starting phase `set-SOURCE-DATE-EPOCH' phase `set-SOURCE-DATE-EPOCH' succeeded after 0.0 seconds starting phase `set-paths' environment variable `PATH' set to `/gnu/store/j3das66pbpfly7gxxb2051h73yj4wkab-r-minimal-4.2.1/bin:/gnu/store/99c25918hl9pihix8hparmc96q6zrpwy-tar-1.34/bin:/gnu/store/l0yga4lrwwf74rz7fb0dadglg27ajpsx-gzip-1.10/bin:/gnu/store/ihakfb51zdgjz3v9nkj0ja9zk9ng8xzl-bzip2-1.0.8/bin:/gnu/store/fk24dx8qz1b5smnc4ljfw25xn7yjps0q-xz-5.2.5/bin:/gnu/store/vl1b3nq6gijpzbl03zq92m5dwgs17nik-file-5.39/bin:/gnu/store/h0rx6y95zin61fp5wlyjly4g9j2hma18-diffutils-3.8/bin:/gnu/store/7j8j7m0kgb7kv2fc18qvrdj7gs3jc4mx-patch-2.7.6/bin:/gnu/store/x4yglk9pn2s2ixl1b4lj151bd2yvlgww-findutils-4.8.0/bin:/gnu/store/vzq0il5z2d6ksllb525m9xaqzv829g3k-gawk-5.1.0/bin:/gnu/store/cnwr7widbi6470kfyb13krx46kz5anmy-sed-4.8/bin:/gnu/store/bx47clwnxn51m7jdwfimz4lw2fh8g21v-grep-3.6/bin:/gnu/store/9a0cjh929maqvkxn3inv6jqbxn72fkx0-coreutils-8.32/bin:/gnu/store/dhx00nrv9r52f6xivg0xa4iihpl9awyk-make-4.3/bin:/gnu/store/7s2zlc4r9wqvlh9x2gqmzm4lnmbsdzmn-bash-minimal-5.1.8/bin:/gnu/store/4bzvr16pyax9224v9r72rqxswj9931sb-ld-wrapper-0/bin:/gnu/store/v4a7zw8w52v64kw5781ypa8gjwd098jz-binutils-2.37/bin:/gnu/store/v5xfd4vy1lvqikdl1rzs8aklgsnqwd26-gcc-10.3.0/bin:/gnu/store/0iapawfss4xnxls622g23qpk4mwb9ihp-glibc-2.33/bin:/gnu/store/0iapawfss4xnxls622g23qpk4mwb9ihp-glibc-2.33/sbin' environment variable `R_LIBS_SITE' set to `/gnu/store/4n3lm4anb2k4xwhdmzr9ra3q1w5lcx4y-r-matrix-1.4-1/site-library/:/gnu/store/h0n8f70hqc3xlyvnwadp1xw3gixcsbz6-r-lattice-0.20-45/site-library/' environment variable `BASH_LOADABLES_PATH' unset environment variable `C_INCLUDE_PATH' set to `/gnu/store/ihakfb51zdgjz3v9nkj0ja9zk9ng8xzl-bzip2-1.0.8/include:/gnu/store/fk24dx8qz1b5smnc4ljfw25xn7yjps0q-xz-5.2.5/include:/gnu/store/vl1b3nq6gijpzbl03zq92m5dwgs17nik-file-5.39/include:/gnu/store/vzq0il5z2d6ksllb525m9xaqzv829g3k-gawk-5.1.0/include:/gnu/store/dhx00nrv9r52f6xivg0xa4iihpl9awyk-make-4.3/include:/gnu/store/v4a7zw8w52v64kw5781ypa8gjwd098jz-binutils-2.37/include:/gnu/store/v5xfd4vy1lvqikdl1rzs8aklgsnqwd26-gcc-10.3.0/include:/gnu/store/0iapawfss4xnxls622g23qpk4mwb9ihp-glibc-2.33/include:/gnu/store/wsx4kz1gh6cpdhx393frhqknmswbggq8-linux-libre-headers-5.10.35/include' environment variable `CPLUS_INCLUDE_PATH' set to `/gnu/store/ihakfb51zdgjz3v9nkj0ja9zk9ng8xzl-bzip2-1.0.8/include:/gnu/store/fk24dx8qz1b5smnc4ljfw25xn7yjps0q-xz-5.2.5/include:/gnu/store/vl1b3nq6gijpzbl03zq92m5dwgs17nik-file-5.39/include:/gnu/store/vzq0il5z2d6ksllb525m9xaqzv829g3k-gawk-5.1.0/include:/gnu/store/dhx00nrv9r52f6xivg0xa4iihpl9awyk-make-4.3/include:/gnu/store/v4a7zw8w52v64kw5781ypa8gjwd098jz-binutils-2.37/include:/gnu/store/v5xfd4vy1lvqikdl1rzs8aklgsnqwd26-gcc-10.3.0/include/c++:/gnu/store/v5xfd4vy1lvqikdl1rzs8aklgsnqwd26-gcc-10.3.0/include:/gnu/store/0iapawfss4xnxls622g23qpk4mwb9ihp-glibc-2.33/include:/gnu/store/wsx4kz1gh6cpdhx393frhqknmswbggq8-linux-libre-headers-5.10.35/include' environment variable `LIBRARY_PATH' set to `/gnu/store/j3das66pbpfly7gxxb2051h73yj4wkab-r-minimal-4.2.1/lib:/gnu/store/ihakfb51zdgjz3v9nkj0ja9zk9ng8xzl-bzip2-1.0.8/lib:/gnu/store/fk24dx8qz1b5smnc4ljfw25xn7yjps0q-xz-5.2.5/lib:/gnu/store/vl1b3nq6gijpzbl03zq92m5dwgs17nik-file-5.39/lib:/gnu/store/vzq0il5z2d6ksllb525m9xaqzv829g3k-gawk-5.1.0/lib:/gnu/store/v4a7zw8w52v64kw5781ypa8gjwd098jz-binutils-2.37/lib:/gnu/store/0iapawfss4xnxls622g23qpk4mwb9ihp-glibc-2.33/lib:/gnu/store/1s4k8h3h1ka9za4yzg0dfjnlhab5k14p-glibc-2.33-static/lib:/gnu/store/6p5m4cv8psfzy5xn5yhvhmjl261wg34m-glibc-utf8-locales-2.33/lib' environment variable `GUIX_LOCPATH' set to `/gnu/store/6p5m4cv8psfzy5xn5yhvhmjl261wg34m-glibc-utf8-locales-2.33/lib/locale' phase `set-paths' succeeded after 0.0 seconds starting phase `install-locale' using 'en_US.utf8' locale for category "LC_ALL" phase `install-locale' succeeded after 0.0 seconds starting phase `unpack' survival/ survival/NAMESPACE survival/noweb/ survival/noweb/cnew2.Rnw survival/noweb/noweb.sty 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survival/R/frailty.gamma.R survival/R/print.summary.survreg.R survival/R/yates.R survival/R/print.summary.survfitms.R survival/R/survexp.cfit.R survival/R/residuals.coxph.penal.R survival/R/summary.coxph.R survival/R/survfitms.R survival/R/is.ratetable.R survival/R/coxph.R survival/R/anova.coxphlist.R survival/R/logLik.coxph.R survival/R/lines.aareg.R survival/R/survdiff.fit.R survival/R/nsk.R survival/R/pspline.R survival/R/print.survcheck.R survival/R/predict.survreg.penal.R survival/R/cluster.R survival/R/predict.coxphms.R survival/R/survobrien.R survival/R/print.survfit.R survival/R/print.aareg.R survival/R/summary.ratetable.R survival/R/survfitKM.R survival/R/survreg.distributions.R survival/R/residuals.coxph.R survival/R/survfit.matrix.R survival/R/frailty.R survival/R/print.ratetable.R