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Revision 396 - (view) (download) (annotate) - [select for diffs]
Modified Tue Feb 18 13:07:32 2014 UTC (5 years, 3 months ago) by markus
File length: 8581 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, 3 months ago) by tdhock
File length: 8709 byte(s)
Diff to previous 392
attr(o, "ex", exact=TRUE)

Revision 392 - (view) (download) (annotate) - [select for diffs]
Modified Tue Sep 3 07:46:16 2013 UTC (5 years, 8 months ago) by tdhock
File length: 8581 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, 8 months ago) by tdhock
File length: 8561 byte(s)
Diff to previous 387
copy utils code to utils.R to avoid utils::: and pass R CMD check

Revision 387 - (view) (download) (annotate) - [select for diffs]
Modified Thu Aug 22 09:28:21 2013 UTC (5 years, 9 months ago) by tdhock
File length: 8434 byte(s)
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update JSS citation

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Modified Wed Jul 24 01:03:22 2013 UTC (5 years, 9 months ago) by tdhock
File length: 8399 byte(s)
Diff to previous 379
citation bugfix and if(interactive()) to reduce check time

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Modified Wed Mar 6 06:53:44 2013 UTC (6 years, 2 months ago) by tdhock
File length: 8294 byte(s)
Diff to previous 376
when did +.method start working?

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

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Modified Fri Jan 25 00:07:58 2013 UTC (6 years, 3 months ago) by tdhock
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default-function bug

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Modified Thu Jun 7 09:38:42 2012 UTC (6 years, 11 months ago) by tdhock
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TODO [.class

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

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Modified Mon Apr 9 21:55:16 2012 UTC (7 years, 1 month ago) by tdhock
File length: 7274 byte(s)
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as-cran for tests

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Modified Mon Apr 9 15:39:09 2012 UTC (7 years, 1 month ago) by tdhock
File length: 7248 byte(s)
Diff to previous 346
debugging CRAN crossref err

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Modified Fri Apr 6 08:40:48 2012 UTC (7 years, 1 month ago) by tdhock
File length: 6720 byte(s)
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NAMESPACE + regexp bug

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

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

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

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

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Modified Fri Oct 21 11:37:19 2011 UTC (7 years, 7 months ago) by tdhock
File length: 5638 byte(s)
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test errors reported more clearly

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

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

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Modified Fri Jun 17 07:39:31 2011 UTC (7 years, 11 months ago) by tdhock
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bugfix when nothing defined in pkg

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Modified Tue May 31 12:21:12 2011 UTC (7 years, 11 months ago) by tdhock
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ideas for tests 1.7

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Modified Mon May 23 16:18:45 2011 UTC (8 years ago) by tdhock
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typo

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

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

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Modified Wed May 11 12:16:29 2011 UTC (8 years ago) by tdhock
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warnings

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Modified Sun May 1 19:15:09 2011 UTC (8 years ago) by tdhock
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definition/news

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Modified Thu Apr 7 14:17:42 2011 UTC (8 years, 1 month ago) by tdhock
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version 1.6, more accurate revision history

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

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

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

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

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

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Modified Mon Jan 10 12:06:48 2011 UTC (8 years, 4 months ago) by tdhock
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parseRd

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Modified Fri Jan 7 12:36:34 2011 UTC (8 years, 4 months ago) by tdhock
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news update

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

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Modified Tue Nov 9 16:56:46 2010 UTC (8 years, 6 months ago) by tdhock
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news update

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Modified Thu Oct 28 16:04:11 2010 UTC (8 years, 6 months ago) by tdhock
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s4 bugfix

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Modified Thu Oct 21 15:36:47 2010 UTC (8 years, 7 months ago) by tdhock
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version bump, ideas for future unit tests

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

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Added Wed May 26 12:00:17 2010 UTC (8 years, 11 months ago) by phgrosjean
File length: 2492 byte(s)
Several bugs corrections and improvements. See NEWS file
More tests temporary in /scratch for difficult cases

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