* Package: sci-biology/rnaplex-0.2 * Repository: science * Maintainer: sci-biology@gentoo.org * USE: abi_x86_64 amd64 elibc_glibc kernel_linux userland_GNU * FEATURES: network-sandbox preserve-libs sandbox userpriv usersandbox >>> Unpacking source... >>> Unpacking RNAplex-0.2.tar.gz to /var/tmp/portage/sci-biology/rnaplex-0.2/work >>> Source unpacked in /var/tmp/portage/sci-biology/rnaplex-0.2/work >>> Preparing source in /var/tmp/portage/sci-biology/rnaplex-0.2/work/RNAplex-0.2 ... >>> Source prepared. >>> Configuring source in /var/tmp/portage/sci-biology/rnaplex-0.2/work/RNAplex-0.2 ... * econf: updating RNAplex-0.2/config.guess with /usr/share/gnuconfig/config.guess * econf: updating RNAplex-0.2/config.sub with /usr/share/gnuconfig/config.sub ./configure --prefix=/usr --build=x86_64-pc-linux-gnu --host=x86_64-pc-linux-gnu --mandir=/usr/share/man --infodir=/usr/share/info --datadir=/usr/share --sysconfdir=/etc --localstatedir=/var/lib --disable-dependency-tracking --libdir=/usr/lib64 checking for a BSD-compatible install... /usr/lib/portage/python3.7/ebuild-helpers/xattr/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking if malloc debugging is wanted... no checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking for x86_64-pc-linux-gnu-gcc... x86_64-pc-linux-gnu-gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether x86_64-pc-linux-gnu-gcc accepts -g... yes checking for x86_64-pc-linux-gnu-gcc option to accept ISO C89... none needed checking for style of include used by make... GNU checking dependency style of x86_64-pc-linux-gnu-gcc... none checking whether x86_64-pc-linux-gnu-gcc accepts -fpic... yes checking for x86_64-pc-linux-gnu-ranlib... x86_64-pc-linux-gnu-ranlib checking whether x86_64-pc-linux-gnu-gcc and cc understand -c and -o together... yes checking how to run the C preprocessor... x86_64-pc-linux-gnu-gcc -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking malloc.h usability... yes checking malloc.h presence... yes checking for malloc.h... yes checking for strings.h... (cached) yes checking for unistd.h... (cached) yes checking for an ANSI C-conforming const... yes checking for size_t... yes checking for inline... inline checking for strdup... yes checking for strstr... yes checking for strchr... yes checking for erand48... yes configure: creating ./config.status config.status: creating Makefile config.status: creating ViennaRNA.spec config.status: creating Progs/Makefile config.status: creating lib/Makefile config.status: creating man/Makefile config.status: creating H/Makefile config.status: creating config.h config.status: executing depfiles commands configure: Files will be installed in the following directories: Executables: /usr/bin Libraries: /usr/lib64 Header files: /usr/include Extra Data: /usr/share Man pages: /usr/share/man >>> Source configured. >>> Compiling source in /var/tmp/portage/sci-biology/rnaplex-0.2/work/RNAplex-0.2 ... make -j1 make all-recursive make[1]: Entering directory '/var/tmp/portage/sci-biology/rnaplex-0.2/work/RNAplex-0.2' Making all in lib make[2]: Entering directory '/var/tmp/portage/sci-biology/rnaplex-0.2/work/RNAplex-0.2/lib' x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -fpic -O2 -pipe -march=native -fno-diagnostics-color -c -o libRNAplex_a-dist_vars.o `test -f 'dist_vars.c' || echo './'`dist_vars.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -fpic -O2 -pipe -march=native -fno-diagnostics-color -c -o libRNAplex_a-fold_vars.o `test -f 'fold_vars.c' || echo './'`fold_vars.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -fpic -O2 -pipe -march=native -fno-diagnostics-color -c -o libRNAplex_a-part_func.o `test -f 'part_func.c' || echo './'`part_func.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -fpic -O2 -pipe -march=native -fno-diagnostics-color -c -o libRNAplex_a-read_epars.o `test -f 'read_epars.c' || echo './'`read_epars.