search for: hilmar

...id. Subsequent write.table / read.table would be another option but I'm not sure if R can guess the factor/char/numeric-type correctly when reading the table. So, is there any way in drop the unused factor levels from *all* factors of a data frame without import/export ? Thanks in advance, Hilmar -- Hilmar Berger Studienkoordinator Institut f?r medizinische Informatik, Statistik und Epidemiologie Universit?t Leipzig H?rtelstr. 16-18 D-04107 Leipzig Tel. +49 341 97 16 101 Fax. +49 341 97 16 109 email: hilmar.berger at imise.uni-leipzig.de

Hi Hilmar, weird. The memory problem seems be due to recursion (my R, version 3.3.3, says: Error: evaluation nested too deeply: infinite recursion / options(expressions=)?, just write traceback() to see how it happens), but why does it segfault with xlsx? Nb xlsx is the culprit: neither rJava nor xlsxjars c...

...4 > rownames(df) = c("ef","gg","hh","efg") > df["e",] a b NA NA NA So, it looks like partial matching is done using pmatch("e",rownames(df)) for "[". If this is true, the help page is not correct. Thanks ! Regards, Hilmar --- Hilmar Berger Integromics S.L. / CNB-CSIC Madrid, Spain [[alternative HTML version deleted]]

...n that the case of the second argument being non-atomic or empty is not handled at all and the function progresses until the end, where it fails in the last step on an empty value: matrix(unlist(value, recursive = FALSE, use.names = FALSE), ??? nrow = nr, dimnames = list(rn, cn)) Best regards, Hilmar -- Dr. Hilmar Berger, MD Max Planck Institute for Infection Biology Charit?platz 1 D-10117 Berlin GERMANY Phone: + 49 30 28460 430 Fax: + 49 30 28460 401 E-Mail: berger at mpiib-berlin.mpg.de Web : www.mpiib-berlin.mpg.de [[alternative HTML version deleted]]

...quot;list") + ) > ma = new("FOOCLASS", list(M=matrix(rnorm(300), 30,10))) > isS4(ma) [1] TRUE > data.frame(a=1:3) == ma Error in matrix(unlist(value, recursive = FALSE, use.names = FALSE), nrow = nr,? : ? length of 'dimnames' [2] not equal to array extent Best, Hilmar On 11/09/2019 12:24, Hilmar Berger wrote: > Another example where a data.frame is compared to (here non-null, > non-empty) non-atomic values in Ops.data.frame, resulting in an error > message: > > setClass("FOOCLASS2", > ???????? slots = c(M="matrix") >...

...= l; Valgrind also reports access to unallocated memory and/or writing past the end of the heap. The crash does not happen if the order is changed: dd2 = c(rep(-1, 144), rep(1, 74), rep(NaN,82)) xx = runmed(dd2,21) Error in if (a < b) { : missing value where TRUE/FALSE needed Best regards, Hilmar -- Dr. Hilmar Berger, MD Max Planck Institute for Infection Biology Charit?platz 1 D-10117 Berlin GERMANY Phone: + 49 30 28460 430 Fax: + 49 30 28460 401 E-Mail: berger at mpiib-berlin.mpg.de Web : www.mpiib-berlin.mpg.de

...t;MAList", list(A=matrix(rnorm(300), 30,10), M=matrix(rnorm(300), 30,10))) > #sweep(ma, 2, c(1:10), "*") > > f = match.fun("*") > f function (e1, e2) .Primitive("*") > f(ma, ma$M) ----> crash to command line with segfault. Best regards, Hilmar -- Dr. Hilmar Berger, MD Max Planck Institute for Infection Biology Charit?platz 1 D-10117 Berlin GERMANY Phone: + 49 30 28460 430 Fax: + 49 30 28460 401 E-Mail: berger at mpiib-berlin.mpg.de Web : www.mpiib-berlin.mpg.de

Dear Hilmar Perhaps this gives an indication of why the infinite recursion happens: ## after calling `*` on ma and a matrix: > showMethods(classes=class(ma), includeDefs=TRUE, inherited = TRUE) Function: * (package base) e1="FOOCLASS", e2="matrix" (inherited from: e1="vecto...

...me that the same problem would occur on Mac, since the behavior of Oracle seems to be Linux specific. Possibly even Linux users on OpenJDK might not encounter any problems (not tested). So possibly the next release of rJava should also fix the xlsx problems with other packages. Best regards, Hilmar On 24/04/17 11:46, January W. wrote: > Hi Hilmar, > > weird. The memory problem seems be due to recursion (my R, version > 3.3.3, says: Error: evaluation nested too deeply: infinite recursion / > options(expressions=)?, just write traceback() to see how it happens), > but why...

