CRAN Package Check Results for Package survival

Last updated on 2020-01-19 23:46:59 CET.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 3.1-8 57.58 535.54 593.12 OK
r-devel-linux-x86_64-debian-gcc 3.1-8 39.78 411.73 451.51 OK
r-devel-linux-x86_64-fedora-clang 3.1-8 722.07 NOTE
r-devel-linux-x86_64-fedora-gcc 3.1-8 696.18 OK
r-devel-windows-ix86+x86_64 3.1-8 162.00 788.00 950.00 NOTE
r-devel-windows-ix86+x86_64-gcc8 3.1-8 119.00 1074.00 1193.00 ERROR
r-patched-linux-x86_64 3.1-8 41.80 486.42 528.22 OK
r-patched-solaris-x86 3.1-8 NOTE
r-release-linux-x86_64 3.1-8 46.36 485.09 531.45 OK
r-release-windows-ix86+x86_64 3.1-8 163.00 731.00 894.00 WARN
r-release-osx-x86_64 3.1-8 NOTE
r-oldrel-windows-ix86+x86_64 3.1-8 107.00 901.00 1008.00 NOTE
r-oldrel-osx-x86_64 3.1-8 NOTE

Check Details

Version: 3.1-8
Check: installed package size
Result: NOTE
     installed size is 8.9Mb
     sub-directories of 1Mb or more:
     R 1.0Mb
     data 3.2Mb
     doc 3.3Mb
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-windows-ix86+x86_64, r-devel-windows-ix86+x86_64-gcc8, r-patched-solaris-x86, r-release-windows-ix86+x86_64, r-release-osx-x86_64, r-oldrel-windows-ix86+x86_64, r-oldrel-osx-x86_64

