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###
### Running command:
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### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL casper
###
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* installing to library 'F:/biocbuild/bbs-3.17-bioc/R/library'
* installing *source* package 'casper' ...
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 12.2.0'
using C++ compiler: 'G__~1.EXE (GCC) 12.2.0'
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c casper.cpp -o casper.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c cstat.cpp -o cstat.o
cstat.cpp: In function 'void free_vector(float*, int, int)':
cstat.cpp:1110:20: warning: comparing the result of pointer addition '(v + ((sizetype)(((long long unsigned int)nl) * 4)))' and NULL [-Waddress]
1110 | if( (v+nl) != NULL ) free((char *) (v+nl));
| ^
cstat.cpp: In function 'void free_dvector(double*, int, int)':
cstat.cpp:1116:20: warning: comparing the result of pointer addition '(v + ((sizetype)(((long long unsigned int)nl) * 8)))' and NULL [-Waddress]
1116 | if( (v+nl) != NULL ) free((char *) (v+nl));
| ^
cstat.cpp: In function 'void free_ivector(int*, int, int)':
cstat.cpp:1122:20: warning: comparing the result of pointer addition '(v + ((sizetype)(((long long unsigned int)nl) * 4)))' and NULL [-Waddress]
1122 | if( (v+nl) != NULL ) free((char *) (v+nl));
| ^
cstat.cpp: In function 'void free_dmatrix(double**, int, int, int, int)':
cstat.cpp:1130:47: warning: comparing the result of pointer addition '((*(m + ((sizetype)(((long long unsigned int)i) * 8)))) + ((sizetype)(((long long unsigned int)ncl) * 8)))' and NULL [-Waddress]
1130 | for(i=nrh;i>=nrl;i--) {if( (m[i]+ncl) != NULL )
| ^
cstat.cpp:1132:21: warning: comparing the result of pointer addition '(m + ((sizetype)(((long long unsigned int)nrl) * 8)))' and NULL [-Waddress]
1132 | if( (m+nrl) != NULL ) free((char *) (m+nrl));
| ^
cstat.cpp: In function 'void free_imatrix(int**, int, int, int, int)':
cstat.cpp:1140:47: warning: comparing the result of pointer addition '((*(m + ((sizetype)(((long long unsigned int)i) * 8)))) + ((sizetype)(((long long unsigned int)ncl) * 4)))' and NULL [-Waddress]
1140 | for(i=nrh;i>=nrl;i--) {if( (m[i]+ncl) != NULL )
| ^
cstat.cpp:1142:21: warning: comparing the result of pointer addition '(m + ((sizetype)(((long long unsigned int)nrl) * 8)))' and NULL [-Waddress]
1142 | if( (m+nrl) != NULL ) free((char *) (m+nrl));
| ^
In function 'void free_dvector(double*, int, int)',
inlined from 'double f1dim(double)' at cstat.cpp:5500:15:
cstat.cpp:1116:34: warning: 'void free(void*)' called on pointer '<unknown>' with nonzero offset 8 [-Wfree-nonheap-object]
1116 | if( (v+nl) != NULL ) free((char *) (v+nl));
| ~~~~^~~~~~~~~~~~~~~~~~
cstat.cpp: In function 'double f1dim(double)':
cstat.cpp:5497:13: note: returned from 'double* dvector(int, int)'
5497 | xt=dvector(1,ncom);
| ~~~~~~~^~~~~~~~
In function 'void free_dvector(double*, int, int)',
inlined from 'void choldc(double**, int, double**, bool*)' at cstat.cpp:1751:15:
cstat.cpp:1116:34: warning: 'void free(void*)' called on pointer '<unknown>' with nonzero offset 8 [-Wfree-nonheap-object]
1116 | if( (v+nl) != NULL ) free((char *) (v+nl));
| ~~~~^~~~~~~~~~~~~~~~~~
cstat.cpp: In function 'void choldc(double**, int, double**, bool*)':
cstat.cpp:1738:13: note: returned from 'double* dvector(int, int)'
1738 | p= dvector(1,n);
| ~~~~~~~^~~~~
In function 'void free_dvector(double*, int, int)',
inlined from 'void choldc(double**, int, double**, bool*)' at cstat.cpp:1751:15:
cstat.cpp:1116:34: warning: 'void free(void*)' called on pointer '<unknown>' with nonzero offset 8 [-Wfree-nonheap-object]
1116 | if( (v+nl) != NULL ) free((char *) (v+nl));
| ~~~~^~~~~~~~~~~~~~~~~~
