From murdoch@dunc@n @ending from gm@il@com  Thu Jul 12 18:29:19 2018
From: murdoch@dunc@n @ending from gm@il@com (Duncan Murdoch)
Date: Thu, 12 Jul 2018 12:29:19 -0400
Subject: [Rd] Top level \Sexpr and R CMD check
In-Reply-To: <CABtg=K=Rvt98Z9XdLLEd7FogzSiXGZRzGOofxP12pzyn5rfr7A@mail.gmail.com>
References: <CABtg=KkE7gNvho-PLvsS-48yOR5nVTTSsekf35uLS4JJiZmjjg@mail.gmail.com>
 <eaf1c672-fb4c-5327-9b5a-4349ef75eec7@gmail.com>
 <CABtg=KkNXXPBg+6yzQZ2FOdWsUqZj0xnbUAaOu=-ZG7pGUOvHQ@mail.gmail.com>
 <b03ecf4b-f59b-eed6-ddb2-4788a4cd98ef@gmail.com>
 <CABtg=KkH8UO93RggxZwtKgJxcN+5JS-HQ0NBQX0yYrLNi5PEXw@mail.gmail.com>
 <CABtg=K=Rvt98Z9XdLLEd7FogzSiXGZRzGOofxP12pzyn5rfr7A@mail.gmail.com>
Message-ID: <f5f9aff9-cca1-9da6-8155-ac4571bc90da@gmail.com>

On 12/07/2018 9:46 AM, G?bor Cs?rdi wrote:
> On Thu, Jul 12, 2018 at 2:30 PM G?bor Cs?rdi <csardi.gabor at gmail.com> wrote:
>>
>> On Thu, Jul 12, 2018 at 2:21 PM Duncan Murdoch <murdoch.duncan at gmail.com> wrote:
>>> I think I found the bug.  The tools::checkRd function only processes
>>> \Sexpr's with "stage=render".  I think the author (who might have been
>>> me, I forget) assumed that would imply all the earlier stages as well,
>>> but apparently it doesn't.
>>>
>>> So you could use that as a workaround.
>>>
>>> I'll do some more checking, then submit a bug report and patch to Bugzilla.
>>>
>>> Duncan Murdoch
>>
>> Thanks much! I tried using stage=render, but then I get an error at
>> install time:
>>
>> Warning: /private/var/folders/59/0gkmw1yj2w7bf2dfc3jznv5w0000gn/T/RtmpCG4Qz9/R.INSTALLec4743ba8cf4/ps/man/ps_handle.Rd:45-48:
>> Section \Sexpr is unrecognized and will be dropped
>>
>> And indeed the whole section is dropped.
>>
>> Seems like there is no clean workaround here.
>>
>> Thanks again,
>> G.
> 
> Btw. would it make sense to just allow \Sexpr as a top level section?
> Maybe here:
> https://github.com/wch/r-source/blob/98e9999eb0e8616550632a1675e4d2dbe630d5e4/src/library/tools/R/RdConv2.R#L500-L503
> 
> At least if stage=render, there is no way to check if the returned
> value is always a valid top level section, anyway.
> If it is not a valid section (or \Sexpr returns some bad markup in
> general), then the user gets a render-time error,
> but with stage=render I guess one cannot do better.
> 

I believe the problem is in the tools:::.check_package_parseRd function. 
  It checks the .Rd files rather than parsed Rd objects, so it needs to 
be told to expand all \Sexpr's, not just render-time ones.  I think it 
is fixed by the below patch to R-devel.  Can you give it a try before I 
submit the bug report?

Duncan Murdoch

Index: src/library/tools/R/QC.R
===================================================================
--- src/library/tools/R/QC.R	(revision 74954)
+++ src/library/tools/R/QC.R	(working copy)
@@ -6430,7 +6430,8 @@
          if(basename(f) %in% c("iconv.Rd", "showNonASCII.Rd")) def_enc 
<- TRUE
  	tmp <- tryCatch(suppressMessages(checkRd(f, encoding = enc,
  						 def_enc = def_enc,
-                                                 macros = macros)),
+                                                 macros = macros,
+                                                 stages = c("build", 
"install", "render"))),
  			error = identity)
  	if(inherits(tmp, "error")) {
  	    bad <- c(bad, f)



[Rd] Top level \Sexpr and R CMD check
Duncan Murdoch