sci-biology:rnaplex-0.2:20201120-032223.log

sci-biology:rnaplex-0.2:20201120-032223.log (text/plain), 41.24 KB, created by Toralf Förster on 2020-11-20 15:54:59 UTC

 * Package:    sci-biology/rnaplex-0.2
 * Repository: science
 * Maintainer: [e-mail]
 * 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'