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Revision 400 - Directory Listing
Modified Wed Apr 29 11:42:12 2015 UTC (4 years ago) by tomaschwutz
fixed failure of S3.tag parser on methods starting with a dot 

Revision 399 - Directory Listing
Modified Wed Apr 29 10:01:10 2015 UTC (4 years ago) by tomaschwutz
quotes in Collate field

roxygen2 surrounds each fileName in the Collate field in DESCRIPTION by single quotes. Without removing those, the files are not sourced.
I inserted two sub statements to omit beginning and ending single quote.

In order to satisfy R CMD check (R 3.1.2) I reintroduced the Author and Maintainer field in addition authors@R
which did not auto-generate these fields as expected.

Revision 397 - Directory Listing
Modified Tue Nov 11 11:22:57 2014 UTC (4 years, 6 months ago) by tomaschwutz
avoid \r\r\n line feeds in Rd when running on windows

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 394 - Directory Listing
Modified Mon Dec 23 15:36:20 2013 UTC (5 years, 5 months ago) by markus
0.) This is an intermediate commit, that will be followed by further tidying. I just got afraid to have to merge branches if I wait longer.

1.) The purposes of the committed changes are 
    a)
    	to enable unittesting for very small units (functions) with the help of a unit testing framework.
    b) 
    	to enable the detailed documentation of S4 methods in separate (signature specific) .Rd files and 
    

2.) Details:
    a) Unittesting:
    	Motivation:
		To implement the changes mentioned above I needed a facility to test very small parts of inlinedocs infrastructure.
    		Just comparing results of all parts combined actions as in the already existent testcases 
    		turned out to be to fragile for my limited understanding of how inlinedocs parts work. 
    		Instead of hoping that package.skeleton.dx would still work after my change and having to write
    		a rather complete result fixture I needed something that would test single functions against a very small 
    		fixture in order to learn what part they were intended to play or how they would have to be tweeaked.
	Existing test tools:
    		Unfortunately it turned out that neither "Runit" nor "testthis" could be applied to test inlinedocs.
    		The reason is that the crucial requirement of test independence was not fulfilled:
    		I was horrified to notice that in both frameworks a test could be reproducibly triggered to fail 
		by code in \emph{another} test.
    		I could  make out a combination of three factors that lead to this unexpected result:
    		- the use of global options and the (necessary) use of environments in inlinedocs
    		- the inability of both testframeworks to isolate such acrobatic behavior to a single test although 
    		  the execution of tests in separated environments is even advertised (in both frameworks!)
    		- the inability of R (at least as far as I know) to provide testframeworks with means of effective isolation
	Adapted test tool:	
    		To make \emph{independent} testing of units possible I went to the rather extreme measure of using a subprocess
    		for each test. The machinery is implemented in  
    		
    		.../testfiles/mm/isolatedTestRunner.R
    		
    		When a test is executed the following things happen:
    		- inside the ...testfiles/mm/tmp a directory is created that reflects the name of the testfunction
    		- source code for a RUnit testsuite (consisting of one test) and a runit.Testfile.R containing the testfunction is created
    		- the suite is run (by means of Rscript ) and the result written to a file 
		  (if it crashes this will be recognized but of course not brake the calling process) 
    		- the result is collected by the isoloatedTestRunner and reported in a very preliminary fashion by isolatedTestrunner.
    		  (RUnit is also used on this level, but could be used more intensly to achieve the same level of reporting and ease of use)
		
		To run all tests just call ./isall.R
		For a single test run use  ./Itest
		Both look nearly like typicla RUnit testsuite with the tiny differece of calling the isolatedTestRunner.R

    	Proposed use:
		For future versions of inlinedocs I strongly recommend a mandatory  extensive testsuite but for the moment 
    		I confined all my unittesting in the directory:

    		.../testfiles/mm

    		because I of course need your agreement, dispute,  opinion or advise for such a change of infrastructure.
                
		At the moment I would just be happy if you run:

		isall.R 	in 

		inlinedocs/inst/testfiles/mm/
		
		before you commit, to see I some of the new tests are broken.



   b) Method documentation:
   	For a generic with the name "GenericName" and the signature c("ClassNameA","ClassNameB") a file with the name GenericName-method-#ClassNameA#ClassNameB.Rd
	is created and populated using the same infrastructe that is used for functions for the actual definition, but a rather different approach
	to find the Generic (forGeneric is not similar enough to forFun to use forAll in both cases)
	I am still struggeling with documentation of operator methods since for them no "srcref" attribute seems to be available but I am working on this.
	
Next Steps and Proposal:
complete operator method description and cleanup (e.g. check if inlinedocs package itself still builds an passed cran checks;-))
 

		

	   

     	






Revision 393 - Directory Listing
Modified Tue Oct 1 07:15:26 2013 UTC (5 years, 7 months ago) by tomaschwutz
fixed error in parsing examples with (yet) empty lines

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 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 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 383 - Directory Listing
Modified Fri Jul 12 12:52:13 2013 UTC (5 years, 10 months ago) by tomaschwutz
expr.type ==  'R.methodsS3::setMethodS3' to support imports instead of depends of R.methodsS3

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

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 370 - Directory Listing
Modified Fri Nov 9 19:48:27 2012 UTC (6 years, 6 months ago) by markus
I made a number of changes:
1.) made inlinedocs a bit more forgiving with respect to  missing parts of the docsstrings which was necessarry for 
the package we just work on. Inlinedocs had stopped with weird error messages while pasting the gathered  bits 
together. (or rather not if some bits where missing...)

2.) R original package.skeleton adds a lot of (duplicated) aliases to method names to a classes Rd file.
These cause R CMD check to complain about the duplication.
I added a new function which is called after modify.Rd.file and comments out the superfluous aliases.

This function does some things that are also done in apply.parsers and modify.Rd.file 
which could (and should) be probably factored out.
For instance the new function also evaluates the whole code in a separate environment (like apply parser) 
and it also could use the more safeguarded way to compute the final name of an Rd.file (like  modify.Rd.file does)

However manipulating environments (explicitly ;-))still scares me a bit.
So I at least wanted to make an intermediate commit to invite discussion and make the changes more reproducible.

3.) I added an additional check before inlinedocs removes the alias to the package name in the package-Rd file.
It had previously removed it from our documentation although there had >> not << been a function of the same name.


Revision 368 - Directory Listing
Modified Thu Oct 25 16:01:50 2012 UTC (6 years, 7 months ago) by tomaschwutz
accessor moved codeBlock

Revision 367 - Directory Listing
Modified Thu Oct 25 10:07:37 2012 UTC (6 years, 7 months ago) by tomaschwutz
tryCatch around parse in gen.Rd, workaround on accessor functions failures

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 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 345 - Directory Listing
Modified Fri Apr 6 08:37:28 2012 UTC (7 years, 1 month ago) by tdhock
use \s space instead of \W not word for deleting sections in Rd

Revision 344 - Directory Listing
Modified Fri Apr 6 08:36:23 2012 UTC (7 years, 1 month ago) by tdhock
copy NAMESPACE from silly package to avoid WARNING

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 334 - Directory Listing
Modified Thu Apr 5 12:06:49 2012 UTC (7 years, 1 month ago) by tdhock
comment debug prints

Revision 332 - Directory Listing
Modified Mon Mar 12 12:12:10 2012 UTC (7 years, 2 months ago) by tdhock
delete debug fun

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

Revision 324 - Directory Listing
Modified Wed Feb 1 17:16:32 2012 UTC (7 years, 3 months ago) by markus
only some changed comments

Revision 323 - Directory Listing
Modified Wed Feb 1 17:14:53 2012 UTC (7 years, 3 months ago) by markus
The call of the old package.skeleton often caused trouble for me, when processing S4 classes. I found out that the trouble could be avoided if the environment that apply.parsers used was changed, which however caused other trouble... So in this commit I just call package.skeleton <<before>> apply.parsers creates a new env. This works fine so far. By the way I probably have deleted some comments, but would opt for descriptive commit messages instead anyway.

Revision 317 - Directory Listing
Modified Fri Jan 13 20:40:49 2012 UTC (7 years, 4 months ago) by tdhock
changes too many dlines to txt, ok now

Revision 316 - Directory Listing
Modified Fri Jan 13 15:56:45 2012 UTC (7 years, 4 months ago) by tdhock
rearrange stuff for escape.percent test

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 307 - Directory Listing
Modified Fri Oct 21 11:37:19 2011 UTC (7 years, 7 months ago) by tdhock
test errors reported more clearly

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 303 - Directory Listing
Modified Tue Jul 19 15:35:23 2011 UTC (7 years, 10 months ago) by tdhock
gregors ideas: whitespace in examples, value, and usage

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 300 - Directory Listing
Modified Fri Jun 17 07:37:46 2011 UTC (7 years, 11 months ago) by tdhock
bugfix when nothing defined in pkg

Revision 275 - Directory Listing
Modified Fri May 27 11:55:21 2011 UTC (8 years ago) by tdhock
disable recursive R CMD check

Revision 274 - Directory Listing
Modified Fri May 27 10:14:41 2011 UTC (8 years ago) by tdhock
try to debug cran err

Revision 271 - Directory Listing
Modified Mon May 23 16:14:49 2011 UTC (8 years ago) by tdhock
suppress warnings when we attempt to detach a pkg

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

Revision 257 - Directory Listing
Modified Sun May 1 17:03:01 2011 UTC (8 years ago) by tdhock
multipar desc

Revision 255 - Directory Listing
Modified Mon Apr 25 13:58:30 2011 UTC (8 years, 1 month ago) by tdhock
check length with sprintf to avoid error

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 248 - Directory Listing
Modified Thu Apr 7 13:54:54 2011 UTC (8 years, 1 month ago) by tdhock
warning bugfix

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 246 - Directory Listing
Modified Thu Apr 7 13:21:39 2011 UTC (8 years, 1 month ago) by tdhock
fixme warning

Revision 239 - Directory Listing
Modified Mon Mar 28 16:07:28 2011 UTC (8 years, 2 months ago) by tdhock
check and test

Revision 236 - Directory Listing
Modified Mon Mar 28 14:03:48 2011 UTC (8 years, 2 months ago) by tdhock
erase \code inside \title in s4 class docs since we cant do bracket matching in regex find/replace in replace.one()

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, 3 months ago) by tdhock
doc updates

Revision 204 - Directory Listing
Modified Fri Feb 18 16:48:22 2011 UTC (8 years, 3 months ago) by tdhock
alternate syntax parser testfile

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 202 - Directory Listing
Modified Fri Feb 18 15:54:00 2011 UTC (8 years, 3 months ago) by tdhock
check outer list in unit tests

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

Revision 200 - Directory Listing
Modified Fri Feb 18 15:02:16 2011 UTC (8 years, 3 months ago) by tdhock
move s3method and collapse to Parser Functions

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

Revision 198 - Directory Listing
Modified Fri Feb 18 14:17:08 2011 UTC (8 years, 3 months ago) by tdhock
s3method -> .s3method

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 196 - Directory Listing
Modified Fri Feb 18 12:52:48 2011 UTC (8 years, 3 months ago) by tdhock
try to recover s3 method

Revision 195 - Directory Listing
Modified Fri Feb 18 12:30:30 2011 UTC (8 years, 3 months ago) by tdhock
title.from.firstline and author

Revision 191 - Directory Listing
Modified Thu Feb 17 14:09:43 2011 UTC (8 years, 3 months ago) by tdhock
length(grep -> grepl, minor

Revision 186 - Directory Listing
Modified Fri Jan 14 18:43:36 2011 UTC (8 years, 4 months ago) by tdhock
make package file before doing global find and replace on doc char vectors

Revision 185 - Directory Listing
Modified Thu Jan 13 16:08:14 2011 UTC (8 years, 4 months ago) by tdhock
new doc keyword

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 162 - Directory Listing
Modified Wed Nov 10 09:18:20 2010 UTC (8 years, 6 months ago) by tdhock
report on which function parsing fails

Revision 159 - Directory Listing
Modified Tue Nov 9 16:42:39 2010 UTC (8 years, 6 months ago) by tdhock
bugfix: dont check for paren matching in comments

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

Revision 156 - Directory Listing
Modified Fri Oct 29 13:06:55 2010 UTC (8 years, 6 months ago) by tdhock
R CMD check for each testfile

