No R binaries and error during 2.9.0 installation

[pawel.matykiewicz@…]

I uninstalled all previous versions of R because I though I will have quick solution but it did not help. Error looked same for upgrade though.

I goes like this:

sudo port install R
--->  Fetching R
--->  Verifying checksum(s) for R
--->  Extracting R
--->  Configuring R
--->  Building R
--->  Staging R into destroot
--->  Installing R @2.9.0_0+gcc43
--->  Activating R @2.9.0_0+gcc43
Error: Target org.macports.activate returned: Image error: /opt/local/lib/R/library/Matrix/CONTENTS already exists and does not belong to a registered port.  Unable to activate port R.
Error: Status 1 encountered during processing.

Do I really have to delete all packages to make it work?

If there is no quick resolution please advise how to install previous version of R through macports.

Thanks

[mf2k (Frank Schima)]

Either manually the delete the file and try again or just do the following:

sudo port -f activate R

[pawel.matykiewicz@…]

It works but you get a lot of warnings. Below example after removing 2 other violating packages:

Warning: File /opt/local/lib/R/library/survival/data/leukemia.dat already exists.  Moving to: /opt/local/lib/R/library/survival/data/leukemia.dat.mp_1240537426.
Warning: File /opt/local/lib/R/library/survival/data/minn2000.dat already exists.  Moving to: /opt/local/lib/R/library/survival/data/minn2000.dat.mp_1240537426.
Warning: File /opt/local/lib/R/library/survival/data/minn2004.dat already exists.  Moving to: /opt/local/lib/R/library/survival/data/minn2004.dat.mp_1240537426.
Warning: File /opt/local/lib/R/library/survival/data/minndecennial.dat already exists.  Moving to: /opt/local/lib/R/library/survival/data/minndecennial.dat.mp_1240537426.
Warning: File /opt/local/lib/R/library/survival/data/minnpred.dat already exists.  Moving to: /opt/local/lib/R/library/survival/data/minnpred.dat.mp_1240537426.
Warning: File /opt/local/lib/R/library/survival/data/pbcseq.dat already exists.  Moving to: /opt/local/lib/R/library/survival/data/pbcseq.dat.mp_1240537426.
Warning: File /opt/local/lib/R/library/survival/data/us1996.dat already exists.  Moving to: /opt/local/lib/R/library/survival/data/us1996.dat.mp_1240537426.
Warning: File /opt/local/lib/R/library/survival/data/us1997.dat already exists.  Moving to: /opt/local/lib/R/library/survival/data/us1997.dat.mp_1240537426.
Warning: File /opt/local/lib/R/library/survival/data/us1998.dat already exists.  Moving to: /opt/local/lib/R/library/survival/data/us1998.dat.mp_1240537426.
Warning: File /opt/local/lib/R/library/survival/data/us1999.dat already exists.  Moving to: /opt/local/lib/R/library/survival/data/us1999.dat.mp_1240537426.
Warning: File /opt/local/lib/R/library/survival/data/us2000.dat already exists.  Moving to: /opt/local/lib/R/library/survival/data/us2000.dat.mp_1240537426.
Warning: File /opt/local/lib/R/library/survival/data/us2001.dat already exists.  Moving to: /opt/local/lib/R/library/survival/data/us2001.dat.mp_1240537426.
Warning: File /opt/local/lib/R/library/survival/data/us2002.dat already exists.  Moving to: /opt/local/lib/R/library/survival/data/us2002.dat.mp_1240537426.
Warning: File /opt/local/lib/R/library/survival/data/us2003.dat already exists.  Moving to: /opt/local/lib/R/library/survival/data/us2003.dat.mp_1240537426.
Warning: File /opt/local/lib/R/library/survival/data/us2004.dat already exists.  Moving to: /opt/local/lib/R/library/survival/data/us2004.dat.mp_1240537426.
Warning: File /opt/local/lib/R/library/survival/data/usdecennial.dat already exists.  Moving to: /opt/local/lib/R/library/survival/data/usdecennial.dat.mp_1240537426.
Warning: File /opt/local/lib/R/library/survival/data/usinfant.dat already exists.  Moving to: /opt/local/lib/R/library/survival/data/usinfant.dat.mp_1240537426.
Warning: File /opt/local/lib/R/library/survival/help/aareg already exists.  Moving to: /opt/local/lib/R/library/survival/help/aareg.mp_1240537426.
Warning: File /opt/local/lib/R/library/survival/help/basehaz already exists.  Moving to: /opt/local/lib/R/library/survival/help/basehaz.mp_1240537426.
Warning: File /opt/local/lib/R/library/survival/help/cgd already exists.  Moving to: /opt/local/lib/R/library/survival/help/cgd.mp_1240537426.
