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  1. ==> Starting build()...
  2. g++ -c -D_FORTIFY_SOURCE=2 -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -Dunix -O3 -I. -Icsrc -DNO_PDF seaview.cxx
  3. g++ -c -D_FORTIFY_SOURCE=2 -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -Dunix -O3 -I. -Icsrc -DNO_PDF custom.cxx
  4. g++ -c -D_FORTIFY_SOURCE=2 -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -Dunix -O3 -I. -Icsrc -DNO_PDF use_mase_files.cxx
  5. g++ -c -D_FORTIFY_SOURCE=2 -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -Dunix -O3 -I. -Icsrc -DNO_PDF regions.cxx
  6. g++ -c -D_FORTIFY_SOURCE=2 -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -Dunix -O3 -I. -Icsrc -DNO_PDF load_seq.cxx
  7. g++ -c -D_FORTIFY_SOURCE=2 -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -Dunix -O3 -I. -Icsrc -DNO_PDF align.cxx
  8. g++ -c -D_FORTIFY_SOURCE=2 -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -Dunix -O3 -I. -Icsrc -DNO_PDF xfmatpt.cxx
  9. g++ -c -D_FORTIFY_SOURCE=2 -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -Dunix -O3 -I. -Icsrc -DNO_PDF comlines.cxx
  10. g++ -c -D_FORTIFY_SOURCE=2 -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -Dunix -O3 -I. -Icsrc -DNO_PDF resource.cxx
  11. g++ -c -D_FORTIFY_SOURCE=2 -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -Dunix -O3 -I. -Icsrc -DNO_PDF nexus.cxx
  12. seaview.cxx:3352:21: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix]
  13. 3352 | strcat(suggested, "."PDF_OR_PS_EXT);
  14. | ^
  15. seaview.cxx:3462:17: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix]
  16. 3462 | pdf_form->label("Set "PDF_OR_PS" output options");
  17. | ^
  18. seaview.cxx:5051:6: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix]
  19. 5051 | {"Prepare "PDF_OR_PS"", 0, file_menu_callback, 0, 0},
  20. | ^
  21. seaview.cxx:5052:6: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix]
  22. 5052 | {""PDF_OR_PS" options...", 0, file_menu_callback, 0, FL_MENU_DIVIDER},
  23. | ^
  24. xfmatpt.cxx:208:79: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix]
  25. 208 | Fl_Widget *postscript = cre_button(fin, curr_y, &width, but_height, fontsize, "Write "PDF_OR_PS);
  26. | ^
  27. xfmatpt.cxx:873:14: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix]
  28. 873 | fl_message("Dot plot is now in file\n%s\nin "PDF_OR_PS" format", surface->outfname());
  29. | ^
  30. g++ -c -D_FORTIFY_SOURCE=2 -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -Dunix -O3 -I. -Icsrc -DNO_PDF viewasprots.cxx
  31. regions.cxx: In function ‘int create_gblocks_mask(SEA_VIEW*, region*, int, int, int, int, int)’:
  32. regions.cxx:305:9: warning: ignoring return value of ‘int system(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  33. 305 | system(cmd);
  34. | ~~~~~~^~~~~
  35. align.cxx: In function ‘void replace_stars(char*)’:
  36. 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]
  37. 1298 | fread(all, 1, l, in);
  38. | ~~~~~^~~~~~~~~~~~~~~
  39. seaview.cxx: In function ‘void delete_tmp_filename(const char*)’:
  40. seaview.cxx:646:9: warning: ignoring return value of ‘int system(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  41. 646 | system(fname);
  42. | ~~~~~~^~~~~~~
  43. seaview.cxx: In function ‘char* run_and_close_native_file_chooser(Fl_Native_File_Chooser*, int)’:
  44. seaview.cxx:2909:38: warning: ignoring return value of ‘int chdir(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  45. 2909 | if( *last_visited_directory )chdir(last_visited_directory);
  46. | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
  47. g++ -c -D_FORTIFY_SOURCE=2 -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -Dunix -O3 -I. -Icsrc -DNO_PDF racnuc_fetch.cxx
