printf ' ' | fink --no-use-binary-dist --yes --build-as-nobody rebuild cran-survival-r30 2>&1 The package 'cran-survival-r30' will be built without being installed. Reading build dependency for cran-survival-r30-2.37-7-2... Reading dependency for cran-survival-r30-2.37-7-2... Reading build conflict for cran-survival-r30-2.37-7-2... The package 'r-base30-dev' will be installed. Reading dependency for r-base30-dev-3.0.3-8... Reading runtime dependency for r-base30-dev-3.0.3-8... The following package will be rebuilt: cran-survival-r30 The following additional package will be installed: r-base30-dev Do you want to continue? [Y/n] (assuming default) Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/dists/stable/main/binary-darwin-x86_64/sci/r-base30-dev_3.0.3-8_darwin-x86_64.deb Selecting previously deselected package r-base30-dev. dpkg: considering removing r-base31-dev in favour of r-base30-dev ... dpkg: yes, will remove r-base31-dev in favour of r-base30-dev. (Reading database ... 11542 files and directories currently installed.) Unpacking r-base30-dev (from .../r-base30-dev_3.0.3-8_darwin-x86_64.deb) ... Setting up r-base30-dev (3.0.3-8) ... Setting runtime build-lock... dpkg-deb -b /sw/build.build/root-fink-buildlock-cran-survival-r30-2.37-7-2 /sw/build.build dpkg-deb: building package `fink-buildlock-cran-survival-r30-2.37-7-2' in `/sw/build.build/fink-buildlock-cran-survival-r30-2.37-7-2_2014.07.27-08.56.00_darwin-x86_64.deb'. Installing build-lock package... /sw/bin/dpkg-lockwait -i /sw/build.build/fink-buildlock-cran-survival-r30-2.37-7-2_2014.07.27-08.56.00_darwin-x86_64.deb Selecting previously deselected package fink-buildlock-cran-survival-r30-2.37-7-2. (Reading database ... 11540 files and directories currently installed.) Unpacking fink-buildlock-cran-survival-r30-2.37-7-2 (from .../fink-buildlock-cran-survival-r30-2.37-7-2_2014.07.27-08.56.00_darwin-x86_64.deb) ... Setting up fink-buildlock-cran-survival-r30-2.37-7-2 (2014.07.27-08.56.00) ... sudo -u fink-bld [ENV] sh -c /tmp/fink.DYtAZ env LANG=C LC_ALL=C /sw/bin/tar --no-same-owner --no-same-permissions -xvf /sw/src/survival_2.37-7.tar.gz survival/ survival/inst/ survival/inst/CITATION survival/inst/NEWS.Rd survival/inst/COPYRIGHTS survival/inst/doc/ survival/inst/doc/adjcurve.Rnw survival/inst/doc/tests.pdf survival/inst/doc/timedep.R survival/inst/doc/adjcurve.pdf survival/inst/doc/validate.pdf survival/inst/doc/tests.Rnw survival/inst/doc/adjcurve.R survival/inst/doc/timedep.Rnw survival/inst/doc/timedep.pdf survival/inst/doc/sourcecode.pdf survival/inst/doc/tests.R survival/tests/ survival/tests/singtest.Rout.save survival/tests/anova.R survival/tests/model.matrix.Rout.save survival/tests/expected.Rout.save survival/tests/factor2.Rout.save survival/tests/strata2.Rout.save survival/tests/r_capacitor.R survival/tests/fr_cancer.Rout.save survival/tests/data.rat2 survival/tests/quantile.R survival/tests/fr_ovarian.Rout.save survival/tests/difftest.Rout.save survival/tests/turnbull.Rout.save survival/tests/aareg.R survival/tests/jasa.R survival/tests/model.matrix.R survival/tests/fr_simple.R survival/tests/difftest.R survival/tests/ovarian.R survival/tests/quantile.Rout.save survival/tests/cancer.Rout.save