sci-biology:seaview-4.6:20200201-230151.log

sci-biology:seaview-4.6:20200201-230151.log (text/plain), 25.32 KB, created by Toralf Förster on 2020-02-02 04:11:56 UTC

 * Package:    sci-biology/seaview-4.6
 * Repository: gentoo
 * Maintainer: [e-mail]
 * USE:        abi_x86_64 amd64 elibc_glibc kernel_linux userland_GNU xft
 * FEATURES:   network-sandbox preserve-libs sandbox userpriv usersandbox
>>> Unpacking source...
>>> Unpacking seaview_4.6.tar.gz to /var/tmp/portage/sci-biology/seaview-4.6/work
>>> Source unpacked in /var/tmp/portage/sci-biology/seaview-4.6/work
>>> Preparing source in /var/tmp/portage/sci-biology/seaview-4.6/work/seaview ...
>>> Source prepared.
>>> Configuring source in /var/tmp/portage/sci-biology/seaview-4.6/work/seaview ...
>>> Source configured.
>>> Compiling source in /var/tmp/portage/sci-biology/seaview-4.6/work/seaview ...
make -j1 
x86_64-pc-linux-gnu-g++ -c   -O2 -pipe -march=native -fno-common -Dunix -O2 -pipe -march=native -fno-common -I. -I/usr/include/fltk -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_THREAD_SAFE -D_REENTRANT -Icsrc  -DDEFAULT_HELPFILE=\"/usr/share/seaview/seaview.html\" -DPHYMLNAME=\"phyml\" -DNO_PDF seaview.cxx
seaview.cxx:3317:21: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix]
 3317 |   strcat(suggested, "."PDF_OR_PS_EXT);
      |                     ^
seaview.cxx:3427:17: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix]
 3427 | pdf_form->label("Set "PDF_OR_PS" output options");
      |                 ^
seaview.cxx:5003:6: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix]
 5003 |     {"Prepare "PDF_OR_PS"", 0, file_menu_callback, 0, 0},
      |      ^
seaview.cxx:5004:6: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix]
 5004 |     {""PDF_OR_PS" options...", 0, file_menu_callback, 0, FL_MENU_DIVIDER},
      |      ^
seaview.cxx: In function ‘void delete_tmp_filename(const char*)’:
seaview.cxx:638:9: warning: ignoring return value of ‘int system(const char*)’, declared with attribute warn_unused_result [-Wunused-result]
  638 |   system(fname);
      |   ~~~~~~^~~~~~~
seaview.cxx: In function ‘char* run_and_close_native_file_chooser(Fl_Native_File_Chooser*, int)’:
seaview.cxx:2876:38: warning: ignoring return value of ‘int chdir(const char*)’, declared with attribute warn_unused_result [-Wunused-result]
 2876 |    if( *last_visited_directory )chdir(last_visited_directory);
      |                                 ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/string.h:494,
                 from seaview.h:5,
                 from seaview.cxx:67:
In function ‘char* strncpy(char*, const char*, size_t)’,
    inlined from ‘void goto_callback(Fl_Widget*, void*)’ at seaview.cxx:2705:9:
/usr/include/bits/string_fortified.h:106:34: warning: ‘char* __builtin___strncpy_chk(char*, const char*, long unsigned int, long unsigned int)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
  106 |   return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
      |          ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
seaview.cxx: In function ‘void goto_callback(Fl_Widget*, void*)’:
seaview.cxx:2703:12: note: length computed here
 2703 |  l = strlen(p);
      |      ~~~~~~^~~
x86_64-pc-linux-gnu-g++ -c   -O2 -pipe -march=native -fno-common -Dunix -O2 -pipe -march=native -fno-common -I. -I/usr/include/fltk -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_THREAD_SAFE -D_REENTRANT -Icsrc  -DDEFAULT_HELPFILE=\"/usr/share/seaview/seaview.html\" -DPHYMLNAME=\"phyml\" -DNO_PDF custom.cxx
x86_64-pc-linux-gnu-g++ -c   -O2 -pipe -march=native -fno-common -Dunix -O2 -pipe -march=native -fno-common -I. -I/usr/include/fltk -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_THREAD_SAFE -D_REENTRANT -Icsrc  -DDEFAULT_HELPFILE=\"/usr/share/seaview/seaview.html\" -DPHYMLNAME=\"phyml\" -DNO_PDF use_mase_files.cxx
x86_64-pc-linux-gnu-g++ -c   -O2 -pipe -march=native -fno-common -Dunix -O2 -pipe -march=native -fno-common -I. -I/usr/include/fltk -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_THREAD_SAFE -D_REENTRANT -Icsrc  -DDEFAULT_HELPFILE=\"/usr/share/seaview/seaview.html\" -DPHYMLNAME=\"phyml\" -DNO_PDF regions.cxx
