Dear All, I've got into the habit of installing R from the precompiled Debian binaries, including many of the packages from the r-cran-* Debian packages, and later building from source (e.g., to link against Goto's BLAS, or to build patched versions, etc). I install the newly built R to the very same place (/usr/lib/R). This allows me to build and update R when I wish, AND provides the ease of quickly updating many packages. Things have always worked fine, but after a few funny problems (which could be unrelated to the process itself) I've started wondering if this is a rather silly thing to do, and if I should keep my own build separate from the Debian stuff. Any advice would be much appreciated. Thanks, R. -- RamÂón DÂÃaz-Uriarte Bioinformatics Unit Centro Nacional de Investigaciones OncolÂógicas (CNIO) (Spanish National Cancer Center) Melchor FernÂández Almagro, 3 28029 Madrid (Spain) Fax: +-34-91-224-6972 Phone: +-34-91-224-6900 http://ligarto.org/rdiaz PGP KeyID: 0xE89B3462 (http://ligarto.org/rdiaz/0xE89B3462.asc) **NOTA DE CONFIDENCIALIDAD** Este correo electrÂónico, y en su caso los ficheros adjuntos, pueden contener informaciÂón protegida para el uso exclusivo de su destinatario. Se prohÂÃbe la distribuciÂón, reproducciÂón o cualquier otro tipo de transmisiÂón por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido. **CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies.
building from source after installing binary package
5 messages · Uwe Ligges, Brian Ripley, Ramon Diaz-Uriarte
Diaz.Ramon wrote:
Dear All, I've got into the habit of installing R from the precompiled Debian binaries, including many of the packages from the r-cran-* Debian packages, and later building from source (e.g., to link against Goto's BLAS, or to build patched versions, etc). I install the newly built R to the very same place (/usr/lib/R). This allows me to build and update R when I wish, AND provides the ease of quickly updating many packages. Things have always worked fine, but after a few funny problems (which could be unrelated to the process itself) I've started wondering if this is a rather silly thing to do, and if I should keep my own build separate from the Debian stuff. Any advice would be much appreciated.
Yes, simply install to another directory, e.g. by telling configure: ./configure --prefix=/I/want/to/have/R/installed/here Uwe Ligges
Thanks, R. -- RamÂón DÂÃaz-Uriarte Bioinformatics Unit Centro Nacional de Investigaciones OncolÂógicas (CNIO) (Spanish National Cancer Center) Melchor FernÂández Almagro, 3 28029 Madrid (Spain) Fax: +-34-91-224-6972 Phone: +-34-91-224-6900 http://ligarto.org/rdiaz PGP KeyID: 0xE89B3462 (http://ligarto.org/rdiaz/0xE89B3462.asc) **NOTA DE CONFIDENCIALIDAD** Este correo electrÂónico, y en su caso los ficheros adjuntos, pueden contener informaciÂón protegida para el uso exclusivo de su destinatario. Se prohÂÃbe la distribuciÂón, reproducciÂón o cualquier otro tipo de transmisiÂón por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido. **CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies.
______________________________________________ R-help at stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
On Fri, 6 May 2005, Uwe Ligges wrote:
Diaz.Ramon wrote:
Dear All, I've got into the habit of installing R from the precompiled Debian binaries, including many of the packages from the r-cran-* Debian packages, and later building from source (e.g., to link against Goto's BLAS, or to build patched versions, etc). I install the newly built R to the very same place (/usr/lib/R). This allows me to build and update R when I wish, AND provides the ease of quickly updating many packages. Things have always worked fine, but after a few funny problems (which could be unrelated to the process itself) I've started wondering if this is a rather silly thing to do, and if I should keep my own build separate from the Debian stuff. Any advice would be much appreciated.
Yes, simply install to another directory, e.g. by telling configure: ./configure --prefix=/I/want/to/have/R/installed/here
I don't think that is the point: Ramon must have done that as the default installation place is /usr/local/lib/R. I think this is a Debian-specific question (there is a R-debian list) and the point may be to make use of the binary Debian packages. I would advocate installing R from the sources into /usr/local, and having separate directory trees both for packages you install and for Debian packages. Then you can manipulate which packages are seen via R_LIBS.
Brian D. Ripley, ripley at stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UK Fax: +44 1865 272595
Dear Uwe, Yes, sure, I understand how to install to another directory. I think I was not very clear, because my doubt is whether I should do that, or if it is OK to install to the very same place where Debian left the previous installation. By doing the later I save myself having to reinstall packages, etc, etc. R.