survival/tests/r_peterson.R survival/tests/rounding.Rout.save survival/tests/r_capacitor.Rout.save survival/tests/summary_survfit.R survival/tests/data.interval survival/tests/testnull.Rout.save survival/tests/bladder.R survival/tests/stratatest.Rout.save survival/tests/gray1.rda survival/tests/strata2.R survival/tests/rounding.R survival/tests/r_tdist.R survival/tests/frank.R survival/tests/expected2.R survival/tests/concordance.R survival/tests/book4.R survival/tests/turnbull.R survival/tests/coxsurv4.Rout.save survival/tests/r_strata.Rout.save survival/tests/r_strata.R survival/tests/book4.Rout.save survival/tests/r_tdist.Rout.save survival/tests/jasa.Rout.save survival/tests/book6.R survival/tests/data.motor survival/tests/fr_resid.R survival/tests/testci.R survival/tests/coxsurv.Rout.save survival/tests/r_user.Rout.save survival/tests/tiedtime.R survival/tests/r_sas.Rout.save survival/tests/r_resid.R survival/tests/fr_lung.R survival/tests/pspline.R survival/tests/book6.Rout.save survival/tests/anova.Rout.save survival/tests/testci2.Rout.save survival/tests/prednew.R survival/tests/survreg2.Rout.save survival/tests/survfit2.Rout.save survival/tests/fr_rat1.Rout.save survival/tests/survreg2.R survival/tests/book3.R survival/tests/book1.Rout.save survival/tests/nested.R survival/tests/book1.R survival/tests/fr_kidney.R survival/tests/r_sas.R survival/tests/fr_ovarian.R survival/tests/survtest.R survival/tests/mrtest.R survival/tests/r_stanford.Rout.save survival/tests/clogit.R survival/tests/factor.R survival/tests/book7.Rout.save survival/tests/r_donnell.R survival/tests/book2.Rout.save survival/tests/testreg.Rout.save survival/tests/doaml.R survival/tests/coxsurv2.R survival/tests/r_donnell.Rout.save survival/tests/prednew.Rout.save survival/tests/r_user.R survival/tests/ratetable.Rout.save survival/tests/book2.R survival/tests/r_scale.R survival/tests/tt.Rout.save survival/tests/ovarian.Rout.save survival/tests/fr_kidney.Rout.save survival/tests/singtest.R survival/tests/data.cracks survival/tests/testci2.R survival/tests/fr_rat2.Rout.save survival/tests/testnull.R survival/tests/fr_cancer.R survival/tests/coxsurv4.R survival/tests/coxsurv3.Rout.save survival/tests/data.valve survival/tests/survtest.Rout.save survival/tests/factor2.R survival/tests/ratetable.R survival/tests/data.donnell survival/tests/nested.Rout.save survival/tests/fr_simple.Rout.save survival/tests/r_scale.Rout.save survival/tests/fr_rat1.R survival/tests/book5.Rout.save survival/tests/r_lung.R survival/tests/detail.Rout.save survival/tests/expected2.Rout.save survival/tests/bladder.Rout.save survival/tests/infcox.Rout.save survival/tests/data.capacitor survival/tests/ties.rda survival/tests/coxsurv2.Rout.save survival/tests/surv.Rout.save survival/tests/doaml.Rout.save survival/tests/r_resid.Rout.save survival/tests/pspline.Rout.save survival/tests/clogit.Rout.save survival/tests/summary_survfit.Rout.save survival/tests/book3.Rout.save survival/tests/frank.Rout.save survival/tests/r_stanford.R survival/tests/infcox.R survival/tests/cancer.R survival/tests/detail.R survival/tests/fr_rat2.R survival/tests/data.peterson survival/tests/frailty.Rout.save survival/tests/counting.R