* installing *source* package ‘BAMMtools’ ...
** package ‘BAMMtools’ 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/BAMMtools/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 BAMMtools_init.c -o BAMMtools_init.o
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 cohort_matrix.c -o cohort_matrix.o
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 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"/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 jenksBrks.c -o jenksBrks.o
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 treetraverse.c -o treetraverse.o
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 BAMMtools.so BAMMtools_init.o cohort_matrix.o dtrates.o jenksBrks.o treetraverse.o
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/BAMMtools/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/BAMMtools/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/BAMMtools/src'
installing to /data/gannet/ripley/R/packages/tests-devel/BAMMtools.Rcheck/00LOCK-BAMMtools/00new/BAMMtools/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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)