Re: [ESS] Error starting R
I've had a chance to play around. I've uninstalled ess-17.11 from the system and installed the latest ess-20181007.1527 and am able to start R under Emacs with M-x R. Reinstalled the most recent ess-smart-underscore-20180911.523 and can still start R under Emacs with M-x R. A couple of other packages have been updated since last week... alert-20181005.2251 ein-20181008.235 elpy-20181006.2226 magit-20181008.1844 projectile-20181008.812 yasnippet-20181007.2230 ..so its possible, but I guess unlikely that they were causing conflict. Thanks to the developers/maintainers for their on-going efforts, really appreciated. Neil -- *Natural selection is a mechanism for generating an exceedingly high **degree of improbability.* - R.A. Fisher *Ignorance more frequently begets confidence than does knowledge* - Charles Darwin PGP Public : https://pgp.mit.edu/pks/lookup?op=get=0x0E7ECE9C10D7B4A0 On Thu, 4 Oct 2018 at 09:40, Neil Shephard wrote: > > > > On Wed, 3 Oct 2018 at 21:08, Alex Branham wrote: > >> >> Thanks. I've tried to reproduce this and am having issues still. Just to >> confirm: you don't have any ess-* packages (ess-smart-underscore, >> ess-R-object-viewer, etc) installed, either system wide or under >> ~/.emacs.d/elpa? >> >> Nope, after removing ess-20181003.1614 and > ess-smart-underscore-20180911.523 from ~/.emacs.d/elpa the only ESS related > package installed on this system is ess-17.11 which is installed under the > system. > > We're getting ready to release ESS 18.10 so if there is some 3rd-party >> package out there that's causing issues with ESS's autoloads, it would >> be nice to figure out who to blame :-) >> > > I've a number of other packages installed (along with their dependencies) > but I've no idea which might be causing a conflict (list at bottom). > > I gave ess-20181002.2153 a whirl this morning but still have the same > issue. Whats even more confusing for me is that I've the same ~/.emacs.d > on other systems (by virtue of using a dotfiles repository to organise > things) and there is no issue on those. Is it possible there is a conflict > between the system installed ess-17.11 and the MELPA installed one? Its > the only thing I can think of at this point (beyond conflicts with other > packages, but I don't think the Backtrace suggests any other culprits). > > I'll find some time to investigate this as a possible cause but may not be > until tomorrow. > > Thanks again, > > Neil > > > Other installed packages (via MELPA)... > > auto-package-update 20180712.2045 installed > Automatically update Emacs packages. > autopair20160304.1237 installed > Automagically pair braces and quotes like TextMate > better-defaults 20170614.404 installed Fixing weird > quirks and poor defaults > company 20180913.2311 installed Modular text > completion framework > darktooth-theme 20180726.302 installed From the > darkness... it watches > ein 20181002.1658 installed Emacs > IPython Notebook > eink-theme 20170717.1507 installed E Ink color > theme > elpy20180924.1634 installed Emacs Python > Development Environment > ess 20181003.1614 installed Emacs Speaks > Statistics > find-file-in-project 20180912.1218 installed Find > file/directory and review Diff/Patch/Commit efficiently everywhere > flycheck20180907.1319 installed On-the-fly > syntax checking > highlight-indentation20171218.937 installed Minor modes > for highlighting indentation > highlight-parentheses20180704.1102 installed highlight > surrounding parentheses > julia-mode 20180816.2117 installed Major mode > for editing Julia source code > magit 20180928.1153 installed A Git > porcelain inside Emacs. > material-theme 20171123.1840 installed A Theme > based on the colors of the Google Material Design > org-time-budgets2015.801 installed Define time > budgets and display clocked time. > package+20170816.256 installed Extensions > for the package library. > package-utils 20180514.1415 installed Extensions > for package.el > polymode20180926.2044 installed Extensible > framework for multiple major modes > projectile 20181003.742 installed Manage and > navigate projects in Emacs easily > projectile-git-auto
Re: [ESS] Error starting R
On Wed, 3 Oct 2018 at 21:08, Alex Branham wrote: > > Thanks. I've tried to reproduce this and am having issues still. Just to > confirm: you don't have any ess-* packages (ess-smart-underscore, > ess-R-object-viewer, etc) installed, either system wide or under > ~/.emacs.d/elpa? > > Nope, after removing ess-20181003.1614 and ess-smart-underscore-20180911.523 from ~/.emacs.d/elpa the only ESS related package installed on this system is ess-17.11 which is installed under the system. We're getting ready to release ESS 18.10 so if there is some 3rd-party > package out there that's causing issues with ESS's autoloads, it would > be nice to figure out who to blame :-) > I've a number of other packages installed (along with their dependencies) but I've no idea which might be causing a conflict (list at bottom). I gave ess-20181002.2153 a whirl this morning but still have the same issue. Whats even more confusing for me is that I've the same ~/.emacs.d on other systems (by virtue of using a dotfiles repository to organise things) and there is no issue on those. Is it possible there is a conflict between the system installed ess-17.11 and the MELPA installed one? Its the only thing I can think of at this point (beyond conflicts with other packages, but I don't think the Backtrace suggests any other culprits). I'll find some time to investigate this as a possible cause but may not be until tomorrow. Thanks again, Neil Other installed packages (via MELPA)... auto-package-update 20180712.2045 installed Automatically update Emacs packages. autopair20160304.1237 installed Automagically pair braces and quotes like TextMate better-defaults 20170614.404 installed Fixing weird quirks and poor defaults company 20180913.2311 installed Modular text completion framework darktooth-theme 20180726.302 installed From the darkness... it watches ein 20181002.1658 installed Emacs IPython Notebook eink-theme 20170717.1507 installed E Ink color theme elpy20180924.1634 installed Emacs Python Development Environment ess 20181003.1614 installed Emacs Speaks Statistics find-file-in-project 20180912.1218 installed Find file/directory and review Diff/Patch/Commit efficiently everywhere flycheck20180907.1319 installed On-the-fly syntax checking highlight-indentation20171218.937 installed Minor modes for highlighting indentation highlight-parentheses20180704.1102 installed highlight surrounding parentheses julia-mode 20180816.2117 installed Major mode for editing Julia source code magit 20180928.1153 installed A Git porcelain inside Emacs. material-theme 20171123.1840 installed A Theme based on the colors of the Google Material Design org-time-budgets2015.801 installed Define time budgets and display clocked time. package+20170816.256 installed Extensions for the package library. package-utils 20180514.1415 installed Extensions for package.el polymode20180926.2044 installed Extensible framework for multiple major modes projectile 20181003.742 installed Manage and navigate projects in Emacs easily projectile-git-autofetch 20180418.2336 installed automatically fetch git repositories py-autopep8 20160925.1052 installed Use autopep8 to beautify a Python buffer pylint 20170402.1255 installed minor mode for running `pylint' pyvenv 20180831.847 installed Python virtual environment interface vimish-fold 20180101.612 installed Fold text like in Vim wide-column 20170925.1613 installed Calls functions dependant on column position. yaml-mode 20180409.607 installed Major mode for editing YAML files yasnippet 20180916.2115 installed Yet another snippet extension for Emacs. alert 20180827.422 dependencyGrowl-style notification system for Emacs apiwrap 20180602.2231 dependencyapi-wrapping macros async 20180527.1730 dependencyAsynchronous processing in Emacs auto-complete 20170125.245 dependencyAuto Completion for GNU Emacs autothemer 20180920.923 dependencyConveniently define themes. cl-generic 0.3 dependency Forward cl-generic compatibility for Emacs<25 dash20180910.1856 dependencyA modern list
Re: [ESS] Error starting R
Thanks for the suggestions. I do already version control some files under
~/.emacs.d (and many other ~/.* files as I'm trying to organise a dotfiles
repo for myself) such as init.el and a sub-dir 'settings' which holds
multiple files that are loaded from init.el. I opted to explicitly ignore
~/.emacs.d/elpa though as it felt like extra work to git add/commit each
time MELPA updated things. I'll look into straight.el and borg though to
see what they're like.
Thanks again for your help trouble-shooting this.
Neil
--
*Natural selection is a mechanism for generating an exceedingly high **degree
of improbability.* - R.A. Fisher
*Ignorance more frequently begets confidence than does knowledge* - Charles
Darwin
PGP Public : https://pgp.mit.edu/pks/lookup?op=get=0x0E7ECE9C10D7B4A0
Website - http://kimura.no-ip.info/
Photos - http://www.flickr.com/photos/slackline/
On Wed, 3 Oct 2018 at 22:26, Alex Branham wrote:
> Version controlling your packages is definitely a good idea if you want
> to be able to switch between versions and rollback when things break.
> There's a few ways to do this:
>
> - relying on your distro's package manager to perform rollbacks when
> needed (guix and nix both do this well. I think nix is available for
> macos as well?).
>
> - use a package manager other than package.el. straight.el is one that
> provides a comparison between itself and a few others:
>
> https://github.com/raxod502/straight.el#comparison-to-other-package-managers
> .
> Personally I use borg.
>
> - Putting ~/.emacs.d/elpa under version control. This has a few
> downsides since packages change directories across updates, and it's
> easy to commit byte-compiled code.
>
> Alex
>
> On Wed 03 Oct 2018 at 15:21, Jeremie Juste via ESS-help <
> ess-help@r-project.org> wrote:
>
> > Hello,
> >
> > Glad you could sort it out.
> > I think version controling the .emacs file and the .emacs.d directory
> > could help solve these issues faster. You could easily go back to a
> > previous working version. This might be helpful if you are in a
> > situation where you really need things to work.
> >
> > I'm currently exploring this idea but I don't know the full pros and
> > cons of this method.
> >
> >
> >
> > Best regards,
> > Jeremie
> >
> >
> >
> >> Timely
> >>
> >> On Wed, 3 Oct 2018 at 20:16, Alex Branham
> wrote:
> >>
> >>>
> >>> > I've tried disabling ess-smart-underscore as Alex suggests but no
> joy.
> >>>
> >>> I'm not familiar with how this package works but disabling it (by
> >>> removing the "require" from your init file) might not be enough.
> Emacs's
> >>> package manager autoloads some functionality if the package is simply
> >>> installed on your system. It doesn't do this if you do "emacs -Q",
> which
> >>> might explain why you don't see this error then.
> >>>
> >>> Timely as I've just been playing around and you are absolutely right,
> >> simply commenting out ess-smart-underscore from the settings wasn't
> >> sufficient. I decided to try manually delete it and ess from
> >> ~/.emacs.d/elpa/ess* completely and lo-and-behold I can now start R
> under
> >> Emacs/ESS with M-x R again.
> >>
> >> However, this is from the system-wide install of Emacs (currently
> ess-17.11
> >> under Gentoo).
> >>
> >> I did try installing just ess-20181003.1614 after seeing it had been
> >> updated today but that didn't work either.
> >>
> >> For me personally thats not a problem as I'm happy with not having the
> >> latest ESS, and I won't miss the functionality of ess-smart-underscore.
> >>
> >> As an aside it doesn't look like ess-smart-underscore is that old,
> current
> >> version on MELPA is from last month 20180911.523, some of the other ess
> >> packages are very old (ess-smart-equals was last updated 2015;
> >> ess-R-data-view 2013).
> >>
> >> If there is anything I can do to help fathom out what is going on let me
> >> know. I've included the debug from installing ess-20181003.1614 below
> for
> >> reference. This happens after installing from MELPA under the same
> Emacs
> >> instance, no restarting. If I delete ~/.emacs.d/elpa/ess-20181003.1614
> and
> >> restart Emacs M-x R works fine (as its using ess-17.11 from the main
> >> system).
