Re: [R] installation of R (14.1 and 15.1) fails: [reg-packages.Rout] Error 1
sorry, I forgot: I'm using gcc and gfortran, version 4.5.4. Oliver On Mon, Oct 08, 2012 at 09:57:00AM +0100, Oliver Kullmann wrote: > Hello, > > I'm trying to install R on two Linux machines: > > 1. > > uname -a > Linux cs-wsok 3.4.6-2.10-desktop #1 SMP PREEMPT Thu Jul 26 09:36:26 UTC > 2012 (641c197) x86_64 x86_64 x86_64 GNU/Linux > 2. > > uname -a > Linux csltok.swansea.ac.uk 3.4.6-2.10-desktop #1 SMP PREEMPT Thu Jul 26 > 09:36:26 UTC 2012 (641c197) x86_64 x86_64 x86_64 GNU/Linux > > I am trying version 14.1 on first machine and 15.1 on second machine. > On both machines I get the same test error: > > 1. > comparing 'reg-tests-2.Rout' to './reg-tests-2.Rout.save' ... OK > running code in 'reg-examples1.R' ... OK > running code in 'reg-examples2.R' ... OK > running code in 'reg-packages.R' ...make[4]: *** [reg-packages.Rout] > Error 1 > make[4]: Leaving directory > `/home/csoliver/OKplatform/ExternalSources/builds/R/R-2.14.1/tests' > make[3]: *** [test-Reg] Error 2 > 2. > comparing 'reg-tests-2.Rout' to './reg-tests-2.Rout.save' ... OK > running code in 'reg-examples1.R' ... OK > running code in 'reg-examples2.R' ... OK > running code in 'reg-packages.R' ...make[4]: *** [reg-packages.Rout] > Error 1 > make[4]: Leaving directory > `/home/kullmann/OKplatform/ExternalSources/builds/R/R-2.15.1/tests' > make[3]: *** [test-Reg] Error 2 > > I looked at > http://www.stats.bris.ac.uk/R/doc/FAQ/R-FAQ.html#R-Bugs > and didn't find specific suggestions about information to provide in > case of building errors. And I don't know how to get more information > about these test-errors. > > Hope somebody can help. > > Best regards > > Oliver > __ 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] installation of R (14.1 and 15.1) fails: [reg-packages.Rout] Error 1
Hello, I'm trying to install R on two Linux machines: 1. > uname -a Linux cs-wsok 3.4.6-2.10-desktop #1 SMP PREEMPT Thu Jul 26 09:36:26 UTC 2012 (641c197) x86_64 x86_64 x86_64 GNU/Linux 2. > uname -a Linux csltok.swansea.ac.uk 3.4.6-2.10-desktop #1 SMP PREEMPT Thu Jul 26 09:36:26 UTC 2012 (641c197) x86_64 x86_64 x86_64 GNU/Linux I am trying version 14.1 on first machine and 15.1 on second machine. On both machines I get the same test error: 1. comparing 'reg-tests-2.Rout' to './reg-tests-2.Rout.save' ... OK running code in 'reg-examples1.R' ... OK running code in 'reg-examples2.R' ... OK running code in 'reg-packages.R' ...make[4]: *** [reg-packages.Rout] Error 1 make[4]: Leaving directory `/home/csoliver/OKplatform/ExternalSources/builds/R/R-2.14.1/tests' make[3]: *** [test-Reg] Error 2 2. comparing 'reg-tests-2.Rout' to './reg-tests-2.Rout.save' ... OK running code in 'reg-examples1.R' ... OK running code in 'reg-examples2.R' ... OK running code in 'reg-packages.R' ...make[4]: *** [reg-packages.Rout] Error 1 make[4]: Leaving directory `/home/kullmann/OKplatform/ExternalSources/builds/R/R-2.15.1/tests' make[3]: *** [test-Reg] Error 2 I looked at http://www.stats.bris.ac.uk/R/doc/FAQ/R-FAQ.html#R-Bugs and didn't find specific suggestions about information to provide in case of building errors. And I don't know how to get more information about these test-errors. Hope somebody can help. Best regards Oliver __ 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] read.table: deciding automatically between two colClasses values
Hi Josh,
thanks, that worked!