regions.cxx: In function ‘int create_gblocks_mask(SEA_VIEW*, region*, int, int, int, int, int)’:
regions.cxx:305:9: warning: ignoring return value of ‘int system(const char*)’, declared with attribute warn_unused_result [-Wunused-result]
  305 |   system(cmd);
      |   ~~~~~~^~~~~
x86_64-pc-linux-gnu-g++ -c   -O2 -pipe -march=native -fno-common -Dunix -O2 -pipe -march=native -fno-common -I. -I/usr/include/fltk -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_THREAD_SAFE -D_REENTRANT -Icsrc  -DDEFAULT_HELPFILE=\"/usr/share/seaview/seaview.html\" -DPHYMLNAME=\"phyml\" -DNO_PDF load_seq.cxx
x86_64-pc-linux-gnu-g++ -c   -O2 -pipe -march=native -fno-common -Dunix -O2 -pipe -march=native -fno-common -I. -I/usr/include/fltk -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_THREAD_SAFE -D_REENTRANT -Icsrc  -DDEFAULT_HELPFILE=\"/usr/share/seaview/seaview.html\" -DPHYMLNAME=\"phyml\" -DNO_PDF align.cxx
align.cxx: In function ‘void replace_stars(char*)’:
align.cxx:1298:7: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
 1298 |  fread(all, 1, l, in);
      |  ~~~~~^~~~~~~~~~~~~~~
x86_64-pc-linux-gnu-g++ -c   -O2 -pipe -march=native -fno-common -Dunix -O2 -pipe -march=native -fno-common -I. -I/usr/include/fltk -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_THREAD_SAFE -D_REENTRANT -Icsrc  -DDEFAULT_HELPFILE=\"/usr/share/seaview/seaview.html\" -DPHYMLNAME=\"phyml\" -DNO_PDF xfmatpt.cxx
xfmatpt.cxx:208:79: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix]
  208 | ript = cre_button(fin, curr_y, &width, but_height, fontsize, "Write "PDF_OR_PS);
      |                                                              ^

xfmatpt.cxx:873:14: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix]
  873 |   fl_message("Dot plot is now in file\n%s\nin "PDF_OR_PS" format", surface->outfname());
      |              ^
x86_64-pc-linux-gnu-g++ -c   -O2 -pipe -march=native -fno-common -Dunix -O2 -pipe -march=native -fno-common -I. -I/usr/include/fltk -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_THREAD_SAFE -D_REENTRANT -Icsrc  -DDEFAULT_HELPFILE=\"/usr/share/seaview/seaview.html\" -DPHYMLNAME=\"phyml\" -DNO_PDF comlines.cxx
x86_64-pc-linux-gnu-g++ -c   -O2 -pipe -march=native -fno-common -Dunix -O2 -pipe -march=native -fno-common -I. -I/usr/include/fltk -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_THREAD_SAFE -D_REENTRANT -Icsrc  -DDEFAULT_HELPFILE=\"/usr/share/seaview/seaview.html\" -DPHYMLNAME=\"phyml\" -DNO_PDF resource.cxx
x86_64-pc-linux-gnu-g++ -c   -O2 -pipe -march=native -fno-common -Dunix -O2 -pipe -march=native -fno-common -I. -I/usr/include/fltk -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_THREAD_SAFE -D_REENTRANT -Icsrc  -DDEFAULT_HELPFILE=\"/usr/share/seaview/seaview.html\" -DPHYMLNAME=\"phyml\" -DNO_PDF nexus.cxx
x86_64-pc-linux-gnu-g++ -c   -O2 -pipe -march=native -fno-common -Dunix -O2 -pipe -march=native -fno-common -I. -I/usr/include/fltk -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_THREAD_SAFE -D_REENTRANT -Icsrc  -DDEFAULT_HELPFILE=\"/usr/share/seaview/seaview.html\" -DPHYMLNAME=\"phyml\" -DNO_PDF viewasprots.cxx
x86_64-pc-linux-gnu-g++ -c   -O2 -pipe -march=native -fno-common -Dunix -O2 -pipe -march=native -fno-common -I. -I/usr/include/fltk -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_THREAD_SAFE -D_REENTRANT -Icsrc  -DDEFAULT_HELPFILE=\"/usr/share/seaview/seaview.html\" -DPHYMLNAME=\"phyml\" -DNO_PDF racnuc_fetch.cxx
x86_64-pc-linux-gnu-g++ -c   -O2 -pipe -march=native -fno-common -Dunix -O2 -pipe -march=native -fno-common -I. -I/usr/include/fltk -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_THREAD_SAFE -D_REENTRANT -Icsrc  -DDEFAULT_HELPFILE=\"/usr/share/seaview/seaview.html\" -DPHYMLNAME=\"phyml\" -DNO_PDF concatenate.cxx