Version: 3.1-8
Check: running tests for arch ‘i386’
Result: ERROR
     Running 'aareg.R' [4s]
     Comparing 'aareg.Rout' to 'aareg.Rout.save' ... OK
     Running 'anova.R' [3s]
     Comparing 'anova.Rout' to 'anova.Rout.save' ... OK
     Running 'bladder.R' [3s]
     Comparing 'bladder.Rout' to 'bladder.Rout.save' ... OK
     Running 'book1.R' [4s]
     Comparing 'book1.Rout' to 'book1.Rout.save' ... OK
     Running 'book2.R' [3s]
     Comparing 'book2.Rout' to 'book2.Rout.save' ... OK
     Running 'book3.R' [3s]
     Comparing 'book3.Rout' to 'book3.Rout.save' ... OK
     Running 'book4.R' [3s]
     Comparing 'book4.Rout' to 'book4.Rout.save' ... OK
     Running 'book5.R' [3s]
     Comparing 'book5.Rout' to 'book5.Rout.save' ... OK
     Running 'book6.R' [3s]
     Comparing 'book6.Rout' to 'book6.Rout.save' ... OK
     Running 'book7.R' [3s]
     Comparing 'book7.Rout' to 'book7.Rout.save' ... OK
     Running 'cancer.R' [4s]
     Comparing 'cancer.Rout' to 'cancer.Rout.save' ... OK
     Running 'clogit.R' [3s]
     Comparing 'clogit.Rout' to 'clogit.Rout.save' ... OK
     Running 'concordance.R' [4s]
     Comparing 'concordance.Rout' to 'concordance.Rout.save' ... OK
     Running 'concordance2.R' [18s]
     Comparing 'concordance2.Rout' to 'concordance2.Rout.save' ... OK
     Running 'concordance3.R' [3s]
     Comparing 'concordance3.Rout' to 'concordance3.Rout.save' ... OK
     Running 'counting.R' [3s]
     Comparing 'counting.Rout' to 'counting.Rout.save' ... OK
     Running 'coxsurv.R' [3s]
     Comparing 'coxsurv.Rout' to 'coxsurv.Rout.save' ... OK
     Running 'coxsurv2.R' [3s]
     Comparing 'coxsurv2.Rout' to 'coxsurv2.Rout.save' ... OK
     Running 'coxsurv3.R' [3s]
     Comparing 'coxsurv3.Rout' to 'coxsurv3.Rout.save' ... OK
     Running 'coxsurv4.R' [3s]
     Comparing 'coxsurv4.Rout' to 'coxsurv4.Rout.save' ... OK
     Running 'coxsurv5.R' [4s]
     Comparing 'coxsurv5.Rout' to 'coxsurv5.Rout.save' ... OK
     Running 'detail.R' [3s]
     Comparing 'detail.Rout' to 'detail.Rout.save' ... OK
     Running 'difftest.R' [3s]
     Comparing 'difftest.Rout' to 'difftest.Rout.save' ... OK
     Running 'doaml.R' [3s]
     Comparing 'doaml.Rout' to 'doaml.Rout.save' ... OK
     Running 'doweight.R' [3s]
     Comparing 'doweight.Rout' to 'doweight.Rout.save' ... OK
     Running 'expected.R' [4s]
     Comparing 'expected.Rout' to 'expected.Rout.save' ... OK
     Running 'expected2.R' [3s]
     Comparing 'expected2.Rout' to 'expected2.Rout.save' ... OK
     Running 'factor.R' [3s]
     Comparing 'factor.Rout' to 'factor.Rout.save' ... OK
     Running 'factor2.R' [3s]
     Comparing 'factor2.Rout' to 'factor2.Rout.save' ... OK
     Running 'finegray.R' [3s]
     Comparing 'finegray.Rout' to 'finegray.Rout.save' ... OK
     Running 'fr_cancer.R' [3s]
     Comparing 'fr_cancer.Rout' to 'fr_cancer.Rout.save' ... OK
     Running 'fr_kidney.R' [3s]
     Comparing 'fr_kidney.Rout' to 'fr_kidney.Rout.save' ... OK
     Running 'fr_lung.R' [3s]
     Comparing 'fr_lung.Rout' to 'fr_lung.Rout.save' ... OK
     Running 'fr_ovarian.R' [3s]
     Comparing 'fr_ovarian.Rout' to 'fr_ovarian.Rout.save' ... OK
     Running 'fr_rat1.R' [3s]
     Comparing 'fr_rat1.Rout' to 'fr_rat1.Rout.save' ... OK
     Running 'fr_resid.R' [3s]
     Comparing 'fr_resid.Rout' to 'fr_resid.Rout.save' ... OK
     Running 'fr_simple.R' [3s]
     Comparing 'fr_simple.Rout' to 'fr_simple.Rout.save' ... OK
     Running 'frailty.R' [2s]
     Comparing 'frailty.Rout' to 'frailty.Rout.save' ... OK
     Running 'frank.R' [3s]
     Comparing 'frank.Rout' to 'frank.Rout.save' ... OK
     Running 'infcox.R' [2s]
     Comparing 'infcox.Rout' to 'infcox.Rout.save' ... OK
     Running 'jasa.R' [3s]
     Comparing 'jasa.Rout' to 'jasa.Rout.save' ... OK
     Running 'model.matrix.R' [3s]
     Comparing 'model.matrix.Rout' to 'model.matrix.Rout.save' ... OK
     Running 'mstate.R' [3s]
     Comparing 'mstate.Rout' to 'mstate.Rout.save' ... OK
     Running 'multi2.R' [4s]
     Comparing 'multi2.Rout' to 'multi2.Rout.save' ... OK
     Running 'multistate.R' [4s]
     Comparing 'multistate.Rout' to 'multistate.Rout.save' ... OK
     Running 'nested.R' [3s]
     Comparing 'nested.Rout' to 'nested.Rout.save' ... OK
     Running 'ovarian.R' [3s]
     Comparing 'ovarian.Rout' to 'ovarian.Rout.save' ... OK
     Running 'overlap.R' [3s]
     Comparing 'overlap.Rout' to 'overlap.Rout.save' ... OK
     Running 'prednew.R' [3s]
     Comparing 'prednew.Rout' to 'prednew.Rout.save' ... OK
     Running 'pspline.R' [3s]
     Comparing 'pspline.Rout' to 'pspline.Rout.save' ... OK
     Running 'pyear.R' [3s]
     Comparing 'pyear.Rout' to 'pyear.Rout.save' ... OK
     Running 'quantile.R' [3s]
     Comparing 'quantile.Rout' to 'quantile.Rout.save' ... OK
     Running 'r_donnell.R' [4s]
     Comparing 'r_donnell.Rout' to 'r_donnell.Rout.save' ... OK
     Running 'r_lung.R' [3s]
     Comparing 'r_lung.Rout' to 'r_lung.Rout.save' ... OK
     Running 'r_peterson.R' [3s]
     Comparing 'r_peterson.Rout' to 'r_peterson.Rout.save' ... OK
     Running 'r_resid.R' [3s]
     Comparing 'r_resid.Rout' to 'r_resid.Rout.save' ... OK
     Running 'r_sas.R' [9s]
     Comparing 'r_sas.Rout' to 'r_sas.Rout.save' ...412,413c412,413
    < null device
    < 1
    ---
    > pdf
    > 2
     Running 'r_scale.R' [4s]
     Comparing 'r_scale.Rout' to 'r_scale.Rout.save' ... OK
     Running 'r_stanford.R' [3s]
     Comparing 'r_stanford.Rout' to 'r_stanford.Rout.save' ... OK
     Running 'r_strata.R' [3s]
     Comparing 'r_strata.Rout' to 'r_strata.Rout.save' ... OK
     Running 'r_tdist.R' [3s]
     Comparing 'r_tdist.Rout' to 'r_tdist.Rout.save' ... OK
     Running 'r_user.R' [3s]
     Comparing 'r_user.Rout' to 'r_user.Rout.save' ... OK
     Running 'ratetable.R' [3s]
     Comparing 'ratetable.Rout' to 'ratetable.Rout.save' ... OK
     Running 'singtest.R' [3s]
     Comparing 'singtest.Rout' to 'singtest.Rout.save' ... OK
     Running 'strata2.R' [3s]
     Comparing 'strata2.Rout' to 'strata2.Rout.save' ... OK
     Running 'stratatest.R' [3s]
     Comparing 'stratatest.Rout' to 'stratatest.Rout.save' ... OK
     Running 'summary_survfit.R' [3s]
     Comparing 'summary_survfit.Rout' to 'summary_survfit.Rout.save' ... OK
     Running 'surv.R' [3s]
     Comparing 'surv.Rout' to 'surv.Rout.save' ... OK
     Running 'survSplit.R' [3s]
     Comparing 'survSplit.Rout' to 'survSplit.Rout.save' ... OK
     Running 'survcheck.R' [3s]
     Comparing 'survcheck.Rout' to 'survcheck.Rout.save' ... OK
     Running 'survfit1.R' [3s]
     Comparing 'survfit1.Rout' to 'survfit1.Rout.save' ... OK
     Running 'survfit2.R' [3s]
     Comparing 'survfit2.Rout' to 'survfit2.Rout.save' ... OK
     Running 'survreg1.R' [3s]
     Comparing 'survreg1.Rout' to 'survreg1.Rout.save' ... OK
     Running 'survreg2.R' [4s]
     Comparing 'survreg2.Rout' to 'survreg2.Rout.save' ... OK
     Running 'survtest.R' [3s]
     Comparing 'survtest.Rout' to 'survtest.Rout.save' ... OK
     Running 'testci.R' [3s]
     Comparing 'testci.Rout' to 'testci.Rout.save' ... OK
     Running 'testci2.R' [3s]
     Comparing 'testci2.Rout' to 'testci2.Rout.save' ... OK
     Running 'testnull.R' [3s]
     Comparing 'testnull.Rout' to 'testnull.Rout.save' ... OK
     Running 'testreg.R' [3s]
     Comparing 'testreg.Rout' to 'testreg.Rout.save' ... OK
     Running 'tiedtime.R' [3s]
     Comparing 'tiedtime.Rout' to 'tiedtime.Rout.save' ... OK
     Running 'tmerge.R' [3s]
     Comparing 'tmerge.Rout' to 'tmerge.Rout.save' ... OK
     Running 'tmerge2.R' [3s]
     Comparing 'tmerge2.Rout' to 'tmerge2.Rout.save' ... OK
     Running 'tmerge3.R' [3s]
     Comparing 'tmerge3.Rout' to 'tmerge3.Rout.save' ... OK
     Running 'tt.R' [3s]
     Comparing 'tt.Rout' to 'tt.Rout.save' ... OK
     Running 'turnbull.R' [3s]
     Comparing 'turnbull.Rout' to 'turnbull.Rout.save' ... OK
     Running 'update.R' [3s]
     Comparing 'update.Rout' to 'update.Rout.save' ... OK
     Running 'yates0.R' [1s]
     Comparing 'yates0.Rout' to 'yates0.Rout.save' ... OK
     Running 'yates1.R' [4s]
     Comparing 'yates1.Rout' to 'yates1.Rout.save' ... OK
     Running 'yates2.R' [3s]
     Running 'zph.R' [4s]
    Running the tests in 'tests/zph.R' failed.
    Complete output:
     > library(survival)
     > aeq <- function(x,y) all.equal(as.vector(x), as.vector(y))
     >
     > test1 <- data.frame(time= c(9, 3,1,1,6,6,8),
     + status=c(1,NA,1,0,1,1,0),
     + x= c(0, 2,1,1,1,0,0))
     >
     > # Verify that cox.zph computes a score test
     > # First for the Breslow estimate
     > r <- (3 + sqrt(33))/2 # actual MLE for log(beta)
     > U <- c(1/(r+1), 3/(r+3), -r/(r+3), 0) # score statistic
     > imat <- c(r/(r+1)^2, 3*r/(r+3)^2, 3*r/(r+3)^2, 0) # information matrix
     > g = c(1, 6, 6, 9) # death times
     >
     > u2 <- c(sum(U), sum(g*U)) # first derivative
     > i2 <- matrix(c(sum(imat), sum(g*imat), sum(g*imat), sum(g^2*imat)),
     + 2,2) # second derivative
     > sctest <- solve(i2, u2) %*% u2
     >
     > # Verify that centering makes no difference for the test (though i2 changes)
     > g2 <- g - mean(g)
     > u2b <- c(sum(U), sum(g2*U))
     > i2b <- matrix(c(sum(imat), sum(g2*imat), sum(g2*imat), sum(g2^2*imat)),
     + 2,2)
     > sctest2 <- solve(i2b, u2b) %*% u2b
     > all.equal(sctest, sctest2)
     [1] TRUE
     >
     > # Now check the program
     > fit1 <- coxph(Surv(time, status) ~ x, test1, ties='breslow')
     > aeq(fit1$coef, log(r))
     [1] TRUE
     > zp1 <- cox.zph(fit1, transform='identity', global=FALSE)
     > aeq(zp1$table[,1], sctest)
     [1] TRUE
     > aeq(zp1$y, resid(fit1, type="scaledsch"))
     [1] TRUE
     >
     > dummy <- rep(0, nrow(test1))
     > fit1b <- coxph(Surv(dummy, time, status) ~ x, test1, ties='breslow')
     > aeq(fit1b$coef, log(r))
     [1] TRUE
     > zp1b <- cox.zph(fit1b, transform='identity', global=FALSE)
     > aeq(zp1b$table[,1], sctest)
     [1] TRUE
     > # the pair of tied times gets reversed in the zph result
     > # but since the 'y' values are only used to plot it doesn't matter
     > aeq(zp1b$y[c(1,3,2,4)], resid(fit1b, type="scaledsch"))
     [1] TRUE
     >
     > # log time check
     > g3 <- log(g) - mean(log(g))
     > u3 <- c(sum(U), sum(g3*U)) # first derivative
     > i3 <- matrix(c(sum(imat), sum(g3*imat), sum(g3*imat), sum(g3^2*imat)),
     + 2,2) # second derivative
     > sctest3 <- solve(i3, u3) %*% u3
     > zp3 <- cox.zph(fit1, transform='log', global=FALSE)
     > aeq(zp3$table[,1], sctest3)
     [1] TRUE
     >
     > # Efron approximation
     > phi <- acos((45/23)*sqrt(3/23))
     > r <- 2*sqrt(23/3)* cos(phi/3) # actual MLE for log(beta)
     > U <- c(1/(r+1), 3/(r+3), -r/(r+5), 0) # score statistic
     > imat <- c(r/(r+1)^2, 3*r/(r+3)^2, 5*r/(r+5)^2, 0) # information matrix
     >
     > u4 <- c(sum(U), sum(g3*U)) # first derivative
     > i4 <- matrix(c(sum(imat), sum(g3*imat), sum(g3*imat), sum(g3^2*imat)),
     + 2,2) # second derivative
     > sctest4 <- solve(i4, u4) %*% u4
     >
     > fit4 <- coxph(Surv(time, status) ~ x, test1, ties='efron')
     > aeq(fit4$coef, log(r))
     [1] TRUE
     > zp4 <- cox.zph(fit4, transform='log', global=FALSE)
     > aeq(zp4$table[,1], sctest4)
     [1] TRUE
     > aeq(zp4$y, resid(fit4, type="scaledsch"))
     [1] TRUE
     >
     > fit5 <- coxph(Surv(dummy, time, status) ~ x, test1, ties="efron")
     > aeq(fit5$coef, log(r))
     [1] TRUE
     > zp5 <- cox.zph(fit5, transform="log", global=FALSE)
     > aeq(zp5$table[,1], sctest4)
     [1] TRUE
     >
     > # Artificial stratification
     > test2 <- rbind(test1, test1)
     > test2$group <- rep(letters[1:2], each=nrow(test1))
     > # U, imat, and sctest will all double
     > dummy <- c(dummy, dummy)
     > fit6 <- coxph(Surv(dummy, time, status) ~ x + strata(group), test2)
     > aeq(fit6$coef, log(r))
     [1] TRUE
     > zp6 <- cox.zph(fit6, transform="log", globa=FALSE)
     > aeq(zp6$table[,1], 2*sctest4)
     [1] TRUE
     >
     > # A multi-state check, 2 covariates
     > # Verify that the multi-state result = the single state Cox models
     > etime <- with(mgus2, ifelse(pstat==0, futime, ptime))
     > event <- with(mgus2, ifelse(pstat==0, 2*death, 1))
     > event <- factor(event, 0:2, labels=c("censor", "pcm", "death"))
     > table(event)
     event
     censor pcm death
     409 115 860
     >
     > ct1 <- coxph(Surv(etime, event) ~ sex + age, mgus2, id=id)
     > ct2 <- coxph(Surv(etime, event=='pcm') ~ sex + age, mgus2)
     > ct3 <- coxph(Surv(etime, event=='death') ~ sex + age, mgus2)
     >
     > zp1 <- cox.zph(ct1, transform='identity')
     > zp2 <- cox.zph(ct2, transform='identity')
     > zp3 <- cox.zph(ct3, transform='identity')
     > aeq(zp1$table[1:2,], zp2$table[1:2,])
     [1] TRUE
     > aeq(zp1$table[3:4,], zp3$table[1:2,])
     [1] TRUE
     >
     > # Now add a starting time of zero
     > dummy <- rep(0, nrow(mgus2))
     > ct4 <- coxph(Surv(dummy, etime, event) ~ sex + age, mgus2, id=id)
     Error in if (flag["teleport"] > 0) { :
     missing value where TRUE/FALSE needed
     Calls: coxph -> survcheck2
     Execution halted
Flavor: r-devel-windows-ix86+x86_64-gcc8

