The help file of the R bitmap function says that I have to set the environment variable R_GSCMD to the path of my Ghostscript installation. How do I set this variable (either by commandline or in R.app for Mac)? Sorry if this sounds like a very basic question, but I could not find the answer anywhere else. Many thanks Andreas -- -------------------------- Andreas Zankl, MD Division of Molecular Pediatrics Clinique Infantile 02/50 CHUV Avenue Pierre Decker 2 CH-1011 Lausanne Switzerland Phone: +41-21-3143778 Fax: +41-21-3143546 Email: andreas.zankl at gmail.com
On Thu, 20 Oct 2005, Andreas Zankl wrote:> The help file of the R bitmap function says that I have to set the > environment variable R_GSCMD to the path of my Ghostscript > installation.Actually, it does not say that. It says you _can_ specify the path to your executable (not the installation) that way. It will work without doing so if the executable 'gs' (on a Unix-alike) is on your path, which it normally is on Unix-alikes.> How do I set this variable (either by commandline or in > R.app for Mac)? Sorry if this sounds like a very basic question, but > I could not find the answer anywhere else.?Sys.putenv for how to do it from R. help.search("environment variable") got me there. -- 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
See the first paragraph of ?Startup. Andy> From: Andreas Zankl > > Thanks. Sys.putenv did work, however this has to be set every > time I start R. > > gs is on my path and works fine under Unix, but I get the following > error when running bitmap (without setting R_GSCMD first): > > /bin/sh: line 1: gs: command not found > > I assume the problem is related to the fact that I am using the csh > shell, while the new Mac OS X default shell is now bash. So I guess > my .csh path settings are ignored by R calling bash. I solved the > problem by adding my R_GSCMD settings to the Renviron file > (R_GSCMD=${RGSCMD-'/sw/bin/gs'} in my case). Hope this helps anyone > with the same problem. > > Thanks again for your help! > Andreas > > > > At 12:51 +0100 20.10.2005, Prof Brian Ripley wrote: > >On Thu, 20 Oct 2005, Andreas Zankl wrote: > > > >>The help file of the R bitmap function says that I have to set the > >>environment variable R_GSCMD to the path of my Ghostscript > >>installation. > > > >Actually, it does not say that. It says you _can_ specify the path > >to your executable (not the installation) that way. It will work > >without doing so if the executable 'gs' (on a Unix-alike) is on your > >path, which it normally is on Unix-alikes. > > > >>How do I set this variable (either by commandline or in > >>R.app for Mac)? Sorry if this sounds like a very basic question, but > >>I could not find the answer anywhere else. > > > >?Sys.putenv for how to do it from R. help.search("environment > >variable") got me there. > > > >-- > >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 > > > -- > PLEASE NOTE MY NEW EMAIL ADDRESS: ANDREAS.ZANKL at GMAIL.COM > > -------------------------- > Andreas Zankl, MD > Division of Molecular Pediatrics > Clinique Infantile 02/50 > CHUV > Avenue Pierre Decker 2 > CH-1011 Lausanne > Switzerland > Phone: +41-21-3143778 > Fax: +41-21-3143546 > Email: andreas.zankl at gmail.com > > ______________________________________________ > 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 > >
Renviron is in an odd places on Macs: /Library/Frameworks/R.framework/Versions/2.1.1/Resources/etc/Renviron As suggested in ?Startup, I added the R_GSCMD variable to Renviron.site instead. Thanks for your help Andreas> > >>See the first paragraph of ?Startup. > >If this is literally `Renviron' (not ~/.Renviron or Renviron.site) >see also the Note in that help file. > >> >>Andy >> >>>From: Andreas Zankl >>> >>>Thanks. Sys.putenv did work, however this has to be set every >>>time I start R. >>> >>>gs is on my path and works fine under Unix, but I get the following >>>error when running bitmap (without setting R_GSCMD first): >>> >>>/bin/sh: line 1: gs: command not found >>> >>>I assume the problem is related to the fact that I am using the csh >>>shell, while the new Mac OS X default shell is now bash. So I guess >>>my .csh path settings are ignored by R calling bash. I solved the >>>problem by adding my R_GSCMD settings to the Renviron file >>>(R_GSCMD=${RGSCMD-'/sw/bin/gs'} in my case). Hope this helps anyone >>>with the same problem. >>> >>>Thanks again for your help! >>>Andreas >>> >>> >>> >>>At 12:51 +0100 20.10.2005, Prof Brian Ripley wrote: >>>>On Thu, 20 Oct 2005, Andreas Zankl wrote: >>>> >>>>>The help file of the R bitmap function says that I have to set the >>>>>environment variable R_GSCMD to the path of my Ghostscript >>>>>installation. >>>> >>>>Actually, it does not say that. It says you _can_ specify the path >>>>to your executable (not the installation) that way. It will work >>>>without doing so if the executable 'gs' (on a Unix-alike) is on your >>>>path, which it normally is on Unix-alikes. >>>> >>>>>How do I set this variable (either by commandline or in >>>>>R.app for Mac)? Sorry if this sounds like a very basic question, but >>>>>I could not find the answer anywhere else. >>>> >>>>?Sys.putenv for how to do it from R. help.search("environment >>>>variable") got me there. >>>> >>>>-- >>>>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 >>> >>> >>>-- >>>PLEASE NOTE MY NEW EMAIL ADDRESS: ANDREAS.ZANKL at GMAIL.COM >>> >>>-------------------------- >>>Andreas Zankl, MD >>>Division of Molecular Pediatrics >>>Clinique Infantile 02/50 >>>CHUV >>>Avenue Pierre Decker 2 >>>CH-1011 Lausanne >>>Switzerland >>>Phone: +41-21-3143778 >>>Fax: +41-21-3143546 >>>Email: andreas.zankl at gmail.com >>> >>>______________________________________________ >>>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 >>> >> >> >>------------------------------------------------------------------------------ >>Notice: This e-mail message, together with any attachments, >>contains information of Merck & Co., Inc. (One Merck Drive, >>Whitehouse Station, New Jersey, USA 08889), and/or its affiliates >>(which may be known outside the United States as Merck Frosst, >>Merck Sharp & Dohme or MSD and in Japan, as Banyu) that may be >>confidential, proprietary copyrighted and/or legally privileged. It >>is intended solely for the use of the individual or entity named on >>this message. If you are not the intended recipient, and have >>received this message in error, please notify us immediately by >>reply e-mail and then delete it from your system. >>------------------------------------------------------------------------------ >> > >-- >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