Problem in vignette packaging of Sweave in utils package
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Problem in vignette packaging of Sweave in utils package
 
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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 ______________________________________________ [hidden email] mailing list https://stat.ethz.ch/mailman/listinfo/r-devel |
Re: Problem in vignette packaging of Sweave in utils package
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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 ______________________________________________ [hidden email] mailing list https://stat.ethz.ch/mailman/listinfo/r-devel |
Re: Problem in vignette packaging of Sweave in utils package
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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 <[hidden email]> 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 <[hidden email]> 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 > > >> >> > 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 > > > ______________________________________________ > [hidden email] mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel ______________________________________________ [hidden email] mailing list https://stat.ethz.ch/mailman/listinfo/r-devel |
Re: Problem in vignette packaging of Sweave in utils package
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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 On Jul 3, 2012, at 12:54 PM, Yihui Xie wrote: > 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 <[hidden email]> > 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 <[hidden email]> 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 ______________________________________________ [hidden email] mailing list https://stat.ethz.ch/mailman/listinfo/r-devel |
Re: Problem in vignette packaging of Sweave in utils package
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In reply to this post by Yihui Xie-2
On Tue, Jul 3, 2012 at 12:54 PM, Yihui Xie <[hidden email]> wrote:
> 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 <[hidden email]> > 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 ______________________________________________ [hidden email] mailing list https://stat.ethz.ch/mailman/listinfo/r-devel |
Re: Problem in vignette packaging of Sweave in utils package
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In reply to this post by PaulJohnson32gmail
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 > > >> 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 ______________________________________________ [hidden email] mailing list https://stat.ethz.ch/mailman/listinfo/r-devel |
Re: Problem in vignette packaging of Sweave in utils package
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New help request below
On Sat, Jul 7, 2012 at 7:25 AM, Duncan Murdoch <[hidden email]> 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@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 ______________________________________________ [hidden email] mailing list https://stat.ethz.ch/mailman/listinfo/r-devel |
Re: Problem in vignette packaging of Sweave in utils package
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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 <[hidden email]> 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 > ______________________________________________ [hidden email] mailing list https://stat.ethz.ch/mailman/listinfo/r-devel |
Re: Problem in vignette packaging of Sweave in utils package
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On Fri, Jul 27, 2012 at 9:54 AM, Duncan Murdoch
<[hidden email]> wrote: > 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 <[hidden email]> >> 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 ______________________________________________ [hidden email] mailing list https://stat.ethz.ch/mailman/listinfo/r-devel |
Re: Problem in vignette packaging of Sweave in utils package
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I believe the issue is actually quite simple: you need to run
make vignettes when building from a tarball if you want the tangled vignettes and the indices. I'll make that automatic after more testing. On 27/07/2012 21:55, Paul Johnson wrote: > On Fri, Jul 27, 2012 at 9:54 AM, Duncan Murdoch > <[hidden email]> wrote: >> 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 <[hidden email]> >>> 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 > -- Brian D. Ripley, [hidden email] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UK Fax: +44 1865 272595 ______________________________________________ [hidden email] mailing list https://stat.ethz.ch/mailman/listinfo/r-devel |
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