printf ' ' | fink --no-use-binary-dist --yes rebuild cran-nlme-r31 2>&1 The package 'cran-nlme-r31' will be built without being installed. Reading build dependency for cran-nlme-r31-3.1-117-2... Reading dependency for cran-nlme-r31-3.1-117-2... Reading build conflict for cran-nlme-r31-3.1-117-2... The following package will be rebuilt: cran-nlme-r31 Setting runtime build-lock... dpkg-deb -b /sw/build.build/root-fink-buildlock-cran-nlme-r31-3.1-117-2 /sw/build.build dpkg-deb: building package `fink-buildlock-cran-nlme-r31-3.1-117-2' in `/sw/build.build/fink-buildlock-cran-nlme-r31-3.1-117-2_2014.07.27-10.01.09_darwin-x86_64.deb'. Installing build-lock package... /sw/bin/dpkg-lockwait -i /sw/build.build/fink-buildlock-cran-nlme-r31-3.1-117-2_2014.07.27-10.01.09_darwin-x86_64.deb Selecting previously deselected package fink-buildlock-cran-nlme-r31-3.1-117-2. (Reading database ... 7428 files and directories currently installed.) Unpacking fink-buildlock-cran-nlme-r31-3.1-117-2 (from .../fink-buildlock-cran-nlme-r31-3.1-117-2_2014.07.27-10.01.09_darwin-x86_64.deb) ... Setting up fink-buildlock-cran-nlme-r31-3.1-117-2 (2014.07.27-10.01.09) ... sudo -u fink-bld [ENV] sh -c /tmp/fink.0XEA7 env LANG=C LC_ALL=C /sw/bin/tar --no-same-owner --no-same-permissions -xvf /sw/src/nlme_3.1-117.tar.gz nlme/ nlme/po/ nlme/po/R-fr.po nlme/po/de.po nlme/po/R-nlme.pot nlme/po/pl.po nlme/po/R-de.po nlme/po/fr.po nlme/po/ko.po nlme/po/nlme.pot nlme/po/R-pl.po nlme/po/R-ko.po nlme/inst/ nlme/inst/po/ nlme/inst/po/pl/ nlme/inst/po/pl/LC_MESSAGES/ nlme/inst/po/pl/LC_MESSAGES/R-nlme.mo nlme/inst/po/pl/LC_MESSAGES/nlme.mo nlme/inst/po/en@quot/ nlme/inst/po/en@quot/LC_MESSAGES/ nlme/inst/po/en@quot/LC_MESSAGES/R-nlme.mo nlme/inst/po/en@quot/LC_MESSAGES/nlme.mo nlme/inst/po/ko/ nlme/inst/po/ko/LC_MESSAGES/ nlme/inst/po/ko/LC_MESSAGES/R-nlme.mo nlme/inst/po/ko/LC_MESSAGES/nlme.mo nlme/inst/po/fr/ nlme/inst/po/fr/LC_MESSAGES/ nlme/inst/po/fr/LC_MESSAGES/R-nlme.mo nlme/inst/po/fr/LC_MESSAGES/nlme.mo nlme/inst/po/de/ nlme/inst/po/de/LC_MESSAGES/ nlme/inst/po/de/LC_MESSAGES/R-nlme.mo nlme/inst/po/de/LC_MESSAGES/nlme.mo nlme/inst/CITATION nlme/inst/scripts/ nlme/inst/scripts/sims.rda nlme/inst/scripts/ch01.R nlme/inst/scripts/ch02.R nlme/inst/scripts/ch06.R nlme/inst/scripts/ch05.R nlme/inst/scripts/ch08.R nlme/inst/scripts/ch04.R nlme/inst/scripts/ch03.R nlme/inst/mlbook/ nlme/inst/mlbook/README nlme/inst/mlbook/ch05.R nlme/inst/mlbook/ch04.R nlme/tests/ nlme/tests/anova.gls.R nlme/tests/nlme.R nlme/tests/lme.Rout.save nlme/tests/data.frame.R nlme/tests/missing.R nlme/tests/contrMat.R nlme/tests/fitted.R nlme/tests/predict.lme.R nlme/tests/update.R nlme/tests/augPredmissing.R nlme/tests/coef.R nlme/tests/deparse.R nlme/tests/nlme.Rout.save nlme/tests/augPred_lab.R nlme/tests/ss2.rda nlme/tests/varIdent.R nlme/tests/updateLme.R nlme/tests/missing.Rout.save nlme/tests/getData.R nlme/tests/lmList.R nlme/tests/gls.R nlme/tests/lme.R nlme/src/ nlme/src/rs.f nlme/src/matrix.c nlme/src/Makevars