From pauljohn32 at gmail.com  Fri Jul 27 07:23:44 2012
From: pauljohn32 at gmail.com (Paul Johnson)
Date: Fri, 27 Jul 2012 00:23:44 -0500
Subject: [Rd] Problem in vignette packaging of Sweave in utils package
In-Reply-To: <4FF82AD0.1020605@gmail.com>
References: <CAErODj_9n7cjy5iPkjr-GOocL23hnJwX2QCYSd+4zJfgu0SUpA@mail.gmail.com>
	<4FF82AD0.1020605@gmail.com>
Message-ID: <CAErODj9Xu=TcHnEzQj6Auq9CO6cEAbvQeW9RTS3j=g60F-BnBA@mail.gmail.com>

New help request below

On Sat, Jul 7, 2012 at 7:25 AM, Duncan Murdoch <murdoch.duncan at gmail.com> wrote:
> On 12-07-03 1:21 PM, Paul Johnson wrote:
>>
>> In ?Sweave, it refers to Sweave User Manual. In the doc folder of
>> utils package, I see "Sweave.pdf".
>>
>> However, I can't find it from within R
>>
>>
>>> vignette("Sweave User Manual")
>>
>> Warning message:
>> vignette ?Sweave User Manual? not found
>
>
> Turns out there was a bug in the code to install from tarballs, so base
> package vignettes weren't fully installed.  I've fixed it; installs from
> R-patched or R-devel revisions after 59750 should be okay.
>
> Duncan Murdoch
>
>

Thanks, Duncan

Can I ask you to check this one again?

I just built RPMS for R-2.15.1-patched 2012-07-25 on a Rocks Cluster
(Centos 5.3).  I still see the trouble that the vignette for Sweave is
missing from the vignette index.

Below I'm showing everything I can think of that is related to this,
hoping it will give you an idea if the problem is on my end.

> sessionInfo()
R version 2.15.1 Patched (2012-07-25 r59963)
Platform: x86_64-redhat-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=C                 LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

loaded via a namespace (and not attached):
[1] tools_2.15.1

> browseVignettes("utils")
No vignettes found by browseVignettes("utils")

> vignette("Sweave")
Warning message:
vignette ?Sweave? not found

As far as I can tell, the vignette WAS built and installed, as evidenced:

$ pwd
/usr/lib64/R/library/utils/doc
[pauljohn at devel doc]$ ls
Sweave.pdf

But it is not found by the vignette indexing system, it's not in the
output from
help(package="utils")

Maybe I did something to break the install when making the RPM.  But I
don't know what:)  I also built R the "old fashioned way" in the shell
and the result is the same.

For the RPM, I used a spec file I've slightly adapted from Tom "Spot"
Calloway's spec file that is used to build R for EPEL and Fedora.
Here's a copy:

http://pj.freefaculty.org/misc/R-2.15.1-patch.spec

And the output (stdout and stderr) from the build process, obtained from

$ rpmbuild -ba R-2.15.1-patch.spec --define "dist kurocks53" >
R-2.15.1-patch.txt 2>&1

http://pj.freefaculty.org/misc/R-2.15.1-patch.txt

In order to make this work, I did one unsavory thing.  I took the
contents of this R-patched_2012-07-25.tar.gz and re-named the
directory R-2.15.1 and then repackaged that as R-2.15.1.tar.gz.  I
know this is unsavory to rename somebody else's packaging, but it was
the only way I could get the RPM build system to accept the version
number and file name. I put the date in the release version to reduce
confusion.  The RPMs have names like:

R-core-2.15.1-20120725kurocks53.x86_64.rpm

Oh, heck. I'm just uploading them all to the same folder as the spec
file, on the off chance you can see what's wrong.

libRmath-2.15.1-20120725kurocks53.x86_64.rpm
libRmath-devel-2.15.1-20120725kurocks53.x86_64.rpm
libRmath-static-2.15.1-20120725kurocks53.x86_64.rpm
R-2.15.1-20120725kurocks53.x86_64.rpm
R-core-2.15.1-20120725kurocks53.x86_64.rpm
R-debuginfo-2.15.1-20120725kurocks53.x86_64.rpm
R-devel-2.15.1-20120725kurocks53.x86_64.rpm

And the SRPM:

R-2.15.1-20120725kurocks53.src.rpm

pj

-- 
Paul E. Johnson
Professor, Political Science    Assoc. Director
1541 Lilac Lane, Room 504     Center for Research Methods
University of Kansas               University of Kansas
http://pj.freefaculty.org            http://quant.ku.edu



[Rd] Problem in vignette packaging of Sweave in utils package
Paul Johnson