Problem in vignette packaging of Sweave in utils package

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
browseVignettes("utils")
No vignettes found by browseVignettes("utils")
library(help=utils)
does not refer to any vignettes.

The vignette does not appear in the main page for utils in help.start().

I checked the source code for the Sweave vignette, but I don't see
anything wrong. It has all of the required elements:

%\VignetteIndexEntry{Sweave User Manual}
%\VignettePackage{utils}
%\VignetteDepends{tools}
%\VignetteDepends{datasets}
%\VignetteDepends{stats}

Am I accessing it incorrectly, or is there something wrong in my
install of R-2.15.1?
sessionInfo()
R version 2.15.1 (2012-06-22)
Platform: x86_64-pc-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
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
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

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

library(help=utils)
does not refer to any vignettes.

The vignette does not appear in the main page for utils in help.start().

I checked the source code for the Sweave vignette, but I don't see
anything wrong. It has all of the required elements:

%\VignetteIndexEntry{Sweave User Manual}
%\VignettePackage{utils}
%\VignetteDepends{tools}
%\VignetteDepends{datasets}
%\VignetteDepends{stats}

Am I accessing it incorrectly, or is there something wrong in my
install of R-2.15.1?
The vignette name is "Sweave", so you should see it when you say

vignette("Sweave")

but you should also have seen it in

browseVignettes("utils")

and

library(help=utils)

and the page for utils in the HTML help.  So it looks as though 
something is wrong in your install.  I do see it in 2.15.1 patched on 
Windows.

Duncan Murdoch

sessionInfo()
R version 2.15.1 (2012-06-22)
Platform: x86_64-pc-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
Strange enough; I just noticed the HTML index pages of several base
packages were gone (e.g. base, stats, tools, utils) under Ubuntu. Not
sure if this is a problem of Debian packages or R itself.
sessionInfo()
R version 2.15.1 (2012-06-22)
Platform: i686-pc-linux-gnu (32-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

Regards,
Yihui
--
Yihui Xie <xieyihui at gmail.com>
Phone: 515-294-2465 Web: http://yihui.name
Department of Statistics, Iowa State University
2215 Snedecor Hall, Ames, IA
On 03/07/2012 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

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

library(help=utils)
does not refer to any vignettes.

The vignette does not appear in the main page for utils in help.start().

I checked the source code for the Sweave vignette, but I don't see
anything wrong. It has all of the required elements:

%\VignetteIndexEntry{Sweave User Manual}
%\VignettePackage{utils}
%\VignetteDepends{tools}
%\VignetteDepends{datasets}
%\VignetteDepends{stats}

Am I accessing it incorrectly, or is there something wrong in my
install of R-2.15.1?

The vignette name is "Sweave", so you should see it when you say

vignette("Sweave")

but you should also have seen it in

browseVignettes("utils")

and

library(help=utils)

and the page for utils in the HTML help.  So it looks as though something is
wrong in your install.  I do see it in 2.15.1 patched on Windows.

Duncan Murdoch

sessionInfo()
R version 2.15.1 (2012-06-22)
Platform: x86_64-pc-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

______________________________________________
R-devel at r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
The HTML help related pages are dynamically generated upon request, so there are no static pages that would exist otherwise. I can get to the index pages for each of the packages mentioned in Yihui's post.

That being said, I can replicate the vignette issue on:

R version 2.15.1 (2012-06-22) -- "Roasted Marshmallows"

which was a clean install on OSX Lion using the OSX binary on CRAN.
browseVignettes("utils")
No vignettes found by browseVignettes("utils")
browseVignettes("grid")
No vignettes found by browseVignettes("grid")
browseVignettes("parallel")
No vignettes found by browseVignettes("parallel")
vignette("Sweave")
Warning message:
vignette ?Sweave? not found 

However, Matrix and survival did work.

Curiously, testInstalledPackages() did work for the vignettes without returning an error:
Result <- testInstalledPackages(types = "vignettes")
Running vignettes for package ?utils?
Running vignettes for package ?grid?
Running vignettes for package ?parallel?
Running vignettes for package ?Matrix?
Running vignettes for package ?survival?
Result
[1] 0

I then installed:

R version 2.15.1 Patched (2012-07-02 r59715) -- "Roasted Marshmallows"

from Simon's site and:
browseVignettes("utils")
browseVignettes("grid")
browseVignettes("parallel")
vignette("Sweave")
all worked. 