For the record, here is a function to determine the
number of strings, space-separated, in the first line
of a file:
# Removes leading and trailing whitespaces from string x:
trim = function(x) gsub("^\\s+|\\s+$", "", x)
# The number of strings in the first line in the file with name f:
lengthfirstline = function(f) {
length(unlist(strsplit(trim(readLines(f,1)), " ")))
}
Oliver
On Sun, Aug 28, 2011 at 07:23:07AM -0700, Joshua Wiley wrote:
> Hi Oliver,
>
> Look at ?readLines
>
> I imagine something like:
>
> tmp <- readLines(filename, n = 1L)
> (do stuff with the first line to decide)
> IntN <- 6 (or 4)
> NumN <- 8 (or whatever)
> E <- read.table(file = filename, header = TRUE, colClasses =
> c(rep("integer", IntN), "numeric", "integer", rep("numeric", NumN)), ...)
>
> Cheers,
>
> Josh
>
> On Sun, Aug 28, 2011 at 7:13 AM, Oliver Kullmann
> wrote:
> > Hello,
> >
> > I have a function for reading a data-frame from a file, which contains
> >
> > E = read.table(file = filename,
> > header = T,
> > colClasses =
> > c(rep("integer",6),"numeric","integer",rep("numeric",8)),
> > ...)
> >
> > Now a small variation arose, where
> >
> > colClasses = c(rep("integer",4),"numeric","integer",rep("numeric",8))
> >
> > needed to be used (so just a small change).
> > I want to have it convenient for the user, so no user intervention shall
> > be needed, but the function should choose between the two different values
> > "4" and "6" here according to the header-line.
> >
> > Now this seems to be a problem: I found only count.fields, which
> > however is not able just to read the first line. Reading the
> > whole file (just to read the first line) is awkward, and also these
> > files typically have millions of lines. The only possibility to influence
> > count.fields seems via skip, but this I could only use to skip to the
> > last line, which reads the file nevertheless, and I also don't know
> > the number of lines in the file.
> >
> > Perhaps one could catch an error, when the first invocation of
> > read.table fails, and try the second one. However tryCatch doesn't
> > seem to make it simple to write something like
> >
> > E = try(expr1 otherwise expr2)
> >
> > (if expr1 fails, evaluate expr2 instead) ?
> >
> > Oliver
> >
> > __
> > 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.
> >
>
>
__
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and provide commented, minimal, self-contained, reproducible code.
[R] read.table: deciding automatically between two colClasses values
Hello,
I have a function for reading a data-frame from a file, which contains
E = read.table(file = filename,
header = T,
colClasses = c(rep("integer",6),"numeric","integer",rep("numeric",8)),
...)
Now a small variation arose, where
colClasses = c(rep("integer",4),"numeric","integer",rep("numeric",8))
needed to be used (so just a small change).
I want to have it convenient for the user, so no user intervention shall
be needed, but the function should choose between the two different values
"4" and "6" here according to the header-line.
Now this seems to be a problem: I found only count.fields, which
however is not able just to read the first line. Reading the
whole file (just to read the first line) is awkward, and also these
files typically have millions of lines. The only possibility to influence
count.fields seems via skip, but this I could only use to skip to the
last line, which reads the file nevertheless, and I also don't know
the number of lines in the file.
Perhaps one could catch an error, when the first invocation of
read.table fails, and try the second one. However tryCatch doesn't
seem to make it simple to write something like
E = try(expr1 otherwise expr2)
(if expr1 fails, evaluate expr2 instead) ?
Oliver
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] how to improve summary.lm
> When you simply type summary.lm there is an implicit call to
> print.summary.lm but its code is not visible unless you use
> getAnywhere(print.summary.lm ).
Aha, that's great -- now I see all the "\n" (and can get rid off
them ;-)).
> Reading the code you find that the
> coefficient matrix and the significance stars are handled by a
> function , so this should give you what you want:
>
> printCoefmat(summary(model)$coefficients)
>
For the record, now I'm using
short_summary_lm = function(L) {
S = summary(L)
printCoefmat(S$coefficients, signif.legend=FALSE)
digits = max(3,getOption("digits")-3)
cat("R-squared:", formatC(S$r.squared, digits = digits), "\n")
}
Thanks!
Oliver
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[R] how to improve summary.lm
Hello, I need a shorter summary.lm, instead of Call: lm(formula = E$t ~ E$cfs) Residuals: Min1QMedian3Q Max -0.239674 -0.007694 0.006430 0.014330 2.496551 Coefficients: Estimate Std. Error t value Pr(>|t|) (Intercept) -1.994e-02 1.419e-04 -140.5 <2e-16 *** E$cfs1.675e-05 4.714e-09 3552.7 <2e-16 *** --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 Residual standard error: 0.03238 on 65268 degrees of freedom Multiple R-squared: 0.9949, Adjusted R-squared: 0.9949 F-statistic: 1.262e+07 on 1 and 65268 DF, p-value: < 2.2e-16 I need lm(formula = E$t ~ E$cfs) Estimate Std. Error t value Pr(>|t|) (Intercept) -1.994e-02 1.419e-04 -140.5 <2e-16 *** E$cfs1.675e-05 4.714e-09 3552.7 <2e-16 *** Multiple R-squared: 0.9949, Adjusted R-squared: 0.9949 I looked at the code of summary.lm, with the intention to copy parts of it into a new function "short_sum_lm", but couldn't find the parts I'm interested in. I hope it's not too complicated to achieve that. (In general it would be great to have more influence on the summary-function -- typically it's too spacious.) Thanks for your attention Oliver __ 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] can't install R with *local* gcc
Hello, I infer from your answer that piece of information which is most important for us now: That my configuration instructions for R should work (should be correct). Given all these unspecified build-systems we have to fight (at least Gmp, Mpfr, Gcc with everything in it, R, and finally our own) one first wants to know where obvious errors are. Thanks! Once I know more (we are in the middle of it) I move to the devel-list. Oliver P.S. Currently it seems that the Gcc-build is not correct (still the same with 4.4.5), not propagating linker-information to the building of libraries (while the compiler-builds seem alright). > > Hint #1: Expect the process to be somewhat painful... > Hint #2: Study the configure script and config.log to the level where you can > reproduce the mixed C/Fortran code that it is trying to build and run and > with which commands it is trying to build it > Hint #3: Figure out what it really should have done to build such code > > An alternative hint is first to try setting up a very simple Fortran function > to, say, double a number, and a C main program that calls it. Then try > figuring out the compiler/linker options to make it work. (That is of course > what configure was trying to do in the first place, but doing it by hand > might be less prone to getting multiple toolchains mixed up.) > > > -- > Peter Dalgaard > Center for Statistics, Copenhagen Business School > Solbjerg Plads 3, 2000 Frederiksberg, Denmark > Phone: (+45)38153501 > Email: pd@cbs.dk Priv: pda...@gmail.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] can't install R with *local* gcc
Hello,
we re-distribute R with our open-source platform http://www.ok-sat-library.org/
where we use R mainly for evaluation of computational experiments.
Due to the various platforms, we build everything from source, and that works
fine.
Until now, that is: there are circumstances (for example in computer-science
computer labs)
where no Fortran-compiler is provided, and the users (students) can't change
that.
Thus we now try to build gfortran as part of the GCC version 4.2.4 suite, and
building
R using that local gcc.
We already use the local C and C++ compiler of the suite extensively, and that
all works. But we don't have any experience with using gfortran.
The gcc-build works fine, everything seems alright --- only R (version 2.11.0)
won't build with it:
We use the configuration
F77=/home/csoliver/SAT-Algorithmen/OKplatform/ExternalSources/Installations/Gcc/4.2.4/bin/gfortran
FC=${F77}
CC=/home/csoliver/SAT-Algorithmen/OKplatform/ExternalSources/Installations/Gcc/4.2.4/bin/gcc
CXX=/home/csoliver/SAT-Algorithmen/OKplatform/ExternalSources/Installations/Gcc/4.2.4/bin/g++
LDFLAGS="-L
/home/csoliver/SAT-Algorithmen/OKplatform/ExternalSources/Installations/Gcc/4.2.4/lib"
./configure
--prefix=/home/csoliver/SAT-Algorithmen/OKplatform/ExternalSources/Installations/R/2.11.0
(the same problems with "lib64" instead of "lib", by the way)
which yields
checking for Fortran 77 libraries of
/home/csoliver/SAT-Algorithmen/OKplatform/ExternalSources/Installations/Gcc/4.2.4/bin/gfortran...
-L/home/csoliver/SAT-Algorithmen/OKplatform/ExternalSources/Installations/Gcc/4.2.4/lib
-L/home/csoliver/SAT-Algorithmen/OKplatform/ExternalSources/Installations/Gcc/4.2.4/lib/gcc/x86_64-unknown-linux-gnu/4.2.4
-L/home/csoliver/SAT-Algorithmen/OKplatform/ExternalSources/Installations/Gcc/4.2.4/lib/gcc/x86_64-unknown-linux-gnu/4.2.4/../../../../lib64
-L/lib/../lib64 -L/usr/lib/../lib64
-L/home/csoliver/SAT-Algorithmen/OKplatform/ExternalSources/Installations/Gcc/4.2.4/lib/gcc/x86_64-unknown-linux-gnu/4.2.4/../../..
