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  1. [sam@Sams-MacBook-Pro src ((776efec...) *%)]$ make
  2. /Applications/Xcode.app/Contents/Developer/usr/bin/make -f Makefile.freec init
  3. make[1]: Nothing to be done for `init'.
  4. /Applications/Xcode.app/Contents/Developer/usr/bin/make -f Makefile.freec depend
  5. /Applications/Xcode.app/Contents/Developer/usr/bin/make -f Makefile.freec all
  6. c++ -O3 -g -DPROFILE_TRACE -Wall -m64 -c -o main.o main.cpp
  7. main.cpp:586:61: warning: equality comparison result unused [-Wunused-comparison]
  8. if (seekSubclones==0 ||seekSubclones==1) {seekSubclones==100;}
  9. ~~~~~~~~~~~~~^~~~~
  10. main.cpp:586:61: note: use '=' to turn this equality comparison into an assignment
  11. if (seekSubclones==0 ||seekSubclones==1) {seekSubclones==100;}
  12. ^~
  13. =
  14. main.cpp:1040:27: warning: '&&' within '||' [-Wlogical-op-parentheses]
  15. if ((!forceGC && !(has_BAF) || (ifTargeted&&forceGC!=1) || (WESanalysis == true &&forceGC==0))) { //normalize sample density with control density
  16. ~~~~~~~~~^~~~~~~~~~~~~ ~~
  17. main.cpp:1040:27: note: place parentheses around the '&&' expression to silence this warning
  18. if ((!forceGC && !(has_BAF) || (ifTargeted&&forceGC!=1) || (WESanalysis == true &&forceGC==0))) { //normalize sample density with control density
  19. ^
  20. ( )
  21. 2 warnings generated.
  22. c++ -O3 -g -DPROFILE_TRACE -Wall -m64 -c -o ConfigFile.o ConfigFile.cpp
  23. c++ -O3 -g -DPROFILE_TRACE -Wall -m64 -c -o Chameleon.o Chameleon.cpp
  24. c++ -O3 -g -DPROFILE_TRACE -Wall -m64 -c -o GenomeDensity.o GenomeDensity.cpp
  25. GenomeDensity.cpp:63:10: warning: unused variable 'length' [-Wunused-variable]
  26. int length = strs[1].length();
  27. ^
  28. 1 warning generated.
  29. c++ -O3 -g -DPROFILE_TRACE -Wall -m64 -c -o Help.o Help.cpp
  30. c++ -O3 -g -DPROFILE_TRACE -Wall -m64 -c -o myFunc.o myFunc.cpp
  31. myFunc.cpp:54:12: warning: using the result of an assignment as a condition without parentheses [-Wparentheses]
  32. for (; c = *str++; ++jj) {
  33. ~~^~~~~~~~
  34. myFunc.cpp:54:12: note: place parentheses around the assignment to silence this warning
  35. for (; c = *str++; ++jj) {
  36. ^
  37. ( )
  38. myFunc.cpp:54:12: note: use '==' to turn this assignment into an equality comparison
  39. for (; c = *str++; ++jj) {
  40. ^
  41. ==
  42. myFunc.cpp:370:26: warning: using the result of an assignment as a condition without parentheses [-Wparentheses]
  43. if (toadd=strccnt(strs[4].c_str(), '^')) {
  44. ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  45. myFunc.cpp:370:26: note: place parentheses around the assignment to silence this warning
  46. if (toadd=strccnt(strs[4].c_str(), '^')) {
  47. ^
  48. ( )
  49. myFunc.cpp:370:26: note: use '==' to turn this assignment into an equality comparison
  50. if (toadd=strccnt(strs[4].c_str(), '^')) {
  51. ^
  52. ==
  53. myFunc.cpp:393:26: warning: using the result of an assignment as a condition without parentheses [-Wparentheses]
  54. if (toadd=strccnt(strs[4].c_str(), '^')) {
  55. ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  56. myFunc.cpp:393:26: note: place parentheses around the assignment to silence this warning
  57. if (toadd=strccnt(strs[4].c_str(), '^')) {
  58. ^
  59. ( )
  60. myFunc.cpp:393:26: note: use '==' to turn this assignment into an equality comparison
  61. if (toadd=strccnt(strs[4].c_str(), '^')) {
  62. ^
  63. ==
  64. myFunc.cpp:1886:141: warning: '&&' within '||' [-Wlogical-op-parentheses]
  65. if (copyNumbers[0]==1 && copyNumbers[1]==2 && copyNumber<1.5 && (medianBAFSym.compare("AA")==0 || medianBAFSym.compare("AB")==0 && uncertainty >0.1)) {
  66. ~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~
  67. myFunc.cpp:1886:141: note: place parentheses around the '&&' expression to silence this warning
  68. if (copyNumbers[0]==1 && copyNumbers[1]==2 && copyNumber<1.5 && (medianBAFSym.compare("AA")==0 || medianBAFSym.compare("AB")==0 && uncertainty >0.1)) {
  69. ^
  70. ( )
  71. 4 warnings generated.
