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Revision 399 - (view) (download) (annotate) - [select for diffs]
Modified Wed Apr 29 10:01:10 2015 UTC (4 years, 1 month ago) by tomaschwutz
File length: 33332 byte(s)
Diff to previous 397
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 - (view) (download) (annotate) - [select for diffs]
Modified Tue Nov 11 11:22:57 2014 UTC (4 years, 7 months ago) by tomaschwutz
File length: 33113 byte(s)
Diff to previous 396
avoid \r\r\n line feeds in Rd when running on windows

Revision 396 - (view) (download) (annotate) - [select for diffs]
Modified Tue Feb 18 13:07:32 2014 UTC (5 years, 4 months ago) by markus
File length: 32958 byte(s)
Diff to previous 395
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 - (view) (download) (annotate) - [select for diffs]
Modified Tue Feb 11 21:51:01 2014 UTC (5 years, 4 months ago) by tdhock
File length: 26019 byte(s)
Diff to previous 394
attr(o, "ex", exact=TRUE)

Revision 394 - (view) (download) (annotate) - [select for diffs]
Modified Mon Dec 23 15:36:20 2013 UTC (5 years, 6 months ago) by markus
File length: 26016 byte(s)
Diff to previous 392
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 392 - (view) (download) (annotate) - [select for diffs]
Modified Tue Sep 3 07:46:16 2013 UTC (5 years, 9 months ago) by tdhock
File length: 24501 byte(s)
Diff to previous 389
delete Maintainer, Author, support Authors@R

Revision 389 - (view) (download) (annotate) - [select for diffs]
Modified Tue Sep 3 04:33:09 2013 UTC (5 years, 9 months ago) by tdhock
File length: 24234 byte(s)
Diff to previous 386
copy utils code to utils.R to avoid utils::: and pass R CMD check

Revision 386 - (view) (download) (annotate) - [select for diffs]
Modified Wed Jul 24 01:03:22 2013 UTC (5 years, 11 months ago) by tdhock
File length: 24250 byte(s)
Diff to previous 380
citation bugfix and if(interactive()) to reduce check time

Revision 380 - (view) (download) (annotate) - [select for diffs]
Modified Mon Mar 18 02:16:14 2013 UTC (6 years, 3 months ago) by tdhock
File length: 24447 byte(s)
Diff to previous 377
reformat doc

Revision 377 - (view) (download) (annotate) - [select for diffs]
Modified Mon Jan 28 01:22:49 2013 UTC (6 years, 4 months ago) by tdhock
File length: 24457 byte(s)
Diff to previous 376
do not alias inlinedocs to package.skeleton.dx

Revision 376 - (view) (download) (annotate) - [select for diffs]
Modified Mon Jan 28 01:08:01 2013 UTC (6 years, 4 months ago) by tdhock
File length: 24397 byte(s)
Diff to previous 370
version 1.9.2 bugfixes

Revision 370 - (view) (download) (annotate) - [select for diffs]
Modified Fri Nov 9 19:48:27 2012 UTC (6 years, 7 months ago) by markus
File length: 23732 byte(s)
Diff to previous 368
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 - (view) (download) (annotate) - [select for diffs]
Modified Thu Oct 25 16:01:50 2012 UTC (6 years, 7 months ago) by tomaschwutz
File length: 20394 byte(s)
Diff to previous 367
accessor moved codeBlock

Revision 367 - (view) (download) (annotate) - [select for diffs]
Modified Thu Oct 25 10:07:37 2012 UTC (6 years, 8 months ago) by tomaschwutz
File length: 20306 byte(s)
Diff to previous 362
tryCatch around parse in gen.Rd, workaround on accessor functions failures

Revision 362 - (view) (download) (annotate) - [select for diffs]
Modified Mon May 21 14:37:49 2012 UTC (7 years, 1 month ago) by tdhock
File length: 20106 byte(s)
Diff to previous 359
do not stop for WARNINGs in package.skeleton.dx example, due to R CMD check --as-cran bug

Revision 359 - (view) (download) (annotate) - [select for diffs]
Modified Mon Apr 9 21:55:16 2012 UTC (7 years, 2 months ago) by tdhock
File length: 19996 byte(s)
Diff to previous 356
as-cran for tests

Revision 356 - (view) (download) (annotate) - [select for diffs]
Modified Mon Apr 9 15:39:09 2012 UTC (7 years, 2 months ago) by tdhock
File length: 19964 byte(s)
Diff to previous 354
debugging CRAN crossref err