survival/R/print.coxph.penal.R survival/R/survreg.control.R survival/R/coxsurvfit.R survival/R/summary.aareg.R survival/R/royston.R survival/R/print.survreg.penal.R survival/R/Surv.R survival/R/survdiff.R survival/R/summary.survexp.R survival/R/finegray.R survival/R/residuals.survfit.R survival/R/blogit.R survival/R/print.survreg.R survival/R/aareg.R survival/R/frailty.controlaic.R survival/R/tmerge.R survival/R/frailty.brent.R survival/R/frailty.controlgam.R survival/R/statefig.R survival/R/survfit.coxph.R survival/R/print.coxph.null.R survival/R/survfitTurnbull.R survival/R/survConcordance.R survival/R/pade.R survival/R/survexp.R survival/R/dsurvreg.R survival/R/lines.survfit.coxph.R survival/R/coxpenal.fit.R survival/R/clogit.R survival/R/quantile.survfit.R survival/R/survfit.R survival/R/survexp.fit.R survival/R/frailty.gammacon.R survival/R/parsecovar.R survival/R/survpenal.fit.R survival/R/survcallback.R survival/R/coxph.getdata.R survival/R/print.survexp.R survival/R/is.na.coxph.penalty.R survival/MD5 survival/inst/ survival/inst/doc/ survival/inst/doc/multi.pdf survival/inst/doc/other.Rnw survival/inst/doc/population.R survival/inst/doc/approximate.R survival/inst/doc/compete.Rnw survival/inst/doc/validate.pdf survival/inst/doc/concordance.pdf survival/inst/doc/discrim.Rnw survival/inst/doc/validate.R survival/inst/doc/compete.pdf survival/inst/doc/concordance.R survival/inst/doc/splines.R survival/inst/doc/tiedtimes.Rnw survival/inst/doc/splines.pdf survival/inst/doc/population.Rnw survival/inst/doc/survival.pdf survival/inst/doc/adjcurve.R survival/inst/doc/adjcurve.Rnw survival/inst/doc/timedep.pdf survival/inst/doc/adjcurve.pdf survival/inst/doc/timedep.R survival/inst/doc/survival.Rnw survival/inst/doc/compete.R survival/inst/doc/discrim.pdf survival/inst/doc/other.pdf survival/inst/doc/tiedtimes.pdf survival/inst/doc/splines.Rnw survival/inst/doc/approximate.pdf survival/inst/doc/population.pdf survival/inst/doc/approximate.Rnw survival/inst/doc/multi.Rnw survival/inst/doc/validate.Rnw survival/inst/doc/survival.R survival/inst/doc/tiedtimes.R survival/inst/doc/timedep.Rnw survival/inst/doc/discrim.R survival/inst/doc/concordance.Rnw survival/inst/COPYRIGHTS survival/inst/CITATION survival/inst/NEWS.Rd phase `unpack' succeeded after 0.1 seconds starting phase `patch-usr-bin-file' phase `patch-usr-bin-file' succeeded after 0.0 seconds starting phase `patch-source-shebangs' phase `patch-source-shebangs' succeeded after 0.1 seconds starting phase `patch-generated-file-shebangs' phase `patch-generated-file-shebangs' succeeded after 0.0 seconds starting phase `install' Warning message: In normalizePath("~") : path[1]="/homeless-shelter": No such file or directory Warning message: In normalizePath("~") : path[1]="/homeless-shelter": No such file or directory * installing *source* package ‘survival’ ... ** package ‘survival’ successfully unpacked and MD5 sums checked ** using staged installation ** libs gcc -I"/gnu/store/j3das66pbpfly7gxxb2051h73yj4wkab-r-minimal-4.2.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c agexact.c -o agexact.o gcc -I"/gnu/store/j3das66pbpfly7gxxb2051h73yj4wkab-r-minimal-4.2.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c agfit4.c -o agfit4.o gcc -I"/gnu/store/j3das66pbpfly7gxxb2051h73yj4wkab-r-minimal-4.2.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c agfit5.c -o agfit5.o gcc -I"/gnu/store/j3das66pbpfly7gxxb2051h73yj4wkab-r-minimal-4.2.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c agmart.c -o agmart.o gcc -I"/gnu/store/j3das66pbpfly7gxxb2051h73yj4wkab-r-minimal-4.2.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c agmart3.c -o agmart3.o gcc -I"/gnu/store/j3das66pbpfly7gxxb2051h73yj4wkab-r-minimal-4.2.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c agscore2.c -o agscore2.o gcc -I"/gnu/store/j3das66pbpfly7gxxb2051h73yj4wkab-r-minimal-4.2.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c agsurv3.c -o agsurv3.o gcc -I"/gnu/store/j3das66pbpfly7gxxb2051h73yj4wkab-r-minimal-4.2.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c agsurv4.c -o agsurv4.o gcc -I"/gnu/store/j3das66pbpfly7gxxb2051h73yj4wkab-r-minimal-4.2.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c agsurv5.c -o agsurv5.o gcc -I"/gnu/store/j3das66pbpfly7gxxb2051h73yj4wkab-r-minimal-4.2.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c cdecomp.c -o cdecomp.o gcc -I"/gnu/store/j3das66pbpfly7gxxb2051h73yj4wkab-r-minimal-4.2.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c chinv2.c -o chinv2.o gcc -I"/gnu/store/j3das66pbpfly7gxxb2051h73yj4wkab-r-minimal-4.2.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c chinv3.c -o chinv3.o gcc -I"/gnu/store/j3das66pbpfly7gxxb2051h73yj4wkab-r-minimal-4.2.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c cholesky2.c -o cholesky2.o gcc -I"/gnu/store/j3das66pbpfly7gxxb2051h73yj4wkab-r-minimal-4.2.