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) -