############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL groHMM ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘groHMM’ ... ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c AnnotateProbes.c -o AnnotateProbes.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c DecayAlgorithm.c -o DecayAlgorithm.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c MLEfit.c -o MLEfit.o In file included from MLEfit.c:43: hmmHeader.h:301:16: warning: ‘expSum’ defined but not used [-Wunused-function] 301 | static double expSum(double *logValues, int length) { | ^~~~~~ hmmHeader.h:281:16: warning: ‘MargainalizeSumLogProbOver’ defined but not used [-Wunused-function] 281 | static double MargainalizeSumLogProbOver(int state, int position, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c RegisterRRoutines.c -o RegisterRRoutines.o gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c Windowing.c -o Windowing.o Windowing.c: In function ‘WindowAnalysis’: Windowing.c:146:13: warning: unused variable ‘II’ [-Wunused-variable] 146 | int II = 0; | ^~ gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c hmmEM.c -o hmmEM.o In file included from hmmEM.c:50: hmmHeader.h:301:16: warning: ‘expSum’ defined but not used [-Wunused-function] 301 | static double expSum(double *logValues, int length) { | ^~~~~~ hmmHeader.h:281:16: warning: ‘MargainalizeSumLogProbOver’ defined but not used [-Wunused-function] 281 | static double MargainalizeSumLogProbOver(int state, int position, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from hmmHeader.h:36: UsefulValues.h:39:15: warning: ‘VERY_LARGE_DOUBLE_VALUE’ defined but not used [-Wunused-variable] 39 | static double VERY_LARGE_DOUBLE_VALUE = 1e20; | ^~~~~~~~~~~~~~~~~~~~~~~ gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c hmmFwBw.c -o hmmFwBw.o hmmFwBw.c: In function ‘forward’: hmmFwBw.c:142:7: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 142 | for(k=1; k<n; k++) | ^~~ hmmFwBw.c:145:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 145 | for (k = 0; k<n; k++) { | ^~~ In file included from hmmFwBw.c:45: hmmHeader.h: At top level: hmmHeader.h:301:16: warning: ‘expSum’ defined but not used [-Wunused-function] 301 | static double expSum(double *logValues, int length) { | ^~~~~~ hmmHeader.h:281:16: warning: ‘MargainalizeSumLogProbOver’ defined but not used [-Wunused-function] 281 | static double MargainalizeSumLogProbOver(int state, int position, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from hmmHeader.h:36: UsefulValues.h:39:15: warning: ‘VERY_LARGE_DOUBLE_VALUE’ defined but not used [-Wunused-variable] 39 | static double VERY_LARGE_DOUBLE_VALUE = 1e20; | ^~~~~~~~~~~~~~~~~~~~~~~ gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -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 ‘SStatsNormExp’: hmmMiscFunctions.c:384:10: warning: unused variable ‘wi’ [-Wunused-variable] 384 | double wi, *newEx; | ^~ hmmMiscFunctions.c: In function ‘UpdateNormExp’: hmmMiscFunctions.c:417:10: warning: unused variable ‘epsilon’ [-Wunused-variable] 417 | double epsilon=0.00001; | ^~~~~~~ In file included from hmmHeader.h:36, from hmmMiscFunctions.c:43: UsefulValues.h: At top level: UsefulValues.h:39:15: warning: ‘VERY_LARGE_DOUBLE_VALUE’ defined but not used [-Wunused-variable] 39 | static double VERY_LARGE_DOUBLE_VALUE = 1e20; | ^~~~~~~~~~~~~~~~~~~~~~~ gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c hmmViterbi.c -o hmmViterbi.o In file included from hmmViterbi.c:48: hmmHeader.h:301:16: warning: ‘expSum’ defined but not used [-Wunused-function] 301 | static double expSum(double *logValues, int length) { | ^~~~~~ hmmHeader.h:281:16: warning: ‘MargainalizeSumLogProbOver’ defined but not used [-Wunused-function] 281 | static double MargainalizeSumLogProbOver(int state, int position, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from hmmHeader.h:36: UsefulValues.h:39:15: warning: ‘VERY_LARGE_DOUBLE_VALUE’ defined but not used [-Wunused-variable] 39 | static double VERY_LARGE_DOUBLE_VALUE = 1e20; | ^~~~~~~~~~~~~~~~~~~~~~~ gcc -shared -L/home/biocbuild/bbs-3.20-bioc/R/lib -L/usr/local/lib -o groHMM.so AnnotateProbes.o DecayAlgorithm.o MLEfit.o RegisterRRoutines.o Windowing.o hmmEM.o hmmFwBw.o hmmMiscFunctions.o hmmViterbi.o -L/home/biocbuild/bbs-3.20-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.20-bioc/R/site-library/00LOCK-groHMM/00new/groHMM/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (groHMM)