Re: [Rd] R crashes if "toFile" given "~/" in Linux envirnonment
Thanks Simon. There was no help page for "toFile" (the first thing I tried)
so I didn't realize it was an Rgraphviz function. I'll contact the
maintainers.
Mark
Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry
Indiana University School of Medicine
15032 Hunter Court, Westfield, IN 46074
(317) 490-5129 Work, & Mobile & VoiceMail
(317) 399-1219 Skype No Voicemail please
On Mon, May 16, 2011 at 11:02 PM, Simon Urbanek wrote:
> Mark,
>
> I think you have the wrong list - this has nothing to do with R. to File()
> is a function in Rgraphviz and it doesn't crash, it simply exits R.
> Obviously it doesn't support path expansion (I suppose it should consider
> calling path.expand()) and it should also consider using R_error() instead
> of quitting -- but both issues should be best addressed to the Rgraphviz
> maintainers.
>
> Cheers,
> Simon
>
>
> On May 16, 2011, at 10:50 PM, Mark Kimpel wrote:
>
> > I was running some sample code from a help page tonight and wished to
> > redirect the sample output to my Desktop under Linux (Mint-Debian 64 if
> it
> > makes a different). I was surprised to find that file name expansion
> using
> > the ubuquitious "~/" was not recognized, in fact it caused R to crash. Is
> > this expected behavior? See my output below and sessionInfo(). Also, not
> > shown, but 'setwd("~/Desktop")' works just fine. Thanks, Mark
> >
> > # sample code from Rgraphviz clusterData help page
> > library(graph)
> > library(Rgraphviz)
> > g1_gz <-
> gzfile(system.file("GXL/graphExample-01.gxl.gz",package="graph"),
> > open="rb")
> > g11_gz <-
> gzfile(system.file("GXL/graphExample-11.gxl.gz",package="graph"),
> > open="rb")
> > g1 <- fromGXL(g1_gz)
> > g11 <- fromGXL(g11_gz)
> > g1_11 <- join(g1, g11)
> > sgl <- vector(mode="list", length=2)
> > sgl[[1]] <- list(graph=g1, cluster=TRUE)
> > sgl[[2]] <- list(graph=g11, cluster=TRUE)
> > ng <- agopenSimple(g1_11, "tmpsg", subGList=sgl)
> > clusterData(ng, 1, c("bgcolor")) <- c("blue")
> > clusterData(ng, 2, c("bgcolor")) <- c("red")
> >
> > # and now 2 usually equivalent ways to specify the location for output
> file,
> > with the second way crashing:
> > toFile(ng, layoutType="dot", filename="/home/mkimpel/Desktop/
> g1_11_dot.ps",
> > fileType="ps")
> > NULL
> > toFile(ng, layoutType="dot", filename="~/Desktop/g1_11_dot.ps",
> > fileType="ps")
> > ~/Desktop/g1_11_dot.ps: No such file or directory
> >
> > Process R exited abnormally with code 1 at Mon May 16 22:42:12 2011
> > #
> > # and my sessionInfo()
> > R version 2.13.0 (2011-04-13)
> > Platform: x86_64-unknown-linux-gnu (64-bit)
> >
> > locale:
> > [1] LC_CTYPE=en_US.utf8 LC_NUMERIC=C
> > LC_TIME=en_US.utf8LC_COLLATE=en_US.utf8 LC_MONETARY=C
> >
> > [6] LC_MESSAGES=en_US.utf8LC_PAPER=en_US.utf8
> > LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C
> >
> > [11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C
> >
> > attached base packages:
> > [1] stats graphics grDevices datasets utils methods base
> >
> > Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry
> > Indiana University School of Medicine
> >
> > 15032 Hunter Court, Westfield, IN 46074
> >
> > (317) 490-5129 Work, & Mobile & VoiceMail
> > (317) 399-1219 Skype No Voicemail please
> >
> > [[alternative HTML version deleted]]
> >
> > __
> > R-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-devel
> >
> >
>
>
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[Rd] R crashes if "toFile" given "~/" in Linux envirnonment
I was running some sample code from a help page tonight and wished to
redirect the sample output to my Desktop under Linux (Mint-Debian 64 if it
makes a different). I was surprised to find that file name expansion using
the ubuquitious "~/" was not recognized, in fact it caused R to crash. Is
this expected behavior? See my output below and sessionInfo(). Also, not
shown, but 'setwd("~/Desktop")' works just fine. Thanks, Mark
# sample code from Rgraphviz clusterData help page
library(graph)
library(Rgraphviz)
g1_gz <- gzfile(system.file("GXL/graphExample-01.gxl.gz",package="graph"),
open="rb")
g11_gz <- gzfile(system.file("GXL/graphExample-11.gxl.gz",package="graph"),
open="rb")
g1 <- fromGXL(g1_gz)
g11 <- fromGXL(g11_gz)
g1_11 <- join(g1, g11)
sgl <- vector(mode="list", length=2)
sgl[[1]] <- list(graph=g1, cluster=TRUE)
sgl[[2]] <- list(graph=g11, cluster=TRUE)
ng <- agopenSimple(g1_11, "tmpsg", subGList=sgl)
clusterData(ng, 1, c("bgcolor")) <- c("blue")
clusterData(ng, 2, c("bgcolor")) <- c("red")
# and now 2 usually equivalent ways to specify the location for output file,
with the second way crashing:
toFile(ng, layoutType="dot", filename="/home/mkimpel/Desktop/g1_11_dot.ps",
fileType="ps")
NULL
toFile(ng, layoutType="dot", filename="~/Desktop/g1_11_dot.ps",
fileType="ps")
~/Desktop/g1_11_dot.ps: No such file or directory
Process R exited abnormally with code 1 at Mon May 16 22:42:12 2011
#
# and my sessionInfo()
R version 2.13.0 (2011-04-13)
Platform: x86_64-unknown-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.utf8 LC_NUMERIC=C
LC_TIME=en_US.utf8LC_COLLATE=en_US.utf8 LC_MONETARY=C
[6] LC_MESSAGES=en_US.utf8LC_PAPER=en_US.utf8
LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices datasets utils methods base
Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry
Indiana University School of Medicine
15032 Hunter Court, Westfield, IN 46074
(317) 490-5129 Work, & Mobile & VoiceMail
(317) 399-1219 Skype No Voicemail please
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Re: [Rd] Best style to organize code, namespaces
I'm going to suggest something that is probably not the coolest thing to do,
but it gets me by with almost all my debugging. I set options(error=recover)
and then in the function I want to debug I put some unassigned variable name
on the first line (example: ThisIsMyDebuggingVariable). Then I will get the
error message "Error: object 'ThisIsMyDebuggingVariable' not found" and, if
the function is nested within other functions, the nice menu that allows me
to choose what level I want to be in. In Emacs I just step through the
function of interest. This allows for Duncan's wish of single stepping
through multiple levels (if I am interpreting him correctly). It's not very
fancy, but it has gotten the job done for me.
Mark
Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry
Indiana University School of Medicine
15032 Hunter Court, Westfield, IN 46074
(317) 490-5129 Work, & Mobile & VoiceMail
(317) 399-1219 Skype No Voicemail please
On Tue, Feb 23, 2010 at 5:42 PM, Duncan Murdoch wrote:
> On 22/02/2010 10:15 PM, Gabor Grothendieck wrote:
>
>> As you mention ease of debugging basically precludes subfunctions so
>> style 1 is left.
>>
>
> I think you are also unaware of setBreakpoint() (and trace(), which
> underlies it). So more detail:
>
> If you put this into file test.R, starting on line 1:
>
> outer <- function(x) {
> inner <- function() {
> if (x > 3) {
> x <- 0
> }
> }
>
> inner()
> print(x)
> }
>
> you might want to debug why outer(10) prints 10, not 0. So set a
> breakpoint on line 4 to see if you get there:
>
> > setBreakpoint("test.R#4")
> c:\temp\test.R#4:
> outer step 2,3,3,2,3,2 in
> > outer(10)
> test.R#4
> Called from: eval(expr, envir, enclos)
> Browse[1]>
>
> Yes, we got there. Take a step:
>
> Browse[1]> n
> debug: x <- 0
>
> Now recognize we should have used x <<- 0.
>
> Now, it would be nice if we had more flexible debugging (e.g. single
> stepping that would stay as single stepping when we exited from inner()),
> but debug() is certainly not the only possibility for debugging. It's not
> even the best choice in a lot of situations where it does work.
>
> Duncan Murdoch
>
>
>
>> Functions can be nested in environments rather than in other functions
>> and this will allow debugging to still occur.
>>
>> The proto package which makes it particularly convenient to nest
>> functions in environments giving an analog to #3 while still allowing
>> debugging. See http//:r-proto.googlecode.com
>>
>> library(proto)
>>> # p is proto object with variable a and method f
>>> p <- proto(a = 1, f = function(., x = 1) .$a <- .$a + 1)
>>> with(p, debug(f))
>>> p$f()
>>>
>> debugging in: get("f", env = p, inherits = TRUE)(p, ...)
>> debug: .$a <- .$a + 1
>> Browse[2]>
>> exiting from: get("f", env = p, inherits = TRUE)(p, ...)
>> [1] 2
>>
>>> p$a
>>>
>> [1] 2
>>
>>
>> On Mon, Feb 22, 2010 at 9:49 PM, Ben wrote:
>>
>>> Hi all,
>>>
>>> I'm hoping someone could tell me what best practices are as far as
>>> keeping programs organized in R. In most languages, I like to keep
>>> things organized by writing small functions. So, suppose I want to
>>> write a function that would require helper functions or would just be
>>> too big to write in one piece. Below are three ways to do this:
>>>
>>>
>>> ### Style 1 (C-style) ###
>>> Foo <- function(x) {
>>>
>>> }
>>> Foo.subf <- function(x, blah) {
>>>
>>> }
>>> Foo.subg <- function(x, bar) {
>>>
>>> }
>>>
>>> ### Style 2 (Lispish?) ##
>>> Foo <- function(x) {
>>> Subf <- function(blah) {
>>>
>>> }
>>> Subg <- function(bar) {
>>>
>>> }
>>>
>>> }
>>>
>>> ### Object-Oriented #
>>> Foo <- function(x) {
>>> Subf <- function(blah) {
>>>
>>> }
>>> Subg <- function(bar) {
>>>
>>> }
>>> Main <- function() {
>>>
>>> }
>>> return(list(subf=subf, subg=subg, foo=foo))
>>> }
>>> ### End examples
>>>
>>> Which of these ways is best? Style 2 seems at first to be the most
>>> natural in R, but I found there are some major drawbacks. First, it
>>> is hard to debug. For instance, if I want to debug Subf, I need to
>>> first "debug(Foo)" and then while Foo is debugging, type
>>> "debug(Subf)". Another big limitation is that I can't write
>>> test-cases (e.g. using RUnit) for Subf and Subg because they aren't
>>> visible in any way at the global level.
>>>
>>> For these reasons, style 1 seems to be better than style 2, if less
>>> elegant. However, style 1 can get awkward because any parameters
>>> passed to the main function are not visible to the others. In the
>>> above case, the value of "x" must be passed to Foo.subf and Foo.subg
>>> explicitly. Also there is no enforcement of code isolation
>>> (i.e. anyone can call Foo.subf).
>>>
>>> Style 3 is more explicitly object oriented. It has the advantage of
>>> style 2 in that you don't
Re: [Rd] Rcpp: Clarifying the meaning of GPL?