Revision 354 - (view) (download) (annotate) - [select for diffs]
Modified Mon Apr 9 14:04:07 2012 UTC (7 years, 2 months ago) by tdhock
File length: 19900 byte(s)
Diff to previous 345
make default description dynamically inside package.skeleton.dx

Revision 345 - (view) (download) (annotate) - [select for diffs]
Modified Fri Apr 6 08:37:28 2012 UTC (7 years, 2 months ago) by tdhock
File length: 19870 byte(s)
Diff to previous 336
use \s space instead of \W not word for deleting sections in Rd

Revision 336 - (view) (download) (annotate) - [select for diffs]
Modified Thu Apr 5 12:44:33 2012 UTC (7 years, 2 months ago) by tdhock
File length: 19870 byte(s)
Diff to previous 334
do.not.generate example, partial arg NOTEs fixed

Revision 334 - (view) (download) (annotate) - [select for diffs]
Modified Thu Apr 5 12:06:49 2012 UTC (7 years, 2 months ago) by tdhock
File length: 19852 byte(s)
Diff to previous 331
comment debug prints

Revision 331 - (view) (download) (annotate) - [select for diffs]
Modified Mon Mar 12 11:53:14 2012 UTC (7 years, 3 months ago) by tdhock
File length: 19849 byte(s)
Diff to previous 323
default DESCRIPTION values

Revision 323 - (view) (download) (annotate) - [select for diffs]
Modified Wed Feb 1 17:14:53 2012 UTC (7 years, 4 months ago) by markus
File length: 19644 byte(s)
Diff to previous 317
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 - (view) (download) (annotate) - [select for diffs]
Modified Fri Jan 13 20:40:49 2012 UTC (7 years, 5 months ago) by tdhock
File length: 19876 byte(s)
Diff to previous 316
changes too many dlines to txt, ok now

Revision 316 - (view) (download) (annotate) - [select for diffs]
Modified Fri Jan 13 15:56:45 2012 UTC (7 years, 5 months ago) by tdhock
File length: 19866 byte(s)
Diff to previous 312
rearrange stuff for escape.percent test

Revision 312 - (view) (download) (annotate) - [select for diffs]
Modified Fri Jan 13 09:22:02 2012 UTC (7 years, 5 months ago) by tdhock
File length: 19881 byte(s)
Diff to previous 311
usage line breaks

Revision 311 - (view) (download) (annotate) - [select for diffs]
Modified Wed Dec 7 19:39:34 2011 UTC (7 years, 6 months ago) by markus
File length: 19779 byte(s)
Diff to previous 308
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 - (view) (download) (annotate) - [select for diffs]
Modified Fri Oct 21 12:08:39 2011 UTC (7 years, 8 months ago) by tdhock
File length: 19469 byte(s)
Diff to previous 303
modify getSource, delete inlinedocExample to pass 2.14 checks

Revision 303 - (view) (download) (annotate) - [select for diffs]
Modified Tue Jul 19 15:35:23 2011 UTC (7 years, 11 months ago) by tdhock
File length: 20093 byte(s)
Diff to previous 274
gregors ideas: whitespace in examples, value, and usage

Revision 274 - (view) (download) (annotate) - [select for diffs]
Modified Fri May 27 10:14:41 2011 UTC (8 years, 1 month ago) by tdhock
File length: 20028 byte(s)
Diff to previous 271
try to debug cran err

Revision 271 - (view) (download) (annotate) - [select for diffs]
Modified Mon May 23 16:14:49 2011 UTC (8 years, 1 month ago) by tdhock
File length: 21932 byte(s)
Diff to previous 255
suppress warnings when we attempt to detach a pkg

Revision 255 - (view) (download) (annotate) - [select for diffs]
Modified Mon Apr 25 13:58:30 2011 UTC (8 years, 2 months ago) by tdhock
File length: 21901 byte(s)
Diff to previous 236
check length with sprintf to avoid error

Revision 236 - (view) (download) (annotate) - [select for diffs]
Modified Mon Mar 28 14:03:48 2011 UTC (8 years, 2 months ago) by tdhock
File length: 21876 byte(s)
Diff to previous 214
erase \code inside \title in s4 class docs since we cant do bracket matching in regex find/replace in replace.one()

Revision 214 - (view) (download) (annotate) - [select for diffs]
Modified Wed Mar 9 18:28:02 2011 UTC (8 years, 3 months ago) by tdhock
File length: 21572 byte(s)
Diff to previous 209
add leadingS3generic, use dos line endings