-lgfortranbegin -lgfortran -lm
/home/csoliver/SAT-Algorithmen/OKplatform/ExternalSources/Installations/Gcc/4.2.4/lib/libgfortran.a
which looks alright to me (but I don't know Fortran), but then we get
checking for dummy main to link with Fortran 77 libraries... none
checking for Fortran 77 name-mangling scheme... lower case, underscore, no
extra underscore
checking whether
/home/csoliver/SAT-Algorithmen/OKplatform/ExternalSources/Installations/Gcc/4.2.4/bin/gfortran
appends underscores to external names... yes
checking whether
/home/csoliver/SAT-Algorithmen/OKplatform/ExternalSources/Installations/Gcc/4.2.4/bin/gfortran
appends extra underscores to external names... no
checking whether mixed C/Fortran code can be run... configure: WARNING: cannot
run mixed C/Fortran code
configure: error: Maybe check LDFLAGS for paths to Fortran libraries?
make: *** [R_base] Error 1
The R installation-documentation doesn't say much on using local compilers
(more or less nothing), and everything we could
get from it are the above settings of environment variables.
Internet search reveals old stuff on "libg2c" which appears not to exist
anymore, some recommendations
not to build from sources (which is not an option for us), an open Sage ticket
(apparently without any
further work on it), and a request to the R-list with apparently no reply.
Since we are working in a well-defined setting (gcc is fully under our
control), and apparently
all the libraries needed are build by gcc (though this is nowhere said or
(dream) specified),
it should be possible to solve that problem.
I very hope to get some hints (we can't get R running (for our system!)
otherwise).
The error is exactly the same on various systems (all 64-bit machines, Intel
and AMD).
If we use the system-gcc (4.5.0 or 4.1.2) then the installation of R works
without problems;
here (for one of the machines) some data
> version
platform x86_64-unknown-linux-gnu
arch x86_64
os linux-gnu
system x86_64, linux-gnu
status
major 2
minor 11.0
year 2010
month 04
day22
svn rev51801
language R
version.string R version 2.11.0 (2010-04-22)
Thanks for you help in any case!
Oliver
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Re: [R] logarithmic integrals in R?
Thanks for the information.
On Sat, May 29, 2010 at 01:15:29PM +, Hans W. Borchers wrote:
> Oliver Kullmann swansea.ac.uk> writes:
>
> >
> > Hello,
> >
> > I couldn't find information on whether the logarithmic integrals
> >
> > Li_m(x) = integral_0^x log(t)^(-m) dt
> >
> > for x >= 0 are available in R?
>
> I saw your request only this weekend.
> The first logarithmic integral can be computed using the exponential
> integral Ei(x) per
>
> li(x) = Ei(log(x))
>
I found gsl at http://cran.r-project.org/web/packages/gsl/index.html.
> and elliptic integrals are part of the 'gsl' package, so
>
> library('gsl')
> x <- seq(2, 10, by=0.5)
> y <- expint_Ei(log(x))
> y
>
> See e.g. the Handbook of Mathematical Functions for how to reduce higher
> logarithmic integrals.
However here I wasn't succesful: Going through the chapter
http://www.math.ucla.edu/~cbm/aands/page_228.htm
I didn't find any mentioning of the higher logarithmic integrals.
> Another possibility is to use the Web API of 'keisan', the calculation
> library of Casio.
>
Interesting; but again only li(x).
Also a google search on "higher logarithmic integrals", "logarithmic integrals"
or "li_n(x)" doesn't reveal anything, so I would be thankful for a hint.
Thanks again!
Oliver
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[R] logarithmic integrals in R?