cstat.cpp: In function 'void choldc(double**, int, double**, bool*)':
cstat.cpp:1738:13: note: returned from 'double* dvector(int, int)'
1738 | p= dvector(1,n);
| ~~~~~~~^~~~~
In function 'void free_dvector(double*, int, int)',
inlined from 'void nn_bayes(double*, double**, double**, int, double, double*, double**, double, double*, double**)' at cstat.cpp:283:15:
cstat.cpp:1116:34: warning: 'void free(void*)' called on pointer '<unknown>' with nonzero offset 8 [-Wfree-nonheap-object]
1116 | if( (v+nl) != NULL ) free((char *) (v+nl));
| ~~~~^~~~~~~~~~~~~~~~~~
cstat.cpp: In function 'void nn_bayes(double*, double**, double**, int, double, double*, double**, double, double*, double**)':
cstat.cpp:276:14: note: returned from 'double* dvector(int, int)'
276 | z = dvector(1,p);
| ~~~~~~~^~~~~
In function 'void free_dvector(double*, int, int)',
inlined from 'double nn_integral(double*, double*, double**, double*, double*, double*, double**, double*, int*, int*)' at cstat.cpp:341:15:
cstat.cpp:1116:34: warning: 'void free(void*)' called on pointer '<unknown>' with nonzero offset 8 [-Wfree-nonheap-object]
1116 | if( (v+nl) != NULL ) free((char *) (v+nl));
| ~~~~^~~~~~~~~~~~~~~~~~
cstat.cpp: In function 'double nn_integral(double*, double*, double**, double*, double*, double*, double**, double*, int*, int*)':
cstat.cpp:328:13: note: returned from 'double* dvector(int, int)'
328 | m= dvector(1,*p);
| ~~~~~~~^~~~~~
In function 'void free_dvector(double*, int, int)',
inlined from 'void ludc(double**, int, int*, double*)' at cstat.cpp:1946:15:
cstat.cpp:1116:34: warning: 'void free(void*)' called on pointer '<unknown>' with nonzero offset 8 [-Wfree-nonheap-object]
1116 | if( (v+nl) != NULL ) free((char *) (v+nl));
| ~~~~^~~~~~~~~~~~~~~~~~
cstat.cpp: In function 'void ludc(double**, int, int*, double*)':
cstat.cpp:1900:13: note: returned from 'double* dvector(int, int)'
1900 | vv=dvector(1,n);
| ~~~~~~~^~~~~
In function 'void free_dvector(double*, int, int)',
inlined from 'void lu_inverse(double**, int, double**)' at cstat.cpp:1998:38:
cstat.cpp:1116:34: warning: 'void free(void*)' called on pointer '<unknown>' with nonzero offset 8 [-Wfree-nonheap-object]
1116 | if( (v+nl) != NULL ) free((char *) (v+nl));
| ~~~~^~~~~~~~~~~~~~~~~~
cstat.cpp: In function 'void lu_inverse(double**, int, double**)':
cstat.cpp:1990:34: note: returned from 'double* dvector(int, int)'
1990 | indx= ivector(1,n); col= dvector(1,n);
| ~~~~~~~^~~~~
In function 'void free_dvector(double*, int, int)',
inlined from 'void eigenvals(double**, int, double*)' at cstat.cpp:2032:15:
cstat.cpp:1116:34: warning: 'void free(void*)' called on pointer '<unknown>' with nonzero offset 8 [-Wfree-nonheap-object]
1116 | if( (v+nl) != NULL ) free((char *) (v+nl));
| ~~~~^~~~~~~~~~~~~~~~~~
cstat.cpp: In function 'void eigenvals(double**, int, double*)':
cstat.cpp:2024:13: note: returned from 'double* dvector(int, int)'
2024 | e= dvector(1,n);
| ~~~~~~~^~~~~
In function 'void free_dvector(double*, int, int)',
inlined from 'double dmvnormC(double*, int, double*, double**, double, int)' at cstat.cpp:2493:15:
cstat.cpp:1116:34: warning: 'void free(void*)' called on pointer '<unknown>' with nonzero offset 8 [-Wfree-nonheap-object]
1116 | if( (v+nl) != NULL ) free((char *) (v+nl));
| ~~~~^~~~~~~~~~~~~~~~~~
cstat.cpp: In function 'double dmvnormC(double*, int, double*, double**, double, int)':
cstat.cpp:2489:13: note: returned from 'double* dvector(int, int)'
2489 | z= dvector(1,n); z2= dvector(1,n);
| ~~~~~~~^~~~~
In function 'void free_dvector(double*, int, int)',
inlined from 'double dmvnormC(double*, int, double*, double**, double, int)' at cstat.cpp:2493:36:
cstat.cpp:1116:34: warning: 'void free(void*)' called on pointer '<unknown>' with nonzero offset 8 [-Wfree-nonheap-object]
