* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘alakazam’ ...
** package ‘alakazam’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++-14 (Debian 14.2.0-1) 14.2.0’
make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmp3xGMWb/R.INSTALL1c423f1851c83c/alakazam/src'
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c RcppDistance.cpp -o RcppDistance.o
g++-14 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG  -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I/usr/local/include -D_FORTIFY_SOURCE=3   -fpic  -g -O2 -Wall -pedantic -mtune=native   -c RcppExports.cpp -o RcppExports.o
g++-14 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o alakazam.so RcppDistance.o RcppExports.o -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmp3xGMWb/R.INSTALL1c423f1851c83c/alakazam/src'
make[1]: Entering directory '/home/hornik/tmp/scratch/Rtmp3xGMWb/R.INSTALL1c423f1851c83c/alakazam/src'
make[1]: Leaving directory '/home/hornik/tmp/scratch/Rtmp3xGMWb/R.INSTALL1c423f1851c83c/alakazam/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-alakazam/00new/alakazam/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package ‘alakazam’
    finding HTML links ... done
    ABBREV_AA                               html  
    AbundanceCurve-class                    html  
    ChangeoClone-class                      html  
    DEFAULT_COLORS                          html  
    DiversityCurve-class                    html  
    EdgeTest-class                          html  
    Example10x                              html  
    ExampleDb                               html  
    ExampleDbChangeo                        html  
    ExampleTrees                            html  
    IMGT_REGIONS                            html  
    IUPAC_CODES                             html  
    MRCATest-class                          html  
    SingleDb                                html  
    alakazam-package                        html  
    alakazam                                html  
    aliphatic                               html  
    alphaDiversity                          html  
    aminoAcidProperties                     html  
    baseTheme                               html  
    buildPhylipLineage                      html  
    bulk                                    html  
    calcCoverage                            html  
    calcDiversity                           html  
    charge                                  html  
    checkColumns                            html  
    collapseDuplicates                      html  
    combineIgphyml                          html  
    countClones                             html  
    countGenes                              html  
    countPatterns                           html  
    cpuCount                                html  
    estimateAbundance                       html  
    extractVRegion                          html  
    getAAMatrix                             html  
    getDNAMatrix                            html  
    getMRCA                                 html  
    getPathLengths                          html  
    getPositionQuality                      html  
    getSegment                              html  
    graphToPhylo                            html  
    gravy                                   html  
    gridPlot                                html  
    finding level-2 HTML links ... done

    groupGenes                              html  
    isValidAASeq                            html  
    junctionAlignment                       html  
    makeChangeoClone                        html  
    makeTempDir                             html  
    maskPositionsByQuality                  html  
    maskSeqEnds                             html  
    maskSeqGaps                             html  
    nonsquareDist                           html  
    padSeqEnds                              html  
    pairwiseDist                            html  
    pairwiseEqual                           html  
    permuteLabels                           html  
    phyloToGraph                            html  
    plotAbundanceCurve                      html  
    plotDiversityCurve                      html  
    plotDiversityTest                       html  
    plotEdgeTest                            html  
    plotMRCATest                            html  
    plotSubtrees                            html  
    polar                                   html  
    progressBar                             html  
    rarefyDiversity                         html  
    readChangeoDb                           html  
    readFastqDb                             html  
    readIgphyml                             html  
    seqDist                                 html  
    seqEqual                                html  
    sortGenes                               html  
    stoufferMeta                            html  
    summarizeSubtrees                       html  
    tableEdges                              html  
    testDiversity                           html  
    testEdges                               html  
    testMRCA                                html  
    translateDNA                            html  
    translateStrings                        html  
    writeChangeoDb                          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 (alakazam)