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### Running command:
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### /home/biocbuild/bbs-3.21-bioc/R/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
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* installing *source* package ‘PICS’ ...
** using staged installation
checking for pkg-config... /usr/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: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -c pics.c -o pics.o
pics.c: In function ‘ECM2’:
pics.c:1009:16: warning: variable ‘chiSum’ set but not used [-Wunused-but-set-variable]
1009 | double chiSum, etaF, etaR, dd, cc;
| ^~~~~~
pics.c: In function ‘getInfMat’:
pics.c:1633:83: warning: unused variable ‘PhiRw’ [-Wunused-variable]
1633 | double aNormF, aNormR, bNormF, bNormR, P0F=1, P0R=1, PhiF, PhiR, PhiFw, PhiRw, wPjF, wPjR;
| ^~~~~
pics.c:1633:76: warning: unused variable ‘PhiFw’ [-Wunused-variable]
1633 | double aNormF, aNormR, bNormF, bNormR, P0F=1, P0R=1, PhiF, PhiR, PhiFw, PhiRw, wPjF, wPjR;
| ^~~~~
pics.c: In function ‘mergePeak’:
pics.c:1889:11: warning: unused variable ‘j’ [-Wunused-variable]
1889 | int i=0,j=0,k=0,l=0,kMerge=0,flag=0;
| ^
pics.c:1889:7: warning: unused variable ‘i’ [-Wunused-variable]
1889 | int i=0,j=0,k=0,l=0,kMerge=0,flag=0;
| ^
pics.c: In function ‘BIC’:
pics.c:1307:13: warning: ‘penalty’ may be used uninitialized [-Wmaybe-uninitialized]
1307 | bic = logDensityMix(yF, w, muF, sigmaSqF, K, NF) + logDensityMix(yR, w, muR, sigmaSqR, K,NR) - penalty;
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pics.c:1275:42: note: ‘penalty’ was declared here
1275 | double bic, tmp, muF[K], muR[K], penalty, distance;
| ^~~~~~~
pics.c: In function ‘fitModelK’:
pics.c:494:23: warning: ‘firstFit’ may be used uninitialized [-Wmaybe-uninitialized]
494 | return(ans);
| ^
pics.c:421:25: note: ‘firstFit’ was declared here
421 | SEXP ans, temp, firstFit;
| ^~~~~~~~
gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -DSTRICT_R_HEADERS=1 -fpic -g -O2 -Wall -c segment.c -o segment.o
segment.c: In function ‘segReads’:
segment.c:147:22: warning: implicit declaration of function ‘Calloc’; did you mean ‘calloc’? [-Wimplicit-function-declaration]
147 | scoreRegionF=(int*)Calloc((M-m)/(2*INTEGER_VALUE(width)), int);
| ^~~~~~
| calloc
segment.c:147:61: error: expected expression before ‘int’
147 | scoreRegionF=(int*)Calloc((M-m)/(2*INTEGER_VALUE(width)), int);
| ^~~
segment.c:148:61: error: expected expression before ‘int’
148 | scoreRegionR=(int*)Calloc((M-m)/(2*INTEGER_VALUE(width)), int);
| ^~~
segment.c: In function ‘getDensity’:
segment.c:1494:19: warning: variable ‘chr’ set but not used [-Wunused-but-set-variable]
1494 | SEXP ans, x, y, chr, names;
| ^~~
segment.c:1490:8: warning: unused variable ‘filter1’ [-Wunused-variable]
1490 | SEXP filter1;
| ^~~~~~~
segment.c:1489:11: warning: unused variable ‘muFilter’ [-Wunused-variable]
1489 | double *muFilter, *deltaFilter, *sFFilter, *sRFilter, *seFilter, *seFilterF, *seFilterR, *scoreFilter, *score;
| ^~~~~~~~
make: *** [/home/biocbuild/bbs-3.21-bioc/R/etc/Makeconf:195: segment.o] Error 1
ERROR: compilation failed for package ‘PICS’
* removing ‘/tmp/RtmppF6dzr/Rinste6cc85a8ffb22/PICS’
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ERROR: package installation failed