nlme/src/pdMat.h nlme/src/nlOptimizer.h nlme/src/base.h nlme/src/nlmefit.h nlme/src/nlme.c nlme/src/chol.f nlme/src/nlmefit.c nlme/src/pdMat.c nlme/src/nls.c nlme/src/nlOptimizer.c nlme/src/gnls.c nlme/src/init.c nlme/src/corStruct.c nlme/src/matrix.h nlme/NAMESPACE nlme/GPL-2 nlme/data/ nlme/data/Cefamandole.rda nlme/data/Quinidine.rda nlme/data/Gun.rda nlme/data/Relaxin.rda nlme/data/Orthodont.rda nlme/data/Ovary.rda nlme/data/Tetracycline1.rda nlme/data/Remifentanil.rda nlme/data/PBG.rda nlme/data/Phenobarb.rda nlme/data/Assay.rda nlme/data/BodyWeight.rda nlme/data/Machines.rda nlme/data/Glucose2.rda nlme/data/Earthquake.rda nlme/data/Milk.rda nlme/data/Wheat.rda nlme/data/bdf.rda nlme/data/Oxboys.rda nlme/data/Muscle.rda nlme/data/Alfalfa.rda nlme/data/Wheat2.rda nlme/data/IGF.rda nlme/data/MathAchieve.rda nlme/data/Fatigue.rda nlme/data/Pixel.rda nlme/data/Nitrendipene.rda nlme/data/Gasoline.rda nlme/data/ergoStool.rda nlme/data/Rail.rda nlme/data/Tetracycline2.rda nlme/data/Soybean.rda nlme/data/MathAchSchool.rda nlme/data/Wafer.rda nlme/data/Dialyzer.rda nlme/data/Oats.rda nlme/data/Spruce.rda nlme/data/Glucose.rda nlme/data/Oxide.rda nlme/data/RatPupWeight.rda nlme/data/Meat.rda nlme/R/ nlme/R/groupedData.R nlme/R/gnls.R nlme/R/zzMethods.R nlme/R/nlme.R nlme/R/newMethods.R nlme/R/corStruct.R nlme/R/newGenerics.R nlme/R/nlsList.R nlme/R/reStruct.R nlme/R/modelStruct.R nlme/R/VarCov.R nlme/R/varFunc.R nlme/R/pdMat.R nlme/R/simulate.R nlme/R/newFunc.R nlme/R/VarCorr.R nlme/R/lmList.R nlme/R/gls.R nlme/R/lme.R nlme/MD5 nlme/README nlme/DESCRIPTION nlme/ChangeLog nlme/man/ nlme/man/getGroups.gls.Rd nlme/man/plot.gls.Rd nlme/man/summary.pdMat.Rd nlme/man/getGroupsFormula.Rd nlme/man/pdIdent.Rd nlme/man/summary.gls.Rd nlme/man/corMatrix.reStruct.Rd nlme/man/Coef.Rd nlme/man/Tetracycline1.Rd nlme/man/getData.lmList.Rd nlme/man/Dim.corStruct.Rd nlme/man/varExp.Rd nlme/man/gnls.Rd nlme/man/VarCorr.Rd nlme/man/pdMat.Rd nlme/man/getData.lme.Rd nlme/man/pdConstruct.Rd nlme/man/as.matrix.pdMat.Rd nlme/man/Names.Rd nlme/man/ACF.gls.Rd nlme/man/coef.reStruct.Rd nlme/man/coef.pdMat.Rd nlme/man/collapse.groupedData.Rd nlme/man/residuals.lmList.Rd nlme/man/recalc.varFunc.Rd nlme/man/Initialize.Rd nlme/man/pdMatrix.Rd nlme/man/corSpher.Rd nlme/man/Glucose2.Rd nlme/man/Dim.corSpatial.Rd nlme/man/Variogram.corRatio.Rd nlme/man/plot.ranef.lmList.Rd nlme/man/getCovariate.corStruct.Rd nlme/man/LDEsysMat.Rd nlme/man/update.modelStruct.Rd nlme/man/coef.varFunc.Rd nlme/man/pdDiag.Rd nlme/man/corCAR1.Rd nlme/man/logDet.corStruct.Rd nlme/man/summary.lme.Rd nlme/man/logLik.reStruct.Rd nlme/man/plot.nffGroupedData.Rd nlme/man/lmList.Rd nlme/man/Meat.Rd nlme/man/pdCompSymm.Rd nlme/man/Variogram.corSpatial.Rd nlme/man/ergoStool.Rd nlme/man/Relaxin.Rd nlme/man/recalc.modelStruct.Rd nlme/man/summary.modelStruct.Rd nlme/man/asOneFormula.Rd nlme/man/coef.lmList.Rd nlme/man/compareFits.Rd nlme/man/Matrix.reStruct.Rd nlme/man/plot.compareFits.Rd nlme/man/Variogram.corExp.Rd nlme/man/varComb.Rd nlme/man/lmList.groupedData.Rd nlme/man/corMatrix.pdMat.Rd nlme/man/pdSymm.Rd nlme/man/lme.lmList.Rd nlme/man/predict.lme.Rd nlme/man/gls-internal.Rd nlme/man/varConstPower.Rd nlme/man/residuals.glsStruct.Rd nlme/man/qqnorm.lme.Rd nlme/man/formula.reStruct.Rd nlme/man/residuals.gls.Rd nlme/man/lmeControl.Rd nlme/man/BodyWeight.Rd nlme/man/coef.gnls.Rd nlme/man/Machines.Rd nlme/man/Names.reStruct.Rd nlme/man/plot.Variogram.Rd nlme/man/Dialyzer.Rd nlme/man/fitted.lmeStruct.Rd nlme/man/gnlsStruct.Rd nlme/man/getGroups.Rd nlme/man/Initialize.glsStruct.Rd nlme/man/Matrix.pdMat.Rd nlme/man/varWeights.glsStruct.Rd nlme/man/nlmeStruct.Rd nlme/man/plot.lme.Rd nlme/man/Glucose.Rd nlme/man/Names.pdBlocked.Rd nlme/man/logLik.lmeStruct.Rd nlme/man/summary.corStruct.Rd nlme/man/corRatio.Rd nlme/man/predict.gnls.Rd nlme/man/glsStruct.Rd nlme/man/varIdent.Rd nlme/man/qqnorm.gls.Rd nlme/man/Wheat2.Rd nlme/man/fdHess.Rd nlme/man/recalc.reStruct.Rd nlme/man/glsControl.Rd nlme/man/Tetracycline2.Rd nlme/man/Names.formula.Rd nlme/man/phenoModel.Rd nlme/man/corCompSymm.Rd nlme/man/Nitrendipene.Rd nlme/man/logLik.varFunc.Rd nlme/man/MathAchieve.Rd nlme/man/asTable.Rd nlme/man/nlsList.selfStart.Rd nlme/man/Variogram.corGaus.Rd nlme/man/summary.nlsList.Rd nlme/man/Variogram.corSpher.Rd nlme/man/formula.pdBlocked.Rd nlme/man/lme.groupedData.Rd nlme/man/Fatigue.Rd nlme/man/Spruce.Rd nlme/man/coef.lme.Rd nlme/man/varWeights.Rd nlme/man/pdNatural.Rd nlme/man/lmeStruct.Rd nlme/man/nlmeObject.Rd nlme/man/as.matrix.corStruct.Rd nlme/man/predict.nlme.Rd nlme/man/Alfalfa.Rd nlme/man/pdConstruct.pdBlocked.Rd nlme/man/Phenobarb.Rd nlme/man/groupedData.Rd nlme/man/print.varFunc.Rd nlme/man/corMatrix.corStruct.Rd nlme/man/corExp.Rd nlme/man/predict.gls.Rd nlme/man/pooledSD.Rd nlme/man/residuals.nlmeStruct.Rd nlme/man/Oats.Rd nlme/man/corClasses.Rd nlme/man/Wheat.Rd nlme/man/Covariate.varFunc.Rd nlme/man/getCovariate.data.frame.Rd nlme/man/getCovariate.Rd nlme/man/pdBlocked.Rd nlme/man/coef.modelStruct.Rd nlme/man/varClasses.Rd nlme/man/corAR1.Rd nlme/man/Pixel.Rd nlme/man/anova.gls.Rd nlme/man/augPred.Rd nlme/man/residuals.lme.Rd nlme/man/Muscle.Rd nlme/man/pairs.lme.Rd nlme/man/nlsList.Rd nlme/man/PBG.Rd nlme/man/nlme.nlsList.Rd nlme/man/varFunc.Rd nlme/man/Variogram.corLin.Rd nlme/man/corARMA.Rd nlme/man/simulate.lme.Rd nlme/man/getCovariate.varFunc.Rd nlme/man/MathAchSchool.Rd nlme/man/Variogram.default.Rd nlme/man/plot.ranef.lme.Rd nlme/man/plot.lmList.Rd nlme/man/intervals.gls.Rd nlme/man/getData.gls.Rd nlme/man/Variogram.gls.Rd nlme/man/Matrix.Rd nlme/man/getVarCov.Rd nlme/man/print.summary.pdMat.Rd nlme/man/corSpatial.Rd nlme/man/corNatural.Rd nlme/man/quinModel.Rd nlme/man/logLik.gnlsStruct.Rd nlme/man/intervals.lmList.Rd nlme/man/logLik.glsStruct.Rd nlme/man/corFactor.Rd nlme/man/Covariate.Rd nlme/man/gapply.Rd nlme/man/ACF.lme.Rd nlme/man/gnlsObject.Rd nlme/man/fitted.lme.Rd nlme/man/logLik.gnls.Rd nlme/man/IGF.Rd nlme/man/lmeObject.Rd nlme/man/fitted.glsStruct.Rd nlme/man/lme.Rd nlme/man/logDet.reStruct.Rd nlme/man/plot.nmGroupedData.Rd nlme/man/Milk.Rd nlme/man/Initialize.corStruct.Rd nlme/man/Cefamandole.Rd nlme/man/getResponse.Rd nlme/man/getGroups.lme.Rd nlme/man/getGroups.varFunc.Rd nlme/man/logLik.corStruct.Rd nlme/man/solve.reStruct.Rd nlme/man/needUpdate.Rd nlme/man/Initialize.reStruct.Rd nlme/man/fitted.lmList.Rd nlme/man/Remifentanil.Rd nlme/man/summary.varFunc.Rd nlme/man/corLin.Rd nlme/man/fixed.effects.Rd nlme/man/Dim.Rd nlme/man/formula.pdMat.Rd nlme/man/pairs.compareFits.Rd nlme/man/Oxboys.Rd nlme/man/recalc.Rd nlme/man/logDet.Rd nlme/man/isInitialized.Rd nlme/man/solve.pdMat.Rd nlme/man/getResponseFormula.Rd nlme/man/Oxide.Rd nlme/man/pdClasses.Rd nlme/man/gsummary.Rd nlme/man/pairs.lmList.Rd nlme/man/Extract.pdMat.Rd nlme/man/intervals.Rd nlme/man/corGaus.Rd nlme/man/Rail.Rd nlme/man/Initialize.varFunc.Rd nlme/man/corFactor.corStruct.Rd nlme/man/Initialize.lmeStruct.Rd nlme/man/Soybean.Rd nlme/man/pdLogChol.Rd nlme/man/isBalanced.Rd nlme/man/update.varFunc.Rd nlme/man/reStruct.Rd nlme/man/logLik.lme.Rd nlme/man/gls.Rd nlme/man/comparePred.Rd nlme/man/allCoef.Rd nlme/man/RatPupWeight.Rd nlme/man/residuals.lmeStruct.Rd nlme/man/collapse.Rd nlme/man/logLik.lmList.Rd nlme/man/Gun.Rd nlme/man/recalc.corStruct.Rd nlme/man/logDet.pdMat.Rd nlme/man/pdMatrix.reStruct.Rd nlme/man/Ovary.Rd nlme/man/pdFactor.Rd nlme/man/ACF.Rd nlme/man/predict.lmList.Rd nlme/man/coef.corStruct.Rd nlme/man/varPower.Rd nlme/man/ranef.lme.Rd nlme/man/Gasoline.Rd nlme/man/plot.nfnGroupedData.Rd nlme/man/Variogram.lme.Rd nlme/man/Variogram.Rd nlme/man/summary.lmList.Rd nlme/man/anova.lme.Rd nlme/man/residuals.gnlsStruct.Rd nlme/man/fitted.gnlsStruct.Rd nlme/man/plot.augPred.Rd nlme/man/getCovariateFormula.Rd nlme/man/Earthquake.Rd nlme/man/pdFactor.reStruct.Rd nlme/man/plot.intervals.lmList.Rd nlme/man/bdf.Rd nlme/man/fixef.lmList.Rd nlme/man/corMatrix.Rd nlme/man/model.matrix.reStruct.Rd nlme/man/corSymm.Rd nlme/man/glsObject.Rd nlme/man/getData.Rd nlme/man/Dim.pdMat.Rd nlme/man/plot.ACF.Rd nlme/man/ranef.lmList.Rd nlme/man/nlme.Rd nlme/man/varFixed.Rd nlme/man/Quinidine.Rd nlme/man/fitted.nlmeStruct.Rd nlme/man/getGroups.data.frame.Rd nlme/man/getGroups.corStruct.Rd nlme/man/Wafer.Rd nlme/man/getGroups.lmList.Rd nlme/man/splitFormula.Rd nlme/man/Names.pdMat.Rd nlme/man/gnlsControl.Rd nlme/man/varWeights.lmeStruct.Rd nlme/man/intervals.lme.Rd nlme/man/random.effects.Rd nlme/man/Assay.Rd nlme/man/as.matrix.reStruct.Rd nlme/man/Orthodont.Rd nlme/man/balancedGrouped.Rd nlme/man/needUpdate.modelStruct.Rd nlme/man/nlmeControl.Rd nlme/LICENCE.note nlme/INDEX sudo -u fink-bld [ENV] sh -c /tmp/fink.ZwJoZ /tmp/fink.PelMN #!