I don't think this is off-topic, in the sense that it is the contribution of the developers of the multitude of packages available that has led to the success of R. How packages are maintained, forked, etc., is an important issue. I should say that I am not a developer, only a user appreciative of the tremendous effort it takes to develop and maintain packages. In the past, however, when I have inquired about developing a BioConductor package for R, I was told that should I do so I should commit to maintain the package. It seems to me, again as a matter of courtesy and cooperation, that should someone wish to make substantive changes to a package that someone else is maintaining, then they should do so in concert with the package maintainer. If the package is "orphaned", however, then the story would be different. If the original developer/maintainer is still active and does not agree with suggested changes, then a fork, with a different name would be the wisest course of action. I am not taking sides here, I have no idea which of my hypothetical scenarios might have in reality taken place with this particular package. I just wanted to say that I think the issue is important, that good communication is important, and that there are some basic principals that seem reasonable to uphold should we wish the R community to continue to be developer friendly. Mark Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry Indiana University School of Medicine 15032 Hunter Court, Westfield, IN 46074 (317) 490-5129 Work, & Mobile & VoiceMail (317) 399-1219 Skype No Voicemail please On Wed, Dec 23, 2009 at 12:32 AM, Jeff Ryan wrote: > This is fantastically off-topic, and has nothing to do with *R*. > > Out of "courtesy" to this list, the subscribers, and future readers, > please take this off-list where it belongs. > > Jeff > > On Tue, Dec 22, 2009 at 11:27 PM, Dominick Samperi > wrote: > > Stavros Macrakis wrote: > >> > >> That said, as a matter of courtesy and clarity, I'd think that a fork > >> should use a different name. > > > > Yes, the point is that this is not a legal or technical matter, it is a > > matter of professional courtesy. > > > > I take this as one vote for the name change. > > > > On US copyright law, this should not be confused with "copyright" notices > > that appear in GPL > > source code. Remember that these are really "copyleft" notices, and > copyleft > > is designed to > > protect the rights of copiers, not original contributors. My concern > about > > the copyright notice > > should be viewed in the same spirit as the name change (professional > > courtesy). > > > > Since GPL is largely silent on these issues I have asked the R community > to > > vote... > > > > Thanks, > > Dominick > > > > __ > > R-devel@r-project.org mailing list > > https://stat.ethz.ch/mailman/listinfo/r-devel > > > > > > -- > Jeffrey Ryan > jeffrey.r...@insightalgo.com > > ia: insight algorithmics > www.insightalgo.com > > __ > R-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel > [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] question about differences in behavior with NA subscripts in matrix vs. data.frame
I ran into a problem today when using a conditional for sub-setting a
data.frame and tracked it down to a difference in behavior between the
treatment of NA when sub-setting matrices and data.frames. A self-contained
example is below followed by sessionInfo(). I'm not questioning the
documentation of the behavior, but the rationale for its existence.
Could someone explain to me why the difference is logical and useful? This
seems more of a devel than a help issue, my apologies if I've posted to the
incorrect list.
Mark
#
a.vec <- c("A", "", "B", "DEF", NA, "", NA, "Q")
a.vec[a.vec == ""] <- NA
a.vec
## [1] "A" NA"B" "DEF" NANANA"Q"
a.mat <- matrix(rep(c("A", "", "B", "DEF", NA, "", NA, "Q"), 5), nrow = 5,
ncol = 8)
a.mat[a.mat[,3] == "", 3] <- NA
a.mat
## [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8]
## [1,] "A" "" "B" "Q" NA ""NA "DEF"
## [2,] ""NA "DEF" "A" "" "B" "Q" NA
## [3,] "B" "Q" NA""NA "DEF" "A" ""
## [4,] "DEF" "A" NA"B" "Q" NA"" NA
## [5,] NA"" NA"DEF" "A" """B" "Q"
a.df <- data.frame(matrix(rep(c("A", "", "B", "DEF", NA, "", NA, "Q"), 5),
nrow = 5, ncol = 8))
a.df[a.df[,3] == "", 3] <- NA
a.df
## Error in `[<-.data.frame`(`*tmp*`, a.df[, 3] == "", 3, value = NA) :
## missing values are not allowed in subscripted assignments of data
frames
## Enter a frame number, or 0 to exit
## 1: `[<-`(`*tmp*`, a.df[, 3] == "", 3, value = NA)
## 2: `[<-.data.frame`(`*tmp*`, a.df[, 3] == "", 3, value = NA)
## remove plain text non-codes from codes.df
sessionInfo()
## R version 2.10.0 Patched (2009-10-27 r50222)
## x86_64-unknown-linux-gnu
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8
## [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8
## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
## attached base packages:
## [1] stats graphics grDevices datasets utils methods base
## loaded via a namespace (and not attached):
## [1] tools_2.10.0
Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry
Indiana University School of Medicine
15032 Hunter Court, Westfield, IN 46074
(317) 490-5129 Work, & Mobile & VoiceMail
(317) 399-1219 Skype No Voicemail please
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Re: [Rd] 2.10.0 Under development (unstable) (2009-09-15 r49711) just built segfaults on Debian Squeeze
Just downloaded and installed "R version 2.10.0 Under development (unstable) (2009-09-21 r49771)" and am happy to report that my .Rprofile loads appropriately with no segfaults. Thanks Duncan! Mark Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry Indiana University School of Medicine 15032 Hunter Court, Westfield, IN 46074 (317) 490-5129 Work, & Mobile & VoiceMail (317) 399-1219 Skype No Voicemail please On Fri, Sep 18, 2009 at 2:11 PM, Duncan Murdoch wrote: > I've just committed (r49747) some changes that should fix the re-entrancy > bug Mark reported the other day. The problem was that R reads some files > (e.g. Mark's .Rprofile) in a read-eval-print loop, and only parses them a > few lines at a time. This means that within that loop, one of the evals > could cause it to start parsing something else. One of the changes I put in > a few days ago got confused by this. > > Hopefully the latest change hasn't introduced a new bug... > > BTW, one of the effects of this change is that a syntax error in .Rprofile > should now be reported on the correct line number. In R 2.9.x the line > number was relative to the current statement, so it was pretty meaningless. > > Duncan Murdoch > [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] 2.10.0 Under development (unstable) (2009-09-15 r49711) just built segfaults on Debian Squeeze
Thanks, no problem for me to wait for the fix. It's just nice to know that I was able to help improve R in a small way by using R-devel. Usually, it is ME making the error! Thanks again for all your development efforts. Cheers, Mark Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry Indiana University School of Medicine 15032 Hunter Court, Westfield, IN 46074 (317) 490-5129 Work, & Mobile & VoiceMail (317) 399-1219 Skype No Voicemail please On Wed, Sep 16, 2009 at 9:49 PM, Duncan Murdoch wrote: > Okay, I've tracked this down, and it's a stupid error I made when trying to > improve the error messages. I tried to make the parser remember its > position in a file when parsing it line by line so that it could report on > syntax errors properly; the trouble is that when it executes one of those > lines (like yours containing source()), it might re-enter the parser. It > needs to save and restore its state around that sort of call. > > This will be fairly easy to fix, but I won't be able to do it until > tomorrow. > > Duncan Murdoch > > > > On 16/09/2009 3:51 PM, Mark Kimpel wrote: > >> I just downloaded R-devel and when loaded it immediately segfaults. I'm >> not >> sure how much or what sort of diagnostic info and can provide, but below >> is >> my build script, my console output, and the output of uname -r. I am >> currently dependent on the development version of a package, so I'd like >> to >> get R-devel up and running if possible. I am sure there is more info I can >> provide, but before deluging the list with unnecessary output, I thought I >> would ask first what would be helpfu. Mark >> > > #Make R >> cd ~/R_HOME >> wget ftp://ftp.stat.math.ethz.ch/Software/R/R-devel.tar.gz >> tar -xzf R-devel.tar.gz >> cd ~/R_HOME/R-devel >> mkdir R-build >> cd R-build >> ../configure --prefix=/home/mkimpel/R_HOME/R-devel/R-build >> make all >> make install >> >> #33 >> # console output >> mkimpel-XPS ~/R_HOME/R-devel/R-build/bin: ./R >> >> R version 2.10.0 Under development (unstable) (2009-09-15 r49711) >> Copyright (C) 2009 The R Foundation for Statistical Computing >> ISBN 3-900051-07-0 >> >> R is free software and comes with ABSOLUTELY NO WARRANTY. >> You are welcome to redistribute it under certain conditions. >> Type 'license()' or 'licence()' for distribution details. >> >> Natural language support but running in an English locale >> >> R is a collaborative project with many contributors. >> Type 'contributors()' for more information and >> 'citation()' on how to cite R or R packages in publications. >> >> Type 'demo()' for some demos, 'help()' for on-line help, or >> 'help.start()' for an HTML browser interface to help. >> Type 'q()' to quit R. >> >> >> *** caught segfault *** >> address (nil), cause 'memory not mapped' >> >> Possible actions: >> 1: abort (with core dump, if enabled) >> 2: normal R exit >> 3: exit R without saving workspace >> 4: exit R saving workspace >> Selection: 2 >> Save workspace image? [y/n/c]: n >> >> ## >> # kernel version >> mkimpel-XPS ~/R_HOME/R-devel/R-build/bin: uname -r >> 2.6.30-1-amd64 >> mkimpel-XPS ~/R_HOME/R-devel/R-build/bin: >> >> >> Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry >> Indiana University School of Medicine >> >> 15032 Hunter Court, Westfield, IN 46074 >> >> (317) 490-5129 Work, & Mobile & VoiceMail >> (317) 399-1219 Skype No Voicemail please >> >>[[alternative HTML version deleted]] >> >> __ >> R-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/r-devel >> > > [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] 2.10.0 Under development (unstable) (2009-09-15 r49711) just built segfaults on Debian Squeeze
Okay, now that I knew what to look at, I've narrowed to the problem down to
the line
'source("~/R.functions/General_Functions/my.update.packages.func.R")'
if just this line is commented out, R loads fine. If not, it crashes
reliably. Interestingly, if commented out, once R is loaded, the function
loads into R just fine and in facts runs as intended. So, perhaps there is
something in the way R is sourcing the file or with the source command
itself?
Thanks for helping me to figure this out, let me know if there is anything
specific you want me to try.
Mark
Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry
Indiana University School of Medicine
15032 Hunter Court, Westfield, IN 46074
(317) 490-5129 Work, & Mobile & VoiceMail
(317) 399-1219 Skype No Voicemail please
On Wed, Sep 16, 2009 at 8:07 PM, Duncan Murdoch wrote:
> On 16/09/2009 7:48 PM, Mark Kimpel wrote:
>
>> Peter,
>>
>> I have not yet tried Simon's suggestion of using gcc 4.3 (just got back
>> from
>> a meeting), but running your commands produces the output below. As you
>> can
>> see, R --vanilla works, but just plain "R" doesn't. See the results of gdb
>> far below.
>>
>
> That's helpful. It died in the parser while trying to read your user
> profile. I can't tell what file it was trying to read, but the order it
> tries them is as follows:
>
> If you have R_PROFILE_USER set, it tries to read the file named there.
>
> It tries to read .Rprofile in the current directory.
>
> If you have HOME set, it tries to read .Rprofile in that directory.
>
> It appears that you found a bug in the parser while trying to read that
> file: you shouldn't be able to get a segfault, at worst you should get a
> syntax error.
>
> Can you work out what file it read, and send me a copy? I'd like to track
> this down.
>
> Duncan Murdoch
>
>
>
>> I do not have a saved workspace in my R_HOME or any of its subdirectories.
>>
>> Will report back on what I get with gcc 4.3 just as soon as I read the
>> R-admin manual and figure out how to get configure configured
>>
>> Mark
>>
>>
>> mkimpel-XPS ~/sshfs: R --vanilla
>>
>> R version 2.10.0 Under development (unstable) (2009-09-15 r49711)
>> Copyright (C) 2009 The R Foundation for Statistical Computing
>> ISBN 3-900051-07-0
>>
>> R is free software and comes with ABSOLUTELY NO WARRANTY.
>> You are welcome to redistribute it under certain conditions.
>> Type 'license()' or 'licence()' for distribution details.
>>
>> Natural language support but running in an English locale
>>
>> R is a collaborative project with many contributors.
>> Type 'contributors()' for more information and
>> 'citation()' on how to cite R or R packages in publications.
