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December 7, 2016 10:39
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| [sam@Sams-MacBook-Pro src ((776efec...) *%)]$ make | |
| /Applications/Xcode.app/Contents/Developer/usr/bin/make -f Makefile.freec init | |
| make[1]: Nothing to be done for `init'. | |
| /Applications/Xcode.app/Contents/Developer/usr/bin/make -f Makefile.freec depend | |
| /Applications/Xcode.app/Contents/Developer/usr/bin/make -f Makefile.freec all | |
| c++ -O3 -g -DPROFILE_TRACE -Wall -m64 -c -o main.o main.cpp | |
| main.cpp:586:61: warning: equality comparison result unused [-Wunused-comparison] | |
| if (seekSubclones==0 ||seekSubclones==1) {seekSubclones==100;} | |
| ~~~~~~~~~~~~~^~~~~ | |
| main.cpp:586:61: note: use '=' to turn this equality comparison into an assignment | |
| if (seekSubclones==0 ||seekSubclones==1) {seekSubclones==100;} | |
| ^~ | |
| = | |
| main.cpp:1040:27: warning: '&&' within '||' [-Wlogical-op-parentheses] | |
| if ((!forceGC && !(has_BAF) || (ifTargeted&&forceGC!=1) || (WESanalysis == true &&forceGC==0))) { //normalize sample density with control density | |
| ~~~~~~~~~^~~~~~~~~~~~~ ~~ | |
| main.cpp:1040:27: note: place parentheses around the '&&' expression to silence this warning | |
| if ((!forceGC && !(has_BAF) || (ifTargeted&&forceGC!=1) || (WESanalysis == true &&forceGC==0))) { //normalize sample density with control density | |
| ^ | |
| ( ) | |
| 2 warnings generated. | |
| c++ -O3 -g -DPROFILE_TRACE -Wall -m64 -c -o ConfigFile.o ConfigFile.cpp | |
| c++ -O3 -g -DPROFILE_TRACE -Wall -m64 -c -o Chameleon.o Chameleon.cpp | |
| c++ -O3 -g -DPROFILE_TRACE -Wall -m64 -c -o GenomeDensity.o GenomeDensity.cpp | |
| GenomeDensity.cpp:63:10: warning: unused variable 'length' [-Wunused-variable] | |
| int length = strs[1].length(); | |
| ^ | |
| 1 warning generated. | |
| c++ -O3 -g -DPROFILE_TRACE -Wall -m64 -c -o Help.o Help.cpp | |
| c++ -O3 -g -DPROFILE_TRACE -Wall -m64 -c -o myFunc.o myFunc.cpp | |
| myFunc.cpp:54:12: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] | |
| for (; c = *str++; ++jj) { | |
| ~~^~~~~~~~ | |
| myFunc.cpp:54:12: note: place parentheses around the assignment to silence this warning | |
| for (; c = *str++; ++jj) { | |
| ^ | |
| ( ) | |
| myFunc.cpp:54:12: note: use '==' to turn this assignment into an equality comparison | |
| for (; c = *str++; ++jj) { | |
| ^ | |
| == | |
| myFunc.cpp:370:26: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] | |
| if (toadd=strccnt(strs[4].c_str(), '^')) { | |
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | |
| myFunc.cpp:370:26: note: place parentheses around the assignment to silence this warning | |
| if (toadd=strccnt(strs[4].c_str(), '^')) { | |
| ^ | |
| ( ) | |
| myFunc.cpp:370:26: note: use '==' to turn this assignment into an equality comparison | |
| if (toadd=strccnt(strs[4].c_str(), '^')) { | |
| ^ | |
| == | |
| myFunc.cpp:393:26: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] | |
| if (toadd=strccnt(strs[4].c_str(), '^')) { | |
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | |
| myFunc.cpp:393:26: note: place parentheses around the assignment to silence this warning | |
| if (toadd=strccnt(strs[4].c_str(), '^')) { | |
| ^ | |
| ( ) | |
| myFunc.cpp:393:26: note: use '==' to turn this assignment into an equality comparison | |
| if (toadd=strccnt(strs[4].c_str(), '^')) { | |
| ^ | |
| == | |
| myFunc.cpp:1886:141: warning: '&&' within '||' [-Wlogical-op-parentheses] | |
| if (copyNumbers[0]==1 && copyNumbers[1]==2 && copyNumber<1.5 && (medianBAFSym.compare("AA")==0 || medianBAFSym.compare("AB")==0 && uncertainty >0.1)) { | |
| ~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ | |
| myFunc.cpp:1886:141: note: place parentheses around the '&&' expression to silence this warning | |
| if (copyNumbers[0]==1 && copyNumbers[1]==2 && copyNumber<1.5 && (medianBAFSym.compare("AA")==0 || medianBAFSym.compare("AB")==0 && uncertainty >0.1)) { | |
| ^ | |
| ( ) | |
| 4 warnings generated. | |
| c++ -O3 -g -DPROFILE_TRACE -Wall -m64 -c -o KernelVector.o KernelVector.cpp | |
| c++ -O3 -g -DPROFILE_TRACE -Wall -m64 -c -o ChrDensity.o ChrDensity.cpp | |
| c++ -O3 -g -DPROFILE_TRACE -Wall -m64 -c -o ChrCopyNumber.o ChrCopyNumber.cpp | |
| c++ -O3 -g -DPROFILE_TRACE -Wall -m64 -c -o GenomeCopyNumber.o GenomeCopyNumber.cpp | |
| GenomeCopyNumber.cpp:3237:8: warning: unused variable 'contam' [-Wunused-variable] | |
| float contam = 0; | |
| ^ | |
| GenomeCopyNumber.cpp:3696:33: warning: unused variable 'maxpos' [-Wunused-variable] | |
| int maxpos=0; | |
| ^ | |
| GenomeCopyNumber.cpp:3826:30: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] | |
| if (valueToReturn=strccnt(strs[4], '^')) { | |
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ | |
| GenomeCopyNumber.cpp:3826:30: note: place parentheses around the assignment to silence this warning | |
| if (valueToReturn=strccnt(strs[4], '^')) { | |
| ^ | |
| ( ) | |
| GenomeCopyNumber.cpp:3826:30: note: use '==' to turn this assignment into an equality comparison | |
| if (valueToReturn=strccnt(strs[4], '^')) { | |
| ^ | |
| == | |
| GenomeCopyNumber.cpp:3882:27: warning: unused variable 'orient2_1' [-Wunused-variable] | |
| MateOrientation orient2_1 = getMateOrientation(orient2+orient1); | |
| ^ | |
| GenomeCopyNumber.cpp:4202:8: warning: unused variable 'startFragment' [-Wunused-variable] | |
| int startFragment = 0; | |
| ^ | |
| GenomeCopyNumber.cpp:4203:8: warning: unused variable 'endFragment' [-Wunused-variable] | |
| int endFragment=0; | |
| ^ | |
| 6 warnings generated. | |
| c++ -O3 -g -DPROFILE_TRACE -Wall -m64 -c -o chisquaredistr.o chisquaredistr.cpp | |
| c++ -O3 -g -DPROFILE_TRACE -Wall -m64 -c -o ap.o ap.cpp | |
| c++ -O3 -g -DPROFILE_TRACE -Wall -m64 -c -o igammaf.o igammaf.cpp | |
| c++ -O3 -g -DPROFILE_TRACE -Wall -m64 -c -o gammafunc.o gammafunc.cpp | |
| c++ -O3 -g -DPROFILE_TRACE -Wall -m64 -c -o normaldistr.o normaldistr.cpp | |
| c++ -O3 -g -DPROFILE_TRACE -Wall -m64 -c -o ablasf.o ablasf.cpp | |
| c++ -O3 -g -DPROFILE_TRACE -Wall -m64 -c -o ablas.o ablas.cpp | |
| c++ -O3 -g -DPROFILE_TRACE -Wall -m64 -c -o ortfac.o ortfac.cpp | |
| c++ -O3 -g -DPROFILE_TRACE -Wall -m64 -c -o sblas.o sblas.cpp | |
| c++ -O3 -g -DPROFILE_TRACE -Wall -m64 -c -o rotations.o rotations.cpp | |
| c++ -O3 -g -DPROFILE_TRACE -Wall -m64 -c -o reflections.o reflections.cpp | |
| c++ -O3 -g -DPROFILE_TRACE -Wall -m64 -c -o linreg.o linreg.cpp | |
| c++ -O3 -g -DPROFILE_TRACE -Wall -m64 -c -o hblas.o hblas.cpp | |
| c++ -O3 -g -DPROFILE_TRACE -Wall -m64 -c -o descriptivestatistics.o descriptivestatistics.cpp | |
| c++ -O3 -g -DPROFILE_TRACE -Wall -m64 -c -o creflections.o creflections.cpp | |
| c++ -O3 -g -DPROFILE_TRACE -Wall -m64 -c -o blas.o blas.cpp | |
| c++ -O3 -g -DPROFILE_TRACE -Wall -m64 -c -o bdsvd.o bdsvd.cpp | |
| c++ -O3 -g -DPROFILE_TRACE -Wall -m64 -c -o svd.o svd.cpp | |
| c++ -O3 -g -DPROFILE_TRACE -Wall -m64 -c -o ialglib.o ialglib.cpp | |
| ialglib.cpp:837:39: warning: conversion from string literal to 'char *' is deprecated [-Wc++11-compat-deprecated-writable-strings] | |
| vcopy_complex(k, arow, 1, abuf, 1, "No conj"); | |
| ^ | |
| ialglib.cpp:842:53: warning: conversion from string literal to 'char *' is deprecated [-Wc++11-compat-deprecated-writable-strings] | |
| vcopy_complex(k, arow, stride, abuf, 1, "No conj"); | |
| ^ | |
| ialglib.cpp:847:53: warning: conversion from string literal to 'char *' is deprecated [-Wc++11-compat-deprecated-writable-strings] | |
| vcopy_complex(k, arow, stride, abuf, 1, "Conj"); | |
| ^ | |
| ialglib.cpp:917:67: warning: conversion from string literal to 'char *' is deprecated [-Wc++11-compat-deprecated-writable-strings] | |
| vcopy_complex(i, abuf+2*i, alglib_c_block, tmpbuf, 1, "No conj"); | |
| ^ | |
| ialglib.cpp:930:85: warning: conversion from string literal to 'char *' is deprecated [-Wc++11-compat-deprecated-writable-strings] | |
| vcopy_complex(n-1-i, pdiag+2*alglib_c_block, alglib_c_block, tmpbuf, 1, "No conj"); | |
| ^ | |
| ialglib.cpp:1069:57: warning: conversion from string literal to 'char *' is deprecated [-Wc++11-compat-deprecated-writable-strings] | |
| vcopy_complex(m-1-i, pdiag+2, 1, tmpbuf, 1, "No conj"); | |
| ^ | |
| ialglib.cpp:1081:50: warning: conversion from string literal to 'char *' is deprecated [-Wc++11-compat-deprecated-writable-strings] | |
| vcopy_complex(i, arow, 1, tmpbuf, 1, "No conj"); | |
| ^ | |
| ialglib.cpp:1229:50: warning: conversion from string literal to 'char *' is deprecated [-Wc++11-compat-deprecated-writable-strings] | |
| vcopy_complex(k, arow, 1, tmpbuf, 1, "Conj"); | |
| ^ | |
| ialglib.cpp:1237:50: warning: conversion from string literal to 'char *' is deprecated [-Wc++11-compat-deprecated-writable-strings] | |
| vcopy_complex(k, arow, 1, tmpbuf, 1, "Conj"); | |
| ^ | |
| ialglib.cpp:12:18: warning: unused variable 'alglib_half_r_block' [-Wunused-const-variable] | |
