* installing *source* package ‘compositions’ ...
** package ‘compositions’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘clang version 18.1.4’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/compositions/src'
/usr/local/clang18/bin/clang -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang18/include -I/usr/local/clang/include -fpic -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3 -c compositions.c -o compositions.o
compositions.c:210:15: warning: unused variable 'D2' [-Wunused-variable]
210 | const int D2=D*D; // size of a error matrix
| ^~
compositions.c:215:16: warning: unused variable 'transA' [-Wunused-variable]
215 | const char transA='N'; // for BLAS
| ^~~~~~
compositions.c:216:16: warning: unused variable 'transB' [-Wunused-variable]
216 | const char transB='T'; // for BLAS
| ^~~~~~
compositions.c:218:18: warning: unused variable 'zero' [-Wunused-variable]
218 | const double zero=0.0; // for BLAS
| ^~~~
compositions.c:219:18: warning: unused variable 'one' [-Wunused-variable]
219 | const double one =1.0; // for BLAS
| ^~~
compositions.c:451:15: warning: unused variable 'D2' [-Wunused-variable]
451 | const int D2=D*D; // size of a error matrix
| ^~
compositions.c:454:15: warning: unused variable 'ldN' [-Wunused-variable]
454 | const int ldN=*ldNp; //MaxFramesize of central matrix
| ^~~
compositions.c:457:16: warning: unused variable 'transA' [-Wunused-variable]
457 | const char transA='N'; // for BLAS
| ^~~~~~
compositions.c:458:16: warning: unused variable 'transB' [-Wunused-variable]
458 | const char transB='T'; // for BLAS
| ^~~~~~
compositions.c:463:11: warning: variable 'l' set but not used [-Wunused-but-set-variable]
463 | int k,l; // actual matrix position
| ^
compositions.c:567:16: warning: unused variable 'transA' [-Wunused-variable]
567 | const char transA='N'; // for BLAS
| ^~~~~~
compositions.c:568:16: warning: unused variable 'transB' [-Wunused-variable]
568 | const char transB='T'; // for BLAS
| ^~~~~~
compositions.c:580:16: warning: unused variable 'uplo' [-Wunused-variable]
580 | const char uplo='U'; // for LAPACK
| ^~~~
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:1068:10: warning: unused variable 'transA' [-Wunused-variable]
1068 | char transA='N'; // parameter for dgelsd
| ^~~~~~
compositions.c:1248:10: warning: unused variable 'transA' [-Wunused-variable]
1248 | char transA='N'; // for dgemv
| ^~~~~~
compositions.c:1511:8: warning: operator '?:' has lower precedence than '+'; '+' will be evaluated first [-Wparentheses]
1509 | clrVar[truei+D*truej]+=Mxlr(k,i)*Mxlr(k,j)+
| ~~~~~~~~~~~~~~~~~~~~
1510 | (i<nMissings&&j<nMissings)
| ~~~~~~~~~~~~~~~~~~~~~~~~~~
1511 | ?imputationCache[DD*type+i+D*j]
| ^
compositions.c:1511:8: note: place parentheses around the '+' expression to silence this warning
1509 | clrVar[truei+D*truej]+=Mxlr(k,i)*Mxlr(k,j)+
| ~~~~~~~~~~~~~~~~~~~~
1510 | (i<nMissings&&j<nMissings)
| ~~~~~~~~~~~~~~~~~~~~~~~~~~
1511 | ?imputationCache[DD*type+i+D*j]
| ^
compositions.c:1511:8: note: place parentheses around the '?:' expression to evaluate it first
1510 | (i<nMissings&&j<nMissings)
| (
1511 | ?imputationCache[DD*type+i+D*j]
| ^
1512 | :0;
|
| )
compositions.c:1433:10: warning: unused variable 'transA' [-Wunused-variable]
1433 | char transA='N'; // for dgemv
| ^~~~~~
compositions.c:1434:10: warning: unused variable 'transAt' [-Wunused-variable]
1434 | char transAt='T'; // for dgemv
| ^~~~~~~
compositions.c:1757:13: 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:1919:6: warning: unused variable 'idx' [-Wunused-variable]
1919 | int idx=i+N*j;
| ^~~
compositions.c:1870:9: warning: unused variable 'p' [-Wunused-variable]
1870 | int p=dimX[1];
| ^
compositions.c:1871:9: warning: unused variable 'NmissingTypes' [-Wunused-variable]
1871 | int NmissingTypes=0;
| ^~~~~~~~~~~~~
compositions.c:1876:13: warning: unused variable 'dl' [-Wunused-variable]
1876 | double *dl=(double *) R_alloc(N*D,sizeof(double));
| ^~
compositions.c:1998:6: warning: unused variable 'idx' [-Wunused-variable]
1998 | int idx=i+N*j;
| ^~~
compositions.c:1945:9: warning: unused variable 'p' [-Wunused-variable]
1945 | int p=dimX[1];
| ^
compositions.c:1946:9: warning: unused variable 'NmissingTypes' [-Wunused-variable]
1946 | int NmissingTypes=0;
| ^~~~~~~~~~~~~
compositions.c:1951:13: warning: unused variable 'dl' [-Wunused-variable]
1951 | double *dl=(double *) R_alloc(N*D,sizeof(double));
| ^~
compositions.c:1973:13: warning: unused variable 'imputationCache' [-Wunused-variable]
1973 | double *imputationCache=(double *) R_alloc(D*D*nTypes*2,sizeof(double));
| ^~~~~~~~~~~~~~~
compositions.c:2083:13: warning: unused variable 'k' [-Wunused-variable]
2083 | int i,j,k;
| ^
compositions.c:2372:12: warning: unused variable 'Pd' [-Wunused-variable]
2372 | double Pd=sqrt(M_PI*sigmaQ);
| ^~
compositions.c:2479:13: warning: unused variable 'k' [-Wunused-variable]
2479 | int i,j,k,r;
| ^
compositions.c:2484:9: warning: unused variable 'D' [-Wunused-variable]
2484 | int D=dimX[1];
| ^
compositions.c:2485:10: warning: unused variable 'tmpIntPtr' [-Wunused-variable]
2485 | int *tmpIntPtr;
| ^~~~~~~~~
compositions.c:2486:9: warning: unused variable 'tmpInt' [-Wunused-variable]
2486 | int tmpInt;
| ^~~~~~
compositions.c:2487:13: warning: unused variable 'tmpDoublePtr' [-Wunused-variable]
2487 | double *tmpDoublePtr;
| ^~~~~~~~~~~~
compositions.c:2489:12: warning: unused variable 'tmp' [-Wunused-variable]
2489 | double tmp;
| ^~~
38 warnings generated.
/usr/local/clang18/bin/clang -shared -L/usr/local/clang/lib64 -L/usr/local/clang18/lib -L/usr/local/clang18/lib/x86_64-unknown-linux-gnu -L/usr/local/gcc13/lib64 -L/usr/local/lib64 -o compositions.so compositions.o -L/data/gannet/ripley/R/R-clang/lib -lRlapack -L/data/gannet/ripley/R/R-clang/lib -lRblas -lFortran_main -lFortranRuntime -lFortranDecimal -lm
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/compositions/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/compositions/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/compositions/src'
installing to /data/gannet/ripley/R/packages/tests-clang/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)