Revision 209 - (view) (download) (annotate) - [select for diffs]
Modified Fri Feb 25 08:15:10 2011 UTC (8 years, 3 months ago) by tdhock
File length: 21463 byte(s)
Diff to previous 201
doc updates

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Modified Fri Feb 18 15:34:51 2011 UTC (8 years, 4 months ago) by tdhock
File length: 21465 byte(s)
Diff to previous 200
doc updates

Revision 200 - (view) (download) (annotate) - [select for diffs]
Modified Fri Feb 18 15:02:16 2011 UTC (8 years, 4 months ago) by tdhock
File length: 21559 byte(s)
Diff to previous 199
move s3method and collapse to Parser Functions

Revision 199 - (view) (download) (annotate) - [select for diffs]
Modified Fri Feb 18 14:37:24 2011 UTC (8 years, 4 months ago) by tdhock
File length: 21558 byte(s)
Diff to previous 198
replace.one function

Revision 198 - (view) (download) (annotate) - [select for diffs]
Modified Fri Feb 18 14:17:08 2011 UTC (8 years, 4 months ago) by tdhock
File length: 21229 byte(s)
Diff to previous 191
s3method -> .s3method

Revision 191 - (view) (download) (annotate) - [select for diffs]
Modified Thu Feb 17 14:09:43 2011 UTC (8 years, 4 months ago) by tdhock
File length: 21217 byte(s)
Diff to previous 147
length(grep -> grepl, minor

Revision 147 - (view) (download) (annotate) - [select for diffs]
Modified Wed Oct 20 11:24:49 2010 UTC (8 years, 8 months ago) by tdhock
File length: 21207 byte(s)
Diff to previous 141
check pkg using R.home("bin")

Revision 141 - (view) (download) (annotate) - [select for diffs]
Modified Wed Oct 20 09:12:53 2010 UTC (8 years, 8 months ago) by tdhock
File length: 21141 byte(s)
Diff to previous 140
dont on.exit in an example

Revision 140 - (view) (download) (annotate) - [select for diffs]
Modified Tue Oct 19 23:24:01 2010 UTC (8 years, 8 months ago) by tdhock
File length: 21150 byte(s)
Diff to previous 130
do ex in tempdir

Revision 130 - (view) (download) (annotate) - [select for diffs]
Modified Thu Sep 30 12:34:15 2010 UTC (8 years, 8 months ago) by tdhock
File length: 21101 byte(s)
Diff to previous 125
report warning encountered in check

Revision 125 - (view) (download) (annotate) - [select for diffs]
Modified Thu Sep 16 09:34:38 2010 UTC (8 years, 9 months ago) by tdhock
File length: 20997 byte(s)
Diff to previous 123
extended package.skeleton.dx example that also checks the silly package and verifies that there are no warnings

Revision 123 - (view) (download) (annotate) - [select for diffs]
Modified Mon Aug 30 09:19:39 2010 UTC (8 years, 9 months ago) by tomaschwutz
File length: 20745 byte(s)
Diff to previous 122
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 - (view) (download) (annotate) - [select for diffs]
Modified Sat Aug 28 21:36:48 2010 UTC (8 years, 9 months ago) by tomaschwutz
File length: 19996 byte(s)
Diff to previous 115
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 115 - (view) (download) (annotate) - [select for diffs]
Modified Fri Jun 18 10:35:11 2010 UTC (9 years ago) by tdhock
File length: 19189 byte(s)
Diff to previous 110
silly example unit test checks

Revision 110 - (view) (download) (annotate) - [select for diffs]
Modified Mon Jun 7 12:08:54 2010 UTC (9 years ago) by tdhock
File length: 19196 byte(s)
Diff to previous 109
unit test for extract.docs.file

Revision 109 - (view) (download) (annotate) - [select for diffs]
Modified Mon Jun 7 08:42:15 2010 UTC (9 years ago) by tdhock
File length: 20011 byte(s)
Diff to previous 108
extract.docs.file new functionality parses files independently

Revision 108 - (view) (download) (annotate) - [select for diffs]
Modified Wed May 26 12:00:17 2010 UTC (9 years, 1 month ago) by phgrosjean
File length: 20366 byte(s)
Diff to previous 105
Several bugs corrections and improvements. See NEWS file
More tests temporary in /scratch for difficult cases

