning: implicit declaration of function 'compile' is invalid in C99 [-Wimplicit-function-declaration] compile( pp, expbuf, e_expbuf, '\0' ); ^ score.c:1299:3: warning: implicit declaration of function 'mm_step' is invalid in C99 [-Wimplicit-function-declaration] mm_step( cp, expbuf, eb_size, &n_mm ); ^ score.c:1453:12: warning: variable 'idx' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized] }else if( v_id->v_type == T_STRING ){ ^~~~~~~~~~~~~~~~~~~~~~~~ score.c:1475:10: note: uninitialized use occurs here return( idx ); ^~~ score.c:1453:8: note: remove the 'if' if its condition is always true }else if( v_id->v_type == T_STRING ){ ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ score.c:1427:12: note: initialize the variable 'idx' to silence this warning int s, idx; ^ = 0 score.c:1777:32: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] for( c_arg = 0, fp = fstr; pp = strchr( fp, '%' ); ){ ~~~^~~~~~~~~~~~~~~~~~~ score.c:1777:32: note: place parentheses around the assignment to silence this warning for( c_arg = 0, fp = fstr; pp = strchr( fp, '%' ); ){ ^ ( ) score.c:1777:32: note: use '==' to turn this assignment into an equality comparison for( c_arg = 0, fp = fstr; pp = strchr( fp, '%' ); ){ ^ == score.c:1784:12: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] if( rval = fmt_1_item( ip, fmt, n_args, &c_arg ) ) ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ score.c:1784:12: note: place parentheses around the assignment to silence this warning if( rval = fmt_1_item( ip, fmt, n_args, &c_arg ) ) ^ ( ) score.c:1784:12: note: use '==' to turn this assignment into an equality comparison if( rval = fmt_1_item( ip, fmt, n_args, &c_arg ) ) ^ == score.c:1826:10: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] if( dot = strchr( work, '.' ) ){ ~~~~^~~~~~~~~~~~~~~~~~~~~ score.c:1826:10: note: place parentheses around the assignment to silence this warning if( dot = strchr( work, '.' ) ){ ^ ( ) score.c:1826:10: note: use '==' to turn this assignment into an equality comparison if( dot = strchr( work, '.' ) ){ ^ == score.c:1841:11: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] if( star = strchr( work, '*' ) ){ ~~~~~^~~~~~~~~~~~~~~~~~~~~ score.c:1841:11: note: place parentheses around the assignment to silence this warning if( star = strchr( work, '*' ) ){ ^ ( ) score.c:1841:11: note: use '==' to turn this assignment into an equality comparison if( star = strchr( work, '*' ) ){ ^ == score.c:1851:14: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] if( dollar = strchr( work, '$' ) ){ ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ score.c:1851:14: note: place parentheses around the assignment to silence this warning if( dollar = strchr( work, '$' ) ){ ^ ( ) score.c:1851:14: note: use '==' to turn this assignment into an equality comparison if( dollar = strchr( work, '$' ) ){ ^ == score.c:1860:19: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] }else if( dollar = strchr( work, '$' ) ){ ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ score.c:1860:19: note: place parentheses around the assignment to silence this warning }else if( dollar = strchr( work, '$' ) ){ ^ ( ) score.c:1860:19: note: use '==' to turn this assignment into an equality comparison }else if( dollar = strchr( work, '$' ) ){ ^ == score.c:2466:2: warning: variable 'rv' is used uninitialized whenever switch default is taken [-Wsometimes-uninitialized] default : ^~~~~~~ score.c:2472:7: note: uninitialized use occurs here if( !rv ) ^~ score.c:2447:15: note: initialize the variable 'rv' to silence this warning int t_top, rv; ^ = 0 score.c:2498:2: warning: variable 'rv' is used uninitialized whenever switch default is taken [-Wsometimes-uninitialized] default : ^~~~~~~ score.c:2504:6: note: uninitialized use occurs here if( rv ) ^~ score.c:2479:15: note: initialize the variable 'rv' to silence this warning int t_top, rv; ^ = 0 score.c:2557:27: warning: implicit declaration of function 'step' is invalid in C99 [-Wimplicit-function-declaration] v_tm1->v_value.v_ival = step( s_tm1, expbuf ); ^ score.c:3267:21: warning: array subscript is of type 'char' [-Wchar-subscripts] if( ( bc = rm_b2bc[ *bp ] ) != BCODE_N ){ ^ ~~~ score.c:3310:26: warning: array subscript is of type 'char' [-Wchar-subscripts] rm_bcseq[ i ] = rm_b2bc[ *bp++ ]; ^ ~~~~~ score.c:3331:27: warning: array subscript is of type 'char' [-Wchar-subscripts] rm_bcseq[ i ] = rm_b2bc[ *bp++ ]; ^ ~~~~~ score.c:3358:26: warning: array subscript is of type 'char' [-Wchar-subscripts] rm_bcseq[ i ] = rm_b2bc[ *bp++ ]; ^ ~~~~~ score.c:3840:13: warning: unused function 'dumpstk' [-Wunused-function] static void dumpstk( FILE *fp, char msg[] ) ^ score.c:3911:13: warning: unused function 'tm_report' [-Wunused-function] static void tm_report( void ) ^ 7 warnings generated. gcc -O2 -Wall -o efn2_drv efn2_drv.o efn2.o errormsg.o split.o -lm In file included from rmgrm.y:544: rmlex.l:202:7: warning: implicit declaration of function 'isspace' is invalid in C99 [-Wimplicit-function-declaration] if( !isspace( *dp ) ) ^ rmlex.l:205:7: warning: implicit declaration of function 'isdigit' is invalid in C99 [-Wimplicit-function-declaration] if( !isdigit( *dp ) ) ^ rmlex.l:216:9: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] if( qp = strchr( dp, '\'' ) ){ ~~~^~~~~~~~~~~~~~~~~~~~ rmlex.l:216:9: note: place parentheses around the assignment to silence this warning if( qp = strchr( dp, '\'' ) ){ ^ ( ) rmlex.l:216:9: note: use '==' to turn this assignment into an equality comparison if( qp = strchr( dp, '\'' ) ){ ^ == rmgrm.y:9:16: warning: unused variable 'np' [-Wunused-variable] static NODE_T *np; ^ In file included from rmgrm.y:544: lex.yy.c:1677:17: warning: unused function 'yyunput' [-Wunused-function] static void yyunput (int c, register char * yy_bp ) ^ 19 warnings generated. gcc -O2 -Wall -I/sw/include -c -o node.o node.c 21 warnings generated. 