Re: [R] [R-sig-ME] Xy plot help
On Sun, 29 Apr 2012 11:27:06 -0700 (PDT) arun smartpink...@yahoo.com wrote: I tried to get xyplot shrink fit for my mixed model._ But, the mixed model line is not seen in the graph. I would like to know if there is anything wrong with my code. Typo? Try panel.abline(fixef(fm1),... or panel.abline(ff), ... __ 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] zoo arithmetics
Dear list members, what is the reason that one obviously can't do arithmetic operations on zoo members with different index positions? require(zoo) z - zoo(c(1,1,1),order.by=c(1,2,3)) z 1 2 3 1 1 1 z[1] + z[1] 1 2 z[1:2] + z[1:2] 1 2 2 2 z[1] + z[2] Data: numeric(0) Index: numeric(0) __ 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] connecting R and PostgreSQL
Marie, you did not say if you work on Windows or Unix. The manual from google belongs to the R package RpostgreSQL. This package makes use the native PostgreSQL driver. As I read the documentation, the package's DBI interface must be somehow binary compatible with the Postgres version installed. It installs and works seamlessly here on Linux, and also works with Windows Vista, but I remember that I had to shuffle some dlls from the postgresql directory. So if you provide some more information, maybe I'll remember what I did to get it running. Best regards Hugo Am 28.06.2011 14:15, schrieb aya74...@gmx.de: Dear R-helpers, I'm an absolute beginner using both R and PostgreSQL, but now I have to work with both programs. I need to connect R and my Postgres-database, but every attempt so far has failed (I tried using the RpgSQL package as well as RdbiPgSQL, the first, following this manual (http://code.google.com/p/rpostgresql/) didn't find any drivers for the database (step no. 1) whereas the second doesn't work with R version 2.13). Could someone please be so kind to either provide a step-by-step instruction on how to make this connection work or direct me to a manual? Thanks in advance. Yours sincerly, Marie -- __ 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-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] Need help on a R script part
Duncan,
it isn't really that difficult to diagnose. A google search for
ss11=sample(x1, n1, replace=TRUE)
turned up this documented R-script
ttp://www2.latech.edu/~dcahoy/TwoSampleEqualVarTest.R
as a likely source for his fragmented and mangled post; other variable
names match as well. But besides this, Lusk also demanded to be
provided with a mathematical notation of the R code he posted. While
he certainly could have followed Dexter O. Cahoy's reference to the
underlying paper at
ttp://www.sciencedirect.com/science/article/pii/S016794731000157X
to get the theoretical background and a formal notation, I do imagine
a tool which takes the R parse tree as input and produces a mathematical
notation as a nicely formatted (LaTex) output, similar to what Mathematica
does on the fly.
At least I like this idea (h/t to Lusk) and think it should be doable for
some less complex functions at first. Such a translator could greatly
enhance function documentation, facilitate debugging and so on, but
may also provide a base implemention for interfaces specific to other
programs, thus giving R the ability to also export algorithms.
Best regards
Hugo Mildenberger
On Saturday 25 June 2011 15:55:51 Duncan Murdoch wrote:
On 11-06-25 11:33 AM, Mike Miller wrote:
I'm curious about what would cause this (see below), if it isn't a joke.
Is it possible that it didn't look ridiculous in the deleted HTML but the
text looked bad? It's almost unreadable. I guess the HTML gets deleted
because it is a waste of space, but I received a 14 MB message from this
list the other day.
I imagine you need to contact the poster, and find out what they sent.
It's hard to diagnose after it's been mangled.
Duncan Murdoch
Mike
On Fri, 24 Jun 2011, Lusk Aris wrote:
Hi all,
I need all your help on this. I have the next part of
code:e1=x1-mean(x1)e2=x2-mean(x2)n1=length(x1)n2=length(x2N=(n1
+
n2)nu2=sum( c( ( x1 -mean(x1) )^2 , ( x2-mean(x2) )^2 ) )/Nss=c(e1,e2) b3=
N*sum(ss^4)/ (sum( ss^2)^2)what do lines 6-8 (mathematical
notation)?Also the, what means part?for(j in 1:B){ ss11=sample(x1,
n1, replace=TRUE) ss12=sample(x2, n2, replace=TRUE)
}I would appreciate you could help on my inquiry,
and I am awaiting for your soon answer Thx in advance, Lusk
[[alternative HTML version deleted]]
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Re: [R] Help with lmer
Sophie, sorry for any possibly duplicate email, my email client currently does not work correctly. I understand this snapshot as being a subset of your data only. But I do miss the factor Sitename, which appears in your lmer model as a random factor. Also, by looking at the subset, Presencebsence appears be a binary response variable. Does your response imply that you tried to call (m1-lmer(Presencebsence~Habitatype*Width+(1|Sitename),family=binomial)) and got the same error? (Note: I previously mispelled family) I also observe that many factors in your data appear to be closely correlated, e.g. Habitatype and Width, at least in the subset you passed along. I suspect this correlation to be the reason for the lmer error. Hence either use Width or Habitatype. Finally I'd propose you to put all your data into a dataframe, e.g. mydata-NULL mydata$PresenceAbsence - as.factor(Presencebsence) mydata$Habitattype - as.factor(Habitatype) mydata$Substratetype - as.factor(Substratetype) mydata$Width - Width mydata$Banktype- as.factor(Banktype) mydata$BankIncline - BankIncline mydata$Bankheight - as.factor(Bankheight) mydata$Waterdepth- as.factor(Waterdepth) mydata$Sitename- as.factor(Sitename) and then pass the dataframe to lmer by using data=mydata; mainly because passing a bunch of variables directly from the environment hightens the risk of inadvertently using stale copies, but also because str(mydata) would then produce a well arranged summary of all your variables. Kind regards Hugo On Sunday 26 June 2011 11:26:45 Sophie Higgins wrote: Hello Hugo, Thank you for your reply. This is a snap shot of what my data looks like: Presencebsence Habitatype Substratetype Width Banktype BankIncline Bankheight Waterdepth 0 Lake Rocksgravel 600 Earth 0.45 less1 greater2 0 Lake Rocksgravel 600 Earth 0.45 less1 greater2 1 Lake Rocksgravel 600 Earth 0.45 less1 greater2 0 Lake Rocksgravel 600 Earth 0.45 less1 greater2 0 Lake Rocksgravel 600 Earth 0.45 less1 greater2 0 Stream Rocksgravel 1 Rocks 0.45 less1 025to05 0 Stream Rocksgravel 1 Rocks 0.45 less1 025to05 0 Stream Rocksgravel 1 Rocks 0.45 less1 025to05 0 Stream Rocksgravel 1 Rocks 0.45 less1 025to05 I am trying to find out if any off the above factors so substrate type, width, bank type etc have an effect on the presence/absence of the species in question. But as stated below I keep getting an error message up and I have no idea how to fix it in order for me to fun the lmer. Sophie From: hugo.mildenber...@web.de To: r-help@r-project.org CC: england...@hotmail.com Subject: Re: [R] Help with lmer Date: Fri, 24 Jun 2011 17:19:00 +0200 Sophie, I'm myself quite new to linear mixed effect models, but PresenceAbsence sounds like a binary response variable. So wouldn't be m1-lmer(Presencebsence~Habitatype*Width+(1|Sitename),familiy=binomial) the first thing to try? There is also a special mailing list for linear - mixed -effect models: r-sig-mixed-mod...@r-project.org But with numeric problems like this one you really should provide a self contained example (i.e. with data), at least the output of str(yourdata), if ever possible. Kind regards Hugo On Friday 24 June 2011 13:11:23 Sophie Higgins wrote: Hey, I am having trouble with lmer. I am looking at the presence/absence of water shrews against habitat and other factors e.g so I used this: m1-lmer(Presencebsence~Habitatype*Width+(1|Sitename))summary(m1) But i keep getting this error up Error in mer_finalize(ans) : Downdated X'X is not positive definite, 16. summary(m1)Error in asMethod(object) : matrix is not symmetric [1,2] What does this mean and now can I fix it? Sophie [[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-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] On .. glibc detected home/sguha/lib64/R/bin/exec/R: realloc(): invalid next size: 0x000000000209e210 ***
Saptarshi, if you look at the sheer number of shared libraries involved, heap corruption may have happened due to errors in any of these. Finding the reason for such problems is usually difficult, but almost impossible without a reproducible example. If you could boil it down to a minimal example still triggering the access violation, one could try to run it under control of a memory guard like valgrind. Best Hugo On Friday 24 June 2011 17:12:26 Saptarshi Guha wrote: Hello, I'm trying to use rjson to parse a JSON object. The object can be found here http://pastebin.com/np0s5hgM (you'll probably need to add quotes around the content) fromJSON returns the error glibc detected home/sguha/lib64/R/bin/exec/R: realloc(): invalid next size: 0x0209e210 *** Is there a fix coming soon? Maybe CRAN should also have an outstanding bug field - packages with unfixed bugs could be removed. Cheers Joy rjson- 0.2.3 and R.version _ platform x86_64-unknown-linux-gnu arch x86_64 os linux-gnu system x86_64, linux-gnu status major 2 minor 13.0 year 2011 month 04 day13 svn rev55427 language R version.string R version 2.13.0 (2011-04-13) __ 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-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] Need help on a R script part
Lusk,
if I were in your business, I would tackle such a problem with
help from a little formatting ...
e1=x1-mean(x1)
e2=x2-mean(x2)
n1=length(x1)
n2=length(x2)
N=(n1 + n2)
nu2=sum( c( ( x1 -mean(x1) )^2 , ( x2-mean(x2) )^2 ) )/N
ss=c(e1,e2)
b3=N*sum(ss^4)/(sum( ss^2)^2)
for(j in 1:B){ ss11=sample(x1, n1, replace=TRUE)
ss12=sample(x2, n2, replace=TRUE) }
... afterwards I'd correct for missing parenthesis and such. But I
understand that this approach was really not conducive when the
main intention was to target the public by giving the unhappy college
student who infelicitously bumped into a mountain of WWI-style
razor wire. The wire-cutter equivalent tool the R interpreter provides
you with is the question mark. Here are some examples how to use it:
?mean
?length
?sum
?sample
?^
?for
?in
?:
?=
?-
?+
?*
?/
Hope this helps.
Kind regards
On Friday 24 June 2011 15:31:44 Lusk Aris wrote:
Hi all,
I need all your help on this. I have the next part of
code:e1=x1-mean(x1)e2=x2-mean(x2)n1=length(x1)n2=length(x2N=(n1 +
n2)nu2=sum( c( ( x1 -mean(x1) )^2 , ( x2-mean(x2) )^2 ) )/Nss=c(e1,e2) b3=
N*sum(ss^4)/ (sum( ss^2)^2)what do lines 6-8 (mathematical
notation)?Also the, what means part?for(j in 1:B){ ss11=sample(x1,
n1, replace=TRUE) ss12=sample(x2, n2, replace=TRUE)
}I would appreciate you could help on my inquiry,
and I am awaiting for your soon answer Thx in advance, Lusk
[[alternative HTML version deleted]]
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] gcc-4.5.2 and install.packages(glmnet)?