  72. c++ -O3 -g -DPROFILE_TRACE -Wall -m64 -c -o KernelVector.o KernelVector.cpp
  73. c++ -O3 -g -DPROFILE_TRACE -Wall -m64 -c -o ChrDensity.o ChrDensity.cpp
  74. c++ -O3 -g -DPROFILE_TRACE -Wall -m64 -c -o ChrCopyNumber.o ChrCopyNumber.cpp
  75. c++ -O3 -g -DPROFILE_TRACE -Wall -m64 -c -o GenomeCopyNumber.o GenomeCopyNumber.cpp
  76. GenomeCopyNumber.cpp:3237:8: warning: unused variable 'contam' [-Wunused-variable]
  77. float contam = 0;
  78. ^
  79. GenomeCopyNumber.cpp:3696:33: warning: unused variable 'maxpos' [-Wunused-variable]
  80. int maxpos=0;
  81. ^
  82. GenomeCopyNumber.cpp:3826:30: warning: using the result of an assignment as a condition without parentheses [-Wparentheses]
  83. if (valueToReturn=strccnt(strs[4], '^')) {
  84. ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
  85. GenomeCopyNumber.cpp:3826:30: note: place parentheses around the assignment to silence this warning
  86. if (valueToReturn=strccnt(strs[4], '^')) {
  87. ^
  88. ( )
  89. GenomeCopyNumber.cpp:3826:30: note: use '==' to turn this assignment into an equality comparison
  90. if (valueToReturn=strccnt(strs[4], '^')) {
  91. ^
  92. ==
  93. GenomeCopyNumber.cpp:3882:27: warning: unused variable 'orient2_1' [-Wunused-variable]
  94. MateOrientation orient2_1 = getMateOrientation(orient2+orient1);
  95. ^
  96. GenomeCopyNumber.cpp:4202:8: warning: unused variable 'startFragment' [-Wunused-variable]
  97. int startFragment = 0;
  98. ^
  99. GenomeCopyNumber.cpp:4203:8: warning: unused variable 'endFragment' [-Wunused-variable]
  100. int endFragment=0;
  101. ^
  102. 6 warnings generated.
