downloading reverse dependencies ... downloading EloOptimized_0.3.2.tar.gz ... ok downloading GD_10.3.tar.gz ... ok downloading binst_0.2.1.tar.gz ... ok installing dependencies ‘BAMMtools’, ‘discretization’ begin installing package ‘BAMMtools’ begin installing package ‘discretization’ * installing *source* package ‘discretization’ ... ** package ‘discretization’ successfully unpacked and MD5 sums checked ** using staged installation ** R ** 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 * DONE (discretization) * installing *source* package ‘BAMMtools’ ... ** using staged installation ** libs using C compiler: ‘gcc-14 (Debian 14.2.0-3) 14.2.0’ make[1]: Entering directory '/home/hornik/tmp/scratch/RtmpuXyYWO/R.INSTALL28fbfd686ab8a4/BAMMtools/src' gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c BAMMtools_init.c -o BAMMtools_init.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c cohort_matrix.c -o cohort_matrix.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -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-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c jenksBrks.c -o jenksBrks.o gcc-14 -I"/home/hornik/tmp/R-d-gcc-14/include" -DNDEBUG -I/usr/local/include -DUSE_TYPE_CHECKING_STRICT -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c treetraverse.c -o treetraverse.o gcc-14 -shared -L/home/hornik/tmp/R-d-gcc-14/lib -Wl,-O1 -o BAMMtools.so BAMMtools_init.o cohort_matrix.o dtrates.o jenksBrks.o treetraverse.o -L/home/hornik/tmp/R-d-gcc-14/lib -lR make[1]: Leaving directory '/home/hornik/tmp/scratch/RtmpuXyYWO/R.INSTALL28fbfd686ab8a4/BAMMtools/src' installing to /home/hornik/tmp/CRAN_recheck/Library/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) checking BAMMtools_2.1.12.tar.gz ... checking EloOptimized_0.3.2.tar.gz ... checking binst_0.2.1.tar.gz ... checking GD_10.3.tar.gz ... Depends: Package: BAMMtools Depends: ape, R (>= 2.10) Imports: Rcpp (>= 0.11.0), gplots, methods Timings: user system elapsed BAMMtools 71.882 4.731 78.423 Results: Check status summary: NOTE OK Source packages 0 1 Reverse depends 1 2 Check results summary: BAMMtools ... OK rdepends_binst ... NOTE * checking LazyData ... NOTE rdepends_EloOptimized ... OK rdepends_GD ... OK