* installing *source* package ‘compositions’ ... ** package ‘compositions’ successfully unpacked and MD5 sums checked ** using staged installation ** libs using C compiler: ‘gcc-13 (GCC) 13.2.0’ make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/compositions/src' gcc-13 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -c compositions.c -o compositions.o compositions.c: In function 'gsiCGSkrigingPrep': compositions.c:219:18: warning: unused variable 'one' [-Wunused-variable] 219 | const double one =1.0; // for BLAS | ^~~ compositions.c:218:18: warning: unused variable 'zero' [-Wunused-variable] 218 | const double zero=0.0; // for BLAS | ^~~~ compositions.c:216:16: warning: unused variable 'transB' [-Wunused-variable] 216 | const char transB='T'; // for BLAS | ^~~~~~ compositions.c:215:16: warning: unused variable 'transA' [-Wunused-variable] 215 | const char transA='N'; // for BLAS | ^~~~~~ compositions.c:210:15: warning: unused variable 'D2' [-Wunused-variable] 210 | const int D2=D*D; // size of a error matrix | ^~ compositions.c: In function 'gsiCGSkrigingPredict': compositions.c:458:16: warning: unused variable 'transB' [-Wunused-variable] 458 | const char transB='T'; // for BLAS | ^~~~~~ compositions.c:457:16: warning: unused variable 'transA' [-Wunused-variable] 457 | const char transA='N'; // for BLAS | ^~~~~~ compositions.c:454:15: warning: unused variable 'ldN' [-Wunused-variable] 454 | const int ldN=*ldNp; //MaxFramesize of central matrix | ^~~ compositions.c:451:15: warning: unused variable 'D2' [-Wunused-variable] 451 | const int D2=D*D; // size of a error matrix | ^~ compositions.c: In function 'gsiCGSkriging': compositions.c:580:16: warning: unused variable 'uplo' [-Wunused-variable] 580 | const char uplo='U'; // for LAPACK | ^~~~ compositions.c:568:16: warning: unused variable 'transB' [-Wunused-variable] 568 | const char transB='T'; // for BLAS | ^~~~~~ compositions.c:567:16: warning: unused variable 'transA' [-Wunused-variable] 567 | const char transA='N'; // for BLAS | ^~~~~~ compositions.c: In function 'gsiCImpAcompNewImputationVariance': compositions.c:1068:10: warning: unused variable 'transA' [-Wunused-variable] 1068 | char transA='N'; // parameter for dgelsd | ^~~~~~ compositions.c:1066:15: warning: unused variable 'DDn' [-Wunused-variable] 1066 | const int DDn=D*D*n; // step in imputationCache to get second type of info | ^~~ compositions.c: In function 'gsiCImpAcompCompleteAlr': compositions.c:1248:10: warning: unused variable 'transA' [-Wunused-variable] 1248 | char transA='N'; // for dgemv | ^~~~~~ compositions.c: In function 'gsiCImpAcompClrExpectation': compositions.c:1434:10: warning: unused variable 'transAt' [-Wunused-variable] 1434 | char transAt='T'; // for dgemv | ^~~~~~~ compositions.c:1433:10: warning: unused variable 'transA' [-Wunused-variable] 1433 | char transA='N'; // for dgemv | ^~~~~~ compositions.c: In function 'gsiCImpAcompFitWithProjection': compositions.c:1757:20: warning: unused variable 'xv' [-Wunused-variable] 1757 | double xv = MX(c,l); | ^~ compositions.c:1735:16: warning: unused variable 'transA' [-Wunused-variable] 1735 | const char transA='N'; | ^~~~~~ compositions.c: In function 'gsiCFitWithProjection': compositions.c:1919:13: warning: unused variable 'idx' [-Wunused-variable] 1919 | int idx=i+N*j; | ^~~ compositions.c:1876:13: warning: unused variable 