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. I'd very much like to avoid having to build as large a Linux package as pandoc, which has given me issues outside of R (it leaves out words, sentences or paragraphs when converting Latex to epub in a novel I'm working on, and does so without warning). Possibly concerns like this are why R has moved to a later pandoc. Suggestions welcome. John Nash
Requirement for pandoc 1.12.3 in R 3.1.3
5 messages · John C Nash, Brian Ripley, Dan Tenenbaum
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) -
Brian D. Ripley, ripley at stats.ox.ac.uk Emeritus Professor of Applied Statistics, University of Oxford 1 South Parks Road, Oxford OX1 3TG, UK
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) -
----- 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
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