* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘BAMMtools’ ...
** package ‘BAMMtools’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc-13 (Debian 13.2.0-23) 13.2.0’
make[1]: Entering directory '/tmp/RtmpjQ5ODH/R.INSTALL7cc1b1655080f/BAMMtools/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 BAMMtools_init.c -o BAMMtools_init.o
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 cohort_matrix.c -o cohort_matrix.o
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 dtrates.c -o dtrates.o
dtrates.c: In function ‘dtrates’:
dtrates.c:188:17: warning: ‘erates’ may be used uninitialized [-Wmaybe-uninitialized]
188 | SET_VECTOR_ELT(retlist, 1, erates);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
dtrates.c:71:21: note: ‘erates’ was declared here
71 | SEXP rates, erates;
| ^~~~~~
dtrates.c:145:44: warning: ‘nnode’ may be used uninitialized [-Wmaybe-uninitialized]
145 | if (node == nnode) {
| ^
dtrates.c:83:25: note: ‘nnode’ was declared here
83 | int nrow, node, nnode, event, nxtevent, isGoodStart, isGoodEnd, place_holder;
| ^~~~~
dtrates.c:157:103: warning: ‘nxtevent’ may be used uninitialized [-Wmaybe-uninitialized]
157 | lam1 = REAL(getListElement(eventData, "lam1"))[nxtevent-1];
| ^
dtrates.c:83:39: note: ‘nxtevent’ was declared here
83 | int nrow, node, nnode, event, nxtevent, isGoodStart, isGoodEnd, place_holder;
| ^~~~~~~~
dtrates.c:140:63: warning: ‘mu1’ may be used uninitialized [-Wmaybe-uninitialized]
140 | ret = getMeanRateExponential(relStart,relEnd,mu1,mu2);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
dtrates.c:84:47: note: ‘mu1’ was declared here
84 | double begin, end, Start, lam1, lam2, mu1, mu2, relStart, relEnd, rightshift, leftshift, erightshift, eleftshift, ret;
| ^~~
dtrates.c:140:63: warning: ‘mu2’ may be used uninitialized [-Wmaybe-uninitialized]
140 | ret = getMeanRateExponential(relStart,relEnd,mu1,mu2);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
dtrates.c:84:52: note: ‘mu2’ was declared here
84 | double begin, end, Start, lam1, lam2, mu1, mu2, relStart, relEnd, rightshift, leftshift, erightshift, eleftshift, ret;
| ^~~
dtrates.c:168:82: warning: ‘eleftshift’ may be used uninitialized [-Wmaybe-uninitialized]
168 | ret = (eleftshift+erightshift)/(getDblMatrixELT(segmat, l, 2) - getDblMatrixELT(segmat, l, 1));
| ~~~~~~~~~~~^~~~~~~~~~~~~
dtrates.c:84:111: note: ‘eleftshift’ was declared here
84 | double begin, end, Start, lam1, lam2, mu1, mu2, relStart, relEnd, rightshift, leftshift, erightshift, eleftshift, ret;
| ^~~~~~~~~~
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 jenksBrks.c -o jenksBrks.o
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 treetraverse.c -o treetraverse.o
gcc-13 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o BAMMtools.so BAMMtools_init.o cohort_matrix.o dtrates.o jenksBrks.o treetraverse.o -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/tmp/RtmpjQ5ODH/R.INSTALL7cc1b1655080f/BAMMtools/src'
make[1]: Entering directory '/tmp/RtmpjQ5ODH/R.INSTALL7cc1b1655080f/BAMMtools/src'
make[1]: Leaving directory '/tmp/RtmpjQ5ODH/R.INSTALL7cc1b1655080f/BAMMtools/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-BAMMtools/00new/BAMMtools/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package ‘BAMMtools’
finding HTML links ... done
BAMMlikelihood html
BAMMtools-data html
BAMMtools html
ShiftProbsTree html
addBAMMlegend html
addBAMMshifts html
assignColorBreaks html
cohorts html
finding level-2 HTML links ... done
computeBayesFactors html
credibleShiftSet html
distinctShiftConfigurations html
dtRates html
generateControlFile html
getBestShiftConfiguration html
getBranchShiftPriors html
getCladeRates html
getCohortMatrix html
getEventData html
getJenksBreaks html
getMarginalBranchRateMatrix html
getMeanBranchLengthTree html
getRateThroughTimeMatrix html
getShiftNodesFromIndex html
getTipRates html
getmrca html
marginalOddsRatioBranches html
maximumShiftCredibility html
plot html
plot.bammshifts html
plot.credibleshiftset html
plotPrior html
plotRateThroughTime html
ratesHistogram html
richColors html
samplingProbs html
setBAMMpriors html
speciesByRatesMatrix html
stepBF html
subsetEventData html
subtreeBAMM html
summary.bammdata html
summary.credibleshiftset html
testTimeVariableBranches html
traitDependentBAMM html
transparentColor html
writeEventData html
** building package indices
** 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 (BAMMtools)