Hello, I couldn't find information on whether the logarithmic integrals Li_m(x) = integral_0^x log(t)^(-m) dt for x >= 0 are available in R? Best wishes Oliver __ 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] question regarding conversion from factor to vector
thank you! (I was on the wrong track, and thinking these would be "levels".) Oliver > In this case where the is only one dimension, the table object is more > like a named vector. The first "vector" in your terminology (but would > be more accurately called "labels") can be accessed with: > > names( table(E$singles) ) > > If you want the counts without the lables , then just use the unname > function: > > unname( table(E$singles) ) > -- > David. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] question regarding conversion from factor to vector
Hello, let me show you the following part of a session: > table(E$singles) 0 1 2 3 4 5 6 7 8 14 15 461752 5487 93224379658 1099 4053 2 1868 1 21 28 29 35 42 49 50 56 63 70 77 904560 1348275126 1156103 71 63 84 91 98105112119126133134140147 51 35 37 16 19 17 14 27 1 20 17 154161168169175182189196203210217 16 8 7 1 7 12 5 6 3 8 4 224231245252259266273280287294301 6 5 5 1 2 3 4 2 2 1 2 315329336343364385386399441476560 2 2 1 2 3 2 1 1 1 1 1 > as.numeric(as.vector(as.data.frame(table(E$singles))$Var1)) %% 7 [1] 0 1 2 3 4 5 6 0 1 0 1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 0 [39] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 As you can see, the values of column "singles" of dataframe E show a strong regularity w.r.t. multiples of 7, and with the second line I checked that. Now I hope that there is a better way to get the vector of values out of the table-result? First I convert it into a dataframe, to get a name for the two vectors constituting the table, then a get a vector of strings(!), which are then converted to integers. By the way, the type of E$singles is integers. Thanks for your help! Oliver __ 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] tree-drawing in R ?
Hello, I wonder whether binary (rooted) trees with simple labels (say, integers) can be drawn by some R-package? Couldn't find one. Just to make sure (since "trees" can be many things): I mean those computer-science creatures, with roots and subtrees. Thanks for your consideration in any case Oliver P.S. Perhaps there is some graph-drawing package? (Here a "graph" consists of vertices and connecting edges.) __ 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] regression tests still fail for R version 2.10.0
On Sat, Dec 05, 2009 at 01:39:03PM -0500, David Winsemius wrote: > The question lacks so many specifics that would be needed to address > problem that I suspect persons with sufficient knowledge to address it > (and I am probably not among that group) simply passed it over and > waited for you to get sufficiently motivated to actually read the > Posting Guide. Thanks for your answer! I'm for quite some time now on that mailing list, and I read quite a few of the e-mails: Most of the e-mails are far worse, but get quite a lot of attention. I can't find anything in the posting guidelines which speakes about installation; I also can't find something on what are "OS specifics", and how to obtain them from R. There is this session-info, which as described seems to be not applicable here, but on the other hand seems to be the only thing which yields some output: > sessionInfo() R version 2.9.2 (2009-08-24) x86_64-unknown-linux-gnu locale: LC_CTYPE=en_GB.UTF-8;LC_NUMERIC=C;LC_TIME=en_GB.UTF-8;LC_COLLATE=en_GB.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_GB.UTF-8;LC_PAPER=en_GB.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_GB.UTF-8;LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base This is of course the old version (where the regression tests didn't fail). What else could be relevant? Linux was already mentioned (Suse 10.0), 64-bit AMD machine. Installation by "./configure --prefix=/path_to_local_directory; make; make check". > gcc --version gcc (GCC) 4.1.2 Copyright (C) 2006 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. I'm not aware that there are different source-packages of R around? Other than R-2.10.0.tar.gz. > md5sum R-2.10.0.tar.gz 4486934883b1dbcd5400135e22b26a75 R-2.10.0.tar.gz Why I am building from sources? Shouldn't this be irrelevant --- in my e-mail I just try to *help* R, and any information on problems should be relevant, irrespective of the person who submits such information? Anyway, I am redistributing R in a open-source package which provides a kind of "complete" environment for some form of scientific investigations; not unlike Sage in some sense. See http://www.ok-sat-library.org/ As such I feel responsible to install only software which is correct (and I need to install from sources). Hope this helps a bit --- feel free to ask! Oliver > Among the missing items are OS specifics, why you need > to install from sources, which version of the source bundle, (perhaps) > which mirror, etc, etc. > > (I surely would not report a bug with so much missing information.) > > -- > David. > On Dec 5, 2009, at 1:25 PM, Oliver Kullmann wrote: > > >Hello, > > > >on Mon Nov 9 17:57:04 CET 2009 I've sent > >an e-mail to the R mailing