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Revision 399 - (view) (download) (annotate) - [select for diffs]
Modified Wed Apr 29 10:01:10 2015 UTC (4 years ago) by tomaschwutz
File length: 1092 byte(s)
Diff to previous 396
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 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: 890 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: 882 byte(s)
Diff to previous 393
attr(o, "ex", exact=TRUE)

Revision 393 - (view) (download) (annotate) - [select for diffs]
Modified Tue Oct 1 07:15:26 2013 UTC (5 years, 7 months ago) by tomaschwutz
File length: 881 byte(s)
Diff to previous 392
fixed error in parsing examples with (yet) empty lines

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: 880 byte(s)
Diff to previous 391
delete Maintainer, Author, support Authors@R

Revision 391 - (view) (download) (annotate) - [select for diffs]
Modified Tue Sep 3 05:41:18 2013 UTC (5 years, 8 months ago) by tdhock
File length: 1003 byte(s)
Diff to previous 390
authors, encoding

Revision 390 - (view) (download) (annotate) - [select for diffs]
Modified Tue Sep 3 05:35:06 2013 UTC (5 years, 8 months ago) by tdhock
File length: 951 byte(s)
Diff to previous 389
contributions from R Core Team

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: 691 byte(s)
Diff to previous 388
copy utils code to utils.R to avoid utils::: and pass R CMD check

Revision 388 - (view) (download) (annotate) - [select for diffs]
Modified Fri Aug 23 00:35:42 2013 UTC (5 years, 8 months ago) by tdhock
File length: 692 byte(s)
Diff to previous 387
GPL-2 or 3

Revision 387 - (view) (download) (annotate) - [select for diffs]
Modified Thu Aug 22 09:28:21 2013 UTC (5 years, 8 months ago) by tdhock
File length: 684 byte(s)
Diff to previous 384
update JSS citation

Revision 384 - (view) (download) (annotate) - [select for diffs]
Modified Tue Jul 23 00:18:14 2013 UTC (5 years, 9 months ago) by tdhock
File length: 684 byte(s)
Diff to previous 379
cran asked for update

Revision 379 - (view) (download) (annotate) - [select for diffs]
Modified Wed Mar 6 06:53:44 2013 UTC (6 years, 2 months ago) by tdhock
File length: 586 byte(s)
Diff to previous 378
when did +.method start working?

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Modified Fri Feb 22 02:42:46 2013 UTC (6 years, 2 months ago) by tdhock
File length: 603 byte(s)
Diff to previous 376
titech email

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Modified Mon Jan 28 01:08:01 2013 UTC (6 years, 3 months ago) by tdhock
File length: 601 byte(s)
Diff to previous 359
version 1.9.2 bugfixes

Revision 359 - (view) (download) (annotate) - [select for diffs]
Modified Mon Apr 9 21:55:16 2012 UTC (7 years, 1 month ago) by tdhock
File length: 601 byte(s)
Diff to previous 356
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: 601 byte(s)
Diff to previous 320
debugging CRAN crossref err

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Modified Fri Jan 27 15:59:35 2012 UTC (7 years, 3 months ago) by tdhock
File length: 599 byte(s)
Diff to previous 312
version 1.8 -> 1.9

Revision 312 - (view) (download) (annotate) - [select for diffs]
Modified Fri Jan 13 09:22:02 2012 UTC (7 years, 4 months ago) by tdhock
File length: 599 byte(s)
Diff to previous 307
usage line breaks

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Modified Fri Oct 21 11:37:19 2011 UTC (7 years, 7 months ago) by tdhock
File length: 598 byte(s)
Diff to previous 305
test errors reported more clearly

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Modified Tue Aug 16 11:48:38 2011 UTC (7 years, 9 months ago) by kmpont
File length: 590 byte(s)
Diff to previous 277
Added default title for setClass when no # title on setClass line

Revision 277 - (view) (download) (annotate) - [select for diffs]
Modified Tue May 31 12:21:12 2011 UTC (7 years, 11 months ago) by tdhock
File length: 588 byte(s)
Diff to previous 254
ideas for tests 1.7

Revision 254 - (view) (download) (annotate) - [select for diffs]
Modified Mon Apr 25 13:57:51 2011 UTC (8 years ago) by tdhock
File length: 580 byte(s)
Diff to previous 250
depend R >= 2.9 for grepl function

Revision 250 - (view) (download) (annotate) - [select for diffs]
Modified Thu Apr 7 14:17:42 2011 UTC (8 years, 1 month ago) by tdhock
File length: 568 byte(s)
Diff to previous 212
version 1.6, more accurate revision history

Revision 212 - (view) (download) (annotate) - [select for diffs]
Modified Wed Mar 9 16:37:25 2011 UTC (8 years, 2 months ago) by kmpont
File length: 570 byte(s)
Diff to previous 150
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 150 - (view) (download) (annotate) - [select for diffs]
Modified Thu Oct 21 15:36:47 2010 UTC (8 years, 7 months ago) by tdhock
File length: 568 byte(s)
Diff to previous 138
version bump, ideas for future unit tests

Revision 138 - (view) (download) (annotate) - [select for diffs]
Modified Tue Oct 19 22:51:59 2010 UTC (8 years, 7 months ago) by tdhock
File length: 568 byte(s)
Diff to previous 108
update examples to pass new more stringent parser checks

Revision 108 - (view) (download) (annotate) - [select for diffs]
Modified Wed May 26 12:00:17 2010 UTC (8 years, 11 months ago) by phgrosjean
File length: 568 byte(s)
Diff to previous 107
Several bugs corrections and improvements. See NEWS file
More tests temporary in /scratch for difficult cases

Revision 107 - (view) (download) (annotate) - [select for diffs]
Modified Wed May 19 08:46:27 2010 UTC (9 years ago) by tdhock
File length: 561 byte(s)
Diff to previous 81
version and maintainer

Revision 81 - (view) (download) (annotate) - [select for diffs]
Modified Mon Apr 19 10:02:10 2010 UTC (9 years, 1 month ago) by tdhock
File length: 570 byte(s)
Diff to previous 70
version bump

Revision 70 - (view) (download) (annotate) - [select for diffs]
Modified Fri Jan 15 09:42:36 2010 UTC (9 years, 4 months ago) by kmpont
File length: 570 byte(s)
Diff to previous 63
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 63 - (view) (download) (annotate) - [select for diffs]
Modified Tue Dec 8 15:01:01 2009 UTC (9 years, 5 months ago) by tdhock
File length: 553 byte(s)
Diff to previous 60
update new email

Revision 60 - (view) (download) (annotate) - [select for diffs]
Modified Mon Nov 30 18:05:13 2009 UTC (9 years, 5 months ago) by kmpont
File length: 556 byte(s)
Diff to previous 51
First implementation of docs within S4 class definitions

Revision 51 - (view) (download) (annotate) - [select for diffs]
Modified Wed Nov 11 15:38:23 2009 UTC (9 years, 6 months ago) by tdhock
File length: 556 byte(s)
Diff to previous 38
update desc with keith as coauthor

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Modified Mon Sep 21 16:54:38 2009 UTC (9 years, 8 months ago) by tdhock
File length: 504 byte(s)
Diff to previous 16
desc and docs update

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Modified Sat Aug 1 08:30:33 2009 UTC (9 years, 9 months ago) by tdhock
File length: 414 byte(s)
Diff to previous 2
website update DESCRIPTION minimal

Revision 2 - (view) (download) (annotate) - [select for diffs]
Added Wed Jul 29 16:59:24 2009 UTC (9 years, 9 months ago) by tdhock
File length: 414 byte(s)
First working version that passes checks successfully

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