Re: [Rd] R CMD build processes inst/doc/Makefile only if there are vignette files?
On 11-04-29 10:36 PM, Prof Brian Ripley wrote: On Fri, 29 Apr 2011, Hervé Pagès wrote: On 11-03-30 01:55 AM, Prof Brian Ripley wrote: What R CMD build (and check) does is to call tools::buildVignettes. That has been true for a while, and buildVignettes() returns if no vignettes are found. The docs are out-of-date. My view is that you are misusing inst/doc: it is intended *only* for files which are going to be installed and hence report.tex should not really be there. So you should be doing this in another source directory and copying report.pdf to inst/doc. Use configure to arrange this. Shortly vignettes to be built will be moved out of inst/doc. Could you please elaborate on this? I just found this in the NEWS for R 2.14.0: o The preferred location for vignette sources is now the directory ‘vignettes’ and not ‘inst/doc’: R CMD build will now re-build vignettes in ‘vignettes’ and copy the ‘.Rnw’ (etc) files and the corresponding PDFs to ‘inst/doc’. Sounds like an important move. What are the long term plans: keep both inst/doc/ and vignettes/ as places for vignettes to be built? Or drop inst/doc/ at some point? Drop inst/doc at some point. May I ask when? It doesn't make much difference to the codebase: all the work is done in pkgVignettes(). Maybe but it will make a big difference from our side: about 450 BioC packages will need to be modified. Thanks, H. Thanks! H. On Tue, 29 Mar 2011, Henrik Bengtsson wrote: Hi, in Section 'Writing package vignettes' of 'Writing R Extensions' it says: Whenever a Makefile is found, then R CMD build will try to run make after the Sweave runs, so PDF manuals can be created from arbitrary source formats (plain LaTeX files, ...). [...] Note that the make step is executed even if there are no files in Sweave format, [...]. In my package, inst/doc/ file contains two files: Makefile, and report.tex. However, when running 'Rcmd build' on Windows with R v2.13.0 alpha (2011-03-27 r55091) I can only get 'make' to run (process inst/doc/Makefile) if I add a inst/doc/dummy.Rnw file, otherwise nothing happens. My Makefile contains: all: pdf pdf: report.tex texi2dvi --pdf report.tex clean: rm dummy.Rnw dummy.tex rm *.aux *.log *.toc Is it really necessary to add dummy.Rnw? Am I missing something? /Henrik sessionInfo() R version 2.13.0 alpha (2011-03-27 r55091) Platform: x86_64-pc-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] tools_2.13.0 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpa...@fhcrc.org Phone: (206) 667-5791 Fax: (206) 667-1319 -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpa...@fhcrc.org Phone: (206) 667-5791 Fax:(206) 667-1319 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] R CMD build processes inst/doc/Makefile only if there are vignette files?
On 11-03-30 01:55 AM, Prof Brian Ripley wrote: What R CMD build (and check) does is to call tools::buildVignettes. That has been true for a while, and buildVignettes() returns if no vignettes are found. The docs are out-of-date. My view is that you are misusing inst/doc: it is intended *only* for files which are going to be installed and hence report.tex should not really be there. So you should be doing this in another source directory and copying report.pdf to inst/doc. Use configure to arrange this. Shortly vignettes to be built will be moved out of inst/doc. Could you please elaborate on this? I just found this in the NEWS for R 2.14.0: o The preferred location for vignette sources is now the directory ‘vignettes’ and not ‘inst/doc’: R CMD build will now re-build vignettes in ‘vignettes’ and copy the ‘.Rnw’ (etc) files and the corresponding PDFs to ‘inst/doc’. Sounds like an important move. What are the long term plans: keep both inst/doc/ and vignettes/ as places for vignettes to be built? Or drop inst/doc/ at some point? Thanks! H. On Tue, 29 Mar 2011, Henrik Bengtsson wrote: Hi, in Section 'Writing package vignettes' of 'Writing R Extensions' it says: Whenever a Makefile is found, then R CMD build will try to run make after the Sweave runs, so PDF manuals can be created from arbitrary source formats (plain LaTeX files, ...). [...] Note that the make step is executed even if there are no files in Sweave format, [...]. In my package, inst/doc/ file contains two files: Makefile, and report.tex. However, when running 'Rcmd build' on Windows with R v2.13.0 alpha (2011-03-27 r55091) I can only get 'make' to run (process inst/doc/Makefile) if I add a inst/doc/dummy.Rnw file, otherwise nothing happens. My Makefile contains: all: pdf pdf: report.tex texi2dvi --pdf report.tex clean: rm dummy.Rnw dummy.tex rm *.aux *.log *.toc Is it really necessary to add dummy.Rnw? Am I missing something? /Henrik sessionInfo() R version 2.13.0 alpha (2011-03-27 r55091) Platform: x86_64-pc-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] tools_2.13.0 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpa...@fhcrc.org Phone: (206) 667-5791 Fax:(206) 667-1319 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] R CMD build processes inst/doc/Makefile only if there are vignette files?