That problem is at least two-fold:
1. A failing heuristic in glmnet/configure.in
2. glmnet/src/glmnet/src/newGLMnet_f.f90 does not compile.
Several problems:
- gfortran does not recognise lines starting with [c|C]
comments
- starting at line 517, a line number column was inserted
after column 72
- long lines had been wrapped by inserting [*], often inside
parameter names
- looks very wrong, much like a listing file
Quick fix procedure:
ad 1. unpack the archive
apply the patch shown below or edit configure.in (replace ${FC}
by ${F77} in line 38)
delete glmnet/configure
repack the archive
try to install the newly packed archive via R CMD INSTALL (will
fail)
ad 2. I could also attach a patch also for glmnet/src/newGLMnet_f.f90
- but it is rather big (you may contact me)
- while the package will compile and load without error,
running example(glmnet) results in:
glmnet fit1=glmnet(x,y)
Error in validObject(.Object) :
invalid class dgCMatrix object: length(Dimnames[[2]])'
must match Dim[2]
In addition: Warning message:
from glmnet Fortran code - Convergence for 1th lambda value
not reached after
maxit=10 iterations; solutions for larger
lambdas returned
So there seem to be many problems worth of a bug report to the author(s) of
glmnet.
Kind regards
Hugo
--- cut here ---
diff -ur a/glmnet/configure.in b/glmnet/configure.in
--- a/glmnet/configure.in 2011-06-15 20:05:30.0 +0200
+++ b/glmnet/configure.in 2011-06-24 10:08:21.0 +0200
@@ -35,7 +35,7 @@
FC=`basename ${FC}`
fi
-case ${FC} in
+case ${F77} in
gfortran*)
echo R configured for gfortran; Good!
AC_SUBST(OUR_FCFLAGS, -fdefault-real-8 -ffixed-form)
--- cut here ---
On Thursday 23 June 2011 22:39:33 Juergen Rose wrote:
Hi,
is there any chance to install glmnet with gcc-4.5.2? For me it fails on
all systems with:
trying URL
'http://mirrors.softliste.de/cran/src/contrib/glmnet_1.7.tar.gz'
Content type 'application/x-gzip' length 522888 bytes (510 Kb)
opened URL
==
downloaded 510 Kb
* installing *source* package ‘glmnet’ ...
This package has only been tested with gfortran.
So some checks are needed.
R_HOME is /usr/lib64/R
Attempting to determine R_ARCH...
R_ARCH is
Attempting to detect how R was configured for Fortran 90
Unsupported Fortran 90 compiler or Fortran 90
compilers unavailable! Stop!
ERROR: configuration failed for package ‘glmnet’
How can I get more information, what a problem has happened?
Otherwise I have no problem to compile a small Fortran 90 program:
root@orca:/home/rose/Txt/src/Test/Fortran(57)# cat hello.f90
program Hello
print *,'Hello world'
end program Hello
root@orca:/home/rose/Txt/src/Test/Fortran(58)# gfortran -cpp -dM
hello.f90
root@orca:/home/rose/Txt/src/Test/Fortran(59)# ./a.out
Hello world
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Re: [R] How to capture console output in a numeric format
One possibility involves applying a regular expression via gsub:
as.numeric(gsub(^\\[1\\] ,,fvals))
On Friday 24 June 2011 14:39:31 Ravi Varadhan wrote:
Hi,
I would like to know how to capture the console output from running an
algorithm for further analysis. I can capture this using capture.output()
but
that yields a character vector. I would like to extract the actual numeric
values. Here is an example of what I am trying to do.
fr - function(x) { ## Rosenbrock Banana function
on.exit(print(f))
x1 - x[1]
x2 - x[2]
f - 100 * (x2 - x1 * x1)^2 + (1 - x1)^2
f
}
fvals - capture.output(ans - optim(c(-1.2,1), fr))
Now, `fvals' contains character elements, but I would like to obtain the
actual numerical values. How can I do this?
Thanks very much for any suggestions.
Best,
Ravi.
---
Ravi Varadhan, Ph.D.
Assistant Professor,
Division of Geriatric Medicine and Gerontology School of Medicine Johns
Hopkins University
Ph. (410) 502-2619
email: rvarad...@jhmi.edumailto:rvarad...@jhmi.edu
[[alternative HTML version deleted]]
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and provide commented, minimal, self-contained, reproducible code.
__
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Re: [R] Help with lmer
Sophie, I'm myself quite new to linear mixed effect models, but PresenceAbsence sounds like a binary response variable. So wouldn't be m1-lmer(Presencebsence~Habitatype*Width+(1|Sitename),familiy=binomial) the first thing to try? There is also a special mailing list for linear - mixed -effect models: r-sig-mixed-mod...@r-project.org But with numeric problems like this one you really should provide a self contained example (i.e. with data), at least the output of str(yourdata), if ever possible. Kind regards Hugo On Friday 24 June 2011 13:11:23 Sophie Higgins wrote: Hey, I am having trouble with lmer. I am looking at the presence/absence of water shrews against habitat and other factors e.g so I used this: m1-lmer(Presencebsence~Habitatype*Width+(1|Sitename))summary(m1) But i keep getting this error up Error in mer_finalize(ans) : Downdated X'X is not positive definite, 16. summary(m1)Error in asMethod(object) : matrix is not symmetric [1,2] What does this mean and now can I fix it? Sophie [[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-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] Rmpi fails to install
Juergen,
I try to install Rmpi as root with install.packages(Rmpi).
It fails with:
...
I encountered a similar problem with openmpi-1.5.3 and
Rmpi_0.5-9.tar.gz. The reason was an unchecked call to
dlopen(libmpi.so.0). At least openmpi-1.5.3 does not provide
libmpi.so.0 anymore. The patch below corrects for this.
According to man dlopen, this should work with all POSIX.1-2001
compliant systems. But possibly R already has an abstraction layer
for loading shared objects?
Here is how to apply this patch locally:
tar -xvzf Rmpi_0.5-9.tar.gz
patch -p1 rmpi-check-dlopen-status.patch
tar -cvzf Rmpi_0.5-9a.tar.gz
R CMD INSTALL --preclean Rmpi_0.5-9a.tar.gz
Best
Hugo
cut
diff -ru a/Rmpi/src/Rmpi.c b/Rmpi/src/Rmpi.c
--- a/Rmpi/src/Rmpi.c 2010-11-30 20:38:01.0 +0100
+++ b/Rmpi/src/Rmpi.c 2011-06-17 12:48:37.0 +0200
@@ -68,7 +68,11 @@
else {
#ifdef OPENMPI
- dlopen(libmpi.so.0, RTLD_GLOBAL | RTLD_LAZY);
+ if (!dlopen(libmpi.so, RTLD_GLOBAL | RTLD_LAZY)) {
+Rprintf(%s\n,dlerror());
+return AsInt(0);
+ }
+
#endif
#ifndef MPI2
--- cut
On Monday 07 March 2011 21:53:05 r...@uni-potsdam.de wrote:
I try to install Rmpi as root with install.packages(Rmpi).
It fails with:
...
checking for x86_64-pc-linux-gnu-gcc -std=gnu99 option to accept ISO
C89... none needed
I am here /usr and it is OpenMPI
Trying to find mpi.h ...
Found in /usr/include
Trying to find libmpi.so or libmpich.a ...
Found libmpi in /usr/lib
checking for openpty in -lutil... yes
checking for main in -lpthread... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
x86_64-pc-linux-gnu-gcc -std=gnu99 -I/usr/lib64/R/include
-DPACKAGE_NAME=\\ -DPACKAGE_TARNAME=\\ -DPACKAGE_VERSION=\\
-DPACKAGE_STRING=\\ -DPACKAGE_BUGREPORT=\\ -I/usr/include -DMPI2
-DOPENMPI -I/usr/local/include-fpic -march=nocona -O2 -pipe
-fomit-frame-pointer -c RegQuery.c -o RegQuery.o
x86_64-pc-linux-gnu-gcc -std=gnu99 -I/usr/lib64/R/include
-DPACKAGE_NAME=\\ -DPACKAGE_TARNAME=\\ -DPACKAGE_VERSION=\\
-DPACKAGE_STRING=\\ -DPACKAGE_BUGREPORT=\\ -I/usr/include -DMPI2
-DOPENMPI -I/usr/local/include-fpic -march=nocona -O2 -pipe
-fomit-frame-pointer -c Rmpi.c -o Rmpi.o
x86_64-pc-linux-gnu-gcc -std=gnu99 -I/usr/lib64/R/include
-DPACKAGE_NAME=\\ -DPACKAGE_TARNAME=\\ -DPACKAGE_VERSION=\\
-DPACKAGE_STRING=\\ -DPACKAGE_BUGREPORT=\\ -I/usr/include -DMPI2
-DOPENMPI -I/usr/local/include-fpic -march=nocona -O2 -pipe
-fomit-frame-pointer -c conversion.c -o conversion.o
x86_64-pc-linux-gnu-gcc -std=gnu99 -I/usr/lib64/R/include
-DPACKAGE_NAME=\\ -DPACKAGE_TARNAME=\\ -DPACKAGE_VERSION=\\
-DPACKAGE_STRING=\\ -DPACKAGE_BUGREPORT=\\ -I/usr/include -DMPI2
-DOPENMPI -I/usr/local/include-fpic -march=nocona -O2 -pipe
-fomit-frame-pointer -c internal.c -o internal.o
x86_64-pc-linux-gnu-gcc -std=gnu99 -shared -Wl,-O1 -Wl,--as-needed -o
Rmpi.so RegQuery.o Rmpi.o conversion.o internal.o -L/usr/lib -lmpi
-lutil -lpthread -L/usr/lib64/R/lib -lR
installing to /usr/lib64/R/library/Rmpi/libs
** R
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded
/usr/lib64/R/bin/exec/R: symbol lookup
error: /usr/lib64/openmpi/mca_paffinity_linux.so: undefined symbol:
mca_base_param_reg_int
The downloaded packages are in
?/tmp/RtmpLvvl9R/downloaded_packages?
Updating HTML index of packages in '.Library'
Warning message:
In install.packages(Rmpi) :
installation of package 'Rmpi' had non-zero exit status
The system is a gentoo system with openmpi-1.5.1. I am thankful for any
hint.
