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.dun...@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@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
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