Re: [R-SIG-Mac] R.app Package Manager Bug?
+1 I see this too, on both mavericks and ordinary mac build of R.app Its because R 3.1.0 has made .find.package a defunct function We'll need to wait for the R.app developers to change the code behind the package manager to use find.package instead of .find.package Hopefully it'll be a simple fix sessionInfo() R version 3.1.0 (2014-04-10) Platform: x86_64-apple-darwin10.8.0 (64-bit) locale: [1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] BiocInstaller_1.15.1 loaded via a namespace (and not attached): [1] tools_3.1.0 On Sunday, 13 April 2014 20:11:44 UTC+1, Neil Tiffin wrote: When I select 'Package Manager' from the 'Packages Data' menu in R.app nothing happens and I get the following in the R Console window: Error: '.find.package' is defunct. Use 'find.package' instead. See help(Defunct) Is this a known problem or do I have something messed up? Thanks, Neil Just upgraded to 3.1.0. sessionInfo() R version 3.1.0 (2014-04-10) Platform: x86_64-apple-darwin10.8.0 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utile datasets methods base ___ R-SIG-Mac mailing list r-si...@r-project.org javascript: https://stat.ethz.ch/mailman/listinfo/r-sig-mac ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] [Rd] R 3.1.0: 'R CMD Sweave' deletes non tex files created upon batch mode exit
On 14/04/2014, 10:23 AM, Marc Schwartz wrote:
Hi Martin,
Thanks for your confirmation on this.
I normally do not use R CMD Sweave, as I too run under ESS in normal day to day
operations. This finding was a quirk of having a particular Rnw document that I
occasionally run using R CMD Sweave and I had done so over the weekend,
realizing this behavior.
This sounds like an argument for dropping R CMD Sweave, rather than
fixing it. The bug was introduced in July, 2013, and nobody noticed it
because so few people use that feature, and apparently nobody who does
use it bothers to test pre-release versions.
Duncan Murdoch
Thanks again.
Regards,
Marc
On Apr 14, 2014, at 7:28 AM, Martin Maechler maech...@stat.math.ethz.ch wrote:
Marc Schwartz marc_schwa...@me.com
on Sun, 13 Apr 2014 10:22:55 -0500 writes:
[on the R-SIG-Mac mailing list] :
Hi all,
With R version 3.1.0 on OSX, using either the Snow Leopard or the Mavericks
binary installation on a Mac with fully updated Mavericks, there has been a
change in behavior since 3.0.3.
I've just written to R-core about this:
R CMD Sweave
has *serious* problems also in the very simple case when it
should produce figures: They are not available after the
completion of R CMD Sweave,
confirming your 'deletes non tex files created upon batch mode exit'
So this is not related to OSX only, but also a big problem
at least on other *nix descendent platforms, such as Linux.
In short, failure (no graphic produce in the example below) by
R CMD Sweave foo.Rnw
but all is fine with using Sweave(), as you Marc, noted, and hence with
Rscript -e 'Sweave(foo.Rnw)'
... and to answer your question:
No this was not intended and is probably one of the bigger /
most embarrassing bugs in a newly released version of R
in my view:
Basically 'R CMD Sweave' is partly broken in R 3.1.0.
Yes, this should never have happened.
I had to partially revert the R 3.1.0 installation here (our
statistics dept), by making R 3.0.3 the default 'R'
for now, as we are relying on 'R CMD Sweave ..' in many places.
Personally I've never noticed the problem, as I seem to always
Sweave from ESS (Emacs speaks statistics) which calls Sweave()
in R, and that works fine, also in R 3.1.0, as you've already
noted
Martin Maechler, ETH Zurich
%
\documentclass[12pt]{article}
\usepackage{Sweave}
\begin{document} Just a simple graphic
qqnorm, fig=TRUE=
qqnorm(rnorm(20))
@
and that's all, folks!
\end{document}
%
I have a master .Rnw file which runs a series of outputs from multiple R code
files, each called in BATCH mode using system() from within the master .Rnw
file. The output of the R code files go to separate text files in order to
catch some of the function call output that would not otherwise be included in
the resultant .tex file due to output redirection.
Those text files are then included in the resultant .tex file using, for
example:
\lstinputlisting[caption={}]{test.out}
directives which are included in the .Rnw source file.
A simple example to replicate the observed behaviors.
The test.Rnw file content:
%% R CMD Sweave test.Rnw
results=tex,echo=false=
system(R CMD BATCH test.R test.out)
@
The test.R file content:
options(echo = FALSE)
options(useFancyQuotes = FALSE)
installed.packages()
On version 3.0.3, the file test.out is created, along with test.tex. test.out
contains the output of installed.packages(). I did not include the
aforementioned listing directive in test.Rnw here for simplicity.
