MacOS Port - Successful venv, Failing tests

[r614]

Added a MacOS port of renv in the 'mac' branch.
This script was used to test the code:

Sys.setenv(LC_COLLATE = "C", LC_TIME = "C", LANGUAGE = "en")
tools::testInstalledBasic("both")
tools::testInstalledPackages(scope = "base")
tools::testInstalledPackages(scope = "recommended")

Results:

> Sys.setenv(LC_COLLATE = "C", LC_TIME = "C", LANGUAGE = "en")
> tools::testInstalledBasic("both")
running strict specific tests
  running code in ‘eval-etc.R’
FAILED
[1] 1
> tools::testInstalledPackages(scope = "base")
Testing examples for package ‘base’
Testing examples for package ‘tools’
  comparing ‘tools-Ex.Rout’ to ‘tools-Ex.Rout.save’ ... OK
Running specific tests for package ‘tools’
  Running ‘Rd2HTML.R’
  Running ‘S3.R’
  Running ‘undoc.R’
Testing examples for package ‘utils’
Running specific tests for package ‘utils’
  Running ‘Sweave-tst.R’
Error: testing 'utils' failed
> tools::testInstalledPackages(scope = "recommended")
Testing examples for package ‘MASS’
  comparing ‘MASS-Ex.Rout’ to ‘MASS-Ex.Rout.save’ ... NOTE
  2348c2348
  < ContHigh                          -2.200e-16  1.690e-01   0.000 1.000000    
  ---
  > ContHigh                          -1.490e-15  1.690e-01   0.000 1.000000    
Running specific tests for package ‘MASS’
  Running ‘confint.R’
  Running ‘fitdistr.R’
  comparing ‘fitdistr.Rout’ to ‘fitdistr.Rout.save’ ... OK
  Running ‘glm.nb.R’
  Running ‘hubers.R’
  Running ‘lme.R’
  Running ‘polr.R’
  Running ‘profile.R’
  Running ‘regression.R’
  comparing ‘regression.Rout’ to ‘regression.Rout.save’ ... OK
  Running ‘rlm.R’
  Running ‘scripts.R’
Testing examples for package ‘lattice’
Running specific tests for package ‘lattice’
  Running ‘MASSch04.R’
  Running ‘dates.R’
  Running ‘dotplotscoping.R’
  Running ‘fontsize.R’
  Running ‘levelplot.R’
  Running ‘scales.R’
  Running ‘summary.R’
  Running ‘temp.R’
  Running ‘test.R’
  Running ‘wireframe.R’
Testing examples for package ‘Matrix’
Running specific tests for package ‘Matrix’
  Running ‘Class+Meth.R’
  Running ‘Simple.R’
  Running ‘abIndex-tsts.R’
  Running ‘base-matrix-fun.R’
  Running ‘bind.R’
  comparing ‘bind.Rout’ to ‘bind.Rout.save’ ... OK
  Running ‘dg_Matrix.R’
  Running ‘dpo-test.R’
  Running ‘dtpMatrix.R’
  Running ‘factorizing.R’
  Running ‘group-methods.R’
  Running ‘indexing.R’
  comparing ‘indexing.Rout’ to ‘indexing.Rout.save’ ... OK
  Running ‘matprod.R’
  Running ‘matr-exp.R’
  Running ‘other-pkgs.R’
  Running ‘spModel.matrix.R’
  Running ‘validObj.R’
  Running ‘write-read.R’
Running vignettes for package ‘Matrix’
  Running ‘Comparisons.Rnw’
  Running ‘Design-issues.Rnw’
  Running ‘Intro2Matrix.Rnw’
  Running ‘Introduction.Rnw’
  Running ‘sparseModels.Rnw’
Testing examples for package ‘nlme’
Running specific tests for package ‘nlme’
  Running ‘anova.gls.R’
  Running ‘augPred_lab.R’
  Running ‘augPredmissing.R’
