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Revision 396 - Directory Listing
Modified Tue Feb 18 13:07:32 2014 UTC (5 years, 3 months ago) by markus
This is the next intermediate commit.
Its main purpose is to make the package pass the cran checks so that further collaboration is not hindered.
Many of the functions I introduced and documented sparsely are not too probable to survive in their current 
form. 
The reason is the following:
Regarding design this version is in the middle of the path from the aspect oriented version I started with to the hierarchical version I have in mind and could maintain much easier.
E.g. I got rid of package.skeleton and inlinedocs now writes (most of ) the rd files.
This is not true for lists and similar stuff yet.
My final goal would be to get also rid of modify.Rd.file and move its functionality to the functions that now replace 
package.skeleton. 
If that is achieved we would be left with only two steps ( or "aspects").
1.) gather the information from the source into an environment
2.) pass the whole environment to the various Rd file writers that write the completed files instead of parsing the templates

The last step
3.) (filling the *.Rd files with  content)
    
would not be necessary any longer.

I also hope to simplify the first step considerably.
1.1)
When I started the most abstract thing we had to deal with was the list of objects.
This however does not contain generics, methods or classes.
To extract those you need the whole (populated) environment.
So step 1) will in future just populate an environment and leave the details to specialized functions. 
E.g. the (present) object list would then only be created by the function that writes Rd files for functions.
The function that document Methods dont need it.
At the moment the interfaces are in the process of change so that objects, the  environment , Methodlists, lists of Generics  are passed around for everyone to pick what he needs. This intermediate mess is not there to stay.

1.2) 
A second thing that caused a lot of work, was the parsing of the code files to produce the doc links.
I introduced a good deal of duplication here, that is however also not there to stay but a step towards reducing this kind of thing altogether but in tiny steps (seperately for classes methods and so on)
I would very much like to avoid parsing a setMethod (or setClass) statement altogether.
Presently this is necessary to find out the signature of the mehtod in question only to store the doc link relevant info  with the right key to rejoin it later with the other docs for that method.
The effort to do so is enormous. E.g. I have to reassemble the argument list of a setMethod( )call to be sure what is what in the following text. The sad thing is that the R parser does this (effortlessly) anyway when the environment is populated.
Therefore I propose to research the  srcref features in R, that would help us to find the src chunk of a method by asking the 
method object in the environment where it came from and find the preceding comments this way.

This is what I am driving towards.
So the apparent inconsistency is a reflection of ongoing design change.

To faciliate this migration I have also included some more unit tests (27 runit tests now) and some small helper scripts to run them continiously and in parallel whenever the tiniest bit of code in inlinedocs/R is touched. 
You find them in

...testfiles/mm. 

The tests duplicate a lot of code (thereby  asking  for a setup mehtod.) 
To use them as extended documentation I however prioritised readability and therefor made every test independent to understand.