list (see below), > >about a failing regression test. Yet nobody > >replied, while (obviously) the situation didn't > >change (installation still fails, and might > >continue to do so in the future). > > > >I wonder whether somebody has to say something here? > >Shall a bug report be submitted? > >Or will R 2.10.1 have fixed the bug? > > > >Oliver > > > >-- > > > >Hello, > > > >I have installed R version 2.9.2, and everything > >works fine, but when attempting to install version 2.10.0 > >I get: > > > >running code in 'datasets.R' ... OK > >comparing 'datasets.Rout' to './datasets.Rout.save' ... OK > >make[4]: Leaving directory `/home/csoliver/SAT-Algorithmen/ > >OKplatform/ExternalSources/builds/R/R-2.10.0/tests' > >make[3]: Leaving directory `/home/csoliver/SAT-Algorithmen/ > >OKplatform/ExternalSources/builds/R/R-2.10.0/tests' > >make[3]: Entering directory `/home/csoliver/SAT-Algorithmen/ > >OKplatform/ExternalSources/builds/R/R-2.10.0/tests' > >running regression tests ... > >make[4]: Entering directory `/home/csoliver/SAT-Algorithmen/ > >OKplatform/ExternalSources/builds/R/R-2.10.0/tests' > >running code in 'reg-tests-1.R' ...make[4]: *** [reg-tests-1.Rout] > >Error 1 > >make[4]: Leaving directory `/home/csoliver/SAT-Algorithmen/ > >OKplatform/ExternalSources/builds/R/R-2.10.0/tests' > >make[3]: *** [test-Reg] Error 2 > >make[3]: Leaving directory `/home/csoliver/SAT-Algorithmen/ > >OKplatform/ExternalSources/builds/R/R-2.10.0/tests' > >make[2]: *** [test-all-basics] Error 1 > >make[2]: Leaving directory `/home/csoliver/SAT-Algorithmen/ >
[R] regression tests still fail for R version 2.10.0
Hello, on Mon Nov 9 17:57:04 CET 2009 I've sent an e-mail to the R mailing list (see below), about a failing regression test. Yet nobody replied, while (obviously) the situation didn't change (installation still fails, and might continue to do so in the future). I wonder whether somebody has to say something here? Shall a bug report be submitted? Or will R 2.10.1 have fixed the bug? Oliver -- Hello, I have installed R version 2.9.2, and everything works fine, but when attempting to install version 2.10.0 I get: running code in 'datasets.R' ... OK comparing 'datasets.Rout' to './datasets.Rout.save' ... OK make[4]: Leaving directory `/home/csoliver/SAT-Algorithmen/OKplatform/ExternalSources/builds/R/R-2.10.0/tests' make[3]: Leaving directory `/home/csoliver/SAT-Algorithmen/OKplatform/ExternalSources/builds/R/R-2.10.0/tests' make[3]: Entering directory `/home/csoliver/SAT-Algorithmen/OKplatform/ExternalSources/builds/R/R-2.10.0/tests' running regression tests ... make[4]: Entering directory `/home/csoliver/SAT-Algorithmen/OKplatform/ExternalSources/builds/R/R-2.10.0/tests' running code in 'reg-tests-1.R' ...make[4]: *** [reg-tests-1.Rout] Error 1 make[4]: Leaving directory `/home/csoliver/SAT-Algorithmen/OKplatform/ExternalSources/builds/R/R-2.10.0/tests' make[3]: *** [test-Reg] Error 2 make[3]: Leaving directory `/home/csoliver/SAT-Algorithmen/OKplatform/ExternalSources/builds/R/R-2.10.0/tests' make[2]: *** [test-all-basics] Error 1 make[2]: Leaving directory `/home/csoliver/SAT-Algorithmen/OKplatform/ExternalSources/builds/R/R-2.10.0/tests' make[1]: *** [check] Error 2 make[1]: Leaving directory `/home/csoliver/SAT-Algorithmen/OKplatform/ExternalSources/builds/R/R-2.10.0' make: *** [R_base] Error 1 Before that the build seems alright. Oliver -- Dr. Oliver Kullmann Computer Science Department Swansea University Faraday Building, Singleton Park Swansea SA2 8PP, UK http://cs.swan.ac.uk/~csoliver/ __ 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] regression tests fail for R version 2.10.0
Hello, I have installed R version 2.9.2, and everything works fine, but when attempting to install version 2.10.0 I get: running code in 'datasets.R' ... OK comparing 'datasets.Rout' to './datasets.Rout.save' ... OK make[4]: Leaving directory `/home/csoliver/SAT-Algorithmen/OKplatform/ExternalSources/builds/R/R-2.10.0/tests' make[3]: Leaving directory `/home/csoliver/SAT-Algorithmen/OKplatform/ExternalSources/builds/R/R-2.10.0/tests' make[3]: Entering directory `/home/csoliver/SAT-Algorithmen/OKplatform/ExternalSources/builds/R/R-2.10.0/tests' running regression tests ... make[4]: Entering directory `/home/csoliver/SAT-Algorithmen/OKplatform/ExternalSources/builds/R/R-2.10.0/tests' running code in 'reg-tests-1.R' ...make[4]: *** [reg-tests-1.Rout] Error 1 make[4]: Leaving directory `/home/csoliver/SAT-Algorithmen/OKplatform/ExternalSources/builds/R/R-2.10.0/tests' make[3]: *** [test-Reg] Error 2 make[3]: Leaving directory `/home/csoliver/SAT-Algorithmen/OKplatform/ExternalSources/builds/R/R-2.10.0/tests' make[2]: *** [test-all-basics] Error 1 make[2]: Leaving directory `/home/csoliver/SAT-Algorithmen/OKplatform/ExternalSources/builds/R/R-2.10.0/tests' make[1]: *** [check] Error 2 make[1]: Leaving directory `/home/csoliver/SAT-Algorithmen/OKplatform/ExternalSources/builds/R/R-2.10.0' make: *** [R_base] Error 1 Before that the build seems alright. Oliver -- Dr. Oliver Kullmann Computer Science Department Swansea University Faraday Building, Singleton Park Swansea SA2 8PP, UK http://cs.swan.ac.uk/~csoliver/ __ 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] error with summary(vector)??
