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  1. =======> Building '/ports/packages/caps-coev-static#2.0-1.pkg.tar.gz'.
  2. bsdtar -p -o -C /ports/build/caps-coev-static-2.0/src -xf /ports/sources/caps2_src.zip
  3. cp caps_verbose.patch /ports/build/caps-coev-static-2.0/src
  4. + build
  5. + cd caps2.0_src
  6. + LIBDIRPATH=-Wl,-L/usr/lib/Bpp1.9,-rpath,/usr/lib/Bpp1.9
  7. + sed -i 's:CFLAGS=:CFLAGS=-O2 -march=x86-64 -static -fPIC -frtti -Wl,-L/usr/lib/Bpp1.9,-rpath,/usr/lib/Bpp1.9:' Makefile
  8. + sed -i 's:-lbpp-phyl:-L/usr/lib/Bpp1.9 -lbpp-phyl:g' Makefile
  9. + sed -i 's:-lbpp-numcalc:-L/usr/lib/Bpp1.9 -lbpp-numcalc:g' Makefile
  10. + sed -i 's:-lbpp-utils:-L/usr/lib/Bpp1.9 -lbpp-utils:g' Makefile
  11. + sed -i 's:-lbpp-seq:-L/usr/lib/Bpp1.9 -lbpp-seq:g' Makefile
  12. + sed -i 's:-o caps:-o vCAPS-static:' Makefile
  13. + patch -p1 -i /ports/build/caps-coev-static-2.0/src/caps_verbose.patch
  14. patching file caps.cpp
  15. + make all
  16. g++ -g -O2 -march=x86-64 -static -fPIC -frtti -Wl,-L/usr/lib/Bpp1.9,-rpath,/usr/lib/Bpp1.9 -c BCFasta.cpp
  17. g++ -g -O2 -march=x86-64 -static -fPIC -frtti -Wl,-L/usr/lib/Bpp1.9,-rpath,/usr/lib/Bpp1.9 -c file_manip.cpp
  18. g++ -g -O2 -march=x86-64 -static -fPIC -frtti -Wl,-L/usr/lib/Bpp1.9,-rpath,/usr/lib/Bpp1.9 -c Blosum.cpp
  19. g++ -g -O2 -march=x86-64 -static -fPIC -frtti -Wl,-L/usr/lib/Bpp1.9,-rpath,/usr/lib/Bpp1.9 -c create.cpp
  20. In file included from create.cpp:1:
  21. create.h:42:6: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
  22. 42 | std::auto_ptr<DistanceMatrix> ScoreDist(vector<string>& names, vector< string >& sequences);
  23. | ^~~~~~~~
  24. In file included from /usr/include/c++/10.3.0/bits/locale_conv.h:41,
  25. from /usr/include/c++/10.3.0/locale:43,
  26. from /usr/include/c++/10.3.0/iomanip:43,
  27. from create.h:3,
  28. from create.cpp:1:
  29. /usr/include/c++/10.3.0/bits/unique_ptr.h:57:28: note: declared here
  30. 57 | template<typename> class auto_ptr;
  31. | ^~~~~~~~
  32. create.cpp: In function 'void create_seq(bpp::TreeTemplate<bpp::Node>*&, std::vector<std::__cxx11::basic_string<char> >&, std::vector<std::__cxx11::basic_string<char> >&, unsigned int)':
  33. create.cpp:23:7: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
  34. 23 | std::auto_ptr<SiteContainer> sites(seqsim.simulate(length));
  35. | ^~~~~~~~
  36. In file included from /usr/include/c++/10.3.0/bits/locale_conv.h:41,
  37. from /usr/include/c++/10.3.0/locale:43,
  38. from /usr/include/c++/10.3.0/iomanip:43,
  39. from create.h:3,
  40. from create.cpp:1:
  41. /usr/include/c++/10.3.0/bits/unique_ptr.h:57:28: note: declared here
  42. 57 | template<typename> class auto_ptr;
  43. | ^~~~~~~~
  44. create.cpp: At global scope:
  45. create.cpp:49:6: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
  46. 49 | std::auto_ptr<DistanceMatrix> ScoreDist(vector<string>& names, vector< string >& sequences){
  47. | ^~~~~~~~
  48. In file included from /usr/include/c++/10.3.0/bits/locale_conv.h:41,
  49. from /usr/include/c++/10.3.0/locale:43,
  50. from /usr/include/c++/10.3.0/iomanip:43,
  51. from create.h:3,
  52. from create.cpp:1:
  53. /usr/include/c++/10.3.0/bits/unique_ptr.h:57:28: note: declared here
  54. 57 | template<typename> class auto_ptr;
  55. | ^~~~~~~~
  56. create.cpp: In function 'std::auto_ptr<bpp::DistanceMatrix> ScoreDist(std::vector<std::__cxx11::basic_string<char> >&, std::vector<std::__cxx11::basic_string<char> >&)':
  57. create.cpp:53:7: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
  58. 53 | std::auto_ptr<DistanceMatrix> DS;
  59. | ^~~~~~~~
