It's the time of the year to test the new upcoming R release, but this time I'd like to ask as many users as possible to give the new R a spin, because there are many new features in the Mac GUI which increases the likelihood of bugs. It can be downloaded, as usual, from http://r.research.att.com/ and for those of you that like deep links you probably want http://r.research.att.com/R-2.13-branch-leopard.pkg The new features in R itself can be found in the usual place, but this time the focus is also on the GUI and you can get list of new features in the GUI at https://svn.r-project.org/R-packages/trunk/Mac-GUI/NEWS Essentially the internal editor has been much re-written thanks to Hans-J?rg Bibiko and thus is much faster, more versatile (encoding selection, better auto-competion) and features shortcuts you know from Xcode (like <Ctrl><H> for help on the current function). Other parts have been improved as well, help pages are now searchable and so is the history, you can use <Cmd><Enter> in most web views and other lists like Data Manager can be sorted. Finally, for your safety document auto-save feature has been added such that open documents are automatically restored even in the [unlikely ;)] case of an R crash. So, please, consider testing the release candidates in the next week or two and report any bugs you should find. This is true both for R itself and the R.app GUI. Thanks, Simon
Call to test current R 2.13.0 beta and RCs - especially new GUI features!
7 messages · Simon Urbanek, Michael Lawrence, Berend Hasselman +3 more
2 days later
I notice that this version hangs when I run the examples for the ezMixed function in the ez package. Some play (https://gist.github.com/909934) reveals that is might have something to do with the custom progress bar I use in ezMixed, but I can get more minimal examples just using the progress bar to work, and furthermore, if one simply runs through the code in ezMixed line-by-line (instead of using it as a function), the hang does not occur. When I replace the custom progress bar with the standard text progress bar, the function works fine. Any thoughts? Mike On Tue, Apr 5, 2011 at 7:19 PM, Simon Urbanek
<simon.urbanek at r-project.org> wrote:
It's the time of the year to test the new upcoming R release, but this time I'd like to ask as many users as possible to give the new R a spin, because there are many new features in the Mac GUI which increases the likelihood of bugs. It can be downloaded, as usual, from http://r.research.att.com/ and for those of you that like deep links you probably want http://r.research.att.com/R-2.13-branch-leopard.pkg The new features in R itself can be found in the usual place, but this time the focus is also on the GUI and you can get list of new features in the GUI at https://svn.r-project.org/R-packages/trunk/Mac-GUI/NEWS Essentially the internal editor has been much re-written thanks to Hans-J?rg Bibiko and thus is much faster, more versatile (encoding selection, better auto-competion) and features shortcuts you know from Xcode (like <Ctrl><H> for help on the current function). Other parts have been improved as well, help pages are now searchable and so is the history, you can use <Cmd><Enter> in most web views and other lists like Data Manager can be sorted. Finally, for your safety document auto-save feature has been added such that open documents are automatically restored even in the [unlikely ;)] case of an R crash. So, please, consider testing the release candidates in the next week or two and report any bugs you should find. This is true both for R itself and the R.app GUI. Thanks, Simon
_______________________________________________ R-SIG-Mac mailing list R-SIG-Mac at r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
On 06-04-2011, at 00:19, Simon Urbanek wrote:
It's the time of the year to test the new upcoming R release, but this time I'd like to ask as many users as possible to give the new R a spin, because there are many new features in the Mac GUI which increases the likelihood of bugs. It can be downloaded, as usual, from http://r.research.att.com/ and for those of you that like deep links you probably want http://r.research.att.com/R-2.13-branch-leopard.pkg The new features in R itself can be found in the usual place, but this time the focus is also on the GUI and you can get list of new features in the GUI at https://svn.r-project.org/R-packages/trunk/Mac-GUI/NEWS Essentially the internal editor has been much re-written thanks to Hans-J?rg Bibiko and thus is much faster, more versatile (encoding selection, better auto-competion) and features shortcuts you know from Xcode (like <Ctrl><H> for help on the current function).
I have been playing around with the editor and the Help on the current function.
Ctrl+H operates reasonably well but the behaviour can be slightly strange
In the examples that follow, | indicates the position of the caret.
So with
aggregate(d|f[.....
Pressing Ctrl+H will give the help page for aggregate.
However in this case
aggre|gate(df[...
the word aggregate is entered in the Help search field.
And in this case
getOption("verbose")
suppressPackageStartupMessages(library(doBy))
summ|aryBy(height + weight + age ~ sample, data = df, FUN = mean)
with the caret within summaryBy I got help for options.
But if the caret is in the word "library" I'll get the help page for message.
I expected that Ctrl+H would first try to get help for the current word containing the caret/cursor just as it does in TextMate using the R bundle. And if that fails looks backwards.
Berend
4 days later
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An issue I have found using with the GUI is in relation with scrolling through an R script open within the R GUI. If one opens an R script long enough to allow for scrolling and places the script window floating over any other window (including other applications), and then scrolls, the scrolling of the script window effects the windows underneath the script window. The effect on the windows behind the script window is minimal, and the scrolling must be at a slow pace. sessionInfo() R version 2.13.0 RC (2011-04-10 r55401) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] en_AU.UTF-8/en_AU.UTF-8/C/C/en_AU.UTF-8/en_AU.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] RSQLite_0.9-4 DBI_0.2-5 loaded via a namespace (and not attached): [1] tools_2.13.0 Thanks for the great build, Im enjoying the new features. Hope this helps Jason
On 12/04/2011, at 11:50 PM, Eric Wooten wrote:
An odd issue: goseq's dependency genLenDataBase won't load in the GUI, but loads without incident when invoked in the terminal. GUI:
library(goseq)
Loading required package: BiasedUrn Loading required package: geneLenDataBase Error in as.environment(pos) : no item called "newtable" on the search list In addition: Warning message: In objects(newtable, all.names = TRUE) : ?newtable? converted to character string Error: package 'geneLenDataBase' could not be loaded
sessionInfo()
R version 2.13.0 RC (2011-04-11 r55409) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] BiasedUrn_1.03 loaded via a namespace (and not attached): [1] biomaRt_2.7.2 Biostrings_2.19.18 BSgenome_1.19.6 DBI_0.2-5 GenomicRanges_1.3.38 [6] IRanges_1.9.31 RCurl_1.5-0 RSQLite_0.9-4 rtracklayer_1.11.12 XML_3.2-0
Terminal version:
library(goseq) Loading required package: BiasedUrn Loading required package: geneLenDataBase
sessionInfo()
R version 2.13.0 RC (2011-04-11 r55409) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] goseq_1.3.3 geneLenDataBase_0.99.7 BiasedUrn_1.03 loaded via a namespace (and not attached): [1] AnnotationDbi_1.13.21 Biobase_2.11.10 biomaRt_2.7.2 [4] Biostrings_2.19.18 BSgenome_1.19.6 DBI_0.2-5 [7] GenomicFeatures_1.3.15 GenomicRanges_1.3.38 grid_2.13.0 [10] IRanges_1.9.31 lattice_0.19-23 Matrix_0.999375-50 [13] mgcv_1.7-5 nlme_3.1-100 RCurl_1.5-0 [16] RSQLite_0.9-4 rtracklayer_1.11.12 XML_3.2-0
Any thoughts on this? Eric On Fri, Apr 8, 2011 at 1:04 PM, Berend Hasselman <bhh at xs4all.nl> wrote:
On 06-04-2011, at 00:19, Simon Urbanek wrote:
It's the time of the year to test the new upcoming R release, but this
time I'd like to ask as many users as possible to give the new R a spin, because there are many new features in the Mac GUI which increases the likelihood of bugs. It can be downloaded, as usual, from
http://r.research.att.com/ and for those of you that like deep links you probably want http://r.research.att.com/R-2.13-branch-leopard.pkg The new features in R itself can be found in the usual place, but this
time the focus is also on the GUI and you can get list of new features in the GUI at
https://svn.r-project.org/R-packages/trunk/Mac-GUI/NEWS Essentially the internal editor has been much re-written thanks to
Hans-J?rg Bibiko and thus is much faster, more versatile (encoding
selection, better auto-competion) and features shortcuts you know from Xcode
(like <Ctrl><H> for help on the current function).
I have been playing around with the editor and the Help on the current
function.
Ctrl+H operates reasonably well but the behaviour can be slightly strange
In the examples that follow, | indicates the position of the caret.
So with
aggregate(d|f[.....
Pressing Ctrl+H will give the help page for aggregate.
However in this case
aggre|gate(df[...
the word aggregate is entered in the Help search field.
And in this case
getOption("verbose")
suppressPackageStartupMessages(library(doBy))
summ|aryBy(height + weight + age ~ sample, data = df, FUN = mean)
with the caret within summaryBy I got help for options.
But if the caret is in the word "library" I'll get the help page for
message.
I expected that Ctrl+H would first try to get help for the current word
containing the caret/cursor just as it does in TextMate using the R bundle.
And if that fails looks backwards.
