From profjcnash at gmail.com  Thu Mar 12 16:15:42 2015
From: profjcnash at gmail.com (John Nash)
Date: Thu, 12 Mar 2015 11:15:42 -0400
Subject: [Rd] Requirement for pandoc 1.12.3 in R 3.1.3
In-Reply-To: <5501A0F3.3060302@stats.ox.ac.uk>
References: <550199C6.1060301@uottawa.ca> <5501A0F3.3060302@stats.ox.ac.uk>
Message-ID: <5501AD9E.4090007@messier.ca>

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.

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) -
>



[Rd] Requirement for pandoc 1.12.3 in R 3.1.3
John Nash