Revision 155 - Directory Listing
Modified Fri Oct 29 12:12:58 2010 UTC (8 years, 6 months ago) by tdhock
erase browser

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 152 - Directory Listing
Modified Thu Oct 28 15:57:51 2010 UTC (8 years, 6 months ago) by tdhock
parsers error catch for s4 classes

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 144 - Directory Listing
Modified Wed Oct 20 09:33:04 2010 UTC (8 years, 7 months ago) by tdhock
only update definition if there is source to put there

Revision 142 - Directory Listing
Modified Wed Oct 20 09:21:53 2010 UTC (8 years, 7 months ago) by tdhock
paste lines together for definition.from.source

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 130 - Directory Listing
Modified Thu Sep 30 12:34:15 2010 UTC (8 years, 7 months ago) by tdhock
report warning encountered in check

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 116 - Directory Listing
Modified Fri Jun 18 15:33:07 2010 UTC (8 years, 11 months ago) by tdhock
autodetect left indent before examples

Revision 115 - Directory Listing
Modified Fri Jun 18 10:35:11 2010 UTC (8 years, 11 months ago) by tdhock
silly example unit test checks

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 111 - Directory Listing
Modified Mon Jun 7 12:33:37 2010 UTC (8 years, 11 months ago) by tdhock
test for sublogo

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 (9 years ago) by phgrosjean
Several bugs corrections and improvements. See NEWS file
More tests temporary in /scratch for difficult cases

Revision 106 - Directory Listing
Modified Tue May 18 17:39:20 2010 UTC (9 years ago) by tdhock
todo

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 104 - Directory Listing
Modified Tue May 18 16:35:08 2010 UTC (9 years ago) by tdhock
hack: more complicated rep key (there really should be a better way to do regexs in R)

Revision 103 - Directory Listing
Modified Tue May 18 16:33:29 2010 UTC (9 years ago) by tdhock
examples.after.return bugfix for multiline examples

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 101 - Directory Listing
Modified Tue May 4 06:57:58 2010 UTC (9 years ago) by tdhock
cat sep

Revision 100 - Directory Listing
Modified Tue May 4 06:55:27 2010 UTC (9 years ago) by tdhock
typo

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

Revision 97 - Directory Listing
Modified Mon May 3 16:07:46 2010 UTC (9 years ago) by tdhock
bugfix for returns in examples-after-comments module

Revision 96 - Directory Listing
Modified Mon May 3 15:57:03 2010 UTC (9 years ago) by tdhock
examples-after-return gives value as well

Revision 95 - Directory Listing
Modified Mon May 3 14:22:42 2010 UTC (9 years ago) by tdhock
collapse line

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

Revision 93 - Directory Listing
Modified Mon May 3 14:18:47 2010 UTC (9 years ago) by tdhock
forall operates on all docs instead of all objects (thus works for s4 classes as well)

Revision 92 - Directory Listing
Modified Mon May 3 14:17:37 2010 UTC (9 years ago) by tdhock
use collate if it exists

Revision 89 - Directory Listing
Modified Mon May 3 13:01:06 2010 UTC (9 years ago) by tdhock
define parsers as a list, allow configuration of parser list from project .inlinedocs.R or options()

Revision 87 - Directory Listing
Modified Sat May 1 12:21:27 2010 UTC (9 years ago) by tdhock
restructure package.skeleton.dx to support modular parser list

Revision 86 - Directory Listing
Modified Fri Apr 30 12:30:34 2010 UTC (9 years ago) by tomaschwutz
1) changed prefix to include tabs

2) added package sillyS3 to tests, to test generation of S3 comments

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 82 - Directory Listing
Modified Tue Apr 20 13:51:01 2010 UTC (9 years, 1 month ago) by tomaschwutz
added support for tabs and indented function arguments and ### comments, added new test package indent

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 73 - Directory Listing
Modified Mon Mar 1 14:28:44 2010 UTC (9 years, 2 months ago) by tdhock
just ignore format field, causes too many problems

Revision 72 - Directory Listing
Modified Thu Feb 25 16:50:15 2010 UTC (9 years, 3 months ago) by tdhock
delete empty sections in Rd files

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 69 - Directory Listing
Modified Mon Jan 11 18:13:14 2010 UTC (9 years, 4 months ago) by kmpont
First version working with R.oo class and method definitions.
Note: R.oo creates S3 generics freely - these still need a
little more thought to eliminate warnings and to avoid
repetitious documentation of class-specific versions.

