+ case "${usergroup_phase}" in + local run_cmd + run_cmd=run_su + shift + run_su /opt/pkg/bin/bmake all BATCH=1 DEPENDS_TARGET=/nonexistent WRKLOG=/tmp/bulklog/gp-0.26/work.log + su pbulk -c '"$@"' make /opt/pkg/bin/bmake all BATCH=1 DEPENDS_TARGET=/nonexistent WRKLOG=/tmp/bulklog/gp-0.26/work.log WARNING: [license.mk] Every package should define a LICENSE. ===> Building for gp-0.26 --- all --- cd src ; make PROGRAMS="gp_acc gp_cusage gp_digest gp_dimer gp_findorf gp_gc gp_getseq gp_matrix gp_mkmtx gp_pars gp_pattern gp_qs gp_randseq gp_scan gp_seq2prot gp_shift gp_slen gp_tm gp_trimer gp_primer gp_adjust gp_cdndev" GDPROGRAMS="" CC=gcc LIBS=" -lm" CFLAGS="-pedantic -O3 -Wall -g" ; --- genpak.o --- gcc -pedantic -O3 -Wall -g -c genpak.c --- gp_acc --- --- gp_cusage --- --- gp_digest --- --- gp_dimer --- --- gp_cusage --- Creating gp_cusage gcc -pedantic -O3 -Wall -g -o gp_cusage genpak.o gp_cusage.c -lm --- gp_digest --- Creating gp_digest gcc -pedantic -O3 -Wall -g -o gp_digest genpak.o gp_digest.c -lm --- gp_acc --- Creating gp_acc gcc -pedantic -O3 -Wall -g -o gp_acc genpak.o gp_acc.c -lm --- gp_dimer --- Creating gp_dimer gcc -pedantic -O3 -Wall -g -o gp_dimer genpak.o gp_dimer.c -lm --- gp_acc --- gp_acc.c: In function 'main': gp_acc.c:64:14: warning: unused variable 'message' [-Wunused-variable] 64 | char message[100] ; | ^~~~~~~ gp_acc.c:59:23: warning: unused variable 'outseq' [-Wunused-variable] 59 | sekw *inseq, *outseq ; | ^~~~~~ gp_acc.c:56:13: warning: unused variable 'width' [-Wunused-variable] 56 | int width = 70 ; /* width with which the sequence gets formatted */ | ^~~~~ gp_acc.c: In function 'FormatHeader': gp_acc.c:289:51: warning: format '%i' expects argument of type 'int', but argument 3 has type 'long int' [-Wformat=] 289 | fprintf(o.out,"z(%i)z(%i)L(%i)\t",i,k,j) ; | ~^ ~ | | | | int long int | %li gp_acc.c:289:56: warning: format '%i' expects argument of type 'int', but argument 4 has type 'long int' [-Wformat=] 289 | fprintf(o.out,"z(%i)z(%i)L(%i)\t",i,k,j) ; | ~^ ~ | | | | int long int | %li gp_acc.c:289:61: warning: format '%i' expects argument of type 'int', but argument 5 has type 'long int' [-Wformat=] 289 | fprintf(o.out,"z(%i)z(%i)L(%i)\t",i,k,j) ; | ~^ ~ | | | | int long int | %li --- gp_digest --- gp_digest.c: In function 'main': gp_digest.c:72:33: warning: variable 'altenzfile' set but not used [-Wunused-but-set-variable] 72 | int c,show_info = FALSE,altenzfile = FALSE; | ^~~~~~~~~~ gp_digest.c:64:13: warning: unused variable 'width' [-Wunused-variable] 64 | int width = 70 ; /* width with which the sequence gets formatted */ | ^~~~~ gp_digest.c: In function 'FindRestrictionSites': gp_digest.c:211:33: error: implicit declaration of function 'Compare' [-Wimplicit-function-declaration] 211 | while(jsequ[i+j],e->sequ[j]) ) j++; | ^~~~~~~ gp_digest.c:197:17: warning: unused variable 'width' [-Wunused-variable] 197 | int i,j,width = 70 ; | ^~~~~ --- gp_dimer --- gp_dimer.c: In function 'main': gp_dimer.c:109:9: error: implicit declaration of function 'PrintHeader' [-Wimplicit-function-declaration] 109 | PrintHeader(options) ; | ^~~~~~~~~~~ gp_dimer.c:57:14: warning: unused variable 'message' [-Wunused-variable] 57 | char message[100] ; | ^~~~~~~ gp_dimer.c:53:23: warning: unused variable 'outseq' [-Wunused-variable] 53 | sekw *inseq, *outseq ; | ^~~~~~ gp_dimer.c:51:13: warning: unused variable 'width' [-Wunused-variable] 51 | int width = 70 ; /* width with which the sequence gets formatted */ | ^~~~~ gp_dimer.c: In function 'GetFtable': gp_dimer.c:219:22: warning: array subscript has type 'char' [-Wchar-subscripts] 219 | i = C[c1] ; j = C[c2] ; | ^ gp_dimer.c:219:34: warning: array subscript has type 'char' [-Wchar-subscripts] 219 | i = C[c1] ; j = C[c2] ; | ^ --- gp_cusage --- gp_cusage.c: In function 'CountCodons': gp_cusage.c:198:65: warning: array subscript has type 'char' [-Wchar-subscripts] 198 | for(i = 0,j = 0;i<3;i++,j++) coord[i] = Conv[inseq->sequ[j]] ; | ~~~~~~~~~~~^~~ gp_cusage.c:215:57: warning: array subscript has type 'char' [-Wchar-subscripts] 215 | else coord[i] = Conv[inseq->sequ[j]] ; | ~~~~~~~~~~~^~~ gp_cusage.c:185:18: warning: unused variable 'tmp' [-Wunused-variable] 185 | char t, *tmp; | ^~~ gp_cusage.c: In function 'ReadCodonTable': gp_cusage.c:280:32: warning: array subscript has type 'char' [-Wchar-subscripts] 280 | if(Conv[t] > 3 || Conv[t] < 0) { | ^ gp_cusage.c:280:47: warning: array subscript has type 'char' [-Wchar-subscripts] 280 | if(Conv[t] > 3 || Conv[t] < 0) { | ^ gp_cusage.c:283:48: warning: array subscript has type 'char' [-Wchar-subscripts] 283 | coord[i] = Conv[t] ; | ^ gp_cusage.c:295:44: warning: array subscript has type 'char' [-Wchar-subscripts] 295 | outtable->tbl[coord[0]][coord[1]][coord[2]] = t ; | ~~~~~^~~ gp_cusage.c:295:54: warning: array subscript has type 'char' [-Wchar-subscripts] 295 | outtable->tbl[coord[0]][coord[1]][coord[2]] = t ; | ~~~~~^~~ gp_cusage.c:295:64: warning: array subscript has type 'char' [-Wchar-subscripts] 295 | outtable->tbl[coord[0]][coord[1]][coord[2]] = t ; | ~~~~~^~~ gp_cusage.c: In function 'PrintCodonUsageTable': gp_cusage.c:332:77: warning: array subscript has type 'char' [-Wchar-subscripts] 332 | one2three[cdtable->tbl[i][j][k]]) ; | ~~~~~~~~~~~~~~~~~~^~~ gp_cusage.c:368:85: warning: array subscript has type 'char' [-Wchar-subscripts] 368 | one2three[cdtable->tbl[i][j][k]], | ~~~~~~~~~~~~~~~~~~^~~ gp_cusage.c:414:85: warning: array subscript has type 'char' [-Wchar-subscripts] 414 | one2three[cdtable->tbl[i][j][k]], | ~~~~~~~~~~~~~~~~~~^~~ gp_cusage.c: In function 'PrintCodonTable': gp_cusage.c:489:85: warning: array subscript has type 'char' [-Wchar-subscripts] 489 | one2three[intable->tbl[i][j][k]]) ; | ~~~~~~~~~~~~~~~~~~^~~ --- gp_digest --- *** [gp_digest] Error code 1 make[1]: stopped making "all" in /home/pbulk/build/biology/gp/work/gp-0.26/src --- gp_dimer --- *** [gp_dimer] Error code 1 make[1]: stopped making "all" in /home/pbulk/build/biology/gp/work/gp-0.26/src make[1]: 2 errors make[1]: stopped making "all" in /home/pbulk/build/biology/gp/work/gp-0.26/src *** [all] Error code 2 bmake: stopped making "all" in /home/pbulk/build/biology/gp/work/gp-0.26 bmake: 1 error bmake: stopped making "all" in /home/pbulk/build/biology/gp/work/gp-0.26 *** Error code 2 Stop. bmake[1]: stopped making "all" in /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/gp *** Error code 1 Stop. bmake: stopped making "all" in /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/gp