/bin/bash -ev export TMPDIR=/sw/build.build/cran-nlme-r31-3.1-117-2/nlme/tmp BIN_R=/sw/Library/Frameworks/R.framework/Versions/3.1/Resources/bin/R pushd .. /sw/build.build/cran-nlme-r31-3.1-117-2 /sw/build.build/cran-nlme-r31-3.1-117-2/nlme if [[ 3.1 > 2.15 ]]; then $BIN_R --verbose CMD build --no-build-vignettes nlme else $BIN_R --verbose CMD build --no-vignettes nlme fi * checking for file 'nlme/DESCRIPTION' ... OK * preparing 'nlme': * checking DESCRIPTION meta-information ... OK * cleaning src * checking whether 'INDEX' is up-to-date ... NO * use '--force' to remove the existing 'INDEX' * 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 'nlme_3.1-117.tar.gz' /bin/rm -rf /sw/build.build/root-cran-nlme-r31-3.1-117-2 /bin/mkdir -p /sw/build.build/root-cran-nlme-r31-3.1-117-2/sw /bin/mkdir -p /sw/build.build/root-cran-nlme-r31-3.1-117-2/DEBIAN /usr/sbin/chown -R fink-bld:fink-bld /sw/build.build/root-cran-nlme-r31-3.1-117-2 sudo -u fink-bld [ENV] sh -c /tmp/fink.Jbz7m /tmp/fink.GABeD #!/bin/sh -ev BIN_R=/sw/Library/Frameworks/R.framework/Versions/3.1/Resources/bin/R mkdir -p /sw/build.build/root-cran-nlme-r31-3.1-117-2/sw/lib/R/3.1/site-library pushd /sw/build.build/cran-nlme-r31-3.1-117-2/nlme/.. && $BIN_R --verbose CMD install --library=/sw/build.build/root-cran-nlme-r31-3.1-117-2/sw/lib/R/3.1/site-library nlme /sw/build.build/cran-nlme-r31-3.1-117-2 /sw/build.build/cran-nlme-r31-3.1-117-2/nlme * installing *source* package 'nlme' ... ** package 'nlme' successfully unpacked and MD5 sums checked ** libs /sw/bin/gfortran-fsf-4.9 -fPIC -g -O3 -c chol.f -o chol.o make: /sw/bin/gfortran-fsf-4.9: No such file or directory make: *** [chol.o] Error 1 ERROR: compilation failed for package 'nlme' * removing '/sw/build.build/root-cran-nlme-r31-3.1-117-2/sw/lib/R/3.1/site-library/nlme' ### execution of /tmp/fink.GABeD failed, exit code 1 ### execution of /tmp/fink.Jbz7m failed, exit code 1 Removing runtime build-lock... Removing build-lock package... /sw/bin/dpkg-lockwait -r fink-buildlock-cran-nlme-r31-3.1-117-2 (Reading database ... 7429 files and directories currently installed.) Removing fink-buildlock-cran-nlme-r31-3.1-117-2 ... Failed: phase installing: cran-nlme-r31-3.1-117-2 failed Before reporting any errors, please run "fink selfupdate" and try again. Also try using "fink configure" to set your maximum build jobs to 1 and attempt to build the package again. If you continue to have issues, please check to see if the FAQ on Fink's website solves the problem. If not, ask on one (not both, please) of these mailing lists: The Fink Users List The Fink Beginners List , with a carbon copy to the maintainer: Jack Howarth Note that this is preferable to emailing just the maintainer directly, since most fink package maintainers do not have access to all possible hardware and software configurations. Please try to include the complete error message in your report. This generally consists of a compiler line starting with e.g. "gcc" or "g++" followed by the actual error output from the compiler. Also include the following system information: Package manager version: 0.37.0 Distribution version: selfupdate-cvs Thu Jul 24 20:26:24 2014, 10.9, x86_64 Trees: local/main stable/main Xcode.app: 5.1.1 Xcode command-line tools: 6.0.0.0.1.1405597879 Max. Fink build jobs: 8