From dtenenba at fredhutch.org  Thu Mar 12 16:21:15 2015
From: dtenenba at fredhutch.org (Dan Tenenbaum)
Date: Thu, 12 Mar 2015 08:21:15 -0700 (PDT)
Subject: [Rd] Requirement for pandoc 1.12.3 in R 3.1.3
In-Reply-To: <5501AD9E.4090007@messier.ca>
Message-ID: <393541412.529282.1426173675674.JavaMail.root@fredhutch.org>



----- Original Message -----
> From: "John Nash" <profjcnash at gmail.com>
> To: "Prof Brian Ripley" <ripley at stats.ox.ac.uk>, r-devel at 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 at 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 at 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 at 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) -
> >
> 
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>



[Rd] Requirement for pandoc 1.12.3 in R 3.1.3
Dan Tenenbaum