x86_64-pc-linux-gnu-g++ -c   -O2 -pipe -march=native -fno-common -Dunix -O2 -pipe -march=native -fno-common -I. -I/usr/include/fltk -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_THREAD_SAFE -D_REENTRANT -Icsrc  -DDEFAULT_HELPFILE=\"/usr/share/seaview/seaview.html\" -DPHYMLNAME=\"phyml\" -DNO_PDF statistics.cxx
x86_64-pc-linux-gnu-g++ -c   -O2 -pipe -march=native -fno-common -Dunix -O2 -pipe -march=native -fno-common -I. -I/usr/include/fltk -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_THREAD_SAFE -D_REENTRANT -Icsrc  -DDEFAULT_HELPFILE=\"/usr/share/seaview/seaview.html\" -DPHYMLNAME=\"phyml\" -DNO_PDF trees.cxx
trees.cxx: In function ‘void run_phyml_callback(Fl_Widget*, void*)’:
trees.cxx:1233:16: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
 1233 |           fread(bootstrap_trees, l, 1, in);
      |           ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
trees.cxx: In function ‘void command_line_phylogeny(int, char**)’:
trees.cxx:2690:12: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
 2690 |       fread(utree, s, 1, in);
      |       ~~~~~^~~~~~~~~~~~~~~~~
x86_64-pc-linux-gnu-g++ -c   -O2 -pipe -march=native -fno-common -Dunix -O2 -pipe -march=native -fno-common -I. -I/usr/include/fltk -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_THREAD_SAFE -D_REENTRANT -Icsrc  -DDEFAULT_HELPFILE=\"/usr/share/seaview/seaview.html\" -DPHYMLNAME=\"phyml\" -DNO_PDF treedraw.cxx
treedraw.cxx:213:6: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix]
  213 |     {"Save as "PDF_OR_PS"", 0, file_callback, NULL, 0},
      |      ^
x86_64-pc-linux-gnu-g++ -c   -O2 -pipe -march=native -fno-common -Dunix -O2 -pipe -march=native -fno-common -I. -I/usr/include/fltk -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_THREAD_SAFE -D_REENTRANT -Icsrc  -DDEFAULT_HELPFILE=\"/usr/share/seaview/seaview.html\" -DPHYMLNAME=\"phyml\" -DNO_PDF addbootstrap.cxx
x86_64-pc-linux-gnu-g++ -c   -O2 -pipe -march=native -fno-common -Dunix -O2 -pipe -march=native -fno-common -I. -I/usr/include/fltk -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_THREAD_SAFE -D_REENTRANT -Icsrc  -DDEFAULT_HELPFILE=\"/usr/share/seaview/seaview.html\" -DPHYMLNAME=\"phyml\" -DNO_PDF least_squares_brl.cxx
x86_64-pc-linux-gnu-g++ -c   -O2 -pipe -march=native -fno-common -Dunix -O2 -pipe -march=native -fno-common -I. -I/usr/include/fltk -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_THREAD_SAFE -D_REENTRANT -Icsrc  -DDEFAULT_HELPFILE=\"/usr/share/seaview/seaview.html\" -DPHYMLNAME=\"phyml\" -DNO_PDF pseudoterminal.cxx
pseudoterminal.cxx: In function ‘int run_external_prog_in_pseudoterm(char*, const char*, const char*)’:
pseudoterminal.cxx:342:11: warning: ignoring return value of ‘FILE* freopen(const char*, const char*, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
  342 |    freopen(dialogfname, "r", stdin);
      |    ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
pseudoterminal.cxx:344:10: warning: ignoring return value of ‘FILE* freopen(const char*, const char*, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
  344 |   freopen(slavename, "a", stderr);
      |   ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
x86_64-pc-linux-gnu-g++ -c   -O2 -pipe -march=native -fno-common -Dunix -O2 -pipe -march=native -fno-common -I. -I/usr/include/fltk -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_THREAD_SAFE -D_REENTRANT -Icsrc  -DDEFAULT_HELPFILE=\"/usr/share/seaview/seaview.html\" -DPHYMLNAME=\"phyml\" -DNO_PDF unrooted.cxx
x86_64-pc-linux-gnu-g++ -c   -O2 -pipe -march=native -fno-common -Dunix -O2 -pipe -march=native -fno-common -I. -I/usr/include/fltk -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_THREAD_SAFE -D_REENTRANT -Icsrc  -DDEFAULT_HELPFILE=\"/usr/share/seaview/seaview.html\" -DPHYMLNAME=\"phyml\" -DNO_PDF pdf_or_ps.cxx
x86_64-pc-linux-gnu-g++ -c   -O2 -pipe -march=native -fno-common -Dunix -O2 -pipe -march=native -fno-common -I. -I/usr/include/fltk -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_THREAD_SAFE -D_REENTRANT -Icsrc  -DDEFAULT_HELPFILE=\"/usr/share/seaview/seaview.html\" -DPHYMLNAME=\"phyml\" -DNO_PDF svg.cxx