1116 | if( (v+nl) != NULL ) free((char *) (v+nl));
| ~~~~^~~~~~~~~~~~~~~~~~
cstat.cpp: In function 'double dmvnormC(double*, int, double*, double**, double, int)':
cstat.cpp:2489:31: note: returned from 'double* dvector(int, int)'
2489 | z= dvector(1,n); z2= dvector(1,n);
| ~~~~~~~^~~~~
In function 'void free_dvector(double*, int, int)',
inlined from 'double dmvtC(double*, int, double*, double**, double, int, int)' at cstat.cpp:2787:15:
cstat.cpp:1116:34: warning: 'void free(void*)' called on pointer '<unknown>' with nonzero offset 8 [-Wfree-nonheap-object]
1116 | if( (v+nl) != NULL ) free((char *) (v+nl));
| ~~~~^~~~~~~~~~~~~~~~~~
cstat.cpp: In function 'double dmvtC(double*, int, double*, double**, double, int, int)':
cstat.cpp:2783:13: note: returned from 'double* dvector(int, int)'
2783 | z= dvector(1,n); z2= dvector(1,n);
| ~~~~~~~^~~~~
In function 'void free_dvector(double*, int, int)',
inlined from 'double dmvtC(double*, int, double*, double**, double, int, int)' at cstat.cpp:2787:36:
cstat.cpp:1116:34: warning: 'void free(void*)' called on pointer '<unknown>' with nonzero offset 8 [-Wfree-nonheap-object]
1116 | if( (v+nl) != NULL ) free((char *) (v+nl));
| ~~~~^~~~~~~~~~~~~~~~~~
cstat.cpp: In function 'double dmvtC(double*, int, double*, double**, double, int, int)':
cstat.cpp:2783:31: note: returned from 'double* dvector(int, int)'
2783 | z= dvector(1,n); z2= dvector(1,n);
| ~~~~~~~^~~~~
In function 'void free_dvector(double*, int, int)',
inlined from 'void rmvnormC(double*, int, double*, double**)' at cstat.cpp:2732:15:
cstat.cpp:1116:34: warning: 'void free(void*)' called on pointer '<unknown>' with nonzero offset 8 [-Wfree-nonheap-object]
1116 | if( (v+nl) != NULL ) free((char *) (v+nl));
| ~~~~^~~~~~~~~~~~~~~~~~
cstat.cpp: In function 'void rmvnormC(double*, int, double*, double**)':
cstat.cpp:2729:13: note: returned from 'double* dvector(int, int)'
2729 | z= dvector(1,n);
| ~~~~~~~^~~~~
In function 'void free_dvector(double*, int, int)',
inlined from 'void lmbayes_knownvar(double*, double*, double**, double**, double**, double*, double*, int*, double*, double**, int*, int*, int*, double*, double**, double*)' at cstat.cpp:498:17:
cstat.cpp:1116:34: warning: 'void free(void*)' called on pointer '<unknown>' with nonzero offset 8 [-Wfree-nonheap-object]
1116 | if( (v+nl) != NULL ) free((char *) (v+nl));
| ~~~~^~~~~~~~~~~~~~~~~~
cstat.cpp: In function 'void lmbayes_knownvar(double*, double*, double**, double**, double**, double*, double*, int*, double*, double**, int*, int*, int*, double*, double**, double*)':
cstat.cpp:492:20: note: returned from 'double* dvector(int, int)'
492 | zeroes= dvector(1,*p);
| ~~~~~~~^~~~~~
In function 'void free_dvector(double*, int, int)',
inlined from 'void lmbayes_knownvar(double*, double*, double**, double**, double**, double*, double*, int*, double*, double**, int*, int*, int*, double*, double**, double*)' at cstat.cpp:502:15:
cstat.cpp:1116:34: warning: 'void free(void*)' called on pointer '<unknown>' with nonzero offset 8 [-Wfree-nonheap-object]
1116 | if( (v+nl) != NULL ) free((char *) (v+nl));
| ~~~~^~~~~~~~~~~~~~~~~~
cstat.cpp: In function 'void lmbayes_knownvar(double*, double*, double**, double**, double**, double*, double*, int*, double*, double**, int*, int*, int*, double*, double**, double*)':
cstat.cpp:479:16: note: returned from 'double* dvector(int, int)'
479 | b_ls= dvector(1,*p); ypred= dvector(1,*n);
| ~~~~~~~^~~~~~
In function 'void free_dvector(double*, int, int)',
inlined from 'void lmbayes_knownvar(double*, double*, double**, double**, double**, double*, double*, int*, double*, double**, int*, int*, int*, double*, double**, double*)' at cstat.cpp:502:40:
cstat.cpp:1116:34: warning: 'void free(void*)' called on pointer '<unknown>' with nonzero offset 8 [-Wfree-nonheap-object]
1116 | if( (v+nl) != NULL ) free((char *) (v+nl));
| ~~~~^~~~~~~~~~~~~~~~~~
cstat.cpp: In function 'void lmbayes_knownvar(double*, double*, double**, double**, double**, double*, double*, int*, double*, double**, int*, int*, int*, double*, double**, double*)':
cstat.cpp:479:38: note: returned from 'double* dvector(int, int)'
479 | b_ls= dvector(1,*p); ypred= dvector(1,*n);
| ~~~~~~~^~~~~~
In function 'void free_dvector(double*, int, int)',
inlined from 'void lmbayes(double*, double*, double*, double**, double*, double*, double**, double**, double*, int*, double*, double**, int*, int*, int*, double*, double**, double*, double*, double*)' at cstat.cpp:439:17:
cstat.cpp:1116:34: warning: 'void free(void*)' called on pointer '<unknown>' with nonzero offset 8 [-Wfree-nonheap-object]
1116 | if( (v+nl) != NULL ) free((char *) (v+nl));
| ~~~~^~~~~~~~~~~~~~~~~~
cstat.cpp: In function 'void lmbayes(double*, double*, double*, double**, double*, double*, double**, double**, double*, int*, double*, double**, int*, int*, int*, double*, double**, double*, double*, double*)':
cstat.cpp:432:20: note: returned from 'double* dvector(int, int)'
432 | zeroes= dvector(1,*p);
| ~~~~~~~^~~~~~
In function 'void free_dvector(double*, int, int)',
inlined from 'void lmbayes(double*, double*, double*, double**, double*, double*, double**, double**, double*, int*, double*, double**, int*, int*, int*, double*, double**, double*, double*, double*)' at cstat.cpp:443:15:
cstat.cpp:1116:34: warning: 'void free(void*)' called on pointer '<unknown>' with nonzero offset 8 [-Wfree-nonheap-object]
1116 | if( (v+nl) != NULL ) free((char *) (v+nl));
| ~~~~^~~~~~~~~~~~~~~~~~
cstat.cpp: In function 'void lmbayes(double*, double*, double*, double**, double*, double*, double**, double**, double*, int*, double*, double**, int*, int*, int*, double*, double**, double*, double*, double*)':
cstat.cpp:417:16: note: returned from 'double* dvector(int, int)'
417 | b_ls= dvector(1,*p); ypred= dvector(1,*n);
| ~~~~~~~^~~~~~
In function 'void free_dvector(double*, int, int)',
inlined from 'void lmbayes(double*, double*, double*, double**, double*, double*, double**, double**, double*, int*, double*, double**, int*, int*, int*, double*, double**, double*, double*, double*)' at cstat.cpp:443:40:
cstat.cpp:1116:34: warning: 'void free(void*)' called on pointer '<unknown>' with nonzero offset 8 [-Wfree-nonheap-object]
1116 | if( (v+nl) != NULL ) free((char *) (v+nl));
| ~~~~^~~~~~~~~~~~~~~~~~
cstat.cpp: In function 'void lmbayes(double*, double*, double*, double**, double*, double*, double**, double**, double*, int*, double*, double**, int*, int*, int*, double*, double**, double*, double*, double*)':
cstat.cpp:417:38: note: returned from 'double* dvector(int, int)'
417 | b_ls= dvector(1,*p); ypred= dvector(1,*n);
| ~~~~~~~^~~~~~
In function 'void free_dvector(double*, int, int)',
inlined from 'void rmvtC(double*, int, double*, double**, int)' at cstat.cpp:2920:15:
cstat.cpp:1116:34: warning: 'void free(void*)' called on pointer '<unknown>' with nonzero offset 8 [-Wfree-nonheap-object]
1116 | if( (v+nl) != NULL ) free((char *) (v+nl));
| ~~~~^~~~~~~~~~~~~~~~~~
cstat.cpp: In function 'void rmvtC(double*, int, double*, double**, int)':
cstat.cpp:2917:13: note: returned from 'double* dvector(int, int)'
2917 | z= dvector(1,n);
| ~~~~~~~^~~~~
In function 'void free_dvector(double*, int, int)',
inlined from 'void polint(double*, double*, int, double, double*, double*)' at cstat.cpp:5135:15:
cstat.cpp:1116:34: warning: 'void free(void*)' called on pointer '<unknown>' with nonzero offset 8 [-Wfree-nonheap-object]
1116 | if( (v+nl) != NULL ) free((char *) (v+nl));
| ~~~~^~~~~~~~~~~~~~~~~~
cstat.cpp: In function 'void polint(double*, double*, int, double, double*, double*)':
cstat.cpp:5107:13: note: returned from 'double* dvector(int, int)'
5107 | d= dvector(1,n);
| ~~~~~~~^~~~~
In function 'void free_dvector(double*, int, int)',
inlined from 'void polint(double*, double*, int, double, double*, double*)' at cstat.cpp:5136:15:
cstat.cpp:1116:34: warning: 'void free(void*)' called on pointer '<unknown>' with nonzero offset 8 [-Wfree-nonheap-object]
1116 | if( (v+nl) != NULL ) free((char *) (v+nl));
| ~~~~^~~~~~~~~~~~~~~~~~
cstat.cpp: In function 'void polint(double*, double*, int, double, double*, double*)':
cstat.cpp:5106:13: note: returned from 'double* dvector(int, int)'
5106 | c= dvector(1,n);
| ~~~~~~~^~~~~
In function 'void free_dvector(double*, int, int)',
inlined from 'void dirmin(double*, double*, int, double*, double (*)(double*), int, double)' at cstat.cpp:5489:14:
cstat.cpp:1116:34: warning: 'void free(void*)' called on pointer 'xicom' with nonzero offset 8 [-Wfree-nonheap-object]
1116 | if( (v+nl) != NULL ) free((char *) (v+nl));
| ~~~~^~~~~~~~~~~~~~~~~~
cstat.cpp: In function 'void dirmin(double*, double*, int, double*, double (*)(double*), int, double)':
cstat.cpp:5456:15: note: declared here
5456 | double *pcom,*xicom,(*nrfunc)(double []);
| ^~~~~
In function 'void free_dvector(double*, int, int)',
inlined from 'void dirmin(double*, double*, int, double*, double (*)(double*), int, double)' at cstat.cpp:5490:14:
cstat.cpp:1116:34: warning: 'void free(void*)' called on pointer 'pcom' with nonzero offset 8 [-Wfree-nonheap-object]
1116 | if( (v+nl) != NULL ) free((char *) (v+nl));
| ~~~~^~~~~~~~~~~~~~~~~~
cstat.cpp: In function 'void dirmin(double*, double*, int, double*, double (*)(double*), int, double)':
cstat.cpp:5456:9: note: declared here
5456 | double *pcom,*xicom,(*nrfunc)(double []);
| ^~~~
In function 'void free_dvector(double*, int, int)',
inlined from 'void minimize(double*, double**, int, double, int*, double*, double (*)(double*), int)' at cstat.cpp:5448:15:
cstat.cpp:1116:34: warning: 'void free(void*)' called on pointer '<unknown>' with nonzero offset 8 [-Wfree-nonheap-object]
1116 | if( (v+nl) != NULL ) free((char *) (v+nl));
| ~~~~^~~~~~~~~~~~~~~~~~
cstat.cpp: In function 'void minimize(double*, double**, int, double, int*, double*, double (*)(double*), int)':
cstat.cpp:5412:18: note: returned from 'double* dvector(int, int)'
5412 | dirinit=dvector(1,n);
| ~~~~~~~^~~~~
In function 'void free_dvector(double*, int, int)',
inlined from 'void minimize(double*, double**, int, double, int*, double*, double (*)(double*), int)' at cstat.cpp:5449:15:
cstat.cpp:1116:34: warning: 'void free(void*)' called on pointer '<unknown>' with nonzero offset 8 [-Wfree-nonheap-object]
1116 | if( (v+nl) != NULL ) free((char *) (v+nl));
| ~~~~^~~~~~~~~~~~~~~~~~
cstat.cpp: In function 'void minimize(double*, double**, int, double, int*, double*, double (*)(double*), int)':
cstat.cpp:5411:15: note: returned from 'double* dvector(int, int)'
5411 | thtt=dvector(1,n);
| ~~~~~~~^~~~~
In function 'void free_dvector(double*, int, int)',
inlined from 'void minimize(double*, double**, int, double, int*, double*, double (*)(double*), int)' at cstat.cpp:5450:15:
cstat.cpp:1116:34: warning: 'void free(void*)' called on pointer '<unknown>' with nonzero offset 8 [-Wfree-nonheap-object]
1116 | if( (v+nl) != NULL ) free((char *) (v+nl));
| ~~~~^~~~~~~~~~~~~~~~~~
cstat.cpp: In function 'void minimize(double*, double**, int, double, int*, double*, double (*)(double*), int)':
cstat.cpp:5410:14: note: returned from 'double* dvector(int, int)'
5410 | tht=dvector(1,n);
| ~~~~~~~^~~~~
