Dear all,
When creating new functions in a package, there is a "See also"
component in
the Rd file.
Usually one uses \link{otherfun}, if the other function is from the same
package, or \link[otherpackage]{otherfun} otherwise.
The trouble is that I install new packages not in the default R library
folder, but into some other subfolder in my home, so the link searches
for "otherpackage" in my home subfolder.
Is there a method to create links to functions from the base package, for
example (which is installed by default in the normal library folder)?
Thank you,
Adrian
--
Adrian Dusa
Romanian Social Data Archive
1, Schitu Magureanu Bd
050025 Bucharest sector 5
Romania
Tel./Fax: +40 21 3126618 \
+40 21 3120210 / int.101
On 11/14/2007 8:49 AM, Adrian Dusa wrote:> Dear all, > > When creating new functions in a package, there is a "See also" component in > the Rd file. > Usually one uses \link{otherfun}, if the other function is from the same > package, or \link[otherpackage]{otherfun} otherwise. > > The trouble is that I install new packages not in the default R library > folder, but into some other subfolder in my home, so the link searches > for "otherpackage" in my home subfolder. > > Is there a method to create links to functions from the base package, for > example (which is installed by default in the normal library folder)?I believe this is normally automatic in platforms other than Windows. On Windows, the answer is no. The problem is that in most cases R isn't in charge of the help file viewing. There isn't a good way to make a link from an HTML file to a location that isn't known in advance, for example. On Unix-alikes, the workaround is to build soft links to all the packages in a standard location; but soft links don't work on Windows (and we don't want to get into the almost-undocumented hard links that exist on some Windows file systems). Duncan Murdoch
On Wed, 14 Nov 2007, Adrian Dusa wrote:> > Dear all, > > When creating new functions in a package, there is a "See also" component in > the Rd file. > Usually one uses \link{otherfun}, if the other function is from the same > package, or \link[otherpackage]{otherfun} otherwise.I think you have misread the manual here: There are two other forms of optional argument specified as \link[pkg]{foo} and \link[pkg:bar]{foo} to link to the package pkg, to files foo.html and bar.html respectively. These are rarely needed, perhaps to refer to not-yet-installed packages (but there the HTML help system will resolve the link at run time) or in the normally undesirable event that more than one package offers help on a topic (in which case the present package has precedence so this is only needed to refer to other packages) Note: 'rarely needed'.> The trouble is that I install new packages not in the default R library > folder, but into some other subfolder in my home, so the link searches > for "otherpackage" in my home subfolder. > > Is there a method to create links to functions from the base package, for > example (which is installed by default in the normal library folder)?What OS is this? (As I recall you used Linux last time you posted.) In any case, on all OSes you will be able to do cross-library links to the base package without having to do anything further (and CRAN packages are full of them). On Unix-alikes the help files are all linked into a single virtual library, and on Windows links to the base package (and a few others) from other libraries are fixed up on installation by link.html.help (see its help). -- 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
On Thu, 15 Nov 2007, Adrian Dusa wrote:> Dear Prof. Ripley, > > On Wednesday 14 November 2007, Prof Brian Ripley wrote: >> On Wed, 14 Nov 2007, Adrian Dusa wrote: >>> Dear all, >>> >>> When creating new functions in a package, there is a "See also" component >>> in the Rd file. >>> Usually one uses \link{otherfun}, if the other function is from the same >>> package, or \link[otherpackage]{otherfun} otherwise. >> >> I think you have misread the manual here: >> >> There are two other forms of optional argument specified as >> \link[pkg]{foo} and \link[pkg:bar]{foo} to link to the package pkg, to >> files foo.html and bar.html respectively. These are rarely needed, >> perhaps to refer to not-yet-installed packages (but there the HTML >> help system will resolve the link at run time) or in the normally >> undesirable event that more than one package offers help on a topic >> (in which case the present package has precedence so this is only >> needed to refer to other packages) >> >> Note: 'rarely needed'. > > Ah-haa, thanks for the clarification. I could have directly used > \code{\link{anova}} > to refer to the anova() from package stats which is also installed by default > in the same installation folder as the base package. > > >>> The trouble is that I install new packages not in the default R library >>> folder, but into some other subfolder in my home, so the link searches >>> for "otherpackage" in my home subfolder. >>> >>> Is there a method to create links to functions from the base package, for >>> example (which is installed by default in the normal library folder)? >> >> What OS is this? (As I recall you used Linux last time you posted.) > > Linux it is, I only thought the question should be platform independent. > >> In any case, on all OSes you will be able to do cross-library links to the >> base package without having to do anything further (and CRAN packages are >> full of them). On Unix-alikes the help files are all linked into a single >> virtual library, and on Windows links to the base package (and a few >> others) from other libraries are fixed up on installation by >> link.html.help (see its help). > > Indeed, link.html.help() resolves all the links under Windows (where I > suspected the biggest trouble would be). It is strangely under Linux that I > am not able to resolve the links (most surely I do something wrong). > > Using as above: > \code{\link{anova}} > > the html help file directs to > file:///home/adi/myRlibrary/stats/html/anova.htmlI hope it is actually ../../stats/html/anova.html and the browser is interpreting that as a full URL.> instead of > file:///usr/lib/R/library/stats/html/anova.htmlBut at run time help.start() creates links into a subdirectory of tempdir(). As in> help.start()Making links in per-session dir ... If '/home/ripley/bin/firefox' is already running, it is *not* restarted, and you must switch to its window. Otherwise, be patient ... and without that> help("anova", htmlhelp=TRUE)Help for 'anova' is shown in browser /home/ripley/bin/firefox ... Use help("anova", htmlhelp = FALSE) or options(htmlhelp = FALSE) to revert. Warning message: In .show_help_on_topic_as_HTML(file, topic) : Using non-linked HTML file: style sheet and hyperlinks may be incorrect and note the last line. (In case anyone wonders about the browser path: I am running 32-bit Firefox on x86_64 Linux.) -- 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
On Thursday 15 November 2007, Prof Brian Ripley wrote:> [...] > > > > Using as above: > > \code{\link{anova}} > > > > the html help file directs to > > file:///home/adi/myRlibrary/stats/html/anova.html > > I hope it is actually ../../stats/html/anova.html and the browser is > interpreting that as a full URL. > > > instead of > > file:///usr/lib/R/library/stats/html/anova.html > > But at run time help.start() creates links into a subdirectory of > tempdir(). As in > > > help.start()I got it. Perhaps it would be useful to have another startup option, something like: options(htmlLinksResolve=TRUE) that one could use in the .First() function from .Rprofile I tried using help.start() in .Rprofile, but it throws a (probably obvious) error: Error: could not find function "help.start" For my personal purposes, all questions have been answered though. Thank you very much, Adrian -- Adrian Dusa Romanian Social Data Archive 1, Schitu Magureanu Bd 050025 Bucharest sector 5 Romania Tel./Fax: +40 21 3126618 \ +40 21 3120210 / int.101
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