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### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data PICS
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* checking for file ‘PICS/DESCRIPTION’ ... OK
* preparing ‘PICS’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* running ‘cleanup’
* installing the package to build vignettes
-----------------------------------
* installing *source* package ‘PICS’ ...
** using staged installation
checking for pkg-config... /opt/R/arm64/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for GSL... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
using C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
using SDK: ‘MacOSX11.3.sdk’
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pics.c -o pics.o
pics.c:1009:9: warning: variable 'chiSum' set but not used [-Wunused-but-set-variable]
double chiSum, etaF, etaR, dd, cc;
^
pics.c:1301:3: warning: variable 'penalty' is used uninitialized whenever switch default is taken [-Wsometimes-uninitialized]
default:
^~~~~~~
pics.c:1307:97: note: uninitialized use occurs here
bic = logDensityMix(yF, w, muF, sigmaSqF, K, NF) + logDensityMix(yR, w, muR, sigmaSqR, K,NR) - penalty;
^~~~~~~
pics.c:1275:42: note: initialize the variable 'penalty' to silence this warning
double bic, tmp, muF[K], muR[K], penalty, distance;
^
= 0.0
pics.c:1633:69: warning: unused variable 'PhiFw' [-Wunused-variable]
double aNormF, aNormR, bNormF, bNormR, P0F=1, P0R=1, PhiF, PhiR, PhiFw, PhiRw, wPjF, wPjR;
^
pics.c:1633:76: warning: unused variable 'PhiRw' [-Wunused-variable]
double aNormF, aNormR, bNormF, bNormR, P0F=1, P0R=1, PhiF, PhiR, PhiFw, PhiRw, wPjF, wPjR;
^
pics.c:1963:10: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
if((gsl_matrix_get(Index,kMerge,k)==1) | (gsl_matrix_get(Index,kMerge+1,k)==1))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
||
pics.c:1963:10: note: cast one or both operands to int to silence this warning
pics.c:1889:7: warning: unused variable 'i' [-Wunused-variable]
int i=0,j=0,k=0,l=0,kMerge=0,flag=0;
^
pics.c:1889:11: warning: unused variable 'j' [-Wunused-variable]
int i=0,j=0,k=0,l=0,kMerge=0,flag=0;
^
7 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c segment.c -o segment.o
segment.c:123:6: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
if((length(contF)>0) & (length(contR)>0))
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
&&
segment.c:123:6: note: cast one or both operands to int to silence this warning
segment.c:147:22: error: call to undeclared function 'Calloc'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration]
scoreRegionF=(int*)Calloc((M-m)/(2*INTEGER_VALUE(width)), int);
^
segment.c:147:61: error: expected expression
scoreRegionF=(int*)Calloc((M-m)/(2*INTEGER_VALUE(width)), int);
^
segment.c:148:61: error: expected expression
scoreRegionR=(int*)Calloc((M-m)/(2*INTEGER_VALUE(width)), int);
^
segment.c:406:6: warning: variable 'pp' is incremented both in the loop header and in the loop body [-Wfor-loop-analysis]
pp++;
^
segment.c:395:27: note: incremented here
for (pp=start; pp<=p; pp++) {
^
segment.c:536:6: warning: variable 'pp' is incremented both in the loop header and in the loop body [-Wfor-loop-analysis]
pp++;
^
segment.c:525:27: note: incremented here
for (pp=start; pp<=p; pp++) {
^
segment.c:1489:11: warning: unused variable 'muFilter' [-Wunused-variable]
double *muFilter, *deltaFilter, *sFFilter, *sRFilter, *seFilter, *seFilterF, *seFilterR, *scoreFilter, *score;
^
segment.c:1490:8: warning: unused variable 'filter1' [-Wunused-variable]
SEXP filter1;
^
segment.c:1494:19: warning: variable 'chr' set but not used [-Wunused-but-set-variable]
SEXP ans, x, y, chr, names;
^
6 warnings and 3 errors generated.
make: *** [segment.o] Error 1
ERROR: compilation failed for package ‘PICS’
* removing ‘/private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpMwyPMO/Rinst7cd83a486f6e/PICS’
-----------------------------------
ERROR: package installation failed
