- using R version 3.1.0 Patched (2014-04-10 r65397)
- using platform: x86_64-unknown-linux-gnu (64-bit)
- using session charset: UTF-8
- checking for file ‘survival/DESCRIPTION’ ... OK
- this is package ‘survival’ version ‘2.37-7’
- checking package namespace information ... OK
- checking package dependencies ... OK
- checking if this is a source package ... OK
- checking if there is a namespace ... OK
- checking for executable files ... OK
- checking for hidden files and directories ... OK
- checking for portable file names ... OK
- checking for sufficient/correct file permissions ... OK
- checking whether package ‘survival’ can be installed ... OK
- checking installed package size ... NOTE

installed size is 5.2Mb

sub-directories of 1Mb or more:

data 1.9Mb

doc 1.8Mb - checking package directory ... OK
- checking ‘build’ directory ... OK
- checking DESCRIPTION meta-information ... OK
- checking top-level files ... OK
- checking for left-over files ... OK
- checking index information ... OK
- checking package subdirectories ... OK
- checking R files for non-ASCII characters ... OK
- checking R files for syntax errors ... OK
- checking whether the package can be loaded ... OK
- checking whether the package can be loaded with stated dependencies ... OK
- checking whether the package can be unloaded cleanly ... OK
- checking whether the namespace can be loaded with stated dependencies ... OK
- checking whether the namespace can be unloaded cleanly ... OK
- checking dependencies in R code ... OK
- checking S3 generic/method consistency ... OK
- checking replacement functions ... OK
- checking foreign function calls ... NOTE

Calls with DUP = FALSE:

.C(Ccoxmart2, as.integer(n), as.double(y[, 1]), as.integer(y[,

2]), newstrat, score, rep(1, n), resid = double(n), DUP = FALSE)

.C(Cpyears1, as.integer(n), as.integer(ncol(Y)), as.integer(is.Surv(Y)),

as.double(Y), as.double(weights), as.integer(length(atts$dim)),

as.integer(rfac), as.integer(atts$dim), as.double(unlist(cuts)),

as.double(ratetable), as.double(R), as.integer(odim), as.integer(ofac),

as.integer(odims), as.double(ocut), as.integer(expect ==

"event"), as.double(X), pyears = double(osize), pn = double(osize),

pcount = double(if (is.Surv(Y)) osize else 1), pexpect = double(osize),

offtable = double(1), DUP = FALSE)

DUP = FALSE is deprecated and may be disabled in future versions of R. - checking R code for possible problems ... OK
- checking Rd files ... OK
- checking Rd metadata ... OK
- checking Rd cross-references ... OK
- checking for missing documentation entries ... OK
- checking for code/documentation mismatches ... OK
- checking Rd \usage sections ... OK
- checking Rd contents ... OK
- checking for unstated dependencies in examples ... OK
- checking contents of ‘data’ directory ... OK
- checking data for non-ASCII characters ... OK
- checking data for ASCII and uncompressed saves ... OK
- checking line endings in C/C++/Fortran sources/headers ... OK
- checking line endings in Makefiles ... OK
- checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
- checking compiled code ... OK
- checking sizes of PDF files under ‘inst/doc’ ... OK
- checking installed files from ‘inst/doc’ ... OK
- checking files in ‘vignettes’ ... OK
- checking examples ... [3s/3s] OK
- checking for unstated dependencies in tests ... OK
- checking tests ... [33s/34s] OK

Running ‘aareg.R’ [1s/1s]

Comparing ‘aareg.Rout’ to ‘aareg.Rout.save’ ... OK

Running ‘anova.R’ [0s/0s]

Comparing ‘anova.Rout’ to ‘anova.Rout.save’ ... OK

Running ‘bladder.R’ [0s/0s]

Comparing ‘bladder.Rout’ to ‘bladder.Rout.save’ ... OK

Running ‘book1.R’ [0s/0s]

Comparing ‘book1.Rout’ to ‘book1.Rout.save’ ... OK

Running ‘book2.R’ [0s/0s]

Comparing ‘book2.Rout’ to ‘book2.Rout.save’ ... OK

Running ‘book3.R’ [0s/0s]

Comparing ‘book3.Rout’ to ‘book3.Rout.save’ ... OK

Running ‘book4.R’ [0s/0s]

Comparing ‘book4.Rout’ to ‘book4.Rout.save’ ... OK

Running ‘book5.R’ [0s/0s]

Comparing ‘book5.Rout’ to ‘book5.Rout.save’ ... OK

Running ‘book6.R’ [0s/0s]

Comparing ‘book6.Rout’ to ‘book6.Rout.save’ ... OK

Running ‘book7.R’ [1s/1s]

Comparing ‘book7.Rout’ to ‘book7.Rout.save’ ... OK

Running ‘cancer.R’ [0s/0s]