x86_64-pc-linux-gnu-g++ -c   -O2 -pipe -march=native -fno-common -Dunix -O2 -pipe -march=native -fno-common -I. -I/usr/include/fltk -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_THREAD_SAFE -D_REENTRANT -Icsrc  -DDEFAULT_HELPFILE=\"/usr/share/seaview/seaview.html\" -DPHYMLNAME=\"phyml\" -DNO_PDF threads.cxx
x86_64-pc-linux-gnu-g++  -c -I.  -O2 -pipe -march=native -fno-common -Dunix -O2 -pipe -march=native -fno-common -I. -I/usr/include/fltk -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_THREAD_SAFE -D_REENTRANT -Icsrc  -DDEFAULT_HELPFILE=\"/usr/share/seaview/seaview.html\" -DPHYMLNAME=\"phyml\" -DNO_PDF FL/Fl_Native_File_Chooser_FLTK.cxx
x86_64-pc-linux-gnu-gcc -c  -O2 -pipe -march=native -fno-common -O2 -pipe -march=native -fno-common -Dunix -Icsrc csrc/raa_acnuc.c
x86_64-pc-linux-gnu-gcc -c  -O2 -pipe -march=native -fno-common -O2 -pipe -march=native -fno-common -Dunix -Icsrc csrc/parser.c
x86_64-pc-linux-gnu-gcc -c  -O2 -pipe -march=native -fno-common -O2 -pipe -march=native -fno-common -Dunix -Icsrc csrc/md5.c
x86_64-pc-linux-gnu-gcc -c  -O2 -pipe -march=native -fno-common -O2 -pipe -march=native -fno-common -Dunix -Icsrc csrc/zsockr.c
x86_64-pc-linux-gnu-gcc -c  -O2 -pipe -march=native -fno-common -O2 -pipe -march=native -fno-common -Dunix -Icsrc csrc/misc_acnuc.c
x86_64-pc-linux-gnu-gcc -c  -O2 -pipe -march=native -fno-common -O2 -pipe -march=native -fno-common -Dunix -Icsrc csrc/dnapars.c
csrc/dnapars.c: In function ‘dnapars’:
csrc/dnapars.c:1685:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 1685 |     fread(tree, L, 1, outtree);
      |     ^~~~~~~~~~~~~~~~~~~~~~~~~~
x86_64-pc-linux-gnu-gcc -c  -O2 -pipe -march=native -fno-common -O2 -pipe -march=native -fno-common -Dunix -Icsrc csrc/protpars.c
csrc/protpars.c: In function ‘protpars’:
csrc/protpars.c:2097:5: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 2097 |     fread(tree, L, 1, outtree);
      |     ^~~~~~~~~~~~~~~~~~~~~~~~~~
x86_64-pc-linux-gnu-gcc -c  -O2 -pipe -march=native -fno-common -O2 -pipe -march=native -fno-common -Dunix -Icsrc csrc/seq.c
x86_64-pc-linux-gnu-gcc -c  -O2 -pipe -march=native -fno-common -O2 -pipe -march=native -fno-common -Dunix -Icsrc csrc/phylip.c
x86_64-pc-linux-gnu-gcc -c  -O2 -pipe -march=native -fno-common -O2 -pipe -march=native -fno-common -Dunix -Icsrc csrc/lwl.c
x86_64-pc-linux-gnu-gcc -c  -O2 -pipe -march=native -fno-common -O2 -pipe -march=native -fno-common -Dunix -Icsrc csrc/bionj.c
x86_64-pc-linux-gnu-gcc -c  -O2 -pipe -march=native -fno-common -O2 -pipe -march=native -fno-common -Dunix -Icsrc csrc/phyml_util.c
csrc/phyml_util.c: In function ‘Warn_And_Exit’:
csrc/phyml_util.c:47:2: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result]
   47 |  fscanf(stdin,"%c",&c);
      |  ^~~~~~~~~~~~~~~~~~~~~
x86_64-pc-linux-gnu-g++ -o seaview  -Wl,-O1 -Wl,--as-needed seaview.o custom.o use_mase_files.o regions.o load_seq.o align.o xfmatpt.o comlines.o resource.o nexus.o viewasprots.o racnuc_fetch.o concatenate.o statistics.o trees.o treedraw.o addbootstrap.o least_squares_brl.o pseudoterminal.o unrooted.o pdf_or_ps.o svg.o threads.o Fl_Native_File_Chooser_FLTK.o raa_acnuc.o parser.o md5.o zsockr.o misc_acnuc.o dnapars.o protpars.o seq.o phylip.o lwl.o bionj.o phyml_util.o  `fltk-config --use-images --ldflags` -ldl -lpthread -lz 
/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: dnapars.o:(.bss+0x0): multiple definition of `progname'; seaview.o:(.data.rel.local+0x0): first defined here
/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: protpars.o:(.bss+0x2420): multiple definition of `chars'; dnapars.o:(.bss+0x20d0): first defined here
/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: protpars.o:(.bss+0x23c0): multiple definition of `treenode'; dnapars.o:(.bss+0x2020): first defined here
/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: protpars.o:(.bss+0x23e5): multiple definition of `usertree'; dnapars.o:(.bss+0x2085): first defined here
/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: protpars.o:(.bss+0x23b0): multiple definition of `threshwt'; dnapars.o:(.bss+0x90): first defined here
/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: protpars.o:(.bss+0x1fb0): multiple definition of `fsteps'; dnapars.o:(.bss+0xb8): first defined here
/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: protpars.o:(.bss+0x20): multiple definition of `nsteps'; dnapars.o:(.bss+0xc0): first defined here
/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: protpars.o:(.bss+0x1f70): multiple definition of `minwhich'; dnapars.o:(.bss+0x2008): first defined here
/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: protpars.o:(.bss+0x2428): multiple definition of `root'; dnapars.o:(.bss+0x20d8): first defined here
/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: protpars.o:(.bss+0x2418): multiple definition of `col'; dnapars.o:(.bss+0x20c8): first defined here
/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: protpars.o:(.bss+0x1f68): multiple definition of `recompute'; dnapars.o:(.bss+0x2000): first defined here
/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: protpars.o:(.bss+0x1f88): multiple definition of `temp1'; dnapars.o:(.bss+0x70): first defined here
/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: protpars.o:(.bss+0x1f90): multiple definition of `temp'; dnapars.o:(.bss+0x78): first defined here
/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: protpars.o:(.bss+0x8): multiple definition of `place'; dnapars.o:(.bss+0xa0): first defined here
/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: protpars.o:(.bss+0x1f69): multiple definition of `lastrearr'; dnapars.o:(.bss+0x2001): first defined here
/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: protpars.o:(.bss+0x1f60): multiple definition of `there'; dnapars.o:(.bss+0xb0): first defined here
/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: protpars.o:(.bss+0x1fa8): multiple definition of `bestrees'; dnapars.o:(.bss+0x98): first defined here
/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: protpars.o:(.bss+0x0): multiple definition of `names'; dnapars.o:(.bss+0x10): first defined here
/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: protpars.o:(.bss+0x23e2): multiple definition of `trout'; dnapars.o:(.bss+0x2080): first defined here
/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: protpars.o:(.bss+0x2360): multiple definition of `enterorder'; dnapars.o:(.bss+0x2018): first defined here
/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: protpars.o:(.bss+0x23e6): multiple definition of `jumble'; dnapars.o:(.bss+0x2086): first defined here
/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: protpars.o:(.bss+0x2400): multiple definition of `njumble'; dnapars.o:(.bss+0x20b0): first defined here
/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: protpars.o:(.bss+0x23f8): multiple definition of `jumb'; dnapars.o:(.bss+0x20a8): first defined here
/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: protpars.o:(.bss+0x2380): multiple definition of `seed'; dnapars.o:(.bss+0x2040): first defined here
/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: protpars.o:(.bss+0x1f78): multiple definition of `progname'; seaview.o:(.data.rel.local+0x0): first defined here
/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: protpars.o:(.bss+0x1f98): multiple definition of `garbage'; dnapars.o:(.bss+0x80): first defined here
/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: protpars.o:(.bss+0x23dd): multiple definition of `mulsets'; dnapars.o:(.bss+0x207c): first defined here
/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: protpars.o:(.bss+0x2410): multiple definition of `msets'; dnapars.o:(.bss+0x20c0): first defined here
/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: protpars.o:(.bss+0x23dc): multiple definition of `firstset'; dnapars.o:(.bss+0x207a): first defined here
/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: protpars.o:(.bss+0x23e3): multiple definition of `thresh'; dnapars.o:(.bss+0x2084): first defined here