Warning: File /opt/local/lib/R/library/survival/help/coxph.control already exists.  Moving to: /opt/local/lib/R/library/survival/help/coxph.control.mp_1240537426.
Warning: File /opt/local/lib/R/library/survival/help/dsurvreg already exists.  Moving to: /opt/local/lib/R/library/survival/help/dsurvreg.mp_1240537426.
Warning: File /opt/local/lib/R/library/survival/help/mgus already exists.  Moving to: /opt/local/lib/R/library/survival/help/mgus.mp_1240537426.
Warning: File /opt/local/lib/R/library/survival/help/pbcseq already exists.  Moving to: /opt/local/lib/R/library/survival/help/pbcseq.mp_1240537426.
Warning: File /opt/local/lib/R/library/survival/help/plot.aareg already exists.  Moving to: /opt/local/lib/R/library/survival/help/plot.aareg.mp_1240537426.
Warning: File /opt/local/lib/R/library/survival/help/print.aareg already exists.  Moving to: /opt/local/lib/R/library/survival/help/print.aareg.mp_1240537426.
Warning: File /opt/local/lib/R/library/survival/help/print.summary.coxph already exists.  Moving to: /opt/local/lib/R/library/survival/help/print.summary.coxph.mp_1240537426.
Warning: File /opt/local/lib/R/library/survival/help/print.summary.survfit already exists.  Moving to: /opt/local/lib/R/library/survival/help/print.summary.survfit.mp_1240537426.
Warning: File /opt/local/lib/R/library/survival/help/summary.aareg already exists.  Moving to: /opt/local/lib/R/library/survival/help/summary.aareg.mp_1240537426.
Warning: File /opt/local/lib/R/library/survival/help/summary.coxph already exists.  Moving to: /opt/local/lib/R/library/survival/help/summary.coxph.mp_1240537426.
Warning: File /opt/local/lib/R/library/survival/help/survConcordance already exists.  Moving to: /opt/local/lib/R/library/survival/help/survConcordance.mp_1240537426.
Warning: File /opt/local/lib/R/library/survival/help/survfit.coxph already exists.  Moving to: /opt/local/lib/R/library/survival/help/survfit.coxph.mp_1240537426.
Warning: File /opt/local/lib/R/library/survival/help/survregDtest already exists.  Moving to: /opt/local/lib/R/library/survival/help/survregDtest.mp_1240537426.
Warning: File /opt/local/lib/R/library/survival/html/aareg.html already exists.  Moving to: /opt/local/lib/R/library/survival/html/aareg.html.mp_1240537426.
Warning: File /opt/local/lib/R/library/survival/html/basehaz.html already exists.  Moving to: /opt/local/lib/R/library/survival/html/basehaz.html.mp_1240537426.
Warning: File /opt/local/lib/R/library/survival/html/cgd.html already exists.  Moving to: /opt/local/lib/R/library/survival/html/cgd.html.mp_1240537426.
Warning: File /opt/local/lib/R/library/survival/html/coxph.control.html already exists.  Moving to: /opt/local/lib/R/library/survival/html/coxph.control.html.mp_1240537426.
Warning: File /opt/local/lib/R/library/survival/html/dsurvreg.html already exists.  Moving to: /opt/local/lib/R/library/survival/html/dsurvreg.html.mp_1240537426.
Warning: File /opt/local/lib/R/library/survival/html/mgus.html already exists.  Moving to: /opt/local/lib/R/library/survival/html/mgus.html.mp_1240537426.
Warning: File /opt/local/lib/R/library/survival/html/pbcseq.html already exists.  Moving to: /opt/local/lib/R/library/survival/html/pbcseq.html.mp_1240537426.
Warning: File /opt/local/lib/R/library/survival/html/plot.aareg.html already exists.  Moving to: /opt/local/lib/R/library/survival/html/plot.aareg.html.mp_1240537426.
Warning: File /opt/local/lib/R/library/survival/html/print.aareg.html already exists.  Moving to: /opt/local/lib/R/library/survival/html/print.aareg.html.mp_1240537426.
Warning: File /opt/local/lib/R/library/survival/html/print.summary.coxph.html already exists.  Moving to: /opt/local/lib/R/library/survival/html/print.summary.coxph.html.mp_1240537426.
Warning: File /opt/local/lib/R/library/survival/html/print.summary.survfit.html already exists.  Moving to: /opt/local/lib/R/library/survival/html/print.summary.survfit.html.mp_1240537426.
Warning: File /opt/local/lib/R/library/survival/html/summary.aareg.html already exists.  Moving to: /opt/local/lib/R/library/survival/html/summary.aareg.html.mp_1240537426.
Warning: File /opt/local/lib/R/library/survival/html/summary.coxph.html already exists.  Moving to: /opt/local/lib/R/library/survival/html/summary.coxph.html.mp_1240537426.