Comparing ‘cancer.Rout’ to ‘cancer.Rout.save’ ... OK

Running ‘clogit.R’ [1s/1s]

Comparing ‘clogit.Rout’ to ‘clogit.Rout.save’ ... OK

Running ‘concordance.R’ [1s/1s]

Comparing ‘concordance.Rout’ to ‘concordance.Rout.save’ ... OK

Running ‘counting.R’ [0s/0s]

Comparing ‘counting.Rout’ to ‘counting.Rout.save’ ... OK

Running ‘coxsurv.R’ [0s/0s]

Comparing ‘coxsurv.Rout’ to ‘coxsurv.Rout.save’ ... OK

Running ‘coxsurv2.R’ [0s/0s]

Comparing ‘coxsurv2.Rout’ to ‘coxsurv2.Rout.save’ ... OK

Running ‘coxsurv3.R’ [0s/0s]

Comparing ‘coxsurv3.Rout’ to ‘coxsurv3.Rout.save’ ... OK

Running ‘coxsurv4.R’ [0s/0s]

Comparing ‘coxsurv4.Rout’ to ‘coxsurv4.Rout.save’ ... OK

Running ‘detail.R’ [0s/0s]

Comparing ‘detail.Rout’ to ‘detail.Rout.save’ ... OK

Running ‘difftest.R’ [0s/0s]

Comparing ‘difftest.Rout’ to ‘difftest.Rout.save’ ... OK

Running ‘doaml.R’ [0s/0s]

Comparing ‘doaml.Rout’ to ‘doaml.Rout.save’ ... OK

Running ‘doweight.R’ [0s/0s]

Comparing ‘doweight.Rout’ to ‘doweight.Rout.save’ ... OK

Running ‘expected.R’ [1s/1s]

Comparing ‘expected.Rout’ to ‘expected.Rout.save’ ... OK

Running ‘expected2.R’ [0s/0s]

Comparing ‘expected2.Rout’ to ‘expected2.Rout.save’ ... OK

Running ‘factor.R’ [0s/0s]

Comparing ‘factor.Rout’ to ‘factor.Rout.save’ ... OK

Running ‘factor2.R’ [0s/0s]

Comparing ‘factor2.Rout’ to ‘factor2.Rout.save’ ... OK

Running ‘fr_cancer.R’ [0s/0s]

Comparing ‘fr_cancer.Rout’ to ‘fr_cancer.Rout.save’ ... OK

Running ‘fr_kidney.R’ [0s/0s]

Comparing ‘fr_kidney.Rout’ to ‘fr_kidney.Rout.save’ ... OK

Running ‘fr_lung.R’ [0s/0s]

Comparing ‘fr_lung.Rout’ to ‘fr_lung.Rout.save’ ... OK

Running ‘fr_ovarian.R’ [0s/0s]

Comparing ‘fr_ovarian.Rout’ to ‘fr_ovarian.Rout.save’ ... OK

Running ‘fr_rat1.R’ [0s/0s]

Comparing ‘fr_rat1.Rout’ to ‘fr_rat1.Rout.save’ ... OK

Running ‘fr_rat2.R’ [0s/0s]

Comparing ‘fr_rat2.Rout’ to ‘fr_rat2.Rout.save’ ... OK

Running ‘fr_resid.R’ [0s/0s]

Comparing ‘fr_resid.Rout’ to ‘fr_resid.Rout.save’ ... OK

Running ‘fr_simple.R’ [0s/0s]

Comparing ‘fr_simple.Rout’ to ‘fr_simple.Rout.save’ ... OK

Running ‘frailty.R’ [0s/0s]

Comparing ‘frailty.Rout’ to ‘frailty.Rout.save’ ... OK

Running ‘frank.R’ [0s/0s]

Comparing ‘frank.Rout’ to ‘frank.Rout.save’ ... OK

Running ‘infcox.R’ [0s/0s]

Comparing ‘infcox.Rout’ to ‘infcox.Rout.save’ ... OK

Running ‘jasa.R’ [0s/0s]

Comparing ‘jasa.Rout’ to ‘jasa.Rout.save’ ... OK

Running ‘model.matrix.R’ [0s/0s]

Comparing ‘model.matrix.Rout’ to ‘model.matrix.Rout.save’ ... OK

Running ‘mrtest.R’ [0s/0s]

Comparing ‘mrtest.Rout’ to ‘mrtest.Rout.save’ ... OK

Running ‘nested.R’ [0s/0s]

Comparing ‘nested.Rout’ to ‘nested.Rout.save’ ... OK

Running ‘ovarian.R’ [0s/0s]

Comparing ‘ovarian.Rout’ to ‘ovarian.Rout.save’ ... OK

Running ‘prednew.R’ [0s/0s]

Comparing ‘prednew.Rout’ to ‘prednew.Rout.save’ ... OK

Running ‘pspline.R’ [0s/0s]