D    pkg/inlinedocs/inst/scratch/inlinedocsTest
D    pkg/inlinedocs/inst/scratch/tw_testIndent.R
D    pkg/inlinedocs/inst/etc/default-function.R
D    pkg/inlinedocs/inst/etc/users.org
D    pkg/inlinedocs/inst/etc/anne-parse.R
D    pkg/inlinedocs/inst/etc/make.R
D    pkg/inlinedocs/inst/etc/tags
D    pkg/inlinedocs/inst/etc/inner.function
D    pkg/inlinedocs/inst/etc/parseRd.R
D    pkg/inlinedocs/inst/etc/anne.R
D    pkg/inlinedocs/inst/etc/minimalErrorPkg
D    pkg/inlinedocs/inst/etc/author.from.author.R
AM   pkg/inlinedocs/inst/testfiles/csall.sh
M    pkg/inlinedocs/inst/testfiles/mm/runit.NamespaceExample.R
A    pkg/inlinedocs/inst/testfiles/mm/srcref.example.R
D    pkg/inlinedocs/inst/testfiles/mm/package.skeleton.R
AM   pkg/inlinedocs/inst/testfiles/mm/cisall.sh
M    pkg/inlinedocs/inst/testfiles/mm/runit.Infrastructure.R
D    pkg/inlinedocs/inst/testfiles/mm/runit.OperatorDoc.R
AM   pkg/inlinedocs/inst/testfiles/mm/continousRunner.sh
M    pkg/inlinedocs/inst/testfiles/mm/runit.AddExampleCodeFromExternalTest.R
A    pkg/inlinedocs/inst/testfiles/mm/help.R
M    pkg/inlinedocs/inst/testfiles/mm/Itest.R
A    pkg/inlinedocs/inst/testfiles/mm/findGenericsAndMethodsWithSrcrefs.R
A    pkg/inlinedocs/inst/testfiles/mm/runit.ClassDoc.R
A    pkg/inlinedocs/inst/testfiles/mm/runit.MethodExample.R
M    pkg/inlinedocs/inst/testfiles/mm/isolatedTestRunner.R
A    pkg/inlinedocs/inst/testfiles/mm/runit.FunctionExample.R
M    pkg/inlinedocs/inst/testfiles/mm/isall.R
AM   pkg/inlinedocs/inst/testfiles/mm/cITest.sh
M    pkg/inlinedocs/inst/testfiles/mm/runit.MethodDoc.R
A    pkg/inlinedocs/inst/testfiles/mm/runit.RepairUsage.R
A    pkg/inlinedocs/inst/testfiles/lastrun
M    pkg/inlinedocs/R/package.skeleton.dx.R
M    pkg/inlinedocs/R/test.R
M    pkg/inlinedocs/R/parsers.R
M    pkg/inlinedocs/R/utils.R
M    pkg/inlinedocs/R/testhelpers.R
M    pkg/inlinedocs/DESCRIPTION
A    pkg/inlinedocs/man/writeMethodRdFiles.Rd
A    pkg/inlinedocs/man/MethodsWithSrcRefForGen.Rd
M    pkg/inlinedocs/man/removeAliasesfrom.Rd.file.Rd
A    pkg/inlinedocs/man/methSrc.Rd
A    pkg/inlinedocs/man/mm.examples.from.testfile.Rd
M    pkg/inlinedocs/man/modify.Rd.file.Rd
A    pkg/inlinedocs/man/sigString.Rd
A    pkg/inlinedocs/man/writeFunctionRdFiles.Rd
A    pkg/inlinedocs/man/removeComma.Rd
A    pkg/inlinedocs/man/rewriteSetMethodArgs.Rd
M    pkg/inlinedocs/man/print.allfun.Rd
A    pkg/inlinedocs/man/extra.class.docs.Rd
A    pkg/inlinedocs/man/pp.Rd
M    pkg/inlinedocs/man/package.skeleton.dx.Rd
A    pkg/inlinedocs/man/definition.from.source.Rd
A    pkg/inlinedocs/man/writePackageRdFile.Rd
A    pkg/inlinedocs/man/extract.docs.Rd
M    pkg/inlinedocs/man/apply.parsers.Rd
A    pkg/inlinedocs/man/z[-methods.Rd
M    pkg/inlinedocs/man/combine.character.Rd
A    pkg/inlinedocs/man/hiddenClasses.Rd
M    pkg/inlinedocs/man/combine.Rd
A    pkg/inlinedocs/man/writeMethodTableRdFiles.Rd
M    pkg/inlinedocs/man/findGeneric.Rd
M    pkg/inlinedocs/man/inlinedocs-package.Rd
A    pkg/inlinedocs/man/getMethodName.Rd
M    pkg/inlinedocs/man/extract.docs.setClass.Rd
A    pkg/inlinedocs/man/exportedFunctions.Rd
M    pkg/inlinedocs/man/extra.code.docs.Rd
M    pkg/inlinedocs/man/make.package.and.check.Rd
A    pkg/inlinedocs/man/allClasses.Rd
M    pkg/inlinedocs/man/save.test.result.Rd
A    pkg/inlinedocs/man/writeClassRdFiles.Rd
A    pkg/inlinedocs/man/exported.Rd
M    pkg/inlinedocs/man/get_S3_primitive_generics.Rd
M    pkg/inlinedocs/man/test.file.Rd
M    pkg/inlinedocs/man/extract.file.parse.Rd
A    pkg/inlinedocs/man/z[_method__listOfMethods_logical.Rd
A    pkg/inlinedocs/man/methodDocName.Rd
A    pkg/inlinedocs/man/exportedClasses.Rd
M    pkg/inlinedocs/man/extract.docs.file.Rd
A    pkg/inlinedocs/man/GenHasAnyMethodWithSrc.Rd
M    pkg/inlinedocs/man/getKnownS3generics.Rd
M    pkg/inlinedocs/man/is_primitive_in_base.Rd
A    pkg/inlinedocs/man/MethodHasSrc.Rd
M    pkg/inlinedocs/man/fixPackageFileNames.Rd
A    pkg/inlinedocs/man/trimmedNonEmptyLines.Rd
A    pkg/inlinedocs/man/getMethodSrc.Rd
A    pkg/inlinedocs/man/methodTable.Rd
A    pkg/inlinedocs/man/MethodSignatureHasOnlyExportedClasses.Rd
M    pkg/inlinedocs/man/replace.one.Rd
A    pkg/inlinedocs/man/CompareTrimmedNonEmptyLines.Rd
M    pkg/inlinedocs/man/get_internal_S3_generics.Rd
M    pkg/inlinedocs/man/forfun.Rd
A    pkg/inlinedocs/man/mmPromptMethods.Rd
M    pkg/inlinedocs/man/getSource.Rd
A    pkg/inlinedocs/man/documentableMeths.Rd
A    pkg/inlinedocs/man/pe.Rd
A    pkg/inlinedocs/man/GenHasAnyExposedMethod.Rd
M    pkg/inlinedocs/man/leadingS3generic.Rd
A    pkg/inlinedocs/man/exportedGenerics.Rd
M    pkg/inlinedocs/man/decomment.Rd
A    pkg/inlinedocs/man/createObjects.Rd
A    pkg/inlinedocs/man/GenHasSrc.Rd
A    pkg/inlinedocs/man/exportedDocumentableMeths.Rd
M    pkg/inlinedocs/man/prefixed.lines.Rd
M    pkg/inlinedocs/man/forall.Rd
A    pkg/inlinedocs/man/title.from.firstline.Rd
M    pkg/inlinedocs/man/kill.prefix.whitespace.Rd
M    pkg/inlinedocs/man/combine.NULL.Rd
M    pkg/inlinedocs/man/combine.list.Rd
A    pkg/inlinedocs/man/extra.method.docs.Rd
A    pkg/inlinedocs/man/inherit.docs.Rd
M    pkg/inlinedocs/man/extract.xxx.chunks.Rd
M    pkg/inlinedocs/man/do.not.generate.Rd
A    pkg/inlinedocs/man/extract.docs.setMethod.Rd
A    pkg/inlinedocs/man/methSig.Rd
A    pkg/inlinedocs/man/manMan
A    pkg/inlinedocs/man/manMan/descfile.names.Rd
A    pkg/inlinedocs/man/manMan/default.parsers.Rd
A    pkg/inlinedocs/man/manMan/lonely.Rd
A    pkg/inlinedocs/man/manMan/nondesc.parsers.Rd
A    pkg/inlinedocs/man/manMan/non.descfile.names.Rd
A    pkg/inlinedocs/man/manMan/forall.parsers.Rd
A    pkg/inlinedocs/man/manMan/forfun.parsers.Rd
A    pkg/inlinedocs/man/manMan/prefix.Rd
M    pkg/inlinedocs/NAMESPACE
M    pkg/inlinedocs/NEWS

Revision 395 - Directory Listing
Modified Tue Feb 11 21:51:01 2014 UTC (5 years, 3 months ago) by tdhock
attr(o, "ex", exact=TRUE)

Revision 392 - Directory Listing
Modified Tue Sep 3 07:46:16 2013 UTC (5 years, 8 months ago) by tdhock
delete Maintainer, Author, support Authors@R

Revision 391 - Directory Listing
Modified Tue Sep 3 05:41:18 2013 UTC (5 years, 8 months ago) by tdhock
authors, encoding

Revision 390 - Directory Listing
Modified Tue Sep 3 05:35:06 2013 UTC (5 years, 8 months ago) by tdhock
contributions from R Core Team

Revision 389 - Directory Listing
Modified Tue Sep 3 04:33:09 2013 UTC (5 years, 8 months ago) by tdhock
copy utils code to utils.R to avoid utils::: and pass R CMD check

Revision 388 - Directory Listing
Modified Fri Aug 23 00:35:42 2013 UTC (5 years, 9 months ago) by tdhock
GPL-2 or 3

Revision 387 - Directory Listing
Modified Thu Aug 22 09:28:21 2013 UTC (5 years, 9 months ago) by tdhock
update JSS citation

Revision 386 - Directory Listing
Modified Wed Jul 24 01:03:22 2013 UTC (5 years, 10 months ago) by tdhock
citation bugfix and if(interactive()) to reduce check time

Revision 380 - Directory Listing
Modified Mon Mar 18 02:16:14 2013 UTC (6 years, 2 months ago) by tdhock
reformat doc

Revision 379 - Directory Listing
Modified Wed Mar 6 06:53:44 2013 UTC (6 years, 2 months ago) by tdhock
when did +.method start working?