Ah, thank you! (A bit strange.) Now looking more closer to it, I wonder whether I could achieve the following output formatting: > fivenum(E$nodes,1) [1] 1 2 3 7 70632 > round(mean(E$nodes),2) [1] 49.85 That's a reasonable way of showing the numbers involved, since E$nodes is declared as integer data. Now could I get "summary" to show me the numbers in this way, i.e. Min. 1st Qu. Median Mean 3rd Qu. Max. 1 2 3 49.85 7 70630 ?? I guess not. Perhaps it would be helpful to see how "summary" achieves its result here --- how to display the code of this function? (Spent some time with the documentation and on the Internet, but can't find the right combination of key words, and a nice section "List everything related to functions" doesn't seem to be available.) Thanks for your help. Oliver On Sun, Aug 30, 2009 at 10:39:48PM +0100, Oliver Kullmann wrote: > Hello, > > I get > > > summary(E) > level nodesave_nodestime > Min. : 1 Min. :1.00 Min. : 10.71 Min. : 0. > 1st Qu.: 237414 1st Qu.:2.00 1st Qu.: 19.70 1st Qu.: 0.0100 > Median : 749229 Median :3.00 Median : 27.01 Median : 0.0100 > Mean : 767902 Mean : 49.85 Mean : 98.89 Mean : 0.2296 > 3rd Qu.:288 3rd Qu.:7.00 3rd Qu.: 80.38 3rd Qu.: 0.0300 > Max. :2097152 Max. :70632.00 Max. :4451.67 Max. :338.9200 > ave_time singlesautarkies depthave_reductions > Min. : 0.0490 Min. :0 Min. :0 Min. :33 Min. : 0.20 > 1st Qu.: 0.0910 1st Qu.:0 1st Qu.:0 1st Qu.:52 1st Qu.: 7.50 > Median : 0.1270 Median :0 Median :0 Median :52 Median : 9.92 > Mean : 0.4636 Mean :0 Mean :0 Mean :52 Mean :11.76 > 3rd Qu.: 0.3860 3rd Qu.:0 3rd Qu.:0 3rd Qu.:52 3rd Qu.:13.46 > Max. :16.2720 Max. :0 Max. :0 Max. :52 Max. :70.00 > > summary(E$nodes) > Min. 1st Qu. Median Mean 3rd Qu. Max. > 1.00 2.00 3.0049.85 7.00 70630.00 > > The max-value for E$nodes is incorrect --- it it 70632, as computed by > summary(E) ?? > > Oliver > > __ > 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-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] error with summary(vector)??