  48. g++ -c -D_FORTIFY_SOURCE=2 -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -Dunix -O3 -I. -Icsrc -DNO_PDF concatenate.cxx
  49. g++ -c -D_FORTIFY_SOURCE=2 -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -Dunix -O3 -I. -Icsrc -DNO_PDF statistics.cxx
  50. g++ -c -D_FORTIFY_SOURCE=2 -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -Dunix -O3 -I. -Icsrc -DNO_PDF trees.cxx
  51. g++ -c -D_FORTIFY_SOURCE=2 -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -Dunix -O3 -I. -Icsrc -DNO_PDF treedraw.cxx
  52. g++ -c -D_FORTIFY_SOURCE=2 -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -Dunix -O3 -I. -Icsrc -DNO_PDF addbootstrap.cxx
  53. treedraw.cxx:325:6: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix]
  54. 325 | {"Save as "PDF_OR_PS"", 0, file_callback, NULL, 0},
  55. | ^
  56. g++ -c -D_FORTIFY_SOURCE=2 -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -Dunix -O3 -I. -Icsrc -DNO_PDF least_squares_brl.cxx
  57. trees.cxx: In function ‘void run_phyml_callback(Fl_Widget*, void*)’:
  58. trees.cxx:1295:16: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  59. 1295 | fread(bootstrap_trees, l, 1, in);
  60. | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
  61. trees.cxx: In function ‘void command_line_phylogeny(int, char**)’:
  62. trees.cxx:2788:12: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  63. 2788 | fread(utree, s, 1, in);
  64. | ~~~~~^~~~~~~~~~~~~~~~~
  65. g++ -c -D_FORTIFY_SOURCE=2 -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -Dunix -O3 -I. -Icsrc -DNO_PDF pseudoterminal.cxx
  66. g++ -c -D_FORTIFY_SOURCE=2 -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -Dunix -O3 -I. -Icsrc -DNO_PDF unrooted.cxx
  67. g++ -c -D_FORTIFY_SOURCE=2 -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -Dunix -O3 -I. -Icsrc -DNO_PDF pdf_or_ps.cxx
  68. pseudoterminal.cxx: In function ‘int run_external_prog_in_pseudoterm(char*, const char*, const char*)’:
  69. pseudoterminal.cxx:342:11: warning: ignoring return value of ‘FILE* freopen(const char*, const char*, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  70. 342 | freopen(dialogfname, "r", stdin);
  71. | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
  72. pseudoterminal.cxx:344:10: warning: ignoring return value of ‘FILE* freopen(const char*, const char*, FILE*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  73. 344 | freopen(slavename, "a", stderr);
  74. | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
  75. g++ -c -D_FORTIFY_SOURCE=2 -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -Dunix -O3 -I. -Icsrc -DNO_PDF svg.cxx
  76. g++ -c -D_FORTIFY_SOURCE=2 -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -Dunix -O3 -I. -Icsrc -DNO_PDF threads.cxx
  77. In file included from /usr/include/string.h:519,
  78. from seaview.h:5,
  79. from seaview.cxx:67:
  80. In function ‘char* strncpy(char*, const char*, size_t)’,
  81. inlined from ‘void goto_callback(Fl_Widget*, void*)’ at seaview.cxx:2738:9:
  82. /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=]
  83. 106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
  84. | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  85. seaview.cxx: In function ‘void goto_callback(Fl_Widget*, void*)’:
  86. seaview.cxx:2736:12: note: length computed here
  87. 2736 | l = strlen(p);
  88. | ~~~~~~^~~
  89. g++ -c -D_FORTIFY_SOURCE=2 -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -Dunix -O3 -I. -Icsrc -DNO_PDF tbe.cxx
  90. g++ -c -I. -D_FORTIFY_SOURCE=2 -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -Dunix -O3 -I. -Icsrc -DNO_PDF FL/Fl_Native_File_Chooser_FLTK.cxx
  91. gcc -c -O3 -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -Dunix -Icsrc csrc/raa_acnuc.c
  92. gcc -c -O3 -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -Dunix -Icsrc csrc/parser.c