Revision 377 - Directory Listing
Modified Mon Jan 28 01:22:49 2013 UTC (6 years, 3 months ago) by tdhock
do not alias inlinedocs to package.skeleton.dx

Revision 376 - Directory Listing
Modified Mon Jan 28 01:08:01 2013 UTC (6 years, 3 months ago) by tdhock
version 1.9.2 bugfixes

Revision 362 - Directory Listing
Modified Mon May 21 14:37:49 2012 UTC (7 years ago) by tdhock
do not stop for WARNINGs in package.skeleton.dx example, due to R CMD check --as-cran bug

Revision 359 - Directory Listing
Modified Mon Apr 9 21:55:16 2012 UTC (7 years, 1 month ago) by tdhock
as-cran for tests

Revision 356 - Directory Listing
Modified Mon Apr 9 15:39:09 2012 UTC (7 years, 1 month ago) by tdhock
debugging CRAN crossref err

Revision 354 - Directory Listing
Modified Mon Apr 9 14:04:07 2012 UTC (7 years, 1 month ago) by tdhock
make default description dynamically inside package.skeleton.dx

Revision 353 - Directory Listing
Modified Mon Apr 9 12:44:43 2012 UTC (7 years, 1 month ago) by tdhock
doc bugfix for some \code blocks

Revision 352 - Directory Listing
Modified Mon Apr 9 12:43:46 2012 UTC (7 years, 1 month ago) by tdhock
wait 1 sec before redoing package.skeleton.dx()

Revision 336 - Directory Listing
Modified Thu Apr 5 12:44:33 2012 UTC (7 years, 1 month ago) by tdhock
do.not.generate example, partial arg NOTEs fixed

Revision 335 - Directory Listing
Modified Thu Apr 5 12:08:07 2012 UTC (7 years, 1 month ago) by tdhock
do.not.generate for static Rd files

Revision 331 - Directory Listing
Modified Mon Mar 12 11:53:14 2012 UTC (7 years, 2 months ago) by tdhock
default DESCRIPTION values

Revision 320 - Directory Listing
Modified Fri Jan 27 15:59:35 2012 UTC (7 years, 3 months ago) by tdhock
version 1.8 -> 1.9

Revision 312 - Directory Listing
Modified Fri Jan 13 09:22:02 2012 UTC (7 years, 4 months ago) by tdhock
usage line breaks

Revision 311 - Directory Listing
Modified Wed Dec 7 19:39:34 2011 UTC (7 years, 5 months ago) by markus
package.skeleton.dx can now be told to exclude files matching a regular expression to avoid the situation where there would be no possibility to build the documentation because of some files that can not be handled yet.

Revision 308 - Directory Listing
Modified Fri Oct 21 12:08:39 2011 UTC (7 years, 7 months ago) by tdhock
modify getSource, delete inlinedocExample to pass 2.14 checks

Revision 305 - Directory Listing
Modified Tue Aug 16 11:48:38 2011 UTC (7 years, 9 months ago) by kmpont
Added default title for setClass when no # title on setClass line

Revision 304 - Directory Listing
Modified Tue Jul 19 17:03:18 2011 UTC (7 years, 10 months ago) by tdhock
doc usage line breaks, works under R-2.13.1

Revision 302 - Directory Listing
Modified Tue Jul 12 12:06:42 2011 UTC (7 years, 10 months ago) by tdhock
getSource(FUN) instead of attr(FUN,"source")

Revision 291 - Directory Listing
Modified Tue Jun 7 08:59:30 2011 UTC (7 years, 11 months ago) by tdhock
linebreak

Revision 270 - Directory Listing
Modified Mon May 23 15:53:47 2011 UTC (8 years ago) by tdhock
delete examples.after.return support

Revision 249 - Directory Listing
Modified Thu Apr 7 13:58:27 2011 UTC (8 years, 1 month ago) by tdhock
docs for make.package.and.check

Revision 247 - Directory Listing
Modified Thu Apr 7 13:22:13 2011 UTC (8 years, 1 month ago) by tdhock
verbose arg for make.package.and.check