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c cholesky3.c -o cholesky3.o gcc -I"/gnu/store/j3das66pbpfly7gxxb2051h73yj4wkab-r-minimal-4.2.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c cholesky5.c -o cholesky5.o gcc -I"/gnu/store/j3das66pbpfly7gxxb2051h73yj4wkab-r-minimal-4.2.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c chsolve2.c -o chsolve2.o gcc -I"/gnu/store/j3das66pbpfly7gxxb2051h73yj4wkab-r-minimal-4.2.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c chsolve3.c -o chsolve3.o gcc -I"/gnu/store/j3das66pbpfly7gxxb2051h73yj4wkab-r-minimal-4.2.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c chsolve5.c -o chsolve5.o gcc -I"/gnu/store/j3das66pbpfly7gxxb2051h73yj4wkab-r-minimal-4.2.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c collapse.c -o collapse.o gcc -I"/gnu/store/j3das66pbpfly7gxxb2051h73yj4wkab-r-minimal-4.2.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c concordance1.c -o concordance1.o gcc -I"/gnu/store/j3das66pbpfly7gxxb2051h73yj4wkab-r-minimal-4.2.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c concordance3.c -o concordance3.o gcc -I"/gnu/store/j3das66pbpfly7gxxb2051h73yj4wkab-r-minimal-4.2.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c concordance5.c -o concordance5.o gcc -I"/gnu/store/j3das66pbpfly7gxxb2051h73yj4wkab-r-minimal-4.2.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c cox_Rcallback.c -o cox_Rcallback.o gcc -I"/gnu/store/j3das66pbpfly7gxxb2051h73yj4wkab-r-minimal-4.2.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c coxcount1.c -o coxcount1.o gcc -I"/gnu/store/j3das66pbpfly7gxxb2051h73yj4wkab-r-minimal-4.2.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c coxdetail.c -o coxdetail.o gcc -I"/gnu/store/j3das66pbpfly7gxxb2051h73yj4wkab-r-minimal-4.2.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c coxexact.c -o coxexact.o gcc -I"/gnu/store/j3das66pbpfly7gxxb2051h73yj4wkab-r-minimal-4.2.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c coxfit5.c -o coxfit5.o gcc -I"/gnu/store/j3das66pbpfly7gxxb2051h73yj4wkab-r-minimal-4.2.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c coxfit6.c -o coxfit6.o gcc -I"/gnu/store/j3das66pbpfly7gxxb2051h73yj4wkab-r-minimal-4.2.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c coxmart.c -o coxmart.o gcc -I"/gnu/store/j3das66pbpfly7gxxb2051h73yj4wkab-r-minimal-4.2.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c coxmart2.c -o coxmart2.o gcc -I"/gnu/store/j3das66pbpfly7gxxb2051h73yj4wkab-r-minimal-4.2.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c coxph_wtest.c -o coxph_wtest.o gcc -I"/gnu/store/j3das66pbpfly7gxxb2051h73yj4wkab-r-minimal-4.2.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c coxsafe.c -o coxsafe.o gcc -I"/gnu/store/j3das66pbpfly7gxxb2051h73yj4wkab-r-minimal-4.2.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c coxscho.c -o coxscho.o gcc -I"/gnu/store/j3das66pbpfly7gxxb2051h73yj4wkab-r-minimal-4.2.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c coxscore2.c -o coxscore2.o gcc -I"/gnu/store/j3das66pbpfly7gxxb2051h73yj4wkab-r-minimal-4.2.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c coxsurv1.c -o coxsurv1.o gcc -I"/gnu/store/j3das66pbpfly7gxxb2051h73yj4wkab-r-minimal-4.2.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c coxsurv2.c -o coxsurv2.o gcc -I"/gnu/store/j3das66pbpfly7gxxb2051h73yj4wkab-r-minimal-4.2.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c dmatrix.c -o dmatrix.o gcc -I"/gnu/store/j3das66pbpfly7gxxb2051h73yj4wkab-r-minimal-4.2.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c doloop.c -o doloop.o gcc -I"/gnu/store/j3das66pbpfly7gxxb2051h73yj4wkab-r-minimal-4.2.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c finegray.c -o finegray.o gcc -I"/gnu/store/j3das66pbpfly7gxxb2051h73yj4wkab-r-minimal-4.2.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c gchol.c -o gchol.o gcc -I"/gnu/store/j3das66pbpfly7gxxb2051h73yj4wkab-r-minimal-4.2.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c init.c -o init.o gcc -I"/gnu/store/j3das66pbpfly7gxxb2051h73yj4wkab-r-minimal-4.2.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c multicheck.c -o multicheck.o gcc -I"/gnu/store/j3das66pbpfly7gxxb2051h73yj4wkab-r-minimal-4.2.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c norisk.c -o norisk.o gcc -I"/gnu/store/j3das66pbpfly7gxxb2051h73yj4wkab-r-minimal-4.2.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c pyears1.c -o pyears1.o gcc -I"/gnu/store/j3das66pbpfly7gxxb2051h73yj4wkab-r-minimal-4.2.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c pyears2.c -o pyears2.o gcc -I"/gnu/store/j3das66pbpfly7gxxb2051h73yj4wkab-r-minimal-4.2.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c pyears3b.c -o pyears3b.o gcc -I"/gnu/store/j3das66pbpfly7gxxb2051h73yj4wkab-r-minimal-4.2.