Version: 3.1-8
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
    --- re-building 'adjcurve.Rnw' using Sweave
    --- finished re-building 'adjcurve.Rnw'
    
    --- re-building 'approximate.Rnw' using Sweave
    --- finished re-building 'approximate.Rnw'
    
    --- re-building 'compete.Rnw' using Sweave
    --- finished re-building 'compete.Rnw'
    
    --- re-building 'concordance.Rnw' using Sweave
    --- finished re-building 'concordance.Rnw'
    
    --- re-building 'multi.Rnw' using Sweave
    --- finished re-building 'multi.Rnw'
    
    --- re-building 'other.Rnw' using Sweave
    --- finished re-building 'other.Rnw'
    
    --- re-building 'population.Rnw' using Sweave
    --- finished re-building 'population.Rnw'
    
    --- re-building 'splines.Rnw' using Sweave
    Loading required package: survival
    --- finished re-building 'splines.Rnw'
    
    --- re-building 'survival.Rnw' using Sweave
    Warning in coxph(Surv(tstart, time, status) ~ trt + celltype + karno + time:karno, :
     a variable appears on both the left and right sides of the formula
    Warning in coxph(Surv(tstart, time, status) ~ trt + celltype + karno + rank(time):karno, :
     a variable appears on both the left and right sides of the formula
    --- finished re-building 'survival.Rnw'
    
