----- Original Message ----- > From: "John Nash" <profjcn...@gmail.com> > To: "Prof Brian Ripley" <rip...@stats.ox.ac.uk>, r-devel@r-project.org > Sent: Thursday, March 12, 2015 8:15:42 AM > Subject: Re: [Rd] Requirement for pandoc 1.12.3 in R 3.1.3 > > Thanks Brian. > > Indeed, the vignette is in markdown form. When I updated my system to > R 3.1.3 I ran update.packages() and this seems to have upset things > (including R-studio processing of markdown files). > > I tried removing rmarkdown and reverting to an older version so that > my > sessionInfo() is > > Loading required package: rmarkdown > > sessionInfo() > R version 3.1.3 (2015-03-09) > Platform: x86_64-pc-linux-gnu (64-bit) > Running under: Ubuntu 14.04.2 LTS > > locale: > [1] LC_CTYPE=en_CA.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_CA.UTF-8 LC_COLLATE=en_CA.UTF-8 > [5] LC_MONETARY=en_CA.UTF-8 LC_MESSAGES=en_CA.UTF-8 > [7] LC_PAPER=en_CA.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_CA.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] rmarkdown_0.3.3 > > loaded via a namespace (and not attached): > [1] digest_0.6.8 htmltools_0.2.6 > > I also made sure to remove all instances of rmarkdown before > installing > the older version. > > However, > > R CMD build nls14 > > still gives lots of errors (these are related to content in the > vignette > source and are, I believe, consequent on the warning about > engine$weave). The warning still refers to the later version of > pandoc > which Ubuntu 14.04 repos don't yet have. >
You can always download the latest version of pandoc; it's available as a .deb file at https://github.com/jgm/pandoc/releases . Dan > My current guess is some mismatch in the software infrastructure. I > have another machine with R 3.1.2 and rmarkdown_0.3.3 that manages to > build the package without complaint, but it would be good to get this > sorted out. Pointers on where to look for a fix are welcome. > > R CMD build nls14 > * checking for file ‘nls14/DESCRIPTION’ ... OK > * preparing ‘nls14’: > * checking DESCRIPTION meta-information ... OK > * installing the package to build vignettes > * creating vignettes ... ERROR > Warning in engine$weave(file, quiet = quiet, encoding = enc) : > Pandoc (>= 1.12.3) and/or pandoc-citeproc is not available. Please > install both. > Error in fnDeriv(r1, "x") : Only single expressions allowed > Error in as.vector(x, "expression") : > cannot coerce type 'closure' to vector of type 'expression' > Error in as.vector(x, "expression") : > cannot coerce type 'closure' to vector of type 'expression' > Error in array(0, c(length(.value), 2L), list(NULL, c("x001", "x002", > : > length of 'dimnames' [2] not equal to array extent > Error in D(~log(x), "x") : Function '`~`' is not in the derivatives > table > Error in D(interme, "x") : Function '`~`' is not in the derivatives > table > Error in deriv.default(interme, "x") : > Function '`~`' is not in the derivatives table > Error in D(expression(log(x, base = 3)), "x") : > only single-argument calls are supported > Error in deriv.formula(~log(x, base = 3), "x") : > only single-argument calls are supported > Error in deriv.default(expression(log(x, base = 3)), "x") : > only single-argument calls are supported > Error in deriv3.default(expression(log(x, base = 3)), "x") : > only single-argument calls are supported > Error in D(expression(abs(x)), "x") : > Function 'abs' is not in the derivatives table > Error in deriv.formula(~abs(x), "x") : > Function 'abs' is not in the derivatives table > Error in D(expression(sign(x)), "x") : > Function 'sign' is not in the derivatives table > Error in deriv.formula(~sign(x), "x") : > Function 'sign' is not in the derivatives table > sh: 1: yacas: not found > Quitting from lines 629-641 (nls14tutorial.Rmd) > Error: processing vignette 'nls14tutorial.Rmd' failed with > diagnostics: > cannot open the connection > Execution halted > > For reference: > > john@john-J6-2015 ~/current/nls14work $ cat /etc/os-release > NAME="Ubuntu" > VERSION="14.04.2 LTS, Trusty Tahr" > ID=ubuntu > ID_LIKE=debian > PRETTY_NAME="Ubuntu 14.04.2 LTS" > VERSION_ID="14.04" > HOME_URL="http://www.ubuntu.com/"; > SUPPORT_URL="http://help.ubuntu.com/"; > BUG_REPORT_URL="http://bugs.launchpad.net/ubuntu/"; > > john@john-J6-2015 ~/current/nls14work $ cat /etc/linuxmint/info > RELEASE=17.1 > CODENAME=rebecca > EDITION="MATE 64-bit" > DESCRIPTION="Linux Mint 17.1 Rebecca" > DESKTOP=MATE > TOOLKIT=GTK > NEW_FEATURES_URL=http://www.linuxmint.com/rel_rebecca_mate_whatsnew.php > RELEASE_NOTES_URL=http://www.linuxmint.com/rel_rebecca_mate.php > USER_GUIDE_URL=help:linuxmint > GRUB_TITLE=Linux Mint 17.1 MATE 64-bit > > > > john@john-J6-2015 ~/current/nls14work $ dpkg -l | grep -i pandoc > ii libghc-pandoc-citeproc-data 0.2-3build1 > all Pandoc support for Citation > Style Language - data files > > ii pandoc 1.12.2.1-1build2 > amd64 general markup converter > > ii pandoc-citeproc 0.2-3build1 > amd64 Pandoc support for Citation > Style Language - tools > > ii pandoc-data 1.12.2.1-1build2 > all general markup converter - > data > files > > JN > > > On 15-03-12 10:21 AM, Prof Brian Ripley wrote: > > On 12/03/2015 13:51, Prof J C Nash (U30A) wrote: > >> Are other developers finding R 3.1.3 problematic because vignette > >> building requires pandoc 1.12.3, while Linux Mint 17 / Ubuntu > >> 14.04 have > >> 1.12.2.1? R 3.1.2 seems to work fine. > > > > R has no built-in support for non-Sweave vignettes, and there is no > > mention of pandoc in the R 3.1.3 sources except for the manual: > > > > 'Complete checking of a package which contains a file > > @file{README.md} > > needs @command{pandoc} installed: see > > @uref{http://johnmacfarlane.net/@/pandoc/@/installing.html}.' > > > > which is true (but is not done with R 3.1.3). > > > > I suspect you are confusing an R update with an update of whatever > > packages you use to process your vignettes: package rmarkdown has a > > pandoc version requirement of > > > > SystemRequirements: pandoc (>= 1.12.3) - > > > > ______________________________________________ > R-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel > ______________________________________________ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
