From murdoch.duncan at gmail.com  Fri Jul 27 16:54:43 2012
From: murdoch.duncan at gmail.com (Duncan Murdoch)
Date: Fri, 27 Jul 2012 10:54:43 -0400
Subject: [Rd] Problem in vignette packaging of Sweave in utils package
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Message-ID: <5012ABB3.3020300@gmail.com>

On 12-07-27 1:23 AM, Paul Johnson wrote:
> 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?

Sorry, I can't help with this.  If you build from svn or from a tarball, 
then I could help, but someone else produces the rpms, and I don't have 
access to a Linux system to try them.

Duncan Murdoch

>
> 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
>



[Rd] Problem in vignette packaging of Sweave in utils package
Duncan Murdoch