Revision 105 - (view) (download) (annotate) - [select for diffs]
Modified Tue May 18 17:32:43 2010 UTC (9 years, 1 month ago) by tdhock
File length: 12713 byte(s)
Diff to previous 102
extract.docs.code for applying Parser Functions to arbitrary code chunks and returning a doc list

Revision 102 - (view) (download) (annotate) - [select for diffs]
Modified Fri May 14 18:48:40 2010 UTC (9 years, 1 month ago) by tdhock
File length: 13402 byte(s)
Diff to previous 101
bugfix for return at end of function

Revision 101 - (view) (download) (annotate) - [select for diffs]
Modified Tue May 4 06:57:58 2010 UTC (9 years, 1 month ago) by tdhock
File length: 13334 byte(s)
Diff to previous 100
cat sep

Revision 100 - (view) (download) (annotate) - [select for diffs]
Modified Tue May 4 06:55:27 2010 UTC (9 years, 1 month ago) by tdhock
File length: 13327 byte(s)
Diff to previous 96
typo

Revision 96 - (view) (download) (annotate) - [select for diffs]
Modified Mon May 3 15:57:03 2010 UTC (9 years, 1 month ago) by tdhock
File length: 13319 byte(s)
Diff to previous 94
examples-after-return gives value as well

Revision 94 - (view) (download) (annotate) - [select for diffs]
Modified Mon May 3 14:21:15 2010 UTC (9 years, 1 month ago) by tdhock
File length: 13389 byte(s)
Diff to previous 92
passes check 

Revision 92 - (view) (download) (annotate) - [select for diffs]
Modified Mon May 3 14:17:37 2010 UTC (9 years, 1 month ago) by tdhock
File length: 13391 byte(s)
Diff to previous 89
use collate if it exists

Revision 89 - (view) (download) (annotate) - [select for diffs]
Modified Mon May 3 13:01:06 2010 UTC (9 years, 1 month ago) by tdhock
File length: 13293 byte(s)
Diff to previous 87
define parsers as a list, allow configuration of parser list from project .inlinedocs.R or options()

Revision 87 - (view) (download) (annotate) - [select for diffs]
Modified Sat May 1 12:21:27 2010 UTC (9 years, 1 month ago) by tdhock
File length: 12281 byte(s)
Diff to previous 86
restructure package.skeleton.dx to support modular parser list

Revision 86 - (view) (download) (annotate) - [select for diffs]
Modified Fri Apr 30 12:30:34 2010 UTC (9 years, 1 month ago) by tomaschwutz
File length: 35369 byte(s)
Diff to previous 84
1) changed prefix to include tabs

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

Revision 84 - (view) (download) (annotate) - [select for diffs]
Modified Thu Apr 22 10:11:18 2010 UTC (9 years, 2 months ago) by kmpont
File length: 35270 byte(s)
Diff to previous 82
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 - (view) (download) (annotate) - [select for diffs]
Modified Tue Apr 20 13:51:01 2010 UTC (9 years, 2 months ago) by tomaschwutz
File length: 33936 byte(s)
Diff to previous 75
added support for tabs and indented function arguments and ### comments, added new test package indent

Revision 75 - (view) (download) (annotate) - [select for diffs]
Modified Mon Apr 12 09:30:28 2010 UTC (9 years, 2 months ago) by tdhock
File length: 33445 byte(s)
Diff to previous 73
docs update, passes r cmd check, upload to cran

Revision 73 - (view) (download) (annotate) - [select for diffs]
Modified Mon Mar 1 14:28:44 2010 UTC (9 years, 3 months ago) by tdhock
File length: 33432 byte(s)
Diff to previous 72
just ignore format field, causes too many problems

Revision 72 - (view) (download) (annotate) - [select for diffs]
Modified Thu Feb 25 16:50:15 2010 UTC (9 years, 3 months ago) by tdhock
File length: 33347 byte(s)
Diff to previous 70
delete empty sections in Rd files

Revision 70 - (view) (download) (annotate) - [select for diffs]
Modified Fri Jan 15 09:42:36 2010 UTC (9 years, 5 months ago) by kmpont
File length: 33239 byte(s)
Diff to previous 69
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 - (view) (download) (annotate) - [select for diffs]
Modified Mon Jan 11 18:13:14 2010 UTC (9 years, 5 months ago) by kmpont
File length: 26470 byte(s)
Diff to previous 68
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 - (view) (download) (annotate) - [select for diffs]
Modified Thu Jan 7 15:56:05 2010 UTC (9 years, 5 months ago) by kmpont
File length: 25102 byte(s)
Diff to previous 67
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 - (view) (download) (annotate) - [select for diffs]
Modified Thu Jan 7 10:31:00 2010 UTC (9 years, 5 months ago) by kmpont
File length: 25006 byte(s)
Diff to previous 66
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 - (view) (download) (annotate) - [select for diffs]
Modified Thu Jan 7 10:12:28 2010 UTC (9 years, 5 months ago) by kmpont
File length: 24962 byte(s)
Diff to previous 65