Hello, I get > summary(E) level nodesave_nodestime Min. : 1 Min. :1.00 Min. : 10.71 Min. : 0. 1st Qu.: 237414 1st Qu.:2.00 1st Qu.: 19.70 1st Qu.: 0.0100 Median : 749229 Median :3.00 Median : 27.01 Median : 0.0100 Mean : 767902 Mean : 49.85 Mean : 98.89 Mean : 0.2296 3rd Qu.:288 3rd Qu.:7.00 3rd Qu.: 80.38 3rd Qu.: 0.0300 Max. :2097152 Max. :70632.00 Max. :4451.67 Max. :338.9200 ave_time singlesautarkies depthave_reductions Min. : 0.0490 Min. :0 Min. :0 Min. :33 Min. : 0.20 1st Qu.: 0.0910 1st Qu.:0 1st Qu.:0 1st Qu.:52 1st Qu.: 7.50 Median : 0.1270 Median :0 Median :0 Median :52 Median : 9.92 Mean : 0.4636 Mean :0 Mean :0 Mean :52 Mean :11.76 3rd Qu.: 0.3860 3rd Qu.:0 3rd Qu.:0 3rd Qu.:52 3rd Qu.:13.46 Max. :16.2720 Max. :0 Max. :0 Max. :52 Max. :70.00 > summary(E$nodes) Min. 1st Qu. Median Mean 3rd Qu. Max. 1.00 2.00 3.0049.85 7.00 70630.00 The max-value for E$nodes is incorrect --- it it 70632, as computed by summary(E) ?? Oliver __ 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] what to do about "face 1 at size 16 could not be loaded"
Hi, on some machines (all Linux, same behaviour with versions 2.9.0 and 2.9.1) I get errors > plot(E2) Error in text.default(x, y, txt, cex = cex, font = font) : X11 font -adobe-helvetica-%s-%s-*-*-%d-*-*-*-*-*-*-*, face 1 at size 16 could not be loaded (but not on others; the R-installation is always the same (from sources), while the Linux-distribution should also be similar; the above failure occurs for Suse 11.0). What to do about such errors? Is it possible to tell R to ignore such errors (likely this is only about some text, but by using options like "ann=F" I didn't succeed to get it working; E2 above by the way is a data frame)? Or could I make a complete installation of R, which includes all the fonts etc. R expects to find? (Apparently there is no standard what fonts should be there, and so failures in this area are to be expected, or?) Thanks for your consideration. Oliver __ 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 install R really *locally*?
Thanks, but this wasn't my problem (I already use --vanilla when *calling* R): The problem is how to get a "vanilla" *installation* (as I said, it was the installation which failed, not later running R, and this failure was caused by the file HOME/.RProfil). Hope that's clearer now. Thanks anyway! Oliver On Mon, Apr 27, 2009 at 10:45:53AM +0200, Uwe Ligges wrote: > Set you system up in a way that its R is started with some of the > options reported by `R --help': > > --no-environ Don't read the site and user environment files > --no-site-fileDon't read the site-wide Rprofile > --no-init-fileDon't read the .Rprofile or ~/.Rprofile files > --no-restore-data Don't restore previously saved objects > --no-restore-history Don't restore the R history file > --no-restore Don't restore anything > --vanilla Combine --no-save, --no-restore, --no-site-file, > --no-init-file and --no-environ > > > Uwe Ligges > > > Oliver Kullmann wrote: > >Hello, > > > >my first attempt at installing version 2.9.0 failed > >because I got an error > >"Error in library(pspline) : there is no package called 'pspline'" > > > >Later I realised that this comes from HOME/.RProfil, and removing > >that files "solves" that problem. > > > >However, I'm actually glad that this error happened, since it shows > >a deeper problem (which is actually not solved yet): > >My context is that I re-distribute R as a part of an open-source > >library I develop, and this library (actually I call it a "research > >environment") installs many things (like R and Maxima, gcc, git, ...), > >and this all purely locally --- it shouldn't interfere with anything > >the user has installed. > > > >So my question is how can I tell R as installation time that it should > >not look at any configuration files or other files whatsoever (so it should > >for example ignore HOME/.RProfil)? > > > >The installation instructions mention the variable "rhome", but I don't > >understand what type of "home" is meant here. What I could need here > >would be a redefinition of the user home-directory (to a local directory > >in my installation), but I guess that is not meant with rhome. > > > >Hope somebody can help here. > > > >Oliver > > > >__ > >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-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] how to install R really *locally*?
Hello, my first attempt at installing version 2.9.0 failed because I got an error "Error in library(pspline) : there is no package called 'pspline'" Later I realised that this comes from HOME/.RProfil, and removing that files "solves" that problem. However, I'm actually glad that this error happened, since it shows a deeper problem (which is actually not solved yet): My context is that I re-distribute R as a part of an open-source library I develop, and this library (actually I call it a "research environment") installs many things (like R and Maxima, gcc, git, ...), and this all purely locally --- it shouldn't interfere with anything the user has installed. So my question is how can I tell R as installation time that it should not look at any configuration files or other files whatsoever (so it should for example ignore HOME/.RProfil)? The installation instructions mention the variable "rhome", but I don't understand what type of "home" is meant here. What I could need here would be a redefinition of the user home-directory (to a local directory in my installation), but I guess that is not meant with rhome. Hope somebody can help here. Oliver __ 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.
