############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data groHMM ### ############################################################################## ############################################################################## * checking for file ‘groHMM/DESCRIPTION’ ... OK * preparing ‘groHMM’: * checking DESCRIPTION meta-information ... OK * cleaning src * installing the package to build vignettes ----------------------------------- * installing *source* package ‘groHMM’ ... ** this is package ‘groHMM’ version ‘1.41.0’ ** using staged installation ** 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 -fpic -g -O2 -c AnnotateProbes.c -o AnnotateProbes.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c DecayAlgorithm.c -o DecayAlgorithm.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c MLEfit.c -o MLEfit.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c RegisterRRoutines.c -o RegisterRRoutines.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c Windowing.c -o Windowing.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c hmmEM.c -o hmmEM.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c hmmFwBw.c -o hmmFwBw.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c hmmMiscFunctions.c -o hmmMiscFunctions.o hmmMiscFunctions.c: In function ‘SStatsGamma’: hmmMiscFunctions.c:235:37: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘double’ [-Wformat=] 235 | if(!(logPP <= epsilon)) Rprintf("[SSallocGamma] -- \ | ^~~~~~~~~~~~~~~~~~~~ 236 | Assertion about to fail! logPP= %d\n", logPP); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~ | | | double hmmMiscFunctions.c: In function ‘UpdateGamma’: hmmMiscFunctions.c:274:27: warning: implicit declaration of function ‘Calloc’; did you mean ‘calloc’? [-Wimplicit-function-declaration] 274 | double *shape= (double*)Calloc(1, double); | ^~~~~~ | calloc hmmMiscFunctions.c:274:37: error: expected expression before ‘double’ 274 | double *shape= (double*)Calloc(1, double); | ^~~~~~ hmmMiscFunctions.c:275:37: error: expected expression before ‘double’ 275 | double *scale= (double*)Calloc(1, double); | ^~~~~~ hmmMiscFunctions.c:287:3: warning: implicit declaration of function ‘Free’; did you mean ‘free’? [-Wimplicit-function-declaration] 287 | Free(shape); | ^~~~ | free make: *** [/home/biocbuild/bbs-3.21-bioc/R/etc/Makeconf:195: hmmMiscFunctions.o] Error 1 ERROR: compilation failed for package ‘groHMM’ * removing ‘/tmp/RtmpjKSrGL/Rinst387a3439cc967a/groHMM’ ----------------------------------- ERROR: package installation failed