| static const int alglib_half_r_block = alglib_r_block/2; | |
| ^ | |
| ialglib.cpp:13:18: warning: unused variable 'alglib_half_c_block' [-Wunused-const-variable] | |
| static const int alglib_half_c_block = alglib_c_block/2; | |
| ^ | |
| 11 warnings generated. | |
| c++ -O3 -g -DPROFILE_TRACE -Wall -m64 -c -o EntryCNV.o EntryCNV.cpp | |
| c++ -O3 -g -DPROFILE_TRACE -Wall -m64 -c -o SNPinGenome.o SNPinGenome.cpp | |
| SNPinGenome.cpp:273:39: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] | |
| if (valueToReturn = strccnt(strs[4], '^')) { | |
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ | |
| SNPinGenome.cpp:273:39: note: place parentheses around the assignment to silence this warning | |
| if (valueToReturn = strccnt(strs[4], '^')) { | |
| ^ | |
| ( ) | |
| SNPinGenome.cpp:273:39: note: use '==' to turn this assignment into an equality comparison | |
| if (valueToReturn = strccnt(strs[4], '^')) { | |
| ^ | |
| == | |
| SNPinGenome.cpp:287:39: warning: using the result of an assignment as a condition without parentheses [-Wparentheses] | |
| if (valueToReturn = strccnt(strs[4], '^')) { | |
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ | |
| SNPinGenome.cpp:287:39: note: place parentheses around the assignment to silence this warning | |
| if (valueToReturn = strccnt(strs[4], '^')) { | |
| ^ | |
| ( ) | |
| SNPinGenome.cpp:287:39: note: use '==' to turn this assignment into an equality comparison | |
| if (valueToReturn = strccnt(strs[4], '^')) { | |
| ^ | |
| == | |
| SNPinGenome.cpp:316:19: warning: unused variable 'localBAF' [-Wunused-variable] | |
| float localBAF=addInfoFromAPileUp(atoi(strs[3]),minimalTotalLetterCountPerPosition,(*SNP_atChr_)[index].getNucleotideAt(positionCount), | |
| ^ | |
| SNPinGenome.cpp:338:27: warning: unused variable 'localBAF' [-Wunused-variable] | |
| float localBAF=addInfoFromAPileUp(atoi(strs[3]),minimalTotalLetterCountPerPosition,(*SNP_atChr_)[index].getNucleotideAt(positionCount), | |
| ^ | |
| 4 warnings generated. | |
| c++ -O3 -g -DPROFILE_TRACE -Wall -m64 -c -o SNPatChr.o SNPatChr.cpp | |
| c++ -O3 -g -DPROFILE_TRACE -Wall -m64 -c -o SNPposition.o SNPposition.cpp | |
| SNPposition.cpp:31:18: warning: unused variable 'strs_cnt' [-Wunused-variable] | |
| unsigned strs_cnt = split(alt, ',', strs); | |
| ^ | |
| SNPposition.cpp:46:14: warning: unused variable 'c_ref' [-Wunused-variable] | |
| char c_ref = ref[0]; | |
| ^ | |
| SNPposition.cpp:47:14: warning: unused variable 'reverse' [-Wunused-variable] | |
| bool reverse = strcmp(strand, "-") == 0; | |
| ^ | |
| SNPposition.cpp:52:18: warning: unused variable 'strs_cnt' [-Wunused-variable] | |
| unsigned strs_cnt = split(letters, '/', strs); | |
| ^ | |
| 4 warnings generated. | |
| c++ -O3 -g -DPROFILE_TRACE -Wall -m64 -c -o binomialdistr.o binomialdistr.cpp | |
| c++ -O3 -g -DPROFILE_TRACE -Wall -m64 -c -o ibetaf.o ibetaf.cpp | |
| ibetaf.cpp:166:16: warning: 'gamma' is deprecated: first deprecated in macOS 10.9 [-Wdeprecated-declarations] | |