survival/tests/testci.Rout.save survival/tests/data.fluid survival/tests/r_lung.Rout.save survival/tests/r_peterson.Rout.save survival/tests/mrtest.Rout.save survival/tests/aareg.Rout.save survival/tests/surv.R survival/tests/factor.Rout.save survival/tests/pyear.R survival/tests/fr_resid.Rout.save survival/tests/frailty.R survival/tests/counting.Rout.save survival/tests/tt.R survival/tests/fr_lung.Rout.save survival/tests/testreg.R survival/tests/book5.R survival/tests/data.smoke survival/tests/concordance.Rout.save survival/tests/pyear.Rout.save survival/tests/stratatest.R survival/tests/survfit2.R survival/tests/doweight.R survival/tests/tiedtime.Rout.save survival/tests/coxsurv3.R survival/tests/r_sas.R.orig survival/tests/book7.R survival/tests/data.turbine survival/tests/coxsurv.R survival/tests/doweight.Rout.save survival/tests/expected.R survival/src/ survival/src/pystep.c survival/src/survfit4.c survival/src/coxcount1.c survival/src/chinv2.c survival/src/pyears3b.c survival/src/msurv.c survival/src/survS.h survival/src/chsolve2.c survival/src/survproto.h survival/src/agmart2.c survival/src/survregc2.c survival/src/coxexact.c survival/src/survdiff2.c survival/src/pyears1.c survival/src/coxmart2.c survival/src/coxfit5.c survival/src/agfit4.c survival/src/survreg6.c survival/src/agscore.c survival/src/survpenal.c survival/src/concordance1.c survival/src/coxmart.c survival/src/agsurv4.c survival/src/cox_Rcallback.c survival/src/coxfit6.c survival/src/cholesky2.c survival/src/agsurv5.c survival/src/chsolve3.c survival/src/coxph_wtest.c survival/src/pyears2.c survival/src/coxdetail.c survival/src/agsurv3.c survival/src/coxscho.c survival/src/agexact.c survival/src/survregc1.c survival/src/doloop.c survival/src/survfitci.c survival/src/init.c survival/src/survConcordance.c survival/src/agfit5.c survival/src/cholesky3.c survival/src/coxscore.c survival/src/coxsafe.c survival/src/dmatrix.c survival/src/chinv3.c survival/src/agmart.c survival/src/survreg7.c survival/NAMESPACE survival/data/ survival/data/rats.rda survival/data/ovarian.rda survival/data/flchain.rda survival/data/pbc.rda survival/data/veteran.rda survival/data/leukemia.rda survival/data/bladder.rda survival/data/survexp.rda survival/data/cgd.rda survival/data/mgus.rda survival/data/nwtco.rda survival/data/logan.rda survival/data/datalist survival/data/cancer.rda survival/data/tobin.txt.gz survival/data/lung.rda survival/data/stanford2.rda survival/data/kidney.rda survival/data/heart.rda survival/data/colon.rda survival/data/uspop2.rda survival/R/ survival/R/survreg.control.S survival/R/print.summary.coxph.S survival/R/print.coxph.penal.S survival/R/survreg.old.S survival/R/summary.coxph.S survival/R/summary.pyears.S survival/R/residuals.survreg.penal.S survival/R/frailty.gaussian.S survival/R/survpenal.fit.S survival/R/tcut.S survival/R/print.coxph.S survival/R/survSplit.R survival/R/print.aareg.S survival/R/plot.aareg.S survival/R/print.survexp.S survival/R/cox.zph.S survival/R/survregDtest.S survival/R/survdiff.S survival/R/coxph.fit.S survival/R/coxph.control.S survival/R/frailty.controlgam.S survival/R/anova.survreglist.S survival/R/survfitms.R survival/R/predict.survreg.S survival/R/print.survfit.S survival/R/predict.coxph.R survival/R/anova.coxmelist.R survival/R/model.matrix.coxph.R survival/R/print.survreg.S survival/R/coxph.detail.S survival/R/residuals.coxph.null.S survival/R/model.frame.survreg.R survival/R/survreg.S survival/R/summary.coxph.penal.S survival/R/frailty.brent.S survival/R/plot.cox.zph.S survival/R/survexp.fit.S survival/R/coxph.rvar.S survival/R/print.coxph.null.S survival/R/ratetableDate.S survival/R/anova.survreg.S survival/R/survexp.cfit.R survival/R/frailty.t.S survival/R/residuals.coxph.S survival/R/basehaz.S survival/R/is.ratetable.S survival/R/survobrien.S survival/R/print.ratetable.S survival/R/summary.ratetable.S survival/R/agsurv.R survival/R/untangle.specials.S survival/R/match.ratetable.S survival/R/ridge.S survival/R/clogit.R survival/R/survexp.R survival/R/pyears.R survival/R/summary.survreg.S survival/R/coxph.wtest.S survival/R/survcallback.S survival/R/Surv.S survival/R/is.na.coxph.penalty.S survival/R/pspline.S survival/R/survfitCI.R survival/R/quantile.survfit.R survival/R/ratetable.S survival/R/cluster.S survival/R/aareg.taper.S survival/R/coxexact.fit.R survival/R/lines.survexp.R survival/R/plot.survfit.R survival/R/survfitKM.S survival/R/survConcordance.R survival/R/frailty.controlaic.S survival/R/strata.S survival/R/survfit.R survival/R/predict.survreg.penal.S survival/R/coxph.getdata.S survival/R/frailty.controlgauss.S survival/R/print.survreg.penal.S survival/R/survreg.fit.S survival/R/survreg.distributions.S survival/R/summary.aareg.S survival/R/predict.coxph.penal.S survival/R/frailty.gamma.S survival/R/survConcordance.fit.R survival/R/print.survdiff.S survival/R/lines.survfit.coxph.S survival/R/coxph.R survival/R/agexact.fit.S survival/R/print.summary.survexp.R survival/R/summary.survexp.R survival/R/survfitcoxph.fit.R survival/R/frailty.S survival/R/residuals.survreg.S survival/R/format.Surv.S survival/R/survfit.formula.S survival/R/logLik.coxph.R survival/R/lines.aareg.S survival/R/print.summary.survfitms.S survival/R/aareg.S survival/R/cch.R survival/R/frailty.controldf.S survival/R/agreg.fit.R survival/R/print.summary.survreg.S survival/R/coxpenal.df.S survival/R/firstlib.R survival/R/survfitTurnbull.S survival/R/survdiff.fit.S survival/R/print.summary.coxph.penal.S survival/R/print.summary.survfit.S survival/R/dsurvreg.S survival/R/anova.coxphlist.S survival/R/survfit.coxph.R survival/R/frailty.gammacon.S survival/R/anova.coxph.S survival/R/xtras.R survival/R/print.cox.zph.S survival/R/labels.survreg.S survival/R/coxpenal.fit.R survival/R/residuals.coxph.penal.S survival/R/attrassign.R survival/vignettes/ survival/vignettes/adjcurve.Rnw survival/vignettes/raheart.rda survival/vignettes/refer.bib survival/vignettes/tests.Rnw survival/vignettes/timedep.Rnw survival/MD5 survival/build/ survival/build/vignette.rds survival/DESCRIPTION survival/man/ survival/man/survexp.Rd survival/man/survreg.control.Rd survival/man/lines.survfit.Rd survival/man/print.summary.survfit.Rd survival/man/colon.Rd survival/man/survreg.distributions.Rd survival/man/attrassign.Rd survival/man/rats2.Rd survival/man/rats.Rd survival/man/survreg.Rd survival/man/uspop2.Rd survival/man/survfitcoxph.fit.Rd survival/man/ratetable.Rd