...<S4 object> ? setClass("FOOCLASS", ????????? representation("list") ) ma = new("FOOCLASS", list(M=matrix(rnorm(300), 30,10))) isS4(ma) d_3 == ma # error A ########################################################################################## Best regards, Hilmar Am 11/09/2019 um 13:26 schrieb Hilmar Berger: > Sorry, I can't reproduce the example below even on the same machine. > However, the following example produces the same error as NULL values > in prior examples: > > > setClass("FOOCLASS", > +????????? representat...

...ndall") Error: 'x' is empty (*translated from german error message*) The behavior is reproducible in R 2.4.1 and 2.6.1 (WinXP). I noticed that in 2.7.0 something was fixed in cor() related to "complete.obs" handling - would that fix my problems ? Any suggestions ? Thanks, Hilmar

...kages. This is fine if one considers R to be a statistical toolkit; as a programming language, however, it introduces inconsistencies and uncertainties which could be avoided if some of the "modern" parts (including language concepts) could be more integrated in core-R. Best regards, Hilmar -- Dr. Hilmar Berger, MD Max Planck Institute for Infection Biology Charit?platz 1 D-10117 Berlin GERMANY Phone: + 49 30 28460 430 Fax: + 49 30 28460 401 E-Mail: berger at mpiib-berlin.mpg.de Web : www.mpiib-berlin.mpg.de

Full_Name: Hilmar Berger Version: 2.4.1/2.6.2alpha OS: WinXP Submission from: (NULL) (84.185.128.110) Hi all, If I use tapply on an empty data.frame I get an error. I'm not quite sure if one can actually expect the function to return with a result. However, the error message suggests that this case does not g...

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...h Java messing with the stack, see e.g. http://r.789695.n4.nabble.com/Error-memory-exhausted-limit-reached-td4729708.html. I'll fix the infinite recursion caused by the methods package. Michael On Wed, Apr 19, 2017 at 1:12 AM, Wolfgang Huber <wolfgang.huber at embl.de> wrote: > Dear Hilmar > > Perhaps this gives an indication of why the infinite recursion happens: > > ## after calling `*` on ma and a matrix: > >> showMethods(classes=class(ma), includeDefs=TRUE, inherited = TRUE) > > > Function: * (package base) > e1="FOOCLASS", e2="matr...

...of other elements in the same layout. In order to use sensitive values for those externally supplied scaling factors (cex) I would like to know how R scales axis font sizes internally. Could someone point me to the method/file in the R-source code (R 2.1.1) where this scaling is done ? Thanks, Hilmar -- Hilmar Berger Studienkoordinator Institut f??r medizinische Informatik, Statistik und Epidemiologie Universit??t Leipzig H??rtelstr. 16-18 D-04107 Leipzig Tel. +49 341 97 16 101 Fax. +49 341 97 16 109 email: hilmar.berger at imise.uni-leipzig.de

...c") a = new("MyClass", x=3, label="FOO") a at .Data > logical(0) a == data.frame(a=1:3) # error I understand that this is all as expected and the error should most likely disappear with the fix you submitted for other 0-extent cases. Thanks again and best regards, Hilmar Am 18/09/2019 um 11:29 schrieb Martin Maechler: >>>>>> Martin Maechler >>>>>> on Wed, 18 Sep 2019 10:35:42 +0200 writes: > >>>>> Hilmar Berger > >>>>> on Sat, 14 Sep 2019 13:31:27 +0200 writes: > >...

...14, so it might fail with more current versions of R or Java (I'm using Oracle Java 8). Still, even if xlsx was the package to be blamed for the crash, I fail to understand what exactly the product operator is trying to do in the multiplication of the matrix with the object. Best regards, Hilmar On 18/04/17 18:57, Hilmar Berger wrote: > Hi, > > this is a problem that occurs in the presence of two libraries (limma, > xlsx) and leads to a crash of R. The problematic code is the wrong > application of sweep or the product ("*") function on an LIMMA MAList > obj...

Hi, I experience surprisingly large timing differences for the multiplication of matrices of the same dimension. An example is given below. How can this be explained? I posted the question on Stackoverflow: https://stackoverflow.com/questions/58886111/r-why-is-matrix-product-slower-when-matrix-has-very-small-values Somebody could reproduce the behavior but I did not get any useful explanations

...uct 1] do not match the length of object [3] As for the NULL/logical(0) cases I would suggest to explicitly test for invalid conditions in Ops.data.frame and generate a comprehensible message (e.g. "comparison is possible only for atomic and list types") if appropriate. Best regards, Hilmar On 11/09/2019 11:55, Hilmar Berger wrote: > > In the data.frame()==NULL cases I have the impression that the fact > that both sides are non-atomic is not properly detected and therefore > R tries to go on with the == method for data.frames. > > From a cursory check in Ops.data...