Revision 65 - (view) (download) (annotate) - [select for diffs]
Modified Fri Dec 11 14:48:30 2009 UTC (9 years, 6 months ago) by tdhock
File length: 24340 byte(s)
Diff to previous 64
erase curly braces from format section

Revision 64 - (view) (download) (annotate) - [select for diffs]
Modified Thu Dec 10 14:57:31 2009 UTC (9 years, 6 months ago) by tdhock
File length: 24017 byte(s)
Diff to previous 60
add definition attribute to result of extract.docs

Revision 60 - (view) (download) (annotate) - [select for diffs]
Modified Mon Nov 30 18:05:13 2009 UTC (9 years, 6 months ago) by kmpont
File length: 23741 byte(s)
Diff to previous 58
First implementation of docs within S4 class definitions

Revision 58 - (view) (download) (annotate) - [select for diffs]
Modified Thu Nov 26 10:35:42 2009 UTC (9 years, 6 months ago) by tdhock
File length: 19128 byte(s)
Diff to previous 57
use prefix instead of hard re

Revision 57 - (view) (download) (annotate) - [select for diffs]
Modified Mon Nov 23 16:46:00 2009 UTC (9 years, 7 months ago) by kmpont
File length: 19126 byte(s)
Diff to previous 56
Initial implementation of 'extra' fields information via ##field<<

Revision 56 - (view) (download) (annotate) - [select for diffs]
Modified Wed Nov 18 09:31:49 2009 UTC (9 years, 7 months ago) by tdhock
File length: 12560 byte(s)
Diff to previous 55
code formatting clearer

Revision 55 - (view) (download) (annotate) - [select for diffs]
Modified Sun Nov 15 22:54:53 2009 UTC (9 years, 7 months ago) by tdhock
File length: 12516 byte(s)
Diff to previous 53
add directlabels test

Revision 53 - (view) (download) (annotate) - [select for diffs]
Modified Wed Nov 11 22:27:13 2009 UTC (9 years, 7 months ago) by tdhock
File length: 12515 byte(s)
Diff to previous 48
load pkg dependencies before sourcing package

Revision 48 - (view) (download) (annotate) - [select for diffs]
Modified Mon Nov 9 18:14:45 2009 UTC (9 years, 7 months ago) by tdhock
File length: 11990 byte(s)
Diff to previous 42
backwards compatible changes from keith

Revision 42 - (view) (download) (annotate) - [select for diffs]
Modified Mon Oct 26 16:36:08 2009 UTC (9 years, 7 months ago) by tdhock
File length: 9182 byte(s)
Diff to previous 39
allow multiline comments before data items

Revision 39 - (view) (download) (annotate) - [select for diffs]
Modified Sat Oct 3 14:14:22 2009 UTC (9 years, 8 months ago) by tdhock
File length: 8748 byte(s)
Diff to previous 37
need even more escapes to accurately replace backslashes

Revision 37 - (view) (download) (annotate) - [select for diffs]
Modified Mon Aug 31 11:52:01 2009 UTC (9 years, 9 months ago) by tdhock
File length: 8705 byte(s)
Diff to previous 36
rebuild examples at the end if we didnt test them

Revision 36 - (view) (download) (annotate) - [select for diffs]
Modified Wed Aug 19 13:18:42 2009 UTC (9 years, 10 months ago) by tdhock
File length: 8598 byte(s)
Diff to previous 35
convert ._ to space for Rd titles

Revision 35 - (view) (download) (annotate) - [select for diffs]
Modified Tue Aug 18 20:57:20 2009 UTC (9 years, 10 months ago) by tdhock
File length: 8574 byte(s)
Diff to previous 34
custom title allowed by commenting first line of function definition

Revision 34 - (view) (download) (annotate) - [select for diffs]
Modified Tue Aug 18 14:05:29 2009 UTC (9 years, 10 months ago) by tdhock
File length: 8349 byte(s)
Diff to previous 33
update docs for new interpretation of check parameter

Revision 33 - (view) (download) (annotate) - [select for diffs]
Modified Tue Aug 18 13:54:20 2009 UTC (9 years, 10 months ago) by tdhock
File length: 8146 byte(s)
Diff to previous 32
package checking can omit examples for speed

Revision 32 - (view) (download) (annotate) - [select for diffs]
Modified Tue Aug 18 13:14:55 2009 UTC (9 years, 10 months ago) by tdhock
File length: 7974 byte(s)
Diff to previous 31
more backslashes needed for percent escaping

Revision 31 - (view) (download) (annotate) - [select for diffs]
Modified Tue Aug 18 12:48:42 2009 UTC (9 years, 10 months ago) by tdhock
File length: 7972 byte(s)
Diff to previous 28
escape percents in Rd files

Revision 28 - (view) (download) (annotate) - [select for diffs]
Modified Wed Aug 5 10:07:40 2009 UTC (9 years, 10 months ago) by tdhock
File length: 7898 byte(s)
Diff to previous 24
extract -package info from DESCRIPTION file

Revision 24 - (view) (download) (annotate) - [select for diffs]
Modified Tue Aug 4 12:40:37 2009 UTC (9 years, 10 months ago) by tdhock
File length: 7643 byte(s)
Diff to previous 23
package.skeleton.dx default filepath .. bugfix, escape backslashes in comments, examples from test files

Revision 23 - (view) (download) (annotate) - [select for diffs]
Modified Mon Aug 3 15:37:42 2009 UTC (9 years, 10 months ago) by tdhock
File length: 7115 byte(s)
Diff to previous 21
first argument changed to pkgdir, on.exit added to package.skeleton.dx

Revision 21 - (view) (download) (annotate) - [select for diffs]
Modified Mon Aug 3 15:09:28 2009 UTC (9 years, 10 months ago) by tdhock
File length: 7047 byte(s)
Diff to previous 20
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 - (view) (download) (annotate) - [select for diffs]
Modified Sun Aug 2 22:55:45 2009 UTC (9 years, 10 months ago) by tdhock
File length: 6643 byte(s)
Diff to previous 18
error checking for extract.docs and extract.docs.fun

Revision 18 - (view) (download) (annotate) - [select for diffs]
Modified Sat Aug 1 22:01:23 2009 UTC (9 years, 10 months ago) by tdhock
File length: 6427 byte(s)
Diff to previous 12
error checking and automatic DESCRIPTION added

Revision 12 - (view) (download) (annotate) - [select for diffs]
Modified Sat Aug 1 07:01:02 2009 UTC (9 years, 10 months ago) by tdhock
File length: 5638 byte(s)
Diff to previous 8
support for check and chdir args for package.skeleton.dx

Revision 8 - (view) (download) (annotate) - [select for diffs]
Modified Fri Jul 31 17:13:17 2009 UTC (9 years, 10 months ago) by tdhock
File length: 5194 byte(s)
Diff to previous 7
dots argument special case, package name alias conflict special case

Revision 7 - (view) (download) (annotate) - [select for diffs]
Modified Fri Jul 31 15:11:15 2009 UTC (9 years, 10 months ago) by tdhock
File length: 4805 byte(s)
Diff to previous 6
works with new find/replace mechanism

Revision 6 - (view) (download) (annotate) - [select for diffs]
Modified Fri Jul 31 12:04:29 2009 UTC (9 years, 10 months ago) by tdhock
File length: 4355 byte(s)
Diff to previous 5
change extract.docs.file so that reading functions should work with arbitrary packages

Revision 5 - (view) (download) (annotate) - [select for diffs]
Modified Fri Jul 31 09:56:58 2009 UTC (9 years, 10 months ago) by tdhock
File length: 4364 byte(s)
Diff to previous 4
author tag, switch statement, more comments

Revision 4 - (view) (download) (annotate) - [select for diffs]
Modified Thu Jul 30 18:39:50 2009 UTC (9 years, 10 months ago) by tdhock
File length: 3930 byte(s)
Diff to previous 3
deleted name argument, infer from DESCRIPTION file

Revision 3 - (view) (download) (annotate) - [select for diffs]
Modified Thu Jul 30 09:43:37 2009 UTC (9 years, 10 months ago) by tdhock
File length: 4030 byte(s)
Diff to previous 2
support for comments about function return values, resulting documentation passes R CMD check with no warnings

Revision 2 - (view) (download) (annotate) - [select for diffs]
Added Wed Jul 29 16:59:24 2009 UTC (9 years, 10 months ago) by tdhock
File length: 3096 byte(s)
First working version that passes checks successfully

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