>>
>> Type 'demo()' for some demos, 'help()' for on-line help, or
>> 'help.start()' for an HTML browser interface to help.
>> Type 'q()' to quit R.
>>
>> q()
>>>
>> mkimpel-XPS ~/sshfs: R
>>
>> R version 2.10.0 Under development (unstable) (2009-09-15 r49711)
>> Copyright (C) 2009 The R Foundation for Statistical Computing
>> ISBN 3-900051-07-0
>>
>> R is free software and comes with ABSOLUTELY NO WARRANTY.
>> You are welcome to redistribute it under certain conditions.
>> Type 'license()' or 'licence()' for distribution details.
>>
>> Natural language support but running in an English locale
>>
>> R is a collaborative project with many contributors.
>> Type 'contributors()' for more information and
>> 'citation()' on how to cite R or R packages in publications.
>>
>> Type 'demo()' for some demos, 'help()' for on-line help, or
>> 'help.start()' for an HTML browser interface to help.
>> Type 'q()' to quit R.
>>
>>
>> *** caught segfault ***
>> address (nil), cause 'memory not mapped'
>>
>> Possible actions:
>> 1: abort (with core dump, if enabled)
>> 2: normal R exit
>> 3: exit R without saving workspace
>> 4: exit R saving workspace
>> Selection: 4
>> mkimpel-XPS ~/sshfs: R -d gdb
>> GNU gdb (GDB) 6.8.50.20090628-cvs-debian
>> Copyright (C) 2009 Free Software Foundation, Inc.
>> License GPLv3+: GNU GPL version 3 or later <
>> http://gnu.org/licenses/gpl.html
>> This is free software: you are free to change and redistribute it.
>> There is NO WARRANTY, to the extent permitted by law. Type "s
Re: [Rd] 2.10.0 Under development (unstable) (2009-09-15 r49711) just built segfaults on Debian Squeeze
Below is my .Rprofile and the my.update.packages function that it calls
(which is in the right place and has not caused problems before). As I was
writing this, R just finished compiling using gcc-4.3. R once again crashes
as it did with the 4.4 compile. Just for completeness, immediately below is
my build script, the followed by .Rprofile. Thanks guys!
#3
# build R-devel
cd ~/R_HOME
wget ftp://ftp.stat.math.ethz.ch/Software/R/R-devel.tar.gz
tar -xzf R-devel.tar.gz
cd ~/R_HOME/R-devel
mkdir R-build
cd R-build
../configure --prefix=/home/mkimpel/R_HOME/R-devel/R-build
CC=/usr/bin/gcc-4.3 CXX=/usr/bin/g++-4.3 F77=/usr/bin/gfortran-4.3
make all
make install
# end build script
#
# .Rprofile
#tell R where site-library is
ver <- getRversion()
options(editor="emacs")
if (ver == "2.9.1"){.libPaths(new= "~/R_HOME/site-library-2.9.0")}
if (ver == "2.10.0"){.libPaths(new= "~/R_HOME/site-library-2.10.0")}
options(htmlhelp=TRUE)
options(browser="firefox newTab")
#update packages
source("~/R.functions/General_Functions/my.update.packages.func.R")
if (interactive()) { #needed to keep R from looping as it calls R for
install scripts
my.update.packages.func(force = FALSE)
##
# source function loader function and execute it
source("~/R.functions/General_Functions/UtilityFunctions/load.R.func.files.R")
get.and.load.functions.func()
##
# set error recovery option
options(error=utils::recover)
}
#
# end .Rprofile
# ~/R.functions/General_Functions/UtilityFunctions/load.R.func.files.R
my.update.packages.func <- function(update.interveral.days = 7, force =
TRUE){
require(utils)
old.wd <- getwd()
setwd("~/")
last.update.error <- try(load(file = ".Rupdate.date"), TRUE)
if(inherits(last.update.error, "try-error")) {last.update <-
as.POSIXct("2007-01-01")} else {
load(file = ".Rupdate.date")} #if .Rupdate.date does not exist or
can't load, update
if(force) {last.update <- as.POSIXct("2007-01-01")} #allow to force
updates
current.time <- Sys.time()
time.diff <- current.time - last.update
if(
(
(units(time.diff) == "days")
&&
(time.diff[[1]][1] >= update.interveral.days)
) ||
inherits(last.update.error, "try-error")
){ #then update
##From Jim McDonald: I just have the above in my .Rprofile file, so
biocLite() is always there for me.
source("http://www.bioconductor.org/biocLite.R";)
biocLite("Biobase")
library("Biobase")
repos <- biocReposList()
update.packages(repos=repos,
ask=FALSE)###
update.packages(repos="http://www.omegahat.org/R";, ask = FALSE)
last.update <- current.time
local(save(last.update, file = ".Rupdate.date"))
print("packages updated")
} else {print("packages do not need updated")}
setwd(old.wd)
}
###
# End file
Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry
Indiana University School of Medicine
15032 Hunter Court, Westfield, IN 46074
(317) 490-5129 Work, & Mobile & VoiceMail
(317) 399-1219 Skype No Voicemail please
On Wed, Sep 16, 2009 at 8:10 PM, Simon Urbanek
wrote:
>
> On Sep 16, 2009, at 7:48 PM, Mark Kimpel wrote:
>
> Peter,
>>
>> I have not yet tried Simon's suggestion of using gcc 4.3 (just got back
>> from
>> a meeting), but running your commands produces the output below. As you
>> can
>> see, R --vanilla works, but just plain "R" doesn't.
>>
>
> Please send us you .Rprofile because that's likely what's causing the crash
> ... (reading a profile causes the crash, so unless you have a custom site
> profile the .Rprofile is the one to blame).
>
> Thanks,
> S
>
>
>
>
> See the results of gdb
>> far below.
>>
>> I do not have a saved workspace in my R_HOME or any of its subdirectories.
>>
>> Will report back on what I get with gcc 4.3 just as soon as I read the
>> R-admin manual and figure out how to get configure configured
>>
>> Mark
>>
>>
>> mkimpel-XPS ~/sshfs: R --vanilla
>>
Re: [Rd] 2.10.0 Under development (unstable) (2009-09-15 r49711) just built segfaults on Debian Squeeze
Peter, I have not yet tried Simon's suggestion of using gcc 4.3 (just got back from a meeting), but running your commands produces the output below. As you can see, R --vanilla works, but just plain "R" doesn't. See the results of gdb far below. I do not have a saved workspace in my R_HOME or any of its subdirectories. Will report back on what I get with gcc 4.3 just as soon as I read the R-admin manual and figure out how to get configure configured Mark mkimpel-XPS ~/sshfs: R --vanilla R version 2.10.0 Under development (unstable) (2009-09-15 r49711) Copyright (C) 2009 The R Foundation for Statistical Computing ISBN 3-900051-07-0 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > q() mkimpel-XPS ~/sshfs: R R version 2.10.0 Under development (unstable) (2009-09-15 r49711) Copyright (C) 2009 The R Foundation for Statistical Computing ISBN 3-900051-07-0 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. *** caught segfault *** address (nil), cause 'memory not mapped' Possible actions: 1: abort (with core dump, if enabled) 2: normal R exit 3: exit R without saving workspace 4: exit R saving workspace Selection: 4 mkimpel-XPS ~/sshfs: R -d gdb GNU gdb (GDB) 6.8.50.20090628-cvs-debian Copyright (C) 2009 Free Software Foundation, Inc. License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html > This is free software: you are free to change and redistribute it. There is NO WARRANTY, to the extent permitted by law. Type "show copying" and "show warranty" for details. This GDB was configured as "x86_64-linux-gnu". For bug reporting instructions, please see: <http://www.gnu.org/software/gdb/bugs/>... (gdb) run Starting program: /home/mkimpel/R_HOME/R-devel/R-build/lib64/R/bin/exec/R R version 2.10.0 Under development (unstable) (2009-09-15 r49711) Copyright (C) 2009 The R Foundation for Statistical Computing ISBN 3-900051-07-0 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. Program received signal SIGSEGV, Segmentation fault. Rf_setAttrib (vec=0x12e3d68, name=0x94d450, val=0x0) at ../../../src/main/attrib.c:226 226if (NAMED(val)) val = duplicate(val); (gdb) bt #0 Rf_setAttrib (vec=0x12e3d68, name=0x94d450, val=0x0) at ../../../src/main/attrib.c:226 #1 0x0056264f in xxexprlist1 () at gram.y:574 #2 Rf_yyparse () at gram.y:337 #3 0x00563469 in R_Parse1 (status=0x94d450) at gram.y:1126 #4 0x00563cfb in R_Parse1File (fp=0x1200920, gencode=1, status=0x7fffcd94, first=) at gram.y:1164 #5 0x00416cb2 in R_ReplFile (fp=0x1200920, rho=0x973338, savestack=0, browselevel=) at ../../../src/main/main.c:87 #6 0x00416e08 in R_LoadProfile (fparg=, env=0x973338) at ../../../src/main/main.c:651 #7 0x004172c2 in setup_Rmainloop () at ../../../src/main/main.c:875 #8 0x004185c9 in Rf_mainloop () at ../../../src/main/main.c:967 #9 0x00415c38 in main (ac=, av=) at ../../../src/main/Rmain.c:33 #10 0x76ed05c6 in __libc_start_main () from /lib/libc.so.6 #11 0x00415b29 in _start () at ../sysdeps/x86_64/elf/start.S:113 (gdb) Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry Indiana University School of Medicine 15032 Hunter Court, Westfield
[Rd] 2.10.0 Under development (unstable) (2009-09-15 r49711) just built segfaults on Debian Squeeze
I just downloaded R-devel and when loaded it immediately segfaults. I'm not sure how much or what sort of diagnostic info and can provide, but below is my build script, my console output, and the output of uname -r. I am currently dependent on the development version of a package, so I'd like to get R-devel up and running if possible. I am sure there is more info I can provide, but before deluging the list with unnecessary output, I thought I would ask first what would be helpfu. Mark #Make R cd ~/R_HOME wget ftp://ftp.stat.math.ethz.ch/Software/R/R-devel.tar.gz tar -xzf R-devel.tar.gz cd ~/R_HOME/R-devel mkdir R-build cd R-build ../configure --prefix=/home/mkimpel/R_HOME/R-devel/R-build make all make install #33 # console output mkimpel-XPS ~/R_HOME/R-devel/R-build/bin: ./R R version 2.10.0 Under development (unstable) (2009-09-15 r49711) Copyright (C) 2009 The R Foundation for Statistical Computing ISBN 3-900051-07-0 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. *** caught segfault *** address (nil), cause 'memory not mapped' Possible actions: 1: abort (with core dump, if enabled) 2: normal R exit 3: exit R without saving workspace 4: exit R saving workspace Selection: 2 Save workspace image? [y/n/c]: n ## # kernel version mkimpel-XPS ~/R_HOME/R-devel/R-build/bin: uname -r 2.6.30-1-amd64 mkimpel-XPS ~/R_HOME/R-devel/R-build/bin: Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry Indiana University School of Medicine 15032 Hunter Court, Westfield, IN 46074 (317) 490-5129 Work, & Mobile & VoiceMail (317) 399-1219 Skype No Voicemail please [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] rJava fails compilation on R-2.9.1 but not R-2.7.1 on Debian Lenny
Well, guess what, rJava also compiles on R-devel (soon to be
R-2.10.0). I'll stick with that for my purposes. Thanks for your
suggestion. Mark
Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry
Indiana University School of Medicine
15032 Hunter Court, Westfield, IN 46074
(317) 490-5129 Work, & Mobile & VoiceMail
"The real problem is not whether machines think but whether men do."
-- B. F. Skinner
**
On Wed, Jul 15, 2009 at 3:13 PM, Joshua Ulrich wrote:
> Hi Mark,
>
> The first thing that jumps out to me is that 2.7.1 compiles JRI, while
> 2.9.1 does not (for some reason, autodetect decides not to compile).