    --- re-building 'tiedtimes.Rnw' using Sweave
    Warning in system(paste(shQuote(texi2dvi), if (quiet) "--quiet" else "", :
     running command '"D:\compiler\texmf\miktex\bin\texify.exe" --quiet --pdf "tiedtimes.tex" --max-iterations=20 -I "D:/RCompile/recent/R-3.6.2/share/texmf/tex/latex" -I "D:/RCompile/recent/R-3.6.2/share/texmf/bibtex/bst"' had status 1
    Error: processing vignette 'tiedtimes.Rnw' failed with diagnostics:
    Failed to locate the 'texi2pdf' output file (by engine 'utils::Sweave') for vignette with name 'tiedtimes'. The following files exist in directory '.': 'Rplots.pdf', 'adjcurve-024.pdf', 'adjcurve-approx1.pdf', 'adjcurve-approx4.pdf', 'adjcurve-flc1.pdf', 'adjcurve-flc2.pdf', 'adjcurve-flc3.pdf', 'adjcurve-flc3a.pdf', 'adjcurve-flc4.pdf', 'adjcurve-flc5.pdf', 'adjcurve-flc6.pdf', 'adjcurve-flc6b.pdf', 'adjcurve-flc7.pdf', 'adjcurve-flc8.pdf', 'adjcurve.Rnw', 'adjcurve.aux', 'adjcurve.bbl', 'adjcurve.blg', 'adjcurve.log', 'adjcurve.pdf', 'adjcurve.tex', 'approximate.Rnw', 'approximate.aux', 'approximate.log', 'approximate.pdf', 'approximate.tex', 'compete-PCMcurve2.pdf', 'compete-crfig2.pdf', 'compete-fg2.pdf', 'compete-finegray-check.pdf', 'compete-finegray2.pdf', 'compete-finegray3.pdf', 'compete-mgus1.pdf', 'compete-mgus2.pdf', 'compete-mgus3.pdf', 'compete-mgus4g.pdf', 'compete-mgus5.pdf', 'compete-rplot.pdf', 'compete-sfig1.pdf', 'compete-tmwt.pdf', 'compete-varest.pdf', 'compete.Rnw', 'compete.aux', 'compete.log', 'compete.pdf', 'compete.tex', 'concordance.Rnw', 'concordance.aux', 'concordance.bbl', 'concordance.blg', 'concordance.log', 'concordance.pdf', 'concordance.tex', 'multi.Rnw', 'multi.aux', 'multi.log', 'multi.pdf', 'multi.tex', 'other.Rnw', 'other.aux', 'other.log', 'other.pdf', 'other.tex', 'population.Rnw', 'population.aux', 'population.bbl', 'population.blg', 'population.log', 'population.pdf', 'population.tex', 'population.toc', 'refer.bib', 'splines-df.pdf', 'splines-fit1.pdf', 'splines-fit2a.pdf', 'splines-fit2b.pdf', 'splines-hgb.pdf', 'splines-mplot.pdf', 'splines-mplot3.pdf', 'splines-nfit2.pdf', 'splines-plot2.pdf', 'splines.Rnw', 'splines.aux', 'splines.log', 'splines.pdf', 'splines.tex', 'surv-011.pdf', 'surv-PCMcurve.pdf', 'surv-badfit.pdf', 'surv-cfit4.pdf', 'surv-cgd1d.pdf', 'surv-cgd3.pdf', 'surv-coarsen.pdf', 'surv-cox13.pdf', 'surv-cr2.pdf', 'surv-curve1.pdf', 'surv-lung2.pdf', 'surv-lung3.pdf', 'surv-mgus2.pdf', 'surv-mgus3.pdf', 'surv-msingle.pdf', 'surv-sfit0.pdf', 'surv-sfit4.pdf', 'surv-state5.pdf', 'surv-states.pdf', 'surv-survfit-mgus1.pdf', 'surv-survfit2.pdf', 'surv-survfit3.pdf', 'surv-survival5.pdf', 'surv-txsurv.pdf', 'surv-zph2.pdf', 'survival.Rnw', 'survival.aux', 'survival.bbl', 'survival.blg', 'survival.log', 'survival.pdf', 'survival.tex', 'survival.toc', 'tests-data.pdf', 'tests-fig1.pdf', 'tests-solder1b.pdf', 'tests-surv3.pdf', 'tiedtimes.Rnw', 'tiedtimes.tex', 'timedep.Rnw', 'validate.Rnw'
    --- failed re-building 'tiedtimes.Rnw'
    
    --- re-building 'timedep.Rnw' using Sweave
    --- finished re-building 'timedep.Rnw'
    
    --- re-building 'validate.Rnw' using Sweave
    Warning in fitter(X, Y, istrat, offset, init, control, weights = weights, :
     Ran out of iterations and did not converge
    Warning in fitter(X, Y, istrat, offset, init, control, weights = weights, :
     Ran out of iterations and did not converge
    --- finished re-building 'validate.Rnw'
    
    SUMMARY: processing the following file failed:
     'tiedtimes.Rnw'
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-release-windows-ix86+x86_64