############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data cn.farms ### ############################################################################## ############################################################################## * checking for file ‘cn.farms/DESCRIPTION’ ... OK * preparing ‘cn.farms’: * checking DESCRIPTION meta-information ... OK * cleaning src * installing the package to build vignettes ----------------------------------- * installing *source* package ‘cn.farms’ ... ** this is package ‘cn.farms’ version ‘1.55.0’ ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c R_init_cnfarms.c -o R_init_cnfarms.o g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c laplace.cpp -o laplace.o laplace.cpp: In function ‘SEXPREC* momentsGauss(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’: laplace.cpp:442:13: warning: unused variable ‘method’ [-Wunused-variable] 442 | int method=0; | ^~~~~~ laplace.cpp: In function ‘void computeParameters(double, double, double, double, double, double, int&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&)’: laplace.cpp:393:93: warning: ‘I1left’ may be used uninitialized [-Wmaybe-uninitialized] 393 | moment2 = (-0.5*a+0.25*(b-1/sigmaZ)*(b-1/sigmaZ)+(b*leftWeight)/(sigmaZ)+(leftWeight*I1left*sqrtMa)/(sqrt(2.0)*sigmaZ))/(a*a); | ~~~~~~~~~~^~~~~~~ laplace.cpp:198:16: note: ‘I1left’ was declared here 198 | double I1left; | ^~~~~~ laplace.cpp:368:63: warning: ‘I1right’ may be used uninitialized [-Wmaybe-uninitialized] 368 | double rightMoment1=1.0*rightMy*I0right+1.0*rightSigma*I1right; | ~~~~~~~~~~~~~~^~~~~~~~ laplace.cpp:199:16: note: ‘I1right’ was declared here 199 | double I1right; | ^~~~~~~ gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c sparse_farms.c -o sparse_farms.o sparse_farms.c: In function ‘normData’: sparse_farms.c:185:20: warning: implicit declaration of function ‘Calloc’; did you mean ‘calloc’? [-Wimplicit-function-declaration] 185 | void** ret=Calloc(1, void*); | ^~~~~~ | calloc sparse_farms.c:185:30: error: expected expression before ‘void’ 185 | void** ret=Calloc(1, void*); | ^~~~ sparse_farms.c:189:39: error: expected expression before ‘double’ 189 | E_SX_n =(double**)Calloc(nn, double*); | ^~~~~~ sparse_farms.c:198:29: error: expected expression before ‘int’ 198 | nna=(int*)Calloc(1, int); | ^~~ sparse_farms.c:204:46: error: expected expression before ‘double’ 204 | E_SX_n[l]=(double*)Calloc(3, double); | ^~~~~~ sparse_farms.c: In function ‘sparseFarmsC’: sparse_farms.c:264:30: error: expected expression before ‘void’ 264 | void** ret=Calloc(4, void*); | ^~~~ sparse_farms.c:272:29: error: expected expression before ‘int’ 272 | nna=(int*)Calloc(1, int); | ^~~ sparse_farms.c:277:31: error: expected expression before ‘double’ 277 | L=(double**)Calloc(2, double*); | ^~~~~~ sparse_farms.c:279:36: error: expected expression before ‘double’ 279 | lapla=(double**)Calloc(nn, double*); | ^~~~~~ sparse_farms.c:281:39: error: expected expression before ‘double’ 281 | E_SX_n =(double**)Calloc(nn, double*); | ^~~~~~ sparse_farms.c:287:41: error: expected expression before ‘double’ 287 | L[l]=(double*)Calloc(3, double); | ^~~~~~ sparse_farms.c:295:45: error: expected expression before ‘double’ 295 | lapla[l]=(double*)Calloc(3, double); | ^~~~~~ sparse_farms.c:297:46: error: expected expression before ‘double’ 297 | E_SX_n[l]=(double*)Calloc(3, double); | ^~~~~~ sparse_farms.c: In function ‘deinit’: sparse_farms.c:642:17: warning: implicit declaration of function ‘Free’; did you mean ‘free’? [-Wimplicit-function-declaration] 642 | Free(L[l]); | ^~~~ | free make: *** [/home/biocbuild/bbs-3.21-bioc/R/etc/Makeconf:202: sparse_farms.o] Error 1 ERROR: compilation failed for package ‘cn.farms’ * removing ‘/tmp/RtmpMpT5Kv/Rinst19368a3c245fe6/cn.farms’ ----------------------------------- ERROR: package installation failed