>
> HTH,
> Josh
> --
> http://www.fosstrading.com
>
>
>
> On Wed, Jul 15, 2009 at 1:46 PM, Mark Kimpel wrote:
>> I have been futzing around for days tying to get rJava to install on
>> my freshly build Debian Lenny installation. I have R-2.9.1 installed
>> from source in my R_HOME directory and R-2.7.1 installed via apt-get
>> install r-recommended. I was tried many different things, but by
>> accident started up R-2.7.1 as root and viola, successful install. I
>> immediately exited out of R-2.7.1 and started R-2.9.1 as root and
>> compilation fails. The file
>>
>> The output is voluminous, but is included below. I had originally
>> thought that my problem had to do with setting environmental
>> variables, but now it seems not.
>>
>> Thanks,
>> Mark
>>
>> mkimpel-debian-xps /usr/lib/jvm/java-6-sun/include: su root
>> Password:
>> mkimpel-debian-xps:/usr/lib/jvm/java-6-sun/include#
>> /home/mkimpel/R_HOME/R-2.9.1/R-build/bin/R
>> WARNING: ignoring environment value of R_HOME
>>
>> R version 2.9.1 (2009-06-26)
>> Copyright (C) 2009 The R Foundation for Statistical Computing
>> ISBN 3-900051-07-0
>>
>> R is free software and comes with ABSOLUTELY NO WARRANTY.
>> You are welcome to redistribute it under certain conditions.
>> Type 'license()' or 'licence()' for distribution details.
>>
>> Natural language support but running in an English locale
>>
>> R is a collaborative project with many contributors.
>> Type 'contributors()' for more information and
>> 'citation()' on how to cite R or R packages in publications.
>>
>> Type 'demo()' for some demos, 'help()' for on-line help, or
>> 'help.start()' for an HTML browser interface to help.
>> Type 'q()' to quit R.
>>
>>> install.packages('rJava')
>> Warning in install.packages("rJava") :
>> argument 'lib' is missing: using '/usr/local/lib/R/site-library'
>> --- Please select a CRAN mirror for use in this session ---
>> Loading Tcl/Tk interface ... done
>> trying URL 'http://cran.fhcrc.org/src/contrib/rJava_0.6-3.tar.gz'
>> Content type 'application/x-gzip' length 240527 bytes (234 Kb)
>> opened URL
>> ==
>> downloaded 234 Kb
>>
>> * 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
&g
Re: [Rd] rJava fails compilation on R-2.9.1 but not R-2.7.1 on Debian Lenny
Sorry, My sentence that starts "The file" was truncated and should say
"The file "jni.h" is present and on my PATH, see output below"
mkimpel-debian-xps /usr/lib/jvm/java-6-sun/include: ls
classfile_constants.h jawt.h jdwpTransport.h jni.h jvmti.h linux
mkimpel-debian-xps /usr/lib/jvm/java-6-sun/include: printenv PATH
/home/mkimpel/bin:/usr/local/bin:/usr/bin:/bin:/usr/games:/usr/lib/jvm/
mkimpel-debian-xps /usr/lib/jvm/java-6-sun/include:
On Wed, Jul 15, 2009 at 2:46 PM, Mark Kimpel wrote:
> I have been futzing around for days tying to get rJava to install on
> my freshly build Debian Lenny installation. I have R-2.9.1 installed
> from source in my R_HOME directory and R-2.7.1 installed via apt-get
> install r-recommended. I was tried many different things, but by
> accident started up R-2.7.1 as root and viola, successful install. I
> immediately exited out of R-2.7.1 and started R-2.9.1 as root and
> compilation fails. The file
>
> The output is voluminous, but is included below. I had originally
> thought that my problem had to do with setting environmental
> variables, but now it seems not.
>
> Thanks,
> Mark
>
> mkimpel-debian-xps /usr/lib/jvm/java-6-sun/include: su root
> Password:
> mkimpel-debian-xps:/usr/lib/jvm/java-6-sun/include#
> /home/mkimpel/R_HOME/R-2.9.1/R-build/bin/R
> WARNING: ignoring environment value of R_HOME
>
> R version 2.9.1 (2009-06-26)
> Copyright (C) 2009 The R Foundation for Statistical Computing
> ISBN 3-900051-07-0
>
> R is free software and comes with ABSOLUTELY NO WARRANTY.
> You are welcome to redistribute it under certain conditions.
> Type 'license()' or 'licence()' for distribution details.
>
> Natural language support but running in an English locale
>
> R is a collaborative project with many contributors.
> Type 'contributors()' for more information and
> 'citation()' on how to cite R or R packages in publications.
>
> Type 'demo()' for some demos, 'help()' for on-line help, or
> 'help.start()' for an HTML browser interface to help.
> Type 'q()' to quit R.
>
>> install.packages('rJava')
> Warning in install.packages("rJava") :
> argument 'lib' is missing: using '/usr/local/lib/R/site-library'
> --- Please select a CRAN mirror for use in this session ---
> Loading Tcl/Tk interface ... done
> trying URL 'http://cran.fhcrc.org/src/contrib/rJava_0.6-3.tar.gz'
> Content type 'application/x-gzip' length 240527 bytes (234 Kb)
> opened URL
> ==
> downloaded 234 Kb
>
> * 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/bin/java'
> archiver : '/usr/bin/jar'
> compiler : '/usr/bin/javac'
> header prep.: '/usr/bin/javah'
> cpp flags : '-I$(JAVA_HOME)/../include -I$(JAVA_HOME)/../include/linux'
> java libs : '-L$(JAVA_HOME)/lib/amd64/server
> -L$(JAVA_HOME)/lib/amd64 -L$(JAVA_HOME)/../lib/amd64 -L
> -L/usr/java/packages/lib/amd64 -L/lib -L/usr/lib -ljvm'
> checking whether JNI programs can be compiled... yes
> checkin
[Rd] rJava fails compilation on R-2.9.1 but not R-2.7.1 on Debian Lenny
I have been futzing around for days tying to get rJava to install on
my freshly build Debian Lenny installation. I have R-2.9.1 installed
from source in my R_HOME directory and R-2.7.1 installed via apt-get
install r-recommended. I was tried many different things, but by
accident started up R-2.7.1 as root and viola, successful install. I
immediately exited out of R-2.7.1 and started R-2.9.1 as root and
compilation fails. The file
The output is voluminous, but is included below. I had originally
thought that my problem had to do with setting environmental
variables, but now it seems not.
Thanks,
Mark
mkimpel-debian-xps /usr/lib/jvm/java-6-sun/include: su root
Password:
mkimpel-debian-xps:/usr/lib/jvm/java-6-sun/include#
/home/mkimpel/R_HOME/R-2.9.1/R-build/bin/R
WARNING: ignoring environment value of R_HOME
R version 2.9.1 (2009-06-26)
Copyright (C) 2009 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
Natural language support but running in an English locale
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> install.packages('rJava')
Warning in install.packages("rJava") :
argument 'lib' is missing: using '/usr/local/lib/R/site-library'
--- Please select a CRAN mirror for use in this session ---
Loading Tcl/Tk interface ... done
trying URL 'http://cran.fhcrc.org/src/contrib/rJava_0.6-3.tar.gz'
Content type 'application/x-gzip' length 240527 bytes (234 Kb)
opened URL
==
downloaded 234 Kb
* 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/bin/java'
archiver: '/usr/bin/jar'
compiler: '/usr/bin/javac'
header prep.: '/usr/bin/javah'
cpp flags : '-I$(JAVA_HOME)/../include -I$(JAVA_HOME)/../include/linux'
java libs : '-L$(JAVA_HOME)/lib/amd64/server
-L$(JAVA_HOME)/lib/amd64 -L$(JAVA_HOME)/../lib/amd64 -L
-L/usr/java/packages/lib/amd64 -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
configure: creating ./config.status
config.status: creating src/Makevars
config.status: creating R/zzz.R
config.status: creating src/config.h
** libs
gcc -std=gnu99 -I/home/mkimpel/R_HOME/R-2.9.1/R-build/lib64/R/include
-I. -I/usr/lib/jvm/java-1.5.0-gcj-4.3-1.5.0.0/jre/../include
-I/usr/lib/jvm/java-1.5.0-gcj-4.3-1.5.0.0/jre/../include/linux
-I/usr/local/include-fpic -g -O2 -c Rglue.c -o Rglue.o
In file included from Rglue.c:2:
rJava.h:17:17: error: jni.h: No such file or directory
In file included from Rglue.c:2:
rJava.h:115: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’
before ‘*’ token
rJava.h:117: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’
before ‘*’ token
rJava.h:120: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’
before ‘*’ token
rJava.h:122: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’
before ‘javaStringClass
Re: [Rd] install.packages now intentionally references .Rprofile?
This was my original post, with the code example only slightly modified by
Martin for clarity. Prior to R-2.9.0, this repeated downloading did not
occur, the code worked as intended. In fact, if memory serves me correctly,
it even worked at least during the first 3 months of R-2.0.0 in its
development stage, before release as a numbered version. Is there a reason
for that? Is there a work-around? As I mentioned in my original post, the
code is actually wrapped in a function that checks the date and the date of
the last update, and proceeds to update package once per week. It was quite
handy when it was working, hence my desire for a fix for my code.
Thanks,
Mark
Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry
Indiana University School of Medicine
15032 Hunter Court, Westfield, IN 46074
(317) 490-5129 Work, & Mobile & VoiceMail
(317) 399-1219 Home
Skype: mkimpel
"The real problem is not whether machines think but whether men do." -- B.
F. Skinner
**
On Thu, May 21, 2009 at 2:17 AM, Prof Brian Ripley wrote:
> On Wed, 20 May 2009, Martin Morgan wrote:
>
> A post on the Bioconductor mailing list
>>
>> https://stat.ethz.ch/pipermail/bioconductor/2009-May/027700.html
>>
>> suggests that install.packages now references .Rprofile (?), whereas
>> in R-2-8 it did not. Is this intentional?
>>
>
> Yes. And in fact it did in earlier versions, to find the default library
> into which to install.
>
>
>
>> The example is, in .Rprofile
>>
>> library(utils)
>> install.packages("Biobase",
>> repos="http://bioconductor.org/packages/2.4/bioc";)
>>
>> then starting R from the command line results in repeated downloads
>> of Biobase
>>
>> mtmor...@mm:~/tmp> R --quiet
>> trying URL
>> '
>> http://bioconductor.org/packages/2.4/bioc/src/contrib/Biobase_2.4.1.tar.gz
>> '
>> Content type 'application/x-gzip' length 1973533 bytes (1.9 Mb)
>> opened URL
>> ==
>> downloaded 1.9 Mb
>>
>> trying URL
>> '
>> http://bioconductor.org/packages/2.4/bioc/src/contrib/Biobase_2.4.1.tar.gz
>> '
>> Content type 'application/x-gzip' length 1973533 bytes (1.9 Mb)
>> opened URL
>> ==
>> downloaded 1.9 Mb
>>
>> ^C
>> Execution halted
>>
>> sessionInfo()
>>>
>> R version 2.9.0 Patched (2009-05-20 r48588)
>> x86_64-unknown-linux-gnu
>>
>> locale:
>>
>> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
>>
>> attached base packages:
>> [1] stats graphics grDevices utils datasets methods base
>>
>> Martin
>> --
>> Martin Morgan
>> Computational Biology / Fred Hutchinson Cancer Research Center
>> 1100 Fairview Ave. N.
>> PO Box 19024 Seattle, WA 98109
>>
>> Location: Arnold Building M1 B861
>> Phone: (206) 667-2793
>>
>> __
>> R-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>
>>
> --
> Brian D. Ripley, rip...@stats.ox.ac.uk
> Professor of Applied Statistics,
> http://www.stats.ox.ac.uk/~ripley/
Re: [Rd] splitting strings efficiently
I knew there HAD to be a basic function, but 'help.search("split string")'
and 'help("string") did not find it. Thanks for the help on this elementary
question.
Mark
Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry
Indiana University School of Medicine
15032 Hunter Court, Westfield, IN 46074
(317) 490-5129 Work, & Mobile & VoiceMail
(317) 399-1219 Home
Skype: mkimpel
**
On Wed, Sep 24, 2008 at 12:17 PM, Erik Iverson <[EMAIL PROTECTED]>wrote:
> ?strsplit
>
> Mark Kimpel wrote:
>
>> I have a very long list of strings. Each string actually contains multiple
>> values separated by a semi-colon. I need to turn each string into a vector
>> of the values delimited by the semi-colons. I know I can do this very
>> laboriously by using loops, nchar, and substr, but it is terribly slow. Is
>> there a basic R function that handles this situation? If not, is there
>> perhaps a faster way to do it than I currently am, which is to lapply the
>> following function? Thanks, Mark
>>
>>
>> ###
>> string.tokenizer.func<-function(string, separator){
>> new.vec<- NULL
>> newString<- ""
>> if(is.null(string)) {new.vec<-""} else {
>>for(i in 1:(nchar(string) + 1)){
>> if(substr(string, i, i) == separator){
>>new.vec<-c(new.vec,newString)
>>newString <- ""
>> } else {
>>newString<-paste(newString, substr(string, i, i), sep="")
>> }
>>}
>>new.vec<-c(new.vec,newString)
>> }
>> new.vec
>> }
>>
>> Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry
>> Indiana University School of Medicine
>>
>> 15032 Hunter Court, Westfield, IN 46074
>>
>> (317) 490-5129 Work, & Mobile & VoiceMail
>> (317) 399-1219 Home
>> Skype: mkimpel
>>
>> **
>>
>>[[alternative HTML version deleted]]
>>
>> __
>> R-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>
>>
>
>
[[alternative HTML version deleted]]
__
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https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] splitting strings efficiently
I have a very long list of strings. Each string actually contains multiple
values separated by a semi-colon. I need to turn each string into a vector
of the values delimited by the semi-colons. I know I can do this very
laboriously by using loops, nchar, and substr, but it is terribly slow. Is
there a basic R function that handles this situation? If not, is there
perhaps a faster way to do it than I currently am, which is to lapply the
following function? Thanks, Mark
###
string.tokenizer.func<-function(string, separator){
new.vec<- NULL
newString<- ""
if(is.null(string)) {new.vec<-""} else {
for(i in 1:(nchar(string) + 1)){
if(substr(string, i, i) == separator){
new.vec<-c(new.vec,newString)
newString <- ""
} else {
newString<-paste(newString, substr(string, i, i), sep="")
}
}
new.vec<-c(new.vec,newString)
}
new.vec
}
Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry
Indiana University School of Medicine
15032 Hunter Court, Westfield, IN 46074
(317) 490-5129 Work, & Mobile & VoiceMail
(317) 399-1219 Home
Skype: mkimpel
**
[[alternative HTML version deleted]]
__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] specifying compiler path in configure
After reading over the relevant sections of the manual more carefully,
I now see where the information is presented and I was able to get R
to compile with an alternate version of gcc. On thing, however,
remains unclear to me. If R is compiled with a non-default version of
a compiler, are subsequent add-on packages and updated automatically
directed to use the alternate or is it necessary to include this
information in 'install.packages' and 'update.packages'? If the
latter, then it is unclear to me how this is accomplished. Below is my
best attempt at putting this instruction into install.packages and it
failed to produce the intended result, with gcc-4.3 being used instead
of 4.2.
install.packages("affxparser", repos=repos,configure.args =
c('CC=/usr/bin/gcc-4.2', 'CXX=/usr/bin/g++-4.2'))
Thanks, Mark
On Wed, Aug 27, 2008 at 4:38 PM, Prof Brian Ripley
<[EMAIL PROTECTED]> wrote:
> On Wed, 27 Aug 2008, Mark Kimpel wrote:
>
>> I'm having trouble building some packages while running Debian Lenny
>> (testing) and suspect that the issues are related to the default use
>> of gcc-4.3.
>
> You might want to compare your problems with the CRAN checks at
>
> http://cran.r-project.org/web/checks/check_summary.html
>
> as those are run with gcc 4.3.x on Debian testing. From memory, the
> problems are confined to C++-(mis)using packages.
>
>> With Lenny, build-essentials depends on 4.3, so I'd like
>> to leave it installed but have also installed 4.2.1. How do I tell
>> ./configure the path to 4.2.1 ? I"m sure it's an option, but I don't
>> see it documented in the R-admin manual.
>
> From configure --help:
>
> CC C compiler command
> CFLAGS C compiler flags
>
> There are many examples of setting CC in the R-admin manual, and the first
> para of 'Essential Programs' seems to me to tell you that as well.
>
> --
> Brian D. Ripley, [EMAIL PROTECTED]
> Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
> University of Oxford, Tel: +44 1865 272861 (self)
> 1 South Parks Road, +44 1865 272866 (PA)
> Oxford OX1 3TG, UKFax: +44 1865 272595
>
--
Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry
Indiana University School of Medicine
15032 Hunter Court, Westfield, IN 46074
(317) 490-5129 Work, & Mobile & VoiceMail
(317) 663-0513 Home (no voice mail please)
__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] specifying compiler path in configure
I'm having trouble building some packages while running Debian Lenny (testing) and suspect that the issues are related to the default use of gcc-4.3. With Lenny, build-essentials depends on 4.3, so I'd like to leave it installed but have also installed 4.2.1. How do I tell ./configure the path to 4.2.1 ? I"m sure it's an option, but I don't see it documented in the R-admin manual. Mark -- Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry Indiana University School of Medicine 15032 Hunter Court, Westfield, IN 46074 (317) 490-5129 Work, & Mobile & VoiceMail (317) 663-0513 Home (no voice mail please) __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] error in help page of function interpSpline of package splines in R-devel
Unless I am misreading something, I believe there is an error in the
help page of function interpSpline of package splines in R-devel.
The function prototype reads:
interpSpline(obj1, obj2, bSpline = FALSE, period = NULL, na.action = na.fail)
whereas in the Arguments section, under na.action, the text reads "The
default action ('na.omit') is to omit any incomplete observations. "
Based on today's experience, I believe the function prototype is
correct and the text description should be amended.
Mark
--
Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry
Indiana University School of Medicine
15032 Hunter Court, Westfield, IN 46074
(317) 490-5129 Work, & Mobile & VoiceMail
(317) 663-0513 Home (no voice mail please)
__
R-devel@r-project.org mailing list
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[Rd] RBGL not compiling on Debian Lenny with c++ (Debian 4.3.1-2) 4.3.1
I've just installed Debian Lenny and RBGL fails compilation with the following errors (sessionInfo() follows). * Installing *source* package 'RBGL' ... untarring boost include tree... ** libs g++ -I/home/mkimpel/R_HOME/R-patched/R-build/lib64/R/include -I/usr/local/include -IboostIncl -fpic -g -O2 -c bbc.cpp -o bbc.o In file included from /usr/include/c++/4.3/ext/hash_set:64, from boostIncl/boost/graph/adjacency_list.hpp:22, from RBGL.hpp:26, from bbc.cpp:1: /usr/include/c++/4.3/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. In file included from boostIncl/boost/graph/dijkstra_shortest_paths.hpp:19, from boostIncl/boost/graph/betweenness_centrality.hpp:14, from bbc.cpp:2: boostIncl/boost/pending/relaxed_heap.hpp: In member function 'size_t boost::relaxed_heap::log_base_2(size_t)': boostIncl/boost/pending/relaxed_heap.hpp:101: error: 'CHAR_BIT' was not declared in this scope make: *** [bbc.o] Error 1 > sessionInfo() R version 2.7.1 Patched (2008-06-26 r45997) x86_64-unknown-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] graph_1.18.1 loaded via a namespace (and not attached): [1] cluster_1.11.11 tcltk_2.7.1 tools_2.7.1 -- Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry Indiana University School of Medicine 15032 Hunter Court, Westfield, IN 46074 (317) 490-5129 Work, & Mobile & VoiceMail (317) 663-0513 Home (no voice mail please) __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Rmpi segfault after install on Ubuntu Hardy Heron
Dirk,
Did R CMD ldd $R_HOME/library/Rmpi/libs/Rmpi.so as suggested and
things looked okay. Not really wanting to mess with the debugger I
decided to use your prepackaged version. I completely uninstalled all
openmpi packages on my system using Synaptic and deleted my compiled
from source Rmpi from my site-library. Then I executed "sudo apt-get
install r-cran-rmpi" and things seemed to go smoothly. I put a soft
link from the library aptitude installed Rmpi into to my
~/R_HOME/site-library. I get exactly the same error as before. Does
the minimal debugging info below "options(error = recover) provide any
insight? Mark
> require(Rmpi)
Loading required package: Rmpi
*** caught segfault ***
address 0x2224008, cause 'memory not mapped'
Traceback:
1: .Call("mpi_initialize", PACKAGE = "Rmpi")
2: f(libname, pkgname)
3: firstlib(which.lib.loc, package)
4: doTryCatch(return(expr), name, parentenv, handler)
5: tryCatchOne(expr, names, parentenv, handlers[[1]])
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatch(expr, error = function(e) {call <- conditionCall(e)
if (!is.null(call)) {if (identical(call[[1]],
quote(doTryCatch))) call <- sys.call(-4)dcall <-
deparse(call)[1]prefix <- paste("Error in", dcall, ": ")
LONG <- 75msg <- conditionMessage(e)sm <-
strsplit(msg, "\n")[[1]]if (14 + nchar(dcall, type = "w") +
nchar(sm[1], type = "w") > LONG) prefix <-
paste(prefix, "\n ", sep = "")}else prefix <- "Error : "
msg <- paste(prefix, conditionMessage(e), "\n", sep = "")
.Internal(seterrmessage(msg[1]))if (!silent &&
identical(getOption("show.error.messages"), TRUE)) {
cat(msg, file = stderr()).Internal(printDeferredWarnings())
}invisible(structure(msg, class = "try-error"))})
8: try(firstlib(which.lib.loc, package))
9: library(package, lib.loc = lib.loc, character.only = TRUE,
logical.return = TRUE, warn.conflicts = warn.conflicts,
keep.source = keep.source, version = version)
10: require(Rmpi)
Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace
Selection: 2
Save workspace image? [y/n/c]: n
[EMAIL PROTECTED]:~/R_HOME/site-library-2.7.0/Rmpi$ R
R version 2.7.0 Patched (2008-05-18 r45728)
#stuff deleted for brevity
__
> sessionInfo()
R version 2.7.0 Patched (2008-05-18 r45728)
x86_64-unknown-linux-gnu
locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] graph_1.18.1
loaded via a namespace (and not attached):
[1] cluster_1.11.10 tools_2.7.0
Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry
Indiana University School of Medicine
15032 Hunter Court, Westfield, IN 46074
(317) 490-5129 Work, & Mobile & VoiceMail
(317) 663-0513 Home (no voice mail please)
__
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Re: [Rd] Rmpi segfault after install on Ubuntu Hardy Heron
Dirk, Configure concluded without errors. I am not running this on the HPC cluster with icc, rather a separate local box used for testing and learning. Its just an 64-bit Ubuntu 8.04 install on a 4-core machine. LAM is not installed (I checked to make sure). So, that leaves me with you last two options. Before I make my first foray into using the R-debugger, I'd like to try you suggestion to "Check ldd on Rmpi.so" but don't have a clue how to do so. Could you instruct me? Thanks to all for the helpful comments. Mark On Wed, Jun 11, 2008 at 8:22 AM, Dirk Eddelbuettel <[EMAIL PROTECTED]> wrote: > > On 11 June 2008 at 00:46, Mark Kimpel wrote: > | I just installed Rmpi on my 64-bit Ubuntu Hardy Heron OS and using the > | following without errors: > | "R CMD INSTALL Rmpi_0.5-5.tar.gz > --configure-args=--with-mpi=/usr/lib64/openmpi" > > And it concluded without warnings or errors? Configure found all the right > files? > > As Paul suggested, make sure you're not getting it mixed with > exisiting LAM headers or MPICH2 headers or, say, that you're getting your gcc > and icc experiemenst mixed up or ... ? > > I control this by locally re-building the Debian packages for Open MPI. That > way I only keep one -dev package for MPI and can ensure that I do not get > mixups with other MPI installation. But then I do buy into the Package > Management mantra, but not everybody does... > > | Immediately at library(Rmpi) I get the segfault displayed in my > | complete output below. My first thought is that perhaps I used the > | wrong library for openmpi, but with my 64 bit install it seemed like a > | logical choice and the install went without a hitch. > > Check ldd on Rmpi.so to ensure that you linked against what you thought you > should link against. > > And if everything else fails, debug the compiled code and run R under the > debuggger. See the 'R Extensions' manual. > > | Two other general comments: > | 1. Am I addressing this to the correct list or should I use R-help? As > | I read the posting guide, I'm not sure. > | 2. Has anyone considered an R-SIG-HPC list? Anyone besides me interested? > > I'd join. > > Dirk > > -- > Three out of two people have difficulties with fractions. > > __ > R-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel > -- Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry Indiana University School of Medicine 15032 Hunter Court, Westfield, IN 46074 (317) 490-5129 Work, & Mobile & VoiceMail (317) 663-0513 Home (no voice mail please) __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Rmpi segfault after install on Ubuntu Hardy Heron
I just installed Rmpi on my 64-bit Ubuntu Hardy Heron OS and using the
following without errors:
"R CMD INSTALL Rmpi_0.5-5.tar.gz --configure-args=--with-mpi=/usr/lib64/openmpi"
Immediately at library(Rmpi) I get the segfault displayed in my
complete output below. My first thought is that perhaps I used the
wrong library for openmpi, but with my 64 bit install it seemed like a
logical choice and the install went without a hitch.
Two other general comments:
1. Am I addressing this to the correct list or should I use R-help? As
I read the posting guide, I'm not sure.
2. Has anyone considered an R-SIG-HPC list? Anyone besides me interested?
Mark
R version 2.7.0 Patched (2008-05-18 r45728)
Copyright (C) 2008 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
Natural language support but running in an English locale
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
Loading required package: datasets
Loading required package: utils
Loading required package: grDevices
Loading required package: graphics
Loading required package: stats
Loading required package: graph
[1] "packages do not need updated"
> options(STERM='iESS', editor='emacsclient')
> library("Rmpi")
*** caught segfault ***
address 0x2104008, cause 'memory not mapped'
Traceback:
1: .Call("mpi_initialize", PACKAGE = "Rmpi")
2: f(libname, pkgname)
3: firstlib(which.lib.loc, package)
4: doTryCatch(return(expr), name, parentenv, handler)
5: tryCatchOne(expr, names, parentenv, handlers[[1]])
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatch(expr, error = function(e) {call <- conditionCall(e)
if (!is.null(call)) {if (identical(call[[1]],
quote(doTryCatch))) call <- sys.call(-4)dcall <-
deparse(call)[1]prefix <- paste("Error in", dcall, ": ")
LONG <- 75msg <- conditionMessage(e)sm <-
strsplit(msg, "\n")[[1]]if (14 + nchar(dcall, type = "w") +
nchar(sm[1], type = "w") > LONG) prefix <-
paste(prefix, "\n ", sep = "")}else prefix <- "Error : "
msg <- paste(prefix, conditionMessage(e), "\n", sep = "")
.Internal(seterrmessage(msg[1]))if (!silent &&
identical(getOption("show.error.messages"), TRUE)) {
cat(msg, file = stderr()).Internal(printDeferredWarnings())
}invisible(structure(msg, class = "try-error"))})
8: try(firstlib(which.lib.loc, package))
9: library("Rmpi")
Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace
Selection:
--
Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry
Indiana University School of Medicine
15032 Hunter Court, Westfield, IN 46074
(317) 490-5129 Work, & Mobile & VoiceMail
(317) 663-0513 Home (no voice mail please)
__
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Re: [Rd] benchmarking R installations
Thanks, once I get my new Intel installation running in tandem with a gcc one, I'll report back. mark On Tue, Jun 3, 2008 at 7:04 PM, Martin Maechler <[EMAIL PROTECTED]> wrote: >>>>>> "SU" == Simon Urbanek <[EMAIL PROTECTED]> >>>>>> on Tue, 3 Jun 2008 11:52:14 -0400 writes: > >SU> On Jun 3, 2008, at 3:58 AM, Ludo Pagie wrote: > >>> recently there was a post on R-help/Rd ?? with this link >>> on benchmarking different 'number crunching >>> packages'. They used a series of tests, although I didn't >>> check they used all the types you mentioned. I couldn't >>> find test code at first glance but myyebe it is available >>> on request??? >>> >>> http://www.sciviews.org/benchmark/ >>> > >SU> It's quite outdated and doesn't work with the current R versions, > > Yes, that was the topic of the recent R-help post mentioned > above. And because of that I did post an updated version back to the > list. > Here's the posting, as found on http://search.r-project.org : >http://finzi.psych.upenn.edu/R/Rhelp02a/archive/130270.html > and the R script here > > https://stat.ethz.ch/pipermail/r-help/attachments/20080514/0ccea72b/attachment.pl > > SU> but I have an updated version that works. I have put some >SU> benchmarks I'm aware of at > >SU> http://r.research.att.com/benchmarks/ > > That's cool! Thanks, Simon! > Martin > >>> On Mon, 2 Jun 2008, Mark Kimpel wrote: >>> >>>> Recently I posted to this list with a question about >>>> using the Intel 10.1 compilers in building R and one >>>> response was basically, "why in the heck would you want >>>> to do that?" The answer is that my sysadmin believes >>>> that there will be a performance boost with the Intel >>>> vs. Gnu compilers on our Linux cluster, of which I am >>>> one of many users. Wanting to be a good citizen and use >>>> my machine time wisely, I'd of course like to use right >>>> tool to build the most efficient installation of R and >>>> associated packages. BTW, we got R to compile nicely >>>> using the settings at the end of this post. >>>> >>>> Looking back on previous posts, however, it seems that >>>> there is no consensus as to how to benchmark R. I >>>> realize such a task is not trivial, nor controversial, >>>> but does anyone have a set of time-consuming tasks that >>>> can be used to compare R installations? It would seem >>>> logical that such a benchmark would include >>>> sub-benchmarks on file access, interpreted intensive >>>> tasks, C intensive tasks, BLAS intensive tasks, etc. You >>>> developers know more about this than I do, but I know >>>> enough to realize that there won't be one simple >>>> answer. Nevertheless, I'd like to make my usage >>>> decisions on something rather than anedotal claims. >>>> >>>> So, does anyone know of a good benchmarking script or >>>> would be willing to contribute one? >>>> >>>> And here are the settings we used to compile R with >>>> Intel 10.1 compilers: >>>> >>>> ../configure >>>> --prefix=/N/u/mkimpel/R_HOME/R-patched/R-build \ >>>> --with-system-zlib=/usr/lib64 >>>> --with-system-bzlib=/usr/lib64 \ >>>> --with-mpi=/N/soft/linux-rhel4-x86_64/openmpi/1.2.5/intel-64 >>>> --with- tcltk \ >>>> --with-tcl-config=/N/soft/linux-rhel4-x86_64/tcl8.4.16/lib64/ >>>> tclConfig.sh \ >>>> --with-tk-config=/N/soft/linux-rhel4-x86_64/tk8.4.16/lib64/ >>>> tkConfig.sh \ --without-x --without-readline >>>> --without-iconv \ >>>> CC="/N/soft/linux-rhel4-x86_64/intel/cce/10.1.013/bin/icc" >>>> \ CFLAGS="-O3 -no-prec-div -unroll" \ >>>> F77="/N/soft/linux-rhel4-x86_64/intel/fce/10.1.013/bin/ifort" >>>> \ FFLAGS="-O3 -no-prec-div -unroll" \ >>>> CXX="/N/soft/linux-rhel4-x86_64/intel/cce/10.1.013/bin/icpc" >>>> \ CXXFLAGS="-O3 -no-prec-div -unroll" \ >>>>
Re: [Rd] benchmarking R installations
Dirk, Thanks for the helpful reply. I agree with the concept of testing an app that is commonly used. I suppose someone who uses R to interface alot with a database could have a very differnt experience that one who uses it mostly for matrix manupulations. Still, as a scientist I like to have some empirical evidence as to why I am doing something, especially when it entails the extra headache of using a compiler wiith which I am not familiar. As a non-computer-scientist, however, I I wasn't sure the best way about finding the answer. Mark On Tue, Jun 3, 2008 at 11:16 AM, Dirk Eddelbuettel <[EMAIL PROTECTED]> wrote: > On Tue, Jun 03, 2008 at 11:09:28AM -0400, Mark Kimpel wrote: > > Dirk, > > > > At the moment, our emphasis is getting an installation that will run Rmpi > in > > batch mode. I imagine my sysadmin put that line in to minimize potential > > problems. To be honest, I didn't catch it, I was just glad to get a > compile > > :) > > > > As to the line that doesn't apply to the R install, I think you are > > referring to the "with mpi", which I think he also slipped in not > realizing > > it should more properly go with the Rmpi install. > > Right. I wasn't implying it would do harm. > > As for the x11 choice: I prefer to keep the change vectors > minimal. Otherwise you go nuts trying to debug things. > > But it's good to see that you now understand that you have to start > 'at the top' with Intel icc, and once you have a working R with you > can start working towards packages. It's like a port to a different > platform as you completely switch the toolchain. > > Good luck and keep us posted. I have looking at icc on the TODO list > too (for my C++ code, though, given R's interactive nature I think > there are lower hanging fruits elsewhere...) > > Lastly, as to the benchmarking: It's difficult. Ripley once snarled > that it is probably the application you want to run the most so > there you go ... > > Dirk > > > > > Mark > > > > On Tue, Jun 3, 2008 at 12:18 AM, Dirk Eddelbuettel <[EMAIL PROTECTED]> > wrote: > > > > > On Mon, Jun 02, 2008 at 11:56:16PM -0400, Mark Kimpel wrote: > > > > ../configure --prefix=/N/u/mkimpel/R_HOME/R-patched/R-build \ > > > > --with-system-zlib=/usr/lib64 --with-system-bzlib=/usr/lib64 \ > > > > --with-mpi=/N/soft/linux-rhel4-x86_64/openmpi/1.2.5/intel-64 > --with-tcltk > > > \ > > > > > > There is no such option for R's configure. > > > > > > > > --with-tcl-config=/N/soft/linux-rhel4-x86_64/tcl8.4.16/lib64/tclConfig.sh > > > \ > > > > > --with-tk-config=/N/soft/linux-rhel4-x86_64/tk8.4.16/lib64/tkConfig.sh \ > > > > --without-x --without-readline --without-iconv \ > > > > > > So you never want your compute cluster to be able to do an interactive > > > plot under x11 ? > > > > > > Dirk > > > > > > -- > > > Three out of two people have difficulties with fractions. > > > > > > > > > > > -- > > Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry > > Indiana University School of Medicine > > > > 15032 Hunter Court, Westfield, IN 46074 > > > > (317) 490-5129 Work, & Mobile & VoiceMail > > (317) 663-0513 Home (no voice mail please) > > > > ** > > -- > Three out of two people have difficulties with fractions. > -- Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry Indiana University School of Medicine 15032 Hunter Court, Westfield, IN 46074 (317) 490-5129 Work, & Mobile & VoiceMail (317) 663-0513 Home (no voice mail please) ** [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] benchmarking R installations
Dirk, At the moment, our emphasis is getting an installation that will run Rmpi in batch mode. I imagine my sysadmin put that line in to minimize potential problems. To be honest, I didn't catch it, I was just glad to get a compile :) As to the line that doesn't apply to the R install, I think you are referring to the "with mpi", which I think he also slipped in not realizing it should more properly go with the Rmpi install. Mark On Tue, Jun 3, 2008 at 12:18 AM, Dirk Eddelbuettel <[EMAIL PROTECTED]> wrote: > On Mon, Jun 02, 2008 at 11:56:16PM -0400, Mark Kimpel wrote: > > ../configure --prefix=/N/u/mkimpel/R_HOME/R-patched/R-build \ > > --with-system-zlib=/usr/lib64 --with-system-bzlib=/usr/lib64 \ > > --with-mpi=/N/soft/linux-rhel4-x86_64/openmpi/1.2.5/intel-64 --with-tcltk > \ > > There is no such option for R's configure. > > > --with-tcl-config=/N/soft/linux-rhel4-x86_64/tcl8.4.16/lib64/tclConfig.sh > \ > > --with-tk-config=/N/soft/linux-rhel4-x86_64/tk8.4.16/lib64/tkConfig.sh \ > > --without-x --without-readline --without-iconv \ > > So you never want your compute cluster to be able to do an interactive > plot under x11 ? > > Dirk > > -- > Three out of two people have difficulties with fractions. > -- Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry Indiana University School of Medicine 15032 Hunter Court, Westfield, IN 46074 (317) 490-5129 Work, & Mobile & VoiceMail (317) 663-0513 Home (no voice mail please) ** [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] benchmarking R installations
Recently I posted to this list with a question about using the Intel 10.1 compilers in building R and one response was basically, "why in the heck would you want to do that?" The answer is that my sysadmin believes that there will be a performance boost with the Intel vs. Gnu compilers on our Linux cluster, of which I am one of many users. Wanting to be a good citizen and use my machine time wisely, I'd of course like to use right tool to build the most efficient installation of R and associated packages. BTW, we got R to compile nicely using the settings at the end of this post. Looking back on previous posts, however, it seems that there is no consensus as to how to benchmark R. I realize such a task is not trivial, nor controversial, but does anyone have a set of time-consuming tasks that can be used to compare R installations? It would seem logical that such a benchmark would include sub-benchmarks on file access, interpreted intensive tasks, C intensive tasks, BLAS intensive tasks, etc. You developers know more about this than I do, but I know enough to realize that there won't be one simple answer. Nevertheless, I'd like to make my usage decisions on something rather than anedotal claims. So, does anyone know of a good benchmarking script or would be willing to contribute one? And here are the settings we used to compile R with Intel 10.1 compilers: ../configure --prefix=/N/u/mkimpel/R_HOME/R-patched/R-build \ --with-system-zlib=/usr/lib64 --with-system-bzlib=/usr/lib64 \ --with-mpi=/N/soft/linux-rhel4-x86_64/openmpi/1.2.5/intel-64 --with-tcltk \ --with-tcl-config=/N/soft/linux-rhel4-x86_64/tcl8.4.16/lib64/tclConfig.sh \ --with-tk-config=/N/soft/linux-rhel4-x86_64/tk8.4.16/lib64/tkConfig.sh \ --without-x --without-readline --without-iconv \ CC="/N/soft/linux-rhel4-x86_64/intel/cce/10.1.013/bin/icc" \ CFLAGS="-O3 -no-prec-div -unroll" \ F77="/N/soft/linux-rhel4-x86_64/intel/fce/10.1.013/bin/ifort" \ FFLAGS="-O3 -no-prec-div -unroll" \ CXX="/N/soft/linux-rhel4-x86_64/intel/cce/10.1.013/bin/icpc" \ CXXFLAGS="-O3 -no-prec-div -unroll" \ FC="/N/soft/linux-rhel4-x86_64/intel/fce/10.1.013/bin/ifort" \ FCFLAGS="-O3 -no-prec-div -unroll" \ OBJC="/N/soft/linux-rhel4-x86_64/intel/cce/10.1.013/bin/icc" \ OBJCFLAGS="-O3 -no-prec-div -unroll" \ --disable-R-profiling --disable-memory-profiling ## make all make install Mark -- Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry Indiana University School of Medicine 15032 Hunter Court, Westfield, IN 46074 (317) 490-5129 Work, & Mobile & VoiceMail (317) 663-0513 Home (no voice mail please) ** [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] configure.args from install.packages passed on to subsequent update.packages?
>From the help pages I see that there is a configure.args argument to install.packages, and I am using that successfully. I do not see anything similar for update.packages(). Does each package keep track of the configure.args used to build in initially and pass this on to subsequent updates or I am missing an argument to update.packages? Thanks, Mark -- Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry Indiana University School of Medicine 15032 Hunter Court, Westfield, IN 46074 (317) 490-5129 Work, & Mobile & VoiceMail (317) 663-0513 Home (no voice mail please) ** [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] problem building R packages on RHEL 4 Linux with Intel compilers
Esmail and Simon, I would direct you to the very first sentence of my original post, "I would like to build R and packages with the Intel 10.1 compilers in RHEL4." I DO NOT want to build with gcc, that is the very point of this thread. Does anyone have an answer to my original question? I need to know what flags to put with configure so that packages will be compiled with Intel 10.1 when I do "install.packages" from within R. Mark On Thu, May 29, 2008 at 5:54 PM, Simon Urbanek <[EMAIL PROTECTED]> wrote: > > On May 29, 2008, at 5:45 PM, Mark Kimpel wrote: > > Simon, I scanned the config.log, which is too voluminous to insert below, >> but it seems that gcc is still being looked for as the compiler. See the >> lines from config.log below. Mark >> >> Thread model: posix >> gcc version 3.4.6 20060404 (Red Hat 3.4.6-9) >> configure:4824: $? = 0 >> configure:4831: gcc -V >&5 >> gcc: `-V' option must have argument >> configure:4834: $? = 1 >> configure:4857: checking for C compiler default output file name >> configure:4884: gcc -fast -unroll -wd188 -I/usr/local/include -L -L >> -L/usr/local/lib64 conftest.c >&5 >> gcc: unrecognized option `-wd188' >> cc1: error: unrecognized command line option "-fast" >> > > ^^ there you go: "-fast" is not supported by your gcc and "-wd188" is > ignored (whatever you're trying achieve with that) ... it's there in plain > english ;). > > Cheers, > Simon > > > > >> configure:4887: $? = 1 >> configure:4925: result: >> configure: failed program was: >> | /* confdefs.h. */ >> >> # Then the tail end of config.log >> >> r_cc_lo_rules_frag='' >> r_cc_rules_frag='' >> r_cxx_rules_frag='' >> r_objc_rules_frag='' >> >> ## --- ## >> ## confdefs.h. ## >> ## --- ## >> >> #define PACKAGE_NAME "R" >> #define PACKAGE_TARNAME "R" >> #define PACKAGE_VERSION "2.7.0" >> #define PACKAGE_STRING "R 2.7.0" >> #define PACKAGE_BUGREPORT "[EMAIL PROTECTED]" >> #define PACKAGE "R" >> #define VERSION "2.7.0" >> #define R_PLATFORM "x86_64-unknown-linux-gnu" >> #define R_CPU "x86_64" >> #define R_VENDOR "unknown" >> #define R_OS "linux-gnu" >> #define Unix 1 >> #define R_ARCH "" >> >> configure: exit 77 >> >> >> On Thu, May 29, 2008 at 5:35 PM, Simon Urbanek < >> [EMAIL PROTECTED]> wrote: >> >> On May 29, 2008, at 5:01 PM, Mark Kimpel wrote: >> >> I am installing within my home folder, see the ./configure options. I've >> never had a permission problem before and, like I said, if I don't put all >> the Intel-specific flags in the ./configure, everything works fine. >> >> >> This has nothing to do with the executable bit and/or permissions - this >> is about the compiler rejecting your flags. Have a look in config.log that's >> where you'll find out what the compiler didn't like (and the error clearly >> tells you that ;)). >> >> Cheers, >> Simon >> >> >> On Thu, May 29, 2008 at 4:41 PM, Esmail Bonakdarian <[EMAIL PROTECTED]> >> wrote: >> >> Mark Kimpel wrote: >> >> >> checking for gcc... gcc >> checking for C compiler default output file name... >> configure: error: C compiler cannot create executables >> See `config.log' for more details. >> >> >> Are you running this as root? Or do you have the right >> privileges for the install? >> >> The "cannot create executables" looks like a permission problem >> >> Esmail >> >> >> >> >> -- >> Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry >> Indiana University School of Medicine >> >> 15032 Hunter Court, Westfield, IN 46074 >> >> (317) 490-5129 Work, & Mobile & VoiceMail >> (317) 663-0513 Home (no voice mail please) >> >> ** >> >> [[alternative HTML version deleted]] >> >> __ >> R-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/r-devel >> >> >> >> >> >> >> -- >> Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry >> Indiana University School of Medicine >> >> 15032 Hunter Court, Westfield, IN 46074 >> >> (317) 490-5129 Work, & Mobile & VoiceMail >> (317) 663-0513 Home (no voice mail please) >> >> ** >> > > -- Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry Indiana University School of Medicine 15032 Hunter Court, Westfield, IN 46074 (317) 490-5129 Work, & Mobile & VoiceMail (317) 663-0513 Home (no voice mail please) ** [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] problem building R packages on RHEL 4 Linux with Intel compilers
Simon, I scanned the config.log, which is too voluminous to insert below, but it seems that gcc is still being looked for as the compiler. See the lines from config.log below. Mark Thread model: posix gcc version 3.4.6 20060404 (Red Hat 3.4.6-9) configure:4824: $? = 0 configure:4831: gcc -V >&5 gcc: `-V' option must have argument configure:4834: $? = 1 configure:4857: checking for C compiler default output file name configure:4884: gcc -fast -unroll -wd188 -I/usr/local/include -L -L -L/usr/local/lib64 conftest.c >&5 gcc: unrecognized option `-wd188' cc1: error: unrecognized command line option "-fast" configure:4887: $? = 1 configure:4925: result: configure: failed program was: | /* confdefs.h. */ # Then the tail end of config.log r_cc_lo_rules_frag='' r_cc_rules_frag='' r_cxx_rules_frag='' r_objc_rules_frag='' ## --- ## ## confdefs.h. ## ## --- ## #define PACKAGE_NAME "R" #define PACKAGE_TARNAME "R" #define PACKAGE_VERSION "2.7.0" #define PACKAGE_STRING "R 2.7.0" #define PACKAGE_BUGREPORT "[EMAIL PROTECTED]" #define PACKAGE "R" #define VERSION "2.7.0" #define R_PLATFORM "x86_64-unknown-linux-gnu" #define R_CPU "x86_64" #define R_VENDOR "unknown" #define R_OS "linux-gnu" #define Unix 1 #define R_ARCH "" configure: exit 77 On Thu, May 29, 2008 at 5:35 PM, Simon Urbanek <[EMAIL PROTECTED]> wrote: > > On May 29, 2008, at 5:01 PM, Mark Kimpel wrote: > > I am installing within my home folder, see the ./configure options. I've >> never had a permission problem before and, like I said, if I don't put all >> the Intel-specific flags in the ./configure, everything works fine. >> >> > This has nothing to do with the executable bit and/or permissions - this is > about the compiler rejecting your flags. Have a look in config.log that's > where you'll find out what the compiler didn't like (and the error clearly > tells you that ;)). > > Cheers, > Simon > > > On Thu, May 29, 2008 at 4:41 PM, Esmail Bonakdarian <[EMAIL PROTECTED]> >> wrote: >> >> Mark Kimpel wrote: >>> >>> >>>> checking for gcc... gcc >>>> checking for C compiler default output file name... >>>> configure: error: C compiler cannot create executables >>>> See `config.log' for more details. >>>> >>>> >>> Are you running this as root? Or do you have the right >>> privileges for the install? >>> >>> The "cannot create executables" looks like a permission problem >>> >>> Esmail >>> >>> >> >> >> -- >> Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry >> Indiana University School of Medicine >> >> 15032 Hunter Court, Westfield, IN 46074 >> >> (317) 490-5129 Work, & Mobile & VoiceMail >> (317) 663-0513 Home (no voice mail please) >> >> ** >> >>[[alternative HTML version deleted]] >> >> __ >> R-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/r-devel >> >> >> > -- Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry Indiana University School of Medicine 15032 Hunter Court, Westfield, IN 46074 (317) 490-5129 Work, & Mobile & VoiceMail (317) 663-0513 Home (no voice mail please) ** [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] problem building R packages on RHEL 4 Linux with Intel compilers