> >>
> >> Thanks to yourself and Jeremie for your help and to all
> >> developers/maintainers.
> >>
> >> Neil
> >>
> >> Debugger entered--Lisp error: (wrong-type-argument consp nil)
> >> byte-code("\301\302 \"\303\241\210\301\304
> >> \"\305\241\210\306\307\300\"\207" [ess-r-customize-alist assoc
> >> ess-font-lock-keywords (quote ess-R-font-lock-keywords)
> >> inferior-ess-font-lock-keywords (quote
> inferior-ess-r-font-lock-keywords)
> >> defalias R-customize-alist] 3)
> >> autoload-do-load((autoload "ess-r-mode" "Call 'R', the 'GNU S' system
> >> from the R Foundation.\nOptional prefix (\\[universal-argument]) allows
> to
> >> set command line arguments, such as\n--vsize. This should be OS
> >> agnostic.\nIf you have certain command line arguments that should
Re: [ESS] Error starting R
Timely
On Wed, 3 Oct 2018 at 20:16, Alex Branham wrote:
>
> > I've tried disabling ess-smart-underscore as Alex suggests but no joy.
>
> I'm not familiar with how this package works but disabling it (by
> removing the "require" from your init file) might not be enough. Emacs's
> package manager autoloads some functionality if the package is simply
> installed on your system. It doesn't do this if you do "emacs -Q", which
> might explain why you don't see this error then.
>
> Timely as I've just been playing around and you are absolutely right,
simply commenting out ess-smart-underscore from the settings wasn't
sufficient. I decided to try manually delete it and ess from
~/.emacs.d/elpa/ess* completely and lo-and-behold I can now start R under
Emacs/ESS with M-x R again.
However, this is from the system-wide install of Emacs (currently ess-17.11
under Gentoo).
I did try installing just ess-20181003.1614 after seeing it had been
updated today but that didn't work either.
For me personally thats not a problem as I'm happy with not having the
latest ESS, and I won't miss the functionality of ess-smart-underscore.
As an aside it doesn't look like ess-smart-underscore is that old, current
version on MELPA is from last month 20180911.523, some of the other ess
packages are very old (ess-smart-equals was last updated 2015;
ess-R-data-view 2013).
If there is anything I can do to help fathom out what is going on let me
know. I've included the debug from installing ess-20181003.1614 below for
reference. This happens after installing from MELPA under the same Emacs
instance, no restarting. If I delete ~/.emacs.d/elpa/ess-20181003.1614 and
restart Emacs M-x R works fine (as its using ess-17.11 from the main
system).
Thanks to yourself and Jeremie for your help and to all
developers/maintainers.
Neil
Debugger entered--Lisp error: (wrong-type-argument consp nil)
byte-code("\301\302 \"\303\241\210\301\304
\"\305\241\210\306\307\300\"\207" [ess-r-customize-alist assoc
ess-font-lock-keywords (quote ess-R-font-lock-keywords)
inferior-ess-font-lock-keywords (quote inferior-ess-r-font-lock-keywords)
defalias R-customize-alist] 3)
autoload-do-load((autoload "ess-r-mode" "Call 'R', the 'GNU S' system
from the R Foundation.\nOptional prefix (\\[universal-argument]) allows to
set command line arguments, such as\n--vsize. This should be OS
agnostic.\nIf you have certain command line arguments that should always be
passed\nto R, put them in the variable `inferior-R-args'.\n\nSTART-ARGS can
be a string representing an argument, a list of\nsuch strings, or any other
non-nil value. In the latter case, you\nwill be prompted to enter
arguments interactively.\n\n(fn START-ARGS)" t nil) R)
command-execute(R record)
execute-extended-command(nil "R" "R")
funcall-interactively(execute-extended-command nil "R" "R")
call-interactively(execute-extended-command nil nil)
command-execute(execute-extended-command)
--
*Natural selection is a mechanism for generating an exceedingly high **degree
of improbability.* - R.A. Fisher
*Ignorance more frequently begets confidence than does knowledge* - Charles
Darwin
PGP Public : https://pgp.mit.edu/pks/lookup?op=get=0x0E7ECE9C10D7B4A0
Website - http://kimura.no-ip.info/
Photos - http://www.flickr.com/photos/slackline/
[[alternative HTML version deleted]]
__
ESS-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/ess-help
Re: [ESS] Error starting R
Apologies Jeremie, stupid *faux pas* not replying to the list. Running... emacs -Q ...and then loading ess from scratch works (bar similar errors about julia that you mention). R starts fine. I've tried disabling ess-smart-underscore as Alex suggests but no joy. I'll have a further play around later this evening and report back. Thanks both for your assistance. Neil -- *Natural selection is a mechanism for generating an exceedingly high **degree of improbability.* - R.A. Fisher *Ignorance more frequently begets confidence than does knowledge* - Charles Darwin PGP Public : https://pgp.mit.edu/pks/lookup?op=get=0x0E7ECE9C10D7B4A0 Website - http://kimura.no-ip.info/ Photos - http://www.flickr.com/photos/slackline/ On Wed, 3 Oct 2018 at 15:44, Alex Branham wrote: > > On Wed 03 Oct 2018 at 05:34, Neil Shephard via ESS-help < > ess-help@r-project.org> wrote: > > > autoload-do-load: Wrong type argument: consp, nil > > > > I'm using Emacs 25.3.1 with ESS installed from ELPA (20181003.755). I've > > asked on the Emacs Stackexchange ( > > https://emacs.stackexchange.com/q/45010/10100) and was advised to > disable > > in turn different settings that are loaded. I've gone through this for > all > > ESS settings (see below) but the problem persists, I then tried disabling > > loading the other modes I have under Emacs but again the problem > persisted. > > I've seen this problem every now and then but mainly when switching > around git branches. Recompiling ESS always fixed it for me. Does > reinstalling ESS from melpa fix the problem? > > > ...and my ESS settings are... > > > > ;;; ESS > > (require 'ess) > > ;;; Some generally useful key-bindings (mostly ESS specific) > > (define-key global-map [f1] 'Control-X-prefix) > > (define-key global-map [f2] 'save-buffer) > > (define-key global-map [f3] 'find-file) > > (define-key global-map [f5] 'switch-to-buffer) > > (define-key global-map [f6] 'other-window) > > (define-key global-map [f8] 'kill-buffer) > > (define-key global-map [f9] 'ess-load-file) > > ;;; Other specific ESS settings you can use are the following: > > (setq comint-input-ring-size 1000) > > (setq ess-indent-level 4) > > (setq ess-arg-function-offset 4) > > (setq ess-else-offset 4) > > (setq ess-eval-visibly-p nil) > > ;;; Set the width of the buffer automatically > > (defun my-ess-post-run-hook () > > (ess-execute-screen-options) > > (local-set-key "\C-cw" 'ess-execute-screen-options)) > > (add-hook 'ess-post-run-hook 'my-ess-post-run-hook) > > I couldn't reproduce this with the settings above, using the same > version of ESS from MELPA that you have. Perhaps it has something to do > with the settings below? In particular, it looks like > ess-smart-underscore hasn't been updated in a long time. I'd suggest > removing it and trying again. > > > ;;; Auto-complete and ESS > > (require 'auto-complete) > > (require 'auto-complete-config) > > (add-to-list 'ac-dictionary-directories > > "~/.emacs.d/site-lisp/auto-complete/dict") > > (ac-config-default) > > (auto-complete-mode) > > (setq ess-use-auto-complete t) > > ;;; Smart underscore > https://www.emacswiki.org/emacs/ess-smart-underscore.el > > (require 'ess-smart-underscore) > > Alex > [[alternative HTML version deleted]] __ ESS-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/ess-help
[ESS] Error starting R
Hi,
I've recently encountered a problem which prevents me from using M-x R to
start an R session under Emacs. On doing so I'm informed that...
autoload-do-load: Wrong type argument: consp, nil
I'm using Emacs 25.3.1 with ESS installed from ELPA (20181003.755). I've
asked on the Emacs Stackexchange (
https://emacs.stackexchange.com/q/45010/10100) and was advised to disable
in turn different settings that are loaded. I've gone through this for all
ESS settings (see below) but the problem persists, I then tried disabling
loading the other modes I have under Emacs but again the problem persisted.
Any ideas or suggestions on how to resolve this would be very much
appreciated.
Thanks in advance.
Neil
The traceback on this error is...
Debugger entered--Lisp error: (wrong-type-argument consp nil)
byte-code("\301\30\"\303\241\210\301\30\"\305\241\210\306\307\300\"\207"
[ess-r-customize-alist assoc ess-font-lock-keywords (quote
ess-R-font-lock-keywords) inferior-ess-font-lock-keywords (quote
inferior-ess-r-font-lock-keywords) defalias R-customize-alist] 3)
autoload-do-load((autoload "ess-r-mode" "Call 'R', the 'GNU S' system
from the R Foundation.\nOptional prefix (\\[universal-argument]) allows to
set command line arguments, such as\n--vsize. This should be OS
agnostic.\nIf you have certain command line arguments that should always be
passed\nto R, put them in the variable `inferior-R-args'.\n\nSTART-ARGS can
be a string representing an argument, a list of\nsuch strings, or any other
non-nil value. In the latter case, you\nwill be prompted to enter
arguments interactively.\n\n(fn START-ARGS)" t nil) R)
command-execute(R record)
execute-extended-command(nil "R" "R")
funcall-interactively(execute-extended-command nil "R" "R")
call-interactively(execute-extended-command nil nil)
command-execute(execute-extended-command)
...and my ESS settings are...
;;; ESS
(require 'ess)
;;; Some generally useful key-bindings (mostly ESS specific)
(define-key global-map [f1] 'Control-X-prefix)
(define-key global-map [f2] 'save-buffer)
(define-key global-map [f3] 'find-file)
(define-key global-map [f5] 'switch-to-buffer)
(define-key global-map [f6] 'other-window)
(define-key global-map [f8] 'kill-buffer)
(define-key global-map [f9] 'ess-load-file)
;;; Other specific ESS settings you can use are the following:
(setq comint-input-ring-size 1000)
(setq ess-indent-level 4)
(setq ess-arg-function-offset 4)
(setq ess-else-offset 4)
(setq ess-eval-visibly-p nil)
;;; Set the width of the buffer automatically
(defun my-ess-post-run-hook ()
(ess-execute-screen-options)
(local-set-key "\C-cw" 'ess-execute-screen-options))
(add-hook 'ess-post-run-hook 'my-ess-post-run-hook)
;;; Auto-complete and ESS
(require 'auto-complete)
(require 'auto-complete-config)
(add-to-list 'ac-dictionary-directories
"~/.emacs.d/site-lisp/auto-complete/dict")
(ac-config-default)
(auto-complete-mode)
(setq ess-use-auto-complete t)
;;; Smart underscore https://www.emacswiki.org/emacs/ess-smart-underscore.el
(require 'ess-smart-underscore)
--
*Natural selection is a mechanism for generating an exceedingly high **degree
of improbability.* - R.A. Fisher
*Ignorance more frequently begets confidence than does knowledge* - Charles
Darwin
PGP Public : https://pgp.mit.edu/pks/lookup?op=get=0x0E7ECE9C10D7B4A0
[[alternative HTML version deleted]]
__
ESS-help@r-project.org mailing list
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[ESS] ess-17.11-tgz is not compressed
Hi, I've only just caught up on the update to ess-17.11 and went to install it using the Gentoo Linux package management system portage. It complained that the ess-17.11.tgz was not a compressed archive and this appears to be true, its just a plain tar-ball. This means that when portage trys to unpack it based on the file extension '.tgz' it tries to uncompress it, which fails. For now I've change the ebuild (the scripts which install programmes under Gentoo/Linux) to use the ess-17.11.zip but thought this worth reporting. I include below downloading the ess-17.11.tgz and attempting to unzip/uncompress manually, what finally worked was renaming to ess-17.11.tar and untar the archive. Details of this are also on Gentoo Buzilla at https://bugs.gentoo.org/639752 Regards, Neil ~/tmp/ess $ wget http://ess.r-project.org/downloads/ess/ess-17.11.tgz --2017-12-05 08:12:09-- http://ess.r-project.org/downloads/ess/ess-17.11.tgz Resolving ess.r-project.org... 129.132.119.195 Connecting to ess.r-project.org|129.132.119.195|:80... connected. HTTP request sent, awaiting response... 200 OK Length: 3275703 (3.1M) [application/x-tar] Saving to: ‘ess-17.11.tgz’ ess-17.11.tgz 100%[===>] 3.12M 6.30MB/sin 0.5s 2017-12-05 08:12:09 (6.30 MB/s) - ‘ess-17.11.tgz’ saved [8898560] ~/tmp/ess $ gunzip ess-17.11.tgz gzip: ess-17.11.tgz: not in gzip format ~/tmp/ess $ tar xzvf ess-17.11.tgz gzip: stdin: not in gzip format tar: Child returned status 1 tar: Error is not recoverable: exiting now ~/tmp/ess $ mv ess-17.11.tgz ess-17.11.tar ~/tmp/ess $ tar xvf ess-17.11.tar ess-17.11/ ess-17.11/.dir-locals.el ess-17.11/.gitignore ess-17.11/COPYING ess-17.11/ChangeLog ess-17.11/LDA/ ess-17.11/LDA/README ess-17.11/LDA/ex1.nw ess-17.11/Makeconf ess-17.11/Makefile ess-17.11/OONEWS ess-17.11/README.md ess-17.11/RPM.spec.in ess-17.11/VERSION ess-17.11/debian/ ess-17.11/debian/changelog ess-17.11/debian/compat ess-17.11/debian/control ess-17.11/debian/copyright ess-17.11/debian/dirs ess-17.11/debian/doc-base ess-17.11/debian/docs ess-17.11/debian/emacsen-compat ess-17.11/debian/emacsen-install ess-17.11/debian/emacsen-remove ess-17.11/debian/emacsen-startup ess-17.11/debian/rules ess-17.11/debian/source/ ess-17.11/debian/source/format ess-17.11/debian/watch ess-17.11/doc/ ess-17.11/doc/ChangeLog ess-17.11/doc/ESS_intro.tex ess-17.11/doc/Makefile ess-17.11/doc/NEWS ess-17.11/doc/README ess-17.11/doc/html/ ess-17.11/doc/html/ess.html ess-17.11/doc/html/readme.html ess-17.11/doc/html/news.html ess-17.11/doc/ess.pdf ess-17.11/doc/TODO ess-17.11/doc/readme.pdf ess-17.11/doc/ajr-talk.tex ess-17.11/doc/allnews.texi ess-17.11/doc/announc.texi ess-17.11/doc/atouchofstyle.css ess-17.11/doc/authors.texi ess-17.11/doc/bugrept.texi ess-17.11/doc/bugs-ms.texi ess-17.11/doc/bugs.texi ess-17.11/doc/credits.texi ess-17.11/doc/currfeat.texi ess-17.11/doc/dir.txt ess-17.11/doc/ediff-sas.gif ess-17.11/doc/ediff-sas.pdf ess-17.11/doc/ess-defs.texi ess-17.11/doc/ess-demo.jpg ess-17.11/doc/ess-demo.pdf ess-17.11/doc/ess-intro-graphs.bib ess-17.11/doc/ess-intro-graphs.pdf ess-17.11/doc/ess-intro-graphs.tex ess-17.11/doc/ess-intro.pdf ess-17.11/doc/ess-intro.tex ess-17.11/doc/ess-manual.org ess-17.11/doc/ess.texi ess-17.11/doc/font-cor-s.gif ess-17.11/doc/font-cor-s.jpg ess-17.11/doc/font-cor-s.pdf ess-17.11/doc/font-incor-s.gif ess-17.11/doc/font-incor-s.jpg ess-17.11/doc/font-incor-s.pdf ess-17.11/doc/getting.texi ess-17.11/doc/help-bugs.texi ess-17.11/doc/help-jags.texi ess-17.11/doc/help-s.texi ess-17.11/doc/help-sas.texi ess-17.11/doc/hilock-sas.gif ess-17.11/doc/hilock-sas.pdf ess-17.11/doc/images/ ess-17.11/doc/images/ess_176_176.gif ess-17.11/doc/images/ess_32_32.ico ess-17.11/doc/images/icons/ ess-17.11/doc/images/icons/icon_external.png ess-17.11/doc/images/icons/icon_mailto.png ess-17.11/doc/images/logoESS.gif ess-17.11/doc/images/skyline.jpg ess-17.11/doc/include-matrix.org ess-17.11/doc/info/ ess-17.11/doc/info/dir ess-17.11/doc/info/ess.info ess-17.11/doc/inst_svn.texi ess-17.11/doc/inst_tar.texi ess-17.11/doc/installation.texi ess-17.11/doc/lectures.txt ess-17.11/doc/license.texi ess-17.11/doc/mailing.texi ess-17.11/doc/name-completion.txt ess-17.11/doc/newfeat.texi ess-17.11/doc/news.texi ess-17.11/doc/onewfeat.texi ess-17.11/doc/onews.texi ess-17.11/doc/readme.texi ess-17.11/doc/refcard/ ess-17.11/doc/refcard/refcard.tex ess-17.11/doc/refcard/refcard.log ess-17.11/doc/refcard/refcard.aux ess-17.11/doc/refcard/refcard.pdf ess-17.11/doc/requires.texi ess-17.11/doc/rgui-doc.txt ess-17.11/doc/rmh-talk.tex ess-17.11/doc/slverb.sty ess-17.11/doc/stabilty.texi ess-17.11/ess-autoloads.el ess-17.11/etc/ ess-17.11/etc/BACKBUG5.BAT ess-17.11/etc/BACKBUGS.BAT ess-17.11/etc/C-cC-c-probl.R ess-17.11/etc/ESSR/ ess-17.11/etc/ESSR/BUILDESSR ess-17.11/etc/ESSR/LOADREMOTE ess-17.11/etc/ESSR/R/ ess-17.11/etc/ESSR/R/.basic.R ess-17.11/etc/ESSR/R/.load.R
Re: [R] Literature analysis
On Fri, Dec 11, 2009 at 2:04 PM, Schwan s.s.hosse...@utwente.nl wrote: Thanks, but how should I put the citation inside a data frame? data.frame(first txt file, second txt file...) plot (what should I insert here) type=p And how should I load the txt files anyway inside the frame? Check out the resources I recommended in my first reply. These are aspects of using R that are fundamental and completely independent of what analysis you want to do. Neil -- The combination of some data and an aching desire for an answer does not ensure that a reasonable answer can be extracted from a given body of data. ~ John Tukey (1986), Sunset salvo. The American Statistician 40(1). Email - nsheph...@gmail.com Website - http://slack.ser.man.ac.uk/ Photos - http://www.flickr.com/photos/slackline/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] multiple hypothesis testing
Vijaykumar Muley wrote: Dear all, Myself Vijaykumar Muley working as senior research fellow. By training I am a computational biologist with not a strong knowledge of statistics. I have done some analysis which is explained as follows, I have 10340 (X) profiles of binary vectors with same length(N=845), I will call then gene profiles for example... v1 v2 v3 v4.vN a 1 01 0 1 b 0 01 0 0 c 1 01 1 1 d 0 11 1 1 e 0 01 1 1 . . .. . . .. . . .. upto 10340 then I have some other binary profiles with same length (N=845), here I will call then expression profile; v1 v2 v3 v4.vN f1 1 01 0 1 f2 0 01 0 0 f3 1 01 1 1 now I am comparing profile f1 with all X profiles using hypergeometic distribution function. What I am getting is p-value(probability) of the similarity between profile f1 and all X profiles i.e. 10340 by random chance alone. for example, #pair p-value f1,a1e-20 f1,b0.01 . . upto f1,10340 0.05 same thing i am doing with f2 and f3. if we arrange this data(output) in better readable format, it looks like f1 f2f3 a 1e-200.01 0.10 b 0.01 1e-9 0.02 c 1e-3 0.1 0.30 d 0.03 0.07 1e-5 e 1e-1 0.01 1e-9 . . .. . . .. . . .. upto 10340 I hope everyone understood what type of output I am getting. Now I want to perform multiple hypothesis comparision(P-value adjustment) on this data , so that I will get the statistically significant associations between various expression profiles and gene profiles at specific alpha level; Most conservative method for p-value adjustment is bonferroni and many others with less conservation, I dont care which method I use but the problem here is according to what parameter I should use for correct or adjust p-values ?. so in case of Bonferroni correction, should I multiply the each p-value with 10340 or as I have compared 3 expression profiles against 10340 gene profiles, should I multiply p-value with 3*10340 I am aksing this for understanding. What I want to do is From the above gene, p-value table, I want to calculate the percentage of false positive rate at each p-values from 0.0001 to 0.05 So that I can use a good cutoff as significance level (alpha) to exclude the gene profiles which are weakly associated with all expression profiles. (If I am correct, to do this I need to use other p-value correction methods, either simulation based, resampling or Benjamini and Hochberg (BH). Please can any one suuggests me about p-value adjustment or p-value correction, I mean statistically or technically which number should I consider for correction, 10340 or 3 * 10340, as I have three features to associate with same 10340 gene set. or if I am wrong, can any one tell me the protocol which I should refer to get fair number of significant associations between genes and expression profiles. I am using package multtest for p-value adjustment but literally I am not getting for correction, should I give p-values for each expression profile alone or give it all p-values ie. 3*10340. I have gone through many tutorials and articles for multiple hypothesis testing but really couldnt get exactly, what is it. Please give me some clues, some of you may be actively working on p-value adjustment / multiple hypothesis testing, I expect some suggestions. I will be grateful for you kind help. sincerely, Please do NOT reply to a digest when posting to the list, you should start a new thread (or at the very least delete the digest to which you are replying from your email). You may be interested False Discovery Rate (FDR) methods proposed by Benjamini Hochberg[1] and various related work/papers/software[2][3] Neil [1] Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Statist Soc B 57:289-300 [2] http://genomics.princeton.edu/storeylab/qvalue/ -- View this message in context: http://www.nabble.com/multiple-hypothesis-testing-tp22512331p22557450.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Fwd: Converting R to Sweave (Rnw)
Rainer M Krug-6 wrote: Hi I am thinking about using Sweave more frequently, especially for documenting code. But the syntax is slightly awkward for me (name= ... @), and I was thinking if there would be a way of importing the type of code extracted from an Rnw file back into an Rnw file? The advantage would be that the code could run in R without tangling. Obviously, sweave options could not be imported, but that would be fine for me. Below an example of the code generated by Rtangle, which I would like to import into a sweave file. Cheers Rainer ### ### chunk number 1: a ### x - 10 ### ### chunk number 2: ### asequence- seq(from=0,to=5,by=0.1) expnegx2 - exp(-asequence^2) plot(asequence,expnegx2,type=l,ylab=expression(exp(-z^2)),xlab=z) ### ### chunk number 3: Normal1 ### mu - 3 sigma - 5 This seems like trying to put the cart before the horse to my mind. A .Rnw is a hybrid of LaTeX and R code the later is delineated from the former by being encapsulated by the (name= ... @) tags which also define whether the results and/or images should be included in the LaTeX output. If you always want to use Sweave to document your code thats you're prerogative, but its really designed for writing a report with the R-code embedded, some of that code (reading in files etc.) is not relevant to the code so is suppressed, whilst others the output of the commands is required (and you duly write the tags around the R code to show the relevant output). If all you want to do is comment you're code, then I see nothing wrong or hard about using the '#' delimiter which comments out all text that follows its insertion in your .R file. Personally when I write Sweave documents I include comments in the R section of the files using this delimiter. Neil -- View this message in context: http://www.nabble.com/Fwd%3A-Converting-R-to-Sweave-%28Rnw%29-tp22288734p22289546.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] installing R on Ubuntu
znmeb wrote: On Mon, Feb 9, 2009 at 4:51 AM, Neil Shephard nsheph...@gmail.com wrote: There are pro's and con's to each of the GNU/Linux flavours and its really a matter of deciding which you like/have invested time in learning. Irrespective its still simple to install R from source under GNU/Linux... 1) Download source tar-ball 2) Extract and cd to the directory 3) ./configure --prefix=/where/you/want/R/to/go (optionally setting the install path at this stage) 4) ./make 5) ./make install ...all documented in the FAQ at http://cran.r-project.org/doc/FAQ/R-FAQ.html#How-can-R-be-installed-_0028Unix_0029 Many Linux distros do *not* install the development tools by default, and which ones live in which packages varies by distro. Fedora in particular is extremely stripped when you install from the LiveCD. You have to install gcc, make and a couple of other things just to install VMware Tools, for example, when running Fedora as a VMware guest. For building R from source and installing R packages, you'll also need to install gfortran. And many libraries with external dependencies, like Rgraphviz, will require not only the package itself (graphviz) but also the C headers, which may have the name graphviz-devel on some distros and some other name on other distros. What, a Linux distro that *doesn't* come with gcc!! I have to say I'm quite amazed at that!! gfortran is usually a component of gcc, no? I agree that ensuring libraries are available for all of the packages can be tricky, but its not insurmountable (although its one of the reasons I left Slackware in favour of Gentoo), but its no different to learning the vagaries of M$-windows. Its a common misconception I see frequently that computers/software should just work, and thats really not the case. They do what they are told to, and the person using them often needs to understand them in a bit of detail, and this detail is often occluded under Windows so when people try to make the transition from to GNU/Linux they are initially over-whelmed. Anyway, all OT. Neil -- View this message in context: http://www.nabble.com/installing-R-on-Ubuntu-tp10025949p21931845.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Best 64-bit Linux distro for R?
KMSL wrote: I'm running R on the current version of Gentoo and had no trouble building the complete system required. The only problem is that the current version in portage (stable) is 2.7.2. The latest _stable_ version (in terms of Gentoo's testing and release policy, NOT R's) is 2.7.2 as you note, but dev-lang/R-2.8.1 is already in portage (I usually request a version bump in Bugzilla when a new version of R or ESS is released). I have no problems running R-2.8.1 (although I am on ARCH=x86), and I have system-wide set ACCEPT_KEYWORDS=~x86 so I always get the unstable versions installed (and duly report back on bugs I encounter with R and other packages). If you don't want to go to testing on your system you can install the newer version of R by adding the relevant entry to /etc/portage/package.keywords... echo 'dev-lan/R' /etc/portage/package.keywords emerge -uDNa dev-lang/R Besides which its easy to bump the version in a local overlay yourself, but I shan't digress further, Neil -- View this message in context: http://www.nabble.com/Best-64-bit-Linux-distro-for-R--tp21904191p21911267.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] installing R on Ubuntu
The preceived difficulty of installing R under whatever flavour of GNU/Linux in this thread stems from being unfamiliar with the process of the package management of the flavour of GNU/Linux you use (and in part by the various distros not having the most recent version of R in their repositories People who say why can't it be as easy as dowloading a self-installing binary and running that are trying to fit a round peg (their experience and understanding of how applications install in M$-windows) in a square hole (or triangular, hexagonal, or whatever depending on the distribution of GNU/Linux). There are pro's and con's to each of the GNU/Linux flavours and its really a matter of deciding which you like/have invested time in learning. Irrespective its still simple to install R from source under GNU/Linux... 1) Download source tar-ball 2) Extract and cd to the directory 3) ./configure --prefix=/where/you/want/R/to/go (optionally setting the install path at this stage) 4) ./make 5) ./make install ...all documented in the FAQ at http://cran.r-project.org/doc/FAQ/R-FAQ.html#How-can-R-be-installed-_0028Unix_0029 This might not be as clean as using the native package management, but does mean that you'll have the latest version installed. Neil (Addendum - I've tried several different distros, starting with RedHat 7.3, then various versions of Slackware 8 through to 9 before settling on Gentoo, all were easy to install R in). -- View this message in context: http://www.nabble.com/installing-R-on-Ubuntu-tp10025949p21912206.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Problems in Recommending R
Adam D. I. Kramer-2 wrote: I respectfully disagree. In my repeated experience, I have seen colleagues in industry and university simply write R off as too difficult or not worth the effort based on purely cosmetic grounds, and then at my urging and after some instruction embrace R as being a fantastic piece of software. The reality of the situation is that before you read a book, you only have its cover to judge. Suggesting that people should read every book regardless of the cover does not make sense for people who have other things to do. I respectfully disagree with your disagreement :-) You don't just have the cover by which to judge a book you have reviews of the book too (unless of course its just been printed, but even then it quickly gets sent out to review which then appear in journals/papers/web-sites/etc.). As it is there are a lot of reviews which extol the virtues of R. If you're colleagues (or anyone else) ignores these in favour of the look of the web-site to determine whether they are to start trying out and using R then that is their loss. Adam D. I. Kramer-2 wrote: In the ecological context of open-source software, the cover or cosmetics of a software program, its documentation, and its support structure are actually quite correlated with overall ease of use, and if functionality is modeled as the factorial interaction of information produced with the amount of time it takes to produce the information, then functionality correlates with ease of use, and so the appearance of the webpage is not a triviality. Again I'd disagree, perhaps the most widely used suite of software has a very simple and clean web-site with few bells and whistles, ditto for one of the most popular text-editors. I am of course referring to the suite of GNU utilities (http://www.gnu.org/) that make a working GNU/Linux distribution and Emacs (http://www.gnu.org/software/emacs/ ). I like the R web-site, its clean and simple, present key information prominently (manuals, docs, CRAN, RNew and mailing lists). Neil -- View this message in context: http://www.nabble.com/Problems-in-Recommending-R-tp21783299p21808549.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Problems in Recommending R
Barry Rowlingson wrote: 2009/2/3 Neil Shephard nsheph...@gmail.com: Again I'd disagree, perhaps the most widely used suite of software has a very simple and clean web-site with few bells and whistles, ditto for one of the most popular text-editors. I am of course referring to the suite of GNU utilities (http://www.gnu.org/) that make a working GNU/Linux distribution and Emacs (http://www.gnu.org/software/emacs/ ). What?!? Surely the most widely-used suite of software is Microsoft Windows, and that has a full-on bells, whistles, activeX, silverlight-powered web site. My apologies I ommitted the 'open-source' caveat that Adam had written and I quoted in my response. Thus of all the _open-source_ software packages I have a strong suspicion that it is the GNU utilities that are the most widely used (since they are what makes up a funtional GNU/Linux installation, the Linux part simply refers to the code that forms the kernel and gets the hardware to communicate). Barry Rowlingson wrote: I'd say there was a direct relationship between website glossiness and amount of usage - more people use Notepad than Emacs. In which direction the causality (if any) works is an interesting question... Notepad doesn't have a web-site! (If your assertion is true it is the perfect vindication of the EU taking M$ to court over bundling IE with their OS ;-) Theres probably also a relationship between the glossiness of a website (or indeed software) and its quality/functionality. Usage is all well and good, but if you get the wrong answers out it doesn't matter how many people use it, they'll all be wrong! (viz. using Excel for statistics). Its a fine balance. Barry Rowlingson wrote: I like the R web-site, its clean and simple, present key information prominently (manuals, docs, CRAN, RNew and mailing lists). The open-source community should encourage contributions from beyond the world of the coder -- graphic designers, translators, writers and so on. Careful contributions from non-coders greatly enhance a project. Certainly style should not triumph over content but help to express the nature of the content. The R website still has a certain y2k feel about it, and although I'm sure we'd agree it would be wrong to make it all web 2.0 with rounded corners and a tag cloud, there's nothing wrong with refreshing a brand every five or six years. The issue of revamping the web-site arises regularly on this discussion list. A few people have said they're willing to help (in this thread and others in the past), but little has come to fruition. Refreshing branding can work two ways though, sometimes the identity and image that has been built up over time is lost. The developers of R have focused on what they are good at, which is developing R. I get the impression that they are willing to embrace graphic designers, translators, writers and so on (with some caveats on how it is to be managed as pointed out by Friedrich), but no one appears to have stepped up to the oche yet. Neil -- View this message in context: http://www.nabble.com/Problems-in-Recommending-R-tp21783299p21810523.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Problems in Recommending R
hadley wrote: The most useful thing (and quite rightly so) on the front page is the link the the FAQ which should be the starting point for anyone looking at any new software, and answers/explains everything thats pertinent! (At least thats what I read first when I start using new software and have questions). Again, have you ever read the FAQ? It is 133 pages! 133 pages (when printed?) that is divivded up into nice sections with sensible, navigable headings so that I can quickly find the relevant information From r-project.org - R FAQ - R Basics - How Can R be Installed - Choose your OS all in 10 seconds. People can only have their hands held for so long (and I'm not for one minute insinuating that you need your hand holding, its a more general comment as the information is out there, it just requires it to be read and understood). Neil -- View this message in context: http://www.nabble.com/Problems-in-Recommending-R-tp21783299p21813384.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Problems in Recommending R
Warren Young wrote: Yyeahhh...look how much that sort of stance has helped the cause of Linux on the desktop. World domination has been a year or two away for the last 10 years. (Speaking as one who uses Linux every day, and used it as his main desktop at home for many years before switching to OS X.) Linux on the desktop is more likely a goal of Ubuntu. The main aims of http://www.kernel.org/ is simply to support the hardware in an open manner. GNU was to develop a UNIX-like standards compliant operating system, not sure getting that onto the desktop of every computer was an aim. Anyway this is a tangent and mostly irrelevant. Warren Young wrote: I think that's the earlier poster's main point: this can be a one-click process. Why make the human tell the computer things it already knows? Because sometimes the human has a better idea as to what they want than the computer? Example - I've found it infuriating when I've wanted to download browser source code (as the distro I use compiles from source) for firefox and only been presented with pre-compiled binaries (if I'm browsing at home) or windows versions (if I'm at work), then wasting more time trying to find FTP mirrors where the most recent source tar-balls are available, and as I remember that took far longer than being able to choose what OS and version I wanted from a series of clearly written pages. Neil -- View this message in context: http://www.nabble.com/Problems-in-Recommending-R-tp21783299p21813695.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How do I get my IT department to bless R?
Daniel Viar wrote: I currently use R at work under the radar, but there's a chance I could loose that access. I'd like to get our company to feel comfortable with open source and R in particular. Does anyone have any experience with their company's IT department and management that they would be willing to share? How does one get an all Microsoft shop on board with allowing users to user R? I know about the recent NY Times article and recent news. I'm afraid I may need some case studies or examples of what other companies have done. Any help would be greatly appreciated. What alternative do they expect you to use? If they expect you to use Excel for statistics then its worth letting them know that this would be a very bad idea as there are many short-comings, some of which I've referenced at.. http://slack.ser.man.ac.uk/progs/stata/avoid_excel.html Neil -- View this message in context: http://www.nabble.com/How-do-I-get-my-IT-department-to-%22bless%22-R--tp21739359p21746356.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Does anyone has this paper in pdf?
Rolf Turner-3 wrote: Is this really a violation of copyright? If I have a copy of a journal I believe it is within the compass of ``fair practice'' (or some such jargon) to make a photocopy of a particular article and give this copy to a colleague or student for research purposes. Likewise I believe it is ``fair practice'' for me to send a copy of a pdf file (that I have legitimately acquired) to a colleague or student for research purposes. Yes I believe it would constitute a breach of copyright. I looked up the copyright information at the local University (see http://www.shef.ac.uk/library/services/copyrigh.html ) and I'd imagine its similar elsewhere. The particular point regarding copying is probably http://www.shef.ac.uk/library/services/copyrules.html and this sentence is the most pertinent... A key feature of the 1988 Act is that anyone wishing to make a single copy of a short extract from any book, journal or newspaper for the purposes of research for a non-commercial purpose or private study, is likely to be able to do so under the fair dealing provisions. Its slightly ambiguous but I'd imagine that its an individual who has to make the copy for themselves. If copying material for others were permissible then as Wacek points out the whole thing would break down as it could then go on ad nauseum. Note there is a link to issues dealing with teaching material, and I'd imagine colleagues at your institution are likely to have the same access rights, so technically its just as easy to send them a link to download a paper themselves. Rolf Turner-3 wrote: It always gets fussy and fiddly whenever legal issues arise. It would be nice if there were no such thing as ``intellectual property'' (which has always seemed to me to be an oymoron) and no such thing as lawyers. I agree access to all research should be open, particularly if its been funded by public bodies. A series of videos from BioMed Central on the issue of Open Acccess is at http://uk.youtube.com/view_play_list?p=49C6909B5770663A Neil -- View this message in context: http://www.nabble.com/Does-anyone-has-this-paper-in-pdf--tp21594321p21622193.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Does anyone has this paper in pdf?
aiminy wrote: de Jong, S. (1993) SIMPLS: an alternative approach to partial least squares regression. Chemometrics and Intelligent Laboratory Systems, 18, 251263 Yes, the publishers do, you can purchase it from http://dx.doi.org/10.1016/0169-7439(93)85002-X Its a shame that not all journals make their back-catalogue available free of charge, but I don't see why you expect people on this list to breach copyright for you? Neil -- View this message in context: http://www.nabble.com/Does-anyone-has-this-paper-in-pdf--tp21594321p21602580.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Perl-R bridge
ANJAN PURKAYASTHA wrote: Hi, I'm planning to access R from my perl scripts. The only noteworthy bridge seems to be Statistics-R-0.03http://search.cpan.org/%7Ectbrown/Statistics-R/lib/Statistics/R.pm. Would anyone like to share their experience with this Perl-R bridge? Irrespective of whether you are working on a Bioinformatics problem I'd imagine you can find some useful information in the recently published book Building Bioinformatics Solutions with Perl, R and MySQL. See http://www.oup.com/uk/catalogue/?ci=9780199230235 ANJAN PURKAYASTHA wrote: I'd like to install it in a Mac OS X. Suggestions on alternate solutions will be appreciated. In theory any solution involving R and Perl should be platform independant. -- View this message in context: http://www.nabble.com/Perl-R-bridge-tp21535807p21561731.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to create a chromosome location map by locus ID
Sake wrote: Hi, I'm trying to make a chromosomal map in R by using the locus. I have a list of genes and their locus, and I want to visualise that so you can see if there are multiple genes on a specific place on a chromosome. A example of what I more or less want is below: http://www.nabble.com/file/p21474206/untitled.JPG untitled.JPG The genes and locus are here: http://www.nabble.com/file/p21474206/genlocus.csv genlocus.csv I've tried some things, but nothing worked like I would like it to see. Maybe there is some kind of package that does this for you, but I did not find it yet. Thanx Sake Whats wrong with things like the HapMap Genome Browser that allows you to zoom in and out and to produce customised annotations of chromosomal regions at varying resolutions (see http://www.hapmap.org/)? Of course I'm assuming that you are looking at human chromosomes ;-) If not then perhaps the UCSC Genome Browser may be of use as it has a large number genomes you can browse (see http://genome.ucsc.edu/cgi-bin/hgGateway ). If you really want to do this in R You might get some mileage out of the lodplot package which can draw ideograms (which is what a schematic of a choromsome with bandings from different stainings is called), although the dataset available for it is again for human chromosomes (see http://cran.r-project.org/web/packages/lodplot/index.html ). Perhaps worth checking out the Genetics Task View too thats linked from CRAN. Neil -- View this message in context: http://www.nabble.com/How-to-create-a-chromosome-location-map-by-locus-ID-tp21474206p21497479.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] PDF slided (beamer or prosper) to an editable PPT
zubin-2 wrote: Hello, I am getting requests to place our PDF slides (output from beamer) into Microsoft Powerpoint formats (.ppt). What's the best practice or any recommended software packages (any success with open or commercial) that we can use to convert PDF slides into an EDITABLE powerpoint deck? Plenty of suggestions out there... http://www.google.co.uk/search?q=pdf+to+powerpoint+converter Never used any of them though, so I can't comment on which is the best or recommend one over the other. Personally though I don't see the need for them to be editable beyond someone wanting to plagirise the work. Neil -- View this message in context: http://www.nabble.com/PDF-slided-%28beamer-or-prosper%29-to-an-editable-PPT-tp21491357p21497540.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to draw a plot like this?
Jinsong Zhao wrote: Hi there, I hope to draw a plot like this: http://www.sg-chem.net/swizard/Ru-bqdi-spectra.gif is it possible to draw it using R? thanks for any suggestions. My intuition would say yes it is possible as R graphics are highly flexible. I'm afraid I don't know how though, but the following may be useful resources in working out the code... R Graphics Gallery (including sample code): http://addictedtor.free.fr/graphiques/ R Graphics by Paul Murrell (web-site to accompany book, which you have to buy) : http://www.stat.auckland.ac.nz/~paul/RGraphics/rgraphics.html Another R Graphics Gallery : http://research.stowers-institute.org/efg/R/ A number of links in the R wiki to graphics resources : http://wiki.r-project.org/rwiki/doku.php?id=links:links ...in particular the following site which contains ~8000 graph examples (again including example code) :http://bm2.genes.nig.ac.jp/RGM2/index.php Neil -- View this message in context: http://www.nabble.com/How-to-draw-a-plot-like-this--tp19486984p19489416.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Spider Graph
Van Patten, Isaac T wrote: Is there an R function to generate a radar or spider graph from a table - e.g.radar(table(x)) or some such? And you may find this a useful site to bookmark... http://addictedtor.free.fr/graphiques/ Neil -- View this message in context: http://www.nabble.com/Spider-Graph-tp19207029p19217333.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] help needed for HWE.exact in library genetics
You could follow the advice given when loading the library (see the code you posted for details) and use the enhanced genetics packages to cross-validate the results (ideally you should get the same answer). The results not weird though. Your working with SNPs and having a homozygote with a frequency of zero isn't that unlikely, it depends on the minor allele frequency (MAF). In this instance its the controls you appear to be concerned about, and for this locus the MAF of the minor allele is 0.0145, so in a sample of 173 individuals you would expect to see 0.0363 individuals with the recessive genotype (basic Mendelian genetics of 173 * 0.0145^2). Thus at best you might expect to see one person in a sample of that size, but its not surprising that you've not seen any. You may also find the following references of interest... Guangyong Zou, Allan Donner The Merits of Testing Hardy-Weinberg Equilibrium in the Analysis of Unmatched Case-Control Data: A Cautionary Note Annals of Human Genetics Volume 70, Issue 6, Pages 923-933 (basically advocates the use of a robust test for association such as the trend test over the two-stage design of testing for HWeqm and then testing for association). There is follow up discussion of the article in Yik Y. Teo, Andrew E. Fry, Taane G. Clark, E. S. Tai, Mark Seielstad On the Usage of HWE for Identifying Genotyping Errors Annals of Human Genetics Volume 71 Issue 5 , Pages 701 - 703 ...and a rejoinder from Zou and Donner... Guangyong Zou, Allan Donner The Reply of Zou Donner to Teo's Commentary on their Manuscript (p 704-704) Annals of Human Genetics Volume 71 Issue 5 , Pages 701 - 703 Neil Sun, Ying [BSD] - HGD wrote: library( genetics ) NOTE: THIS PACKAGE IS NOW OBSOLETE. The R-Genetics project has developed an set of enhanced genetics packages to replace 'genetics'. Please visit the project homepage at http://rgenetics.org for informtion. -- View this message in context: http://www.nabble.com/help-needed-for-HWE.exact-in-library-%22genetics%22-tp19100974p19105112.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Pros and Cons of R
I feel the discussion about ease of installation on Linux (/*NIX type systems) isn't really relevant to the Pros and Cons of R. The problems encountered by people are often a consequence of their lack of knowledge/understanding of the operating system, and not a deficiency of R itself. Just my tuppence, but I consider myself to be competent in using Linux so this view may be somewhat biased, Neil -- View this message in context: http://www.nabble.com/Pros-and-Cons-of-R-tp17407521p17510625.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Pros and Cons of R
Installation under Gentoo is straightforward too (emerge dev-lang/R). Updating has never really been a problem. CRAN packages are rebuilt if needed when updating R, and periodically all you need to do is fire up R and use update.packages() to update any packages you've installed. Another pro to consider is the cost, you can obtain R for free, SAS/S-Plus/Stata all have licenses of some sort that require purchasing. Neil -- View this message in context: http://www.nabble.com/Pros-and-Cons-of-R-tp17407521p17423145.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] scrime Package simulatedSNP function
Claire_6700 wrote: Hello, I need some help with the simulatedSNPs function from scrime package. I am trying to simulate some genotype of a case/control disease locus. The allele frequence are cases/controls Sample cases controls 2000 .5.10 1500 .6.40 In each of the row, i need to simulate 100 snp and calculate the pvalue ##Download Scrime Package### library(scrime) n.obs-1000 n.snp-100 vec.ia-1 simulateSNPs(n.obs, n.snp, vec.ia, prop.explain = 1, list.ia.val = NULL, vec.ia.num = NULL, maf = c(0.1, 0.12), prob.val = rep(1/3, 3), list.equal = NULL, prob.equal = 0.8, rm.redundancy = TRUE, shuffle = FALSE, shuffle.obs = FALSE, rand = NA) What is the right parameter. I am pretty new with R. wrong result. Interaction Cases Controls 1 SNP1 == 2 5000 any help will be appreciated. thanks Claire Check the help for the ?simulateSNPs() function. It provides clear examples of how to use it. In this instance you need to assign the results of running simulateSNPs to an object. So, in your above code you need to have... Start library(scrime) n.obs-1000 n.snp-100 vec.ia-1 ## Note the assignment in the below statement sim1- simulateSNPs(n.obs, n.snp, vec.ia, prop.explain = 1, \\ list.ia.val = NULL, vec.ia.num = NULL, maf = c(0.1, 0.12), \\ prob.val = rep(1/3, 3), list.equal = NULL, prob.equal = 0.8, \\ rm.redundancy = TRUE, shuffle = FALSE, shuffle.obs = FALSE, rand = NA) Finish You now have an object 'sim1' that contains the results of the simulation. To find out what these are you type... Start names(sim1) [1] datacl tab.explain ia maf Finish What you are seeing with out assigning the results from calling simulateSNPs() to an object is sim1$tab.explain To get the raw data from the simulations into its own object you can... Start sim1.data - sim1$data ## Print summary information on allele frequencies of simulated data sim1$maf [1] 0.1019921 0.1166833 0.1162599 0.1032456 0.1144771 0.1067833 0.1023612 [8] 0.1168232 0.1066618 0.1172988 0.1049692 0.1006477 0.1124793 0.1086271 [15] 0.1181598 0.1038002 0.1150600 0.1029935 0.1196051 0.1015223 0.1045593 [22] 0.1089789 0.1180688 0.1006122 0.1196565 0.1131580 0.1131264 0.1022888 [29] 0.1158212 0.1118635 0.1077083 0.1151471 0.1023238 0.1012435 0.1044028 [36] 0.1047839 0.1007996 0.1030058 0.1180583 0.1003964 0.1051847 0.1183929 [43] 0.1061727 0.1118420 0.1192968 0.1040632 0.1051112 0.1186949 0.1042196 [50] 0.1009020 0.1113263 0.1130648 0.1094135 0.1168967 0.1187118 0.1085089 [57] 0.1199226 0.1143786 0.1159529 0.1014398 0.1104690 0.1050063 0.1009227 [64] 0.1102197 0.1030258 0.1109929 0.1001394 0.1106730 0.1054413 0.1044738 [71] 0.1080446 0.1003916 0.1094400 0.1086378 0.1059338 0.1039598 0.1043444 [78] 0.1102694 0.1017065 0.1154185 0.1177336 0.1095213 0.1171060 0.1103163 [85] 0.1089563 0.1080247 0.1088396 0.1157875 0.1179325 0.1041557 0.1095087 [92] 0.1013651 0.1044949 0.1084277 0.1163425 0.1061450 0.1015519 0.1029643 [99] 0.1126980 0.1023006 Start Neil -- View this message in context: http://www.nabble.com/scrime-Package-simulatedSNP-function-tp17138820p17146486.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Importing data
Yemi Oyeyemi wrote: Hi everyone, please I'm having problem importing data from Stata and excel. Help me out. Thanks You don't provide... a) the code that you've tried b) the error message that relates to the problem you are having ...without these people have little information on what _exactly_ your problem is. Please read the R-help posting guide as advised in the signature of every mail that appears on the list. For clarity its... PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. In this instance you would also do well to read the R Data Import/Export manual at http://cran.r-project.org/doc/manuals/R-data.html and pay particular attention to section 3 titled Importing from other Statistical Systems (http://cran.r-project.org/doc/manuals/R-data.html#Importing-from-other-statistical-systems). This would lead you to the read.dta() and write.dta() functions for respectively reading and writing Stata formatted data sets. Neil -- View this message in context: http://www.nabble.com/Importing-data-tp17104951p17106184.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] genotypes simulation
Claire_6700 wrote: Hello, I am having really hard time finding a good article about simulating genotypes of cases and controls at a disease locus using R. if you guys can point me or guide me where i can find more information, it will be helpful. The popgen() package allows the simulation of genotype data under a coalescent model (via the treesim() function) or Multinomial-Drichlet model (via the simMD() function). These won't quite simulate case-control data, but can no doubt be tweaked to get two sets of data (cases and controls) with the desired allele frequencies, LD etc. There is also the rmetasim() package which interfaces R with metasim. Alternatively if your after validation of p-values derived from genotypic tests of association via simulation there is also the Direction Simulation Approach (DSA) which is implemented in R (http://www.mpipsykl.mpg.de/pages/english/research/mueller_downloads.htm). There is also an R plugin for plink (http://pngu.mgh.harvard.edu/~purcell/plink/) which performs simulation of unlinked loci that are in linkage equilibrium (although you may specifically want to model linkage disequilibrium). And there is an R-plugin for PBAT which is for Population Based Association Tests (http://people.fas.harvard.edu/~tjhoffm/pbatR.html). For other R-genetics information you may find the task-view at http://cran.r-project.org/web/views/Genetics.html useful as well as http://rgenetics.org/ There are also a host of other non-R options available though. Many under the coalescent model (including one of the first by Richard Hudson, the ms program) are linked from http://en.wikipedia.org/wiki/Coalescent_theory#Software and additional software for genetic analysis (including simulation in some instances) at http://linkage.rockefeller.edu/soft/ . The vast majority will simply dump output to text files, so its straight-forward to call them from within R via a system call and then read the results into R. Neil -- View this message in context: http://www.nabble.com/genotypes-simulation-tp17065607p17066332.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] problem in installing R packages on linux
man4ish wrote: No i am trying to install BART which is valid name , i have 30-40 times for other packages still facing the same pblm .How can i rectify this.Please help me out. Rather than sending a screenshot of a terminal (and note the posting guidelines with regards to attachments), if you copy and paste the text that shows the commands you are typing and the errors you are getting it will be more informative to those who you are seeking help from. Otherwise its people are just left to guess what the cause is. Neil -- View this message in context: http://www.nabble.com/problem-in-installing-R--packages-on-linux-tp16760370p16763346.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Graphic text
Hi Maura, I'm afraid that your message below only came to me, and wasn't copied to R-help. I'm useless at graphics in R, but I'd recommend posting exactly what R-code that your writing, this will show what plotting commands your using and the syntax, and will allow others to provide insightful comments, otherwise they're just guessing at what your already doing. A very vague guess that I can offer would be that the argument to main or sub could be split over multiple lines by writing it like this... main=c(This is the first line, and this is the second line) ...but as I say, I'm not great with graphics, and don't know what function/commands your using. For your convenience I've CC'd this to R-help so that if you hit Reply to all then your message with your examples will go to the list too. Neil On Fri, Feb 29, 2008 at 1:44 PM, Maura E Monville [EMAIL PROTECTED] wrote: MY OS is Linux/SuSE 10.3 R version is 2.6.1 The pop-up message is my goal. So far it only appears in the text terminal window where I started R. I would like to show the quantitative results of my calculations superimposed to a 2x2 graphic layout.. This is a textual data spread on a number of lines that cannot be placed in the MAIN or SUB text fields of any of the 4 plots. I do not know how to split the MAIN or the SUB text onto two or more lines. Anyway, both MAIN and SUB text fields are designed to accommodate short text data ... I guess. Thank you so much, Maura E.M. On Fri, Feb 29, 2008 at 3:00 AM, [EMAIL PROTECTED] wrote: Maura E Monville wrote: Can R handle graphic text ? I mean something like a pop-up message window or a text widget ? A little more context would probably be useful. * What OS are you using? * What version of R are you using? * Where is the pop-up message coming from? * What does the pop-up message signify and how do you want it to be handled? Might be worth reading the posting guide and re-posting your question (see the signature in all posts from R-help for the posting guide URL). R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. Quoted from: http://www.nabble.com/Graphic-text-tp15754012p15754012.html -- Maura E.M -- Email - [EMAIL PROTECTED] / [EMAIL PROTECTED] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Graphic text
Hi Maura, Compound quotes can become an absolute nightmare (in any language). R already has Tcl/TK packages, check out the following from CRAN... ade4TKGUI gWidgetstcltk plotAndPlayGTK * RGtk2 * possibly what your after? Also you might find some of the packages listed at the Graphics Task View of use (http://cran.r-project.org/web/views/Graphics.html), perhaps something under the Dynamic Graphics section? Personally if I wanted fancy graphics for a presentation I'd go down the line of LaTeX to produce nice PDF's which can have nice grahpics and pop up's. LaTeX is well supported in R via the Sweave suite and various other packages such as xtable() and the latex functions in Hmisc() and many other packages. Sorry I've not provided any direct solution, Neil On Fri, Feb 29, 2008 at 5:23 PM, Maura E Monville [EMAIL PROTECTED] wrote: I will try. It looks like the new-line sequence is to be enclosed in single quotes '' because the whole text is inside double quotes . Still it would be nice to have the possibility to pop up a text widget. I know R is a serious statistical tool. But when you have to present your project then pretty pictures,widgets, and gadgets capture the attention of the audience. Maybe R can be interfaced with GL and/or Tcl/Tk. Thanks, Maura On Fri, Feb 29, 2008 at 10:43 AM, Neil Shephard [EMAIL PROTECTED] wrote: Hi Maura, I was for sent this instead of it being sent to the list or yourself. Neil -- Forwarded message -- From: Horan, Brian [EMAIL PROTECTED] Date: Fri, Feb 29, 2008 at 4:30 PM Subject: RE: [R] Graphic text To: Neil Shephard [EMAIL PROTECTED] Putting a newline, '\n' works in your main/sub text string works for me on both *NIX and Windows... -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Neil Shephard Sent: Friday, February 29, 2008 9:50 AM To: Maura E Monville Cc: r-help Subject: Re: [R] Graphic text Hi Maura, I'm afraid that your message below only came to me, and wasn't copied to R-help. I'm useless at graphics in R, but I'd recommend posting exactly what R-code that your writing, this will show what plotting commands your using and the syntax, and will allow others to provide insightful comments, otherwise they're just guessing at what your already doing. A very vague guess that I can offer would be that the argument to main or sub could be split over multiple lines by writing it like this... main=c(This is the first line, and this is the second line) but as I say, I'm not great with graphics, and don't know what function/commands your using. For your convenience I've CC'd this to R-help so that if you hit Reply to all then your message with your examples will go to the list too. Neil On Fri, Feb 29, 2008 at 1:44 PM, Maura E Monville [EMAIL PROTECTED] wrote: MY OS is Linux/SuSE 10.3 R version is 2.6.1 The pop-up message is my goal. So far it only appears in the text terminal window where I started R. I would like to show the quantitative results of my calculations superimposed to a 2x2 graphic layout.. This is a textual data spread on a number of lines that cannot be placed in the MAIN or SUB text fields of any of the 4 plots. I do not know how to split the MAIN or the SUB text onto two or more lines. Anyway, both MAIN and SUB text fields are designed to accommodate short text data ... I guess. Thank you so much, Maura E.M. On Fri, Feb 29, 2008 at 3:00 AM, [EMAIL PROTECTED] wrote: Maura E Monville wrote: Can R handle graphic text ? I mean something like a pop-up message window or a text widget ? A little more context would probably be useful. * What OS are you using? * What version of R are you using? * Where is the pop-up message coming from? * What does the pop-up message signify and how do you want it to be handled? Might be worth reading the posting guide and re-posting your question (see the signature in all posts from R-help for the posting guide URL). R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. Quoted from: http://www.nabble.com/Graphic-text-tp15754012p15754012.html -- Maura E.M -- Email - [EMAIL PROTECTED] / [EMAIL
[R] Errors melt()ing data...
Hi,
I'm trying to melt() some data for subsequent cast()ing and am
encoutering errors.
The overall process requires a couple of casts()s and melt()s.
Start Session 1##
## I have the data in a (fully) melted format and can cast it fine...
norm1[1:10,]
Pool SNP Sample.Name variable value
1 1 rs1045485 CA0092 Height.1 0.003488853
2 1 rs1045485 CA0142 Height.2 0.333274200
3 1 rs1045485 CO0007 Height.2 0.396250961
4 1 rs1045485 CA0047 Height.2 0.535686831
5 1 rs1045485 CO0149 Height.2 0.296611673
6 1 rs1045485 CA0106 Height.2 0.786115546
7 1 rs1045485 CO0191 Height.1 0.669268523
8 1 rs1045485 CA0097 Height.2 0.609603217
9 1 rs1045485 CA0076 Height.1 0.004257584
101 rs1045485 CO0017 Height.2 0.589261427
## This gets the data
t.norm1- cast(norm1, Sample.Name + SNP + Pool ~ variable, sum)
t.norm1[1:10,]
Sample.NameSNP PoolHeight.1 Height.2
1 CA0001 rs10454851 0.003311454 0.4789782
2 CA0001 rs10454871 0.001818583 0.5089827
3 CA0001 rs112125701 0.006078444 0.4496129
4 CA0001 rs130106271 0.008753049 0.5424499
5 CA0001rs131131 0.186821486 0.2294912
6 CA0001 rs134026161 0.012030235 0.4161610
7 CA0001 rs1705481 0.002425579 0.3111907
8 CA0001 rs175039081 0.002179705 0.3063292
9 CA0001 rs17997941 0.003632984 0.5049848
10 CA0001 rs17997961 0.389774160 0.000
## I now melt it and cast again to the desired format
t - melt(t.norm1, id = c(Sample.Name, SNP))
cast.height.norm1 - cast(t, SNP ~ Sample.Name + variable, sum)
cast.height.norm1[1:10,1:5]
SNP CA0001_Height.1 CA0001_Height.2 CA0002_Height.1 CA0002_Height.2
1 rs1045485 0.003311454 0.4789782 0.401218142 0.343031163
2 rs1045487 0.001818583 0.5089827 0.007329439 0.453102612
3 rs11212570 0.006078444 0.4496129 0.015164118 0.434320814
4 rs13010627 0.008753049 0.5424499 0.013440474 0.463863778
5 rs13113 0.186821486 0.2294912 0.224865477 0.272916077
6 rs13402616 0.012030235 0.4161610 0.191099755 0.285744704
7rs170548 0.002425579 0.3111907 0.365986770 0.240187431
8 rs17503908 0.002179705 0.3063292 0.011100347 0.232259627
9 rs1799794 0.003632984 0.5049848 0.430635350 0.008364312
10 rs1799796 0.389774160 0.000 0.173564141 0.235928006
Finish Session 1##
This is the format that I'm aiming for and everythings worked fine.
However, I wish to derive two transformed variables (polar.1 and
polar.2) based on each row of t.norm1 and then melt() and cast() the
data into the same desired format.
Start Session 2##
## Now generate polar co-ordinates
t.norm1$polar.1 - log10(sqrt(t.norm1$Height.1^2 + t.norm1$Height.2^2))
t.norm1$polar.2 - atan((t.norm1$Height.2 / t.norm1$Height.1))
## And cast the polar data
t - melt(subset(t.norm1, select= c(Sample.Name, SNP, Pool, polar.1,
polar.2)), id=c(Sample.Name, SNP))
Error in if (!missing(id.var) !(id.var %in% varnames)) { :
missing value where TRUE/FALSE needed
traceback()
4: melt_check(data, id.var, measure.var)
3: melt.data.frame(as.data.frame(data), id = attr(data, idvars))
2: melt.cast_df(subset(t.norm1, select = c(Sample.Name, SNP,
Pool, polar.1, polar.2)), id = c(Sample.Name, SNP),
measure = c(polar.1, polar.2))
1: melt(subset(t.norm1, select = c(Sample.Name, SNP, Pool,
polar.1, polar.2)), id = c(Sample.Name, SNP), measure =
c(polar.1,
polar.2))
Finish Session 2##
As far as I can tell the error is occurring within melt_check() where
there is a check to see if the id.var is missing and whether the
id.var exists within the data frames names, both of which are true
since the subset() call works fine on its own...
Start Session 3##
test - subset(t.norm1, select= c(Sample.Name, SNP, Pool, polar.1,
polar.2))
names(test)
[1] Sample.Name SNP Poolpolar.1 polar.2
Start Session 3##
What I find particularly strange is that there isn't really any
difference between
Session 1
t - melt(t.norm1, id = c(Sample.Name, SNP))
and
Session 2
t - melt(subset(t.norm1, select= c(Sample.Name, SNP, Pool,
polar.1, polar.2)), id=c(Sample.Name, SNP))
..since I've done nothing to alter the Sample.Name and SNP
columns, all thats changing is the names of the two columns that are
the measure.var which in this instance is everything thats not defined
as being and id.var in the call to melt().
If anyone can provide any insight to what I'm doing wrong I'd be very grateful.
Thanks,
Neil
--
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Re: [R] Errors melt()ing data...
Hi Hadley, On Thu, Feb 28, 2008 at 1:15 PM, hadley wickham [EMAIL PROTECTED] wrote: I think the problem is that reshape adds some extra information to the cast data.frame, but this info is no longer relevant when you've removed some of the columns. Try as.data.frame to strip off this extra info. t - melt(subset(as.data.frame(t.norm1), select= c(Sample.Name, SNP, Pool, polar.1, polar.2)), id=c(Sample.Name, SNP)) Thats done the trick, thank you very much. (Also, can't you get to cast.height.norm1 directly from norm1 ? cast.height.norm1 - cast(norm1, SNP ~ Sample.Name + variable, sum) Yep, you can, but I need t.norm1 as an intermediate for deriving polar.1 and polar.2 for each Sample.Name and SNP, although I wouldn't be surprised if this can be done at the same time, as your reshape() package is exceptionally flexible (and as you can probably tell, I'm still climbing the R learning curve!). In fact I think I shall sit down and work out how to do this! Thanks for your help (again), Neil -- Email - [EMAIL PROTECTED] / [EMAIL PROTECTED] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Logical statements and subseting data...
Hi, I'm scratching my head as to why I can't use the subset() command to remove one line of data from a data frame. There is just one row (out of 45840) that I'd like to remove and it can be identified using dim(raw.all.clean) [1] 4584010 subset(raw.all.clean, Height.1 == 0 Height.2 == 0) Sample.Name Well SNP Allele.1 Allele.2 Size.1 Size.2 Height.1 47068 CA0153 O02 rs2106776 NA NA0 Height.2 Pool 4706803 (Note that the row index of 47068 which is higher than the rows reported by dim() is simply because I have already removed a number of rows). So I want to remove this one instance where Height.1 == 0 Height.2 == 0. I'd have thought that a logical expression where Height.1 != 0 Height.2 != 0 would have achieved this, but it doesn't seem to correctly drop out this one observation, instead its dropping out far more observations... t - subset(raw.all.clean, Height.1 != 0 Height.2 != 0) dim(t) [1] 3815010 Thus 7690 rows have been removed. It seems to be that the '' operator is being interparated as an 'OR' (|) since... dim(subset(raw.all.clean, Height.1 != 0)) [1] 4215210 dim(subset(raw.all.clean, Height.2 != 0)) [1] 4183710 ...and... dim(raw.all.clean) - dim(subset(raw.all.clean, Height.1 != 0)) [1] 36880 dim(raw.all.clean) - dim(subset(raw.all.clean, Height.2 != 0)) [1] 40030 3688 + 4003 [1] 7691 (This is one more than the number of rows being removed, but given that there is one sample where both Height.1 and Height.2 are '0' thats fine). I thought I understood how logical expressions are constructed, and have gone back and read the entries on precedence, but can't work out why the above is happening? Whats particularly perplexing (to me) is that the test for exact equality works, but not for inequality? I feel like I'm missing something blatantly obvious, but can't work out what it is. Cheers, Neil -- Email - [EMAIL PROTECTED] / [EMAIL PROTECTED] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Logical statements and subseting data...
Thanks Thierry, they do both leave me with what I expected. On Mon, Feb 25, 2008 at 2:28 PM, ONKELINX, Thierry [EMAIL PROTECTED] wrote: The negation of Height.1 == 0 Height.2 == 0 was incorrect. Use subset(raw.all.clean, !(Height.1 == 0 Height.2 == 0)) I can see clearly how this expression works (negating the whole test), but... or subset(raw.all.clean, Height.1 != 0 | Height.2 != 0) ...not how this works, since the above to me is saying Height.1 is NOT zero OR Height.2 is NOT zero, which to my mind would pick out samples where either one or the other is not equal to zero (and of course those instances where both are equal to zero)? It seems to me that (AND) and | (OR) are used the wrong way round in this case, since the intersection of the two tests for inequality is what is required? Neil -- Email - [EMAIL PROTECTED] / [EMAIL PROTECTED] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] CRAN Taskviews returns 404
On Feb 18, 2008 2:02 PM, Peter Dalgaard [EMAIL PROTECTED] wrote: But what gave you the idea that http://cran.r-project.org/web/packages/Views/ should work? Google seems not to know it. Its the target for the link to the TaskViews from http://cran.r-project.org/web/packages/index.html (which was reached itself by following the packages link at http://cran.r-project.org/). Google does know about http://cran.r-project.org/src/contrib/Views/ but that simply redirects to the current location. Its a tangled web out there! Neil __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Using R in a university course: dealing with proposal comments
Neil Shephard wrote: (Most) of this problem isn't negated when using R. Start a new job and use the (excellent, extensible, and free) software that you've been using for years. Apologies for the double negative, that should have read (Most) of this problem _is_ negated when using R. Neil -- View this message in context: http://www.nabble.com/Using-R-in-a-university-course%3A-dealing-with-proposal-comments-tp15405138p15416301.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Using R in a university course: dealing with proposal comments
Arin Basu-3 wrote: Comment 2: Finally, on a minor point, why is R the statistical software being used? SPSS is probably more widely available in the workplace – certainly in areas of social policy etc. (Prof NB) What struck me in the above is the probably. How probable is it, anything to substantiate the claim? Anyway, whether one package is more widely available in the workplace than another is somewhat of a moot point. If a student learns how to use one software package then they start to get pigeon-holed into using that particular software package. Many jobs are advertised with SPSS/SAS/Stata/S-Plus (add/subtract at will) skills/knowledge required (or at least desirable). The prospective job applicant may think Well I don't know how to use that so I shan't bother applying or they may be unwilling to re-learn how to use a new stats package after months/years of investment in learning how to use another package, alternatively they may well just loose out to someone who already has the experience/skills. (Most) of this problem isn't negated when using R. Start a new job and use the (excellent, extensible, and free) software that you've been using for years. I'd stick with using R to teach your statistics, in the long-run any of them who continue to perform statistical analysis will be grateful. Neil -- View this message in context: http://www.nabble.com/Using-R-in-a-university-course%3A-dealing-with-proposal-comments-tp15405138p15413122.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] kinship package: drawing pedigree error
You can also draw pedigrees using the pedtodot() function from the gap package. It does however depend on graphviz (http://www.graphviz.org). An article on drawing pedigrees in R is available in Bioinformatics 22(8):1013-1014 (see http://forums.gentoo.org/viewtopic-t-641204) There _may_ also be some pedigree drawing functionality in the GeneticsPed package thats part of the RGenetics project (see http://rgenetics.org/) although at present there are a few unresolved problems with the package and only the SVN version is available. Neil Iris Kolder wrote: Hi Im using the kinship package to draw a pedigree. On my data set this works fine but when i add indivudals to the pedigree i keep getting an error i hope someone can help me! This is the code im using: Data-read.table(Tree.txt, header=T, sep=,) attach(Data) ped-pedigree(id, dadid, momid, sex, aff) par(xpd=T) plot.pedigree(ped) -- View this message in context: http://www.nabble.com/kinship-package%3A-drawing-pedigree-error-tp15314771p15352813.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Problems reshaping data with cast()
Hi, I'm trying to cast() some data, but keep on getting the following error... norm.all.melted.height - transform(all.melted.height, + norm.height = value / ave(value, SNP, Pool, FUN = max) + ) Warning messages: 1: In FUN(X[[147L]], ...) : no non-missing arguments to max; returning -Inf 2: In FUN(X[[147L]], ...) : no non-missing arguments to max; returning -Inf 3: In FUN(X[[147L]], ...) : no non-missing arguments to max; returning -Inf norm.all.melted.height - subset(norm.all.melted.height, select=c(Sample.Name, SNP, Pool, variable, norm.height)) names(norm.all.melted.height) - c(Sample.Name, SNP, Pool, variable, value) ## Now reshape the data normalised - cast(norm.all.melted.height, Sample.Name + SNP + Pool ~ value, sum) Error in rep.int(rep.int(seq_len(nx), rep.int(rep.fac, nx)), orep) : negative length vectors are not allowed Is the error thats occuring with cast() likely to be caused by the previous warnings? As far as I can work out rep.int() is called to expand the data based on the grouping specified (in this case the left hand portion of the cast formula, i.e. Sample.Name + SNP + Pool), but how would there be a negative index in this data? I had previously melted the data into this format. Apologies for not providing a reproducible example, I suspect the problem lies within the data structure I'm using. Thanks for reading this question, Neil -- Email - [EMAIL PROTECTED] / [EMAIL PROTECTED] Photos - http://www.flickr.com/photos/slackline/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Problems reshaping data with cast()
On Feb 7, 2008 2:21 PM, hadley wickham [EMAIL PROTECTED] wrote: Hi Neil, I think your cast statement is wrong. You have cast(norm.all.melted.height, Sample.Name + SNP + Pool ~ value, sum) but I think you want cast(norm.all.melted.height, Sample.Name + SNP + Pool ~ ., sum) i.e. value never appears in the cast formula. Hi Hadley, Your right, my formula was wrong. I should have had 'variable' in place of 'value'. cast(norm.all.melted.height, Sample.Name + SNP + Pool ~ variable, sum) Thanks for the help, and apologies for the dumb mistake (I even have your paper from Journal of Statistical Software sat on my desk and still managed to miss the glaringly obvious). Everyone is entitled to be stupid, but some abuse the privilege. - Unknown I guess I've been abusing my privilege a bit today. Neil -- Email - [EMAIL PROTECTED] / [EMAIL PROTECTED] Photos - http://www.flickr.com/photos/slackline/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to search for packages - wrap up!
Charilaos Skiadas-3 wrote: On Feb 5, 2008, at 10:37 AM, Monica Pisica wrote: But perhaps I am missing something very obvious? I thought the task views were located where they are (linked from the page that lists packages) as they summarise the available packages for the given topic. Neil -- View this message in context: http://www.nabble.com/Re%3A-How-to-search-for-packages---wrap-up%21-tp15297545p15306481.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to search for packages - wrap up!
I'm not sure that this would make any difference to someone considering using R. Would they know what CRAN stands for? Probably not unless they've used CPAN or equivalent in the past. Would they know what a 'Task View' is? Again probably not as its not patently obvious what it is, it doesn't click (at least not to my mind if I take a step back from already knowing what a Task View is). I think the current set up with mirrors is fine, it only takes a few seconds to click on a mirror and find that it takes you to a page that isn't simply for downloading software. Discussions of how the R web-site can be improved/altered seem to crop up periodically on the list. At the end of the day someone (who?) has to make the changes to the site. R developers already sacrifice their own time to improving the software. If you want to see changes, then volunteer to (I presume) the R-core team and enter into dialogue with them. Neil On Feb 6, 2008 12:02 PM, Charilaos Skiadas [EMAIL PROTECTED] wrote: On Feb 6, 2008, at 6:23 AM, Neil Shephard wrote: Charilaos Skiadas-3 wrote: On Feb 5, 2008, at 10:37 AM, Monica Pisica wrote: But perhaps I am missing something very obvious? I thought the task views were located where they are (linked from the page that lists packages) as they summarise the available packages for the given topic. That would make sense, and brings up the other point, that the package directory is nontrivial to find as well. I'm thinking here of someone who has not used R yet, but is considering it. One approach those people would take, it seems to me, is to go to the main page and look around at the links to see if there is any information that would help them decide if R is right for what they want it. They have not heard of packages, and have no idea that a lot of the functionality is in the packages. So they would look on the list on the left looking for something that clicks, and none of the items there would. If they eventually decide to click on the CRAN link, they are now faced with a long list of mirrors, and no further explanation of what is behind that. If they have seen mirror systems elsewhere, they would immediately come to the conclusion that this page will simply lead to downloading the software, and dismiss it as not useful. Just reading Gavin's reply, and he makes a good point about the difficulties related to the CRAN master. But couldn't we simply have the links to packages from the task views send someone through the mirror list? I would imagine something like that should be doable. Or we could simply have the Task Views link on the main page send you to a mirrors list, with perhaps a one-line explanation on the top of why this part is necessary. But at least at that point the user has selected Task Views and is more certain that they are on the right track. Even better, this step could be even one step deeper, after the user has selected which task view they want to see. Neil Haris Skiadas Department of Mathematics and Computer Science Hanover College -- Do you really need to send me the email I just sent to you? - Me Email - [EMAIL PROTECTED] / [EMAIL PROTECTED] Website - http://slack.ser.man.ac.uk/ Photos - http://www.flickr.com/photos/slackline/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] I need arguments pro-S-PLUS and against SAS...
You might find this article useful Kellie B. Keeling and Robert J. Pavur, A comparative study of the reliability of nine statistical software packages, Computational Statistics Data Analysis, Volume 51, Issue 8, 1 May 2007, Pages 3811-3831. (http://www.sciencedirect.com/science/article/B6V8V-4JHMGWJ-1/2/77a29a95c2071997f13fcca7267711d1) Alberto Monteiro wrote: I need arguments pro-S-PLUS and against SAS for a meeting I will have next week. S-Plus is (90 - 99)% compatible with R, so using S-Plus will make things much easier for everyone. But I can't use this argument. What other arguments could I use? Alberto Monteiro __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- View this message in context: http://www.nabble.com/I-need-arguments-pro-S-PLUS-and-against-SAS...-tp14621011p14713230.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] editor under MAC system
YIHSU CHEN-3 wrote: Dear R-user; I recently switched from PC to MAC. Is there a compatible editor as Win-editor with package RWinEdit for MAC? I'd recommend using Emacs with ESS (see http://ess.r-project.org/). The advantage of this (beyond the seamless integration) is that its pretty platform neutral, and what you learn on your new Mac system will be portable (i.e. the same method of writing/interacting with your R script/session whether your on Mac/M$-windows/*NIX variant). Neil -- View this message in context: http://www.nabble.com/editor-under-MAC-system-tp14249571p14272456.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Package specific dependencies...
On Nov 22, 2007 4:14 PM, Gabor Grothendieck [EMAIL PROTECTED] wrote: The SystemRequirements field on the DESCRIPTION file is used to document the system requirements. For example, the DESCRIPTION file for Ryacas (which requires yacas) is shown below. Package: Ryacas Version: 0.2-8 Date: 2007-08-22 Title: R interface to the yacas computer algebra system Author: Rob Goedman [EMAIL PROTECTED], Gabor Grothendieck [EMAIL PROTECTED], Søren Højsgaard [EMAIL PROTECTED], Ayal Pinkus [EMAIL PROTECTED] Maintainer: G Grothendieck [EMAIL PROTECTED] Encoding: latin1 Description: An interface to the yacas computer algebra system. Depends: R (= 2.5.1), XML SystemRequirements: yacas (= 1.0.63) # instructions on home page License: GPL URL: http://ryacas.googlecode.com Thats very useful to know and something that I wasn't aware of. But (in my mind) there is a subtle difference between installing packages that require specific libraries and those that require a specific piece of software. Taking the Ryacas package as an example, anyone installing that would automatically know that its required, and in all likelihood would probably have it installed on their system already and have been using it but then decided they want to interface with it from R. This isn't necessarily the case with libraries, you wouldn't know that a dependency is required until you come to try and install the package and get error messages that something is missing. There is also the rather striking difference (taking the two packages that have been discussed) in that Ryacas will install on a system that doesn't have the SystemRequirement met (i.e. without yacas installed) whereas GDD won't install unless the system has the SystemRequirement (libgd) is installed, and it is this problem that I am trying to help address. I do realise that in either instance a user could find this out in advance of installing any package by simply reading the DESCRIPTION file. I suspect that the ultimate answer to the question that I'm asking (i.e. how can dependencies for CRAN packages be pulled in *automatically* when installing them) will simply be that its down to the user/sysadmin to sort this out. Neil -- Don't remember what you can infer. - Harry Tennant Email - [EMAIL PROTECTED] / [EMAIL PROTECTED] Website - http://slack.ser.man.ac.uk/ Photos - http://www.flickr.com/photos/slackline/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Package specific dependencies...
Hi, I noticed recently when installing the GDD package for R under GNU/Linux that it required the gd library (http://libgd.org/) for generating graphics. The resolution of this was to simply install the library on my system, and then GDD successfully installed without any complaints. However, the variant of GNU/Linux that I use is Gentoo, so I filed a bug requesting that a USE flag be set for the R ebuild so that users could automatically pull in the library when installing R simply by setting a flag for the package (Gentoo's package management system Portage allows specific packages to have USE flags for setting a packages ./configure flags and pulling in package dependencies and so forth, this isn't particularly relevant to the question, but more info can be found at http://www.gentoo.org/doc/en/handbook/handbook-x86.xml?part=3). A recent revision of the ebuild for R removed this flag as there was no direct requirement of the gd library by R. Anyway, after a few short discussions with one of the Gentoo maintainers for R I was asked various questions about how this should be dealt with, and being unable to answer everything I am asking the wider R community for assistance and advice. The main aim is to improve the way in which Gentoo handles the various packages that are available for R, and improve on the way in which dependencies such as the above are handle when compiling R. Q.1 How many packages on CRAN have package specific dependencies? Only using a subset of the R packages I'm only aware of the GDD dependency on libgd. Are there others out there? Q.2. Is R capable of tracking dependencies of packages on CRAN? To my knowledge it isn't, as (to the best of memory, it was about six months ago now) I simply received a non-zero exit when trying to install GDD when I didn't have libgd installed. R had no way of saying Hang on this package needs this library, lets install it and I wouldn't expect R to as it would make it particularly problematic if a user has installed locally or doesn't have the correct permissions etc. But would it be appropriate for R to have a configure option to check for a dependency required by various packages? I do realise that this is putting the cart before the horse. Perhaps 'stricter' management of package inclusion would help so that all dependencies of a submitted package are passed onto R developers and appropriate configure flags can be added (although again this still leaves the horse behind the cart). Q.3. Does anyone have experience of dealing with this on other distributions? How does Debian/Slackware/Fedora etc. deal with problems like this? Particularly given that these are often pre-compiled (under Gentoo everything is compiled from source), does this mean that package maintainers of R for these various distros are aware of the dependencies of all packages and include the relevant libraries when compiling? The Gentoo R maintainer is going to look at alternatives for managing CRAN packages (one possible option is http://paludis.pioto.org/ which has some CRAN support already). Something similar has been done for Perl/CPAN (see http://www.gentoo.org/proj/en/perl/g-cpan.xml) and this may be an option for CRAN. Any and all comments and thoughts are more than welcome. Regards Neil -- Don't remember what you can infer. - Harry Tennant Email - [EMAIL PROTECTED] / [EMAIL PROTECTED] Website - http://slack.ser.man.ac.uk/ Photos - http://www.flickr.com/photos/slackline/ -- Don't remember what you can infer. - Harry Tennant Email - [EMAIL PROTECTED] / [EMAIL PROTECTED] Website - http://slack.ser.man.ac.uk/ Photos - http://www.flickr.com/photos/slackline/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