  Running ‘coef.R’
  comparing ‘coef.Rout’ to ‘coef.Rout.save’ ... OK
  Running ‘contrMat.R’
  Running ‘data.frame.R’
  Running ‘deparse.R’
  Running ‘deviance.R’
  Running ‘fitted.R’
  Running ‘getData.R’
  Running ‘gls.R’
  Running ‘gnls-ch8.R’
  Running ‘lmList.R’
  Running ‘lme.R’
  comparing ‘lme.Rout’ to ‘lme.Rout.save’ ... OK
  Running ‘missing.R’
  comparing ‘missing.Rout’ to ‘missing.Rout.save’ ... OK
  Running ‘nlme-stall.R’
  Running ‘nlme.R’
  Running ‘nlme2.R’
  Running ‘predict.lme.R’
  Running ‘sigma-fixed-etc.R’
  Running ‘updateLme.R’
  Running ‘varIdent.R’
Testing examples for package ‘survival’
Running specific tests for package ‘survival’
  Running ‘aareg.R’
  comparing ‘aareg.Rout’ to ‘aareg.Rout.save’ ... OK
  Running ‘anova.R’
  comparing ‘anova.Rout’ to ‘anova.Rout.save’ ... OK
  Running ‘bladder.R’
  comparing ‘bladder.Rout’ to ‘bladder.Rout.save’ ... OK
  Running ‘book1.R’
  comparing ‘book1.Rout’ to ‘book1.Rout.save’ ... OK
  Running ‘book2.R’
  comparing ‘book2.Rout’ to ‘book2.Rout.save’ ... OK
  Running ‘book3.R’
  comparing ‘book3.Rout’ to ‘book3.Rout.save’ ... OK
  Running ‘book4.R’
  comparing ‘book4.Rout’ to ‘book4.Rout.save’ ... OK
  Running ‘book5.R’
  comparing ‘book5.Rout’ to ‘book5.Rout.save’ ... OK
  Running ‘book6.R’
  comparing ‘book6.Rout’ to ‘book6.Rout.save’ ... OK
  Running ‘book7.R’
  comparing ‘book7.Rout’ to ‘book7.Rout.save’ ... OK
  Running ‘cancer.R’
  comparing ‘cancer.Rout’ to ‘cancer.Rout.save’ ... OK
  Running ‘clogit.R’
  comparing ‘clogit.Rout’ to ‘clogit.Rout.save’ ... OK
  Running ‘concordance.R’
  comparing ‘concordance.Rout’ to ‘concordance.Rout.save’ ... OK
  Running ‘concordance2.R’
  comparing ‘concordance2.Rout’ to ‘concordance2.Rout.save’ ... OK
  Running ‘concordance3.R’
  comparing ‘concordance3.Rout’ to ‘concordance3.Rout.save’ ... OK
  Running ‘counting.R’
  comparing ‘counting.Rout’ to ‘counting.Rout.save’ ... OK
  Running ‘coxsurv.R’
  comparing ‘coxsurv.Rout’ to ‘coxsurv.Rout.save’ ... OK
  Running ‘coxsurv2.R’
  comparing ‘coxsurv2.Rout’ to ‘coxsurv2.Rout.save’ ... OK
  Running ‘coxsurv3.R’
  comparing ‘coxsurv3.Rout’ to ‘coxsurv3.Rout.save’ ... OK
  Running ‘coxsurv4.R’
  comparing ‘coxsurv4.Rout’ to ‘coxsurv4.Rout.save’ ... OK
  Running ‘detail.R’
  comparing ‘detail.Rout’ to ‘detail.Rout.save’ ... OK
  Running ‘difftest.R’
  comparing ‘difftest.Rout’ to ‘difftest.Rout.save’ ... OK
  Running ‘doaml.R’
  comparing ‘doaml.Rout’ to ‘doaml.Rout.save’ ... OK
  Running ‘doweight.R’
  comparing ‘doweight.Rout’ to ‘doweight.Rout.save’ ... OK
  Running ‘expected.R’
  comparing ‘expected.Rout’ to ‘expected.Rout.save’ ... OK
  Running ‘expected2.R’
  comparing ‘expected2.Rout’ to ‘expected2.Rout.save’ ... OK
  Running ‘factor.R’
  comparing ‘factor.Rout’ to ‘factor.Rout.save’ ... OK
  Running ‘factor2.R’
  comparing ‘factor2.Rout’ to ‘factor2.Rout.save’ ... OK
  Running ‘finegray.R’
  comparing ‘finegray.Rout’ to ‘finegray.Rout.save’ ... OK
  Running ‘fr_cancer.R’
  comparing ‘fr_cancer.Rout’ to ‘fr_cancer.Rout.save’ ... OK
  Running ‘fr_kidney.R’
  comparing ‘fr_kidney.Rout’ to ‘fr_kidney.Rout.save’ ... OK
  Running ‘fr_lung.R’
  comparing ‘fr_lung.Rout’ to ‘fr_lung.Rout.save’ ... OK
  Running ‘fr_ovarian.R’
  comparing ‘fr_ovarian.Rout’ to ‘fr_ovarian.Rout.save’ ... OK
  Running ‘fr_rat1.R’
  comparing ‘fr_rat1.Rout’ to ‘fr_rat1.Rout.save’ ... OK
  Running ‘fr_rat2.R’
  comparing ‘fr_rat2.Rout’ to ‘fr_rat2.Rout.save’ ... OK
  Running ‘fr_resid.R’
  comparing ‘fr_resid.Rout’ to ‘fr_resid.Rout.save’ ... OK
  Running ‘fr_simple.R’
  comparing ‘fr_simple.Rout’ to ‘fr_simple.Rout.save’ ... OK
  Running ‘frailty.R’
  comparing ‘frailty.Rout’ to ‘frailty.Rout.save’ ... OK
  Running ‘frank.R’
  comparing ‘frank.Rout’ to ‘frank.Rout.save’ ... OK
  Running ‘infcox.R’
  comparing ‘infcox.Rout’ to ‘infcox.Rout.save’ ... OK
  Running ‘jasa.R’
  comparing ‘jasa.Rout’ to ‘jasa.Rout.save’ ... OK
  Running ‘model.matrix.R’
  comparing ‘model.matrix.Rout’ to ‘model.matrix.Rout.save’ ... OK
  Running ‘mstate.R’
  comparing ‘mstate.Rout’ to ‘mstate.Rout.save’ ... OK
  Running ‘nested.R’
  comparing ‘nested.Rout’ to ‘nested.Rout.save’ ... OK
  Running ‘ovarian.R’
  comparing ‘ovarian.Rout’ to ‘ovarian.Rout.save’ ... OK
  Running ‘prednew.R’
  comparing ‘prednew.Rout’ to ‘prednew.Rout.save’ ... OK
  Running ‘pspline.R’
  comparing ‘pspline.Rout’ to ‘pspline.Rout.save’ ... OK
  Running ‘pyear.R’
  comparing ‘pyear.Rout’ to ‘pyear.Rout.save’ ... OK
  Running ‘quantile.R’
  comparing ‘quantile.Rout’ to ‘quantile.Rout.save’ ... OK
  Running ‘r_donnell.R’
  comparing ‘r_donnell.Rout’ to ‘r_donnell.Rout.save’ ... OK
  Running ‘r_lung.R’
  comparing ‘r_lung.Rout’ to ‘r_lung.Rout.save’ ... OK
  Running ‘r_peterson.R’
  comparing ‘r_peterson.Rout’ to ‘r_peterson.Rout.save’ ... OK
  Running ‘r_resid.R’
  comparing ‘r_resid.Rout’ to ‘r_resid.Rout.save’ ... OK
  Running ‘r_sas.R’
  comparing ‘r_sas.Rout’ to ‘r_sas.Rout.save’ ... OK
  Running ‘r_scale.R’
  comparing ‘r_scale.Rout’ to ‘r_scale.Rout.save’ ... OK
  Running ‘r_stanford.R’
  comparing ‘r_stanford.Rout’ to ‘r_stanford.Rout.save’ ... OK
  Running ‘r_strata.R’
  comparing ‘r_strata.Rout’ to ‘r_strata.Rout.save’ ... OK
  Running ‘r_tdist.R’
  comparing ‘r_tdist.Rout’ to ‘r_tdist.Rout.save’ ... OK
  Running ‘r_user.R’
  comparing ‘r_user.Rout’ to ‘r_user.Rout.save’ ... OK
  Running ‘ratetable.R’
  comparing ‘ratetable.Rout’ to ‘ratetable.Rout.save’ ... OK
  Running ‘singtest.R’
  comparing ‘singtest.Rout’ to ‘singtest.Rout.save’ ... OK
  Running ‘strata2.R’
  comparing ‘strata2.Rout’ to ‘strata2.Rout.save’ ... OK
  Running ‘stratatest.R’
  comparing ‘stratatest.Rout’ to ‘stratatest.Rout.save’ ... OK
  Running ‘summary_survfit.R’
  comparing ‘summary_survfit.Rout’ to ‘summary_survfit.Rout.save’ ... OK
  Running ‘surv.R’
  comparing ‘surv.Rout’ to ‘surv.Rout.save’ ... OK
  Running ‘survSplit.R’
  comparing ‘survSplit.Rout’ to ‘survSplit.Rout.save’ ... OK
  Running ‘survfit1.R’
  comparing ‘survfit1.Rout’ to ‘survfit1.Rout.save’ ... OK
  Running ‘survfit2.R’
  comparing ‘survfit2.Rout’ to ‘survfit2.Rout.save’ ... OK
  Running ‘survreg1.R’
  Running ‘survreg2.R’
  comparing ‘survreg2.Rout’ to ‘survreg2.Rout.save’ ... OK
  Running ‘survtest.R’
  comparing ‘survtest.Rout’ to ‘survtest.Rout.save’ ... OK
  Running ‘testci.R’
  comparing ‘testci.Rout’ to ‘testci.Rout.save’ ... OK
  Running ‘testci2.R’
  comparing ‘testci2.Rout’ to ‘testci2.Rout.save’ ... OK
  Running ‘testnull.R’
  comparing ‘testnull.Rout’ to ‘testnull.Rout.save’ ... OK
  Running ‘testreg.R’
  comparing ‘testreg.Rout’ to ‘testreg.Rout.save’ ... OK
  Running ‘tiedtime.R’
  comparing ‘tiedtime.Rout’ to ‘tiedtime.Rout.save’ ... OK
  Running ‘tmerge.R’
  comparing ‘tmerge.Rout’ to ‘tmerge.Rout.save’ ... OK
  Running ‘tmerge2.R’
  comparing ‘tmerge2.Rout’ to ‘tmerge2.Rout.save’ ... OK
  Running ‘tmerge3.R’
  comparing ‘tmerge3.Rout’ to ‘tmerge3.Rout.save’ ... OK
  Running ‘tt.R’
  comparing ‘tt.Rout’ to ‘tt.Rout.save’ ... OK
  Running ‘turnbull.R’
  comparing ‘turnbull.Rout’ to ‘turnbull.Rout.save’ ... OK
  Running ‘yates0.R’
  comparing ‘yates0.Rout’ to ‘yates0.Rout.save’ ...
50c50
< [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’ ... OK
  Running ‘yates2.R’
Running vignettes for package ‘survival’
  Running ‘adjcurve.Rnw’
  Running ‘compete.Rnw’
  Running ‘concordance.Rnw’
  Running ‘multi.Rnw’
  Running ‘population.Rnw’
  Running ‘splines.Rnw’
  Running ‘survival.Rnw’
  Running ‘tests.Rnw’
  Running ‘tiedtimes.Rnw’
  Running ‘timedep.Rnw’
  Running ‘validate.Rnw’
Testing examples for package ‘boot’
  comparing ‘boot-Ex.Rout’ to ‘boot-Ex.Rout.save’ ... OK
Running specific tests for package ‘boot’
Testing examples for package ‘cluster’
Running specific tests for package ‘cluster’
  Running ‘agnes-ex.R’
  comparing ‘agnes-ex.Rout’ to ‘agnes-ex.Rout.save’ ... OK
  Running ‘clara-NAs.R’
  comparing ‘clara-NAs.Rout’ to ‘clara-NAs.Rout.save’ ... OK
  Running ‘clara-ex.R’
  Running ‘clara.R’
  comparing ‘clara.Rout’ to ‘clara.Rout.save’ ... OK
  Running ‘clusplot-out.R’
  comparing ‘clusplot-out.Rout’ to ‘clusplot-out.Rout.save’ ... OK
  Running ‘daisy-ex.R’
  comparing ‘daisy-ex.Rout’ to ‘daisy-ex.Rout.save’ ... OK
  Running ‘diana-boots.R’
  Running ‘diana-ex.R’
  comparing ‘diana-ex.Rout’ to ‘diana-ex.Rout.save’ ... OK
  Running ‘ellipsoid-ex.R’
  comparing ‘ellipsoid-ex.Rout’ to ‘ellipsoid-ex.Rout.save’ ... OK
  Running ‘fanny-ex.R’
  Running ‘mona.R’
  comparing ‘mona.Rout’ to ‘mona.Rout.save’ ... OK
  Running ‘pam.R’
  comparing ‘pam.Rout’ to ‘pam.Rout.save’ ... OK
  Running ‘silhouette-default.R’
  comparing ‘silhouette-default.Rout’ to ‘silhouette-default.Rout.save’ ... OK
