Displaying 20 results from an estimated 100 matches similar to: "S3 methods in packages. Change in R 4.0.0?"
2019 Nov 16
0
S3 methods in packages. Change in R 4.0.0?
On 15/11/2019 8:42 a.m., Herbert Braselmann wrote:
> Hello,
>
> since Bioconductor devel branch 3.11 started, which is operating with
> R-devel 4.0.0 (for e.g. 2019-11-03 r77362 on OS X 10.11.6 El Capitan),
> my package CFAssay 1.21.0 is not built on none of all three Systems,
> Linux, Windos and Mac. The error message refers to xy.coords which is
> called by R function
2005 Feb 16
4
festival text for weather report
http://www.srh.noaa.gov/fwd/productviewnation.php?pil=OKXZFPOKX&version=
0
can anyone suggest how I could set up asterisk@home to read out allowed
the following text when I dial extension 850?
815 PM EST WED FEB 16 2005
.OVERNIGHT...MOSTLY CLEAR. LOWS 30 TO 35. NORTHWEST WINDS 15 TO 20
MPH WITH GUSTS UP TO 30 MPH...DIMINISHING TO 10 TO 15 MPH LATE.
.THURSDAY...PARTLY CLOUDY. COOLER
2010 Sep 13
4
Problem with WARNING...headers with CRLF line endings
Dear all,
When running R CMD check on Windows XP to test my package I get the
following warning message:
"* checking line endings in C/C++/Fortran sources/headers ... WARNING
Found the following sources/headers with CR or CRLF line endings:
src/xpsDict.h"
The problem is that this file is created by the compiler AUTOMATICALLY
during the compilation process, and since the file is
2023 Nov 03
2
'R CMD INSTALL' keeps going on despite serious errors, and returns exit code 0
Hi list,
Here is an example:
??? hpages at XPS15:~$ R CMD INSTALL CoreGx
??? * installing to library ?/home/hpages/R/R-4.4.r85388/site-library?
??? * installing *source* package ?CoreGx? ...
??? ** using staged installation
??? ** R
??? ** data
??? *** moving datasets to lazyload DB
??? ** inst
??? ** byte-compile and prepare package for lazy loading
??? Error : in method for
2010 Jun 21
1
No output/no source tarball produced by 'R CMD build' on Windows (but ret code is 0)
Hi,
After updating R-2.12 on the Bioconductor build system about 1 week ago
(we update R every 4-6 weeks for our devel builds), we've started to see
something never seen before on Windows: for some BioC packages,
'R CMD build' would produce no output at all (0 byte) and, of course,
no source tarball. Even though, the code returned by the command is 0!
See an example of this is here:
2023 Nov 04
1
'R CMD INSTALL' keeps going on despite serious errors, and returns exit code 0
>>>>> Herv? Pag?s
>>>>> on Fri, 3 Nov 2023 15:10:40 -0700 writes:
> Hi list,
> Here is an example:
> ??? hpages at XPS15:~$ R CMD INSTALL CoreGx ??? * installing
> ??? hpages at XPS15:~$ R CMD INSTALL CoreGx
> ??? * installing to library ?/home/hpages/R/R-4.4.r85388/site-library?
2014 Jun 23
1
operation on ‘numsels’ may be undefined
Dear all,
Since many years the following C++ code does compile on ALL Bioconductor
servers (Linux, Windows, Mac) without any warnings:
Int_t numsels = 0; //number of selected entries
...
for (Int_t i=0; i<size; i++) {
numsels = (arrMask[i] == 1) ? ++numsels : numsels;
}//for_i
Even on the recently added release server 'zin2' Linux (Ubuntu 12.04.4
LTS) the
2011 Feb 03
1
bug in codetools/R CMD check?
Hi Mr Tierney,
I have noticed an error message from R 1.12.x's CMD check for a while (apparently prof Ripley completely rewrote CMD check in R 1.12+)
e.g.:
http://bioconductor.org/checkResults/2.7/bioc-LATEST/snpMatrix/lamb2-checksrc.html
----------------
* checking R code for possible problems ... NOTE
Warning: non-unique value when setting 'row.names': ?new?
Error in
2005 Oct 03
0
unable to compute MAD in aCGH package
Hi,
I am currently using the aCGH package in R version 2.1.0 Windows with some
supporting packages (eg. cluster) built under R 2.1.1.Using aCGH package,
I am able to identify regions of genomic aberrations in my cell lines
using the HMM model. However, when I tried to use aCGH for my paraffin
embeded tumour sample, I got the following warning.
Warning: MAD could not ben computed for one of
2012 Jul 27
2
R bioconductor agilent aCGH analysis
Hi,
I would like to analyze some agilent aCGH copy number files. As a start, I
would like to normalize this data. I don't know what is the standard way to
do this. Which package is the standard one that people use for this
purpose? The chips that I am looking at are the agilent sure print 1M
(G4447a) array and a custom chip with similar format. My raw data is a text
file with spot locations
2011 Oct 25
1
Windows download.file sometimes pauses / truncates large files
With
C:\Users\User>R --version
R version 2.14.0 RC (2011-10-23 r57410)
Copyright (C) 2011 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: x86_64-pc-mingw32/x64 (64-bit)
running
download.file('http://www.ebi.ac.uk/microarray-as/ae/files/E-TABM-25/E-TABM-25.raw.1.zip',
tempfile())
sometimes gets 52% (according to the dialog box) of the way through, and
then
2012 Feb 09
1
scan() doesn't like '1.#IND'
Hi,
Since C++ code compiled with g++ 4.6.3 on Windows (the version included
in latest Rtools) now can produce things like '1.#IND' when writing
doubles to a file (using the << operator), I wonder whether scan()
shouldn't support those things. Right now (with recent R devel and
latest Rtools) we get errors like:
Error in scan(file, what, nmax, sep, dec, quote, skip, nlines,
2018 Feb 07
1
release build of ChemmineR failing
The release version of ChemmineR is failing on windows. It seems to be a
build script issue though, possibly something on your side. The package
was building fine a few weeks ago and I have not modified it. Can you
please have a look? Thanks.
"C:/Users/BIOCBU?1/BBS-3?1.6-B/R/bin/Rscript" -e "library(rmarkdown); library(BiocStyle); rmarkdown::render('ChemmineR.Rmd')"
2008 Oct 03
1
Problem with read.table in Windows and Linux
Hello everyone,
I'm trying to open the same file under Linux and Windows. Under Windows everything is ok but when I try to do it under Linux I have a mistake and I don't know why. This is the mistake:
Error in make.names(col.names,unique=TRUE):
string multibyte 1 invalid
why?
I write this when I want to do it under Windows: zz.info<-read.table(file("C:/Documents and
2010 Jun 10
1
R-based version of R CMD build broken on Windows
Hi,
The R-based version of R CMD build doesn't work for me on Windows:
E:\biocbld\bbs-2.7-bioc>R\bin\R CMD build meat\Biobase
* checking for file 'meat\Biobase/DESCRIPTION' ... OK
* preparing 'Biobase':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to re-build vignettes
Warning in shell(sprintf("%s > %s
2011 Apr 11
1
R CMD build --resave-data
Hi,
More about the new --resave-data option
As mentioned previously here
https://stat.ethz.ch/pipermail/r-devel/2011-April/060511.html
'R CMD build' and 'R CMD INSTALL' handle this new option
inconsistently. The former does --resave-data="gzip" by default.
The latter doesn't seem to support the --resave-data= syntax:
the --resave-data flag must either be
2023 Mar 08
1
Default Generic function for: args(name, default = TRUE)
?.S3methods
f <- function()(2)
> length(.S3methods(f))
[1] 0
> length(.S3methods(print))
[1] 206
There may be better ways, but this is what came to my mind.
-- Bert
On Wed, Mar 8, 2023 at 11:09?AM Leonard Mada via R-help <
r-help at r-project.org> wrote:
> Dear R-Users,
>
> I want to change the args() function to return by default the arguments
> of the default
2003 Jul 12
1
AGI script sample using bash shell script
Hi,
A quick and dirty (aka Rapid Application Developement) AGI script
implement using bash shell. No need to invoke a 10MB perl engine to
process simple asterisk agi scripts.
I found it to be very useful in learning the AGI interface. For example,
I learn that AGI won't execute the next command until you read the
results from STDIN.
Enjoy,
Sunny Woo
Solution Consultant
Avantnix
2013 Mar 03
1
Missing PROTECT in mkPRIMSXP ?
The Bioconductor build for a package DirichletMultinomial on
R Under development (unstable) (2013-02-26 r62077) -- "Unsuffered Consequences"
at
http://bioconductor.org/checkResults/devel/bioc-LATEST/DirichletMultinomial/george2-buildsrc.html
shows
* creating vignettes ... ERROR
...
Error: processing vignette ?DirichletMultinomial.Rnw? failed with diagnostics:
chunk 21 (label
2019 Feb 18
2
Error in rbind(info, getNamespaceInfo(env, "S3methods"))
Dear all,
I'm experiencing an unusual installation error for one package. Could
anyone suggest how I can best investigate this from here please? I'm sorry
this isn't very much to go on. Hopefully someone can point me in the right
direction.
The problem seems to be my library. It is large (3,418 packages) and I'd
like to avoid rebuilding it, if possible. All packages are up to