I've hit a roadblock debugging a new update to the survival package. I do debugging in a developement envinment, i.e. I don't create and load a package but rather source all the .R files and dyn.load an .so file, which makes things a bit easier.
Running with R -d "valgrind --tool=memcheck --leak-check=full" one of my test files crashes in simple R code a dozen lines after the likely culprit has been called, i.e, the survfit function for an Aalen-Johansen, containing a .Call to the new C code. The valgrind approach had already allowed me to find a few other (mostly dumb) errors that led to an out of bounds access, e.g., the wrong endpoint variable in a for( ) loop. What would others advise as a next step? Here is the last part of the screen > fit2 <- coxph(list(Surv(tstart, tstop, bstat) ~ 1, + c(1:4):5 ~ age / common + shared), id= id, istate=bili4, + data=pbc2, ties='breslow', x=TRUE) > surv2 <- survfit(fit2, newdata=list(age=50), p0=c(.4, .3, .2, .1, 0)) > test2 <- mysurv(fit2, pbc2$bili4, p0= 4:0/10, fit2, x0 =50) ==31730== Invalid read of size 8 ==31730== at 0x298A07: Rf_allocVector3 (memory.c:2861) ==31730== by 0x299B2C: Rf_allocVector (Rinlinedfuns.h:595) ==31730== by 0x299B2C: R_alloc (memory.c:2330) ==31730== by 0x3243C6: do_which (summary.c:1152) ==31730== by 0x23D8EF: bcEval (eval.c:7724) ==31730== by 0x25731F: Rf_eval (eval.c:1152) ==31730== by 0x25927D: R_execClosure (eval.c:2362) ==31730== by 0x25A35A: R_execMethod (eval.c:2535) ==31730== by 0x887E93F: R_dispatchGeneric (methods_list_dispatch.c:1151) ==31730== by 0x2A0E72: do_standardGeneric (objects.c:1344) ==31730== by 0x2577E7: Rf_eval (eval.c:1254) ==31730== by 0x25927D: R_execClosure (eval.c:2362) ==31730== by 0x25A01C: applyClosure_core (eval.c:2250) ==31730== Address 0x10 is not stack'd, malloc'd or (recently) free'd ==31730== *** caught segfault *** address 0x10, cause 'memory not mapped' Traceback: 1: which(smap == j) 2: which(smap == j) 3: mysurv(fit2, pbc2$bili4, p0 = 4:0/10, fit2, x0 = 50) The offending call is amost certainly the one to survfit; mysurv() is a local function that caculates some things 'by hand'. It does nothing complex: counts, loops, etc, the only non-base action is a call to Matrix::exp near the end, but the which() failure is well before that. The session info just before the offending material: > sessionInfo() R Under development (unstable) (2024-02-07 r85873) Platform: x86_64-pc-linux-gnu Running under: Ubuntu 22.04.3 LTS Matrix products: default BLAS: /usr/local/src/R-devel/lib/libRblas.so LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0 locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=C [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C time zone: America/Chicago tzcode source: system (glibc) attached base packages: [1] splines stats graphics grDevices utils datasets methods [8] base other attached packages: [1] Matrix_1.6-0 loaded via a namespace (and not attached): [1] compiler_4.4.0 tools_4.4.0 grid_4.4.0 lattice_0.22-5 --- Footnote. The impetus for this is realizing that the robust variance for an Aalen-Johansen was incorrect when there are case weights for a subject that vary over time; a rare case but will occur with time dependent IPC weights. Carefully figuring this out has been all I did for the last week, leading to a new routine survfitaj.c and approx 14 pages of derivation and explanation in the methods.Rnw vignette. Subjects who "change horses in midstream", i.e., swap from one curve to another mid-followup make the code more complex. This arises out of the "extended Kaplan-Meier"; I am not a fan of this statistically, but some will use it and expect my code to work. -- Terry M Therneau, PhD Department of Quantitative Health Sciences Mayo Clinic thern...@mayo.edu "TERR-ree THUR-noh" [[alternative HTML version deleted]] ______________________________________________ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel