[R] set attribute method question
Hi, All;
Suppose I have a class 'dat' such that setClass('dat', representation
(.version='character', x='numeric', y='numeric')).
If I want to make a method that changes the .version slot of 'dat'
class in a way like set.version(d) - '0.2' when d is an object of
'dat' class, how can I do this? Thanks in advance.
Tae-Hoon Chung
Post-Doctoral Researcher
Computational Biology Division, TGEN
445 N 5th St. Phoenix, AZ 85004 USA
O: 1-602-343-8724
F: 1-602-343-8840
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[R] set class attribute method question
Hi, All;
Suppose I have a class 'dat' such that setClass('dat', representation
(.version='character', x='numeric', y='numeric')).
If I want to make a method that changes the .version slot of 'dat'
class in a way like set.version(d) - '0.2' when d is an object of
'dat' class, how can I do this? Thanks in advance.
Tae-Hoon Chung
Post-Doctoral Researcher
Computational Biology Division, TGEN
445 N 5th St. Phoenix, AZ 85004 USA
O: 1-602-343-8724
F: 1-602-343-8840
[[alternative HTML version deleted]]
__
R-help@stat.math.ethz.ch 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 dyn.load()
Hi, All; I tried to load the 'genetics' library but it failed with the following message. Can you help me with this? Thanks in advance. library(genetics) Loading required package: gdata Error in dyn.load(x, as.logical(local), as.logical(now)) : unable to load shared library '/Library/Frameworks/R.framework/ Versions/2.5/Resources/library/gtools/libs/ppc/gtools.so': dlopen(/Library/Frameworks/R.framework/Versions/2.5/Resources/ library/gtools/libs/ppc/gtools.so, 6): Library not loaded: /Library/ Frameworks/R.framework/Versions/2.4/Resources/lib/libR.dylib Referenced from: /Library/Frameworks/R.framework/Versions/2.5/ Resources/library/gtools/libs/ppc/gtools.so Reason: Incompatible library version: gtools.so requires version 2.4.0 or later, but libR.dylib provides version 2.2.0 Error: package 'gdata' could not be loaded I am using Mac OS X R 2.5.0. The libraries, 'genetics' v1.2.1, 'gtools' v2.3.1, and 'gdata' v2.3.1 are already installed. Tae-Hoon Chung Post-Doctoral Researcher Computational Biology Division, TGEN 445 N 5th St. Phoenix, AZ 85004 USA O: 1-602-343-8724 F: 1-602-343-8840 [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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] Resolved: Error in dyn.load()
Hi, All; I simply upgraded my R from version 2.5.0 to 2.5.1 and the whole problems disappeared. So I am closing the question myself. It could have been the R version problem. Tae-Hoon Chung Post-Doctoral Researcher Computational Biology Division, TGEN 445 N 5th St. Phoenix, AZ 85004 USA O: 1-602-343-8724 F: 1-602-343-8840 [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch 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] Way to make R idle for some time and try something again later
Hi, All; I have a question. In R, what is the best way to make R idle for a while and try something again later? For example, suppose there is an R job which accesses a file that may be shared with other active jobs. So when the file is being accessed by other job, your job will not be able to access the file and your job will crash because of that. To avoid this, you want your job to try to access the file repeatedly with some time interval, say every 10 seconds or something like that. Which is the best way to do this in R? Thanks in advance, Tae-Hoon Chung Post-Doctoral Researcher Translational Genomics Research Institute (TGen) 445 N. 5th Street (Suite 530) Phoenix, AZ 85004 1-602-343-8724 (Direct) 1-480-323-9820 (Mobile) 1-602-343-8840 (Fax) __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Library mclust in 64bit compiled R
Hi, All;
I tried to use library mclust in 64-bit compiled R 2.0.1 but failed.
Installation went smoothly without any warning or error. However, when I
tried to use them with the following simple code, it crashed.
Library(mclust)
Dat - c(rnorm(20, mean=0, sd=0.2), rnorm(30, mean=1, sd=0.2))
Ind - Mclust(dat, 1, 5)$classification
cbind(Dat, Ind)
The error message was:
/usr/local/R-2.0.1_64bit/lib/R/bin/BATCH: line 55: 18097 Done
( echo invisible(options(echo = TRUE)); cat ${in}; echo proc.time() )
18099 Segmentation fault | ${R_HOME}/bin/R ${opts} ${out} 21
Can anybody help me with this?