survival/man/residuals.survreg.Rd survival/man/print.survfit.Rd survival/man/summary.survexp.Rd survival/man/survdiff.Rd survival/man/bladder.Rd survival/man/pbcseq.Rd survival/man/frailty.Rd survival/man/print.summary.coxph.Rd survival/man/cluster.Rd survival/man/tobin.Rd survival/man/is.ratetable.Rd survival/man/survexp.fit.Rd survival/man/ovarian.Rd survival/man/anova.coxph.Rd survival/man/summary.survfit.Rd survival/man/quantile.survfit.Rd survival/man/flchain.Rd survival/man/survival-internal.Rd survival/man/survfit.formula.Rd survival/man/ridge.Rd survival/man/survregDtest.Rd survival/man/predict.survreg.Rd survival/man/survConcordance.Rd survival/man/model.frame.coxph.Rd survival/man/coxph.detail.Rd survival/man/agreg.fit.Rd survival/man/strata.Rd survival/man/stanford2.Rd survival/man/lung.Rd survival/man/survreg.object.Rd survival/man/untangle.specials.Rd survival/man/summary.aareg.Rd survival/man/survexp.us.Rd survival/man/ratetableDate.Rd survival/man/predict.coxph.Rd survival/man/cgd.Rd survival/man/plot.survfit.Rd survival/man/summary.coxph.Rd survival/man/mgus.Rd survival/man/kidney.Rd survival/man/survfit.object.Rd survival/man/pspline.Rd survival/man/pyears.Rd survival/man/nwtco.Rd survival/man/survfit.Rd survival/man/model.matrix.coxph.Rd survival/man/plot.aareg.Rd survival/man/coxph.Rd survival/man/survfit.coxph.Rd survival/man/residuals.coxph.Rd survival/man/coxph.control.Rd survival/man/cox.zph.Rd survival/man/print.summary.survexp.Rd survival/man/tcut.Rd survival/man/aml.Rd survival/man/pbc.Rd survival/man/Surv.Rd survival/man/coxph.object.Rd survival/man/veteran.Rd survival/man/coxph.wtest.Rd survival/man/survobrien.Rd survival/man/basehaz.Rd survival/man/aareg.Rd survival/man/plot.cox.zph.Rd survival/man/dsurvreg.Rd survival/man/survSplit.Rd survival/man/clogit.Rd survival/man/print.aareg.Rd survival/man/logan.Rd survival/man/cch.Rd survival/man/heart.Rd sudo -u fink-bld [ENV] sh -c /tmp/fink.47E94 /tmp/fink.crS3R #!/bin/sh -ev export TMPDIR=/sw/build.build/cran-survival-r30-2.37-7-2/survival/tmp BIN_R=/sw/Library/Frameworks/R.framework/Versions/3.0/Resources/bin/R pushd .. /sw/build.build/cran-survival-r30-2.37-7-2 /sw/build.build/cran-survival-r30-2.37-7-2/survival if [[ 3.0 > 2.15 ]]; then $BIN_R --verbose CMD build --no-build-vignettes survival else $BIN_R --verbose CMD build --no-vignettes survival fi WARNING: ignoring environment value of R_HOME * checking for file 'survival/DESCRIPTION' ... OK * preparing 'survival': * checking DESCRIPTION meta-information ... OK * cleaning src * checking vignette meta-information ... OK * checking for LF line-endings in source and make files * checking for empty or unneeded directories * looking to see if a 'data/datalist' file should be added * building 'survival_2.37-7.tar.gz' /bin/rm -rf /sw/build.build/root-cran-survival-r30-2.37-7-2 /bin/mkdir -p /sw/build.build/root-cran-survival-r30-2.37-7-2/sw /bin/mkdir -p /sw/build.build/root-cran-survival-r30-2.37-7-2/DEBIAN /usr/sbin/chown -R fink-bld:fink-bld /sw/build.build/root-cran-survival-r30-2.37-7-2 sudo -u fink-bld [ENV] sh -c /tmp/fink.KXVkL /tmp/fink.JIn33 #!/bin/sh -ev BIN_R=/sw/Library/Frameworks/R.framework/Versions/3.0/Resources/bin/R mkdir -p /sw/build.build/root-cran-survival-r30-2.37-7-2/sw/lib/R/3.0/site-library pushd /sw/build.build/cran-survival-r30-2.37-7-2/survival/.. && $BIN_R --verbose CMD install --library=/sw/build.build/root-cran-survival-r30-2.37-7-2/sw/lib/R/3.0/site-library survival /sw/build.build/cran-survival-r30-2.37-7-2 /sw/build.build/cran-survival-r30-2.37-7-2/survival WARNING: ignoring environment value of R_HOME * installing *source* package 'survival' ... ** package 'survival' successfully unpacked and MD5 sums checked ** libs flag-sort -r gcc -ffor-scope -I/sw/Library/Frameworks/R.framework/Versions/3.0/Resources/include -DNDEBUG -I/sw/include -fPIC -g -O3 -c agexact.c -o agexact.o flag-sort -r gcc -ffor-scope -I/sw/Library/Frameworks/R.framework/Versions/3.0/Resources/include -DNDEBUG -I/sw/include -fPIC -g -O3 -c agfit4.c -o agfit4.o flag-sort -r gcc -ffor-scope -I/sw/Library/Frameworks/R.framework/Versions/3.0/Resources/include -DNDEBUG -I/sw/include -fPIC -g -O3 -c agfit5.c -o agfit5.o flag-sort -r gcc -ffor-scope -I/sw/Library/Frameworks/R.framework/Versions/3.0/Resources/include -DNDEBUG -I/sw/include -fPIC -g -O3 -c agmart.c -o agmart.o flag-sort -r gcc -ffor-scope -I/sw/Library/Frameworks/R.framework/Versions/3.0/Resources/include -DNDEBUG -I/sw/include -fPIC -g -O3 -c agmart2.c -o agmart2.o flag-sort -r gcc -ffor-scope -I/sw/Library/Frameworks/R.framework/Versions/3.0/Resources/include -DNDEBUG -I/sw/include -fPIC -g -O3 -c agscore.c -o agscore.o flag-sort -r gcc -ffor-scope -I/sw/Library/Frameworks/R.framework/Versions/3.0/Resources/include -DNDEBUG -I/sw/include -fPIC -g -O3 -c agsurv3.c -o agsurv3.o flag-sort -r gcc -ffor-scope -I/sw/Library/Frameworks/R.framework/Versions/3.0/Resources/include -DNDEBUG -I/sw/include -fPIC -g -O3 -c agsurv4.c -o agsurv4.o flag-sort -r gcc -ffor-scope -I/sw/Library/Frameworks/R.framework/Versions/3.0/Resources/include -DNDEBUG -I/sw/include -fPIC -g -O3 -c agsurv5.c -o agsurv5.o flag-sort -r gcc -ffor-scope -I/sw/Library/Frameworks/R.framework/Versions/3.0/Resources/include -DNDEBUG -I/sw/include -fPIC -g -O3 -c chinv2.c -o chinv2.o flag-sort -r gcc -ffor-scope -I/sw/Library/Frameworks/R.framework/Versions/3.0/Resources/include -DNDEBUG -I/sw/include -fPIC -g -O3 -c chinv3.c -o chinv3.o flag-sort -r gcc -ffor-scope -I/sw/Library/Frameworks/R.framework/Versions/3.0/Resources/include -DNDEBUG -I/sw/include -fPIC -g -O3 -c cholesky2.c -o cholesky2.o flag-sort -r gcc -ffor-scope -I/sw/Library/Frameworks/R.framework/Versions/3.0/Resources/include -DNDEBUG -I/sw/include -fPIC -g -O3 -c cholesky3.c -o cholesky3.o flag-sort -r gcc -ffor-scope -I/sw/Library/Frameworks/R.framework/Versions/3.0/Resources/include -DNDEBUG -I/sw/include -fPIC -g -O3 -c chsolve2.c -o chsolve2.o flag-sort -r gcc -ffor-scope -I/sw/Library/Frameworks/R.framework/Versions/3.0/Resources/include -DNDEBUG -I/sw/include -fPIC -g -O3 -c chsolve3.c -o chsolve3.o flag-sort -r gcc -ffor-scope -I/sw/Library/Frameworks/R.framework/Versions/3.0/Resources/include -DNDEBUG -I/sw/include -fPIC -g -O3 -c concordance1.c -o concordance1.o flag-sort -r gcc -ffor-scope -I/sw/Library/Frameworks/R.framework/Versions/3.0/Resources/include -DNDEBUG -I/sw/include -fPIC -g -O3 -c cox_Rcallback.c -o cox_Rcallback.o flag-sort -r gcc -ffor-scope -I/sw/Library/Frameworks/R.framework/Versions/3.0/Resources/include -DNDEBUG -I/sw/include -fPIC -g -O3 -c coxcount1.c -o coxcount1.o flag-sort -r gcc -ffor-scope -I/sw/Library/Frameworks/R.framework/Versions/3.0/Resources/include -DNDEBUG -I/sw/include -fPIC -g -O3 -c coxdetail.c -o coxdetail.o flag-sort -r gcc -ffor-scope -I/sw/Library/Frameworks/R.framework/Versions/3.0/Resources/include -DNDEBUG -I/sw/include -fPIC -g -O3 -c coxexact.c -o coxexact.o flag-sort -r gcc -ffor-scope -I/sw/Library/Frameworks/R.framework/Versions/3.0/Resources/include -DNDEBUG -I/sw/include -fPIC -g -O3 -c coxfit5.c -o coxfit5.o flag-sort -r gcc -ffor-scope -I/sw/Library/Frameworks/R.framework/Versions/3.0/Resources/include -DNDEBUG -I/sw/include -fPIC -g -O3 -c coxfit6.c -o coxfit6.o flag-sort -r gcc -ffor-scope -I/sw/Library/Frameworks/R.framework/Versions/3.0/Resources/include -DNDEBUG -I/sw/include -fPIC -g -O3 -c coxmart.c -o coxmart.o flag-sort -r gcc -ffor-scope -I/sw/Library/Frameworks/R.framework/Versions/3.0/Resources/include -DNDEBUG -I/sw/include -fPIC -g -O3 -c coxmart2.c -o coxmart2.o flag-sort -r gcc -ffor-scope -I/sw/Library/Frameworks/R.framework/Versions/3.0/Resources/include -DNDEBUG -I/sw/include -fPIC -g -O3 -c coxph_wtest.c -o coxph_wtest.o flag-sort -r gcc -ffor-scope -I/sw/Library/Frameworks/R.framework/Versions/3.0/Resources/include -DNDEBUG -I/sw/include -fPIC -g -O3 -c coxsafe.c -o coxsafe.o flag-sort -r gcc -ffor-scope -I/sw/Library/Frameworks/R.framework/Versions/3.0/Resources/include -DNDEBUG -I/sw/include -fPIC -g -O3 -c coxscho.c -o coxscho.o flag-sort -r gcc -ffor-scope -I/sw/Library/Frameworks/R.framework/Versions/3.0/Resources/include -DNDEBUG -I/sw/include -fPIC -g -O3 -c coxscore.c -o coxscore.o flag-sort -r gcc -ffor-scope -I/sw/Library/Frameworks/R.framework/Versions/3.0/Resources/include -DNDEBUG -I/sw/include -fPIC -g -O3 -c dmatrix.c -o dmatrix.o flag-sort -r gcc -ffor-scope -I/sw/Library/Frameworks/R.framework/Versions/3.0/Resources/include -DNDEBUG -I/sw/include -fPIC -g -O3 -c doloop.c -o doloop.o flag-sort -r gcc -ffor-scope -I/sw/Library/Frameworks/R.framework/Versions/3.0/Resources/include -DNDEBUG -I/sw/include -fPIC -g -O3 -c init.c -o init.o flag-sort -r gcc -ffor-scope -I/sw/Library/Frameworks/R.framework/Versions/3.0/Resources/include -DNDEBUG -I/sw/include -fPIC -g -O3 -c msurv.c -o msurv.o flag-sort -r gcc -ffor-scope -I/sw/Library/Frameworks/R.framework/Versions/3.0/Resources/include -DNDEBUG -I/sw/include -fPIC -g -O3 -c pyears1.c -o pyears1.o flag-sort -r gcc -ffor-scope -I/sw/Library/Frameworks/R.framework/Versions/3.0/Resources/include -DNDEBUG -I/sw/include -fPIC -g -O3 -c pyears2.c -o pyears2.o flag-sort -r gcc -ffor-scope -I/sw/Library/Frameworks/R.framework/Versions/3.0/Resources/include -DNDEBUG -I/sw/include -fPIC -g -O3 -c pyears3b.c -o pyears3b.o flag-sort -r gcc -ffor-scope -I/sw/Library/Frameworks/R.framework/Versions/3.0/Resources/include -DNDEBUG -I/sw/include -fPIC -g -O3 -c pystep.c -o pystep.o flag-sort -r gcc -ffor-scope -I/sw/Library/Frameworks/R.framework/Versions/3.0/Resources/include -DNDEBUG -I/sw/include -fPIC -g -O3 -c survConcordance.c -o survConcordance.o flag-sort -r