  Running ‘sweep-ex.R’
  Running ‘withAutoprint.R’
Testing examples for package ‘codetools’
Running specific tests for package ‘codetools’
  Running ‘tests.R’
Testing examples for package ‘foreign’
Running specific tests for package ‘foreign’
  Running ‘S3.R’
  comparing ‘S3.Rout’ to ‘S3.Rout.save’ ... OK
  Running ‘arff.R’
  comparing ‘arff.Rout’ to ‘arff.Rout.save’ ... OK
  Running ‘download.R’
  Running ‘minitab.R’
  comparing ‘minitab.Rout’ to ‘minitab.Rout.save’ ... OK
  Running ‘mval_bug.R’
  comparing ‘mval_bug.Rout’ to ‘mval_bug.Rout.save’ ... OK
  Running ‘octave.R’
  comparing ‘octave.Rout’ to ‘octave.Rout.save’ ... OK
  Running ‘sas.R’
  Running ‘spss.R’
  comparing ‘spss.Rout’ to ‘spss.Rout.save’ ... OK
  Running ‘stata.R’
  comparing ‘stata.Rout’ to ‘stata.Rout.save’ ... OK
  Running ‘testEmpty.R’
  comparing ‘testEmpty.Rout’ to ‘testEmpty.Rout.save’ ... OK
  Running ‘writeForeignSPSS.R’
  comparing ‘writeForeignSPSS.Rout’ to ‘writeForeignSPSS.Rout.save’ ... OK
  Running ‘xport.R’
  comparing ‘xport.Rout’ to ‘xport.Rout.save’ ... OK
Testing examples for package ‘KernSmooth’
Running specific tests for package ‘KernSmooth’
  Running ‘bkfe.R’
Testing examples for package ‘rpart’
  comparing ‘rpart-Ex.Rout’ to ‘rpart-Ex.Rout.save’ ... OK
Running specific tests for package ‘rpart’
  Running ‘backticks.R’
  comparing ‘backticks.Rout’ to ‘backticks.Rout.save’ ... OK
  Running ‘cost.R’
  comparing ‘cost.Rout’ to ‘cost.Rout.save’ ... OK
  Running ‘cptest.R’
  comparing ‘cptest.Rout’ to ‘cptest.Rout.save’ ... OK
  Running ‘priors.R’
  comparing ‘priors.Rout’ to ‘priors.Rout.save’ ... OK
  Running ‘rescale.R’
  comparing ‘rescale.Rout’ to ‘rescale.Rout.save’ ... OK
  Running ‘testall.R’
  comparing ‘testall.Rout’ to ‘testall.Rout.save’ ... OK
  Running ‘treble.R’
  comparing ‘treble.Rout’ to ‘treble.Rout.save’ ... OK
  Running ‘treble2.R’
  comparing ‘treble2.Rout’ to ‘treble2.Rout.save’ ... OK
  Running ‘treble3.R’
  comparing ‘treble3.Rout’ to ‘treble3.Rout.save’ ... OK
  Running ‘treble4.R’
  comparing ‘treble4.Rout’ to ‘treble4.Rout.save’ ... OK
  Running ‘usersplits.R’
  comparing ‘usersplits.Rout’ to ‘usersplits.Rout.save’ ... OK
  Running ‘xpred1.R’
  comparing ‘xpred1.Rout’ to ‘xpred1.Rout.save’ ... OK
  Running ‘xpred2.R’
  comparing ‘xpred2.Rout’ to ‘xpred2.Rout.save’ ... OK
Running vignettes for package ‘rpart’
  Running ‘longintro.Rnw’
  Running ‘usercode.Rnw’
Testing examples for package ‘class’
Testing examples for package ‘nnet’
Testing examples for package ‘spatial’
  comparing ‘spatial-Ex.Rout’ to ‘spatial-Ex.Rout.save’ ... OK
Running specific tests for package ‘spatial’
Testing examples for package ‘mgcv’
Running specific tests for package ‘mgcv’
  Running ‘bam.R’
  Running ‘coxpht.R’
  Running ‘gam.R’
  Running ‘mgcv-parallel.R’
  Running ‘missing.data.R’
  Running ‘single.index.R’
  Running ‘smooth.construct.so.smooth.spec.R’