Juergen
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Rmpi installation
Kristian, Another update: I ditched the pre-installed version of openmpi and installed openmpi from source (./configure --without-openib). A very reasonable approach. Remembering my own struggles with SuSE years ago, I did not dare to propose that procedure. Compiling and running your test programme gives me the following error: unger@zytosrv01dmi:~/R_projects/OS ./mtest [zytosrv01dmi:6094] *** An error occurred in MPI_Send [zytosrv01dmi:6094] *** on communicator MPI_COMM_WORLD [zytosrv01dmi:6094] *** MPI_ERR_RANK: invalid rank [zytosrv01dmi:6094] *** MPI_ERRORS_ARE_FATAL (your MPI job will now abort) Same here. For the moment I can't figure out why this happens, also because the parameters of the openmpi functions are scarcely documented. Try one of the demo programs in the openmpi examples directory instead, e.g. the attached one However, Rmpi installs happily and it is also possible to call the package in R. When it comes to running a job under snowfall sfInit( parallel=TRUE,type=MPI, cpus=8) the job is split into eight separate processes which all run on the same CPU. So it seems that the processes are not distributed across the 8 CPUs available. sfSetMaxCPUs(number=8) should fix at least the thread distribution. However, on my notebook all cores are kept busy with 100% load after sfInit(), with nothing obvious to compute. I don't know if this has to be considered a bug or a feature. Kind regards Hugo Best wishes Kristian Am 15.06.11 19:25 schrieb Hugo Mildenberger unter hugo.mildenber...@web.de: Dear Kristian, please run exactly mpicc mtest.c -o mtest If you really need it, add -v separately. mpicc is nothing but a compiler wrapper. The -o switch specifies the outfile name, which has to follow immediately after -o, with or without a blank character in between. I'm not sure about what happens with -ov mtest. Probably an output file named v is produced on disk, in addition to the file mtest stemming from a previous with -o mtest Depending on mpicc's, gcc's and ld's version, gcc may instruct the linker to link the previously produced executable mtest with the object newly compiled from mtest.c plus several implicit libraries and startup objects, and output the result to v. ld would then be faced with duplicate defined symbols and output a list of these doublets. My proposal was meant as a test for an else correct openmpi installation, perhaps I should have said this. On successful completion, no message should be printed, but an executable named mtest should have been produced, which could then be run typing ./mtest. If the link process failed, then the openmpi installation was inconsistent. Kind regards Hugo On Wednesday 15 June 2011 17:45:41 Unger, Kristian, Dr. wrote: Dear Hugo I ran the command with the verbose switch and get the following output: mpicc mtest.c -ov mtest mtest: In function `_start': /usr/src/packages/BUILD/glibc-2.11.1/csu/../sysdeps/x86_64/elf/start.S:65 : multiple definition of `_start' /usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../lib64/crt1.o:/usr/src/pa ck ages/BUILD/glibc-2.11.1/csu/../sysdeps/x86_64/elf/start.S:65: first defined here mtest: In function `_fini': (.fini+0x0): multiple definition of `_fini' /usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../lib64/crti.o:initfini.c: (. fini+0x0): first defined here mtest:(.rodata+0x0): multiple definition of `_IO_stdin_used' /usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../lib64/crt1.o:(.rodata.cs t4 +0x0): first defined here mtest: In function `__data_start': (.data+0x0): multiple definition of `__data_start' /usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../lib64/crt1.o:(.data+0x0) : first defined here mtest: In function `main': (.text+0xec): multiple definition of `main' /tmp/ccUyk8e9.o:mtest.c:(.text+0x0): first defined here mtest: In function `_init': (.init+0x0): multiple definition of `_init' /usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../lib64/crti.o:initfini.c: (. init+0x0): first defined here /usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../x86_64-suse-linux/bin/ld : error in mtest(.eh_frame); no .eh_frame_hdr table will be created. collect2: ld returned 1 exit status Not sure if this makes any sense? Best wishes Kristian Dr. Kristian Unger Arbeitsgruppenleiter Integrative Biologie / Head of Integrative Biology Group Abteilung für Strahlenzytogenetik / Research Unit of Radiation Cytogenetics Tel.: +49-89-3187-3515 Mob.: +49-160-90641879 Am 15.06.11 17:25 schrieb Hugo Mildenberger unter hugo.mildenber...@web.de: Kristian, these are the usual problems with binary distributions. Regarding --with-Rmpi-include=/usr/lib64/mpi/gcc/openmpi/include and configure output
Re: [R] Rmpi installation
Hmm, looks like there was a trailing blank after the backslash and before end of line, resulting in --with-Rmpi-libpath possibly not recognised: \--with-Rmpi-libpath=/usr/lib64/mpi/gcc/openmpi/lib64 \ I also doubt there is real need to escape newlines within a string. But another possible problem source is that according to R CMD INSTALL --help, the parameter is called --configure-args, not configure.args. $ R CMD INSTALL --configure-args=--with-Rmpi-include=/usr/lib64/mpi/gcc/openmpi/include --with-Rmpi-libpath=/usr/lib64/mpi/gcc/openmpi/lib64 -- with-Rmpi-type=OPENMPI Rmpi_0.5-4.tar.gz Best On Wednesday 15 June 2011 14:25:46 Unger, Kristian, Dr. wrote: Hi there I am trying to install Rmpi (version 0.5-4) on our 8-core SUSE Linux Enterprise Server 11 SP1. I read all I could find about Rmpi installation but still cannot get it working. Here the last command that I used: R CMD INSTALL --configure.args=--with-Rmpi-include=/usr/lib64/mpi/gcc/openmpi/include \ --with-Rmpi-libpath=/usr/lib64/mpi/gcc/openmpi/lib64 \ --with-Rmpi-type=OPENMPI Rmpi_0.5-4.tar.gz Resulting in the following: zytosrv01dmi:/home/unger/R_projects/OS # R CMD INSTALL --configure-args=--with-Rmpi-include=/usr/lib64/mpi/gcc/openmpi/include \--with-Rmpi-libpath=/usr/lib64/mpi/gcc/openmpi/lib64 \ --with-Rmpi-type=OPENMPI Rmpi_0.5-4.tar.gz * installing to library Œ/usr/local/lib64/R/library¹ * installing *source* package ŒRmpi¹ ... checking for gcc... gcc 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 accepts -g... yes checking for gcc option to accept ISO C89... none needed checking how to run the C preprocessor... gcc -E checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for ANSI C header files... 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 mpi.h usability... no checking mpi.h presence... no checking for mpi.h... no Try to find libmpi or libmpich ... checking for main in -lmpi... no libmpi not found. exiting... ERROR: configuration failed for package ŒRmpi¹ * removing Œ/usr/local/lib64/R/library/Rmpi¹ So obviously libmpi is not found. Doing a locate search for libmpi (straight after updatedb) shows: zytosrv01dmi:/home/unger/R_projects/OS # locate libmpi /opt/mpich/ch-p4/lib64/libmpich.a /opt/mpich/ch-p4/lib64/libmpichf90.a /opt/mpich/ch-p4/lib64/libmpichf90nc.a /opt/mpich/ch-p4/lib64/libmpichfarg.a /opt/mpich/ch-p4/lib64/libmpichfsup.a /opt/mpich/ch-p4mpd/lib64/libmpich.a /opt/mpich/ch-p4mpd/lib64/libmpichf90.a /opt/mpich/ch-p4mpd/lib64/libmpichf90nc.a /opt/mpich/ch-p4mpd/lib64/libmpichfarg.a /opt/mpich/ch-p4mpd/lib64/libmpichfsup.a /usr/lib64/mpi/gcc/openmpi/lib64/libmpi_cxx.la /usr/lib64/mpi/gcc/openmpi/lib64/libmpi_cxx.so /usr/lib64/mpi/gcc/openmpi/lib64/libmpi_cxx.so.0 /usr/lib64/mpi/gcc/openmpi/lib64/libmpi_cxx.so.0.0.0 /usr/lib64/mpi/gcc/openmpi/lib64/libmpi_f77.la /usr/lib64/mpi/gcc/openmpi/lib64/libmpi_f77.so /usr/lib64/mpi/gcc/openmpi/lib64/libmpi_f77.so.0 /usr/lib64/mpi/gcc/openmpi/lib64/libmpi_f77.so.0.0.0 /usr/lib64/mpi/gcc/openmpi/lib64/libmpi_f90.la /usr/lib64/mpi/gcc/openmpi/lib64/libmpi_f90.so /usr/lib64/mpi/gcc/openmpi/lib64/libmpi_f90.so.0 /usr/lib64/mpi/gcc/openmpi/lib64/libmpi_f90.so.0.0.0 /usr/lib64/mpi/gcc/openmpi/lib64/libmpi.la /usr/lib64/mpi/gcc/openmpi/lib64/libmpi.so /usr/lib64/mpi/gcc/openmpi/lib64/libmpi.so.0 /usr/lib64/mpi/gcc/openmpi/lib64/libmpi.so.0.0.0 What lets me assume that the path to libmpi is /usr/lib64/mpi/gcc/openmpi/lib64 which I already included in the options... How can I get this working? I would highly appreciate any help on this! Best wishes Kristian Dr. Kristian Unger Arbeitsgruppenleiter Integrative Biologie / Head of Integrative Biology Group Abteilung für Strahlenzytogenetik / Research Unit of Radiation Cytogenetics Helmholtz Zentrum München Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH) Ingolstädter Landstr. 1 85764 Neuherberg www.helmholtz-muenchen.de Aufsichtsratsvorsitzende: MinDir´in Bärbel Brumme-Bothe Geschäftsführer: Prof. Dr. Günther Wess und Dr. Nikolaus Blum Registergericht: Amtsgericht München HRB 6466 USt-IdNr: DE 129521671 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide
Re: [R] Rmpi installation
