Hello: Changes in R seem to have broken the sos vignette, and I don't know how to fix it. The build on R-forge, "https://r-forge.r-project.org/R/?group_id=235&log=build_src&pkg=sos&flavor=patched", ends as follows: Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, : Running 'texi2dvi' on 'sos.tex' failed. LaTeX errors: ! Undefined control sequence. l.1 \Sconcordance {concordance:sos.tex:sos.Rnw:% The control sequence at the end of the top line of your error message was never \def'ed. If you have Calls: -> texi2pdf -> texi2dvi Execution halted I stepped through the vignette line by line without seeing an error message. However, when I do "R CMD build sos" on my own computer, it stops with a similar error message: Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, : Running 'texi2dvi' on 'sos.tex' failed. BibTeX errors: The top-level auxiliary file: sos.aux The style file: abbrvnat.bst I found no \bibdata command---while reading file sos.aux Calls: <Anonymous> -> texi2pdf -> texi2dvi When I clicked, "Compile PDF" in RStudio, I first got a pop-up saying, 'Sweave Noweb syntax? It seems you are using the Sweave-specific syntax in line(s) 9, 15, 145, 172, 186, 189, 208, 211, 218, 225, 231, 243, 246, 283, 365, 390; you may need Sweave2knitr("sos.Rnw") to convert it to knitr'. When I click, "OK", it stops on LIne 146, "Error in eval(expr, envir, enclos) : object 'hide' not found". Line 145 reads, "<<summary.PL,results=hide>>=". What can I do to get this vignette to working again with the least amount of work? Thanks, Spencer Graves
On 17/06/2016 10:21 PM, Spencer Graves wrote:> Hello: > > > Changes in R seem to have broken the sos vignette, and I don't > know how to fix it. The build on R-forge, > "https://r-forge.r-project.org/R/?group_id=235&log=build_src&pkg=sos&flavor=patched", > ends as follows: > > > Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, : > Running 'texi2dvi' on 'sos.tex' failed. > LaTeX errors: > ! Undefined control sequence. > l.1 \Sconcordance > {concordance:sos.tex:sos.Rnw:% > The control sequence at the end of the top line > of your error message was never \def'ed. If you have > Calls: -> texi2pdf -> texi2dvi > Execution halted > > > I stepped through the vignette line by line without seeing an > error message. However, when I do "R CMD build sos" on my own computer, > it stops with a similar error message: > > > Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, : > Running 'texi2dvi' on 'sos.tex' failed. > BibTeX errors: > The top-level auxiliary file: sos.aux > The style file: abbrvnat.bst > I found no \bibdata command---while reading file sos.aux > Calls: <Anonymous> -> texi2pdf -> texi2dvi >I can't help you with R-forge. You'll need to write to their admin to ask.> > When I clicked, "Compile PDF" in RStudio, I first got a pop-up > saying, 'Sweave Noweb syntax? It seems you are using the Sweave-specific > syntax in line(s) 9, 15, 145, 172, 186, 189, 208, 211, 218, 225, 231, > 243, 246, 283, 365, 390; you may need Sweave2knitr("sos.Rnw") to convert > it to knitr'. When I click, "OK", it stops on LIne 146, "Error in > eval(expr, envir, enclos) : object 'hide' not found". Line 145 reads, > "<<summary.PL,results=hide>>=".In RStudio, you are running knitr rather than Sweave, but your vignette uses Sweave syntax. This is an option you can set in "Global options" and "Project options"; the latter take precedence. Duncan Murdoch> > > What can I do to get this vignette to working again with the > least amount of work? > > > Thanks, > Spencer Graves > > ______________________________________________ > R-devel at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel >
Hi, Duncan: Please excuse: I mixed 2 questions in one email. My first question was why "texi2dvi" failed. It fails with "R CMD build" on my notebook computer and on R-Forge, but don't know how to make it fail otherwise. AND it fails in something I don't think I've changed in years. I mentioned R-Forge, because that provides a replicable example. All CRAN tests now show Status: NOTE, but when I click on "NOTE", I get nothing. In Safari and FireFox, nothing happens. In Chrome, the screen goes blank. I'll try to refer the second question to someone at RStudio. Thanks, Spencer Graves On 6/18/2016 6:20 AM, Duncan Murdoch wrote:> On 17/06/2016 10:21 PM, Spencer Graves wrote: >> Hello: >> >> >> Changes in R seem to have broken the sos vignette, and I don't >> know how to fix it. The build on R-forge, >> "https://r-forge.r-project.org/R/?group_id=235&log=build_src&pkg=sos&flavor=patched", >> >> ends as follows: >> >> >> Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = >> quiet, : >> Running 'texi2dvi' on 'sos.tex' failed. >> LaTeX errors: >> ! Undefined control sequence. >> l.1 \Sconcordance >> {concordance:sos.tex:sos.Rnw:% >> The control sequence at the end of the top line >> of your error message was never \def'ed. If you have >> Calls: -> texi2pdf -> texi2dvi >> Execution halted >> >> >> I stepped through the vignette line by line without seeing an >> error message. However, when I do "R CMD build sos" on my own computer, >> it stops with a similar error message: >> >> >> Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = >> quiet, : >> Running 'texi2dvi' on 'sos.tex' failed. >> BibTeX errors: >> The top-level auxiliary file: sos.aux >> The style file: abbrvnat.bst >> I found