  93. gcc -c -O3 -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -Dunix -Icsrc csrc/md5.c
  94. gcc -c -O3 -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -Dunix -Icsrc csrc/zsockr.c
  95. gcc -c -O3 -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -Dunix -Icsrc csrc/misc_acnuc.c
  96. gcc -c -O3 -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -Dunix -Icsrc csrc/dnapars.c
  97. gcc -c -O3 -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -Dunix -Icsrc csrc/protpars.c
  98. gcc -c -O3 -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -Dunix -Icsrc csrc/seq.c
  99. gcc -c -O3 -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -Dunix -Icsrc csrc/phylip.c
  100. gcc -c -O3 -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -Dunix -Icsrc csrc/lwl.c
  101. gcc -c -O3 -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -Dunix -Icsrc csrc/bionj.c
  102. gcc -c -O3 -march=x86-64 -mtune=generic -O2 -pipe -fno-plt -Dunix -Icsrc csrc/phyml_util.c
  103. g++ -o seaview -Wl,-O1,--sort-common,--as-needed,-z,relro,-z,now 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 tbe.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
  104. /usr/bin/ld: dnapars.o:(.bss+0x0): multiple definition of `progname'; seaview.o:(.data.rel.local+0x0): first defined here
  105. /usr/bin/ld: protpars.o:(.bss+0x2420): multiple definition of `chars'; dnapars.o:(.bss+0x20d0): first defined here
  106. /usr/bin/ld: protpars.o:(.bss+0x23e5): multiple definition of `usertree'; dnapars.o:(.bss+0x2085): first defined here
  107. /usr/bin/ld: protpars.o:(.bss+0x23b0): multiple definition of `threshwt'; dnapars.o:(.bss+0x90): first defined here
  108. /usr/bin/ld: protpars.o:(.bss+0x1fb0): multiple definition of `fsteps'; dnapars.o:(.bss+0xb8): first defined here
  109. /usr/bin/ld: protpars.o:(.bss+0x20): multiple definition of `nsteps'; dnapars.o:(.bss+0xc0): first defined here
  110. /usr/bin/ld: protpars.o:(.bss+0x1f70): multiple definition of `minwhich'; dnapars.o:(.bss+0x2008): first defined here
  111. /usr/bin/ld: protpars.o:(.bss+0x23c0): multiple definition of `treenode'; dnapars.o:(.bss+0x2020): first defined here
  112. /usr/bin/ld: protpars.o:(.bss+0x2428): multiple definition of `root'; dnapars.o:(.bss+0x20d8): first defined here
  113. /usr/bin/ld: protpars.o:(.bss+0x1f68): multiple definition of `recompute'; dnapars.o:(.bss+0x2000): first defined here
  114. /usr/bin/ld: protpars.o:(.bss+0x1f88): multiple definition of `temp1'; dnapars.o:(.bss+0x70): first defined here
  115. /usr/bin/ld: protpars.o:(.bss+0x1f90): multiple definition of `temp'; dnapars.o:(.bss+0x78): first defined here
  116. /usr/bin/ld: protpars.o:(.bss+0x8): multiple definition of `place'; dnapars.o:(.bss+0xa0): first defined here
  117. /usr/bin/ld: protpars.o:(.bss+0x1f69): multiple definition of `lastrearr'; dnapars.o:(.bss+0x2001): first defined here
  118. /usr/bin/ld: protpars.o:(.bss+0x1f60): multiple definition of `there'; dnapars.o:(.bss+0xb0): first defined here
  119. /usr/bin/ld: protpars.o:(.bss+0x1fa8): multiple definition of `bestrees'; dnapars.o:(.bss+0x98): first defined here
  120. /usr/bin/ld: protpars.o:(.bss+0x0): multiple definition of `names'; dnapars.o:(.bss+0x10): first defined here
  121. /usr/bin/ld: protpars.o:(.bss+0x23e2): multiple definition of `trout'; dnapars.o:(.bss+0x2080): first defined here
  122. /usr/bin/ld: protpars.o:(.bss+0x2360): multiple definition of `enterorder'; dnapars.o:(.bss+0x2018): first defined here
  123. /usr/bin/ld: protpars.o:(.bss+0x23e6): multiple definition of `jumble'; dnapars.o:(.bss+0x2086): first defined here
  124. /usr/bin/ld: protpars.o:(.bss+0x2400): multiple definition of `njumble'; dnapars.o:(.bss+0x20b0): first defined here