Revision 68 - Directory Listing
Modified Thu Jan 7 15:56:05 2010 UTC (9 years, 4 months ago) by kmpont
Bug fix: when ... was used with ##<< argument documentation, it was
matching _any_ three character argument, which meant that ... was
documented repeatedly and the three character argument was
undocumented.

Also minor tweak so works with rare case when there are no ###
documentation lines.

Revision 67 - Directory Listing
Modified Thu Jan 7 10:31:00 2010 UTC (9 years, 4 months ago) by kmpont
Almost dummy commit to insert log message which got lost for version 66.

Version 66 fixed various matters to do with S4 classes:

1) Previous versions crashed looking for missing print.Rd when
   attempting to define a method for "print" generic for S4 classes, using
      setMethod("print" ...)
   Note that this was misconceived, as "print" does not seem to be
   generic for S4 classes.
2) When "show" generic is defined with setMethod("show" ...) an
   additional alias is defined in the class skeleton documentation.
   This revealed a problem with alias handling - multiple aliases from
   package.skeleton were all replaced by the aliases from the inline docs.
3) Class documentation extracted from setClass)("class.name" ...) now
   automatically includes "class.name" as an alias (default was only
   to have "class.name-class", which makes referencing from other
   documentation more clumsy.

Revision 66 - Directory Listing
Modified Thu Jan 7 10:12:28 2010 UTC (9 years, 4 months ago) by kmpont


Revision 65 - Directory Listing
Modified Fri Dec 11 14:48:30 2009 UTC (9 years, 5 months ago) by tdhock
erase curly braces from format section

Revision 64 - Directory Listing
Modified Thu Dec 10 14:57:31 2009 UTC (9 years, 5 months ago) by tdhock
add definition attribute to result of extract.docs

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 58 - Directory Listing
Modified Thu Nov 26 10:35:42 2009 UTC (9 years, 6 months ago) by tdhock
use prefix instead of hard re

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 56 - Directory Listing
Modified Wed Nov 18 09:31:49 2009 UTC (9 years, 6 months ago) by tdhock
code formatting clearer

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

Revision 53 - Directory Listing
Modified Wed Nov 11 22:27:13 2009 UTC (9 years, 6 months ago) by tdhock
load pkg dependencies before sourcing package

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 42 - Directory Listing
Modified Mon Oct 26 16:36:08 2009 UTC (9 years, 7 months ago) by tdhock
allow multiline comments before data items

Revision 39 - Directory Listing
Modified Sat Oct 3 14:14:22 2009 UTC (9 years, 7 months ago) by tdhock
need even more escapes to accurately replace backslashes

Revision 37 - Directory Listing
Modified Mon Aug 31 11:52:01 2009 UTC (9 years, 8 months ago) by tdhock
rebuild examples at the end if we didnt test them

Revision 36 - Directory Listing
Modified Wed Aug 19 13:18:42 2009 UTC (9 years, 9 months ago) by tdhock
convert ._ to space for Rd titles

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 33 - Directory Listing
Modified Tue Aug 18 13:54:20 2009 UTC (9 years, 9 months ago) by tdhock
package checking can omit examples for speed

Revision 32 - Directory Listing
Modified Tue Aug 18 13:14:55 2009 UTC (9 years, 9 months ago) by tdhock
more backslashes needed for percent escaping

Revision 31 - Directory Listing
Modified Tue Aug 18 12:48:42 2009 UTC (9 years, 9 months ago) by tdhock
escape percents in Rd files

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 21 - Directory Listing
Modified Mon Aug 3 15:09:28 2009 UTC (9 years, 9 months ago) by tdhock
bugfix for returned docs of length 1 (was matrix, needed list), allow description for functions on line before def if its undocumented (ie constructed by a function call), allow Rd files to be manually updated if there are no significant docs in code

Revision 20 - Directory Listing
Modified Sun Aug 2 22:55:45 2009 UTC (9 years, 9 months ago) by tdhock
error checking for extract.docs and extract.docs.fun

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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