no \bibdata command---while reading file sos.aux >> Calls: <Anonymous> -> texi2pdf -> texi2dvi >> > > I can't help you with R-forge. You'll need to write to their admin to > ask. > >> >> When I clicked, "Compile PDF" in RStudio, I first got a pop-up >> saying, 'Sweave Noweb syntax? It seems you are using the Sweave-specific >> syntax in line(s) 9, 15, 145, 172, 186, 189, 208, 211, 218, 225, 231, >> 243, 246, 283, 365, 390; you may need Sweave2knitr("sos.Rnw") to convert >> it to knitr'. When I click, "OK", it stops on LIne 146, "Error in >> eval(expr, envir, enclos) : object 'hide' not found". Line 145 reads, >> "<<summary.PL,results=hide>>=". > > In RStudio, you are running knitr rather than Sweave, but your > vignette uses Sweave syntax. This is an option you can set in "Global > options" and "Project options"; the latter take precedence. > > Duncan Murdoch > >> >> >> What can I do to get this vignette to working again with the >> least amount of work? >> >> >> Thanks, >> Spencer Graves >> >> ______________________________________________ >> R-devel at r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/r-devel >> > >
On 18/06/16 05:21, Spencer Graves wrote:> Hello: > > > Changes in R seem to have broken the sos vignette, and I don't > know how to fix it. The build on R-forge, > "https://r-forge.r-project.org/R/?group_id=235&log=build_src&pkg=sos&flavor=patched", > ends as follows: > > > Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, : > Running 'texi2dvi' on 'sos.tex' failed. > LaTeX errors: > ! Undefined control sequence. > l.1 \Sconcordance > {concordance:sos.tex:sos.Rnw:% > The control sequence at the end of the top line > of your error message was never \def'ed. If you have > Calls: -> texi2pdf -> texi2dvi > Execution halted >...> What can I do to get this vignette to working again with the > least amount of work?Try commenting out (removing) the following line in your vignette: \SweaveOpts{concordance=TRUE} The package builds just fine after doing that, on this computer. The R-Forge history of sos.Rnw shows the line was added on May 12, revision 237. -- Mikko Korpela Department of Geosciences and Geography University of Helsinki
On 20/06/2016 11:50 p.m., Mikko Korpela wrote:> On 18/06/16 05:21, Spencer Graves wrote: >> Hello: >> >> >> Changes in R seem to have broken the sos vignette, and I don't >> know how to fix it. The build on R-forge, >> "https://r-forge.r-project.org/R/?group_id=235&log=build_src&pkg=sos&flavor=patched", >> >> ends as follows: >> >> >> Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = >> quiet, : >> Running 'texi2dvi' on 'sos.tex' failed. >> LaTeX errors: >> ! Undefined control sequence. >> l.1 \Sconcordance >> {concordance:sos.tex:sos.Rnw:% >> The control sequence at the end of the top line >> of your error message was never \def'ed. If you have >> Calls: -> texi2pdf -> texi2dvi >> Execution halted >> > > ... > >> What can I do to get this vignette to working again with the >> least amount of work? > > Try commenting out (removing) the following line in your vignette: > > \SweaveOpts{concordance=TRUE} > > The package builds just fine after doing that, on this computer. The > R-Forge history of sos.Rnw shows the line was added on May 12, > revision 237. >This is an annoying RStudio *feature*. Much as I appreciate RStudio's contribution to the R community, I don't approve of software which adds code to your document without informing you. David Scott -- _________________________________________________________________ David Scott Department of Statistics The University of Auckland, PB 92019 Auckland 1142, NEW ZEALAND Phone: +64 9 923 5055, or +64 9 373 7599 ext 85055 Email: d.scott at auckland.ac.nz, Fax: +64 9 373 7018
On 6/20/2016 6:50 AM, Mikko Korpela wrote:> On 18/06/16 05:21, Spencer Graves wrote: >> Hello: >> >> >> Changes in R seem to have broken the sos vignette, and I don't >> know how to fix it. The build on R-forge, >> "https://r-forge.r-project.org/R/?group_id=235&log=build_src&pkg=sos&flavor=patched", >> >> ends as follows: >> >> >> Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = >> quiet, : >> Running 'texi2dvi' on 'sos.tex' failed. >> LaTeX errors: >> ! Undefined control sequence. >> l.1 \Sconcordance >> {concordance:sos.tex:sos.Rnw:% >> The control sequence at the end of the top line >> of your error message was never \def'ed. If you have >> Calls: -> texi2pdf -> texi2dvi >> Execution halted >> > > ... > >> What can I do to get this vignette to working again with the >> least amount of work? > > Try commenting out (removing) the following line in your vignette: > > \SweaveOpts{concordance=TRUE} > > The package builds just fine after doing that, on this computer. The > R-Forge history of sos.Rnw shows the line was added on May 12, > revision 237. >Thanks so much. It worked like you indicated. That offending line is added automatically by RStudio. I must have saved it without realizing it. Then it either passed "R CMD build" under R 3.2 or I committed that change without realizing I had not tested it with "R CMD check". RStudio is a great product -- except for this feature. I documented this on Stackoverflow and sent an email to Yihui Xe, who works for (or did work for) RStudio, reporting the issue. I did not mention your name, as I assumed you would have published your answer. Thanks again, Spencer Graves