From nashjc at uottawa.ca  Thu Mar 12 18:09:42 2015
From: nashjc at uottawa.ca (Prof J C Nash (U30A))
Date: Thu, 12 Mar 2015 13:09:42 -0400
Subject: [Rd] Requirement for pandoc 1.12.3 in R 3.1.3
In-Reply-To: <393541412.529282.1426173675674.JavaMail.root@fredhutch.org>
References: <393541412.529282.1426173675674.JavaMail.root@fredhutch.org>
Message-ID: <5501C856.4020707@uottawa.ca>

Dan's suggestion to get latest pandoc got me part of the way to a
workaround. The other part was removing references in the vignette to
alpha versions of some software.

For info: pandoc 1.13.2 seems to have some bugs for conversion of LaTeX
to html or epub still (or at least the error messages point to the wrong
place). However, these are in work I'm doing outside of R, and I'll
pursue them with the pandoc developer(s).

JN


On 15-03-12 11:21 AM, Dan Tenenbaum wrote:
> 
> 
> ----- 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) -
>>>
>>
>> ______________________________________________
>> R-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>



[Rd] Requirement for pandoc 1.12.3 in R 3.1.3
Prof J C Nash (U30A