On version 3.1.0, the file test.out is created, but when the R CMD Sweave
command exits and returns to the CLI in the console, test.out is deleted,
presumably as part of a post R batch session clean up process. The file
test.tex is retained.
I uninstalled 3.1.0 and reinstalled 3.0.3 and observed the prior behavior. I
then tried clean installs of both the Snow Leopard and Mavericks 3.1.0
binaries, with the new behavior observed in both cases.
In reading the NEWS file for 3.1.0, there are multiple references to Sweave,
but there is nothing explicit about this new behavior.
I should note that when the .Rnw file is run from within an R 3.1.0 interactive
session using:
Sweave(test.Rnw)
the test.out file is created and not deleted upon the function exit, or when
exiting the R session back to the console.
Thus, this new behavior seems to be limited to running Sweave from the CLI
using R CMD. It is not clear to me if this new behavior is by design or perhaps
an unintended consequence of changes elsewhere in Sweave processing or in the
handling of R in BATCH mode.
When watching the folder where the file output activity takes place, I note
that a file .build.timestamp is created and then deleted, which leads me to
believe that the new functions fileSnapshot() and changedFiles()
Re: [R-SIG-Mac] [Rd] R 3.1.0: 'R CMD Sweave' deletes non tex files created upon batch mode exit
On 15 Apr 2014, at 13:14 , Duncan Murdoch murdoch.dun...@gmail.com wrote: On 14/04/2014, 10:23 AM, Marc Schwartz wrote: Hi Martin, Thanks for your confirmation on this. I normally do not use R CMD Sweave, as I too run under ESS in normal day to day operations. This finding was a quirk of having a particular Rnw document that I occasionally run using R CMD Sweave and I had done so over the weekend, realizing this behavior. This sounds like an argument for dropping R CMD Sweave, rather than fixing it. The bug was introduced in July, 2013, and nobody noticed it because so few people use that feature, and apparently nobody who does use it bothers to test pre-release versions. I'd say that that cat is out of the bag. There are probably umpteen documents around suggesting R CMD Sweave. As people use Sweave only sporadically, it could take years before the old usage got stamped out. And anyways, the command format is the obvious way to generate documents in scripts and makefiles, isn't it? -pd -- Peter Dalgaard, Professor, Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Email: pd@cbs.dk Priv: pda...@gmail.com ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] [Rd] R 3.1.0: 'R CMD Sweave' deletes non tex files created upon batch mode exit
On Tue, Apr 15, 2014 at 7:14 AM, Duncan Murdoch murdoch.dun...@gmail.comwrote: On 14/04/2014, 10:23 AM, Marc Schwartz wrote: Hi Martin, Thanks for your confirmation on this. I normally do not use R CMD Sweave, as I too run under ESS in normal day to day operations. This finding was a quirk of having a particular Rnw document that I occasionally run using R CMD Sweave and I had done so over the weekend, realizing this behavior. This sounds like an argument for dropping R CMD Sweave, rather than fixing it. The bug was introduced in July, 2013, and nobody noticed it because so few people use that feature, and apparently nobody who does use it bothers to test pre-release versions. Or they just fix it for themselves, and do not report it. At least I know of one such case Gabor [[alternative HTML version deleted]] ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
[R-SIG-Mac] Cairo: Fontconfig error: Cannot load default config file
Running on R 3.1 on my Mavericks laptop: options(bitmapType = cairo); svg(cars.svg, width=11.69, height=8.27) plot(cars) dev.off() Gives a message: Fontconfig error: Cannot load default config file. The text in the svg seems heavily pixelated. The same happens when using png(). IIRC, this did not happen on R 3.0, although I am now starting to doubt this. Is there anything on my machine that I try to update/reinstall to fix this? ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] Cairo: Fontconfig error: Cannot load default config file
Can you try setting FC_DEBUG environment variable to see what fonts.conf file it is loading, what fonts it tries to read, etc? The fontconfig library will print useful output to stderr when the right env bars are set. Murray (mobile) On Apr 15, 2014 7:57 PM, Jeroen Ooms jeroen.o...@stat.ucla.edu wrote: Running on R 3.1 on my Mavericks laptop: options(bitmapType = cairo); svg(cars.svg, width=11.69, height=8.27) plot(cars) dev.off() Gives a message: Fontconfig error: Cannot load default config file. The text in the svg seems heavily pixelated. The same happens when using png(). IIRC, this did not happen on R 3.0, although I am now starting to doubt this. Is there anything on my machine that I try to update/reinstall to fix this? ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac [[alternative HTML version deleted]] ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