  60. In file included from /usr/include/c++/10.3.0/bits/locale_conv.h:41,
  61. from /usr/include/c++/10.3.0/locale:43,
  62. from /usr/include/c++/10.3.0/iomanip:43,
  63. from create.h:3,
  64. from create.cpp:1:
  65. /usr/include/c++/10.3.0/bits/unique_ptr.h:57:28: note: declared here
  66. 57 | template<typename> class auto_ptr;
  67. | ^~~~~~~~
  68. create.cpp:84:13: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
  69. 84 | DS = (std::auto_ptr<DistanceMatrix>)(MyDS.getMatrix());
  70. | ^~~~~~~~
  71. In file included from /usr/include/c++/10.3.0/bits/locale_conv.h:41,
  72. from /usr/include/c++/10.3.0/locale:43,
  73. from /usr/include/c++/10.3.0/iomanip:43,
  74. from create.h:3,
  75. from create.cpp:1:
  76. /usr/include/c++/10.3.0/bits/unique_ptr.h:57:28: note: declared here
  77. 57 | template<typename> class auto_ptr;
  78. | ^~~~~~~~
  79. g++ -g -O2 -march=x86-64 -static -fPIC -frtti -Wl,-L/usr/lib/Bpp1.9,-rpath,/usr/lib/Bpp1.9 -lgsl -lgslcblas -L/usr/lib/Bpp1.9 -lbpp-phyl -L/usr/lib/Bpp1.9 -lbpp-utils -L/usr/lib/Bpp1.9 -lbpp-numcalc -L/usr/lib/Bpp1.9 -lbpp-seq -o vCAPS-static caps.cpp file_manip.o BCFasta.o create.o Blosum.o
  80. In file included from caps.cpp:5:
  81. caps.h:83:69: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
  82. 83 | vector<Node *> Put_distances_on_tree(TreeTemplate<Node> *tree, std::auto_ptr< DistanceMatrix >DS );
  83. | ^~~~~~~~
  84. In file included from /usr/include/c++/10.3.0/bits/locale_conv.h:41,
  85. from /usr/include/c++/10.3.0/locale:43,
  86. from /usr/include/c++/10.3.0/iomanip:43,
  87. from /usr/include/Utils/TextTools.h:50,
  88. from /usr/include/NumCalc/VectorExceptions.h:45,
  89. from /usr/include/NumCalc/VectorTools.h:43,
  90. from /usr/include/Phyl/TreeTools.h:52,
  91. from /usr/include/Phyl/TreeTemplateTools.h:45,
  92. from /usr/include/Phyl/TreeTemplate.h:45,
  93. from /usr/include/Phyl/Newick.h:44,
  94. from BCFasta.h:5,
  95. from caps.cpp:3:
  96. /usr/include/c++/10.3.0/bits/unique_ptr.h:57:28: note: declared here
  97. 57 | template<typename> class auto_ptr;
  98. | ^~~~~~~~
  99. In file included from caps.cpp:5:
  100. caps.h:84:167: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
  101. 84 | ate<Node>* tree, map<int, int>& idmap, vector< vector<double> >& pol, int l, vector<double>& ans, std::auto_ptr<DistanceMatrix> DS );
  102. | ^~~~~~~~
  103.  
  104. In file included from /usr/include/c++/10.3.0/bits/locale_conv.h:41,
  105. from /usr/include/c++/10.3.0/locale:43,
  106. from /usr/include/c++/10.3.0/iomanip:43,
  107. from /usr/include/Utils/TextTools.h:50,
  108. from /usr/include/NumCalc/VectorExceptions.h:45,
  109. from /usr/include/NumCalc/VectorTools.h:43,
  110. from /usr/include/Phyl/TreeTools.h:52,
  111. from /usr/include/Phyl/TreeTemplateTools.h:45,
  112. from /usr/include/Phyl/TreeTemplate.h:45,
  113. from /usr/include/Phyl/Newick.h:44,
  114. from BCFasta.h:5,
  115. from caps.cpp:3:
  116. /usr/include/c++/10.3.0/bits/unique_ptr.h:57:28: note: declared here
  117. 57 | template<typename> class auto_ptr;
  118. | ^~~~~~~~
  119. In file included from caps.cpp:6:
  120. create.h:42:6: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
  121. 42 | std::auto_ptr<DistanceMatrix> ScoreDist(vector<string>& names, vector< string >& sequences);
  122. | ^~~~~~~~
  123. In file included from /usr/include/c++/10.3.0/bits/locale_conv.h:41,
  124. from /usr/include/c++/10.3.0/locale:43,
  125. from /usr/include/c++/10.3.0/iomanip:43,
  126. from /usr/include/Utils/TextTools.h:50,
  127. from /usr/include/NumCalc/VectorExceptions.h:45,
  128. from /usr/include/NumCalc/VectorTools.h:43,
  129. from /usr/include/Phyl/TreeTools.h:52,