  103. c++ -O3 -g -DPROFILE_TRACE -Wall -m64 -c -o chisquaredistr.o chisquaredistr.cpp
  104. c++ -O3 -g -DPROFILE_TRACE -Wall -m64 -c -o ap.o ap.cpp
  105. c++ -O3 -g -DPROFILE_TRACE -Wall -m64 -c -o igammaf.o igammaf.cpp
  106. c++ -O3 -g -DPROFILE_TRACE -Wall -m64 -c -o gammafunc.o gammafunc.cpp
  107. c++ -O3 -g -DPROFILE_TRACE -Wall -m64 -c -o normaldistr.o normaldistr.cpp
  108. c++ -O3 -g -DPROFILE_TRACE -Wall -m64 -c -o ablasf.o ablasf.cpp
  109. c++ -O3 -g -DPROFILE_TRACE -Wall -m64 -c -o ablas.o ablas.cpp
  110. c++ -O3 -g -DPROFILE_TRACE -Wall -m64 -c -o ortfac.o ortfac.cpp
  111. c++ -O3 -g -DPROFILE_TRACE -Wall -m64 -c -o sblas.o sblas.cpp
  112. c++ -O3 -g -DPROFILE_TRACE -Wall -m64 -c -o rotations.o rotations.cpp
  113. c++ -O3 -g -DPROFILE_TRACE -Wall -m64 -c -o reflections.o reflections.cpp
  114. c++ -O3 -g -DPROFILE_TRACE -Wall -m64 -c -o linreg.o linreg.cpp
  115. c++ -O3 -g -DPROFILE_TRACE -Wall -m64 -c -o hblas.o hblas.cpp
  116. c++ -O3 -g -DPROFILE_TRACE -Wall -m64 -c -o descriptivestatistics.o descriptivestatistics.cpp
  117. c++ -O3 -g -DPROFILE_TRACE -Wall -m64 -c -o creflections.o creflections.cpp
  118. c++ -O3 -g -DPROFILE_TRACE -Wall -m64 -c -o blas.o blas.cpp
  119. c++ -O3 -g -DPROFILE_TRACE -Wall -m64 -c -o bdsvd.o bdsvd.cpp
  120. c++ -O3 -g -DPROFILE_TRACE -Wall -m64 -c -o svd.o svd.cpp
  121. c++ -O3 -g -DPROFILE_TRACE -Wall -m64 -c -o ialglib.o ialglib.cpp
  122. ialglib.cpp:837:39: warning: conversion from string literal to 'char *' is deprecated [-Wc++11-compat-deprecated-writable-strings]
  123. vcopy_complex(k, arow, 1, abuf, 1, "No conj");
  124. ^
  125. ialglib.cpp:842:53: warning: conversion from string literal to 'char *' is deprecated [-Wc++11-compat-deprecated-writable-strings]
  126. vcopy_complex(k, arow, stride, abuf, 1, "No conj");
  127. ^
  128. ialglib.cpp:847:53: warning: conversion from string literal to 'char *' is deprecated [-Wc++11-compat-deprecated-writable-strings]
  129. vcopy_complex(k, arow, stride, abuf, 1, "Conj");
  130. ^
  131. ialglib.cpp:917:67: warning: conversion from string literal to 'char *' is deprecated [-Wc++11-compat-deprecated-writable-strings]
  132. vcopy_complex(i, abuf+2*i, alglib_c_block, tmpbuf, 1, "No conj");
  133. ^
  134. ialglib.cpp:930:85: warning: conversion from string literal to 'char *' is deprecated [-Wc++11-compat-deprecated-writable-strings]
  135. vcopy_complex(n-1-i, pdiag+2*alglib_c_block, alglib_c_block, tmpbuf, 1, "No conj");
  136. ^
  137. ialglib.cpp:1069:57: warning: conversion from string literal to 'char *' is deprecated [-Wc++11-compat-deprecated-writable-strings]
  138. vcopy_complex(m-1-i, pdiag+2, 1, tmpbuf, 1, "No conj");
  139. ^
  140. ialglib.cpp:1081:50: warning: conversion from string literal to 'char *' is deprecated [-Wc++11-compat-deprecated-writable-strings]
  141. vcopy_complex(i, arow, 1, tmpbuf, 1, "No conj");
  142. ^
  143. ialglib.cpp:1229:50: warning: conversion from string literal to 'char *' is deprecated [-Wc++11-compat-deprecated-writable-strings]
  144. vcopy_complex(k, arow, 1, tmpbuf, 1, "Conj");
  145. ^
  146. ialglib.cpp:1237:50: warning: conversion from string literal to 'char *' is deprecated [-Wc++11-compat-deprecated-writable-strings]
  147. vcopy_complex(k, arow, 1, tmpbuf, 1, "Conj");
  148. ^
  149. ialglib.cpp:12:18: warning: unused variable 'alglib_half_r_block' [-Wunused-const-variable]
  150. static const int alglib_half_r_block = alglib_r_block/2;
  151. ^
  152. ialglib.cpp:13:18: warning: unused variable 'alglib_half_c_block' [-Wunused-const-variable]
  153. static const int alglib_half_c_block = alglib_c_block/2;
  154. ^
  155. 11 warnings generated.
  156. c++ -O3 -g -DPROFILE_TRACE -Wall -m64 -c -o EntryCNV.o EntryCNV.cpp
  157. c++ -O3 -g -DPROFILE_TRACE -Wall -m64 -c -o SNPinGenome.o SNPinGenome.cpp
  158. SNPinGenome.cpp:273:39: warning: using the result of an assignment as a condition without parentheses [-Wparentheses]
  159. if (valueToReturn = strccnt(strs[4], '^')) {
  160. ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
  161. SNPinGenome.cpp:273:39: note: place parentheses around the assignment to silence this warning
  162. if (valueToReturn = strccnt(strs[4], '^')) {
  163. ^
  164. ( )
  165. SNPinGenome.cpp:273:39: note: use '==' to turn this assignment into an equality comparison
  166. if (valueToReturn = strccnt(strs[4], '^')) {
  167. ^
  168. ==
  169. SNPinGenome.cpp:287:39: warning: using the result of an assignment as a condition without parentheses [-Wparentheses]
  170. if (valueToReturn = strccnt(strs[4], '^')) {
  171. ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
  172. SNPinGenome.cpp:287:39: note: place parentheses around the assignment to silence this warning
  173. if (valueToReturn = strccnt(strs[4], '^')) {
  174. ^
  175. ( )
  176. SNPinGenome.cpp:287:39: note: use '==' to turn this assignment into an equality comparison
  177. if (valueToReturn = strccnt(strs[4], '^')) {
  178. ^
  179. ==
  180. SNPinGenome.cpp:316:19: warning: unused variable 'localBAF' [-Wunused-variable]
  181. float localBAF=addInfoFromAPileUp(atoi(strs[3]),minimalTotalLetterCountPerPosition,(*SNP_atChr_)[index].getNucleotideAt(positionCount),
  182. ^
  183. SNPinGenome.cpp:338:27: warning: unused variable 'localBAF' [-Wunused-variable]
  184. float localBAF=addInfoFromAPileUp(atoi(strs[3]),minimalTotalLetterCountPerPosition,(*SNP_atChr_)[index].getNucleotideAt(positionCount),
  185. ^
  186. 4 warnings generated.
  187. c++ -O3 -g -DPROFILE_TRACE -Wall -m64 -c -o SNPatChr.o SNPatChr.cpp
  188. c++ -O3 -g -DPROFILE_TRACE -Wall -m64 -c -o SNPposition.o SNPposition.cpp
  189. SNPposition.cpp:31:18: warning: unused variable 'strs_cnt' [-Wunused-variable]
  190. unsigned strs_cnt = split(alt, ',', strs);
  191. ^
  192. SNPposition.cpp:46:14: warning: unused variable 'c_ref' [-Wunused-variable]
  193. char c_ref = ref[0];
  194. ^
  195. SNPposition.cpp:47:14: warning: unused variable 'reverse' [-Wunused-variable]
  196. bool reverse = strcmp(strand, "-") == 0;
  197. ^
  198. SNPposition.cpp:52:18: warning: unused variable 'strs_cnt' [-Wunused-variable]
  199. unsigned strs_cnt = split(letters, '/', strs);
  200. ^
  201. 4 warnings generated.
  202. c++ -O3 -g -DPROFILE_TRACE -Wall -m64 -c -o binomialdistr.o binomialdistr.cpp
  203. c++ -O3 -g -DPROFILE_TRACE -Wall -m64 -c -o ibetaf.o ibetaf.cpp
  204. ibetaf.cpp:166:16: warning: 'gamma' is deprecated: first deprecated in macOS 10.9 [-Wdeprecated-declarations]
  205. t = t*(gamma(a+b)/(gamma(a)*gamma(b)));
  206. ^
  207. /usr/include/math.h:759:15: note: 'gamma' has been explicitly marked deprecated here
  208. extern double gamma(double) __OSX_AVAILABLE_BUT_DEPRECATED(__MAC_10_0, __MAC_10_9, __IPHONE_NA, __IPHONE_NA);
  209. ^
  210. ibetaf.cpp:166:28: warning: 'gamma' is deprecated: first deprecated in macOS 10.9 [-Wdeprecated-declarations]
  211. t = t*(gamma(a+b)/(gamma(a)*gamma(b)));
  212. ^
  213. /usr/include/math.h:759:15: note: 'gamma' has been explicitly marked deprecated here
  214. extern double gamma(double) __OSX_AVAILABLE_BUT_DEPRECATED(__MAC_10_0, __MAC_10_9, __IPHONE_NA, __IPHONE_NA);
  215. ^
  216. ibetaf.cpp:166:37: warning: 'gamma' is deprecated: first deprecated in macOS 10.9 [-Wdeprecated-declarations]
  217. t = t*(gamma(a+b)/(gamma(a)*gamma(b)));
  218. ^
  219. /usr/include/math.h:759:15: note: 'gamma' has been explicitly marked deprecated here
  220. extern double gamma(double) __OSX_AVAILABLE_BUT_DEPRECATED(__MAC_10_0, __MAC_10_9, __IPHONE_NA, __IPHONE_NA);
  221. ^
  222. ibetaf.cpp:928:13: warning: 'gamma' is deprecated: first deprecated in macOS 10.9 [-Wdeprecated-declarations]
  223. t = gamma(a+b)/(gamma(a)*gamma(b));
  224. ^
  225. /usr/include/math.h:759:15: note: 'gamma' has been explicitly marked deprecated here
  226. extern double gamma(double) __OSX_AVAILABLE_BUT_DEPRECATED(__MAC_10_0, __MAC_10_9, __IPHONE_NA, __IPHONE_NA);
  227. ^
  228. ibetaf.cpp:928:25: warning: 'gamma' is deprecated: first deprecated in macOS 10.9 [-Wdeprecated-declarations]
  229. t = gamma(a+b)/(gamma(a)*gamma(b));
  230. ^
  231. /usr/include/math.h:759:15: note: 'gamma' has been explicitly marked deprecated here
  232. extern double gamma(double) __OSX_AVAILABLE_BUT_DEPRECATED(__MAC_10_0, __MAC_10_9, __IPHONE_NA, __IPHONE_NA);
  233. ^
  234. ibetaf.cpp:928:34: warning: 'gamma' is deprecated: first deprecated in macOS 10.9 [-Wdeprecated-declarations]
  235. t = gamma(a+b)/(gamma(a)*gamma(b));
  236. ^
  237. /usr/include/math.h:759:15: note: 'gamma' has been explicitly marked deprecated here
  238. extern double gamma(double) __OSX_AVAILABLE_BUT_DEPRECATED(__MAC_10_0, __MAC_10_9, __IPHONE_NA, __IPHONE_NA);
  239. ^
  240. 6 warnings generated.
  241. c++ -O3 -g -DPROFILE_TRACE -Wall -m64 -c -o ThreadPool.o ThreadPool.cpp
  242. c++ -O3 -g -DPROFILE_TRACE -Wall -m64 -c -o BAFpileup.o BAFpileup.cpp
  243. BAFpileup.cpp:58:25: warning: unused variable 'matesOrientation' [-Wunused-variable]
  244. MateOrientation matesOrientation = getMateOrientation(matesOrientation_str);
  245. ^
  246. BAFpileup.cpp:55:20: warning: unused variable 't0' [-Wunused-variable]
  247. time_t t0 = time(NULL);
  248. ^
  249. 2 warnings generated.
  250. c++ -O3 -g -DPROFILE_TRACE -Wall -m64 -c -o SeekSubclones.o SeekSubclones.cpp
  251. g++ -m64 -O3 -g -o freec main.o ConfigFile.o Chameleon.o GenomeDensity.o Help.o myFunc.o KernelVector.o ChrDensity.o ChrCopyNumber.o GenomeCopyNumber.o chisquaredistr.o ap.o igammaf.o gammafunc.o normaldistr.o ablasf.o ablas.o ortfac.o sblas.o rotations.o reflections.o linreg.o hblas.o descriptivestatistics.o creflections.o blas.o bdsvd.o svd.o ialglib.o EntryCNV.o SNPinGenome.o SNPatChr.o SNPposition.o binomialdistr.o ibetaf.o ThreadPool.o BAFpileup.o SeekSubclones.o -lpthread
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