'dl' [-Wunused-variable] 1876 | double *dl=(double *) R_alloc(N*D,sizeof(double)); | ^~ compositions.c:1871:9: warning: unused variable 'NmissingTypes' [-Wunused-variable] 1871 | int NmissingTypes=0; | ^~~~~~~~~~~~~ compositions.c:1870:9: warning: unused variable 'p' [-Wunused-variable] 1870 | int p=dimX[1]; | ^ compositions.c: In function 'gsiCFitWithEM': compositions.c:1998:13: warning: unused variable 'idx' [-Wunused-variable] 1998 | int idx=i+N*j; | ^~~ compositions.c:1973:13: warning: unused variable 'imputationCache' [-Wunused-variable] 1973 | double *imputationCache=(double *) R_alloc(D*D*nTypes*2,sizeof(double)); | ^~~~~~~~~~~~~~~ compositions.c:1951:13: warning: unused variable 'dl' [-Wunused-variable] 1951 | double *dl=(double *) R_alloc(N*D,sizeof(double)); | ^~ compositions.c:1946:9: warning: unused variable 'NmissingTypes' [-Wunused-variable] 1946 | int NmissingTypes=0; | ^~~~~~~~~~~~~ compositions.c:1945:9: warning: unused variable 'p' [-Wunused-variable] 1945 | int p=dimX[1]; | ^ compositions.c: In function 'gsiAitchisonDistributionIntegral': compositions.c:2083:13: warning: unused variable 'k' [-Wunused-variable] 2083 | int i,j,k; | ^ compositions.c: In function 'gsiDensityCheck2': compositions.c:2372:12: warning: unused variable 'Pd' [-Wunused-variable] 2372 | double Pd=sqrt(M_PI*sigmaQ); | ^~ compositions.c: In function 'gsiDensityCheck': compositions.c:2489:12: warning: unused variable 'tmp' [-Wunused-variable] 2489 | double tmp; | ^~~ compositions.c:2487:13: warning: unused variable 'tmpDoublePtr' [-Wunused-variable] 2487 | double *tmpDoublePtr; | ^~~~~~~~~~~~ compositions.c:2486:9: warning: unused variable 'tmpInt' [-Wunused-variable] 2486 | int tmpInt; | ^~~~~~ compositions.c:2485:10: warning: unused variable 'tmpIntPtr' [-Wunused-variable] 2485 | int *tmpIntPtr; | ^~~~~~~~~ compositions.c:2484:9: warning: unused variable 'D' [-Wunused-variable] 2484 | int D=dimX[1]; | ^ compositions.c:2479:13: warning: unused variable 'k' [-Wunused-variable] 2479 | int i,j,k,r; | ^ compositions.c: In function 'gsiCGSkriging': compositions.c:628:24: warning: 'mt' may be used uninitialized [-Wmaybe-uninitialized] 628 | type[i+n*p]=mt; | ~~~~~~~~~~~^~~ compositions.c:590:12: note: 'mt' was declared here 590 | int mt; // temporary for missingType | ^~ compositions.c: In function 'gsiCGSkrigingPrep': compositions.c:259:24: warning: 'mt' may be used uninitialized [-Wmaybe-uninitialized] 259 | type[i+n*p]=mt; | ~~~~~~~~~~~^~~ compositions.c:227:12: note: 'mt' was declared here 227 | int mt; // temporary for missingType | ^~ gcc-13 -shared -g -O2 -Wall -pedantic -mtune=native -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection -Werror=implicit-function-declaration -Wstrict-prototypes -fpic -L/usr/local/gcc13/lib64 -L/usr/local/lib64 -L/usr/local/clang18/lib/x86_64-unknown-linux-gnu -o compositions.so compositions.o -llapack -L/data/gannet/ripley/R/R-devel/lib -lRblas -lgfortran -lm -lquadmath make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/compositions/src' make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/compositions/src' make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/compositions/src' installing to /data/gannet/ripley/R/packages/tests-devel/compositions.Rcheck/00LOCK-compositions/00new/compositions/libs ** R ** data ** demo ** 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 (compositions)