So it would appear that there was something amiss with the 2.15.1 release packaging or something involving the vignettes at least for those packages. A review of the NEWS file did not reveal anything obvious to me that would be relevant.

Regards,

Marc Schwartz

Strange enough; I just noticed the HTML index pages of several base
packages were gone (e.g. base, stats, tools, utils) under Ubuntu. Not
sure if this is a problem of Debian packages or R itself.

sessionInfo()
R version 2.15.1 (2012-06-22)
Platform: i686-pc-linux-gnu (32-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

Regards,
Yihui
--
Yihui Xie <xieyihui at gmail.com>
Phone: 515-294-2465 Web: http://yihui.name
Department of Statistics, Iowa State University
2215 Snedecor Hall, Ames, IA

On Tue, Jul 3, 2012 at 1:34 PM, Duncan Murdoch <murdoch.duncan at gmail.com> wrote:
On 03/07/2012 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

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

library(help=utils)
does not refer to any vignettes.

The vignette does not appear in the main page for utils in help.start().

I checked the source code for the Sweave vignette, but I don't see
anything wrong. It has all of the required elements:

%\VignetteIndexEntry{Sweave User Manual}
%\VignettePackage{utils}
%\VignetteDepends{tools}
%\VignetteDepends{datasets}
%\VignetteDepends{stats}

Am I accessing it incorrectly, or is there something wrong in my
install of R-2.15.1?

The vignette name is "Sweave", so you should see it when you say

vignette("Sweave")

but you should also have seen it in

browseVignettes("utils")

and

library(help=utils)

and the page for utils in the HTML help.  So it looks as though something is
wrong in your install.  I do see it in 2.15.1 patched on Windows.

Duncan Murdoch
Strange enough; I just noticed the HTML index pages of several base
packages were gone (e.g. base, stats, tools, utils) under Ubuntu. Not
sure if this is a problem of Debian packages or R itself.

It is not only on Debian where I see:
vignette("Sweave")
Warning message:
vignette ?Sweave? not found

This afflicts RPM based installs as well. It is not a new problem, AFAICT.

Here's output from R-2.15.0 on a Centos Linux cluster node.:
vignette("Sweave")
Warning message:
vignette 'Sweave' not found
sessionInfo()
R version 2.15.0 (2012-03-30)
Platform: x86_64-redhat-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.iso885915       LC_NUMERIC=C
 [3] LC_TIME=en_US.iso885915        LC_COLLATE=en_US.iso885915
 [5] LC_MONETARY=en_US.iso885915    LC_MESSAGES=en_US.iso885915
 [7] LC_PAPER=C                     LC_NAME=C
 [9] LC_ADDRESS=C                   LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.iso885915 LC_IDENTIFICATION=C

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

loaded via a namespace (and not attached):
[1] tools_2.15.0
--
Yihui Xie <xieyihui at gmail.com>
Phone: 515-294-2465 Web: http://yihui.name
Department of Statistics, Iowa State University
2215 Snedecor Hall, Ames, IA

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
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

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

library(help=utils)
does not refer to any vignettes.

The vignette does not appear in the main page for utils in help.start().

I checked the source code for the Sweave vignette, but I don't see
anything wrong. It has all of the required elements:

%\VignetteIndexEntry{Sweave User Manual}
%\VignettePackage{utils}
%\VignetteDepends{tools}
%\VignetteDepends{datasets}
%\VignetteDepends{stats}

Am I accessing it incorrectly, or is there something wrong in my
install of R-2.15.1?

sessionInfo()
R version 2.15.1 (2012-06-22)
Platform: x86_64-pc-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
New help request below
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
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

On Fri, Jul 27, 2012 at 9:54 AM, Duncan Murdoch
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

Sorry I was unclear. I did build from R-patched tarball, from here:

ftp://ftp.stat.math.ethz.ch/Software/R/R-patched_2012-07-25.tar.gz

I get the same result whether I build that into an RPM or if I build
and install the "old fashioned" way (configure, make, make install).
The Sweave pdf is created, but not found inside R.

I just re-ran the compilation in an Emacs shell and you can see
everything that goes on:

http://pj.freefaculty.org/misc/R-patched-build-20120725.txt

As you will see, I run into problems with pdf creation in

make pdf

dealing with refman. I think that links back to the ancient tetex
toolkit and the lack of incolsolata font.  If that is the reason R
can't find the vignette, I would be glad to know.

I do get the Sweave.pdf vignette created, just not indexed.

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