| t = t*(gamma(a+b)/(gamma(a)*gamma(b))); | |
| ^ | |
| /usr/include/math.h:759:15: note: 'gamma' has been explicitly marked deprecated here | |
| extern double gamma(double) __OSX_AVAILABLE_BUT_DEPRECATED(__MAC_10_0, __MAC_10_9, __IPHONE_NA, __IPHONE_NA); | |
| ^ | |
| ibetaf.cpp:166:28: warning: 'gamma' is deprecated: first deprecated in macOS 10.9 [-Wdeprecated-declarations] | |
| t = t*(gamma(a+b)/(gamma(a)*gamma(b))); | |
| ^ | |
| /usr/include/math.h:759:15: note: 'gamma' has been explicitly marked deprecated here | |
| extern double gamma(double) __OSX_AVAILABLE_BUT_DEPRECATED(__MAC_10_0, __MAC_10_9, __IPHONE_NA, __IPHONE_NA); | |
| ^ | |
| ibetaf.cpp:166:37: warning: 'gamma' is deprecated: first deprecated in macOS 10.9 [-Wdeprecated-declarations] | |
| t = t*(gamma(a+b)/(gamma(a)*gamma(b))); | |
| ^ | |
| /usr/include/math.h:759:15: note: 'gamma' has been explicitly marked deprecated here | |
| extern double gamma(double) __OSX_AVAILABLE_BUT_DEPRECATED(__MAC_10_0, __MAC_10_9, __IPHONE_NA, __IPHONE_NA); | |
| ^ | |
| ibetaf.cpp:928:13: warning: 'gamma' is deprecated: first deprecated in macOS 10.9 [-Wdeprecated-declarations] | |
| t = gamma(a+b)/(gamma(a)*gamma(b)); | |
| ^ | |
| /usr/include/math.h:759:15: note: 'gamma' has been explicitly marked deprecated here | |
| extern double gamma(double) __OSX_AVAILABLE_BUT_DEPRECATED(__MAC_10_0, __MAC_10_9, __IPHONE_NA, __IPHONE_NA); | |
| ^ | |
| ibetaf.cpp:928:25: warning: 'gamma' is deprecated: first deprecated in macOS 10.9 [-Wdeprecated-declarations] | |
| t = gamma(a+b)/(gamma(a)*gamma(b)); | |
| ^ | |
| /usr/include/math.h:759:15: note: 'gamma' has been explicitly marked deprecated here | |
| extern double gamma(double) __OSX_AVAILABLE_BUT_DEPRECATED(__MAC_10_0, __MAC_10_9, __IPHONE_NA, __IPHONE_NA); | |
| ^ | |
| ibetaf.cpp:928:34: warning: 'gamma' is deprecated: first deprecated in macOS 10.9 [-Wdeprecated-declarations] | |
| t = gamma(a+b)/(gamma(a)*gamma(b)); | |
| ^ | |
| /usr/include/math.h:759:15: note: 'gamma' has been explicitly marked deprecated here | |
| extern double gamma(double) __OSX_AVAILABLE_BUT_DEPRECATED(__MAC_10_0, __MAC_10_9, __IPHONE_NA, __IPHONE_NA); | |
| ^ | |
| 6 warnings generated. | |
| c++ -O3 -g -DPROFILE_TRACE -Wall -m64 -c -o ThreadPool.o ThreadPool.cpp | |
| c++ -O3 -g -DPROFILE_TRACE -Wall -m64 -c -o BAFpileup.o BAFpileup.cpp | |
| BAFpileup.cpp:58:25: warning: unused variable 'matesOrientation' [-Wunused-variable] | |
| MateOrientation matesOrientation = getMateOrientation(matesOrientation_str); | |
| ^ | |
| BAFpileup.cpp:55:20: warning: unused variable 't0' [-Wunused-variable] | |
| time_t t0 = time(NULL); | |
| ^ | |
| 2 warnings generated. | |
| c++ -O3 -g -DPROFILE_TRACE -Wall -m64 -c -o SeekSubclones.o SeekSubclones.cpp | |
| 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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I have cleaned the code a little bit in v10.2. and the "==" typo was fixed.