[R] using boost in R package
Hi All, I am making a R package which is using a boost c++ library. Can some suggest how can I compile the dll in windows using boost. It makes a package but during installation in fails to link boost and give errors Any help will be useful Thanks Vidhu __ 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] Making R Package (how to include a library)
Hi All, I am making a R package which uses some C code. and existing library.My src folder has some .c files. and a Makevars.in Makevars.in contains export PKG_LIBS=-L. -lbz2 R CMD SHLIB bed2vector.C R CMD SHLIB wdl.C R CMD SHLIB peaks.C R CMD SHLIB cdensum.c When I try library(libraryname). It gives me error undefined symbol: BZ2_bzRead Can anyone please suggest how to include a exiting library along with .c files to make a Rpackage thank you vidhu [[alternative HTML version deleted]] __ 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] Reading the data from specific columns
Hi All, I have a huge tab separated file which a many columns. I want to read only few specific columns in R object. There are no column names/headers in the file. Can someone please suggest how can I do that. I checked the help of read.delim but wasnt able to find such option Thank you Reagards Vidhu [[alternative HTML version deleted]] __ 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] RSQLite maximum table size
Hi All, I am trying to make write a table in RSQLite. And I get the error mentioned below mat-as.data.frame(matrix(rnorm(n=24400),nrow=244000,ncol=1000)) dbWriteTable(con, array, mat) [1] FALSE *Warning message: In value[[3]](cond) : RS-DBI driver: (error in statement: too many SQL variables)* Can someone please tell me what is maximum size of a table( max number of rows and cols) we can have in RSQLite and how big the database can grow Thank you Regards Vidhu [[alternative HTML version deleted]] __ 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] Possible cause of the error: unknown c standard 'gnu99'
Hi All, I am getting error unknown c standard 'gnu99'. I have attached the screen shot. Can anyone suggest what is causing this error thank you Best regards Vidhu __ 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 in `[.matrix.coo`(x, rw, cl) : Subscripts out of bound
Hi All,
I am facing a strange problem. I am making a R Package that internally run
various packages and summarizes the results from them.
I am getting this error from the piece of code written below. The text in
red color is throwing
Error in `[.matrix.coo`(x, rw, cl) : Subscripts out of bound
Value of m is 99
This code works fine when I tested it. But money I make library it gives me
error.
I have attached the file names messages.txt which contains the
warnings/messages generated while making R package.
I am out of ideas
Kindly suggest something
regards
vidhu
`sm.quantreg` -
function(y, lambda = 1.0, tau = 0.5, interpolate = FALSE) {
nona - !is.na(y)
## Sparse matrices: E, D, and B
if(!interpolate) {
y.nona - y[nona]
m - length(y.nona) *1.0
E - as.matrix.csr(0,m,m)
diag(E) - 1
*D - diff(E)*
B - rbind(E, lambda * D)
ystar - c(y.nona, rep(0,m-1))
}else {
## interpolate missing values via weighting
y[!nona] - 0
m - length(y) *1.0
E - as.matrix.csr(0,m,m)
diag(E) - 1
D - diff(E)
tmp - as.matrix.csr(0,m,m)
diag(tmp) - as.numeric(nona)
B - rbind(tmp, lambda * D)
ystar - c(y, rep(0,m-1))
}
## use sparse matrices and accompanying mathematical operations
cat (before try\n)
try(myrq - rq.fit.sfn(as.matrix.csr(B), ystar, tau))
cat (after try\n)
if(exists(myrq)) {
if(!interpolate) {
ys - rep(NA, length(y))
ys[nona] - myrq$coef
}else {
ys - myrq$coef
}
}else {
cat(Error triggered within Quantreg algorithm!\n)
ys - NULL
}
return(ys)
}
##
C:\Documents and Settings\Administrator\My DocumentsR CMD INSTALL t1
installing to 'c:/R/R-2.6.2/library'
-- Making package t1
adding build stamp to DESCRIPTION
installing NAMESPACE file and metadata
making DLL ...
gcc-sjlj -std=gnu99 -IC:/R/R-2.6.2/include -O3 -Wall -c CGHseg_rewrite.c
-o CGHseg_rewrite.o
gcc-sjlj -std=gnu99 -IC:/R/R-2.6.2/include -O3 -Wall -c rowMedians.c -o r
owMedians.o
gcc-sjlj -std=gnu99 -IC:/R/R-2.6.2/include -O3 -Wall -c runavg.c -o runav
g.o
windres --preprocessor=gcc-sjlj -E -xc -DRC_INVOKED -I C:/R/R-2.6.2/include -
i t1_res.rc -o t1_res.o
gcc-sjlj -std=gnu99 -shared -s -o t1.dll t1.def CGHseg_rewrite.o rowMedians.o
runavg.o t1_res.o -LC:/R/R-2.6.2/bin-lR
... DLL made
installing DLL
installing R files
installing data files
installing man source files
installing indices
not zipping data
installing help
Building/Updating help pages for package 't1'
Formats: text html latex example chm
checkUploadFileFormat texthtmllatex example
runAnalysis texthtmllatex example
runCGHAnalysistexthtmllatex example
preparing package t1 for lazy loading
Loading required package: waveslim
Loading required package: quantreg
Loading required package: SparseM
Loading required package: snapCGH
Loading required package: limma
Loading required package: tilingArray
Loading required package: Biobase
Loading required package: tools
Welcome to Bioconductor
Vignettes contain introductory material. To view, type
'openVignette()'. To cite Bioconductor, see
'citation(Biobase)' and for packages 'citation(pkgname)'.
Loading required package: affy
Loading required package: affyio
Loading required package: preprocessCore
Attaching package: 'affy'
The following object(s) are masked from package:waveslim :
pm
Loading required package: RColorBrewer
Loading required package: grid
Loading required package: strucchange
Loading required package: zoo
Loading required package: sandwich
Loading required package: vsn
Loading required package: genefilter
Loading required package: survival
Loading required package: splines
Attaching package: 'survival'
The following object(s) are masked from package:quantreg :
untangle.specials
Loading required package: geneplotter
Loading required package: annotate
Loading required package: AnnotationDbi
Loading required package: DBI
Loading required package: RSQLite
Loading required package: xtable
Loading required package: lattice
KernSmooth 2.22 installed
Copyright M. P. Wand 1997
Loading required package: pixmap
Loading required package: DNAcopy
Attaching package: 'DNAcopy'
The following object(s) are masked from package:tilingArray :
segment
Loading required package: GLAD
Loading required package: aws
Loading required package: tcltk
Loading Tcl/Tk interface ... done
Loading required package: cluster
Loading required package: aCGH
Loading required package: multtest
Loading required package: sma
Attaching package: 'aCGH'
The following object(s) are masked from package:stats :
heatmap
Attaching package: 'snapCGH'
The following object(s) are masked from
Re: [R] Error while making R package
Hi All, *I am still facing the problems in making R package on windows. * -- Making package t1 adding build stamp to DESCRIPTION installing NAMESPACE file and metadata making DLL ... making CGHseg_rewrite.d from CGHseg_rewrite.c making rowMedians.d from rowMedians.c making runavg.d from runavg.c gcc-sjlj -std=gnu99 -IC:/R/R-2.6.2/include -O3 -Wall -c CGHseg_rewrite.c -o CGHseg_rewrite.o gcc-sjlj -std=gnu99 -IC:/R/R-2.6.2/include -O3 -Wall -c rowMedians.c -o rowMedians.o gcc-sjlj -std=gnu99 -IC:/R/R-2.6.2/include -O3 -Wall -c runavg.c -o runavg.o windres --preprocessor=gcc-sjlj -E -xc -DRC_INVOKED -I C:/R/R-2.6.2/include -i t1_res.rc -o t1_res. o gcc-sjlj -std=gnu99 -shared -s -o t1.dll t1.def CGHseg_rewrite.o rowMedians.o runavg.o t1_res.o -L C:/R/R-2.6.2/bin-lR ... DLL made installing DLL installing R files installing data files rm: failed to get attributes of `/': No such file or directory make[2]: *** [c:/R/R-2.6.2/library/t1/data] Error 1 make[1]: *** [all] Error 2 make: *** [pkg-t1] Error 2 *** Installation of t1 failed *** Removing 'c:/R/R-2.6.2/library/t1' Restoring previous 'c:/R/R-2.6.2/library/t1' *I have made registry changes also as per the link : https://stat.ethz.ch/pipermail/r-devel/2008-January/048059.html * *I can successfully make the package on Linux. * But when I try to R CMD INSTALL on windows( package made in linux) I get the same error of rm: failed to get attributes of `/': No such file or directory make[2]: *** [c:/R/R-2.6.2/library/t1/data] Error 1 I am attaching the .tar file made on windows2000 Thank you Best Regards Vidhu __ 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 while making R package
Hi All, I am trying to make R package using R 2.6.2 And I am getting following error. When I give R CMD check t1\ -- Making package t1 adding build stamp to DESCRIPTION making DLL ... making CGHseg_rewrite.d from CGHseg_rewrite.c making rowMedians.d from rowMedians.c making runavg.d from runavg.c gcc-sjlj -std=gnu99 -Ic:/R/R-2.6.2/include -O3 -Wall -c CGHseg_rewrite.c -o CGHseg_rewrite.o gcc-sjlj -std=gnu99 -Ic:/R/R-2.6.2/include -O3 -Wall -c rowMedians.c -o rowMedians.o gcc-sjlj -std=gnu99 -Ic:/R/R-2.6.2/include -O3 -Wall -c runavg.c -o runavg.o windres --preprocessor=gcc-sjlj -E -xc -DRC_INVOKED -I c:/R/R-2.6.2/include -i t1_res.rc -o t1_res.o gcc-sjlj -std=gnu99 -shared -s -o t1.dll t1.def CGHseg_rewrite.o rowMedians.o runavg.o t1_res.o -Lc:/R/R-2.6.2/bin-lR ... DLL made installing DLL installing R files installing data files rm: failed to get attributes of `/': No such file or directory make[2]: *** [C:/Vidhu/CGH/RPackage/t1.Rcheck/t1/data] Error 1 make[1]: *** [all] Error 2 make: *** [pkg-t1] Error 2 *** Installation of t1 failed *** Can you please suggest what could be the probable cause of the error Thank you Vidhu [[alternative HTML version deleted]] __ 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 stop buffering of cat
Hi All, My R code takes very long time to finish the processing. I want to see at what stage the script is running. So I wrote some output messages using cat. But instead of displaying the cat messages at different stages they are buffered and displayed in the end when entire processing is done. Can you please suggest how to stop this buffering or some alternative way to display messages Thank you Vidhu [[alternative HTML version deleted]] __ 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 hide the warnings
Hi All, I want to hide all the system(R) generated warning messages and want only the messages from my script should be shown when i run myscript.R Can you please suggest how can I hide the warnings Thank you Vidhu [[alternative HTML version deleted]] __ 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] c code working in linux and hanging in windows
Hi All, I am calling some c code from R. It successfully makes the dll and .so files. When I run .so in Linux is works prefect but hangs in windows. Though the dll loads but it never returns back from the c function Can you please suggest the possible cause of this thank you vidhu [[alternative HTML version deleted]] __ 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] FASeg
Hi All, I was using FASeg package. Now when I am trying to install this library I get the message Warning message: package 'FASeg' is not available Can someone please suggest something. Thank you vidhu [[alternative HTML version deleted]] __ 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] making a dll for windows eviornment for R
Hi All, I have a .c file and I need to make a dll so that it could be called by R. I have successfully made .so from .c file and its working great. But i have no clue of making dll. I tried googling for help ...but not much of use Please suggest something regards Vidhu [[alternative HTML version deleted]] __ 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] read table not reading lines containing single quotes
Hi, * I am using read.table command as follow kegg-read.table(c:/IDs.tab,header =TRUE,quote= ', sep=\t) * Fragment of file is as follow: ID Pathway 04916Melanogenesis 04920Adipocytokine signaling pathway 04930Type II diabetes mellitus 04940Type I diabetes mellitus 04950Maturity onset diabetes of the young 05010Alzheimer's disease 05020Parkinson's disease 05030Amyotrophic lateral sclerosis (ALS) 05040Huntington's disease 05050Dentatorubropallidoluysian atrophy (DRPLA) *It doesnot read from Alzheimer's disease. Due the single qoutes in it. Can you please suggest something so that I can read full file. * Thank you Vidhu [[alternative HTML version deleted]] __ 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] Cannot run R from command prompt
Hello, I have installed R 2.6 on windows 2000 and now from the command prompt when I type R it show 'R' is not recognized as an internal or external command, operable program or batch file. If I change the path to C:\R\R-2.6.2\bin and then type R it runs fine. I have changed my envionment variable Path to C:\R\R-2.6.2\bin; Still its not working. Can you please give some suggestion Thank you Vidhu [[alternative HTML version deleted]] __ 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 in plot.new() : figure margins too large
Hi
I am getting error :
Error in plot.new() : figure margins too large
Can you please help
-code is
temp - seq(550/2, 2200, 550/2)
sV2 - c(1, 1+temp[-length(temp)])
eV2 - temp
i=1
bitmap(paste(c:/vidhu/poster/poster_56half_2, LETTERS[i], .png, sep =
), png256,width = 55.5, height = 8.875, res = 300)
par(mfrow = c(28,1), mar = c(0.5,3,0.5,0.5), mgp = c(2,0.65,0))
for(i in 1:length(sV2)) {
cat(i = , i, \n, sep = )
if (i%%2)
{
pSL(sV2[i], eV2[i], 5)}
}
dev.off()
windows()
[[alternative HTML version deleted]]
__
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.