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -fpic -O2 -pipe -march=native -fno-diagnostics-color -c -o libRNAplex_a-treedist.o `test -f 'treedist.c' || echo './'`treedist.c treedist.c: In function ‘print_postorder_list’: treedist.c:437:13: warning: type defaults to ‘int’ in declaration of ‘i’ [-Wimplicit-int] 437 | register i; | ^ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -fpic -O2 -pipe -march=native -fno-diagnostics-color -c -o libRNAplex_a-energy_par.o `test -f 'energy_par.c' || echo './'`energy_par.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -fpic -O2 -pipe -march=native -fno-diagnostics-color -c -o libRNAplex_a-inverse.o `test -f 'inverse.c' || echo './'`inverse.c inverse.c: In function ‘pf_cost’: inverse.c:488:16: warning: passing argument 1 of ‘pf_fold’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 488 | f = pf_fold(string, structure); | ^~~~~~ In file included from inverse.c:20: ./../H/part_func.h:6:29: note: expected ‘char *’ but argument is of type ‘const char *’ 6 | extern float pf_fold(char *sequence, char *structure); | ~~~~~~^~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -fpic -O2 -pipe -march=native -fno-diagnostics-color -c -o libRNAplex_a-ProfileDist.o `test -f 'ProfileDist.c' || echo './'`ProfileDist.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -fpic -O2 -pipe -march=native -fno-diagnostics-color -c -o libRNAplex_a-RNAstruct.o `test -f 'RNAstruct.c' || echo './'`RNAstruct.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -fpic -O2 -pipe -march=native -fno-diagnostics-color -c -o libRNAplex_a-utils.o `test -f 'utils.c' || echo './'`utils.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -fpic -O2 -pipe -march=native -fno-diagnostics-color -c -o libRNAplex_a-fold.o `test -f 'fold.c' || echo './'`fold.c fold.c:936:2: warning: ‘P’ is static but used in inline function ‘LoopEnergy’ which is not static 936 | P->mismatchI[type_2][sq1][sp1]; | ^ fold.c:935:17: warning: ‘P’ is static but used in inline function ‘LoopEnergy’ which is not static 935 | energy += P->mismatchI[type][si1][sj1]+ | ^ fold.c:933:41: warning: ‘P’ is static but used in inline function ‘LoopEnergy’ which is not static 933 | energy += MIN2(MAX_NINIO, (nl-ns)*P->F_ninio[2]); | ^ fold.c:74:45: note: in definition of macro ‘MIN2’ 74 | #define MIN2(A, B) ((A) < (B) ? (A) : (B)) | ^ fold.c:933:41: warning: ‘P’ is static but used in inline function ‘LoopEnergy’ which is not static 933 | energy += MIN2(MAX_NINIO, (nl-ns)*P->F_ninio[2]); | ^ fold.c:74:33: note: in definition of macro ‘MIN2’ 74 | #define MIN2(A, B) ((A) < (B) ? (A) : (B)) | ^ fold.c:931:30: warning: ‘P’ is static but used in inline function ‘LoopEnergy’ which is not static 931 | (P->internal_loop[30]+(int)(P->lxc*log((n1+n2)/30.))); | ^ fold.c:931:3: warning: ‘P’ is static but used in inline function ‘LoopEnergy’ which is not static 931 | (P->internal_loop[30]+(int)(P->lxc*log((n1+n2)/30.))); | ^ fold.c:930:34: warning: ‘P’ is static but used in inline function ‘LoopEnergy’ which is not static 930 | energy = (n1+n2<=MAXLOOP)?(P->internal_loop[n1+n2]): | ^ fold.c:928:14: warning: ‘P’ is static but used in inline function ‘LoopEnergy’ which is not static 928 | return P->int22[type][type_2][si1][sp1][sq1][sj1]; | ^ fold.c:923:13: warning: ‘P’ is static but used in inline function ‘LoopEnergy’ which is not static 923 | energy = P->int21[type_2][type][sq1][si1][sp1]; | ^ fold.c:921:13: warning: ‘P’ is static but used in inline function ‘LoopEnergy’ which is not static 921 | energy = P->int21[type][type_2][si1][sq1][sj1]; | ^ fold.c:918:9: warning: ‘P’ is static but used in inline function ‘LoopEnergy’ which is not static 918 | return P->int11[type][type_2][si1][sj1]; | ^ fold.c:911:31: warning: ‘P’ is static but used in inline function ‘LoopEnergy’ which is not static 911 | if (type_2>2) energy += P->TerminalAU; | ^ fold.c:910:29: warning: ‘P’ is static but used in inline function ‘LoopEnergy’ which is not static 910 | if (type>2) energy += P->TerminalAU; | ^ fold.c:908:26: warning: ‘P’ is static but used in inline function ‘LoopEnergy’ which is not static 908 | if (nl==1) energy += P->stack[type][type_2]; | ^ fold.c:907:27: warning: ‘P’ is static but used in inline function ‘LoopEnergy’ which is not static 907 | (P->bulge[30]+(int)(P->lxc*log(nl/30.))); | ^ fold.c:907:8: warning: ‘P’ is static but used in inline function ‘LoopEnergy’ which is not static 907 | (P->bulge[30]+(int)(P->lxc*log(nl/30.))); | ^ fold.c:906:28: warning: ‘P’ is static but used in inline function ‘LoopEnergy’ which is not static 906 | energy = (nl<=MAXLOOP)?P->bulge[nl]: | ^ fold.c:903:12: warning: ‘P’ is static but used in inline function ‘LoopEnergy’ which is not static 903 | return P->stack[type][type_2]; /* stack */ | ^ fold.c:845:15: warning: ‘P’ is static but used in inline function ‘HairpinE’ which is not static 845 | energy += P->mismatchH[type][si1][sj1]; | ^ fold.c:842:17: warning: ‘P’ is static but used in inline function ‘HairpinE’ which is not static 842 | energy += P->TerminalAU; /* penalty for closing AU GU pair */ | ^ fold.c:839:36: warning: ‘P’ is static but used in inline function ‘HairpinE’ which is not static 839 | energy += P->Triloop_E[(ts - P->Triloops)/6]; | ^ fold.c:839:17: warning: ‘P’ is static but used in inline function ‘HairpinE’ which is not static 839 | energy += P->Triloop_E[(ts - P->Triloops)/6]; | ^ fold.c:838:20: warning: ‘P’ is static but used in inline function ‘HairpinE’ which is not static 838 | if ((ts=strstr(P->Triloops, tl))) | ^ fold.c:833:34: warning: ‘P’ is static but used in inline function ‘HairpinE’ which is not static 833 | energy += P->TETRA_ENERGY[(ts - P->Tetraloops)/7]; | ^ fold.c:833:12: warning: ‘P’ is static but used in inline function ‘HairpinE’ which is not static 833 | energy += P->TETRA_ENERGY[(ts - P->Tetraloops)/7]; | ^ fold.c:832:22: warning: ‘P’ is static but used in inline function ‘HairpinE’ which is not static 832 | if ((ts=strstr(P->Tetraloops, tl))) | ^ fold.c:827:26: warning: ‘P’ is static but used in inline function ‘HairpinE’ which is not static 827 | P->hairpin[30]+(int)(P->lxc*log((size)/30.)); | ^ fold.c:827:5: warning: ‘P’ is static but used in inline function ‘HairpinE’ which is not static 827 | P->hairpin[30]+(int)(P->lxc*log((size)/30.)); | ^ fold.c:826:27: warning: ‘P’ is static but used in inline function ‘HairpinE’ which is not static 826 | energy = (size <= 30) ? P->hairpin[size] : | ^ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -fpic -O2 -pipe -march=native -fno-diagnostics-color -c -o libRNAplex_a-naview.o `test -f 'naview.c' || echo './'`naview.c naview.c: In function ‘dump_loops’: naview.c:334:28: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘long int’ [-Wformat=] 334 | printf("\nRoot loop is #%d\n",(root-loops)+1); | ~^ ~~~~~~~~~~~~~~ | | | | int long int | %ld x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -fpic -O2 -pipe -march=native -fno-diagnostics-color -c -o libRNAplex_a-PS_dot.o `test -f 'PS_dot.c' || echo './'`PS_dot.c PS_dot.c: In function ‘PS_rna_plot_a’: PS_dot.c:341:36: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘double’ [-Wformat=] 341 | printf("nt %d pairs with %d X %d Y %d\n", i, pair_table[i],X[i],Y[i]); | ~^ ~~~~ | | | | int double | %f PS_dot.c:341:41: warning: format ‘%d’ expects argument of type ‘int’, but argument 5 has type ‘double’ [-Wformat=] 341 | printf("nt %d pairs with %d X %d Y %d\n", i, pair_table[i],X[i],Y[i]); | ~^ ~~~~ | | | | int double | %f In file included from /usr/include/string.h:519, from PS_dot.c:13: In function ‘strncpy’, inlined from ‘PS_color_aln’ at PS_dot.c:1655:4: /usr/include/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PS_dot.c: In function ‘PS_color_aln’: PS_dot.c:1655:4: note: length computed here 1655 | strncpy(ruler+i,tmpBuffer,strlen(tmpBuffer)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/string.h:519, from PS_dot.c:13: In function ‘strncpy’, inlined from ‘aliPS_color_aln’ at PS_dot.c:1926:4: /usr/include/bits/string_fortified.h:106:10: warning: ‘__builtin_strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PS_dot.c: In function ‘aliPS_color_aln’: PS_dot.c:1926:4: note: length computed here 1926 | strncpy(ruler+i,tmpBuffer,strlen(tmpBuffer)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -fpic -O2 -pipe -march=native -fno-diagnostics-color -c -o libRNAplex_a-stringdist.o `test -f 'stringdist.c' || echo './'`stringdist.c stringdist.c:24: warning: "INFINITY" redefined 24 | #define INFINITY 10000 | In file included from stringdist.c:12: /usr/include/math.h:91: note: this is the location of the previous definition 91 | # define INFINITY (__builtin_inff ()) | x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -fpic -O2 -pipe -march=native -fno-diagnostics-color -c -o libRNAplex_a-params.o `test -f 'params.c' || echo './'`params.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -fpic -O2 -pipe -march=native -fno-diagnostics-color -c -o libRNAplex_a-subopt.o `test -f 'subopt.c' || echo './'`subopt.c subopt.c: In function ‘subopt’: subopt.c:507:37: warning: implicit declaration of function ‘initialize_cofold’; did you mean ‘initialize_fold’? [-Wimplicit-function-declaration] 507 | (circ)? initialize_fold(length) : initialize_cofold(length); | ^~~~~~~~~~~~~~~~~ | initialize_fold subopt.c:508:49: warning: implicit declaration of function ‘cofold’; did you mean ‘fold’? [-Wimplicit-function-declaration] 508 | min_en = (circ) ? circfold(sequence, struc) : cofold(sequence, struc); | ^~~~~~ | fold subopt.c:647:26: warning: implicit declaration of function ‘free_co_arrays’; did you mean ‘free_arrays’? [-Wimplicit-function-declaration] 647 | (circ) ? free_arrays():free_co_arrays(); | ^~~~~~~~~~~~~~ | free_arrays x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -fpic -O2 -pipe -march=native -fno-diagnostics-color -c -o libRNAplex_a-list.o `test -f 'list.c' || echo './'`list.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -fpic -O2 -pipe -march=native -fno-diagnostics-color -c -o libRNAplex_a-Lfold.o `test -f 'Lfold.c' || echo './'`Lfold.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -fpic -O2 -pipe -march=native -fno-diagnostics-color -c -o libRNAplex_a-cofold.o `test -f 'cofold.c' || echo './'`cofold.c cofold.c:1303:8: warning: return type defaults to ‘int’ [-Wimplicit-int] 1303 | static comp_pair(const void *A, const void *B) { | ^~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -fpic -O2 -pipe -march=native -fno-diagnostics-color -c -o libRNAplex_a-part_func_co.o `test -f 'part_func_co.c' || echo './'`part_func_co.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -fpic -O2 -pipe -march=native -fno-diagnostics-color -c -o libRNAplex_a-ProfileAln.o `test -f 'ProfileAln.c' || echo './'`ProfileAln.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -fpic -O2 -pipe -march=native -fno-diagnostics-color -c -o libRNAplex_a-duplex.o `test -f 'duplex.c' || echo './'`duplex.c duplex.c: In function ‘aliduplexfold’: duplex.c:385:38: warning: passing argument 3 of ‘alibacktrack’ from incompatible pointer type [-Wincompatible-pointer-types] 385 | struc = alibacktrack(i_min, j_min, S1, S2); | ^~ | | | short int ** duplex.c:37:56: note: expected ‘const short int **’ but argument is of type ‘short int **’ 37 | PRIVATE char * alibacktrack(int i, int j, const short *S1[], const short *S2[]); | ~~~~~~~~~~~~~^~~~ duplex.c:385:42: warning: passing argument 4 of ‘alibacktrack’ from incompatible pointer type [-Wincompatible-pointer-types] 385 | struc = alibacktrack(i_min, j_min, S1, S2); | ^~ | | | short int ** duplex.c:37:75: note: expected ‘const short int **’ but argument is of type ‘short int **’ 37 | har * alibacktrack(int i, int j, const short *S1[], const short *S2[]); | ~~~~~~~~~~~~~^~~~ duplex.c: In function ‘aliduplex_subopt’: duplex.c:463:32: warning: passing argument 3 of ‘alibacktrack’ from incompatible pointer type [-Wincompatible-pointer-types] 463 | struc = alibacktrack(i,j,S1,S2); | ^~ | | | short int ** duplex.c:37:56: note: expected ‘const short int **’ but argument is of type ‘short int **’ 37 | PRIVATE char * alibacktrack(int i, int j, const short *S1[], const short *S2[]); | ~~~~~~~~~~~~~^~~~ duplex.c:463:35: warning: passing argument 4 of ‘alibacktrack’ from incompatible pointer type [-Wincompatible-pointer-types] 463 | struc = alibacktrack(i,j,S1,S2); | ^~ | | | short int ** duplex.c:37:75: note: expected ‘const short int **’ but argument is of type ‘short int **’ 37 | har * alibacktrack(int i, int j, const short *S1[], const short *S2[]); | ~~~~~~~~~~~~~^~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -fpic -O2 -pipe -march=native -fno-diagnostics-color -c -o libRNAplex_a-alifold.o `test -f 'alifold.c' || echo './'`alifold.c alifold.c: In function ‘make_pscores’: alifold.c:722:25: warning: passing argument 1 of ‘get_ribosum’ from incompatible pointer type [-Wincompatible-pointer-types] 722 | else dm=get_ribosum(AS,n_seq,n); | ^~ | | | const char * const* In file included from alifold.c:23: ./../H/ribo.h:1:34: note: expected ‘char **’ but argument is of type ‘const char * const*’ 1 | extern float **get_ribosum(char *Alseq[], int n_seq, int length); | ~~~~~~^~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -fpic -O2 -pipe -march=native -fno-diagnostics-color -c -o libRNAplex_a-alipfold.o `test -f 'alipfold.c' || echo './'`alipfold.c alipfold.c: In function ‘make_pscores’: alipfold.c:1154:25: warning: passing argument 1 of ‘get_ribosum’ from incompatible pointer type [-Wincompatible-pointer-types] 1154 | else dm=get_ribosum(AS,n_seq,n); | ^~ | | | const char * const* In file included from alipfold.c:22: ./../H/ribo.h:1:34: note: expected ‘char **’ but argument is of type ‘const char * const*’ 1 | extern float **get_ribosum(char *Alseq[], int n_seq, int length); | ~~~~~~^~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -fpic -O2 -pipe -march=native -fno-diagnostics-color -c -o libRNAplex_a-aln_util.o `test -f 'aln_util.c' || echo './'`aln_util.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -fpic -O2 -pipe -march=native -fno-diagnostics-color -c -o libRNAplex_a-LPfold.o `test -f 'LPfold.c' || echo './'`LPfold.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -fpic -O2 -pipe -march=native -fno-diagnostics-color -c -o libRNAplex_a-part_func_up.o `test -f 'part_func_up.c' || echo './'`part_func_up.c In file included from /usr/include/stdio.h:866, from part_func_up.c:56: In function ‘sprintf’, inlined from ‘plot_free_pu_out’ at part_func_up.c:1449:3: /usr/include/bits/stdio2.h:38:10: warning: ‘__builtin___sprintf_chk’ writing 3 bytes into a region of size 2 overflows the destination [-Wstringop-overflow=] 38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 39 | __bos (__s), __fmt, __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -fpic -O2 -pipe -march=native -fno-diagnostics-color -c -o libRNAplex_a-ribo.o `test -f 'ribo.c' || echo './'`ribo.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -fpic -O2 -pipe -march=native -fno-diagnostics-color -c -o libRNAplex_a-findpath.o `test -f 'findpath.c' || echo './'`findpath.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -fpic -O2 -pipe -march=native -fno-diagnostics-color -c -o libRNAplex_a-MEA.o `test -f 'MEA.c' || echo './'`MEA.c x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -fpic -O2 -pipe -march=native -fno-diagnostics-color -c -o libRNAplex_a-ali_plex.o `test -f 'ali_plex.c' || echo './'`ali_plex.c ali_plex.c: In function ‘alifind_max’: ali_plex.c:586:35: warning: format ‘%d’ expects argument of type ‘int’, but argument 6 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=] 586 | printf("%s %3d,%-3d : %3d,%-3d (%5.2f)\n", test.structure, | ~~~^ | | | int | %-3ld ...... 590 | begin_q-11 + test.j +strlen(test.structure) -l1 -2 , test.energy); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | size_t {aka long unsigned int} ali_plex.c: In function ‘aliplot_max’: ali_plex.c:634:34: warning: format ‘%d’ expects argument of type ‘int’, but argument 6 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=] 634 | printf("%s %3d,%-3d : %3d,%-3d (%5.2f)", | ~~~^ | | | int | %-3ld ...... 639 | begin_q -11 + test.j +strlen(test.structure) - l1 - 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | size_t {aka long unsigned int} x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -fpic -O2 -pipe -march=native -fno-diagnostics-color -c -o libRNAplex_a-plex.o `test -f 'plex.c' || echo './'`plex.c plex.c: In function ‘find_max_XS’: plex.c:1113:33: warning: format ‘%d’ expects argument of type ‘int’, but argument 6 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=] 1113 | printf("%s %3d,%-3d : %3d,%-3d (%5.2f = %5.2f + %5.2f + %5.2f) [%5.2f = %5.2f + %5.2f + %5.2f] \n", test.structure, | ~~~^ | | | int | %-3ld ...... 1117 | (begin_q -11) + test.j + strlen(test.structure)-l1-2-10, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | size_t {aka long unsigned int} plex.c: In function ‘plot_max_XS’: plex.c:1206:34: warning: format ‘%d’ expects argument of type ‘int’, but argument 6 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=] 1206 | printf("%s %3d,%-3d : %3d,%-3d (%5.2f = %5.2f + %5.2f + %5.2f) [%5.2f = %5.2f + %5.2f + %5.2f] \n", test.structure, | ~~~^ | | | int | %-3ld ...... 1210 | (begin_q -11) + test.j + strlen(test.structure)-l1-2-10, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | size_t {aka long unsigned int} plex.c: In function ‘find_max’: plex.c:1998:33: warning: format ‘%d’ expects argument of type ‘int’, but argument 6 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=] 1998 | printf("%s %3d,%-3d : %3d,%-3d (%5.2f) [%5.2f]\n", test.structure, | ~~~^ | | | int | %-3ld ...... 2002 | (begin_q -11) + test.j + strlen(test.structure)-l1-2-10, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | size_t {aka long unsigned int} plex.c:2045:33: warning: format ‘%d’ expects argument of type ‘int’, but argument 6 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=] 2045 | printf("%s %3d,%-3d : %3d,%-3d (%5.2f)\n", test.structure, | ~~~^ | | | int | %-3ld ...... 2049 | (begin_q -11) + test.j + strlen(test.structure)-l1-2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | size_t {aka long unsigned int} plex.c: In function ‘plot_max’: plex.c:2080:34: warning: format ‘%d’ expects argument of type ‘int’, but argument 6 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=] 2080 | printf("%s %3d,%-3d : %3d,%-3d (%5.2f) [%5.2f]", test.structure, | ~~~^ | | | int | %-3ld ...... 2084 | (begin_q -11) + test.j + strlen(test.structure)-l1-2-10, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | size_t {aka long unsigned int} plex.c:2102:34: warning: format ‘%d’ expects argument of type ‘int’, but argument 6 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=] 2102 | printf("%s %3d,%-3d : %3d,%-3d (%5.2f)", test.structure, | ~~~^ | | | int | %-3ld ...... 2106 | (begin_q -11) + test.j + strlen(test.structure)-l1-2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | size_t {aka long unsigned int} x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -fpic -O2 -pipe -march=native -fno-diagnostics-color -c -o libRNAplex_a-c_plex.o `test -f 'c_plex.c' || echo './'`c_plex.c c_plex.c: In function ‘find_max_C’: c_plex.c:1092:35: warning: format ‘%d’ expects argument of type ‘int’, but argument 6 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=] 1092 | printf("%s %3d,%-3d : %3d,%-3d (%5.2f)\n", test.structure, | ~~~^ | | | int | %-3ld ...... 1096 | (begin_q -11) + test.j + strlen(test.structure)-l1-2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | size_t {aka long unsigned int} c_plex.c: In function ‘plot_max_C’: c_plex.c:1133:36: warning: format ‘%d’ expects argument of type ‘int’, but argument 6 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=] 1133 | printf("%s %3d,%-3d : %3d,%-3d (%5.2f)\n", test.structure, | ~~~^ | | | int | %-3ld 1134 | begin_t-10+test.i-l1, begin_t-10+test.i-1, begin_q-10 +test.j-1 , 1135 | (begin_q -11) + test.j + strlen(test.structure)-l1-2 , test.energy); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | size_t {aka long unsigned int} rm -f libRNAplex.a ar cru libRNAplex.a libRNAplex_a-dist_vars.o libRNAplex_a-fold_vars.o libRNAplex_a-part_func.o libRNAplex_a-read_epars.o libRNAplex_a-treedist.o libRNAplex_a-energy_par.o libRNAplex_a-inverse.o libRNAplex_a-ProfileDist.o libRNAplex_a-RNAstruct.o libRNAplex_a-utils.o libRNAplex_a-fold.o libRNAplex_a-naview.o libRNAplex_a-PS_dot.o libRNAplex_a-stringdist.o libRNAplex_a-params.o libRNAplex_a-subopt.o libRNAplex_a-list.o libRNAplex_a-Lfold.o libRNAplex_a-cofold.o libRNAplex_a-part_func_co.o libRNAplex_a-ProfileAln.o libRNAplex_a-duplex.o libRNAplex_a-alifold.o libRNAplex_a-alipfold.o libRNAplex_a-aln_util.o libRNAplex_a-LPfold.o libRNAplex_a-part_func_up.o libRNAplex_a-ribo.o libRNAplex_a-findpath.o libRNAplex_a-MEA.o libRNAplex_a-ali_plex.o libRNAplex_a-plex.o libRNAplex_a-c_plex.o x86_64-pc-linux-gnu-ranlib libRNAplex.a make[2]: Leaving directory '/var/tmp/portage/sci-biology/rnaplex-0.2/work/RNAplex-0.2/lib' Making all in Progs make[2]: Entering directory '/var/tmp/portage/sci-biology/rnaplex-0.2/work/RNAplex-0.2/Progs' x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I./../H -O2 -pipe -march=native -fno-diagnostics-color -c RNAplex.c RNAplex.c: In function ‘main’: RNAplex.c:1007:21: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=] 1007 | printf("lengths = %d,%d\n", strlen(s1), strlen(s2)); | ~^ ~~~~~~~~~~ | | | | int size_t {aka long unsigned int} | %ld RNAplex.c:1007:24: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=] 1007 | printf("lengths = %d,%d\n", strlen(s1), strlen(s2)); | ~^ ~~~~~~~~~~ | | | | int size_t {aka long unsigned int} | %ld RNAplex.c: In function ‘linear_fit’: RNAplex.c:1733:5: warning: implicit declaration of function ‘error’; did you mean ‘perror’? [-Wimplicit-function-declaration] 1733 | error("Problem in fitting"); | ^~~~~ | perror RNAplex.c: In function ‘read_plfold_i_bin’: RNAplex.c:1389:3: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1389 | fread(first_line,sizeof(int),(end-beg)+1,fp); //get the value of the u option | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ RNAplex.c:1412:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1412 | fread(access[count],sizeof(int),(end-beg)+1,fp); //read the needed number of accessibility values | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-pc-linux-gnu-gcc -O2 -pipe -march=native -fno-diagnostics-color -Wl,-O1 -Wl,--as-needed -Wl,--defsym=__gentoo_check_ldflags__=0 -o RNAplex RNAplex.o ../lib/libRNAplex.a -lm /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: ../lib/libRNAplex.a(libRNAplex_a-subopt.o):(.bss+0x0): multiple definition of `FcM'; ../lib/libRNAplex.a(libRNAplex_a-fold.o):(.bss+0x0): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: ../lib/libRNAplex.a(libRNAplex_a-subopt.o):(.bss+0x4): multiple definition of `FcI'; ../lib/libRNAplex.a(libRNAplex_a-fold.o):(.bss+0x4): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: ../lib/libRNAplex.a(libRNAplex_a-subopt.o):(.bss+0x8): multiple definition of `FcH'; ../lib/libRNAplex.a(libRNAplex_a-fold.o):(.bss+0x8): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: ../lib/libRNAplex.a(libRNAplex_a-subopt.o):(.bss+0xc): multiple definition of `Fc'; ../lib/libRNAplex.a(libRNAplex_a-fold.o):(.bss+0xc): first defined here /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: ../lib/libRNAplex.a(libRNAplex_a-fold.o): in function `backtrack': fold.c:(.text+0x138d): undefined reference to `LoopEnergy' /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: ../lib/libRNAplex.a(libRNAplex_a-fold.o): in function `fill_arrays': fold.c:(.text+0x263d): undefined reference to `LoopEnergy' /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: ../lib/libRNAplex.a(libRNAplex_a-fold.o): in function `stack_energy': fold.c:(.text+0x3689): undefined reference to `LoopEnergy' /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: ../lib/libRNAplex.a(libRNAplex_a-fold.o): in function `circfold': fold.c:(.text+0x4985): undefined reference