* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘compositions’ ...
** package ‘compositions’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc-13 (Debian 13.3.0-1) 13.3.0’
make[1]: Entering directory '/tmp/RtmppqfP6M/R.INSTALL19d77c3da2efa8/compositions/src'
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG   -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native  -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 -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o compositions.so compositions.o -llapack -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lRblas -lgfortran -lm -lquadmath -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/tmp/RtmppqfP6M/R.INSTALL19d77c3da2efa8/compositions/src'
make[1]: Entering directory '/tmp/RtmppqfP6M/R.INSTALL19d77c3da2efa8/compositions/src'
make[1]: Leaving directory '/tmp/RtmppqfP6M/R.INSTALL19d77c3da2efa8/compositions/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-compositions/00new/compositions/libs
** R
** data
** demo
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package ‘compositions’
    finding HTML links ... done
    Aar                                     html  
    Activity10                              html  
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    AnimalVegetation                        html  
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    compositional-class                     html  
    compositions                            html  
    cor                                     html  
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    gsigetbalstruct                         html  
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    ilt                                     html  
    ipt                                     html  
    isAcomp                                 html  
    ismahalanobisoutlier                    html  
    isoportion                              html  
    jura                                    html  
    kdeDirichlet                            html  
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    lines                                   html  
    logratioVariogram                       html  
    lrvgram                                 html  
    mahalanobisdist                         html  
    matmult                                 html  
    matmultacomp                            html  
    meanAcomp                               html  
    meanrow                                 html  
    missingProjector                        html  
    missingsummary                          html  
    mix2compositions                        html  
    mixRead                                 html  
    mvar                                    html  
    names                                   html  
    norm                                    html  
    normalize                               html  
    oneOrDataset                            html  
    outlierclassifier                       html  
    outlierplot                             html  
    outliers                                html  
    pairwisePlot                            html  
    finding level-2 HTML links ... done

    panelAcomp                              html  
    parametricMat                           html  
    perturbe                                html  
    plot                                    html  
    plot3d                                  html  
    plot3dacomp                             html  
    plot3daplus                             html  
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    plotlogratioVariogram                   html  
    plotmissingsummary                      html  
    plotpos                                 html  
    powerofmatrix                           html  
    princompacomp                           html  
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    qqnorm                                  html  
    rDirichlet                              html  
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    ratioLoadings                           html  
    rcomp-class                             html  
    rcomp                                   html  
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    rcompmargin                             html  
    readgeoeas                              html  
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    segments                                html  
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    tests                                   html  
    totals                                  html  
    tryDebugger                             html  
    ult                                     html  
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    varmlm                                  html  
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    wrapped_functions                       html  
    zeroreplace                             html  
** 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)