Revision 240 - Directory Listing
Modified Mon Mar 28 16:09:23 2011 UTC (8 years, 1 month ago) by tdhock
add make.package.and.check doc

Revision 214 - Directory Listing
Modified Wed Mar 9 18:28:02 2011 UTC (8 years, 2 months ago) by tdhock
add leadingS3generic, use dos line endings

Revision 213 - Directory Listing
Modified Wed Mar 9 16:49:46 2011 UTC (8 years, 2 months ago) by kmpont
Options fix just introduced now correctly restores original settings

Revision 212 - Directory Listing
Modified Wed Mar 9 16:37:25 2011 UTC (8 years, 2 months ago) by kmpont
Fix parser to avoid breaking when processing inlinedocs source. (Problem
was redefinition of class DocLink into inlinedocs environment, where it
already existed).

First attempt at adding sections and thoughts to JSS article

silly.example.R now includes some R.oo class and method declarations to
test that aspect; the previous "detect the first ." approach has been
erased in favour of the better method now extracted as a separate
"leadingS3generic" function.


Revision 209 - Directory Listing
Modified Fri Feb 25 08:15:10 2011 UTC (8 years, 2 months ago) by tdhock
doc updates

Revision 203 - Directory Listing
Modified Fri Feb 18 15:59:29 2011 UTC (8 years, 3 months ago) by tdhock
Unit tests accept .parsers variable

Revision 201 - Directory Listing
Modified Fri Feb 18 15:34:51 2011 UTC (8 years, 3 months ago) by tdhock
doc updates

Revision 199 - Directory Listing
Modified Fri Feb 18 14:37:24 2011 UTC (8 years, 3 months ago) by tdhock
replace.one function

Revision 197 - Directory Listing
Modified Fri Feb 18 14:09:37 2011 UTC (8 years, 3 months ago) by tdhock
doc rebuilt, passes checks

Revision 175 - Directory Listing
Modified Thu Jan 6 15:24:45 2011 UTC (8 years, 4 months ago) by tdhock
seealso after return ok

Revision 163 - Directory Listing
Modified Tue Nov 16 12:06:29 2010 UTC (8 years, 6 months ago) by tdhock
kill.prefix.whitespace

Revision 158 - Directory Listing
Modified Mon Nov 8 12:26:12 2010 UTC (8 years, 6 months ago) by tdhock
bug comment

Revision 154 - Directory Listing
Modified Fri Oct 29 12:11:52 2010 UTC (8 years, 6 months ago) by tdhock
parsefun and extract.docs.fun consolidated into extract.xxx.chunks in ongoing effort to make parser functions more readable and modular

Revision 147 - Directory Listing
Modified Wed Oct 20 11:24:49 2010 UTC (8 years, 7 months ago) by tdhock
check pkg using R.home("bin")

Revision 141 - Directory Listing
Modified Wed Oct 20 09:12:53 2010 UTC (8 years, 7 months ago) by tdhock
dont on.exit in an example

Revision 140 - Directory Listing
Modified Tue Oct 19 23:24:01 2010 UTC (8 years, 7 months ago) by tdhock
do ex in tempdir

Revision 138 - Directory Listing
Modified Tue Oct 19 22:51:59 2010 UTC (8 years, 7 months ago) by tdhock
update examples to pass new more stringent parser checks

Revision 137 - Directory Listing
Modified Tue Oct 19 22:36:28 2010 UTC (8 years, 7 months ago) by tdhock
new man pages for new parser stuff

Revision 128 - Directory Listing
Modified Wed Sep 22 09:24:39 2010 UTC (8 years, 8 months ago) by tdhock
examples in attr forall, lonely gets an example

Revision 125 - Directory Listing
Modified Thu Sep 16 09:34:38 2010 UTC (8 years, 8 months ago) by tdhock
extended package.skeleton.dx example that also checks the silly package and verifies that there are no warnings

Revision 123 - Directory Listing
Modified Mon Aug 30 09:19:39 2010 UTC (8 years, 8 months ago) by tomaschwutz
added alias inlinedocs to function package.skeleton.dx (to be displayed on ?inlinedocs)
added an example to package.skeleton.dx
added the silly package to inst directory, so that a package for examples is available at installation time 


Revision 122 - Directory Listing
Modified Sat Aug 28 21:36:48 2010 UTC (8 years, 8 months ago) by tomaschwutz
implemented Claudia's suggestion about the assignment function of example code to attribute ex:
added function inlinedocExample<- in file package.skeleton.dx.R with specifying the example already using this mechanism
added testfile attrExamples.R

in addition added suppressWarnings() around the call to package.skeleton, because it always gave a warning of non-exisiting package with my Windows version of R 10.1.

Revision 118 - Directory Listing
Modified Fri Jun 18 16:32:29 2010 UTC (8 years, 11 months ago) by tdhock
fermat-inline test, extract.docs.fun now uses nondesc.parsers as the parser list

Revision 114 - Directory Listing
Modified Fri Jun 18 09:42:18 2010 UTC (8 years, 11 months ago) by tdhock
verbose arg doc

Revision 113 - Directory Listing
Modified Fri Jun 18 09:40:30 2010 UTC (8 years, 11 months ago) by tdhock
test.file verbose, tags test, save.test.result doc

Revision 110 - Directory Listing
Modified Mon Jun 7 12:08:54 2010 UTC (8 years, 11 months ago) by tdhock
unit test for extract.docs.file

Revision 109 - Directory Listing
Modified Mon Jun 7 08:42:15 2010 UTC (8 years, 11 months ago) by tdhock
extract.docs.file new functionality parses files independently

Revision 108 - Directory Listing
Modified Wed May 26 12:00:17 2010 UTC (8 years, 11 months ago) by phgrosjean
Several bugs corrections and improvements. See NEWS file
More tests temporary in /scratch for difficult cases

Revision 105 - Directory Listing
Modified Tue May 18 17:32:43 2010 UTC (9 years ago) by tdhock
extract.docs.code for applying Parser Functions to arbitrary code chunks and returning a doc list

Revision 102 - Directory Listing
Modified Fri May 14 18:48:40 2010 UTC (9 years ago) by tdhock
bugfix for return at end of function

Revision 99 - Directory Listing
Modified Mon May 3 18:31:40 2010 UTC (9 years ago) by tdhock
update some docs

Revision 94 - Directory Listing
Modified Mon May 3 14:21:15 2010 UTC (9 years ago) by tdhock
passes check 

Revision 91 - Directory Listing
Modified Mon May 3 14:17:02 2010 UTC (9 years ago) by tdhock
doc update after added new parser list feature

Revision 90 - Directory Listing
Modified Mon May 3 14:03:10 2010 UTC (9 years ago) by tdhock
unix line endings

Revision 84 - Directory Listing
Modified Thu Apr 22 10:11:18 2010 UTC (9 years, 1 month ago) by kmpont
Further fixes for S3 methods declared with setMethodS3

1) automatically generates \method{}{} markup which should be correct if
and only if the generic name is everything up to but not including the
first period in the function name. Thus this will not work properly if a
generic function has a name like "my.generic" so that the specific function
is "my.generic.my_type".

2) fix for behaviour of package.skeleton, which, as used within this
package, for a function "[[.Distribution" generates a file with name
"z[[.Distribution.Rd"

3) prints S3method calls suitable for inclusion in a NAMESPACE file

The mechanism depends on the parse of the source file picking up and
setting the "created" field to "setMethodS3". Something similar might work
for other ways of creating S3 generics, but I am not currently clear how to
pick those up reliably.

Revision 75 - Directory Listing
Modified Mon Apr 12 09:30:28 2010 UTC (9 years, 1 month ago) by tdhock
docs update, passes r cmd check, upload to cran

Revision 70 - Directory Listing
Modified Fri Jan 15 09:42:36 2010 UTC (9 years, 4 months ago) by kmpont
Completed experimental implementation for S3 classes using R.oo.

1) Search for comments preceding definition now uses parse on file
   insteadof grep via new method extract.file.parse. This works for more
   ways of defining values and does not require blank lines after
   definitions.

2) When an S3 generic is defined using setMethodS3:
a) the generic is documented with a copy of the inline documentation for the
   specific.
b) (Very experimental!) further definitions of the same generic inherit
   documentation from the first version defined in the same source file.
   The idea is to avoid repeating documentation when defining the generic
   repeatedly for an inheritance hierarchy.
   Thus if an argument is not documented, the documentation from the first
   version of the generic will be used. At present this applies to _all_
   documentation entries, but that may be reduced in the future.

3) Further minor tweaks:
a) fixes to work around package.skeleton issue: if a default argument
   contains a "%" character, then it should be escaped in the skeleton
   \usage, but is not, causing things to break nastily.
b) If documentation for an object contains an explicit title but no
   description, then the title is copied into the description in order
   to avoid warnings from the package checking process which requires
   description to be present. The idea here is to simplify generating
   documentation for small methods by reducing it to the bare minimum.

Revision 62 - Directory Listing
Modified Tue Dec 8 15:00:47 2009 UTC (9 years, 5 months ago) by tdhock
update email address, add new extract pages

Revision 60 - Directory Listing
Modified Mon Nov 30 18:05:13 2009 UTC (9 years, 5 months ago) by kmpont
First implementation of docs within S4 class definitions

Revision 57 - Directory Listing
Modified Mon Nov 23 16:46:00 2009 UTC (9 years, 6 months ago) by kmpont
Initial implementation of 'extra' fields information via ##field<<

Revision 55 - Directory Listing
Modified Sun Nov 15 22:54:53 2009 UTC (9 years, 6 months ago) by tdhock
add directlabels test

Revision 52 - Directory Listing
Modified Wed Nov 11 22:26:18 2009 UTC (9 years, 6 months ago) by tdhock
remove Rdversion lines, R-2.10

Revision 51 - Directory Listing
Modified Wed Nov 11 15:38:23 2009 UTC (9 years, 6 months ago) by tdhock
update desc with keith as coauthor

Revision 48 - Directory Listing
Modified Mon Nov 9 18:14:45 2009 UTC (9 years, 6 months ago) by tdhock
backwards compatible changes from keith

Revision 44 - Directory Listing
Modified Mon Nov 9 12:22:59 2009 UTC (9 years, 6 months ago) by tdhock
add prefix doc

Revision 38 - Directory Listing
Modified Mon Sep 21 16:54:38 2009 UTC (9 years, 8 months ago) by tdhock
desc and docs update

Revision 35 - Directory Listing
Modified Tue Aug 18 20:57:20 2009 UTC (9 years, 9 months ago) by tdhock
custom title allowed by commenting first line of function definition

Revision 34 - Directory Listing
Modified Tue Aug 18 14:05:29 2009 UTC (9 years, 9 months ago) by tdhock
update docs for new interpretation of check parameter

Revision 28 - Directory Listing
Modified Wed Aug 5 10:07:40 2009 UTC (9 years, 9 months ago) by tdhock
extract -package info from DESCRIPTION file

Revision 24 - Directory Listing
Modified Tue Aug 4 12:40:37 2009 UTC (9 years, 9 months ago) by tdhock
package.skeleton.dx default filepath .. bugfix, escape backslashes in comments, examples from test files

Revision 23 - Directory Listing
Modified Mon Aug 3 15:37:42 2009 UTC (9 years, 9 months ago) by tdhock
first argument changed to pkgdir, on.exit added to package.skeleton.dx

Revision 18 - Directory Listing
Modified Sat Aug 1 22:01:23 2009 UTC (9 years, 9 months ago) by tdhock
error checking and automatic DESCRIPTION added

Revision 12 - Directory Listing
Modified Sat Aug 1 07:01:02 2009 UTC (9 years, 9 months ago) by tdhock
support for check and chdir args for package.skeleton.dx

Revision 8 - Directory Listing
Modified Fri Jul 31 17:13:17 2009 UTC (9 years, 9 months ago) by tdhock
dots argument special case, package name alias conflict special case

Revision 7 - Directory Listing
Modified Fri Jul 31 15:11:15 2009 UTC (9 years, 9 months ago) by tdhock
works with new find/replace mechanism

Revision 6 - Directory Listing
Modified Fri Jul 31 12:04:29 2009 UTC (9 years, 9 months ago) by tdhock
change extract.docs.file so that reading functions should work with arbitrary packages

Revision 5 - Directory Listing
Modified Fri Jul 31 09:56:58 2009 UTC (9 years, 9 months ago) by tdhock
author tag, switch statement, more comments

Revision 4 - Directory Listing
Modified Thu Jul 30 18:39:50 2009 UTC (9 years, 9 months ago) by tdhock
deleted name argument, infer from DESCRIPTION file

Revision 3 - Directory Listing
Modified Thu Jul 30 09:43:37 2009 UTC (9 years, 9 months ago) by tdhock
support for comments about function return values, resulting documentation passes R CMD check with no warnings

Revision 2 - Directory Listing
Added Wed Jul 29 16:59:24 2009 UTC (9 years, 9 months ago) by tdhock
First working version that passes checks successfully

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