/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: protpars.o:(.bss+0x23e4): multiple definition of `weights'; dnapars.o:(.bss+0x2083): first defined here
/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: protpars.o:(.bss+0x23e1): multiple definition of `progress'; dnapars.o:(.bss+0x207f): first defined here
/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: protpars.o:(.bss+0x23e0): multiple definition of `stepbox'; dnapars.o:(.bss+0x207e): first defined here
/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: protpars.o:(.bss+0x23de): multiple definition of `ancseq'; dnapars.o:(.bss+0x207d): first defined here
/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: protpars.o:(.bss+0x2408): multiple definition of `ith'; dnapars.o:(.bss+0x20b8): first defined here
/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: protpars.o:(.bss+0x23df): multiple definition of `justwts'; dnapars.o:(.bss+0x207b): first defined here
/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: protpars.o:(.bss+0x23b8): multiple definition of `threshold'; dnapars.o:(.bss+0x2088): first defined here
/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: protpars.o:(.bss+0x2508): multiple definition of `outtreename'; dnapars.o:(.bss+0x21a8): first defined here
/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: protpars.o:(.bss+0x23e8): multiple definition of `inseed0'; dnapars.o:(.bss+0x2090): first defined here
/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: protpars.o:(.bss+0x23f0): multiple definition of `inseed'; dnapars.o:(.bss+0x2098): first defined here
/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: protpars.o:(.bss+0x2440): multiple definition of `weightfilename'; dnapars.o:(.bss+0x20e0): first defined here
/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: protpars.o:(.bss+0x2520): multiple definition of `intreename'; dnapars.o:(.bss+0x21c0): first defined here
/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: protpars.o:(.bss+0x2600): multiple definition of `outfilename'; dnapars.o:(.bss+0x22a0): first defined here
/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: protpars.o:(.bss+0x26e0): multiple definition of `infilename'; dnapars.o:(.bss+0x2380): first defined here
/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: protpars.o:(.bss+0x27a8): multiple definition of `firstplotblock'; dnapars.o:(.bss+0x2448): first defined here
/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: protpars.o:(.bss+0x27a9): multiple definition of `javarun'; dnapars.o:(.bss+0x2449): first defined here
/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: seq.o:(.bss+0x60): multiple definition of `firstplotblock'; dnapars.o:(.bss+0x2448): first defined here
/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: seq.o:(.bss+0x61): multiple definition of `javarun'; dnapars.o:(.bss+0x2449): first defined here
/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: phylip.o:(.bss+0x79): multiple definition of `javarun'; dnapars.o:(.bss+0x2449): first defined here
/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: phylip.o:(.bss+0x78): multiple definition of `firstplotblock'; dnapars.o:(.bss+0x2448): first defined here
collect2: error: ld returned 1 exit status
make: *** [Makefile:46: seaview] Error 1
 * ERROR: sci-biology/seaview-4.6::gentoo failed (compile phase):
 *   emake failed
 * 
 * If you need support, post the output of `emerge --info '=sci-biology/seaview-4.6::gentoo'`,
 * the complete build log and the output of `emerge -pqv '=sci-biology/seaview-4.6::gentoo'`.
 * The complete build log is located at '/var/log/portage/sci-biology:seaview-4.6:20200201-230151.log'.
 * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-biology/seaview-4.6/temp/build.log'.
 * The ebuild environment file is located at '/var/tmp/portage/sci-biology/seaview-4.6/temp/environment'.
 * Working directory: '/var/tmp/portage/sci-biology/seaview-4.6/work/seaview'
 * S: '/var/tmp/portage/sci-biology/seaview-4.6/work/seaview'