Comparing ‘pspline.Rout’ to ‘pspline.Rout.save’ ... OK

Running ‘pyear.R’ [0s/0s]

Comparing ‘pyear.Rout’ to ‘pyear.Rout.save’ ... OK

Running ‘quantile.R’ [0s/0s]

Comparing ‘quantile.Rout’ to ‘quantile.Rout.save’ ... OK

Running ‘r_capacitor.R’ [0s/0s]

Comparing ‘r_capacitor.Rout’ to ‘r_capacitor.Rout.save’ ... OK

Running ‘r_donnell.R’ [1s/1s]

Comparing ‘r_donnell.Rout’ to ‘r_donnell.Rout.save’ ... OK

Running ‘r_lung.R’ [0s/0s]

Comparing ‘r_lung.Rout’ to ‘r_lung.Rout.save’ ... OK

Running ‘r_peterson.R’ [0s/0s]

Comparing ‘r_peterson.Rout’ to ‘r_peterson.Rout.save’ ... OK

Running ‘r_resid.R’ [0s/0s]

Comparing ‘r_resid.Rout’ to ‘r_resid.Rout.save’ ... OK

Running ‘r_sas.R’ [5s/5s]

Comparing ‘r_sas.Rout’ to ‘r_sas.Rout.save’ ... OK

Running ‘r_scale.R’ [0s/0s]

Comparing ‘r_scale.Rout’ to ‘r_scale.Rout.save’ ... OK

Running ‘r_stanford.R’ [0s/0s]

Comparing ‘r_stanford.Rout’ to ‘r_stanford.Rout.save’ ... OK

Running ‘r_strata.R’ [0s/0s]

Comparing ‘r_strata.Rout’ to ‘r_strata.Rout.save’ ... OK

Running ‘r_tdist.R’ [0s/0s]

Comparing ‘r_tdist.Rout’ to ‘r_tdist.Rout.save’ ... OK

Running ‘r_user.R’ [0s/0s]

Comparing ‘r_user.Rout’ to ‘r_user.Rout.save’ ... OK

Running ‘ratetable.R’ [0s/0s]

Comparing ‘ratetable.Rout’ to ‘ratetable.Rout.save’ ... OK

Running ‘rounding.R’ [0s/0s]

Comparing ‘rounding.Rout’ to ‘rounding.Rout.save’ ... OK

Running ‘singtest.R’ [0s/0s]

Comparing ‘singtest.Rout’ to ‘singtest.Rout.save’ ... OK

Running ‘strata2.R’ [0s/0s]

Comparing ‘strata2.Rout’ to ‘strata2.Rout.save’ ... OK

Running ‘stratatest.R’ [0s/0s]

Comparing ‘stratatest.Rout’ to ‘stratatest.Rout.save’ ... OK

Running ‘summary_survfit.R’ [0s/0s]

Comparing ‘summary_survfit.Rout’ to ‘summary_survfit.Rout.save’ ... OK

Running ‘surv.R’ [0s/0s]

Comparing ‘surv.Rout’ to ‘surv.Rout.save’ ... OK

Running ‘survfit2.R’ [0s/0s]

Comparing ‘survfit2.Rout’ to ‘survfit2.Rout.save’ ... OK

Running ‘survreg2.R’ [1s/1s]

Comparing ‘survreg2.Rout’ to ‘survreg2.Rout.save’ ... OK

Running ‘survtest.R’ [0s/0s]

Comparing ‘survtest.Rout’ to ‘survtest.Rout.save’ ... OK

Running ‘testci.R’ [0s/0s]

Comparing ‘testci.Rout’ to ‘testci.Rout.save’ ... OK

Running ‘testci2.R’ [0s/0s]

Comparing ‘testci2.Rout’ to ‘testci2.Rout.save’ ... OK

Running ‘testnull.R’ [0s/0s]

Comparing ‘testnull.Rout’ to ‘testnull.Rout.save’ ... OK

Running ‘testreg.R’ [0s/0s]

Comparing ‘testreg.Rout’ to ‘testreg.Rout.save’ ... OK

Running ‘tiedtime.R’ [0s/0s]

Comparing ‘tiedtime.Rout’ to ‘tiedtime.Rout.save’ ... OK

Running ‘tt.R’ [6s/6s]

Comparing ‘tt.Rout’ to ‘tt.Rout.save’ ... OK

Running ‘turnbull.R’ [0s/0s]

Comparing ‘turnbull.Rout’ to ‘turnbull.Rout.save’ ... OK - checking for unstated dependencies in vignettes ... OK
- checking package vignettes in ‘inst/doc’ ... OK
- checking running R code from vignettes ... [10s/10s] OK
- checking re-building of vignette outputs ... [11s/12s] OK
- checking PDF version of manual ... OK