Warning: File /opt/local/lib/R/library/survival/html/survConcordance.html already exists.  Moving to: /opt/local/lib/R/library/survival/html/survConcordance.html.mp_1240537426.
Warning: File /opt/local/lib/R/library/survival/html/survfit.coxph.html already exists.  Moving to: /opt/local/lib/R/library/survival/html/survfit.coxph.html.mp_1240537426.
Warning: File /opt/local/lib/R/library/survival/html/survregDtest.html already exists.  Moving to: /opt/local/lib/R/library/survival/html/survregDtest.html.mp_1240537426.
Warning: File /opt/local/lib/R/library/survival/latex/aareg.tex already exists.  Moving to: /opt/local/lib/R/library/survival/latex/aareg.tex.mp_1240537426.
Warning: File /opt/local/lib/R/library/survival/latex/basehaz.tex already exists.  Moving to: /opt/local/lib/R/library/survival/latex/basehaz.tex.mp_1240537426.
Warning: File /opt/local/lib/R/library/survival/latex/cgd.tex already exists.  Moving to: /opt/local/lib/R/library/survival/latex/cgd.tex.mp_1240537426.
Warning: File /opt/local/lib/R/library/survival/latex/coxph.control.tex already exists.  Moving to: /opt/local/lib/R/library/survival/latex/coxph.control.tex.mp_1240537426.
Warning: File /opt/local/lib/R/library/survival/latex/dsurvreg.tex already exists.  Moving to: /opt/local/lib/R/library/survival/latex/dsurvreg.tex.mp_1240537426.
Warning: File /opt/local/lib/R/library/survival/latex/mgus.tex already exists.  Moving to: /opt/local/lib/R/library/survival/latex/mgus.tex.mp_1240537426.
Warning: File /opt/local/lib/R/library/survival/latex/pbcseq.tex already exists.  Moving to: /opt/local/lib/R/library/survival/latex/pbcseq.tex.mp_1240537426.
Warning: File /opt/local/lib/R/library/survival/latex/plot.aareg.tex already exists.  Moving to: /opt/local/lib/R/library/survival/latex/plot.aareg.tex.mp_1240537426.
Warning: File /opt/local/lib/R/library/survival/latex/print.aareg.tex already exists.  Moving to: /opt/local/lib/R/library/survival/latex/print.aareg.tex.mp_1240537426.
Warning: File /opt/local/lib/R/library/survival/latex/print.summary.coxph.tex already exists.  Moving to: /opt/local/lib/R/library/survival/latex/print.summary.coxph.tex.mp_1240537426.
Warning: File /opt/local/lib/R/library/survival/latex/print.summary.survfit.tex already exists.  Moving to: /opt/local/lib/R/library/survival/latex/print.summary.survfit.tex.mp_1240537426.
Warning: File /opt/local/lib/R/library/survival/latex/summary.aareg.tex already exists.  Moving to: /opt/local/lib/R/library/survival/latex/summary.aareg.tex.mp_1240537426.
Warning: File /opt/local/lib/R/library/survival/latex/summary.coxph.tex already exists.  Moving to: /opt/local/lib/R/library/survival/latex/summary.coxph.tex.mp_1240537426.
Warning: File /opt/local/lib/R/library/survival/latex/survConcordance.tex already exists.  Moving to: /opt/local/lib/R/library/survival/latex/survConcordance.tex.mp_1240537426.
Warning: File /opt/local/lib/R/library/survival/latex/survfit.coxph.tex already exists.  Moving to: /opt/local/lib/R/library/survival/latex/survfit.coxph.tex.mp_1240537426.
Warning: File /opt/local/lib/R/library/survival/latex/survregDtest.tex already exists.  Moving to: /opt/local/lib/R/library/survival/latex/survregDtest.tex.mp_1240537426.
Warning: File /opt/local/lib/R/library/survival/R-ex/aareg.R already exists.  Moving to: /opt/local/lib/R/library/survival/R-ex/aareg.R.mp_1240537426.
Warning: File /opt/local/lib/R/library/survival/R-ex/dsurvreg.R already exists.  Moving to: /opt/local/lib/R/library/survival/R-ex/dsurvreg.R.mp_1240537426.
Warning: File /opt/local/lib/R/library/survival/R-ex/summary.aareg.R already exists.  Moving to: /opt/local/lib/R/library/survival/R-ex/summary.aareg.R.mp_1240537426.
Warning: File /opt/local/lib/R/library/survival/R-ex/summary.coxph.R already exists.  Moving to: /opt/local/lib/R/library/survival/R-ex/summary.coxph.R.mp_1240537426.
Warning: File /opt/local/lib/R/library/survival/R-ex/survConcordance.R already exists.  Moving to: /opt/local/lib/R/library/survival/R-ex/survConcordance.R.mp_1240537426.
Warning: File /opt/local/lib/R/library/survival/R-ex/survfit.coxph.R already exists.  Moving to: /opt/local/lib/R/library/survival/R-ex/survfit.coxph.R.mp_1240537426.
Warning: File /opt/local/lib/R/library/survival/R-ex/survregDtest.R already exists.  Moving to: /opt/local/lib/R/library/survival/R-ex/survregDtest.R.mp_1240537426.