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c pystep.c -o pystep.o gcc -I"/gnu/store/j3das66pbpfly7gxxb2051h73yj4wkab-r-minimal-4.2.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c survConcordance.c -o survConcordance.o gcc -I"/gnu/store/j3das66pbpfly7gxxb2051h73yj4wkab-r-minimal-4.2.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c survdiff2.c -o survdiff2.o gcc -I"/gnu/store/j3das66pbpfly7gxxb2051h73yj4wkab-r-minimal-4.2.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c survfit4.c -o survfit4.o gcc -I"/gnu/store/j3das66pbpfly7gxxb2051h73yj4wkab-r-minimal-4.2.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c survfitci.c -o survfitci.o gcc -I"/gnu/store/j3das66pbpfly7gxxb2051h73yj4wkab-r-minimal-4.2.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c survfitkm.c -o survfitkm.o gcc -I"/gnu/store/j3das66pbpfly7gxxb2051h73yj4wkab-r-minimal-4.2.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c survfitresid.c -o survfitresid.o gcc -I"/gnu/store/j3das66pbpfly7gxxb2051h73yj4wkab-r-minimal-4.2.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c survpenal.c -o survpenal.o gcc -I"/gnu/store/j3das66pbpfly7gxxb2051h73yj4wkab-r-minimal-4.2.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c survreg6.c -o survreg6.o gcc -I"/gnu/store/j3das66pbpfly7gxxb2051h73yj4wkab-r-minimal-4.2.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c survreg7.c -o survreg7.o gcc -I"/gnu/store/j3das66pbpfly7gxxb2051h73yj4wkab-r-minimal-4.2.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c survregc1.c -o survregc1.o gcc -I"/gnu/store/j3das66pbpfly7gxxb2051h73yj4wkab-r-minimal-4.2.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c survregc2.c -o survregc2.o gcc -I"/gnu/store/j3das66pbpfly7gxxb2051h73yj4wkab-r-minimal-4.2.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c survsplit.c -o survsplit.o gcc -I"/gnu/store/j3das66pbpfly7gxxb2051h73yj4wkab-r-minimal-4.2.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c tmerge.c -o tmerge.o gcc -I"/gnu/store/j3das66pbpfly7gxxb2051h73yj4wkab-r-minimal-4.2.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c zph1.c -o zph1.o gcc -I"/gnu/store/j3das66pbpfly7gxxb2051h73yj4wkab-r-minimal-4.2.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c zph2.c -o zph2.o gcc -shared -L/gnu/store/j3das66pbpfly7gxxb2051h73yj4wkab-r-minimal-4.2.1/lib/R/lib -L/usr/local/lib -o survival.so agexact.o agfit4.o agfit5.o agmart.o agmart3.o agscore2.o agsurv3.o agsurv4.o agsurv5.o cdecomp.o chinv2.o chinv3.o cholesky2.o cholesky3.o cholesky5.o chsolve2.o chsolve3.o chsolve5.o collapse.o concordance1.o concordance3.o concordance5.o cox_Rcallback.o coxcount1.o coxdetail.o coxexact.o coxfit5.o coxfit6.o coxmart.o coxmart2.o coxph_wtest.o coxsafe.o coxscho.o coxscore2.o coxsurv1.o coxsurv2.o dmatrix.o doloop.o finegray.o gchol.o init.o multicheck.o norisk.o pyears1.o pyears2.o pyears3b.o pystep.o survConcordance.o survdiff2.o survfit4.o survfitci.o survfitkm.o survfitresid.o survpenal.o survreg6.o survreg7.o survregc1.o survregc2.o survsplit.o tmerge.o zph1.o zph2.o -L/gnu/store/j3das66pbpfly7gxxb2051h73yj4wkab-r-minimal-4.2.1/lib/R/lib -lR installing to /gnu/store/f2dxjsgjlfdlzm8z2nxcnawcpqg4x3mn-r-survival-3.3-1/site-library/00LOCK-survival/00new/survival/libs ** R ** data *** moving datasets to lazyload DB ** inst ** tests ** byte-compile and prepare package for lazy loading Warning message: In normalizePath("~") : path[1]="/homeless-shelter": No such file or directory Warning message: In normalizePath("~") : path[1]="/homeless-shelter": No such file or directory ** help *** installing help indices *** copying figures ** building package indices Warning message: In normalizePath("~") : path[1]="/homeless-shelter": No such file or directory Warning message: In normalizePath("~") : path[1]="/homeless-shelter": No such file or directory ** installing vignettes ** testing if installed package can be loaded from temporary location Warning message: In normalizePath("~") : path[1]="/homeless-shelter": No such file or directory Warning message: In normalizePath("~") : path[1]="/homeless-shelter": No such file or directory ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location Warning message: In normalizePath("~") : path[1]="/homeless-shelter": No such file or directory Warning message: In normalizePath("~") : path[1]="/homeless-shelter": No such file or directory ** testing if installed package keeps a record of temporary installation path * DONE (survival) phase `install' succeeded after 64.3 seconds starting phase `check' Warning message: In normalizePath("~") : path[1]="/homeless-shelter": No such file or directory Warning message: In normalizePath("~") : path[1]="/homeless-shelter": No such file or directory Testing examples for package ‘survival’ comparing ‘survival-Ex.Rout’ to ‘survival-Ex.Rout.save’ ... NOTE Warning message: In normalizePath("~") : path[1]="/homeless-shelter": No such file or directory Warning message: In normalizePath("~") : path[1]="/homeless-shelter": No such file or directory Running specific tests for package ‘survival’ Running ‘aareg.R’ comparing ‘aareg.Rout’ to ‘aareg.Rout.save’ ... files differ in number of lines: 1,6d0 < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory Running ‘aareg2.R’ Running ‘anova.R’ comparing ‘anova.Rout’ to ‘anova.Rout.save’ ... files differ in number of lines: 1,6d0 < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory Running ‘bladder.R’ comparing ‘bladder.Rout’ to ‘bladder.Rout.save’ ... files differ in number of lines: 1,6d0 < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory Running ‘book1.R’ comparing ‘book1.Rout’ to ‘book1.Rout.save’ ... files differ in number of lines: 1,6d0 < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory Running ‘book2.R’ comparing ‘book2.Rout’ to ‘book2.Rout.save’ ... files differ in number of lines: 1,6d0 < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory Running ‘book3.R’ comparing ‘book3.Rout’ to ‘book3.Rout.save’ ... files differ in number of lines: 1,6d0 < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory Running ‘book4.R’ comparing ‘book4.Rout’ to ‘book4.Rout.save’ ... files differ in number of lines: 1,6d0 < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory Running ‘book5.R’ comparing ‘book5.Rout’ to ‘book5.Rout.save’ ... files differ in number of lines: 1,6d0 < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory Running ‘book6.R’ comparing ‘book6.Rout’ to ‘book6.Rout.save’ ... files differ in number of lines: 1,6d0 < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory Running ‘book7.R’ comparing ‘book7.Rout’ to ‘book7.Rout.save’ ... files differ in number of lines: 1,6d0 < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory Running ‘brier.R’ Running ‘cancer.R’ comparing ‘cancer.Rout’ to ‘cancer.Rout.save’ ... files differ in number of lines: 1,6d0 < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory Running ‘checkSurv2.R’ comparing ‘checkSurv2.Rout’ to ‘checkSurv2.Rout.save’ ... files differ in number of lines: 1,6d0 < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory Running ‘clogit.R’ comparing ‘clogit.Rout’ to ‘clogit.Rout.save’ ... files differ in number of lines: 1,6d0 < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory Running ‘concordance.R’ comparing ‘concordance.Rout’ to ‘concordance.Rout.save’ ... files differ in number of lines: 1,6d0 < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory Running ‘concordance2.R’ comparing ‘concordance2.Rout’ to ‘concordance2.Rout.save’ ... files differ in number of lines: 1,6d0 < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory Running ‘concordance3.R’ comparing ‘concordance3.Rout’ to ‘concordance3.Rout.save’ ... files differ in number of lines: 1,6d0 < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory Running ‘counting.R’ comparing ‘counting.Rout’ to ‘counting.Rout.save’ ... files differ in number of lines: 1,6d0 < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory Running ‘coxsurv.R’ comparing ‘coxsurv.Rout’ to ‘coxsurv.Rout.save’ ... files differ in number of lines: 1,6d0 < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory Running ‘coxsurv2.R’ comparing ‘coxsurv2.Rout’ to ‘coxsurv2.Rout.save’ ... files differ in number of lines: 1,6d0 < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory Running ‘coxsurv3.R’ comparing ‘coxsurv3.Rout’ to ‘coxsurv3.Rout.save’ ... files differ in number of lines: 1,6d0 < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory Running ‘coxsurv4.R’ comparing ‘coxsurv4.Rout’ to ‘coxsurv4.Rout.save’ ... files differ in number of lines: 1,6d0 < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory Running ‘coxsurv5.R’ comparing ‘coxsurv5.Rout’ to ‘coxsurv5.Rout.save’ ... files differ in number of lines: 1,6d0 < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory Running ‘detail.R’ comparing ‘detail.Rout’ to ‘detail.Rout.save’ ... files differ in number of lines: 1,6d0 < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory Running ‘difftest.R’ comparing ‘difftest.Rout’ to ‘difftest.Rout.save’ ... files differ in number of lines: 1,6d0 < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory Running ‘doaml.R’ comparing ‘doaml.Rout’ to ‘doaml.Rout.save’ ... files differ in number of lines: 1,6d0 < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory Running ‘doweight.R’ comparing ‘doweight.Rout’ to ‘doweight.Rout.save’ ... files differ in number of lines: 1,6d0 < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory Running ‘expected.R’ comparing ‘expected.Rout’ to ‘expected.Rout.save’ ... files differ in number of lines: 1,6d0 < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory Running ‘expected2.R’ comparing ‘expected2.Rout’ to ‘expected2.Rout.save’ ... files differ in number of lines: 1,6d0 < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory Running ‘factor.R’ comparing ‘factor.Rout’ to ‘factor.Rout.save’ ... files differ in number of lines: 1,6d0 < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory Running ‘factor2.R’ comparing ‘factor2.Rout’ to ‘factor2.Rout.save’ ... files differ in number of lines: 1,6d0 < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory Running ‘finegray.R’ comparing ‘finegray.Rout’ to ‘finegray.Rout.save’ ... files differ in number of lines: 1,6d0 < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory Running ‘fr_cancer.R’ comparing ‘fr_cancer.Rout’ to ‘fr_cancer.Rout.save’ ... files differ in number of lines: 1,6d0 < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory Running ‘fr_kidney.R’ comparing ‘fr_kidney.Rout’ to ‘fr_kidney.Rout.save’ ... files differ in number of lines: 1,6d0 < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory Running ‘fr_lung.R’ comparing ‘fr_lung.Rout’ to ‘fr_lung.Rout.save’ ... files differ in number of lines: 1,6d0 < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory Running ‘fr_ovarian.R’ comparing ‘fr_ovarian.Rout’ to ‘fr_ovarian.Rout.save’ ... files differ in number of lines: 1,6d0 < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory Running ‘fr_rat1.R’ comparing ‘fr_rat1.Rout’ to ‘fr_rat1.Rout.save’ ... files differ in number of lines: 1,6d0 < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory Running ‘fr_resid.R’ comparing ‘fr_resid.Rout’ to ‘fr_resid.Rout.save’ ... files differ in number of lines: 1,6d0 < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory Running ‘fr_simple.R’ comparing ‘fr_simple.Rout’ to ‘fr_simple.Rout.save’ ... files differ in number of lines: 1,6d0 < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory Running ‘frailty.R’ comparing ‘frailty.Rout’ to ‘frailty.Rout.save’ ... files differ in number of lines: 1,6d0 < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory Running ‘frank.R’ comparing ‘frank.Rout’ to ‘frank.Rout.save’ ... files differ in number of lines: 1,6d0 < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory Running ‘infcox.R’ comparing ‘infcox.Rout’ to ‘infcox.Rout.save’ ... files differ in number of lines: 1,6d0 < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory Running ‘jasa.R’ comparing ‘jasa.Rout’ to ‘jasa.Rout.save’ ... files differ in number of lines: 1,6d0 < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory Running ‘model.matrix.R’ comparing ‘model.matrix.Rout’ to ‘model.matrix.Rout.save’ ... files differ in number of lines: 1,6d0 < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory Running ‘mstate.R’ comparing ‘mstate.Rout’ to ‘mstate.Rout.save’ ... files differ in number of lines: 1,6d0 < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory Running ‘mstrata.R’ comparing ‘mstrata.Rout’ to ‘mstrata.Rout.save’ ... files differ in number of lines: 1,6d0 < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory Running ‘multi2.R’ comparing ‘multi2.Rout’ to ‘multi2.Rout.save’ ... files differ in number of lines: 1,6d0 < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory 55c49 < [1] "Component "trt": 'current' is not a factor" --- > [1] "Component \"trt\": 'current' is not a factor" Running ‘multistate.R’ comparing ‘multistate.Rout’ to ‘multistate.Rout.save’ ... files differ in number of lines: 1,6d0 < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory Running ‘neardate.R’ comparing ‘neardate.Rout’ to ‘neardate.Rout.save’ ... files differ in number of lines: 1,6d0 < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory Running ‘nested.R’ comparing ‘nested.Rout’ to ‘nested.Rout.save’ ... files differ in number of lines: 1,6d0 < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory Running ‘nsk.R’ comparing ‘nsk.Rout’ to ‘nsk.Rout.save’ ... files differ in number of lines: 1,6d0 < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory Running ‘ovarian.R’ comparing ‘ovarian.Rout’ to ‘ovarian.Rout.save’ ... files differ in number of lines: 1,6d0 < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory Running ‘overlap.R’ comparing ‘overlap.Rout’ to ‘overlap.Rout.save’ ... files differ in number of lines: 1,6d0 < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory Running ‘prednew.R’ comparing ‘prednew.Rout’ to ‘prednew.Rout.save’ ... files differ in number of lines: 1,6d0 < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory Running ‘pseudo.R’ comparing ‘pseudo.Rout’ to ‘pseudo.Rout.save’ ... files differ in number of lines: 1,6d0 < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory Running ‘pspline.R’ comparing ‘pspline.Rout’ to ‘pspline.Rout.save’ ... files differ in number of lines: 1,6d0 < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory Running ‘pyear.R’ comparing ‘pyear.Rout’ to ‘pyear.Rout.save’ ... files differ in number of lines: 1,6d0 < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory Running ‘quantile.R’ comparing ‘quantile.Rout’ to ‘quantile.Rout.save’ ... files differ in number of lines: 1,6d0 < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory Running ‘r_lung.R’ comparing ‘r_lung.Rout’ to ‘r_lung.Rout.save’ ... files differ in number of lines: 1,6d0 < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory Running ‘r_resid.R’ comparing ‘r_resid.Rout’ to ‘r_resid.Rout.save’ ... files differ in number of lines: 1,6d0 < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory Running ‘r_sas.R’ comparing ‘r_sas.Rout’ to ‘r_sas.Rout.save’ ... files differ in number of lines: 1,6d0 < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory Running ‘r_scale.R’ comparing ‘r_scale.Rout’ to ‘r_scale.Rout.save’ ... files differ in number of lines: 1,6d0 < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory Running ‘r_stanford.R’ comparing ‘r_stanford.Rout’ to ‘r_stanford.Rout.save’ ... files differ in number of lines: 1,6d0 < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory Running ‘r_strata.R’ comparing ‘r_strata.Rout’ to ‘r_strata.Rout.save’ ... files differ in number of lines: 1,6d0 < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory Running ‘r_tdist.R’ comparing ‘r_tdist.Rout’ to ‘r_tdist.Rout.save’ ... files differ in number of lines: 1,6d0 < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory Running ‘r_user.R’ comparing ‘r_user.Rout’ to ‘r_user.Rout.save’ ... files differ in number of lines: 1,6d0 < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory Running ‘ratetable.R’ comparing ‘ratetable.Rout’ to ‘ratetable.Rout.save’ ... files differ in number of lines: 1,6d0 < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory Running ‘residsf.R’ comparing ‘residsf.Rout’ to ‘residsf.Rout.save’ ... files differ in number of lines: 1,6d0 < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory Running ‘royston.R’ comparing ‘royston.Rout’ to ‘royston.Rout.save’ ... files differ in number of lines: 1,6d0 < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory Running ‘rttright.R’ comparing ‘rttright.Rout’ to ‘rttright.Rout.save’ ... files differ in number of lines: 1,6d0 < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory Running ‘singtest.R’ comparing ‘singtest.Rout’ to ‘singtest.Rout.save’ ... files differ in number of lines: 1,6d0 < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory Running ‘strata2.R’ comparing ‘strata2.Rout’ to ‘strata2.Rout.save’ ... files differ in number of lines: 1,6d0 < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory Running ‘stratatest.R’ comparing ‘stratatest.Rout’ to ‘stratatest.Rout.save’ ... files differ in number of lines: 1,6d0 < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory Running ‘summary_survfit.R’ comparing ‘summary_survfit.Rout’ to ‘summary_survfit.Rout.save’ ... files differ in number of lines: 1,6d0 < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory Running ‘surv.R’ comparing ‘surv.Rout’ to ‘surv.Rout.save’ ... files differ in number of lines: 1,6d0 < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory Running ‘survcheck.R’ comparing ‘survcheck.Rout’ to ‘survcheck.Rout.save’ ... files differ in number of lines: 1,6d0 < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory Running ‘survfit1.R’ comparing ‘survfit1.Rout’ to ‘survfit1.Rout.save’ ... files differ in number of lines: 1,6d0 < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory Running ‘survfit2.R’ comparing ‘survfit2.Rout’ to ‘survfit2.Rout.save’ ... files differ in number of lines: 1,6d0 < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory Running ‘survreg1.R’ comparing ‘survreg1.Rout’ to ‘survreg1.Rout.save’ ... files differ in number of lines: 1,6d0 < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory Running ‘survreg2.R’ comparing ‘survreg2.Rout’ to ‘survreg2.Rout.save’ ... files differ in number of lines: 1,6d0 < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory Running ‘survSplit.R’ comparing ‘survSplit.Rout’ to ‘survSplit.Rout.save’ ... files differ in number of lines: 1,6d0 < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory Running ‘survtest.R’ comparing ‘survtest.Rout’ to ‘survtest.Rout.save’ ... files differ in number of lines: 1,6d0 < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory Running ‘testci.R’ comparing ‘testci.Rout’ to ‘testci.Rout.save’ ... files differ in number of lines: 1,6d0 < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory Running ‘testci2.R’ comparing ‘testci2.Rout’ to ‘testci2.Rout.save’ ... files differ in number of lines: 