D: [iurt_root_command] chroot Installing /home/pterjan/rpmbuild/SRPMS/wise2-2.4.1-10.mga10.src.rpm Building target platforms: x86_64 Building for target x86_64 Executing(%prep): /bin/sh -e /home/pterjan/rpmbuild/tmp/rpm-tmp.tnzEI1 + umask 022 + cd /home/pterjan/rpmbuild/BUILD + '[' 1 -eq 1 ']' + '[' 1 -eq 1 ']' + '[' 1 -eq 1 ']' + cd /home/pterjan/rpmbuild/BUILD + rm -rf wise2.4.1 + /usr/lib/rpm/rpmuncompress -x /home/pterjan/rpmbuild/SOURCES/wise2.4.1.tar.gz + STATUS=0 + '[' 0 -ne 0 ']' + cd wise2.4.1 + rm -rf /home/pterjan/rpmbuild/BUILD/wise2.4.1-SPECPARTS + /usr/bin/mkdir -p /home/pterjan/rpmbuild/BUILD/wise2.4.1-SPECPARTS + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w . + /usr/lib/rpm/rpmuncompress /home/pterjan/rpmbuild/SOURCES/fix_getline.patch + /usr/bin/patch -p0 -s --fuzz=0 --no-backup-if-mismatch -f + /usr/lib/rpm/rpmuncompress /home/pterjan/rpmbuild/SOURCES/wise2.4.1-replace-isnumber.patch + /usr/bin/patch -p0 -s --fuzz=0 --no-backup-if-mismatch -f + /usr/lib/rpm/rpmuncompress /home/pterjan/rpmbuild/SOURCES/wise2.4.1-fix-makefile.patch + /usr/bin/patch -p0 -s --fuzz=0 --no-backup-if-mismatch -f + /usr/lib/rpm/rpmuncompress /home/pterjan/rpmbuild/SOURCES/wise2.4.1-clean-makefile.patch + /usr/bin/patch -p0 -s --fuzz=0 --no-backup-if-mismatch -f + RPM_EC=0 ++ jobs -p + exit 0 Executing(%build): /bin/sh -e /home/pterjan/rpmbuild/tmp/rpm-tmp.kBUBYL + umask 022 + cd /home/pterjan/rpmbuild/BUILD + cd wise2.4.1 + '[' 1 -eq 1 ']' + '[' 1 -eq 1 ']' + cd src + /usr/bin/make -O -j16 V=1 VERBOSE=1 all (cd base ; /usr/bin/make CC="cc" CFLAGS="-c -O3 `pkg-config --cflags glib-2.0 --libs glib-2.0`" libwisebase.a ) make[1]: Entering directory '/home/pterjan/rpmbuild/BUILD/wise2.4.1/src/base' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-6 -pthread -lglib-2.0 wisetime.c make[1]: Leaving directory '/home/pterjan/rpmbuild/BUILD/wise2.4.1/src/base' make[1]: Entering directory '/home/pterjan/rpmbuild/BUILD/wise2.4.1/src/base' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-6 -pthread -lglib-2.0 wiserandom.c make[1]: Leaving directory '/home/pterjan/rpmbuild/BUILD/wise2.4.1/src/base' make[1]: Entering directory '/home/pterjan/rpmbuild/BUILD/wise2.4.1/src/base' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-6 -pthread -lglib-2.0 wiseoverlay.c make[1]: Leaving directory '/home/pterjan/rpmbuild/BUILD/wise2.4.1/src/base' make[1]: Entering directory '/home/pterjan/rpmbuild/BUILD/wise2.4.1/src/base' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-6 -pthread -lglib-2.0 wisememman.c make[1]: Leaving directory '/home/pterjan/rpmbuild/BUILD/wise2.4.1/src/base' make[1]: Entering directory '/home/pterjan/rpmbuild/BUILD/wise2.4.1/src/base' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-6 -pthread -lglib-2.0 wisestreaminterface.c make[1]: Leaving directory '/home/pterjan/rpmbuild/BUILD/wise2.4.1/src/base' make[1]: Entering directory '/home/pterjan/rpmbuild/BUILD/wise2.4.1/src/base' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-6 -pthread -lglib-2.0 wisefile.c make[1]: Leaving directory '/home/pterjan/rpmbuild/BUILD/wise2.4.1/src/base' make[1]: Entering directory '/home/pterjan/rpmbuild/BUILD/wise2.4.1/src/base' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-6 -pthread -lglib-2.0 linesubs.c make[1]: Leaving directory '/home/pterjan/rpmbuild/BUILD/wise2.4.1/src/base' make[1]: Entering directory '/home/pterjan/rpmbuild/BUILD/wise2.4.1/src/base' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-6 -pthread -lglib-2.0 wiseconfig.c make[1]: Leaving directory '/home/pterjan/rpmbuild/BUILD/wise2.4.1/src/base' make[1]: Entering directory '/home/pterjan/rpmbuild/BUILD/wise2.4.1/src/base' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-6 -pthread -lglib-2.0 commandline.c make[1]: Leaving directory '/home/pterjan/rpmbuild/BUILD/wise2.4.1/src/base' make[1]: Entering directory '/home/pterjan/rpmbuild/BUILD/wise2.4.1/src/base' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-6 -pthread -lglib-2.0 wiseerror.c make[1]: Leaving directory '/home/pterjan/rpmbuild/BUILD/wise2.4.1/src/base' make[1]: Entering directory '/home/pterjan/rpmbuild/BUILD/wise2.4.1/src/base' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-6 -pthread -lglib-2.0 wisestring.c make[1]: Leaving directory '/home/pterjan/rpmbuild/BUILD/wise2.4.1/src/base' make[1]: Entering directory '/home/pterjan/rpmbuild/BUILD/wise2.4.1/src/base' ar ru libwisebase.a wiseconfig.o wisestring.o wiseerror.o wisememman.o wisefile.o wiserandom.o wisetime.o wiseoverlay.o wisestreaminterface.o commandline.o linesubs.o ar: creating libwisebase.a if test -x /bin/ranlib; then /bin/ranlib libwisebase.a; else exit 0; fi if test -x /usr/bin/ranlib; then /usr/bin/ranlib libwisebase.a; else exit 0; fi make[1]: Leaving directory '/home/pterjan/rpmbuild/BUILD/wise2.4.1/src/base' (cd HMMer2 ; /usr/bin/make CC="cc" CFLAGS="-c -O3 `pkg-config --cflags glib-2.0 --libs glib-2.0`" libhmmer.a ) make[1]: Entering directory '/home/pterjan/rpmbuild/BUILD/wise2.4.1/src/HMMer2' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-6 -pthread -lglib-2.0 -c prior.c prior.c: In function 'P7ReadPrior': prior.c:102:12: error: implicit declaration of function 'strcmp' [-Wimplicit-function-declaration] 102 | if (strcmp(sptr, "DIRICHLET") == 0) pri->strategy = PRI_DCHLET; | ^~~~~~ prior.c:10:1: note: include '' or provide a declaration of 'strcmp' 9 | #include "funcs.h" +++ |+#include 10 | #include "squid.h" make[1]: *** [Makefile:69: prior.o] Error 1 make[1]: Leaving directory '/home/pterjan/rpmbuild/BUILD/wise2.4.1/src/HMMer2' make[1]: *** Waiting for unfinished jobs.... make[1]: Entering directory '/home/pterjan/rpmbuild/BUILD/wise2.4.1/src/HMMer2' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-6 -pthread -lglib-2.0 -c misc.c make[1]: Leaving directory '/home/pterjan/rpmbuild/BUILD/wise2.4.1/src/HMMer2' make[1]: Entering directory '/home/pterjan/rpmbuild/BUILD/wise2.4.1/src/HMMer2' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-6 -pthread -lglib-2.0 -c emulation.c make[1]: Leaving directory '/home/pterjan/rpmbuild/BUILD/wise2.4.1/src/HMMer2' make[1]: Entering directory '/home/pterjan/rpmbuild/BUILD/wise2.4.1/src/HMMer2' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-6 -pthread -lglib-2.0 -c plan9.c make[1]: Leaving directory '/home/pterjan/rpmbuild/BUILD/wise2.4.1/src/HMMer2' make[1]: Entering directory '/home/pterjan/rpmbuild/BUILD/wise2.4.1/src/HMMer2' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-6 -pthread -lglib-2.0 -c emit.c