to `LoopEnergy' /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: ../lib/libRNAplex.a(libRNAplex_a-fold.o): in function `energy_of_circ_struct': fold.c:(.text+0x5bdb): undefined reference to `LoopEnergy' /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: ../lib/libRNAplex.a(libRNAplex_a-fold.o):fold.c:(.text+0x6474): more undefined references to `LoopEnergy' follow /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: ../lib/libRNAplex.a(libRNAplex_a-subopt.o): in function `repeat': subopt.c:(.text+0xbd4): undefined reference to `HairpinE' /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: ../lib/libRNAplex.a(libRNAplex_a-subopt.o): in function `subopt': subopt.c:(.text+0x217f): undefined reference to `HairpinE' /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: subopt.c:(.text+0x2510): undefined reference to `LoopEnergy' /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: ../lib/libRNAplex.a(libRNAplex_a-ali_plex.o): in function `aliduplexfold': ali_plex.c:(.text+0xb5c): undefined reference to `LoopEnergy' /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: ali_plex.c:(.text+0x107c): undefined reference to `LoopEnergy' /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: ../lib/libRNAplex.a(libRNAplex_a-ali_plex.o): in function `aliduplexfold_XS': ali_plex.c:(.text+0x1dd1): undefined reference to `LoopEnergy' /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: ali_plex.c:(.text+0x2438): undefined reference to `LoopEnergy' /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: ../lib/libRNAplex.a(libRNAplex_a-plex.o):plex.c:(.text+0x1d4e): more undefined references to `LoopEnergy' follow /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: ../lib/libRNAplex.a(libRNAplex_a-alifold.o): in function `backtrack': alifold.c:(.text+0xb38): undefined reference to `HairpinE' /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: alifold.c:(.text+0xcdc): undefined reference to `LoopEnergy' /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: ../lib/libRNAplex.a(libRNAplex_a-alifold.o): in function `stack_energy.isra.0': alifold.c:(.text+0x14c0): undefined reference to `LoopEnergy' /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: alifold.c:(.text+0x16cf): undefined reference to `HairpinE' /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: ../lib/libRNAplex.a(libRNAplex_a-alifold.o): in function `fill_arrays.isra.0': alifold.c:(.text+0x1fc7): undefined reference to `HairpinE' /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: alifold.c:(.text+0x2286): undefined reference to `LoopEnergy' /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: ../lib/libRNAplex.a(libRNAplex_a-alifold.o): in function `circalifold': alifold.c:(.text+0x42e2): undefined reference to `HairpinE' /usr/lib/gcc/x86_64-pc-linux-gnu/10.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: alifold.c:(.text+0x459e): undefined reference to `LoopEnergy' collect2: error: ld returned 1 exit status make[2]: *** [Makefile:241: RNAplex] Error 1 make[2]: Leaving directory '/var/tmp/portage/sci-biology/rnaplex-0.2/work/RNAplex-0.2/Progs' make[1]: *** [Makefile:318: all-recursive] Error 1 make[1]: Leaving directory '/var/tmp/portage/sci-biology/rnaplex-0.2/work/RNAplex-0.2' make: *** [Makefile:234: all] Error 2 * ERROR: sci-biology/rnaplex-0.2::science failed (compile phase): * emake failed * * If you need support, post the output of `emerge --info '=sci-biology/rnaplex-0.2::science'`, * the complete build log and the output of `emerge -pqv '=sci-biology/rnaplex-0.2::science'`. * The complete build log is located at '/var/log/portage/sci-biology:rnaplex-0.2:20201120-032223.log'. * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-biology/rnaplex-0.2/temp/build.log'. * The ebuild environment file is located at '/var/tmp/portage/sci-biology/rnaplex-0.2/temp/environment'. * Working directory: '/var/tmp/portage/sci-biology/rnaplex-0.2/work/RNAplex-0.2' * S: '/var/tmp/portage/sci-biology/rnaplex-0.2/work/RNAplex-0.2'