[R] automated image processing
Hi, I am looking for a R package which is capable to process and analysis pictures of tissues (stained) in an automatic way. I had a look on biops and EBImage (Bioconductor) but they are not automatic... Did you already use/know a such package ? Thanks, - Martial _ Tchattez en direct en en vidéo avec vos amis ! [[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] outlier detection test for large data set
Hello, Which outlier detection test is robust for large dataset ? I think the detection test in the package 'outliers' are suitable for small data set (between 3 and 100). Do you know one for 2 or more values ? Thanks, - Martial _ Inédit ! Des Emoticônes Déjantées! Installez les dans votre Messenger ! [[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] R function found in two packages !
Hi,
Is there a mean to automatically choose one version of the 'rbind' function ?
By default, R chose the 'rbind' from {base}, i would lke to use the one from
{IRanges}...
Is it possible to set that using 'par' ?
?rbind
Help on topic 'rbind' was found in the following packages:
Package Library
IRanges /us3/gcg18/martial/local/R_lib
base /usr/local/lib64/R/library
Choose one
1: External Data Frame {IRanges}
2: Combine R Objects by Rows or Columns {base}
Thanks,
- Martial
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Re: [R] R function found in two packages !
Thanks,
Date: Thu, 18 Jun 2009 11:21:29 +0200
Subject: Re: [R] R function founRd in two packages !
From: landronim...@gmail.com
To: martial100...@hotmail.com
CC: r-help@r-project.org
On 6/18/09, Martial Sankar martial100...@hotmail.com wrote:
Is there a mean to automatically choose one version of the 'rbind'
function ? By default, R chose the 'rbind' from {base}, i would lke to use
the one from {IRanges}...
I am usually solving these issues with:
base::rbind() or IRanges::rbind().
Liviu
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[R] Unable to use jpeg(), png() etc.....
Hello, I 've just re-installed R 2.9.0 on ubuntu 9.04. I do not understand why I am unable to use simple device function such as jpeg(), png()... png() Error in X11(paste(png::, filename, sep = ), width, height, pointsize, : unable to start device PNG In addition: Warning message: In png() : no png support in this version of R capabilities() jpeg png tifftcltk X11 aqua http/ftp sockets FALSEFALSEFALSEFALSE TRUEFALSE TRUE TRUE libxml fifo clediticonv NLS profmemcairo TRUE TRUEFALSE TRUE TRUEFALSEFALSE It's not really a problem because i use cairo but i would like to know the source of this error. I checked the library as proposed in previous post : https://stat.ethz.ch/pipermail/r-help/2005-December/085177.html but all of them (libpng, libjpeg...) are already installed. Did someone ever find the source of this R Error ? Thanks ! - Martial _ ? Lancez-vous ! [[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.
Re: [R] shall I uninstall an old R installation in advance of installing a new one ?
Hello Maura, Date: Wed, 17 Jun 2009 14:07:44 +0200 From: mau...@alice.it To: r-h...@stat.math.ethz.ch Subject: [R] shall I uninstall an old R installation in advance of installing a new one ? I have resumed developing R code on SuSE/Linux version 11.1 I installed the latest 64-bit R version available for my platform. Accidentally I figured out I still had an old R installation that, surprisingly, was not wiped out by the new SuSE installation from scratch. I suspect the new and old R versions got mixed up. I would greatly appreciate some suggestions about restarting from scratch a new R installation. My question is: how can I remove the old R installation so that no old files are left in the system ? I am not familar with Suse, maybe you should remove R with a Suse equivalent of the command line apt-get remove 'name of the R package in Suse' After that if some files or directory are not removed manually removed them with rm. Moreover, if I choose to install the new R version without previous disk saving ... where does R get installed (path) ? For default path installation, please refer to the R-admin manual. http://cran.r-project.org/doc/manuals/R-admin.html Cheers, - Martial Thank you. Maura tutti i telefonini TIM! [[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. _ Inédit ! Des Emoticônes Déjantées! Installez les dans votre Messenger ! [[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] web interface for R script??
Dear All, I requiered your feedbacks about a web interface for R scripts. I already tested RGG ( but it's not web). and two of the CRAN list : Rserve Rpad. However, Rpad requieres some knowledge in Javascript, php etc... and with Rserve I have to create a web interface entirely. Rwui from the cran list seems attractive. Did you ever test this one ? Other suggestions are welcomed too ^^ Thanks, - Martial _ Découvrez toutes les possibilités de communication avec vos proches [[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] access to the current element of lapply
Dear All,
I would like to use the 'split' function on the dataframe elements contained in
a list L.
For example :
(df - data.frame(cbind(c(rep('A',2), rep('B',2)), rep(1:4
X1 X2
1 A 1
2 A 2
3 B 3
4 B 4
(L-split(df, df$X1))
$A
X1 X2
1 A 1
2 A 2
$B
X1 X2
3 B 3
4 B 4
Now, I would like to split EACH data frame, ie, according to column 2(X2).
lapply(L, split, df$X2)
$A
$A$`1`
X1 X2
1 A 1
$A$`2`
X1 X2
2 A 2
$A$`3`
[1] X1 X2
0 rows (or 0-length row.names)
$A$`4`
[1] X1 X2
0 rows (or 0-length row.names)
$B
$B$`1`
X1 X2
3 B 3
$B$`2`
X1 X2
4 B 4
$B$`3`
[1] X1 X2
0 rows (or 0-length row.names)
$B$`4`
[1] X1 X2
0 rows (or 0-length row.names)
Warning messages:
1: In split.default(seq_len(nrow(x)), f, drop = drop, ...) :
data length is not a multiple of split variable
2: In split.default(seq_len(nrow(x)), f, drop = drop, ...) :
data length is not a multiple of split variable
I works but it's dirty.
How could I do it properly, without warnings and 0 rows data frame in output ?
I thought accessing to the current element of 'lapply' to recuperate the vector
of the column 2 would work.
i.e:
lapply(L,split, L[[current]][,2])
Is there a way to do something like that in R ?
Thanks in advance !
- Martial
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[R] 'Dynamic' 3D plot
Hi, I am looking for a R package to draw 3d plot. But not in a static way like scatterplot3d or stuff like that. I would like to make rotate the plot, to zoom/unzoom etc..., actually to render the graph 'dynamic'... (for the biologist and bioinformatician, a R package which permitts to reproduce what pdb viewer does). Does a Way exist to do something like that in R ? Thanks, _ Inédit ! Des Emoticônes Déjantées! Installez les dans votre Messenger ! [[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] normality test for large a large dataset ?
Hello, Do you know a R implemented normality test like the shapiro test but more suitable for large data set ? Thanks, _ Découvrez toutes les possibilités de communication avec vos proches [[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] rjava - JDK not found
Hi, I would like to test the new package RGG (R Gui Generator). This package requires the installation of several other package. One of them is rJava. I installed sun-java6-jdk and run the R CMD javareconf but the installation still fails ! Do you have any ideas ? * Installing *source* package rJava ... checking for gcc... gcc -std=gnu99 checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc -std=gnu99 accepts -g... yes checking for gcc -std=gnu99 option to accept ISO C89... none needed checking how to run the C preprocessor... gcc -std=gnu99 -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/wait.h that is POSIX.1 compatible... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for string.h... (cached) yes checking sys/time.h usability... yes checking sys/time.h presence... yes checking for sys/time.h... yes checking for unistd.h... (cached) yes checking for an ANSI C-conforming const... yes checking whether time.h and sys/time.h may both be included... yes configure: checking whether gcc -std=gnu99 supports static inline... yes checking Java support in R... present: interpreter : '/usr/lib/jvm/java-6-sun/jre/bin/java' archiver: '/usr/lib/jvm/java-6-sun/bin/jar' compiler: '/usr/lib/jvm/java-6-sun/bin/javac' header prep.: '/usr/lib/jvm/java-6-sun/bin/javah' cpp flags : '-I/usr/lib/jvm/java-6-sun/include -I/usr/lib/jvm/java-6-sun/include/linux' java libs : '-L/usr/lib/jvm/java-6-sun-1.6.0.07/jre/lib/amd64/server -L/usr/lib/jvm/java-6-sun-1.6.0.07/jre/lib/amd64 -L/usr/lib/jvm/java-6-sun-1.6.0.07/jre/../lib/amd64 -L -L/usr/java/packages/lib/amd64 -L/lib -L/usr/lib -ljvm:-L/usr/lib32:-L/usr/lib64' checking whether JNI programs can be compiled... configure: error: Cannot compile a simple JNI program. See config.log for details. Make sure you have Java Development Kit installed and correctly registered in R. If in doubt, re-run R CMD javareconf as root. ERROR: configuration failed for package rJava _ Découvrez toutes les possibilités de communication avec vos proches [[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.