Thanks in advance,
Tae-Hoon Chung
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Re: [R] x[x$a==q,,drop=TRUE]
Hi, Mikkel; The problem here, I think, is that spray$PD is NOT recognized as character in R. Actually, R understands it as factors according to your printout. This happens quite a lot if you use read.table and come across characters within the data file. One remedy I use often use is doing something like spray$PD - as.character(spray$PD) to make it sure that spray$PD is character. Tae-Hoon Chung -- Tae-Hoon Chung Post-Doctoral Researcher Translational Genomics Research Institute (TGen) 445 N. 5th Street (Suite 530) Phoenix, AZ 85004 1-602-343-8724 (Direct) 1-480-323-9820 (Mobile) 1-602-343-8840 (Fax) -- On 6/1/05 11:08 AM, Mikkel Grum [EMAIL PROTECTED] wrote: I'm trying to select a subset of a dataframe while dropping some factors. While the dataset gets smaller all Factor levels remain and I need to get rid of them. Strangely enough, I am almost certain that the same code on the same data worked OK earlier today - and it is not the first time that I'm not able to replicate earlier results with this command (I know, I might just be going crazy). What am I doing wrong? I'm working on Windows Server 2003, R 2.1.0 (2005-04-18). str(spray) `data.frame': 370 obs. of 7 variables: $ PD: Factor w/ 8 levels Botrytis,Downy,..: 2 2 2 2 4 2 2 5 5 5 ... $ postSpmtsQ: num 1309 1309 384 384 1044 ... $ ante62Q : num 284 284 218 218 366 ... $ ante08Q : num 331 331 228 228 492 ... $ ante29Q : num 297 297 1067 1067 1034 ... $ ante16Q : num 0 0 0.2 0.2 0 0 0 6.7 0 31.5 ... $ Trt : Factor w/ 41 levels Acrobat MZ WP,..: 27 5 27 5 36 27 5 24 24 24 ... sprayS - spray[spray$PD == Spidermites, , drop = TRUE] str(sprayS) `data.frame': 111 obs. of 7 variables: $ PD: Factor w/ 8 levels Botrytis,Downy,..: 5 5 5 5 5 5 5 5 5 5 ... $ postSpmtsQ: num 13395 31588 84254 136 619 ... $ ante62Q : num 1357 21187 21819 218 237 ... $ ante08Q : num973 21740 25112 228 134 ... $ ante29Q : num2103 106970 66676 1067119 ... $ ante16Q : num 6.7 0 31.5 0.2 0 0 0 0 14.3 0 ... $ Trt : Factor w/ 41 levels Acrobat MZ WP,..: 24 24 24 24 24 24 24 24 24 24 ... table(sprayS$Trt) Acrobat MZ WP Agrifos Apollo 50 SC CALMAG 0 013 0 DM-31Dynamec 1.8 EC Equation Pro DF Evisect S 013 0 0 Flint Floramite Impulse Karate 015 0 0 Karate zeonMelodyMeltatox 40 EC MKP 0 0 0 0 Molasses Nembicidine Nimrod 250 EC Nissorun 10 EC 0 0 0 12 Oberon Orthene 75 WP Oscar 20 SC Pegasus 15 0 9 26 Polar 50 WSGPotfos Proplant Pyrus 0 0 0 0 Ridomil MZ 63 5WP Rovral aqua flo Score 250 EC Secure 36 SC 0 0 0 8 Sequestrone Shavit f Sporekill Stroby 50 WG 0 0 0 0 SwitchTracer Trafos K Vandozeb 0 0 0 0 Vitomex 0 cheers, Mikkel __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Plotting dendrogram horizontally
Hi, All; I tried to plot a dendrogram horizontally using following codes: hc.g - hclust(dist(mat), method=single) plot(as.dendrogram(hc.g), horiz=T, ...) While I was trying this (single linkage was IMPORTANT) with a matrix with size 587 rows, an error happened with a message saying [1] Error in match.fun(FUN) : evaluation nested too deeply: infinite recursion options(expression=)?\n attr(,class) [1] try-error If I used other linkage methods, this error didn't happen. Only for single linkage method, this error took place. Is there any other way I can plot dendrogram horizontally without using as.dendrogram? Thanks in advance, Tae-Hoon Chung -- Tae-Hoon Chung Post-Doctoral Researcher Translational Genomics Research Institute (TGen) 445 N. 5th Street (Suite 530) Phoenix, AZ 85004 1-602-343-8724 (Direct) 1-480-323-9820 (Mobile) 1-602-343-8840 (Fax) __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Error while generating dendrogram
Hi, All; When I was trying to convert the result object of hierarchical clustering into an instance of dendrogram class using as.dendrogram() and plot the resulting dendrogram horizontally, I got the following error message: [1] evaluation nested too deeply: infinite recursion\ Options(expression=)? Attr(,class) [1] try-error This error happened while I was experimenting a function generating a composite plot of heatmap + dendrogram of gene clusters + dendrogram of sample clusters in microarray data analysis. The source chunk is a bit long but the part of origin for error is like this: ... hc - hclust(mat, single) ### THIS WORKED FINE! plot(hc, hang=-1) ### THIS ALSO WORKED FINE! IMAGE GENERATED ... dend - as.dendrogram(hc) ### THIS SEEMS TO WORK FINE! plot(dend, horizontal=T, axes=F, ann=F, yaxs=i, leaflab=none) ### ERROR! ... 1. Can anyone suggest solutions? Actually this is first time I get this type of error message. 2. If converting hc to dendrogram class causes the trouble, is there anyone who can suggest a simple method of generating a dendrogram in horizontal direction not in vertical direction? Thanks in advance; Tae-Hoon Chung -- Tae-Hoon Chung Post-Doctoral Researcher Translational Genomics Research Institute (TGen) 445 N. 5th Street (Suite 530) Phoenix, AZ 85004 1-602-343-8724 (Direct) 1-480-323-9820 (Mobile) 1-602-343-8840 (Fax) __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Special paper for postscript
Hi, All; When I generate a special paper postscript image larger than a4 or letter using R, I can only see one-page portion of all image, of course. What will be the simple solution for this? Is there any way I can set the bounding box information on the image? Or any other suggestions? Thanks in advance; Tae-Hoon Chung -- Tae-Hoon Chung Post-Doctoral Researcher Translational Genomics Research Institute (TGen) 445 N. 5th Street (Suite 530) Phoenix, AZ 85004 1-602-343-8724 (Direct) 1-480-323-9820 (Mobile) 1-602-343-8840 (Fax) __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Segmentation fault while using Mclust function of mclust library in R-2.0.1
Hi, all; I got an unusual error while using mclust library 2.1-7 on R 2.0.1. When I tried to run Mclust(rnorm(100)), I got segmentation fault error. Does anyone know what causes this problem? I came across the same problem even when I tried to run the example shown in Mclust help using iris data. Thanks in advance, Tae-Hoon Chung -- Tae-Hoon Chung Post-Doctoral Researcher Translational Genomics Research Institute (TGen) 445 N. 5th Street (Suite 530) Phoenix, AZ 85004 1-602-343-8724 (Direct) 1-480-323-9820 (Mobile) 1-602-343-8840 (Fax) __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Memory problem ... Again
Happy new year to all; A few days ago, I posted similar problem. At that time, I found out that our R program had been 32-bit compiled, not 64-bit compiled. So the R program has been re-installed in 64-bit and run the same job, reading in 150 Affymetrix U133A v2 CEL files and perform dChip processing. However, the memory problem happened again. Since the amount of physical memory is 64GB, I think it should not be a problem. Is there anyway we can configure memory usage so that all physical memory can be utilized? Our system is like this: System type: IBM AIX Symmetric Multiprocessing (SMP) OS version: SuSe 8 SP3a CPU: 8 Memory: 64GB The codes are as follows: Data - ReadAffy(filenames = paste(HOME, CelData/, fname, sep=)) eset - expresso(Data, normalize.method=invariantset, bg.correct=FALSE, pmc\ orrect.method=pmonly, summary.method=liwong) normalization: invariantset PM/MM correction : pmonly expression values: liwong normalizing...Error: cannot allocate vector of size 594075 Kb gc() used (Mb) gc trigger (Mb) Ncells 797971 21.41710298 45.7 Vcells 76716794 585.4 305954055 2334.3 ... mem.limits() nsize vsize NANA object.size(Data) [1] 608355664 memory.profile() NILSXP SYMSXPLISTSXP CLOSXP ENVSXPPROMSXPLANGSXP 1 30484 372383 4845420180 127274 SPECIALSXP BUILTINSXPCHARSXP LGLSXP INTSXP 203 1168 111430 5296 0 0 44650 REALSXPCPLXSXP STRSXP DOTSXP ANYSXP VECSXPEXPRSXP 13382 9 60170 0 0 26003 0 BCODESXP EXTPTRSXP WEAKREFSXP 0106 0 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Memory problem ... Again = False Alarm !!!
Thanks Peter and Andy; I just found it was not due to memory problem. It was false alarm ... 64-bit compiled program works fine! On 1/3/05 3:39 PM, Peter Dalgaard [EMAIL PROTECTED] wrote: Tae-Hoon Chung [EMAIL PROTECTED] writes: Happy new year to all; A few days ago, I posted similar problem. At that time, I found out that our R program had been 32-bit compiled, not 64-bit compiled. So the R program has been re-installed in 64-bit and run the same job, reading in 150 Affymetrix U133A v2 CEL files and perform dChip processing. However, the memory problem happened again. Since the amount of physical memory is 64GB, I think it should not be a problem. Is there anyway we can configure memory usage so that all physical memory can be utilized? Our system is like this: System type: IBM AIX Symmetric Multiprocessing (SMP) OS version: SuSe 8 SP3a CPU: 8 Memory: 64GB . expression values: liwong normalizing...Error: cannot allocate vector of size 594075 Kb gc() used (Mb) gc trigger (Mb) Ncells 797971 21.41710298 45.7 As Brian Ripley told you, 64-bit builds of R has 56byte Ncells, so if yours was one, you should have 797971*56/1024/1024 [1] 42.61625 i.e. 42.6Mb used for your Ncells, and it seems that you don't __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Configuration of memory usage
Hi, all; I know there has been a lot of discussions on memory usage in R. However, I have some odd situation here. Basically, I have a rare opportunity to run R in a system with 64GB memory without any limit on memory usage for any person or process. However, I encountered the memory problem error message like this: Error: cannot allocate vector of size 594075 Kb I got this error message while I was trying to apply dChip preprocessing procedures for 150 Affymetrix U133v2 chips that has 22,000 probe sets on them. The actual codes I ran was like this: Data - ReadAffy(filenames = paste(HOME, CelData/, fname, sep=)) mem.limits() nsize vsize NANA gc() used (Mb) gc trigger (Mb) Ncells 530216 14.2 899071 24.1 Vcells 76196137 581.4 243983468 1861.5 eset - expresso(Data, normalize.method=invariantset, bg.correct=FALSE, pmc\ orrect.method=pmonly, summary.method=liwong) normalization: invariantset PM/MM correction : pmonly expression values: liwong normalizing...Error: cannot allocate vector of size 594075 Kb gc() used (Mb) gc trigger (Mb) Ncells 797983 21.41710298 45.7 Vcells 76716811 585.4 305954068 2334.3 object.size(Data) [1] 608355664 memory.profile() NILSXP SYMSXPLISTSXP CLOSXP ENVSXPPROMSXPLANGSXP 1 30484 372373 4845420180 127274 SPECIALSXP BUILTINSXPCHARSXP LGLSXP INTSXP 203 1168 111434 5296 0 0 44649 REALSXPCPLXSXP STRSXP DOTSXP ANYSXP VECSXPEXPRSXP 13382 9 60173 0 0 26002 0 BCODESXP EXTPTRSXP WEAKREFSXP 0106 0 Although I have no idea of memory allocation in R, apparently something's wrong with this. The memory problem must have nothing to do with physical memory. My question is this. Is this memory problem due to some non-optimal configuration of memory usage? If so, then what will be the optimal configuration for this? If not, then there must be problems on actual implementations of functions I used here, right? The reason I am asking this is that, according to the reference manual, the error message I got can be brought up by roughly three reasons. First, when the system is unable to provide the R requested memory. Second, when the requested memory size exceeds the address-space limit for a process. Finally, when the length of a vector is larger than 2^31-1. I wonder the problem has anything to do with the third case. (If so, then I think I am hopeless unless the internal implementations change...) __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] R on IBM P-Series either with AIX or Linux
Hi, all; I have a quick question. Does R work properly on IBM P-series? Is there any technical catches that should be payed special attention to? Currently, we tried to install and run R on an IBM P-series machine with AIX 5.1 but we experienced some technical difficulties. In particular, R does not properly use all available memory and there seems to be some other minor difficulties. Thanks in advance; Tae-Hoon Chung, Ph.D Post-doctoral Research Fellow Molecular Diagnostics and Target Validation Division Translational Genomics Research Institute 1275 W Washington St, Tempe AZ 85281 USA Phone: 602-343-8724 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] e1071 question: what's the definition of performance in t une.* functions?
Thank you Andy. It seems like this can be the reason for the confusion. I never thought that there can be this kind of catches for using tune.* functions. For the record, I actually emailed to Dr. Friedrich Leisch the author of this library. When I get some reply, I will post it also. Regards, TH On Jul 12, 2004, at 6:40 PM, Liaw, Andy wrote: Looking at the body of tune(), it has: ... repeat.errors[reps] - if (is.factor(true.y)) 1 - classAgreement(table(pred, true.y)) else crossprod(pred - true.y)/length(pred) ... where classAgreement() is a function defined inside tune() that computes the fraction of correctly predicted cases. So it looks like tune() and friends are returning error rates as fractions, not percentages. You're right that the fraction shouldn't be larger than 1. Did you make sure that tune() sees the data as classification, not regression (i.e., did you make sure that the class labels given to tune.*() are factor)? HTH, Andy Tae-Hoon Chung, Ph.D Post-doctoral Research Fellow Molecular Diagnostics and Target Validation Division Translational Genomics Research Institute 1275 W Washington St, Tempe AZ 85281 USA Phone: 602-343-8724 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Re: R library(e1071) question: definition of performance in tune.* functions
Thank you David and Andy. Now, everything is clear. For others, the problem is the one said in the subject, and the answer is the one excerpted from reply from David. TH. On Jul 13, 2004, at 1:54 PM, David Meyer wrote: Tae-Hoon: When we run tune.* for parameter tuning, we get performance value. Can you tell me what the definition of it is? The values returned by tune() are Mean Squared Errors in case of regression, and simple rates (*no* percentages) in case of classification. As Andy already suggested, you might want to check if your target variable is indeed a factor. In case it is and you still get values greater than 1, drop me a mail with a piece of code (and data) enabling me to reproduce the phenomenon. Best, David -- Dr. David Meyer Department of Information Systems Vienna University of Economics and Business Administration Augasse 2-6, A-1090 Wien, Austria, Europe Fax: +43-1-313 36x746 Tel: +43-1-313 36x4393 HP: http://wi.wu-wien.ac.at/Wer_sind_wir/meyer/ Tae-Hoon Chung, Ph.D Post-doctoral Research Fellow Molecular Diagnostics and Target Validation Division Translational Genomics Research Institute 1275 W Washington St, Tempe AZ 85281 USA Phone: 602-343-8724 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] e1071 question: what's the definition of performance in tune.* functions?
Hi, all; Basically, the subject contains the all information I need to know. In e1071 library, there are functions to tune parameters. They provide several values one of which is the performance. Does any body know the definition of performance here? Is it percentage of error or just the error rate or anything else? Thanks in advance! Tae-Hoon Chung, Ph.D Post-doctoral Research Fellow Molecular Diagnostics and Target Validation Division Translational Genomics Research Institute 1275 W Washington St, Tempe AZ 85281 USA Phone: 602-343-8724 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] ESS does not recognize installed libraries
Hi, all. Something strange happened to my ESS. I use Mac OS X. When R is used in stand alone mode, it recognizes external libraries like affy, e1071 etc. However, when R is invoked through ESS in Emacs, it produces errors like: Error in library(affy) : There is no package called 'affy' Interestingly, I remember I successfully used these libraries through ESS in Emacs before. I became unable to use these libraries at one moment but I don't recall anything strange happened before that. This kind of strange thing happened sometimes to my R. In those cases, things restored smoothly when the system is restarted. However, this time, this trick does not work. Thanks in advance Tae-Hoon Chung, Ph.D Post-doctoral Research Fellow Molecular Diagnostics and Target Validation Division Translational Genomics Research Institute 1275 W Washington St, Tempe AZ 85281 USA Phone: 602-343-8724 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] ESS does not recognize installed libraries
Hi, Sean. For this part, I am not quite sure because I don't know how internal implementation of ESS handles R under Emacs. It is definitely a possibility that stand-alone version of R and ESS-version of R can use a little bit different library paths. However, I don't think R program itself is different between stand-alone version and ESS-version. Tae-Hoon On Jul 6, 2004, at 2:58 AM, Sean Davis wrote: Are you sure that the R executable is the same when used stand-alone and in ESS? Sean On 7/6/04 5:12 AM, Tae-Hoon Chung [EMAIL PROTECTED] wrote: Hi, all. Something strange happened to my ESS. I use Mac OS X. When R is used in stand alone mode, it recognizes external libraries like affy, e1071 etc. However, when R is invoked through ESS in Emacs, it produces errors like: Error in library(affy) : There is no package called 'affy' Interestingly, I remember I successfully used these libraries through ESS in Emacs before. I became unable to use these libraries at one moment but I don't recall anything strange happened before that. This kind of strange thing happened sometimes to my R. In those cases, things restored smoothly when the system is restarted. However, this time, this trick does not work. Thanks in advance Tae-Hoon Chung, Ph.D Post-doctoral Research Fellow Molecular Diagnostics and Target Validation Division Translational Genomics Research Institute 1275 W Washington St, Tempe AZ 85281 USA Phone: 602-343-8724 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Tae-Hoon Chung, Ph.D Post-doctoral Research Fellow Molecular Diagnostics and Target Validation Division Translational Genomics Research Institute 1275 W Washington St, Tempe AZ 85281 USA Phone: 602-343-8724 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] ESS does not recognize installed libraries
Thank you Adaikalavan. The problem was not due to simultaneous multiple versions of R. The problem was due to missing directories in library path and this has been cured by adding the missing library path using .libPaths(). However, it is uncertain how the same R program has different library paths and how it disappeared in some previous R sessions. Tae-Hoon. On Jul 6, 2004, at 3:04 AM, Adaikalavan Ramasamy wrote: Do you by any chance have multiple versions of R installed ? The first two lines of the header in the iESS buffer should give a clue. Example : R : Copyright 2004, The R Foundation for Statistical Computing Version 1.9.1 (2004-06-21), ISBN 3-900051-00-3 How does that compare to the header in your terminal/standalone mode. If different, then you may have to set your global path to R correctly. Other than that, it could be that some of your library paths are missing. Try '.find.package(affy)' on your terminal. See if this path is included in '.libPaths()' on your emacs/ESS interface. Tae-Hoon Chung, Ph.D Post-doctoral Research Fellow Molecular Diagnostics and Target Validation Division Translational Genomics Research Institute 1275 W Washington St, Tempe AZ 85281 USA Phone: 602-343-8724 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Absolute ceiling on R's memory usage = 4 gigabytes?
Hi, Eric.
It seems a little bit puzzling to me. Which Affymetrix chip do you use?
The reason I'm asking this is that yesterday I was able to normalize
150 HU-133A CEL files (containing 22283 probes) using R 1.9.1 in Mac OS
X 10.3.3 with 1.5 GB memory. If your chip has more probes than this,
then it must be understandable ...
On Jul 1, 2004, at 2:59 PM, Kort, Eric wrote:
Hello. By way of background, I am running out of memory when
attempting to normalize the data from 160 affymetrix microarrays using
justRMA (from the affy package). This is despite making 6 gigabytes
of swap space available on our sgi irix machine (which has 2 gigabytes
of ram). I have seen in various discussions statements such as you
will need at least 6 gigabytes of memory to normalize that many
chips, but my question is this:
I cannot set the memory limits of R (1.9.1) higher than 4 gigabytes as
attempting to do so results in this message:
WARNING: --max-vsize=4098M=4098`M': too large and ignored
I experience this both on my windows box (on which I cannot allocate
more than 4 gigabytes of swap space anyway), and on an the above
mentioned sgi irix machine (on which I can). In view of that, I do
not see what good it does to make 4 gigabytes of ram+swap space
available. Does this mean 4 gigabytes is the absolute upper limit of
R's memory usage...or perhaps 8 gigabytes since you can set both the
stack and the heap size to 4 gigabytes?
Thanks,
Eric
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Tae-Hoon Chung, Ph.D
Post-doctoral Research Fellow
Molecular Diagnostics and Target Validation Division
Translational Genomics Research Institute
1275 W Washington St, Tempe AZ 85281 USA
Phone: 602-343-8724
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