Hi all, A list of some possible issues: 1. In R 2.11.x, in: http://svn.r-project.org/R/branches/R-2-11-branch/share/texmf/ there are two files, jss.cls and jss.bst (for JSS), which appear to be new since 2.10.x. These files are not installed when building/installing R. It would appear that they are not included in: https://svn.r-project.org/R/branches/R-2-11-branch/share/Makefile.in The relevant code there is: @for f in $(srcdir)/texmf/*.sty \ $(srcdir)/texmf/*.fd; do \ $(INSTALL_DATA) $${f} "$(DESTDIR)$(rsharedir)/texmf"; \ done which would skip over the two jss files. This issue came up when another useR (on F12) was building the zoo package with its vignette, which apparently uses jss.cls. Errors were of course observed. I thought that the error was limited to Fedora, but this is an issue in the source. 2. On a related issue, the texmf tree appears to be modified in 2.12.x, with the latex and bibtex files being put into separate folders: https://svn.r-project.org/R/trunk/share/texmf/ The makefile.in: https://svn.r-project.org/R/trunk/share/Makefile.in appears to be modified to handle that split: @for f in $(srcdir)/texmf/bibtex/bst/*; do \ $(INSTALL_DATA) $${f} "$(DESTDIR)$(rsharedir)/texmf/bibtex/bst"; \ done @for f in $(srcdir)/texmf/tex/latex/*; do \ $(INSTALL_DATA) $${f} "$(DESTDIR)$(rsharedir)/texmf/tex/latex"; \ done So there was perhaps an oversight of sorts for 2.11.x in handling these two JSS related files. 3. A final note, which is that the NEWS file appears to be missing from R-Devel tonight: https://svn.r-project.org/R/trunk/ I was trying to read it to note any comments relevant to the above. HTH, Marc Schwartz
Possible bug in 2.11.x texmf makefile.in and some related things...
5 messages · Brian Ripley, Peter Dalgaard, Marc Schwartz
On Sun, 4 Jul 2010, Marc Schwartz wrote:
Hi all, A list of some possible issues: 1. In R 2.11.x, in: http://svn.r-project.org/R/branches/R-2-11-branch/share/texmf/ there are two files, jss.cls and jss.bst (for JSS), which appear to be new since 2.10.x. These files are not installed when building/installing R. It would appear that they are not included in: https://svn.r-project.org/R/branches/R-2-11-branch/share/Makefile.in The relevant code there is: @for f in $(srcdir)/texmf/*.sty \ $(srcdir)/texmf/*.fd; do \ $(INSTALL_DATA) $${f} "$(DESTDIR)$(rsharedir)/texmf"; \ done which would skip over the two jss files. This issue came up when another useR (on F12) was building the zoo package with its vignette, which apparently uses jss.cls. Errors were of course observed. I thought that the error was limited to Fedora, but this is an issue in the source.
But there are a fair number of packages which need extra LaTeX files to build their vignettes, and e.g. the CRAN test systems have had to have these installed for a long time. Certainly zoo has needed them from before 2.11.0, and many believe that a Open Source package needs to include copies of such files (see 'Writing R Extensions').
2. On a related issue, the texmf tree appears to be modified in 2.12.x, with the latex and bibtex files being put into separate folders:
More precisely, it is a TDS-comformant tree now.
https://svn.r-project.org/R/trunk/share/texmf/ The makefile.in: https://svn.r-project.org/R/trunk/share/Makefile.in appears to be modified to handle that split: @for f in $(srcdir)/texmf/bibtex/bst/*; do \ $(INSTALL_DATA) $${f} "$(DESTDIR)$(rsharedir)/texmf/bibtex/bst"; \ done @for f in $(srcdir)/texmf/tex/latex/*; do \ $(INSTALL_DATA) $${f} "$(DESTDIR)$(rsharedir)/texmf/tex/latex"; \ done So there was perhaps an oversight of sorts for 2.11.x in handling these two JSS related files.
That's a different hand. I don't know if the files were intended to be installed in 2.11.x: they are in R-devel so eventually packages depending on R >= 2.12.0 will be able to rely on them.
3. A final note, which is that the NEWS file appears to be missing from R-Devel tonight: https://svn.r-project.org/R/trunk/ I was trying to read it to note any comments relevant to the above.
Correct. You need to look in https://svn.r-project.org/R/trunk/doc/NEWS.Rd which says \item File \file{NEWS} is now generated at installation with a slightly different format: it will be in UTF-8 on platforms using UTF-8, and otherwise in ASCII. \item \file{NEWS} is no longer in the sources, but generated as part of the installation. The primary source for changes is now \file{doc/NEWS.Rd}. A version of the NEWS file will be in the tarballs.
HTH, Marc Schwartz
______________________________________________ R-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Brian D. Ripley, ripley at 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, UK Fax: +44 1865 272595
Prof Brian Ripley wrote:
....
So there was perhaps an oversight of sorts for 2.11.x in handling these two JSS related files.
That's a different hand. I don't know if the files were intended to be installed in 2.11.x: they are in R-devel so eventually packages depending on R >= 2.12.0 will be able to rely on them.
Looking through the logs, those two files were indeed committed to r-devel, but long before the creation of R-2-11-branch. They appear not to be used in any other part of the sources, so are indeed pretty useless if not copied to the tarball (since we should not assume that people in general build from svn checkouts). But as Brian points out, they are only two out of many files that could be included as a service to the user.
3. A final note, which is that the NEWS file appears to be missing from R-Devel tonight:
...
\item \file{NEWS} is no longer in the sources, but generated as
part of the installation. The primary source for changes is now
\file{doc/NEWS.Rd}.
A version of the NEWS file will be in the tarballs.
Yes. It's generally a bad principle to have anything but the base sources in the repository, although we have had so for some things in the past (notably Java class files), because we couldn't rely on everyone having the appropriate tools. Especially with text files there will always be the risk of editing the target file instead of the source. (Just ask the editor of The R Journal how easy it is to remember to edit RJournal.dtx and not RJournal.sty...)
Peter Dalgaard Center for Statistics, Copenhagen Business School Phone: (+45)38153501 Email: pd.mes at cbs.dk Priv: PDalgd at gmail.com
On Jul 5, 2010, at 1:50 AM, Prof Brian Ripley wrote:
On Sun, 4 Jul 2010, Marc Schwartz wrote:
Hi all, A list of some possible issues: 1. In R 2.11.x, in: http://svn.r-project.org/R/branches/R-2-11-branch/share/texmf/ there are two files, jss.cls and jss.bst (for JSS), which appear to be new since 2.10.x. These files are not installed when building/installing R. It would appear that they are not included in: https://svn.r-project.org/R/branches/R-2-11-branch/share/Makefile.in The relevant code there is: @for f in $(srcdir)/texmf/*.sty \ $(srcdir)/texmf/*.fd; do \ $(INSTALL_DATA) $${f} "$(DESTDIR)$(rsharedir)/texmf"; \ done which would skip over the two jss files. This issue came up when another useR (on F12) was building the zoo package with its vignette, which apparently uses jss.cls. Errors were of course observed. I thought that the error was limited to Fedora, but this is an issue in the source.
But there are a fair number of packages which need extra LaTeX files to build their vignettes, and e.g. the CRAN test systems have had to have these installed for a long time. Certainly zoo has needed them from before 2.11.0, and many believe that a Open Source package needs to include copies of such files (see 'Writing R Extensions').
OK...so strictly speaking then, this is a bug in zoo(?), since it does not include those two files to build the relevant documents and would appear to presume that they are available on target build systems? This is not an issue when installing the package, only when building it locally AFAICS, but lacking the two files, it would not otherwise pass R CMD check. The resultant PDF files are in the zoo source tarball and of course in the binaries. What is interesting is that if one reviews the CRAN checks for zoo, there are notes for OSX related to jss.cls not being present. So I am guessing that the other OS CRAN build systems have the two files, but the OSX build system does not? That led to some confusion, as I was not sure whether the files were expected to be present, given that zoo passes the checks on the other OS's.
2. On a related issue, the texmf tree appears to be modified in 2.12.x, with the latex and bibtex files being put into separate folders:
More precisely, it is a TDS-comformant tree now.
Makes sense....thanks.
https://svn.r-project.org/R/trunk/share/texmf/ The makefile.in: https://svn.r-project.org/R/trunk/share/Makefile.in appears to be modified to handle that split: @for f in $(srcdir)/texmf/bibtex/bst/*; do \ $(INSTALL_DATA) $${f} "$(DESTDIR)$(rsharedir)/texmf/bibtex/bst"; \ done @for f in $(srcdir)/texmf/tex/latex/*; do \ $(INSTALL_DATA) $${f} "$(DESTDIR)$(rsharedir)/texmf/tex/latex"; \ done So there was perhaps an oversight of sorts for 2.11.x in handling these two JSS related files.
That's a different hand. I don't know if the files were intended to be installed in 2.11.x: they are in R-devel so eventually packages depending on R >= 2.12.0 will be able to rely on them.
3. A final note, which is that the NEWS file appears to be missing from R-Devel tonight: https://svn.r-project.org/R/trunk/ I was trying to read it to note any comments relevant to the above.
Correct. You need to look in https://svn.r-project.org/R/trunk/doc/NEWS.Rd which says \item File \file{NEWS} is now generated at installation with a slightly different format: it will be in UTF-8 on platforms using UTF-8, and otherwise in ASCII. \item \file{NEWS} is no longer in the sources, but generated as part of the installation. The primary source for changes is now \file{doc/NEWS.Rd}. A version of the NEWS file will be in the tarballs.
OK. Again, thanks for the clarifications. Regards, Marc
On Jul 5, 2010, at 2:52 AM, Peter Dalgaard wrote:
Prof Brian Ripley wrote: ....
So there was perhaps an oversight of sorts for 2.11.x in handling these two JSS related files.
That's a different hand. I don't know if the files were intended to be installed in 2.11.x: they are in R-devel so eventually packages depending on R >= 2.12.0 will be able to rely on them.
Looking through the logs, those two files were indeed committed to r-devel, but long before the creation of R-2-11-branch. They appear not to be used in any other part of the sources, so are indeed pretty useless if not copied to the tarball
So R has an appendix... ;-) Actually, they are in the 2.11.x tarballs. They are just not installed to the target directory tree after a build, given the code in the Makefile.in.
(since we should not assume that people in general build from svn checkouts).
I do and have been for quite some time, but maybe I am just weird that way... :-) Perhaps starting with 2.12.x, I will modify my build script to download the tarball instead.
But as Brian points out, they are only two out of many files that could be included as a service to the user.
3. A final note, which is that the NEWS file appears to be missing from R-Devel tonight:
...
\item \file{NEWS} is no longer in the sources, but generated as
part of the installation. The primary source for changes is now
\file{doc/NEWS.Rd}.
A version of the NEWS file will be in the tarballs.
Yes. It's generally a bad principle to have anything but the base sources in the repository, although we have had so for some things in the past (notably Java class files), because we couldn't rely on everyone having the appropriate tools. Especially with text files there will always be the risk of editing the target file instead of the source. (Just ask the editor of The R Journal how easy it is to remember to edit RJournal.dtx and not RJournal.sty...)
Yep. Thanks Peter. Regards, Marc