  130. from /usr/include/Phyl/TreeTemplateTools.h:45,
  131. from /usr/include/Phyl/TreeTemplate.h:45,
  132. from /usr/include/Phyl/Newick.h:44,
  133. from BCFasta.h:5,
  134. from caps.cpp:3:
  135. /usr/include/c++/10.3.0/bits/unique_ptr.h:57:28: note: declared here
  136. 57 | template<typename> class auto_ptr;
  137. | ^~~~~~~~
  138. caps.cpp: In function 'int main(int, char**)':
  139. caps.cpp:323:9: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
  140. 323 | std::auto_ptr<DistanceMatrix> DS;
  141. | ^~~~~~~~
  142. In file included from /usr/include/c++/10.3.0/bits/locale_conv.h:41,
  143. from /usr/include/c++/10.3.0/locale:43,
  144. from /usr/include/c++/10.3.0/iomanip:43,
  145. from /usr/include/Utils/TextTools.h:50,
  146. from /usr/include/NumCalc/VectorExceptions.h:45,
  147. from /usr/include/NumCalc/VectorTools.h:43,
  148. from /usr/include/Phyl/TreeTools.h:52,
  149. from /usr/include/Phyl/TreeTemplateTools.h:45,
  150. from /usr/include/Phyl/TreeTemplate.h:45,
  151. from /usr/include/Phyl/Newick.h:44,
  152. from BCFasta.h:5,
  153. from caps.cpp:3:
  154. /usr/include/c++/10.3.0/bits/unique_ptr.h:57:28: note: declared here
  155. 57 | template<typename> class auto_ptr;
  156. | ^~~~~~~~
  157. caps.cpp:548:16: warning: unknown escape sequence: '\F'
  158. 548 | OUTPUT << "\n\File1: " << files[i] << endl;
  159. | ^~~~~~~~~~~~
  160. caps.cpp: In function 'bpp::TreeTemplate<bpp::Node>* create_input_tree(std::vector<std::__cxx11::basic_string<char> >&, std::vector<std::__cxx11::basic_string<char> >&)':
  161. caps.cpp:3040:7: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
  162. 3040 | std::auto_ptr<DistanceMatrix> DS;
  163. | ^~~~~~~~
  164. In file included from /usr/include/c++/10.3.0/bits/locale_conv.h:41,
  165. from /usr/include/c++/10.3.0/locale:43,
  166. from /usr/include/c++/10.3.0/iomanip:43,
  167. from /usr/include/Utils/TextTools.h:50,
  168. from /usr/include/NumCalc/VectorExceptions.h:45,
  169. from /usr/include/NumCalc/VectorTools.h:43,
  170. from /usr/include/Phyl/TreeTools.h:52,
  171. from /usr/include/Phyl/TreeTemplateTools.h:45,
  172. from /usr/include/Phyl/TreeTemplate.h:45,
  173. from /usr/include/Phyl/Newick.h:44,
  174. from BCFasta.h:5,
  175. from caps.cpp:3:
  176. /usr/include/c++/10.3.0/bits/unique_ptr.h:57:28: note: declared here
  177. 57 | template<typename> class auto_ptr;
  178. | ^~~~~~~~
  179. caps.cpp: At global scope:
  180. caps.cpp:3348:69: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
  181. 3348 | vector<Node *> Put_distances_on_tree(TreeTemplate<Node> *tree, std::auto_ptr<DistanceMatrix> DS ){
  182. | ^~~~~~~~
  183. In file included from /usr/include/c++/10.3.0/bits/locale_conv.h:41,
  184. from /usr/include/c++/10.3.0/locale:43,
  185. from /usr/include/c++/10.3.0/iomanip:43,
  186. from /usr/include/Utils/TextTools.h:50,
  187. from /usr/include/NumCalc/VectorExceptions.h:45,
  188. from /usr/include/NumCalc/VectorTools.h:43,
  189. from /usr/include/Phyl/TreeTools.h:52,
  190. from /usr/include/Phyl/TreeTemplateTools.h:45,
  191. from /usr/include/Phyl/TreeTemplate.h:45,
  192. from /usr/include/Phyl/Newick.h:44,
  193. from BCFasta.h:5,
  194. from caps.cpp:3:
  195. /usr/include/c++/10.3.0/bits/unique_ptr.h:57:28: note: declared here
  196. 57 | template<typename> class auto_ptr;
  197. | ^~~~~~~~
  198. caps.cpp:3505:167: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
  199. 3505 | ate<Node>* tree, map<int, int>& idmap, vector< vector<double> >& pol, int l, vector<double>& ans, std::auto_ptr<DistanceMatrix> DS ){
  200. |
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