9 warnings generated. gcc -O2 -Wall -o rnamotif rnamot.o compile.o dbutil.o dump.o efn.o efn2.o errormsg.o find_motif.o getargs.o mm_regexp.o node.o preprocessor.o regexp.o score.o split.o y.tab.o -lm rm -f src/*.o /bin/rm -rf /sw/build.build/root-rnamotif-3.0.7-1 /bin/mkdir -p /sw/build.build/root-rnamotif-3.0.7-1/sw /bin/mkdir -p /sw/build.build/root-rnamotif-3.0.7-1/DEBIAN /usr/sbin/chown -R fink-bld:fink-bld /sw/build.build/root-rnamotif-3.0.7-1 sudo -u fink-bld [ENV] sh -c /tmp/fink.C5jH_ mkdir -p /sw/build.build/root-rnamotif-3.0.7-1/sw/share mkdir -p /sw/build.build/root-rnamotif-3.0.7-1/sw/share/rnamotif cp -R * /sw/build.build/root-rnamotif-3.0.7-1/sw/share/rnamotif/. mkdir -p /sw/build.build/root-rnamotif-3.0.7-1/sw/bin ln -s /sw/share/rnamotif/src/rnamotif /sw/build.build/root-rnamotif-3.0.7-1/sw/bin/rnamotif ln -s /sw/share/rnamotif/src/rmfmt /sw/build.build/root-rnamotif-3.0.7-1/sw/bin/rmfmt ln -s /sw/share/rnamotif/src/rmprune /sw/build.build/root-rnamotif-3.0.7-1/sw/bin/rmprune ln -s /sw/share/rnamotif/src/rm2ct /sw/build.build/root-rnamotif-3.0.7-1/sw/bin/rm2ct mkdir -p /sw/build.build/root-rnamotif-3.0.7-1/sw/share/doc mkdir -p /sw/build.build/root-rnamotif-3.0.7-1/sw/share/doc/rnamotif sudo -u fink-bld [ENV] sh -c /tmp/fink.Bg__x /usr/bin/install -d -m 700 /sw/build.build/root-rnamotif-3.0.7-1/sw/share/doc/rnamotif /bin/cp -r README /sw/build.build/root-rnamotif-3.0.7-1/sw/share/doc/rnamotif/ /bin/cp -r COPYING.GNU /sw/build.build/root-rnamotif-3.0.7-1/sw/share/doc/rnamotif/ /bin/cp -r doc/rnamotif.pdf /sw/build.build/root-rnamotif-3.0.7-1/sw/share/doc/rnamotif/ /bin/chmod -R go=u-w /sw/build.build/root-rnamotif-3.0.7-1/sw/share/doc/rnamotif /usr/bin/install -d -m 755 /sw/build.build/root-rnamotif-3.0.7-1/sw/etc/profile.d echo "setenv EFNDATA '/sw/share/rnamotif/efndata'" >> /sw/build.build/root-rnamotif-3.0.7-1/sw/etc/profile.d/rnamotif.csh.env echo "export EFNDATA='/sw/share/rnamotif/efndata'" >> /sw/build.build/root-rnamotif-3.0.7-1/sw/etc/profile.d/rnamotif.sh.env /usr/bin/touch /sw/build.build/root-rnamotif-3.0.7-1/sw/etc/profile.d/rnamotif.csh /usr/bin/touch /sw/build.build/root-rnamotif-3.0.7-1/sw/etc/profile.d/rnamotif.sh /bin/cat /sw/build.build/root-rnamotif-3.0.7-1/sw/etc/profile.d/rnamotif.csh >> /sw/build.build/root-rnamotif-3.0.7-1/sw/etc/profile.d/rnamotif.csh.env /bin/cat /sw/build.build/root-rnamotif-3.0.7-1/sw/etc/profile.d/rnamotif.sh >> /sw/build.build/root-rnamotif-3.0.7-1/sw/etc/profile.d/rnamotif.sh.env /bin/mv -f /sw/build.build/root-rnamotif-3.0.7-1/sw/etc/profile.d/rnamotif.csh.env /sw/build.build/root-rnamotif-3.0.7-1/sw/etc/profile.d/rnamotif.csh /bin/mv -f /sw/build.build/root-rnamotif-3.0.7-1/sw/etc/profile.d/rnamotif.sh.env /sw/build.build/root-rnamotif-3.0.7-1/sw/etc/profile.d/rnamotif.sh /bin/chmod 755 /sw/build.build/root-rnamotif-3.0.7-1/sw/etc/profile.d/rnamotif.* /bin/rm -f /sw/build.build/root-rnamotif-3.0.7-1/sw/info/dir /sw/build.build/root-rnamotif-3.0.7-1/sw/info/dir.old /sw/build.build/root-rnamotif-3.0.7-1/sw/share/info/dir /sw/build.build/root-rnamotif-3.0.7-1/sw/share/info/dir.old Reverting ownership of install dir to root Writing control file... Writing md5sums file... env LANG=C LC_ALL=C dpkg-deb -b root-rnamotif-3.0.7-1 /sw/fink/10.9/stable/main/binary-darwin-x86_64/sci dpkg-deb: building package `rnamotif' in `/sw/fink/10.9/stable/main/binary-darwin-x86_64/sci/rnamotif_3.0.7-1_darwin-x86_64.deb'. Removing runtime build-lock... Removing build-lock package... /sw/bin/dpkg-lockwait -r fink-buildlock-rnamotif-3.0.7-1 (Reading database ... 4297 files and directories currently installed.) Removing fink-buildlock-rnamotif-3.0.7-1 ...