similar to: 3 minor issues with getClass 'resolve.msg' arg

>>>>> Herv? Pag?s <hpages at fredhutch.org> >>>>> on Sun, 26 Jun 2016 13:21:00 -0700 writes: > Hi, > It turns out that two packages (1 Bioconductor, 1 CRAN) define an > S4 class called "Annotated": > library(S4Vectors) # see (*) at bottom for how to install > library(RNeXML) > 1st issue >

Hello, I apologize that I am cross posting here after getting no answer from my initial question on stack overflow <http://stackoverflow.com/questions/33492601/r-setoldclass-only-if-needed>. I should certainly have posted it first here.. I am using 3 packages: - xts - quantmod - 'myPackage' quantmod is creating a union class by doing: setOldClass("xts");

On 05/16/2018 01:24 PM, Michael Lawrence wrote: > On Wed, May 16, 2018 at 12:23 PM, Herv? Pag?s <hpages at fredhutch.org> wrote: >> On 05/16/2018 10:22 AM, Michael Lawrence wrote: >>> >>> Factors and data.frames are not structures, because they must have a >>> class attribute. Just call them "objects". They are higher level than >>>

Hi, Can anyone help? I get the following error when trying to complie the h323 channel under the source installation directory asterisk/channels/h323 i have read the readme file and kept to the recomended versions; h.323 v1.12.2 and PWLIB v1.5.2 Thanks in advance [root@gw01 h323]# make g++ -g -c -fno-rtti -o ast_h323.o -march=i686 -DPBYTE_ORDER=PLITTLE_ENDIAN -DNDE BUG -DDO_CRASH

On 06/08/2018 10:15 AM, Michael Lawrence wrote: > There probably should be an abstraction for this. In S4Vectors, we > have extractROWS(). FWIW the code in S4Vectors that does what your subset_ROW() does is: https://github.com/Bioconductor/S4Vectors/blob/04cc9516af986b30445e99fd1337f13321b7b4f6/R/subsetting-utils.R#L466-L476 (This is the default "extractROWS" method.) Except

Dear list, I'm just getting started learning how to use remote supercomputers for execution of parallelized code. I got a lot of initial help from this <http://stackoverflow.com/questions/14553357/parallelizing-on-a-supercomputer-and-then-combining-the-parallel-results-r> previous post, as well as one particularly helpful and patient XSEDE guy. I'm only using one node (for the

Hi, I am having trouble installing the Open H.323 Channel driver in Asterisk. I have installed PWLib and OpenH323 V.1.11.7 This is the output l get before it bails out. asterisk:/usr/src/asterisk/channels/h323# make g++ -g -c -o ast_h323.o -march=i686 -DPBYTE_ORDER=PLITTLE_ENDIAN -DNDEBUG -DDO_CRASH -DDEBUG_THREADS -pipe -Wall -fPIC -Wmissing-prototypes -Wmissing-declarations -DP_LINUX

Good day, If the library path is changed with .libPaths, the command install.packages("/nb/dario/Biostrings_2.39.9.tar.gz", repos=NULL) fails with ** testing if installed package can be loaded Error : package ?S4Vectors? required by ?Biostrings? could not be found However, running library(S4Vectors) followed by sessionInfo() after the error shows that the package can indeed be

Hello, am I using 'setIs' in the correct way in the subsequent (artifical) example? Do I have to specify explicit 'setAs' for 'list' and 'vector' or should this work automatically, since "getClass("List1")" states an explicit coerce also for these classes. I'm working with R 2.0.0 Patched (2004-10-06) on windows 2000. Thanks for your

On 05/16/2018 10:22 AM, Michael Lawrence wrote: > Factors and data.frames are not structures, because they must have a > class attribute. Just call them "objects". They are higher level than > structures, which in practice just shape data without adding a lot of > semantics. Compare getClass("matrix") and getClass("factor"). > > I agree that

Hi All, I've just rebuild the latest R with the Goto BLAS on our new Intel quad core machines. I did a few basic matrix calculations, and I was very impressed by the performance I saw. I wonder if anyone has a more rigorous benchmarking program for R. I downloaded a old R test/benchmarking program (see below), and this didn't work with the current R, and so I wondered if anyone could

A generic for displaying an object in a cell would be a reasonable solution for this particular problem. However, as soon as you start treating these objects as data (like putting them into a matrix), you're likely going to want vectorized operations over them, which means formalized vector and matrix classes. S4Vectors in Bioconductor facilitates this for vectors, but not for higher-order

Encountered an error in scripting, which can be reproduced using Rscript as follows: $ Rscript -e "library(httr); handle('http://cran.r-project.org')" Error in getCurlHandle(cookiefile = cookie_path, .defaults = list()) : could not find function "getClass" Calls: handle -> getCurlHandle or by starting R without the methods package attached: $

Malcolm, I tested the code on a clean R 3.2.0 session. Not even in RStudio, just to rule that out. > sessionInfo() R version 3.2.0 (2015-04-16) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 8 x64 (build 9200) locale: [1] LC_COLLATE=English_United Kingdom.1252 [2] LC_CTYPE=English_United Kingdom.1252 [3] LC_MONETARY=English_United Kingdom.1252 [4] LC_NUMERIC=C [5]

Hi all, I am using R and JRI under Windows XP Pro. I am posting this question here since the reason might be R related (since I am running an R script) but there is also a very good chance that it is JRI only (since I am using the JRI interface to activate the script) -- in which case I want to apologize for misplacing this message. I have a method that instantiates an REngine object every time

I have an S4 class with a slot of class "array", and in upgrading to 2.0.1 (from 1.9.1) I have encountered a change in behaviour. This causes me some difficulties if I want to allow 2-dimensional arrays in the slot. The following (in 2.0.1) illustrates the point: > setClass("foo",representation("array")) [1] "foo" > a <-

Hi, ?pairlist gives no explanation about what exactly is the difference between a pairlist and a list (except that a pairlist of length 0 is 'NULL'). So, what's a pairlist? class(.Options) [1] "pairlist" Some strange things about the "pairlist" type: > showClass("pairlist") Error in getClass(Class) : "pairlist" is not a defined class

I noticed about a couple weeks ago that my R start up script starting showing the below errors, following the line "Type 'q()' to quit R" Not sure what I did different and so far it hasn't caused major problems but kind of fear that it will. Can you please help? I also posted my Rprofile below. Attempting to load the environment 'package:R.utils' R.methodsS3 v1.2.2

I'm having trouble using binomial(link="cloglog") with GLMM in lme4, Version: 0.5-2, Date: 2004/03/11. The example in the Help file works fine, even simplified as follows: fm0 <- GLMM(immun~1, data=guImmun, family=binomial, random=~1|comm) However, for another application, I need binomial(link="cloglog"), and this generates an error for me: >

Hi, further down from the problem I asked about yesterday I encounter the following problem (please appologize for the lengthy mail - I have not found a brief example making the issue clear): - using R packages making use of namespaces & - S4 classes when using --with-package-versions in the install call: Pkgs install ok and the first pkg 'base' can be loaded in R