* installing *source* package 'BAMMtools' ...
** package 'BAMMtools' successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 12.3.0'
make[1]: Entering directory '/d/temp/2024_12_25_01_50_00_20757/Rtmp44atG0/R.INSTALL197f01f1951c6/BAMMtools/src'
gcc  -I"D:/RCompile/recent/R-4.3.3/include" -DNDEBUG     -I"d:/rtools43/x86_64-w64-mingw32.static.posix/include"     -pedantic -Wstrict-prototypes -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c BAMMtools_init.c -o BAMMtools_init.o
gcc  -I"D:/RCompile/recent/R-4.3.3/include" -DNDEBUG     -I"d:/rtools43/x86_64-w64-mingw32.static.posix/include"     -pedantic -Wstrict-prototypes -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c cohort_matrix.c -o cohort_matrix.o
gcc  -I"D:/RCompile/recent/R-4.3.3/include" -DNDEBUG     -I"d:/rtools43/x86_64-w64-mingw32.static.posix/include"     -pedantic -Wstrict-prototypes -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c dtrates.c -o dtrates.o
dtrates.c: In function 'dtrates':
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;
      |                                                                                                               ^~~~~~~~~~
dtrates.c:153:78: warning: 'mu2' may be used uninitialized [-Wmaybe-uninitialized]
  153 |                                                                 eleftshift = getTimeIntegratedBranchRate(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:153:78: warning: 'mu1' may be used uninitialized [-Wmaybe-uninitialized]
  153 |                                                                 eleftshift = getTimeIntegratedBranchRate(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: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: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:169:65: warning: 'erates' may be used uninitialized [-Wmaybe-uninitialized]
  169 |                                                                 REAL(erates)[l] += ret/((double) nsamples);
      |                                                                 ^~~~~~~~~~~~
dtrates.c:71:21: note: 'erates' was declared here
   71 |         SEXP rates, erates;
      |                     ^~~~~~
gcc  -I"D:/RCompile/recent/R-4.3.3/include" -DNDEBUG     -I"d:/rtools43/x86_64-w64-mingw32.static.posix/include"     -pedantic -Wstrict-prototypes -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c jenksBrks.c -o jenksBrks.o
gcc  -I"D:/RCompile/recent/R-4.3.3/include" -DNDEBUG     -I"d:/rtools43/x86_64-w64-mingw32.static.posix/include"     -pedantic -Wstrict-prototypes -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c treetraverse.c -o treetraverse.o
gcc -shared -s -static-libgcc -o BAMMtools.dll tmp.def BAMMtools_init.o cohort_matrix.o dtrates.o jenksBrks.o treetraverse.o -Ld:/rtools43/x86_64-w64-mingw32.static.posix/lib/x64 -Ld:/rtools43/x86_64-w64-mingw32.static.posix/lib -LD:/RCompile/recent/R-4.3.3/bin/x64 -lR
make[1]: Leaving directory '/d/temp/2024_12_25_01_50_00_20757/Rtmp44atG0/R.INSTALL197f01f1951c6/BAMMtools/src'
make[1]: Entering directory '/d/temp/2024_12_25_01_50_00_20757/Rtmp44atG0/R.INSTALL197f01f1951c6/BAMMtools/src'
make[1]: Leaving directory '/d/temp/2024_12_25_01_50_00_20757/Rtmp44atG0/R.INSTALL197f01f1951c6/BAMMtools/src'
installing to d:/Rcompile/CRANpkg/lib/4.3/00LOCK-BAMMtools/00new/BAMMtools/libs/x64
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* MD5 sums
packaged installation of 'BAMMtools' as BAMMtools_2.1.12.zip
* DONE (BAMMtools)