  125. /usr/bin/ld: protpars.o:(.bss+0x23f8): multiple definition of `jumb'; dnapars.o:(.bss+0x20a8): first defined here
  126. /usr/bin/ld: protpars.o:(.bss+0x2418): multiple definition of `col'; dnapars.o:(.bss+0x20c8): first defined here
  127. /usr/bin/ld: protpars.o:(.bss+0x2380): multiple definition of `seed'; dnapars.o:(.bss+0x2040): first defined here
  128. /usr/bin/ld: protpars.o:(.bss+0x1f78): multiple definition of `progname'; seaview.o:(.data.rel.local+0x0): first defined here
  129. /usr/bin/ld: protpars.o:(.bss+0x1f98): multiple definition of `garbage'; dnapars.o:(.bss+0x80): first defined here
  130. /usr/bin/ld: protpars.o:(.bss+0x23dd): multiple definition of `mulsets'; dnapars.o:(.bss+0x207c): first defined here
  131. /usr/bin/ld: protpars.o:(.bss+0x2410): multiple definition of `msets'; dnapars.o:(.bss+0x20c0): first defined here
  132. /usr/bin/ld: protpars.o:(.bss+0x23dc): multiple definition of `firstset'; dnapars.o:(.bss+0x207a): first defined here
  133. /usr/bin/ld: protpars.o:(.bss+0x23e3): multiple definition of `thresh'; dnapars.o:(.bss+0x2084): first defined here
  134. /usr/bin/ld: protpars.o:(.bss+0x23e4): multiple definition of `weights'; dnapars.o:(.bss+0x2083): first defined here
  135. /usr/bin/ld: protpars.o:(.bss+0x23e1): multiple definition of `progress'; dnapars.o:(.bss+0x207f): first defined here
  136. /usr/bin/ld: protpars.o:(.bss+0x23e0): multiple definition of `stepbox'; dnapars.o:(.bss+0x207e): first defined here
  137. /usr/bin/ld: protpars.o:(.bss+0x23de): multiple definition of `ancseq'; dnapars.o:(.bss+0x207d): first defined here
  138. /usr/bin/ld: protpars.o:(.bss+0x2408): multiple definition of `ith'; dnapars.o:(.bss+0x20b8): first defined here
  139. /usr/bin/ld: protpars.o:(.bss+0x23df): multiple definition of `justwts'; dnapars.o:(.bss+0x207b): first defined here
  140. /usr/bin/ld: protpars.o:(.bss+0x23b8): multiple definition of `threshold'; dnapars.o:(.bss+0x2088): first defined here
  141. /usr/bin/ld: protpars.o:(.bss+0x2508): multiple definition of `outtreename'; dnapars.o:(.bss+0x21a8): first defined here
  142. /usr/bin/ld: protpars.o:(.bss+0x23e8): multiple definition of `inseed0'; dnapars.o:(.bss+0x2090): first defined here
  143. /usr/bin/ld: protpars.o:(.bss+0x23f0): multiple definition of `inseed'; dnapars.o:(.bss+0x2098): first defined here
  144. /usr/bin/ld: protpars.o:(.bss+0x2440): multiple definition of `weightfilename'; dnapars.o:(.bss+0x20e0): first defined here
  145. /usr/bin/ld: protpars.o:(.bss+0x2520): multiple definition of `intreename'; dnapars.o:(.bss+0x21c0): first defined here
  146. /usr/bin/ld: protpars.o:(.bss+0x2600): multiple definition of `outfilename'; dnapars.o:(.bss+0x22a0): first defined here
  147. /usr/bin/ld: protpars.o:(.bss+0x26e0): multiple definition of `infilename'; dnapars.o:(.bss+0x2380): first defined here
  148. /usr/bin/ld: protpars.o:(.bss+0x27a8): multiple definition of `firstplotblock'; dnapars.o:(.bss+0x2448): first defined here
  149. /usr/bin/ld: protpars.o:(.bss+0x27a9): multiple definition of `javarun'; dnapars.o:(.bss+0x2449): first defined here
  150. /usr/bin/ld: seq.o:(.bss+0x60): multiple definition of `firstplotblock'; dnapars.o:(.bss+0x2448): first defined here
  151. /usr/bin/ld: seq.o:(.bss+0x61): multiple definition of `javarun'; dnapars.o:(.bss+0x2449): first defined here
  152. /usr/bin/ld: phylip.o:(.bss+0x79): multiple definition of `javarun'; dnapars.o:(.bss+0x2449): first defined here
  153. /usr/bin/ld: phylip.o:(.bss+0x78): multiple definition of `firstplotblock'; dnapars.o:(.bss+0x2448): first defined here
  154. collect2: error: ld returned 1 exit status
  155. make: *** [Makefile:46: seaview] Error 1
  156. ==> ERROR: A failure occurred in build().
  157. Aborting...
  158.  
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