make[1]: Leaving directory '/home/pterjan/rpmbuild/BUILD/wise2.4.1/src/HMMer2' make[1]: Entering directory '/home/pterjan/rpmbuild/BUILD/wise2.4.1/src/HMMer2' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-6 -pthread -lglib-2.0 -c masks.c make[1]: Leaving directory '/home/pterjan/rpmbuild/BUILD/wise2.4.1/src/HMMer2' make[1]: Entering directory '/home/pterjan/rpmbuild/BUILD/wise2.4.1/src/HMMer2' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-6 -pthread -lglib-2.0 -c mathsupport.c make[1]: Leaving directory '/home/pterjan/rpmbuild/BUILD/wise2.4.1/src/HMMer2' make[1]: Entering directory '/home/pterjan/rpmbuild/BUILD/wise2.4.1/src/HMMer2' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-6 -pthread -lglib-2.0 -c tophits.c make[1]: Leaving directory '/home/pterjan/rpmbuild/BUILD/wise2.4.1/src/HMMer2' make[1]: Entering directory '/home/pterjan/rpmbuild/BUILD/wise2.4.1/src/HMMer2' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-6 -pthread -lglib-2.0 -c debug.c make[1]: Leaving directory '/home/pterjan/rpmbuild/BUILD/wise2.4.1/src/HMMer2' make[1]: Entering directory '/home/pterjan/rpmbuild/BUILD/wise2.4.1/src/HMMer2' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-6 -pthread -lglib-2.0 -c alphabet.c make[1]: Leaving directory '/home/pterjan/rpmbuild/BUILD/wise2.4.1/src/HMMer2' make[1]: Entering directory '/home/pterjan/rpmbuild/BUILD/wise2.4.1/src/HMMer2' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-6 -pthread -lglib-2.0 -c modelmakers.c make[1]: Leaving directory '/home/pterjan/rpmbuild/BUILD/wise2.4.1/src/HMMer2' make[1]: Entering directory '/home/pterjan/rpmbuild/BUILD/wise2.4.1/src/HMMer2' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-6 -pthread -lglib-2.0 -c trace.c make[1]: Leaving directory '/home/pterjan/rpmbuild/BUILD/wise2.4.1/src/HMMer2' make[1]: Entering directory '/home/pterjan/rpmbuild/BUILD/wise2.4.1/src/HMMer2' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-6 -pthread -lglib-2.0 -c plan7.c make[1]: Leaving directory '/home/pterjan/rpmbuild/BUILD/wise2.4.1/src/HMMer2' make[1]: Entering directory '/home/pterjan/rpmbuild/BUILD/wise2.4.1/src/HMMer2' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-6 -pthread -lglib-2.0 -c histogram.c make[1]: Leaving directory '/home/pterjan/rpmbuild/BUILD/wise2.4.1/src/HMMer2' make[1]: Entering directory '/home/pterjan/rpmbuild/BUILD/wise2.4.1/src/HMMer2' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-6 -pthread -lglib-2.0 -c hmmio.c make[1]: Leaving directory '/home/pterjan/rpmbuild/BUILD/wise2.4.1/src/HMMer2' make[1]: Entering directory '/home/pterjan/rpmbuild/BUILD/wise2.4.1/src/HMMer2' cc -c -O3 -I/usr/include/glib-2.0 -I/usr/lib64/glib-2.0/include -I/usr/include/sysprof-6 -pthread -lglib-2.0 -c core_algorithms.c make[1]: Leaving directory '/home/pterjan/rpmbuild/BUILD/wise2.4.1/src/HMMer2' make: *** [makefile:88: realall] Error 2 + : + cd ../src/dyc/ + /usr/bin/make -O -j16 V=1 VERBOSE=1 newdyc make: *** No rule to make target 'newdyc'. Stop. + : + export PATH=/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/home/pterjan/.local/bin:/home/pterjan/bin:/home/pterjan/rpmbuild/BUILD/wise2.4.1/src/dyc + PATH=/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/home/pterjan/.local/bin:/home/pterjan/bin:/home/pterjan/rpmbuild/BUILD/wise2.4.1/src/dyc + /usr/bin/make -O -j16 V=1 VERBOSE=1 linux cc -pthread -c -g -DUNIX -I../base/ -I../base/ inputfile.c inputfile.c:8:8: error: type defaults to 'int' in declaration of 'linecount' [-Wimplicit-int] 8 | static linecount = 0; | ^~~~~~~~~ make: *** [makefile:60: inputfile.o] Error 1 make: *** Waiting for unfinished jobs.... cc -pthread -c -g -DUNIX -I../base/ -I../base/ variable.c cc -pthread -c -g -DUNIX -I../base/ -I../base/ friend.c cc -pthread -c -g -DUNIX -I../base/ -I../base/ dynafunc.c dynafunc.dy: In function 'write_GenericMatrix_func': dynafunc.dy:2355:3: error: implicit declaration of function 'write_shatter_functions'; did you mean 'write_dc_functions'? [-Wimplicit-function-declaration] 2355 | write_shatter_functions(dfp,gm,dpi); | ^~~~~~~~~~~~~~~~~~~~~~~ | write_dc_functions make: *** [makefile:60: dynafunc.o] Error 1 cc -pthread -c -g -DUNIX -I../base/ -I../base/ modulefunc.c cc -pthread -c -g -DUNIX -I../base/ -I../base/ dynadb.c cc -pthread -c -g -DUNIX -I../base/ -I../base/ dyc.c cc -pthread -c -g -DUNIX -I../base/ -I../base/ module.c cc -pthread -c -g -DUNIX -I../base/ -I../base/ type.c cc -pthread -c -g -DUNIX -I../base/ -I../base/ dynfile.c cc -pthread -c -g -DUNIX -I../base/ -I../base/ method.c cc -pthread -c -g -DUNIX -I../base/ -I../base/ wisec.c cc -pthread -c -g -DUNIX -I../base/ -I../base/ display.c cc -pthread -c -g -DUNIX -I../base/ -I../base/ api.c cc -pthread -c -g -DUNIX -I../base/ -I../base/ dynashadow.c dynashadow.dy: In function 'optimised_shadow_GenericMatrix': dynashadow.dy:2180:31: warning: passing argument 2 of 'write_main_shadow_block' discards 'const' qualifier from pointer target type [-Wdiscarded-qualifiers] 2180 | write_main_shadow_block(dfp,gm,"DC_OPT_SHADOW_MATRIX","mat","DC_OPT_SHADOW_SPECIAL","DC_OPT_SHADOW_MATRIX_SP","DC_OPT_SHADOW_SPECIAL_SP",7,TRUE,TRUE,0,TRUE); | ^~ In file included from dynashadow.c:4: dynashadow.h:163:60: note: expected 'GenericMatrix *' but argument is of type 'const GenericMatrix *' 163 | void write_main_shadow_block(DYNFILE * dfp,GenericMatrix * gm,char * matrixtag,char * pointer_tag,char * specialtag,char * shadow_main_tag,char * shadow_special_tag,int shadow_length,boolean shadow_on_special,boolean use_special,int debug,int use_shadow_pointer); | ~~~~~~~~~~~~~~~~^~ dynashadow.dy:2187:36: warning: passing argument 2 of 'write_special_shadow_block' discards 'const' qualifier from pointer target type [-Wdiscarded-qualifiers] 2187 | write_special_shadow_block(dfp,gm,"DC_OPT_SHADOW_MATRIX","mat","DC_OPT_SHADOW_SPECIAL","DC_OPT_SHADOW_MATRIX_SP","DC_OPT_SHADOW_SPECIAL_SP",7,TRUE,0); | ^~ dynashadow.h:189:63: note: expected 'GenericMatrix *' but argument is of type 'const GenericMatrix *' 189 | void write_special_shadow_block(DYNFILE * dfp,GenericMatrix * gm,char * matrix,char * pointer_tag,char * special,char * shadow_main_tag,char * shadow_special_tag,int shadow_length,boolean shadow_on_special,int debug); | ~~~~~~~~~~~~~~~~^~ cc -pthread -c -g -DUNIX -I../base/ -I../base/ dyna2.c error: Bad exit status from /home/pterjan/rpmbuild/tmp/rpm-tmp.kBUBYL (%build) RPM build errors: Bad exit status from /home/pterjan/rpmbuild/tmp/rpm-tmp.kBUBYL (%build) I: [iurt_root_command] ERROR: chroot