1,6d0 < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory Running ‘testnull.R’ comparing ‘testnull.Rout’ to ‘testnull.Rout.save’ ... files differ in number of lines: 1,6d0 < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory Running ‘testreg.R’ comparing ‘testreg.Rout’ to ‘testreg.Rout.save’ ... files differ in number of lines: 1,6d0 < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory Running ‘tiedtime.R’ comparing ‘tiedtime.Rout’ to ‘tiedtime.Rout.save’ ... files differ in number of lines: 1,6d0 < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory Running ‘tmerge.R’ comparing ‘tmerge.Rout’ to ‘tmerge.Rout.save’ ... files differ in number of lines: 1,6d0 < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory Running ‘tmerge2.R’ comparing ‘tmerge2.Rout’ to ‘tmerge2.Rout.save’ ... files differ in number of lines: 1,6d0 < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory Running ‘tmerge3.R’ comparing ‘tmerge3.Rout’ to ‘tmerge3.Rout.save’ ... files differ in number of lines: 1,6d0 < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory Running ‘tt.R’ comparing ‘tt.Rout’ to ‘tt.Rout.save’ ... files differ in number of lines: 1,6d0 < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory Running ‘turnbull.R’ comparing ‘turnbull.Rout’ to ‘turnbull.Rout.save’ ... files differ in number of lines: 1,6d0 < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory Running ‘update.R’ comparing ‘update.Rout’ to ‘update.Rout.save’ ... files differ in number of lines: 1,6d0 < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory Running ‘yates0.R’ comparing ‘yates0.Rout’ to ‘yates0.Rout.save’ ... files differ in number of lines: 1,6d0 < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory 57c51 < [1] "Attributes: < Component "dimnames": Component 2: 1 string mismatch >" --- > [1] "Attributes: < Component \"dimnames\": Component 2: 1 string mismatch >" Running ‘yates1.R’ comparing ‘yates1.Rout’ to ‘yates1.Rout.save’ ... files differ in number of lines: 1,6d0 < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory Running ‘yates2.R’ Running ‘zph.R’ comparing ‘zph.Rout’ to ‘zph.Rout.save’ ... files differ in number of lines: 1,6d0 < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory < Warning message: < In normalizePath("~") : < path[1]="/homeless-shelter": No such file or directory Running vignettes for package ‘survival’ Running ‘adjcurve.Rnw’ Running ‘approximate.Rnw’ Running ‘compete.Rnw’ Running ‘concordance.Rnw’ Running ‘discrim.Rnw’ Running ‘multi.Rnw’ Running ‘other.Rnw’ Running ‘population.Rnw’ Running ‘splines.Rnw’ Running ‘survival.Rnw’ Running ‘tiedtimes.Rnw’ Running ‘timedep.Rnw’ Running ‘validate.Rnw’ Warning messages: 1: In coxph(Surv(tstart, time, status) ~ trt + celltype + karno + time:karno, : a variable appears on both the left and right sides of the formula 2: 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 3: In tmerge(jasa, tdata, id = subject, death = event(futime, fustat), : replacement of variable 'transplant' 4: In coxph.fit(X, Y, istrat, offset, init, control, weights = weights, : Ran out of iterations and did not converge 5: In coxph.fit(X, Y, istrat, offset, init, control, weights = weights, : Ran out of iterations and did not converge 6: In coxph(Surv(tstart, time, status) ~ trt + celltype + karno + time:karno, : a variable appears on both the left and right sides of the formula 7: 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 8: In tmerge(jasa, tdata, id = subject, death = event(futime, fustat), : replacement of variable 'transplant' 9: In coxph.fit(X, Y, istrat, offset, init, control, weights = weights, : Ran out of iterations and did not converge 10: In coxph.fit(X, Y, istrat, offset, init, control, weights = weights, : Ran out of iterations and did not converge phase `check' succeeded after 387.2 seconds starting phase `patch-shebangs' phase `patch-shebangs' succeeded after 0.0 seconds starting phase `strip' phase `strip' succeeded after 0.0 seconds starting phase `validate-runpath' phase `validate-runpath' succeeded after 0.0 seconds starting phase `validate-documentation-location' phase `validate-documentation-location' succeeded after 0.0 seconds starting phase `delete-info-dir-file' phase `delete-info-dir-file' succeeded after 0.0 seconds starting phase `patch-dot-desktop-files' phase `patch-dot-desktop-files' succeeded after 0.0 seconds starting phase `make-dynamic-linker-cache' phase `make-dynamic-linker-cache' succeeded after 0.0 seconds starting phase `install-license-files' installing 0 license files from '.' phase `install-license-files' succeeded after 0.0 seconds starting phase `reset-gzip-timestamps' phase `reset-gzip-timestamps' succeeded after 0.0 seconds starting phase `compress-documentation' phase `compress-documentation' succeeded after 0.0 seconds