[kjell.konis@…]

If I were you I would (1) uninstall the R port, (2) delete the directory /opt/local/lib/R then (3) reinstall the R port without forcing. You will need to reinstall all your packages (from source) after this - but you should do this anyways when upgrading from R 2.x._ to R 2.(x+1)._. Right now you have packages built for R 2.8.x installed in R 2.9.0 and they may or may not be compatible. In the case of packages for numerical computations (e.g., Matrix) this may take the form of appearing to work but giving the wrong answer.

You can avoid R package issues in the future by not using root privileges when installing packages. R will then put them in a personal library for you.

Cheers.

Replying to pawel.matykiewicz@…:

I uninstalled all previous versions of R because I though I will have quick solution but it did not help. Error looked same for upgrade though.

I goes like this:

sudo port install R
--->  Fetching R
--->  Verifying checksum(s) for R
--->  Extracting R
--->  Configuring R
--->  Building R
--->  Staging R into destroot
--->  Installing R @2.9.0_0+gcc43
--->  Activating R @2.9.0_0+gcc43
Error: Target org.macports.activate returned: Image error: /opt/local/lib/R/library/Matrix/CONTENTS already exists and does not belong to a registered port.  Unable to activate port R.
Error: Status 1 encountered during processing.

Do I really have to delete all packages to make it work?

If there is no quick resolution please advise how to install previous version of R through macports.

Thanks

[(none)]

Milestone Port Bugs deleted