Berend
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Simon, I'd like to give this a test, but I can't afford to loose the use of my current installation. The installer says: Requirements: - Mac OS X 10.5 (Leopard) or 10.6 (Snow Leopard) Note: By default the installer upgrades previous Leopard build of R if present. If you want to keep the previous Leopard build, use pkgutil --forget org.r-project.R.Leopard.fw.pkg I thought it would just be installed in the Versions directory of the R.framework and the symlink changed, but maybe this is not so? I'm on 10.6.6 - I'm not sure if that means that it will replace any leopard versions that exist (but not snow leopard?), of if I need to use the "pkgutil --forget org.r-project.R.Leopard.fw.pkg" command. Not knowing anything about this, do I just run that command in terminal in my home directory, or does it need to be done in the R directory. Will it then go ahead and install, or do I run it and then use the installer? Will it mean I can use RSwitch? Sorry about the lack of adventurousness, but I really can't afford to loose my current stable install as I'm "on-demand" to produce and modify analyses. Cheers Ben
On 06/04/2011, at 6:19 AM, Simon Urbanek wrote:
It's the time of the year to test the new upcoming R release, but this time I'd like to ask as many users as possible to give the new R a spin, because there are many new features in the Mac GUI which increases the likelihood of bugs. It can be downloaded, as usual, from http://r.research.att.com/ and for those of you that like deep links you probably want http://r.research.att.com/R-2.13-branch-leopard.pkg The new features in R itself can be found in the usual place, but this time the focus is also on the GUI and you can get list of new features in the GUI at https://svn.r-project.org/R-packages/trunk/Mac-GUI/NEWS Essentially the internal editor has been much re-written thanks to Hans-J?rg Bibiko and thus is much faster, more versatile (encoding selection, better auto-competion) and features shortcuts you know from Xcode (like <Ctrl><H> for help on the current function). Other parts have been improved as well, help pages are now searchable and so is the history, you can use <Cmd><Enter> in most web views and other lists like Data Manager can be sorted. Finally, for your safety document auto-save feature has been added such that open documents are automatically restored even in the [unlikely ;)] case of an R crash. So, please, consider testing the release candidates in the next week or two and report any bugs you should find. This is true both for R itself and the R.app GUI. Thanks, Simon
_______________________________________________ R-SIG-Mac mailing list R-SIG-Mac at r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Ben,
On Apr 13, 2011, at 10:59 PM, Ben Madin wrote:
Simon, I'd like to give this a test, but I can't afford to loose the use of my current installation.
It's way to late - R 2.13.0 is already released so you may as well forget it all and install the new version ;).
The installer says: Requirements: - Mac OS X 10.5 (Leopard) or 10.6 (Snow Leopard) Note: By default the installer upgrades previous Leopard build of R if present. If you want to keep the previous Leopard build, use pkgutil --forget org.r-project.R.Leopard.fw.pkg I thought it would just be installed in the Versions directory of the R.framework and the symlink changed, but maybe this is not so?
No, Apple's installer keeps track of files installed by the same product and will upgrade it - i.e. remove files that are not in the new version. Unfortunately AFAIK the Installer has no provision to change that behavior (there is a reason for that since that would make it much harder to keep track which files were installed by which package and which version ...).
I'm on 10.6.6 - I'm not sure if that means that it will replace any leopard versions that exist (but not snow leopard?),
There is no "snow leopard" version.
of if I need to use the "pkgutil --forget org.r-project.R.Leopard.fw.pkg" command. Not knowing anything about this, do I just run that command in terminal in my home directory, or does it need to be done in the R directory. Will it then go ahead and install, or do I run it and then use the installer? Will it mean I can use RSwitch?
The pkgutil just tells the system to forget about the installed R framework so it won't know about it when upgrading and thus it won't delete its files. It doesn't install anything.
Sorry about the lack of adventurousness, but I really can't afford to loose my current stable install as I'm "on-demand" to produce and modify analyses.
As I said, you're way too late anyway, but thanks for the thought. Cheers, Simon
On 06/04/2011, at 6:19 AM, Simon Urbanek wrote:
It's the time of the year to test the new upcoming R release, but this time I'd like to ask as many users as possible to give the new R a spin, because there are many new features in the Mac GUI which increases the likelihood of bugs. It can be downloaded, as usual, from http://r.research.att.com/ and for those of you that like deep links you probably want http://r.research.att.com/R-2.13-branch-leopard.pkg The new features in R itself can be found in the usual place, but this time the focus is also on the GUI and you can get list of new features in the GUI at https://svn.r-project.org/R-packages/trunk/Mac-GUI/NEWS Essentially the internal editor has been much re-written thanks to Hans-J?rg Bibiko and thus is much faster, more versatile (encoding selection, better auto-competion) and features shortcuts you know from Xcode (like <Ctrl><H> for help on the current function). Other parts have been improved as well, help pages are now searchable and so is the history, you can use <Cmd><Enter> in most web views and other lists like Data Manager can be sorted. Finally, for your safety document auto-save feature has been added such that open documents are automatically restored even in the [unlikely ;)] case of an R crash. So, please, consider testing the release candidates in the next week or two and report any bugs you should find. This is true both for R itself and the R.app GUI. Thanks, Simon
_______________________________________________ R-SIG-Mac mailing list R-SIG-Mac at r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac