[Rd] Problem running checks after building R-patched

2014-05-07 Thread Berend Hasselman
I am compiling the latest R-patched (Revision: 65533) Ubuntu Lucid (10.04). Building succeeds but make check stops with an error. The output in the terminal from make check: Testing examples for package ‘base’ Testing examples for package ‘tools’ Error: testing 'tools' failed Execution halted m

Re: [Rd] Problem running checks after building R-patched

2014-05-07 Thread Martin Maechler
> Berend Hasselman > on Wed, 7 May 2014 09:24:46 +0200 writes: > I am compiling the latest R-patched (Revision: 65533) Ubuntu Lucid (10.04). > Building succeeds but make check stops with an error. > The output in the terminal from make check: > Testing examples for

Re: [Rd] Problem running checks after building R-patched

2014-05-07 Thread Berend Hasselman
On 07-05-2014, at 11:23, Martin Maechler wrote: >> Berend Hasselman >>on Wed, 7 May 2014 09:24:46 +0200 writes: > >> I am compiling the latest R-patched (Revision: 65533) Ubuntu Lucid (10.04). > >> Building succeeds but make check stops with an error. >> The output in the terminal

Re: [Rd] precedence (was 'historical NA question')

2014-05-07 Thread Therneau, Terry M., Ph.D.
Hadley asked about the Blue book; my shelf still has the earlier brown book Becker and Chambers, 1984, S: An interactive environment for data analysis and graphics. The manual page for precedence is $ component select %x special operator - unary minus

[Rd] historical significance of Pr(>Chisq) < 2.2e-16

2014-05-07 Thread Michael Friendly
Where does the value 2.2e-16 come from in p-values for chisq tests such as those reported below? > Anova(cm.mod2) Analysis of Deviance Table (Type II tests) Response: Freq LR Chisq Df Pr(>Chisq) B 11026.2 1 < 2.2e-16 *** W 7037.5 1 < 2.2e-16 *** Age 886.6 8 < 2.2e-16 *** B:W 3025.2 1 < 2.2e-16

Re: [Rd] historical significance of Pr(>Chisq) < 2.2e-16

2014-05-07 Thread John Nolan
Presumably from > .Machine$double.eps [1] 2.220446e-16 Whether this means the tail probability is actually that small, or that the routine that computes it can't get any more accuracy than that, you'll have to dig deeper. John .. John

Re: [Rd] historical significance of Pr(>Chisq) < 2.2e-16

2014-05-07 Thread Jari Oksanen
See ?format.pval cheers, jari oksanen From: r-devel-boun...@r-project.org [r-devel-boun...@r-project.org] on behalf of Michael Friendly [frien...@yorku.ca] Sent: 07 May 2014 17:02 To: r-devel Subject: [Rd] historical significance of Pr(>Chisq) < 2.2e-16 W

Re: [Rd] precedence (was 'historical NA question')

2014-05-07 Thread luke-tierney
On Wed, 7 May 2014, Therneau, Terry M., Ph.D. wrote: Hadley asked about the Blue book; my shelf still has the earlier brown book Becker and Chambers, 1984, S: An interactive environment for data analysis and graphics. The manual page for precedence is $ component select %x

Re: [Rd] precedence (was 'historical NA question')

2014-05-07 Thread John Chambers
On 5/7/14, 5:21 AM, Therneau, Terry M., Ph.D. wrote: Hadley asked about the Blue book; my shelf still has the earlier brown book Becker and Chambers, 1984, S: An interactive environment for data analysis and graphics. Historically interesting, but there was never a guarantee that Version 3

[Rd] yinch() is NOT nonsense with log='y'

2014-05-07 Thread Spencer Graves
May I request a modest change in the documentation and warning for "xinch", "yinch", and "xyinch"? Consider the following example: > plot(1:2, log='y') > yinch(1) [1] 0.1961134 Warning message: In yinch(1) : y log scale: yinch() is nonsense In fact, in this environment, "

Re: [Rd] Historical NA question (Herv? Pag?s)

2014-05-07 Thread Georgi Boshnakov
"Equivalence" certainly does not mean that literally replacing some text will not change the result. >From "R language definition", p. 11: > Except for the syntax, there is no difference between applying an operator > and calling a function. In fact, x + y can equivalently be written ‘+‘(x, y)

Re: [Rd] precedence (was 'historical NA question')

2014-05-07 Thread Hervé Pagès
No big deal. These things can be tricky: https://stat.ethz.ch/pipermail/r-devel/2006-January/036022.html Sorry I couldn't resist ;-) H. On 05/07/2014 09:16 AM, John Chambers wrote: On 5/7/14, 5:21 AM, Therneau, Terry M., Ph.D. wrote: Hadley asked about the Blue book; my shelf still has the

Re: [Rd] precedence (was 'historical NA question')

2014-05-07 Thread Simon Urbanek
On May 7, 2014, at 3:37 PM, Hervé Pagès wrote: > No big deal. These things can be tricky: > > https://stat.ethz.ch/pipermail/r-devel/2006-January/036022.html > > Sorry I couldn't resist ;-) > Yeah, but that's just yet another trip down the rabbit hole - why is -2 parsed as `-`(2) and not a s

Re: [Rd] historical significance of Pr(>Chisq) < 2.2e-16

2014-05-07 Thread William Dunlap
It may come a time before the pchisq() function had the lower.tail argument. In those days you had the compute the upper tail as 1-pchisq(x2, df). For any eps<2.2e-16 (.Machine$double.eps), 1-eps==1 so 1-(1-eps)==0 so you would get, e.g., > 1-pchisq(100,2) [1] 0 and people would say 'but the

Re: [Rd] precedence (was 'historical NA question')

2014-05-07 Thread peter dalgaard
On 07 May 2014, at 21:52 , Simon Urbanek wrote: > On May 7, 2014, at 3:37 PM, Hervé Pagès wrote: > >> No big deal. These things can be tricky: >> >> https://stat.ethz.ch/pipermail/r-devel/2006-January/036022.html >> >> Sorry I couldn't resist ;-) >> > > Yeah, but that's just yet another tr

Re: [Rd] precedence (was 'historical NA question')

2014-05-07 Thread Hervé Pagès
On 05/07/2014 12:52 PM, Simon Urbanek wrote: On May 7, 2014, at 3:37 PM, Hervé Pagès wrote: No big deal. These things can be tricky: https://stat.ethz.ch/pipermail/r-devel/2006-January/036022.html Sorry I couldn't resist ;-) Yeah, but that's just yet another trip down the rabbit hole - wh

Re: [Rd] precedence (was 'historical NA question')

2014-05-07 Thread Hervé Pagès
On 05/07/2014 02:01 PM, peter dalgaard wrote: On 07 May 2014, at 21:52 , Simon Urbanek wrote: On May 7, 2014, at 3:37 PM, Hervé Pagès wrote: No big deal. These things can be tricky: https://stat.ethz.ch/pipermail/r-devel/2006-January/036022.html Sorry I couldn't resist ;-) Yeah, but t

Re: [Rd] precedence (was 'historical NA question')

2014-05-07 Thread Simon Urbanek
On May 7, 2014, at 5:17 PM, Hervé Pagès wrote: > On 05/07/2014 12:52 PM, Simon Urbanek wrote: >> On May 7, 2014, at 3:37 PM, Hervé Pagès wrote: >> >>> No big deal. These things can be tricky: >>> >>> https://stat.ethz.ch/pipermail/r-devel/2006-January/036022.html >>> >>> Sorry I couldn't res

Re: [Rd] precedence (was 'historical NA question')

2014-05-07 Thread Simon Urbanek
On May 7, 2014, at 5:41 PM, Hervé Pagès wrote: > On 05/07/2014 02:01 PM, peter dalgaard wrote: >> >> On 07 May 2014, at 21:52 , Simon Urbanek wrote: >> >>> On May 7, 2014, at 3:37 PM, Hervé Pagès wrote: >>> No big deal. These things can be tricky: https://stat.ethz.ch/piperm

Re: [Rd] precedence (was 'historical NA question')

2014-05-07 Thread Duncan Murdoch
On 07/05/2014, 5:55 PM, Simon Urbanek wrote: On May 7, 2014, at 5:41 PM, Hervé Pagès wrote: On 05/07/2014 02:01 PM, peter dalgaard wrote: On 07 May 2014, at 21:52 , Simon Urbanek wrote: On May 7, 2014, at 3:37 PM, Hervé Pagès wrote: No big deal. These things can be tricky: https://st

Re: [Rd] precedence (was 'historical NA question')

2014-05-07 Thread Hervé Pagès
On 05/07/2014 02:55 PM, Simon Urbanek wrote: On May 7, 2014, at 5:41 PM, Hervé Pagès wrote: On 05/07/2014 02:01 PM, peter dalgaard wrote: On 07 May 2014, at 21:52 , Simon Urbanek wrote: On May 7, 2014, at 3:37 PM, Hervé Pagès wrote: No big deal. These things can be tricky: https://

Re: [Rd] precedence (was 'historical NA question')

2014-05-07 Thread Hervé Pagès
On 05/07/2014 02:45 PM, Simon Urbanek wrote: On May 7, 2014, at 5:17 PM, Hervé Pagès wrote: On 05/07/2014 12:52 PM, Simon Urbanek wrote: On May 7, 2014, at 3:37 PM, Hervé Pagès wrote: No big deal. These things can be tricky: https://stat.ethz.ch/pipermail/r-devel/2006-January/036022.html

Re: [Rd] precedence (was 'historical NA question')

2014-05-07 Thread Hervé Pagès
On 05/07/2014 02:45 PM, Simon Urbanek wrote: On May 7, 2014, at 5:17 PM, Hervé Pagès wrote: On 05/07/2014 12:52 PM, Simon Urbanek wrote: On May 7, 2014, at 3:37 PM, Hervé Pagès wrote: No big deal. These things can be tricky: https://stat.ethz.ch/pipermail/r-devel/2006-January/036022.ht

[Rd] checking dependencies in R code ... WARNING

2014-05-07 Thread Knut Krueger
I am trying to update an unsupported package and got the warning: * checking dependencies in R code ... WARNING 'library' or 'require' calls not declared from: 'Hmisc' 'R2HTML' 'tcltk' Missing or unexported object: 'utils::.win32consoleCompletion' See the information on DESCRIPTION files in the c

Re: [Rd] checking dependencies in R code ... WARNING

2014-05-07 Thread Tobias Verbeke
Hi Knut, The code will contain library or require statements, which do not belong there, but need to replaced by specifying the dependencies on these packages in the DESCRIPTION file (Depends / Imports field). For imports you also need to make sure the NAMESPACE file contains the intended state

Re: [Rd] historical significance of Pr(>Chisq) < 2.2e-16

2014-05-07 Thread Prof Brian Ripley
On 07/05/2014 21:41, William Dunlap wrote: It may come a time before the pchisq() function had the lower.tail argument. In those days you had the compute the upper tail as 1-pchisq(x2, df). For any eps<2.2e-16 (.Machine$double.eps), 1-eps==1 so 1-(1-eps)==0 so you would get, e.g., > 1-pchisq