Kristian, I just tried that particular command here on a Gentoo system with openmpi-1.5.3 installed, because I wondered why the Rmpi configure script tests for main function in a shared library ... But I got a completly different output from configure. While the linker succeeds here, the package load test does not. However, on your system, may be the openmpi installation really is a kinda private one of gcc? I heard gcc makes use of openmpi internally. So is openmpi really installed? I just recognize that you are trying to use Rmpi_0.5-4.tar.gz while current version on CRAN is Rmpi_0.5-9.tar.gz. Best Hugo R CMD INSTALL --configure-args=--with-Rmpi-include=/usr/include --with-Rmpi-libpath=/usr/lib64/openmpi --with-Rmpi-type=OPENMPI Rmpi_0.5-9.tar.gz * installing to library ‘/home/hm/R/x86_64-pc-linux-gnu-library/2.13’ * installing *source* package ‘Rmpi’ ... checking for openpty in -lutil... no checking for main in -lpthread... no configure: creating ./config.status config.status: creating src/Makevars ** libs ** libs x86_64-pc-linux-gnu-gcc -std=gnu99 -I/usr/lib64/R/include -DPACKAGE_NAME=\\ -DPACKAGE_TARNAME=\\ -DPACKAGE_VERSION=\\ - DPACKAGE_STRING=\\ -DPACKAGE_BUGREPORT=\\ -I/usr/include -DMPI2 -DOPENMPI -I/usr/local/include-fpic -O3 -pipe -march=core2 - mtune=core2 -ggdb -c RegQuery.c -o RegQuery.o x86_64-pc-linux-gnu-gcc -std=gnu99 -I/usr/lib64/R/include -DPACKAGE_NAME=\\ -DPACKAGE_TARNAME=\\ -DPACKAGE_VERSION=\\ - DPACKAGE_STRING=\\ -DPACKAGE_BUGREPORT=\\ -I/usr/include -DMPI2 -DOPENMPI -I/usr/local/include-fpic -O3 -pipe -march=core2 - mtune=core2 -ggdb -c Rmpi.c -o Rmpi.o x86_64-pc-linux-gnu-gcc -std=gnu99 -I/usr/lib64/R/include -DPACKAGE_NAME=\\ -DPACKAGE_TARNAME=\\ -DPACKAGE_VERSION=\\ - DPACKAGE_STRING=\\ -DPACKAGE_BUGREPORT=\\ -I/usr/include -DMPI2 -DOPENMPI -I/usr/local/include-fpic -O3 -pipe -march=core2 - mtune=core2 -ggdb -c conversion.c -o conversion.o x86_64-pc-linux-gnu-gcc -std=gnu99 -I/usr/lib64/R/include -DPACKAGE_NAME=\\ -DPACKAGE_TARNAME=\\ -DPACKAGE_VERSION=\\ - DPACKAGE_STRING=\\ -DPACKAGE_BUGREPORT=\\ -I/usr/include -DMPI2 -DOPENMPI -I/usr/local/include-fpic -O3 -pipe -march=core2 - mtune=core2 -ggdb -c internal.c -o internal.o x86_64-pc-linux-gnu-gcc -std=gnu99 -shared -Wl,-O1 -Wl,--as-needed -o Rmpi.so RegQuery.o Rmpi.o conversion.o internal.o -L/usr/lib64/openmpi -lmpi -L/usr/lib64/R/lib -lR installiert nach /home/hm/R/x86_64-pc-linux-gnu-library/2.13/Rmpi/libs [...] ompi_mpi_init: orte_init failed -- Returned Not found (-13) instead of Success (0) On Wednesday 15 June 2011 15:19:22 Unger, Kristian, Dr. wrote: Thank you very much Hugo. Using the command as suggested results exactly the same error: # R CMD INSTALL --configure-args=--with-Rmpi-include=/usr/lib64/mpi/gcc/openmpi/include --with-Rmpi-libpath=/usr/lib64/mpi/gcc/openmpi/lib64 --with-Rmpi-type=OPENMPI Rmpi_0.5-4.tar.gz * installing to library ‘/usr/local/lib64/R/library’ * installing *source* package ‘Rmpi’ ... checking for gcc... gcc 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 accepts -g... yes checking for gcc option to accept ISO C89... none needed checking how to run the C preprocessor... gcc -E checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for ANSI C header files... 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 mpi.h usability... no checking mpi.h presence... no checking for mpi.h... no Try to find libmpi or libmpich ... checking for main in -lmpi... no libmpi not found. exiting... ERROR: configuration failed for package ‘Rmpi’ * removing ‘/usr/local/lib64/R/library/Rmpi’ Best wishes Kristian Dr. Kristian Unger Arbeitsgruppenleiter Integrative Biologie / Head of Integrative Biology Group Abteilung für Strahlenzytogenetik / Research Unit of Radiation Cytogenetics Tel.: +49-89-3187-3515 Mob.: +49-160-90641879 Am 15.06.11 15:12 schrieb Hugo Mildenberger unter hugo.mildenber...@web.de: Hmm, looks like there was a trailing blank after the backslash and before end of line, resulting in --with-Rmpi-libpath possibly not recognised: \--with-Rmpi-libpath=/usr/lib64/mpi/gcc/openmpi/lib64 \ I also doubt there is real need to escape newlines within a string. But another possible problem source is that according to R CMD INSTALL --help, the parameter is called --configure
Re: [R] Rmpi installation
Kristian, these are the usual problems with binary distributions. Regarding --with-Rmpi-include=/usr/lib64/mpi/gcc/openmpi/include and configure output checking for mpi.h... no ... so does /usr/lib64/mpi/gcc/openmpi/include really exist? At least, that appears to be a very unusual place to look for mpi.h (normally to be found in /usr/include ). And if you try to compile link the attached demo program: does the link phase succeed? Compile link using $ mpicc mtest.c -o mtest Presumably you have already tried to run install.packages(Rmpi). Kind regards Hugo On Wednesday 15 June 2011 16:22:07 Unger, Kristian, Dr. wrote: Thanks Hugo. I am pretty sure openmpi is installed: # zypper se openmpi Loading repository data... Reading installed packages... S | Name | Summary | Type --+---+-+--- i | openmpi | A powerful implementaion of MPI | package | openmpi | A powerful implementaion of MPI | srcpackage i | openmpi-devel | A powerful implementaion of MPI | package I got the same error message with the latest version available. The reason why I took the somewhat older version is that I wanted to make sure that it is not related to any libraries used by the newest version. Best wishes Kristian Dr. Kristian Unger Arbeitsgruppenleiter Integrative Biologie / Head of Integrative Biology Group Abteilung für Strahlenzytogenetik / Research Unit of Radiation Cytogenetics Tel.: +49-89-3187-3515 Mob.: +49-160-90641879 Am 15.06.11 16:16 schrieb Hugo Mildenberger unter hugo.mildenber...@web.de: Kristian, I just tried that particular command here on a Gentoo system with openmpi-1.5.3 installed, because I wondered why the Rmpi configure script tests for main function in a shared library ... But I got a completly different output from configure. While the linker succeeds here, the package load test does not. However, on your system, may be the openmpi installation really is a kinda private one of gcc? I heard gcc makes use of openmpi internally. So is openmpi really installed? I just recognize that you are trying to use Rmpi_0.5-4.tar.gz while current version on CRAN is Rmpi_0.5-9.tar.gz. Best Hugo R CMD INSTALL --configure-args=--with-Rmpi-include=/usr/include --with-Rmpi-libpath=/usr/lib64/openmpi --with-Rmpi-type=OPENMPI Rmpi_0.5-9.tar.gz * installing to library ‘/home/hm/R/x86_64-pc-linux-gnu-library/2.13’ * installing *source* package ‘Rmpi’ ... checking for openpty in -lutil... no checking for main in -lpthread... no configure: creating ./config.status config.status: creating src/Makevars ** libs ** libs x86_64-pc-linux-gnu-gcc -std=gnu99 -I/usr/lib64/R/include -DPACKAGE_NAME=\\ -DPACKAGE_TARNAME=\\ -DPACKAGE_VERSION=\\ - DPACKAGE_STRING=\\ -DPACKAGE_BUGREPORT=\\ -I/usr/include -DMPI2 -DOPENMPI -I/usr/local/include-fpic -O3 -pipe -march=core2 - mtune=core2 -ggdb -c RegQuery.c -o RegQuery.o x86_64-pc-linux-gnu-gcc -std=gnu99 -I/usr/lib64/R/include -DPACKAGE_NAME=\\ -DPACKAGE_TARNAME=\\ -DPACKAGE_VERSION=\\ - DPACKAGE_STRING=\\ -DPACKAGE_BUGREPORT=\\ -I/usr/include -DMPI2 -DOPENMPI -I/usr/local/include-fpic -O3 -pipe -march=core2 - mtune=core2 -ggdb -c Rmpi.c -o Rmpi.o x86_64-pc-linux-gnu-gcc -std=gnu99 -I/usr/lib64/R/include -DPACKAGE_NAME=\\ -DPACKAGE_TARNAME=\\ -DPACKAGE_VERSION=\\ - DPACKAGE_STRING=\\ -DPACKAGE_BUGREPORT=\\ -I/usr/include -DMPI2 -DOPENMPI -I/usr/local/include-fpic -O3 -pipe -march=core2 - mtune=core2 -ggdb -c conversion.c -o conversion.o x86_64-pc-linux-gnu-gcc -std=gnu99 -I/usr/lib64/R/include -DPACKAGE_NAME=\\ -DPACKAGE_TARNAME=\\ -DPACKAGE_VERSION=\\ - DPACKAGE_STRING=\\ -DPACKAGE_BUGREPORT=\\ -I/usr/include -DMPI2 -DOPENMPI -I/usr/local/include-fpic -O3 -pipe -march=core2 - mtune=core2 -ggdb -c internal.c -o internal.o x86_64-pc-linux-gnu-gcc -std=gnu99 -shared -Wl,-O1 -Wl,--as-needed -o Rmpi.so RegQuery.o Rmpi.o conversion.o internal.o -L/usr/lib64/openmpi -lmpi -L/usr/lib64/R/lib -lR installiert nach /home/hm/R/x86_64-pc-linux-gnu-library/2.13/Rmpi/libs [...] ompi_mpi_init: orte_init failed -- Returned Not found (-13) instead of Success (0) On Wednesday 15 June 2011 15:19:22 Unger, Kristian, Dr. wrote: Thank you very much Hugo. Using the command as suggested results exactly the same error: # R CMD INSTALL --configure-args=--with-Rmpi-include=/usr/lib64/mpi/gcc/openmpi/include --with-Rmpi-libpath=/usr/lib64/mpi/gcc/openmpi/lib64 --with-Rmpi-type=OPENMPI Rmpi_0.5-4.tar.gz * installing to library ‘/usr/local/lib64/R/library’ * installing *source* package ‘Rmpi’ ... checking for gcc... gcc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling
Re: [R] Rmpi installation
Dear Kristian, please run exactly mpicc mtest.c -o mtest If you really need it, add -v separately. mpicc is nothing but a compiler wrapper. The -o switch specifies the outfile name, which has to follow immediately after -o, with or without a blank character in between. I'm not sure about what happens with -ov mtest. Probably an output file named v is produced on disk, in addition to the file mtest stemming from a previous with -o mtest Depending on mpicc's, gcc's and ld's version, gcc may instruct the linker to link the previously produced executable mtest with the object newly compiled from mtest.c plus several implicit libraries and startup objects, and output the result to v. ld would then be faced with duplicate defined symbols and output a list of these doublets. My proposal was meant as a test for an else correct openmpi installation, perhaps I should have said this. On successful completion, no message should be printed, but an executable named mtest should have been produced, which could then be run typing ./mtest. If the link process failed, then the openmpi installation was inconsistent. Kind regards Hugo On Wednesday 15 June 2011 17:45:41 Unger, Kristian, Dr. wrote: Dear Hugo I ran the command with the verbose switch and get the following output: mpicc mtest.c -ov mtest mtest: In function `_start': /usr/src/packages/BUILD/glibc-2.11.1/csu/../sysdeps/x86_64/elf/start.S:65: multiple definition of `_start' /usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../lib64/crt1.o:/usr/src/pack ages/BUILD/glibc-2.11.1/csu/../sysdeps/x86_64/elf/start.S:65: first defined here mtest: In function `_fini': (.fini+0x0): multiple definition of `_fini' /usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../lib64/crti.o:initfini.c:(. fini+0x0): first defined here mtest:(.rodata+0x0): multiple definition of `_IO_stdin_used' /usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../lib64/crt1.o:(.rodata.cst4 +0x0): first defined here mtest: In function `__data_start': (.data+0x0): multiple definition of `__data_start' /usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../lib64/crt1.o:(.data+0x0): first defined here mtest: In function `main': (.text+0xec): multiple definition of `main' /tmp/ccUyk8e9.o:mtest.c:(.text+0x0): first defined here mtest: In function `_init': (.init+0x0): multiple definition of `_init' /usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../lib64/crti.o:initfini.c:(. init+0x0): first defined here /usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../x86_64-suse-linux/bin/ld: error in mtest(.eh_frame); no .eh_frame_hdr table will be created. collect2: ld returned 1 exit status Not sure if this makes any sense? Best wishes Kristian Dr. Kristian Unger Arbeitsgruppenleiter Integrative Biologie / Head of Integrative Biology Group Abteilung für Strahlenzytogenetik / Research Unit of Radiation Cytogenetics Tel.: +49-89-3187-3515 Mob.: +49-160-90641879 Am 15.06.11 17:25 schrieb Hugo Mildenberger unter hugo.mildenber...@web.de: Kristian, these are the usual problems with binary distributions. Regarding --with-Rmpi-include=/usr/lib64/mpi/gcc/openmpi/include and configure output checking for mpi.h... no ... so does /usr/lib64/mpi/gcc/openmpi/include really exist? At least, that appears to be a very unusual place to look for mpi.h (normally to be found in /usr/include ). And if you try to compile link the attached demo program: does the link phase succeed? Compile link using $ mpicc mtest.c -o mtest Presumably you have already tried to run install.packages(Rmpi). Kind regards Hugo On Wednesday 15 June 2011 16:22:07 Unger, Kristian, Dr. wrote: Thanks Hugo. I am pretty sure openmpi is installed: # zypper se openmpi Loading repository data... Reading installed packages... S | Name | Summary | Type --+---+-+--- i | openmpi | A powerful implementaion of MPI | package | openmpi | A powerful implementaion of MPI | srcpackage i | openmpi-devel | A powerful implementaion of MPI | package I got the same error message with the latest version available. The reason why I took the somewhat older version is that I wanted to make sure that it is not related to any libraries used by the newest version. Best wishes Kristian Dr. Kristian Unger Arbeitsgruppenleiter Integrative Biologie / Head of Integrative Biology Group Abteilung für Strahlenzytogenetik / Research Unit of Radiation Cytogenetics Tel.: +49-89-3187-3515 Mob.: +49-160-90641879 Am 15.06.11 16:16 schrieb Hugo Mildenberger unter hugo.mildenber...@web.de: Kristian, I just tried that particular command here
Re: [R] predictive logistic model cell-biology, non-dichotomous data
Andreas, the jpg files you linked below do not exist, but if all you need for the moment is a predictive model and graphical displays of the fitted model and the calibrated sample data, then the R - package calib will do it very well. Usage is very simple. Best, Hugo On Tuesday 14 June 2011 00:11:37 andreasss wrote: Hi everyone, I would like to fit a predictive model to my data in order to compare absorbance readings to a toxin standard. This data was obtained by exposing red blood cells to different toxin concentrations, which lead to the lysis of the red blood cells, increasing the absorbance (hemoglobin is freed). The data has a sigmoid shape (see below), so I thought about fitting a logistic model to the data so that I will be able to determine the toxin equivalent of new absorbance readings. http://r.789695.n4.nabble.com/file/n3595812/Unbenannt.jpg The data points for this curve are: http://r.789695.n4.nabble.com/file/n3595812/qweqwe.jpg I must admit that I am totally lost. I have done a fair bit of reading on logistic regression, but most seem to focus on binary outcomes or multinomial analysis. Do I have to somehow assign 'pass' or 'fail' to this data, maybe 0 and 100% lysis? Or is the logistic model not suitable for what I am planning. All I want to do is to fit a predictive model to this data and to graphically represent the 'best fit'. Any help will be greatly appreciated. Thanks in advance, Andreas -- View this message in context: http://r.789695.n4.nabble.com/predictive-logistic-model-cell-biology-non-dichotomous-data-tp3595812p3595812.html Sent from the R help mailing list archive at Nabble.com. __ 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-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] R-2.10.1 to R-2.13.0
Ogbos, I don't use Ubunto too, but X-11 headers should be installable running apt-get xorg-dev and/or (possibly) apt-get libx11-dev xlibs-dev Best On Thursday 26 May 2011 16:13:36 Duncan Murdoch wrote: On 26/05/2011 10:05 AM, ogbos okike wrote: Hi Duncan, Thanks for your time. Using ./configure as specified in the installation manual, I attempted to install R-2.13.0 but it reported an error message: checking for IceConnectionNumber in -lICE... no checking X11/Intrinsic.h usability... no checking X11/Intrinsic.h presence... no checking for X11/Intrinsic.h... no configure: error: --with-x=yes (default) and X11 headers/libs are not available Could you please advise further. I am attempting this for the first time on my laptop (ubuntu os). I don't use Ubuntu, but that looks as though you don't have the development headers for X11 available. The usual advice I've seen on this is to install an Ubuntu binary rather than building yourself, but I don't remember the details of where to get it (and I don't remember how to get the X11 headers you need). Duncan Murdoch Regards Ogbos On 26 May 2011 12:45, Duncan Murdochmurdoch.dun...@gmail.com wrote: On 26/05/2011 6:02 AM, ogbos okike wrote: Dear List, I am currently running R-2.10.1. I wish to install R-2.13.0 or update my R-2.10.1 to the R-2.13.0. I have downloaded R-2.13.0 but wish to seek your advice before installing that. Please is there a better way of updating to the newer version other than downloading and installing the version? Thanks for your suggestions. There is some advice on this in the Windows FAQ. You can see the current version online at http://cran.r-project.org/bin/windows/base/rw-FAQ.html#What_0027s-the-best-way-to-upgrade_003f If you're not using Windows, most of the advice in that FAQ item is still good (though the paths filenames will be different). Duncan Murdoch __ 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-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] Processing large datasets
With PostgreSQL at least, R can also be used as implementation
language for stored procedures. Hence data transfers between
processes can be avoided alltogether.
http://www.joeconway.com/plr/
Implemention of such a procedure in R appears to be straighforward:
CREATE OR REPLACE FUNCTION overpaid (emp) RETURNS bool AS '
if (20 arg1$salary) {
return(TRUE)
}
if (arg1$age 30 10 arg1$salary) {
return(TRUE)
}
return(FALSE)
' LANGUAGE 'plr';
CREATE TABLE emp (name text, age int, salary numeric(10,2));
INSERT INTO emp VALUES ('Joe', 41, 25.00);
INSERT INTO emp VALUES ('Jim', 25, 12.00);
INSERT INTO emp VALUES ('Jon', 35, 5.00);
SELECT name, overpaid(emp) FROM emp;
name | overpaid
--+--
Joe | t
Jim | t
Jon | f
(3 rows)
Best
On Wednesday 25 May 2011 14:12:23 Jonathan Daily wrote:
In cases where I have to parse through large datasets that will not
fit into R's memory, I will grab relevant data using SQL and then
analyze said data using R. There are several packages designed to do
this, like [1] and [2] below, that allow you to query a database using
SQL and end up with that data in an R data.frame.
[1] http://cran.cnr.berkeley.edu/web/packages/RMySQL/index.html
[2] http://cran.cnr.berkeley.edu/web/packages/RSQLite/index.html
On Wed, May 25, 2011 at 12:29 AM, Roman Naumenko ro...@bestroman.com wrote:
Hi R list,
I'm new to R software, so I'd like to ask about it is capabilities.
What I'm looking to do is to run some statistical tests on quite big
tables which are aggregated quotes from a market feed.
This is a typical set of data.
Each day contains millions of records (up to 10 non filtered).
2011-05-24 750 Bid DELL14130770400
15.4800 BATS35482391Y 1 1 0 0
2011-05-24 904 Bid DELL14130772300
15.4800 BATS35482391Y 1 0 0 0
2011-05-24 904 Bid DELL14130773135
15.4800 BATS35482391Y 1 0 0 0
I'll need to filter it out first based on some criteria.
Since I keep it mysql database, it can be done through by query. Not
super efficient, checked it already.
Then I need to aggregate dataset into different time frames (time is
represented in ms from midnight, like 35482391).
Again, can be done through a databases query, not sure what gonna be faster.
Aggregated tables going to be much smaller, like thousands rows per
observation day.
Then calculate basic statistic: mean, standard deviation, sums etc.
After stats are calculated, I need to perform some statistical
hypothesis tests.
So, my question is: what tool faster for data aggregation and filtration
on big datasets: mysql or R?
Thanks,
--Roman N.
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Re: [R] source and localhost
Thomas, your example works with R-2.13.0 and Apache running on Gentoo. You may try to use http://127.0.0.1:5984/path/fn.R;, just to exclude that this problem has anything to do with name resolution. Best Hugo Dear List, I have problems with the function source() using a url of the kind: http://localhost:5984/path/fn.R I receive Fehler in file(file, r, encoding = encoding) : kann Verbindung nicht öffnen Zusätzlich: Warnmeldung: In file(file, r, encoding = encoding) : Öffnen fehlgeschlagen: HTTP Status war '502 cannotconnect' The url itself is ok since I can: - use a browser - use curl - use download.file() function - use getURL() (out of Duncans RCurl) furthermore it works, when I use the full host + domain name. So I think it is about dns stuff. I get a nice: Sys.getenv(no_proxy) [1] localhost, 127.0.0.1 and work on 32bit opensuse 11.4 with R version 2.13.0 (2011-04-13) Can someone give me a hint? Best regards Thomas __ 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-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] Loop stopping after 1 iteration
William,
num_obs obviously isn't a vector, therefore length(num_obs) will
evaluate to one. Hence your for loop control part will expand to
for (i in 1:1)
while it should probably read:
for (i in 1:num_obs)
Best
Hugo
On Wednesday 18 May 2011 17:18:15 armstrwa wrote:
Hi all,
This is a very basic question, but I just can't figure out why R is handling
a loop I'm writing the way it is.
Here is the script I have written:
grid_2_series-function(gage_handle,data_type,filename)
series_name-paste(gage_handle,data_type,sep=_)
data_grid-read.table(file=paste(filename,.txt,sep=))
num_rows_data-nrow(data_grid)-1
num_cols_data-ncol(data_grid)-4
num_obs-num_rows_data*num_cols_data
time_series-matrix(nrow=0,ncol=2)
for(i in 1:length(num_obs)){
rownum-ceiling(i/31)+1
colnum-if(i%%31==0){
35
}else{
(i%%31)+4
}
year-data_grid[rownum,2]
month-data_grid[rownum,3]
day-colnum-4
date_string-paste(month,day,year,sep=/)
date-as.Date(date_string,format='%m/%d/%Y')
value-as.character(data_grid[rownum,colnum])
time_series-rbind(time_series,c(date,value))
}
The script is working as I intended it to (goes through a matrix of data
where column 2 is the year, column 3 is the month, and row 1 columns 5-35
are the day of the month the observation was recorded [I have included a
screenshot below to help visualize what I'm talking about] and converts the
grid into a 2 column time series where column 1 is the date and column 2 is
the value of the observation), but it is stopping after only 1 iteration.
nabble_img src=matrix_screenshot.jpg border=0/
Two questions:
1.) Does anyone know of an existing function to accomplish this task?
2.) Why is the loop stopping after 1 iteration? I have it written to
iterate up to the total number of observations (20,615 in one case).
Thank you for your help and sorry for this question which I'm sure has a
very simple answer.
Thanks again,
Billy
--
View this message in context:
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Sent from the R help mailing list archive at Nabble.com.
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Re: [R] Dotplot (package Hmisc) with groups: colours and symbols
Hello Esther,
you left out the ellipsis argument (...) to the panel function.
That argument serves a placeholder for the rest of the parameters
you did not want to name and pass explicitely. If you don't pass the
ellipsis to panel.Dotplot, all unnamed parameters will get default
values. You can see these defaults by typing panel.dotplot or
edit(panel.dotplot) on the command line.
Dotplot( site~Cbind(yield, yield+5, yield-5)|variety,
groups = year,
data = barley,
pch= c(1,2),
panel = function(x,y,...){
panel.Dotplot(x,y,col=black,...);
})
Best
On Wednesday 11 May 2011 11:11:50 E Hofstadler wrote:
Hello all,
This question concerns the function Dotplot from the Hmisc package.
My aim is to compare values between groups in each panel of the
Dotplot, with the values of different groups clearly distinguishable
by different symbols. All lines and symbols should be coloured in
black.
Before adding the panel function to the Dotplot, the groups behaved as
desired and were marked by different symbols, but the error bands were
blue instead of black. After adding the panel function and changing
the trellis colour settings, the error bars are now black, but now the
groups are suddenly marked by the same rather than different symbols.
I've tried several ways to change the group symbols but to no avail.
## set CI lines to black
t1 = trellis.par.get(plot.line)
t1$col - black
trellis.par.set(plot.line,t1)
## load example data
require(lattice)
data(barley)
## example plot (problem: groups marked by the same symbol)
require(Hmisc)
Dotplot(site~Cbind(yield, yield+5, yield-5)|variety, groups=year,
data=barley, pch=c(1,2), col=black,
panel=function(x,y){
panel.Dotplot(x,y,col=black)})
Key()
What am I doing wrong?
Many thanks in advance.
Esther
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Re: [R] Insert variable in RMySQL-Statement
Arne,
there might be faster or more elegant solutions, but this is a possibility:
for ( a in values ) {
Temp - dbGetQuery(con, paste(select * from db where id = ,a,sep=)));
print(Temp);
}
There must be also a way to make use of the in - operator:
select * from db where id in (1,2,3);
but I can't figure it out at the moment.
Best
Hugo
On Wednesday 09 February 2011 10:09:34 Arne H. Schulz wrote:
Dear list,
I'm working with a MySQL-Table and would like to extract selected ids that
are stored in a vector:
Ids - c(1,2,3)
How do I insert this variable in a for loop like this:
For (a in values) {
Temp - dbGetQuery(con,
select * from db
Where id = ID;)
}
My problem is to split the select-statement and insert the current id. How
can I handle this problem?
Best regards,
Arne
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Re: [R] Insert variable in RMySQL-Statement
This should be much faster:
idx - c(1,2,3)
res - dbGetQuery(con,paste(select * from db where id in
(,paste(idx,collapse=,),),sep=));
print(res);
On Wednesday 09 February 2011 14:13:17 Hugo Mildenberger wrote:
Arne,
there might be faster or more elegant solutions, but this is a possibility:
for ( a in values ) {
Temp - dbGetQuery(con, paste(select * from db where id =
,a,sep=)));
print(Temp);
}
There must be also a way to make use of the in - operator:
select * from db where id in (1,2,3);
but I can't figure it out at the moment.
Best
Hugo
On Wednesday 09 February 2011 10:09:34 Arne H. Schulz wrote:
Dear list,
I'm working with a MySQL-Table and would like to extract selected ids that
are stored in a vector:
Ids - c(1,2,3)
How do I insert this variable in a for loop like this:
For (a in values) {
Temp - dbGetQuery(con,
select * from db
Where id = ID;)
}
My problem is to split the select-statement and insert the current id. How
can I handle this problem?
Best regards,
Arne
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Re: [R] Finding non-normal distributions per row of data frame?
Danny, sounds like you already have a certain idea how a 'nugget' distribution could look like. Maybe you also could intentionally produce some experimental data having such distributions, harvest the related patterns from the microarray and then apply a method as it was described in http://www.cs.uwaterloo.ca/~shai/TALKS/NIPS07_prob_wkshp.pdf But this is an uneducated guess only. Best Hugo On Saturday 05 February 2011 00:21:01 DB1984 wrote: Greg, Dennis - thanks for your input, I really appreciate the feedback, as it is not easy to source. In terms of the data; I've described it as 20 columns, which is the smallest dataset, but this can run to 320 columns, so in some cases there is likely to be enough power to detect non-normality. That said, a better solution would be useful. As a first approximation, I looked at the mean/median ratio to indicate simple skew in the data - which suggested that most of the data was normally distributed. I took the 'nuggets' to be those with a mean/median ratio in the top or bottom 1% of the data. This was a small group - overall the data appears relatively normally distributed within rows. The aim is really to find those nuggets with significantly non-normal distributions. My hope was to be able to take the tails of the p-values for Shapiro-Wilk, or some similar test, and find these enriched with nuggets. This may not be an appropriately robust approach - but is there a better option? One idea was to sort the data in each row, and perform a linear regression. For normal distributions I am expecting the intercept to be close to the mean. Using the (intercept-mean) and p-values for the fit of the regression was again another way to filter out the nuggets in the dataset. If it helps, the nuggets I am expecting are either grouped 80% grouped around the mean with 20% forming a uni-directional tail, or an approximate bimodal distribution. As I'd imagine is obvious - I don't have an ideal solution to finding these nuggets, and so coming up with the R code to do so is harder still. If anybody has insight into this sort of problem, and can point me in the direction of further reading, that would be helpful. If there is a ready-made solution, even better! As I said, thanks for your time with this... __ 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] Fitting ELISA measurements unknowns to 4 parameter logistic model
Hello Chris, You may also use the R-package calib. Hugo On Tuesday 01 February 2011 17:08:13 Christopher Anderson wrote: Hello, I am trying to fit my Elisa results (absorbance readings) to a standard curve. To create the standard curve model, I performed a 4-parameter logistic fit using the 'drc' package (ExpectedConc~Absorbance). This gave me the following: FourP A 'drc' model. Call: drm(formula = Response ~ Expected, data = SC, fct = LL.4()) Coefficients: b:(Intercept) c:(Intercept) d:(Intercept) e:(Intercept) 1.336 6.236 85.521 59.598 summary(FourP) Model fitted: Log-logistic (ED50 as parameter) (4 parms) Parameter estimates: Estimate Std. Error t-value p-value b:(Intercept) 1.335960.15861 8.42309 0.0011 c:(Intercept) 6.235573.18629 1.95700 0.1220 d:(Intercept) 85.521402.15565 39.67313 0. e:(Intercept) 59.598355.18781 11.48815 0.0003 Residual standard error: 1.866876 (4 degrees of freedom) Now that I have the 4 parameters, how do I fit the absorbance readings for the analytical unknowns to the standard curve model (as to estimate the concentrations of my unknown analytical samples)? I can use the argument 'predict', but this predicts absorbance given concentrations (y given x), I need to predict concentrations give absorbance (x given y). Thanks! Chris [[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-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] using gsarima package with R
On Sunday 23 January 2011 20:52:21 nandan amar wrote: I am trying to use function garsim from package gsarima. I can download gsarima package from http://cran.fyxm.net/web/packages/gsarima/index.html for linux. But how I can add it to R. For example by entering R CMD INSTALL /path/to/gsarima_0.0-2.tar.gz __ 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] Debian ?Ubuntu version of latest R using synaptic in Ubuntu 10.10
Ajay, you may try to run R as root while updating packages. Some packages insist to install in directories writeable only by root. On Saturday 22 January 2011 07:50:10 Ajay Ohri wrote: Dear List I use synaptic to download R on my Ubuntu 10.10. It seems latest version of R on Ubuntu is 2.11.1 Even when I use debian.cran.r-project.org to update my packages the problem remains (latest versions on CRAN are almost always 2 updates ahead of Debian packages) This is also true for a lot of other packages as well My specific problem is while I can use sudo apt-get to update packages from Debian repository I get a permission denied when I am trying to update from CRAN from within R. I am a Linux newbie Please help Regards Ajay Websites- http://decisionstats.com [[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-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] User input in R program
Hello Christian, for an example of interacting with graphic output, just run example(getGraphicsEvent) However, on X11, that feature had ceased to work since a pre-release of R-2.12 if Cairo support was enabled at compile time. The reason for this defect had already been documented in R's bugs database for long. Maybe getGraphicsEvent still runs on Windows. Best Hugo On Friday 21 January 2011 13:26:26 christiaan pauw wrote: HI Everybody Does anyone know of documentation about different ways of obtaining user input in R. I have used readline() but I wondered is there are sophisticated packages that does things like validate answers or generate selection lists. bets regards Christaan [[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-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] cannot allocate vector of size ... in RHLE5 PAE kernel
I got the following warning:
memorytest.c: In function ‘main’:
memorytest.c:5: warning: return type of ‘main’ is not ‘int’
Is this important ?
Hello Mauricio,
No, your gcc version is unduly puristic here. The traditional return
type of the main function in C should be int, and if that is given,
main has to return an integer number explicitly. By convention,
a main function returning 0 indicates success, and anything other
is considered as an error or warning condition. Specifying void main()
normally implies returning zero. But if you are still worried simply
change void main into int main() and add the statement return 0;
just before the last curly bracket (without quotation marks, of course):
int main() {
[...]
return 0;
}
Best
Hugo
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Re: [R] cannot allocate vector of size ... in RHLE5 PAE kernel
Dear Mauricio,
what I do not understand at all is the message:
Error: cannot allocate vector of size 476.2 Mb
Have you tried to allocate a big matrix in between, whith
the R - statement not being shown in the output? Probably
not. If not, your local R version is buggy for sure. The test shows
that the OS imposes no artificial constraint on memory consumption,
at least not up to ~ 1GB. But because you said that you're running a
32 - bit version of R (in a virtual machine?), the question is now
wether gcc also compiles the test program as a 32 - bit program. I'm
unsure because a 64 - bit system can be configured to compile and
run programs using either environment. Regrettably I previously
did not include a test for that.
--- snip ---
#include stdio.h
int main() {
printf(The size of a pointer is %lu bytes\n, (unsigned
long)sizeof(void *));
return 0;
}
--- snip ---
If the program says The size of a pointer is 4 bytes then you're
running the test program in a 32 bit environment. Then the
allocation problem could possibly be solved by recompiling/updating
your R version. The system is called Redhat Enterprise Linux after
all, so calling in Redhat support at that point and ask them to do
something for their money should be an option.
Best
Hugo
On Wednesday 19 January 2011 12:54:38 Mauricio Zambrano wrote:
Dear Hugo,
I tried your memory test program (without further modifications) just
after the gc() command:
print(gc())
print(gcinfo(TRUE))
system(/mypath/memorytest.out)
and the result that I got was:
Number of simulations read from ' Particles.txt ' : 9000
---
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 480114 12.91816453 48.6 5543382 148.1
Vcells 5256970 40.2 119171871 909.3 322607910 2461.4
[1] TRUE
Trying to allocate 10 bytes ... success. Now trying to commit
memory ... succeeded.
Garbage collection 2667 = 2286+194+187 (level 2) ...
12.9 Mbytes of cons cells used (26%)
278.4 Mbytes of vectors used (29%)
Error: cannot allocate vector of size 476.2 Mb
What do you understand of this result ?
Thanks in advance,
Mauricio
I got the following warning:
memorytest.c: In function ‘main’:
memorytest.c:5: warning: return type of ‘main’ is not ‘int’
Is this important ?
Hello Mauricio,
No, your gcc version is unduly puristic here. The traditional return
type of the main function in C should be int, and if that is given,
main has to return an integer number explicitly. By convention,
a main function returning 0 indicates success, and anything other
is considered as an error or warning condition. Specifying void main()
normally implies returning zero. But if you are still worried simply
change void main into int main() and add the statement return 0;
just before the last curly bracket (without quotation marks, of course):
int main() {
[...]
return 0;
}
Best
Hugo
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Re: [R] Time and xts
Nicos,
there are certainly better / faster methods to compare a time range which I
simply don't know of, but the condensed code below should do it. Your main
problem was that you can't compare time(x) to 7:55, since the
latter expression denotes a sequence from 7 to 55 in R. Consequently, such
an expression compares time(x) with all integer numbers between 7 and 55:
time(z[1]) = 7:55
[1] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
[13] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
[25] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
[37] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
[49] FALSE
length(z[time(z) = 2 time(z) = 7:55])
[1] 0
Your while loop was therefore equivalent to
m=vector(numeric,0);
while(m) print(1);
Best
Hugo
-- snip --
library(zoo)
library(chron)
Lines- DateTimeOpenHighLow Close
1/2/200517:05 1.3546 1.3553 1.3546 1.35495
1/2/200517:10 1.3553 1.3556 1.3549 1.35525
1/2/200517:15 1.3556 1.35565 1.35515 1.3553
1/2/200517:25 1.355 1.3556 1.355 1.3555
3/14/2006 5:211.18895 2.18925 1.18835 1.1885
3/14/2006 7:562.18895 3.18925 1.18835 1.1885
2/13/2006 5:201.18895 1.18925 1.18835 1.1885
z- read.zoo(con-textConnection(Lines), header = TRUE, index = list(1, 2), FUN
= function(d,t) as.chron(paste(d, t), format = %m/%d/%Y %H:%M))
close(con);
entrytrade - function(k) { k$Open+k$High }
#Note: A binary and operator () instead a logical () is needed here
new - entrytrade( z[hours(time(z)) = 2 ( hours(time(z)) +
minutes(time(z))/100 = 7.55 ) ] );
print(new);
--- snip ---
On Tuesday 18 January 2011 22:36:12 rnick wrote:
Hi all,
Gabor came up with a very nice of code for my request:
Lines - DateTimeOpenHighLow Close
1/2/200517:05 1.3546 1.3553 1.3546 1.35495
1/2/200517:10 1.3553 1.3556 1.3549 1.35525
1/2/200517:15 1.3556 1.35565 1.35515 1.3553
1/2/200517:25 1.355 1.3556 1.355 1.3555
2/13/2006 5:201.18895 1.18925 1.18835 1.1885
library(zoo)
library(chron)
z - read.zoo(textConnection(Lines), header = TRUE, index = list(1, 2),
FUN = function(d,t) as.chron(paste(d, t), format = %m/%d/%Y %H:%M))
z$New - z$Open + z$High
zz - z[hours(time(z)) = 2 hours(time(z)) = 8]
The result is:
zz
Open High Low Close New
(02/13/06 05:20:00) 1.19 1.19 1.19 1.19 2.38
However, my original code needs a for loop.
Any ideas on how to identify the z positions where time is between 2:00:00
and 07:55:00.
Could i do it with the following structure?
Lines- DateTimeOpenHighLow Close
1/2/200517:05 1.3546 1.3553 1.3546 1.35495
1/2/200517:10 1.3553 1.3556 1.3549 1.35525
1/2/200517:15 1.3556 1.35565 1.35515 1.3553
1/2/200517:25 1.355 1.3556 1.355 1.3555
2/13/2006 5:201.18895 1.18925 1.18835 1.1885
library(zoo)
library(chron)
z- read.zoo(textConnection(Lines), header = TRUE, index = list(1, 2), FUN =
function(d,t) as.chron(paste(d, t), format = %m/%d/%Y %H:%M))
n=5
entrytrade-function(k)
{
new[k]-open[k]+high[k]
}
for (x in seq(from=1,to=n,by=1))
{
while (z[time(x)=2 time(x)=7:55])
{
entrytrade(x)
}
}
Based on what i have seen the problem lies in the for loop and more
specifically in the while statement. That's the error i get:
Error in while (z[time(x) = 2 time(x) = 7:55]) { :
argument is of length zero
Thanks
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Re: [R] cannot allocate vector of size ... in RHLE5 PAE kernel
Mauricio,
I tried your matrix allocation on Gentoo-hardened 32 and
64 bit systems. Both work ok, using R-2.11.1 and R-2.12.2 respectively,
and both use a recent 2.6.36 kernel revision.
This is from the 32 bit system with 512 MB physical memory:
system(free)
total used free sharedbuffers
cached
Mem:469356 61884 407472 0 1368 21592
-/+ buffers/cache: 38924 430432
Swap: 1927796 360961891700
gc()
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 120116 3.3 35 9.4 35 9.4
Vcells 78413 0.6 786432 6.0 391299 3.0
bs - matrix(NA, nrow=6940,ncol=9000)
gc()
used (Mb)gc trigger (Mb) max used (Mb)
Ncells 120123 3.3 35 9.4 359.4
Vcells 31308414 238.9 34854943 266.0 31308428 238.9
system(free)
total used free sharedbuffers cached
Mem:469356 307528 161828 0 1404 22508
-/+ buffers/cache: 283616 185740
Swap: 1927796 360841891712
MZ I tried to increase the memory limit available for R by using:
MZ $ R --min-vsize=10M --max-vsize=5000M --min-nsize=500k --max-nsize=5000M
Hmm, I wonder if specifying 5000M is a good idea within a 32-bit environment.
Depending on R's internal implementation, maybe that value could overflow an
tacitly wrap around on a 32 bit integer. (5000M 2^32 - 1) You may try to
specify
1000M instead. But I think it's more probable that the system or VM
configuration
had setup a memory usage limit per user or per process. How to view/change this
on redhat I don't know. But you may try to compile a small C programm using
malloc() and see what happens if you request say 1Gigabyte:
#include stdlib.h
#include stdio.h
void main() {
const size_t size = 10LU;
void* p = malloc(size);
if ( p ) {
fprintf(stderr,successfully allocated %lu bytes\n,size);
}else {
fprintf(stderr,allocation of %lu bytes failed:%m\n,size);
}
}
put this into a file named, say, tmalloc.c and compile it using
gcc tmalloc.c -o tmalloc
Hugo
On Monday 17 January 2011 16:42:43 Mauricio Zambrano wrote:
Following the advice a colleague, I put the gc() and gcinfo(TRUE)
commands just before the line I got the problem, and their output
were:
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 471485 12.61704095 45.6 7920371 211.5
Vcells 6408885 48.9 113919753 869.2 347651599 2652.4
Garbage collection 538 = 323+101+114 (level 2) ...
13.0 Mbytes of cons cells used (29%)
49.0 Mbytes of vectors used (7%)
Error: cannot allocate vector of size 238.1 Mb
If I understood correctly, I should have enough memory for allocating
the new matrix (Q.obs - matrix(NA, nrow=6940, MZ ncol=9000) ))
Thanks in advance for any help,
Mauricio
MZ == Mauricio Zambrano hzambran.newsgro...@gmail.com
on Mon, 17 Jan 2011 11:46:44 +0100 writes:
MZ Dear R community,
MZ I'm running R 32 bits in a 64-bits machine (with 16Gb of Ram) using a
MZ PAE kernel, as you can see here:
MZ $ uname -a
MZ Linux mymachine 2.6.18-238.el5PAE #1 SMP Sun Dec 19 14:42:44 EST 2010
MZ i686 i686 i386 GNU/Linux
MZ When I try to create a large matrix ( Q.obs - matrix(NA, nrow=6940,
MZ ncol=9000) ), I got the following error:
Error: cannot allocate vector of size 238.3 Mb
MZ However, the amount of free memory in my machine seems to be much
MZ larger than this:
MZ system(free)
MZ \ total used free sharedbuffers
cached
MZ Mem: 1246623663541166112120 0 67596
2107556
MZ -/+ buffers/cache:41789648287272
MZ Swap: 12582904 0 12582904
MZ I tried to increase the memory limit available for R by using:
MZ $ R --min-vsize=10M --max-vsize=5000M --min-nsize=500k
--max-nsize=5000M
MZ but it didn't work.
MZ Any hint about how can I get R using all the memory available in the
machine ?
Install a 64-bit version of Linux, i.e., ubuntu in your case
and work from there.
I don't think there's a way around that.
Martin
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Re: [R] How to still processing despite bug errors?
Altay, simply run your tests under control of an exception handler: help(try) help(tryCatch) On Monday 17 January 2011 22:05:07 Altay wrote: Hi, everybody. I am working processing EEG data from 1000 pacients. I have a specific syntax to perform the Spectral Analysis and a loop to analyse all subjects. each subject data are in separate folders (P1, P2 P3...) My question is: in some cases, some errors can appear in one subject. I want to know if is possible to jump to the next subject and perform the same syntax , exibiting an error like: Working on P1 Error X in P1 Working on P2... The idea is to let the computer processing continuosly all the subjects and at the end only see the problems in the subjects that R could not perform the analysis. Each Subject takes 20 minutes to perform the analysis and I don't want to stay days in front of PC, waiting for the next error in order to start the syntax again with the next subject. Any ideas? Thanks in Advance. Altay Lino de Souza. [[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-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] rootogram for normal distributions
Using R-2.12.1 and latticeExtra-0.6-14, I would like to understand why a rootogram displaying samples from the Poisson distribution looks like I expected it, whereas a rootogram using the normal distribution does not: library(latticeExtra) rootogram(~rpois(1000, lambda = 50), dfun = function(x) dpois(x, lambda = 50)) rootogram(~rnorm(1000), dfun = function(x) dnorm(x,mean(x),sd(x))) I probably can't attach figures here. Thus a textual description of what I get may suffice: With increasing sample size, the rootogram using random samples from the Poisson distribution shows decreasing differences (bars are quickly approaching the zero line), whereas the displayed differences for random samples of the normal distribution are always large. The differences even increase with sample size, i.e, the hanging bars tend to vanish for very large samples. __ 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] xyplot: modify axis tick marks
Using lattice and the rainfall$Time series as proposed below by Dennis
gives also a nice result:
rainfall$Time - seq(from = as.Date('1993-01-01'),
to = as.Date('2007-12-01'), by = 'month')
xyplot(rainfall~Time,data=rainfall,type=c(g,p,l,smooth))
On Sunday 16 January 2011 17:33:18 Dennis Murphy wrote:
Hi:
Try this, since your data have no missing months:
rainfall$Time - seq(from = as.Date('1993-01-01'), to =
as.Date('2007-12-01'), by = 'month')
g - ggplot(rainfall, aes(x = Time, y = rainfall))
g + geom_path()
HTH,
Dennis
On Sun, Jan 16, 2011 at 5:01 AM, Kang Min ngokang...@gmail.com wrote:
Hi,
I would like to plot time against rainfall data (data is at the end)
using xyplot.
The basic code looks like this: xyplot(rainfall~time, type=a)
When I do this, the graph looks ok except that the x-axis has too many
values. I would just like to display the years and not the months on
the x-axis. I've been fiddling around with 'scales', and read previous
posts about axis problems but I still can't find the solution.
Thanks in advance.
Kang Min
timerainfall
Jan1993 176.4
Feb1993 69.2
Mar1993 250.5
Apr1993 283.9
May1993 129.9
Jun1993 115.5
Jul1993 240
Aug1993 106.8
Sep1993 61.7
Oct1993 175.5
Nov1993 250.8
Dec1993 308.5
Jan1994 56.9
Feb1994 133.5
Mar1994 288.2
Apr1994 154
May1994 169.6
Jun1994 184.7
Jul1994 53.8
Aug1994 45.1
Sep1994 23.7
Oct1994 84.7
Nov1994 322.2
Dec1994 425.4
Jan1995 349.4
Feb1995 334
Mar1995 67.7
Apr1995 242.3
May1995 84.4
Jun1995 63.7
Jul1995 173.6
Aug1995 211.6
Sep1995 29.5
Oct1995 101.1
Nov1995 372.8
Dec1995 302.5
Jan1996 173.2
Feb1996 180.2
Mar1996 129.7
Apr1996 178.2
May1996 107.5
Jun1996 265.8
Jul1996 162.3
Aug1996 258.4
Sep1996 297
Oct1996 300
Nov1996 180.2
Dec1996 185.5
Jan1997 15.4
Feb1997 105.4
Mar1997 34.3
Apr1997 118.4
May1997 41.6
Jun1997 78.9
Jul1997 18.6
Aug1997 86.6
Sep1997 31.1
Oct1997 78.4
Nov1997 158.3
Dec1997 351.9
Jan1998 268.8
Feb1998 32.5
Mar1998 58.8
Apr1998 187.7
May1998 370.8
Jun1998 198.8
Jul1998 259.2
Aug1998 195
Sep1998 258.2
Oct1998 222.7
Nov1998 107.2
Dec1998 463.4
Jan1999 193.9
Feb1999 67.4
Mar1999 181.4
Apr1999 88.5
May1999 157.1
Jun1999 103.4
Jul1999 225.4
Aug1999 204
Sep1999 125.9
Oct1999 205
Nov1999 241.5
Dec1999 340.5
Jan2000 275.2
Feb2000 237.8
Mar2000 238.3
Apr2000 311.6
May2000 96.8
Jun2000 157.5
Jul2000 116.1
Aug2000 113.5
Sep2000 81.1
Oct2000 120.9
Nov2000 385.7
Dec2000 236
Jan2001 425.8
Feb2001 86.6
Mar2001 297.3
Apr2001 203.3
May2001 164.9
Jun2001 137.1
Jul2001 111.3
Aug2001 158.3
Sep2001 162
Oct2001 252.2
Nov2001 175.3
Dec2001 609
Jan2002 221.2
Feb2002 50.8
Mar2002 55.6
Apr2002 116.5
May2002 236.6
Jun2002 83.1
Jul2002 233.7
Aug2002 54.2
Sep2002 124.2
Oct2002 10.8
Nov2002 307.2
Dec2002 255
Jan2003 444.2
Feb2003 172.9
Mar2003 154.6
Apr2003 159.9
May2003 81.8
Jun2003 50.3
Jul2003 170.4
Aug2003 193.6
Sep2003 205.3
Oct2003 351.4
Nov2003 133.8
Dec2003 273
Jan2004 600.9
Feb2004 31.9
Mar2004 269.4
Apr2004 57.1
May2004 137.6
Jun2004 127.2
Jul2004 166.6
Aug2004 185.2
Sep2004 128.9
Oct2004 125.6
Nov2004 166.2
Dec2004 139.8
Jan2005 163.2
Feb2005 8.4
Mar2005 82.4
Apr2005 81.7
May2005 331.1
Jun2005 82.3
Jul2005 104
Aug2005 58.5
Sep2005 175.7
Oct2005 314.5
Nov2005 362.9
Dec2005 166
Jan2006 454.4
Feb2006 115.5
Mar2006 83.1
Apr2006 239.8
May2006 205.7
Jun2006 236.8
Jul2006 153.8
Aug2006 127.3
Sep2006 83.3
Oct2006 102
Nov2006 185.6
Dec2006 765.9
Jan2007 450.1
Feb2007 105.5
Mar2007 269.1
Apr2007 240.2
May2007 127.2
Jun2007 139
Jul2007 141.7
Aug2007 190.7
Sep2007 149
Oct2007 237.2
Nov2007 367.9
Dec2007 468.6
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[[alternative HTML version deleted]]
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Re: [R] rootogram for normal distributions
Thank you very much for your qualified answers, and also for the
link to the Tukey paper. I appreciate Tukey's writings very much.
Looking at the lattice code (below), a possible implementation might
involve binning, not so?
I see a problematic part here:
xx - sort(unique(x))
Unique certainly works well with Poisson distributed data, but is
essentially a no-op when confronted with continous floating-point
numbers.
Best
Hugo
prepanel.rootogram
function (x, y = table(x), dfun = NULL, transformation = sqrt,
hang = TRUE, ...)
{
plot.line - trellis.par.get(plot.line)
stopifnot(is.function(dfun))
yy - transformation(y/sum(y))
xx - sort(unique(x))
dotArgs - list(...)
dfunArgs - names(formals(dfun))
if (!(... %in% dfunArgs))
dotArgs - dotArgs[dfunArgs[-1]]
dd - transformation(do.call(dfun, c(list(xx), dotArgs)))
list(xlim = range(xx), ylim = if (hang) range(dd, dd - yy,
0) else range(dd, yy, 0), dx = diff(xx), dy = diff(dd))
}
panel.rootogram
function (x, y = table(x), dfun = NULL, col = plot.line$col,
lty = plot.line$lty, lwd = plot.line$lwd, alpha = plot.line$alpha,
transformation = sqrt, hang = TRUE, ...)
{
plot.line - trellis.par.get(plot.line)
ref.line - trellis.par.get(reference.line)
stopifnot(is.function(dfun))
yy - transformation(y/sum(y))
xx - sort(unique(x))
dotArgs - list(...)
dfunArgs - names(formals(dfun))
if (!(... %in% dfunArgs))
dotArgs - dotArgs[dfunArgs[-1]]
dd - transformation(do.call(dfun, c(list(xx), dotArgs)))
panel.abline(h = 0, col = ref.line$col, lty = ref.line$lty,
lwd = ref.line$lwd, alpha = ref.line$alpha)
panel.segments(xx, if (hang)
dd
else 0, xx, if (hang)
(dd - yy)
else yy, col = col, lty = lty, lwd = lwd, alpha = alpha,
...)
panel.lines(xx, dd)
}
environment: namespace:latticeExtra
On Sunday 16 January 2011 15:59:58 Achim Zeileis wrote:
On Sun, 16 Jan 2011, Hadley Wickham wrote:
The normal distribution is a continuous distribution, i.e., the frequency
for each observed value will essentially be 1/n and not converge to the
density function. Hence, you would need to look at histogram or smoothed
densities. Rootograms, on the other hand, are intended for discrete
distributions.
I don't think that's true - rootograms are useful for both continuous
and discrete distributions. See (e.g.) p 314 at
http://www.edwardtufte.com/tufte/tukey, where Tukey himself uses a
rootogram with a normal distribution.
OK, let me rephrase: Rootograms as implemented in rootogram() are intended
for discrete distributions. At least that's my reading. But maybe I've
missed a trick that you can point us to.
Z
Hadley
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Re: [R] a remove question
How about ls(pattern=NY) #rm(list=ls(pattern=NY)) On Sunday 16 January 2011 22:08:16 Erin Hodgess wrote: Dear R People: I have the following: ls(pattern=NY*) [1] CRAN_df CRAN_df0 CRAN_df1 CRAN_mat CRAN_sp [6] CRAN_spdf1 CRAN_spdf2 CRAN_spdf4 delauney_NY dist2_NY [11] dist3_NY Gabriel_NY NY8a_nb rel_neigh_NY scot_BNG [16] SOI_NY rm(pattern=NY*) Warning message: In rm(pattern = NY*) : object 'NY*' not found How do I remove all of NY* items, please? I suspect it might be an sapply issue thanks, Erin __ 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.