gcc -ffor-scope -I/sw/Library/Frameworks/R.framework/Versions/3.0/Resources/include -DNDEBUG -I/sw/include -fPIC -g -O3 -c survdiff2.c -o survdiff2.o flag-sort -r gcc -ffor-scope -I/sw/Library/Frameworks/R.framework/Versions/3.0/Resources/include -DNDEBUG -I/sw/include -fPIC -g -O3 -c survfit4.c -o survfit4.o flag-sort -r gcc -ffor-scope -I/sw/Library/Frameworks/R.framework/Versions/3.0/Resources/include -DNDEBUG -I/sw/include -fPIC -g -O3 -c survfitci.c -o survfitci.o flag-sort -r gcc -ffor-scope -I/sw/Library/Frameworks/R.framework/Versions/3.0/Resources/include -DNDEBUG -I/sw/include -fPIC -g -O3 -c survpenal.c -o survpenal.o flag-sort -r gcc -ffor-scope -I/sw/Library/Frameworks/R.framework/Versions/3.0/Resources/include -DNDEBUG -I/sw/include -fPIC -g -O3 -c survreg6.c -o survreg6.o flag-sort -r gcc -ffor-scope -I/sw/Library/Frameworks/R.framework/Versions/3.0/Resources/include -DNDEBUG -I/sw/include -fPIC -g -O3 -c survreg7.c -o survreg7.o flag-sort -r gcc -ffor-scope -I/sw/Library/Frameworks/R.framework/Versions/3.0/Resources/include -DNDEBUG -I/sw/include -fPIC -g -O3 -c survregc1.c -o survregc1.o flag-sort -r gcc -ffor-scope -I/sw/Library/Frameworks/R.framework/Versions/3.0/Resources/include -DNDEBUG -I/sw/include -fPIC -g -O3 -c survregc2.c -o survregc2.o flag-sort -r gcc -ffor-scope -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/sw/lib -o survival.dylib agexact.o agfit4.o agfit5.o agmart.o agmart2.o agscore.o agsurv3.o agsurv4.o agsurv5.o chinv2.o chinv3.o cholesky2.o cholesky3.o chsolve2.o chsolve3.o concordance1.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 coxscore.o dmatrix.o doloop.o init.o msurv.o pyears1.o pyears2.o pyears3b.o pystep.o survConcordance.o survdiff2.o survfit4.o survfitci.o survpenal.o survreg6.o survreg7.o survregc1.o survregc2.o -L/sw/Library/Frameworks/R.framework/Versions/3.0/Resources/lib -lR -lintl -Wl,-framework -Wl,CoreFoundation installing to /sw/build.build/root-cran-survival-r30-2.37-7-2/sw/lib/R/3.0/site-library/survival/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (survival) install_name_tool -id /sw/lib/R/3.0/site-library/survival/libs/survival.dylib /sw/build.build/root-cran-survival-r30-2.37-7-2/sw/lib/R/3.0/site-library/survival/libs/survival.dylib sudo -u fink-bld [ENV] sh -c /tmp/fink.H9qNz /bin/rm -f /sw/build.build/root-cran-survival-r30-2.37-7-2/sw/info/dir /sw/build.build/root-cran-survival-r30-2.37-7-2/sw/info/dir.old /sw/build.build/root-cran-survival-r30-2.37-7-2/sw/share/info/dir /sw/build.build/root-cran-survival-r30-2.37-7-2/sw/share/info/dir.old Reverting ownership of install dir to root Writing control file... Creating shlibs files... Writing md5sums file... env LANG=C LC_ALL=C dpkg-deb -b root-cran-survival-r30-2.37-7-2 /sw/fink/10.9/stable/main/binary-darwin-x86_64/libs/rmods dpkg-deb: building package `cran-survival-r30' in `/sw/fink/10.9/stable/main/binary-darwin-x86_64/libs/rmods/cran-survival-r30_2.37-7-2_darwin-x86_64.deb'. Removing runtime build-lock... Removing build-lock package... /sw/bin/dpkg-lockwait -r fink-buildlock-cran-survival-r30-2.37-7-2 (Reading database ... 11541 files and directories currently installed.) Removing fink-buildlock-cran-survival-r30-2.37-7-2 ...