On Friday 06 May 2005 08:53, Uwe Ligges wrote:
Diaz.Ramon wrote:
Dear All, I've got into the habit of installing R from the precompiled Debian binaries, including many of the packages from the r-cran-* Debian packages, and later building from source (e.g., to link against Goto's BLAS, or to build patched versions, etc). I install the newly built R to the very same place (/usr/lib/R). This allows me to build and update R when I wish, AND provides the ease of quickly updating many packages. Things have always worked fine, but after a few funny problems (which could be unrelated to the process itself) I've started wondering if this is a rather silly thing to do, and if I should keep my own build separate from the Debian stuff. Any advice would be much appreciated.
Yes, simply install to another directory, e.g. by telling configure: ./configure --prefix=/I/want/to/have/R/installed/here Uwe Ligges
Thanks, R. -- RamÂón DÂÃaz-Uriarte Bioinformatics Unit Centro Nacional de Investigaciones OncolÂógicas (CNIO) (Spanish National Cancer Center) Melchor FernÂández Almagro, 3 28029 Madrid (Spain) Fax: +-34-91-224-6972 Phone: +-34-91-224-6900 http://ligarto.org/rdiaz PGP KeyID: 0xE89B3462 (http://ligarto.org/rdiaz/0xE89B3462.asc) **NOTA DE CONFIDENCIALIDAD** Este correo electrÂónico, y en su caso los ficheros adjuntos, pueden contener informaciÂón protegida para el uso exclusivo de su destinatario. Se prohÂÃbe la distribuciÂón, reproducciÂón o cualquier otro tipo de transmisiÂón por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido. **CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies.
______________________________________________ R-help at stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RamÂón DÂÃaz-Uriarte Bioinformatics Unit Centro Nacional de Investigaciones OncolÂógicas (CNIO) (Spanish National Cancer Center) Melchor FernÂández Almagro, 3 28029 Madrid (Spain) Fax: +-34-91-224-6972 Phone: +-34-91-224-6900 http://ligarto.org/rdiaz PGP KeyID: 0xE89B3462 (http://ligarto.org/rdiaz/0xE89B3462.asc) **NOTA DE CONFIDENCIALIDAD** Este correo electrÂónico, y en su caso los ficheros adjuntos, pueden contener informaciÂón protegida para el uso exclusivo de su destinatario. Se prohÂÃbe la distribuciÂón, reproducciÂón o cualquier otro tipo de transmisiÂón por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido. **CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies.
On Friday 06 May 2005 09:48, Prof Brian Ripley wrote:
On Fri, 6 May 2005, Uwe Ligges wrote:
Diaz.Ramon wrote:
Dear All, I've got into the habit of installing R from the precompiled Debian binaries, including many of the packages from the r-cran-* Debian packages, and later building from source (e.g., to link against Goto's BLAS, or to build patched versions, etc). I install the newly built R to the very same place (/usr/lib/R). This allows me to build and update R when I wish, AND provides the ease of quickly updating many packages. Things have always worked fine, but after a few funny problems (which could be unrelated to the process itself) I've started wondering if this is a rather silly thing to do, and if I should keep my own build separate from the Debian stuff. Any advice would be much appreciated.
Yes, simply install to another directory, e.g. by telling configure: ./configure --prefix=/I/want/to/have/R/installed/here
I don't think that is the point: Ramon must have done that as the default installation place is /usr/local/lib/R.
Yes, I did change the --prefix because Debian installs to /usr/lib.
I think this is a Debian-specific question (there is a R-debian list) and the point may be to make use of the binary Debian packages. I would
Yes, that is correct (I guess I was not being very clear... too late last night). I'll ask in the debian list; I asked here just in case people with other GNU/Linux distributions did (or did not) do similar things.
advocate installing R from the sources into /usr/local, and having separate directory trees both for packages you install and for Debian packages. Then you can manipulate which packages are seen via R_LIBS.
Thanks. I'll try that. Best, R.
Ram??n D??az-Uriarte Bioinformatics Unit Centro Nacional de Investigaciones Oncol??gicas (CNIO) (Spanish National Cancer Center) Melchor Fern??ndez Almagro, 3 28029 Madrid (Spain) Fax: +-34-91-224-6972 Phone: +-34-91-224-6900 http://ligarto.org/rdiaz PGP KeyID: 0xE89B3462 (http://ligarto.org/rdiaz/0xE89B3462.asc) **NOTA DE CONFIDENCIALIDAD** Este correo electr??nico, y en su caso los ficheros adjuntos, pueden contener informaci??n protegida para el uso exclusivo de su destinatario. Se proh??be la distribuci??n, reproducci??n o cualquier otro tipo de transmisi??n por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido. **CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies.