[Rd] Bug (PR#13987)
Full_Name: Clemens Bockmeyer Version: 2.9.0 OS: Submission from: (NULL) (193.174.111.250) Dear helpdesk, the following bug occurs when working with BRB Array tools trying to generate a heat map: Error in rgb (bitAnd(Max color 255), bit and Max color %/%256, 255 bit And Max color... could not find function bitAnd. Error occured while executing the following R command: myplot.image.array (TRUE). Error may be memory related or due to size of graphic file. Try again with fewer genes or... My question is: What to do, that R works? I am sure that I do NOT have to much genes! Thank you in advance. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] how to document stuff most users don't want to see
Under the system of development we now have, I agreee with Seth's assertion. But if there were people dedicated to documentation, then I think something like what I described could be workable. Pat Seth Falcon wrote: Writing good documentation is hard. I can appreciate the desire to find technological solutions that improve documentation. However, the benefit of a help system that allows for varying degrees of verbosity is very likely to be overshadowed by the additional complexity imposed on the help system. Users would need to learn how to tune the help system. Developers would need to learn and follow the system of variable verbosity. This time would be better spent by developers simply improving the documentation and by users by simply reading the improved documentation. My $0.02. + seth __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Bug (PR#13987)
Please do read the FAQ and R posting guide. (i) You were asked not to report on obselete versions of R (2.9.2 and 2.10.0 alpha are current). (ii) There is no reproducible code here, but the error is almost certainly not in R but in a contributed package or in 'BRB Array tools' (whatever that is, and if you mean 'BRB-Array Tools', that is not freely distributable). 'Finally, check carefully whether the bug is with R, or a contributed package. Bug reports on contributed packages should be sent first to the package maintainer, and only submitted to the R-bugs repository by package maintainers, mentioning the package in the subject line.' (iii) R-bugs is explicitly not a place to ask questions. On Wed, 7 Oct 2009, bockme...@gmail.com wrote: Full_Name: Clemens Bockmeyer Version: 2.9.0 OS: Hmm, 'Always include the version of R, machine, and operating system that you are using; type `version' in R to print this.' Submission from: (NULL) (193.174.111.250) Dear helpdesk, the following bug occurs when working with BRB Array tools trying to generate a heat map: Error in rgb (bitAnd(Max color 255), bit and Max color %/%256, 255 bit And Max color... could not find function bitAnd. Error occured while executing the following R command: myplot.image.array (TRUE). Error may be memory related or due to size of graphic file. Try again with fewer genes or... My question is: What to do, that R works? I am sure that I do NOT have to much genes! Thank you in advance. -- Brian D. Ripley, rip...@stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] inconsistency in return value of peaks() {splus2R} (PR#13988)
vi...@phil.uu.nl wrote: Full_Name: Benny van der Vijgh Version: 2.7.2 OS: Windows Vista Submission from: (NULL) (194.171.252.108) The return value of peaks() in package splus2R is not consistent. This is not an R bug. Please contact the author of that package. Duncan Murdoch This is because of the call to max.col() without additional parameters which peaks() makes. max.col() has a parameter 'ties.method' which specifies how ties are handled, with random by default. This means that when peaks() is called on a vector with two (or more) neighbouring elements in a tie for the local maximum, these end up in the same row in the embedded matrix after which max.col() at random chooses which will be considered the maximum, thereby yielding inconsistent results, for example: a - c(3,5,5,3) peaks(a) [1] FALSE FALSE FALSE FALSE peaks(a) [1] FALSE TRUE FALSE FALSE this can be easily fixed by setting the parameter 'ties.method' for max.col() to first or last, which is a matter of application and taste I think, perhaps it can even be considered to make this parameter also a parameter of peaks() and pass it to max.col() in the execution. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Buglet in qbeta?
Hi, I sometimes play around with extreme parameters for distributions and found that qbeta is not always monotone as the following example shows. I don't know whether this is serious enough to submit a bug report (as this example is near to the limitations of floating point arithmetic). Josef x - qbeta((0:100)/100,0.01,5) x [1] 0.00e+00 1.253990e-201 1.589622e-171 6.462785e-154 2.015085e-141 [6] 9.892240e-132 8.192553e-124 4.056003e-117 2.554424e-111 3.330774e-106 [11] 1.253990e-101 1.728076e-97 1.038529e-93 3.109063e-90 5.141594e-87 [16] 5.098238e-84 3.238117e-81 1.390549e-78 4.58e-76 9.411402e-74 [21] 1.589622e-71 2.090373e-69 2.190596e-67 1.866714e-65 1.316493e-63 [26] 7.803602e-62 3.941205e-60 1.716606e-58 6.517745e-57 2.178181e-55 [31] 6.462785e-54 1.715788e-52 4.104801e-51 8.906113e-50 1.762731e-48 [36] 3.199622e-47 5.352348e-46 8.288322e-45 1.193037e-43 1.602341e-42 [41] 2.015085e-41 2.380564e-40 2.649862e-39 2.787018e-38 2.776910e-37 [46] 2.627517e-36 2.366341e-35 2.032732e-34 1.668853e-33 1.311905e-32 [51] 9.892240e-32 2.220446e-15 2.331468e-15 2.553513e-15 1.110223e-16 [56] 3.330669e-16 9.992007e-16 8.881784e-16 4.440892e-16 7.771561e-16 [61] 1.554312e-15 8.881784e-16 9.992007e-16 2.109424e-15 2.331468e-15 [66] 2.553513e-15 2.553513e-15 1.110223e-16 6.661338e-16 1.221245e-15 [71] 1.443290e-15 2.220446e-16 6.661338e-16 2.664535e-15 1.054712e-14 [76] 4.019007e-14 1.512124e-13 5.589973e-13 2.031153e-12 7.261081e-12 [81] 2.554423e-11 8.847001e-11 3.017724e-10 1.014153e-09 3.359099e-09 [86] 1.096950e-08 3.532966e-08 1.122586e-07 3.520157e-07 1.089674e-06 [91] 3.330818e-06 1.005659e-05 3.50e-05 8.845884e-05 2.579427e-04 [96] 7.446202e-04 2.133444e-03 6.108393e-03 1.783085e-02 5.699554e-02 [101] 1.00e+00 order(x) [1] 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 [19] 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 [37] 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 55 68 72 [55] 56 59 69 73 60 58 62 57 63 70 71 61 64 52 53 65 54 66 [73] 67 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 [91] 91 92 93 94 95 96 97 98 99 100 101 pbeta(x,0.01,5) [1] 0.000 0.010 0.020 0.030 0.040 0.050 0.060 [8] 0.070 0.080 0.090 0.100 0.110 0.120 0.130 [15] 0.140 0.150 0.160 0.170 0.180 0.190 0.200 [22] 0.210 0.220 0.230 0.240 0.250 0.260 0.270 [29] 0.280 0.290 0.300 0.310 0.320 0.330 0.340 [36] 0.350 0.360 0.370 0.380 0.390 0.400 0.410 [43] 0.420 0.430 0.440 0.450 0.460 0.470 0.480 [50] 0.490 0.500 0.7285871 0.7289426 0.7296061 0.7070842 0.7148952 [57] 0.7227924 0.7219416 0.7169548 0.7209782 0.7259930 0.7219416 0.7227924 [64] 0.7282134 0.7289426 0.7296061 0.7296061 0.7070842 0.7198677 0.7242443 [71] 0.7254552 0.7120024 0.7198677 0.7299167 0.7400284 0.7499948 0.7599988 [78] 0.778 0.778 0.790 0.800 0.810 0.820 0.830 [85] 0.840 0.850 0.860 0.870 0.880 0.890 0.900 [92] 0.910 0.920 0.930 0.940 0.950 0.960 0.970 [99] 0.980 0.990 1.000 version _ platform x86_64-unknown-linux-gnu arch x86_64 os linux-gnu system x86_64, linux-gnu status Under development (unstable) major 2 minor 11.0 year 2009 month 10 day07 svn rev49963 language R version.string R version 2.11.0 Under development (unstable) (2009-10-07 r49963) p.s. there are similar results for R-2.9.2 in Windows (with different round-off errors). -- - Josef Leydold | WU (Vienna University of Economics and Business) | Department of Statistics and Mathematics - Augasse 2-6 | Tel. +43 1 31336 4695 A-1090
Re: [Rd] how to document stuff most users don't want to see
If help was only displayed in the form of html pages, one could perhaps mimic the javascript trick sometimes found in wikipedia, e.g. http://en.wikipedia.org/wiki/Mathematical_induction#Example; (see the show/hide toggle at the bottom). I don't see how this could work with plain text or pdf output. Regards, baptiste __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Improved Function Information with TAB Key
Hello,
Pressing the TAB key when typing a function into an R terminal does not
produce the expected output. Currently, R will order all of the available
function inputs into alphabetical order and present them as options, whereas
it should display the inputs in the order they appear in the function.
For example:
test = function(b,a,c){
print(b)
a*c
}
test( TABTAB
a= b= c=
where TAB indicates pressing the Tab key.
It's easy to see that if the function were designed to accept 'b' as a
string, and 'a' and 'c' as numerics that this function would fail if the
user made the assumption that the TAB output is in the correct order, and
input 'a' as a string.
This is a simple example, however I have several functions that I use often
and each has many possible inputs. It would be useful to not have to
remember the order the inputs are in for each function, or have to use
args(function) beforehand. It is also on occasion useful not to have to
explicitly name each input in your function.
Im using Ubuntu Linux 9.04 and a standard install of R 2.9.2 (unfortunately
not the polished R.app available on Macs - which coincidentally do display
function inputs in the correct order).
I welcome any thoughts, disagreements or tips any of you may have,
Thanks in advance,
Lee Kelvin
--
Lee Kelvin
School of Physics Astronomy
University of St Andrews
North Haugh
St Andrews KY16 9SS
United Kingdom
Phone (+44) [0]1334461668
Email l...@st-andrews.ac.uk
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