On Fri, 29 Apr 2011, Hervé Pagès wrote: On 11-03-30 01:55 AM, Prof Brian Ripley wrote: What R CMD build (and check) does is to call tools::buildVignettes. That has been true for a while, and buildVignettes() returns if no vignettes are found. The docs are out-of-date. My view is that you are misusing inst/doc: it is intended *only* for files which are going to be installed and hence report.tex should not really be there. So you should be doing this in another source directory and copying report.pdf to inst/doc. Use configure to arrange this. Shortly vignettes to be built will be moved out of inst/doc. Could you please elaborate on this? I just found this in the NEWS for R 2.14.0: o The preferred location for vignette sources is now the directory ‘vignettes’ and not ‘inst/doc’: R CMD build will now re-build vignettes in ‘vignettes’ and copy the ‘.Rnw’ (etc) files and the corresponding PDFs to ‘inst/doc’. Sounds like an important move. What are the long term plans: keep both inst/doc/ and vignettes/ as places for vignettes to be built? Or drop inst/doc/ at some point? Drop inst/doc at some point. It doesn't make much difference to the codebase: all the work is done in pkgVignettes(). Thanks! H. On Tue, 29 Mar 2011, Henrik Bengtsson wrote: Hi, in Section 'Writing package vignettes' of 'Writing R Extensions' it says: Whenever a Makefile is found, then R CMD build will try to run make after the Sweave runs, so PDF manuals can be created from arbitrary source formats (plain LaTeX files, ...). [...] Note that the make step is executed even if there are no files in Sweave format, [...]. In my package, inst/doc/ file contains two files: Makefile, and report.tex. However, when running 'Rcmd build' on Windows with R v2.13.0 alpha (2011-03-27 r55091) I can only get 'make' to run (process inst/doc/Makefile) if I add a inst/doc/dummy.Rnw file, otherwise nothing happens. My Makefile contains: all: pdf pdf: report.tex texi2dvi --pdf report.tex clean: rm dummy.Rnw dummy.tex rm *.aux *.log *.toc Is it really necessary to add dummy.Rnw? Am I missing something? /Henrik sessionInfo() R version 2.13.0 alpha (2011-03-27 r55091) Platform: x86_64-pc-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] tools_2.13.0 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpa...@fhcrc.org Phone: (206) 667-5791 Fax:(206) 667-1319 -- Brian D. Ripley, rip...@stats.ox.ac.uk 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, UKFax: +44 1865 272595__ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] R CMD build processes inst/doc/Makefile only if there are vignette files?
Hi, in Section 'Writing package vignettes' of 'Writing R Extensions' it says: Whenever a Makefile is found, then R CMD build will try to run make after the Sweave runs, so PDF manuals can be created from arbitrary source formats (plain LaTeX files, ...). [...] Note that the make step is executed even if there are no files in Sweave format, [...]. In my package, inst/doc/ file contains two files: Makefile, and report.tex. However, when running 'Rcmd build' on Windows with R v2.13.0 alpha (2011-03-27 r55091) I can only get 'make' to run (process inst/doc/Makefile) if I add a inst/doc/dummy.Rnw file, otherwise nothing happens. My Makefile contains: all: pdf pdf: report.tex texi2dvi --pdf report.tex clean: rm dummy.Rnw dummy.tex rm *.aux *.log *.toc Is it really necessary to add dummy.Rnw? Am I missing something? /Henrik sessionInfo() R version 2.13.0 alpha (2011-03-27 r55091) Platform: x86_64-pc-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] tools_2.13.0 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] R CMD build processes inst/doc/Makefile only if there are vignette files?
What R CMD build (and check) does is to call tools::buildVignettes. That has been true for a while, and buildVignettes() returns if no vignettes are found. The docs are out-of-date. My view is that you are misusing inst/doc: it is intended *only* for files which are going to be installed and hence report.tex should not really be there. So you should be doing this in another source directory and copying report.pdf to inst/doc. Use configure to arrange this. Shortly vignettes to be built will be moved out of inst/doc. On Tue, 29 Mar 2011, Henrik Bengtsson wrote: Hi, in Section 'Writing package vignettes' of 'Writing R Extensions' it says: Whenever a Makefile is found, then R CMD build will try to run make after the Sweave runs, so PDF manuals can be created from arbitrary source formats (plain LaTeX files, ...). [...] Note that the make step is executed even if there are no files in Sweave format, [...]. In my package, inst/doc/ file contains two files: Makefile, and report.tex. However, when running 'Rcmd build' on Windows with R v2.13.0 alpha (2011-03-27 r55091) I can only get 'make' to run (process inst/doc/Makefile) if I add a inst/doc/dummy.Rnw file, otherwise nothing happens. My Makefile contains: all: pdf pdf: report.tex texi2dvi --pdf report.tex clean: rm dummy.Rnw dummy.tex rm *.aux *.log *.toc Is it really necessary to add dummy.Rnw? Am I missing something? /Henrik sessionInfo() R version 2.13.0 alpha (2011-03-27 r55091) Platform: x86_64-pc-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] tools_2.13.0 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel -- Brian D. Ripley, rip...@stats.ox.ac.uk 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, UKFax: +44 1865 272595 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