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c dataframe.cpp -o dataframe.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c discretedf.cpp -o discretedf.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c dropVariant.cpp -o dropVariant.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c exon.cpp -o exon.o
gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c fragFunc.c -o fragFunc.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c fragment.cpp -o fragment.o
gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c functions.c -o functions.o
gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c hash.c -o hash.o
gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c join_exons.c -o join_exons.o
gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c makeIslands.c -o makeIslands.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c model.cpp -o model.o
model.cpp: In member function 'char* Model::toString()':
model.cpp:147:24: warning: 'sprintf' argument 3 overlaps destination object '<unknown>' [-Wrestrict]
147 | sprintf(str, "%s {%s}", str, vstr);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c model_cmp.cpp -o model_cmp.o
gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c pathCounts.c -o pathCounts.o
gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c procBam.c -o procBam.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c rcasper.cpp -o rcasper.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c seppel.cpp -o seppel.o
seppel.cpp: In member function 'void Seppel::exploreUnif(int, std::set<Variant*, VariantCmp>*)':
seppel.cpp:484:9: warning: array subscript -1 is outside array bounds of 'void [24]' [-Warray-bounds]
484 | delete [] possiblemodels;
| ^~~~~~~~~~~~~~~~~~~~~~~~
seppel.cpp:402:55: note: at offset -8 into object of size 24 allocated by 'operator new'
402 | vector<Model*>* possiblemodels = new vector<Model*>();
| ^
seppel.cpp:484:19: warning: 'void operator delete [](void*)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
484 | delete [] possiblemodels;
| ^~~~~~~~~~~~~~
seppel.cpp:402:55: note: returned from 'void* operator new(std::size_t)'
402 | vector<Model*>* possiblemodels = new vector<Model*>();
| ^
gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c simReads.c -o simReads.o
gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c simReadsfunc.c -o simReadsfunc.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c smartmodeldist.cpp -o smartmodeldist.o
gcc -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c uniqQname.c -o uniqQname.o
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c variant.cpp -o variant.o
variant.cpp: In member function 'void Variant::toString(char*)':
variant.cpp:164:52: warning: 'sprintf' argument 3 overlaps destination object 'str' [-Wrestrict]
164 | for (int e = 0; e < exonCount; e++) sprintf(str, "%s,%i", str, exons[e]->id);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
variant.cpp:156:30: note: destination object referenced by 'restrict'-qualified argument 1 was declared here
156 | void Variant::toString(char *str)
| ~~~~~~^~~
g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c variant_cmp.cpp -o variant_cmp.o
g++ -std=gnu++11 -shared -s -static-libgcc -o casper.dll tmp.def casper.o cstat.o dataframe.o discretedf.o dropVariant.o exon.o fragFunc.o fragment.o functions.o hash.o join_exons.o makeIslands.o model.o model_cmp.o pathCounts.o procBam.o rcasper.o seppel.o simReads.o simReadsfunc.o smartmodeldist.o uniqQname.o variant.o variant_cmp.o -Lc:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -Lc:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.17-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.17-bioc/R/library/00LOCK-casper/00new/casper/libs/x64
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for 'transcripts' in package 'casper'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (casper)