Re: [R] rjava - JDK not found
I completely removed the java-sun version and install the openjdk instead. I re-launched the R CMD reconf. The installation still failed ! install.packages(rJava) Warning in install.packages(rJava) : argument 'lib' is missing: using '/home/martial/R/x86_64-unknown-linux-gnu-library/2.9' trying URL 'http://cran.fr.r-project.org/src/contrib/rJava_0.6-2.tar.gz' Content type 'application/x-tar' length 237115 bytes (231 Kb) opened URL == downloaded 231 Kb * Installing *source* package rJava ... checking Java support in R... present: interpreter : '/usr/bin/java' archiver: '' compiler: '' header prep.: '' cpp flags : '-I/usr/lib/jvm/java-6-openjdk/jre/../include' java libs : '-L/usr/lib/jvm/java-6-openjdk/jre/lib/amd64/server -L/usr/lib/jvm/java-6-openjdk/jre/lib/amd64 -L/usr/lib/jvm/java-6-openjdk/jre/../lib/amd64 -L -L/usr/java/packages/lib/amd64 -L/usr/lib64 -L/lib64 -L/lib -L/usr/lib -ljvm' configure: error: Java Development Kit (JDK) is missing or not registered in R Make sure R is configured with full Java support (including JDK). Run R CMD javareconf as root to add Java support to R. It's interesting to notice that the result of the javareconf is totally different: ~$ R CMD javareconf -e /bin/bash Java interpreter : /usr/lib/jvm/java-6-openjdk//jre/bin/java Java version : 1.6.0_0 Java home path : /usr/lib/jvm/java-6-openjdk/ Java compiler: /usr/lib/jvm/java-6-openjdk//bin/javac Java headers gen.: /usr/lib/jvm/java-6-openjdk//bin/javah Java archive tool: /usr/lib/jvm/java-6-openjdk//bin/jar Java library path: $(JAVA_HOME)jre/lib/amd64/server:$(JAVA_HOME)jre/lib/amd64:$(JAVA_HOME)jre/../lib/amd64::/usr/java/packages/lib/amd64:/usr/lib64:/lib64:/lib:/usr/lib JNI linker flags : -L$(JAVA_HOME)jre/lib/amd64/server -L$(JAVA_HOME)jre/lib/amd64 -L$(JAVA_HOME)jre/../lib/amd64 -L -L/usr/java/packages/lib/amd64 -L/usr/lib64 -L/lib64 -L/lib -L/usr/lib -ljvm JNI cpp flags: -I$(JAVA_HOME)/include The following Java variables have been exported: JAVA_HOME JAVA JAVAC JAVAH JAR JAVA_LIBS JAVA_CPPFLAGS JAVA_LD_LIBRARY_PATH Runnig: /bin/bash However, ~$ sudo R CMD javareconf Java interpreter : /usr/bin/java Java version : 1.6.0_0 Java home path : /usr/lib/jvm/java-6-openjdk/jre Java compiler: not present Java headers gen.: Java archive tool: Java library path: $(JAVA_HOME)/lib/amd64/server:$(JAVA_HOME)/lib/amd64:$(JAVA_HOME)/../lib/amd64::/usr/java/packages/lib/amd64:/usr/lib64:/lib64:/lib:/usr/lib JNI linker flags : -L$(JAVA_HOME)/lib/amd64/server -L$(JAVA_HOME)/lib/amd64 -L$(JAVA_HOME)/../lib/amd64 -L -L/usr/java/packages/lib/amd64 -L/usr/lib64 -L/lib64 -L/lib -L/usr/lib -ljvm JNI cpp flags: -I$(JAVA_HOME)/../include Updating Java configuration in /usr/local/lib64/R Done. In fact the javareconf is called in sudo mode during the installation of the package rjava. How can I fix the java support in sudo mode ? Any ideas ?? From: martial100...@hotmail.com To: r-help@r-project.org Date: Thu, 30 Apr 2009 10:43:38 + Subject: [R] rjava - JDK not found Hi, I would like to test the new package RGG (R Gui Generator). This package requires the installation of several other package. One of them is rJava. I installed sun-java6-jdk and run the R CMD javareconf but the installation still fails ! Do you have any ideas ? * Installing *source* package rJava ... checking for gcc... gcc -std=gnu99 checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc -std=gnu99 accepts -g... yes checking for gcc -std=gnu99 option to accept ISO C89... none needed checking how to run the C preprocessor... gcc -std=gnu99 -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/wait.h that is POSIX.1 compatible... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for string.h... (cached) yes checking sys/time.h usability... yes checking sys/time.h presence... yes checking for sys/time.h... yes checking for unistd.h... (cached) yes checking for an ANSI C-conforming const... yes checking whether time.h and sys/time.h may both be included... yes configure: checking whether gcc -std=gnu99 supports static inline... yes checking Java support in R... present: interpreter : '/usr/lib/jvm/java-6-sun/jre/bin/java' archiver: '/usr/lib/jvm/java-6-sun/bin/jar' compiler:
Re: [R] rjava - JDK not found
Done ! install.packages(rJava) Warning in install.packages(rJava) : argument 'lib' is missing: using '/home/martial/R/x86_64-unknown-linux-gnu-library/2.9' trying URL 'http://cran.fr.r-project.org/src/contrib/rJava_0.6-2.tar.gz' Content type 'application/x-tar' length 237115 bytes (231 Kb) opened URL == downloaded 231 Kb * Installing *source* package rJava ... checking Java support in R... present: interpreter : '/usr/bin/java' archiver: '' compiler: '' header prep.: '' cpp flags : '-I/usr/lib/jvm/java-6-openjdk/jre/../include' java libs : '-L/usr/lib/jvm/java-6-openjdk/jre/lib/amd64/server -L/usr/lib/jvm/java-6-openjdk/jre/lib/amd64 -L/usr/lib/jvm/java-6-openjdk/jre/../lib/amd64 -L -L/usr/java/packages/lib/amd64 -L/usr/lib64 -L/lib64 -L/lib -L/usr/lib -ljvm' configure: error: Java Development Kit (JDK) is missing or not registered in R Make sure R is configured with full Java support (including JDK). Run R CMD javareconf as root to add Java support to R. The fact is that some the path for the archiver, the compiler and the header are missing. Thus, when doing the javareconf, just add the path for the missing variables. ~$ sudo R CMD javareconf JAVAC=/usr/lib/jvm/java-6-openjdk/jre/../bin/javac JAR=/usr/bin/jar JAVAH=/usr/bin/javah Java interpreter : /usr/bin/java Java version : 1.6.0_0 Java home path : /usr/lib/jvm/java-6-openjdk/jre Java compiler: /usr/lib/jvm/java-6-openjdk/jre/../bin/javac Java headers gen.: /usr/bin/javah Java archive tool: /usr/bin/jar Java library path: $(JAVA_HOME)/lib/amd64/server:$(JAVA_HOME)/lib/amd64:$(JAVA_HOME)/../lib/amd64::/usr/java/packages/lib/amd64:/usr/lib64:/lib64:/lib:/usr/lib JNI linker flags : -L$(JAVA_HOME)/lib/amd64/server -L$(JAVA_HOME)/lib/amd64 -L$(JAVA_HOME)/../lib/amd64 -L -L/usr/java/packages/lib/amd64 -L/usr/lib64 -L/lib64 -L/lib -L/usr/lib -ljvm JNI cpp flags: -I$(JAVA_HOME)/../include Updating Java configuration in /usr/local/lib64/R Done. Then launch the R and install the package: ~$ sudo R install.packages(rJava) (...) checking Java support in R... present: interpreter : '/usr/bin/java' archiver: '/usr/bin/jar' compiler: '/usr/lib/jvm/java-6-openjdk/jre/../bin/javac' header prep.: '/usr/bin/javah' cpp flags : '-I/usr/lib/jvm/java-6-openjdk/jre/../include' java libs : '-L/usr/lib/jvm/java-6-openjdk/jre/lib/amd64/server -L/usr/lib/jvm/java-6-openjdk/jre/lib/amd64 -L/usr/lib/jvm/java-6-openjdk/jre/../lib/amd64 -L -L/usr/java/packages/lib/amd64 -L/usr/lib64 -L/lib64 -L/lib -L/usr/lib -ljvm' checking whether JNI programs can be compiled... yes checking JNI data types... ok checking whether JRI should be compiled (autodetect)... no checking whether debugging output should be enabled... no checking whether memory profiling is desired... no checking whether threads support is requested... no checking whether callbacks support is requested... no checking whether JNI cache support is requested... no checking whether JRI is requested... no (...) ** building package indices ... * DONE (rJava) That's all ! ^^ _ r ! Téléchargez-le maintenant ! [[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.