I am installing within my home folder, see the ./configure options. I've never had a permission problem before and, like I said, if I don't put all the Intel-specific flags in the ./configure, everything works fine. On Thu, May 29, 2008 at 4:41 PM, Esmail Bonakdarian <[EMAIL PROTECTED]> wrote: > Mark Kimpel wrote: > >> >> checking for gcc... gcc >> checking for C compiler default output file name... >> configure: error: C compiler cannot create executables >> See `config.log' for more details. >> > > Are you running this as root? Or do you have the right > privileges for the install? > > The "cannot create executables" looks like a permission problem > > Esmail > -- Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry Indiana University School of Medicine 15032 Hunter Court, Westfield, IN 46074 (317) 490-5129 Work, & Mobile & VoiceMail (317) 663-0513 Home (no voice mail please) ** [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] problem building R packages on RHEL 4 Linux with Intel compilers
I would like to build R and packages with the Intel 10.1 compilers in RHEL4. Using the flags below, I can successfully build R using a vanilla ./configure, but when I install new packages they build with gcc. My sysadmin suggested adding the flags to ./configure as illustrated below, but then the R build blows up with the config tail output that follows far below. It looks like gcc is still being searched for. I did read the R install and admin manual but could not find an answer. Help? CC=icc CFLAGS="-fast -unroll" F77=ifort FLAGS="-fast -unroll" CXX=icpc CXXFLAGS="-fast -unroll" FC=ifort FCFLAGS="-fast -unroll" LDFLAGS="-L$ICC_LIBS -L$IFC_LIBS -L/usr/local/lib64" SHLIB_CXXLD=icpc ../configure --prefix=/N/u/mkimpel/Quarry/R_HOME/R-patched/R-build\ CC=icc CFLAGS="-fast -unroll -wd188" F77=ifort FFLAGS="-fast -unroll" \ CXX=icpc CXXFLAGS="-fast -unroll" FC=ifort FCFLAGS="-fast -unroll" \ ICC_LIBS=/N/soft/linux-rhel4-x86_64/intel/cce/10.1.013/lib \ IFC_LIBS=/N/soft/linux-rhel4-x86_64/intel/fce/10.1.013/lib \ LDFLAGS="-L$ICC_LIBS -L$IFC_LIBS -L/usr/local/lib64" \ SHLIB_CXXLD=icpc; gmake; gmake install ### checking for gcc... gcc checking for C compiler default output file name... configure: error: C compiler cannot create executables See `config.log' for more details. -- Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry Indiana University School of Medicine 15032 Hunter Court, Westfield, IN 46074 (317) 490-5129 Work, & Mobile & VoiceMail (317) 663-0513 Home (no voice mail please) ** [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] error with R-patched (2008-05-02 r45591)
You're correct, bad form on my part. In reality, I did it in two steps as you suggested, just condensed for purposes of a brief communication. mark On Mon, May 5, 2008 at 1:52 AM, Peter Dalgaard <[EMAIL PROTECTED]> wrote: > Mark Kimpel wrote: > > > Thanks guys. For the benefit of anyone following up on this in the > > future, I > > solved my problem in my offending file with: > > > > iconv -f LATIN1 -t UTF-8 methods.output.func.R >> methods.output.func.R > > > > Mark > > > > > That line triggers a knee-jerk reflex with me (possibly unfairly since it > apparently did the job). I have always learned that using the same file for > input and output is asking for trouble: if something goes wrong on the way, > you end with neither of them. I'd do > > iconv -f LATIN1 -t UTF-8 methods.output.func.R > > mv methods.output.func.R > > > > > -- > O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B > c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K > (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 > ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 > > > -- Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry Indiana University School of Medicine 15032 Hunter Court, Westfield, IN 46074 (317) 490-5129 Work, & Mobile & VoiceMail (317) 663-0513 Home (no voice mail please) ** [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] error with R-patched (2008-05-02 r45591)
Thanks guys. For the benefit of anyone following up on this in the future, I
solved my problem in my offending file with:
iconv -f LATIN1 -t UTF-8 methods.output.func.R >> methods.output.func.R
Mark
On Sun, May 4, 2008 at 4:13 AM, Peter Dalgaard <[EMAIL PROTECTED]>
wrote:
> Prof Brian Ripley wrote:
>
> > From the NEWS file for R-patchd:
> > >
> >
> > BUG FIXES
> >
> >oThe parser sometimes accepted invalid quoted strings in a UTF-8
> >locale.
> >
> > This is likely to be the issue, but we still don't have a reproducible
> > example (see the posting guide).
> >
> > As Brian probably already knows, the issue is likely to be that your
> source file is in a non-UTF-8 encoding. (Emacs has become a little too
> smooth in handling such files almost invisibly. The magic incantation is
>
> C-x RET f utf-8
>
> before saving.)
>
> It can be reproduces as follows:
>
> [EMAIL PROTECTED] ~]$ cat > xxx.R
> "æøå"
> [EMAIL PROTECTED] ~]$ iconv -t latin1 xxx.R > .R
>
> and then R-patched gives
>
> > source("~/.R")
> Error in source("~/.R") :
> invalid multibyte character in mbcs_get_next at line 1
>
> whereas R-2.6.2 gives
>
> > source(".R")
> > .Last.value
> $value
> [1] "\xe6\xf8\xe5"
>
> $visible
> [1] TRUE
>
>
>
>
>
>
> > On Sat, 3 May 2008, Mark Kimpel wrote:
> >
> > I have found the cause of the problem I am having with R-patched. In my
> > > .Rprofile I have a function that loads a bunch of my own functions,
> > > one
> > > of which contains the character "(R)". No other version of R I have used
> > > since writing this function ~2 yrs. ago has had a problem reading in
> > > this
> > > character, but apparently R-patched does (invalid multibyte character
> > > in
> > > mbcs_get_next at line 17).
> > >
> >
> > That is a parser error message.
> >
> > Has something intentional or unintentional
> > > occured to cause this? I suspect unintentional since this would seem
> > > to
> > > be a loss of functionalilty unlikely to be introduced in a patch of a
> > > release.
> > >
> > > Anyway, that's the issue, R-patched doesn't like "(R)".
> > >
> >
> > I get
> >
> > "(R)"
> > >
> > [1] "(R)"
> >
> > in R-patched in UTF-8.
> >
> >
> > > Mark
> > >
> > >
> > > On Sat, May 3, 2008 at 4:20 PM, Prof Brian Ripley <
> > > [EMAIL PROTECTED]>
> > > wrote:
> > > On Sat, 3 May 2008, Mark Kimpel wrote:
> > >
> > >Just installed the latest R-patched and get the
> > >error seen at the end of the
> > >output below. Don't know what to make of this but
> > >thought I should report
> > >it.
> > >
> > >
> > > Nor do we. You have something incorrect in your startup files, but
> > > we don't have those.
> > >
> > > In general, when installing the latest version of R,
> > > should one use
> > > R-latest or R-patched? R-latest is stable, but one
> > > would assume that
> > > R-patched includes the latest bug fixes.
> > >
> > >
> > > And you terminolgy is from where? (Not e.g. the R FAQ.)
> > >
> > > Mark
> > >
> > > mkimpel-m90 ~/R_HOME/R-patched/R-build/bin: ./R
> > >
> > > R version 2.7.0 Patched (2008-05-02 r45591)
> > > Copyright (C) 2008 The R Foundation for Statistical Computing
> > > ISBN 3-900051-07-0
> > >
> > > R is free software and comes with ABSOLUTELY NO WARRANTY.
> > > You are welcome to redistribute it under certain conditions.
> > > Type 'license()' or 'licence()' for distribution details.
> > >
> > > Natural language support but running in an English locale
> > >
> > > R is a collaborative project with many contributors.
> > > Type 'contributors()' for more information and
> > > 'citation()' on how to cite R or R packages in publications.
> > >
> > > Type 'demo()' for some demos, 'help()' for on-line help, or
> > > 'help.start()' for an HTML browser
Re: [Rd] error with R-patched (2008-05-02 r45591)
I have found the cause of the problem I am having with R-patched. In my .Rprofile I have a function that loads a bunch of my own functions, one of which contains the character "(R)". No other version of R I have used since writing this function ~2 yrs. ago has had a problem reading in this character, but apparently R-patched does (invalid multibyte character in mbcs_get_next at line 17). Has something intentional or unintentional occured to cause this? I suspect unintentional since this would seem to be a loss of functionalilty unlikely to be introduced in a patch of a release. Anyway, that's the issue, R-patched doesn't like "(R)". Mark On Sat, May 3, 2008 at 4:20 PM, Prof Brian Ripley <[EMAIL PROTECTED]> wrote: > On Sat, 3 May 2008, Mark Kimpel wrote: > > Just installed the latest R-patched and get the error seen at the end of > > the > > output below. Don't know what to make of this but thought I should > > report > > it. > > > > Nor do we. You have something incorrect in your startup files, but we > don't have those. > > In general, when installing the latest version of R, should one use > > R-latest or R-patched? R-latest is stable, but one would assume that > > R-patched includes the latest bug fixes. > > > > And you terminolgy is from where? (Not e.g. the R FAQ.) > > Mark > > > > mkimpel-m90 ~/R_HOME/R-patched/R-build/bin: ./R > > > > R version 2.7.0 Patched (2008-05-02 r45591) > > Copyright (C) 2008 The R Foundation for Statistical Computing > > ISBN 3-900051-07-0 > > > > R is free software and comes with ABSOLUTELY NO WARRANTY. > > You are welcome to redistribute it under certain conditions. > > Type 'license()' or 'licence()' for distribution details. > > > > Natural language support but running in an English locale > > > > R is a collaborative project with many contributors. > > Type 'contributors()' for more information and > > 'citation()' on how to cite R or R packages in publications. > > > > Type 'demo()' for some demos, 'help()' for on-line help, or > > 'help.start()' for an HTML browser interface to help. > > Type 'q()' to quit R. > > > > Loading required package: utils > > [1] "packages do not need updated" > > Error in source(source.files[i]) : > > invalid multibyte character in mbcs_get_next at line 17 > > [Previously saved workspace restored] > > > > sessionInfo() > > > > > R version 2.7.0 Patched (2008-05-02 r45591) > > x86_64-unknown-linux-gnu > > > > locale: > > > > LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C > > > > attached base packages: > > [1] stats graphics grDevices datasets utils methods base > > > > > > -- > > Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry > > Indiana University School of Medicine > > > > 15032 Hunter Court, Westfield, IN 46074 > > > > (317) 490-5129 Work, & Mobile & VoiceMail > > (317) 663-0513 Home (no voice mail please) > > > > ** > > > >[[alternative HTML version deleted]] > > > > __ > > R-devel@r-project.org mailing list > > https://stat.ethz.ch/mailman/listinfo/r-devel > > > > > -- > Brian D. Ripley, [EMAIL PROTECTED] > Professor of Applied Statistics, > http://www.stats.ox.ac.uk/~ripley/<http://www.stats.ox.ac.uk/%7Eripley/> > University of Oxford, Tel: +44 1865 272861 (self) > 1 South Parks Road, +44 1865 272866 (PA) > Oxford OX1 3TG, UKFax: +44 1865 272595 > -- Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry Indiana University School of Medicine 15032 Hunter Court, Westfield, IN 46074 (317) 490-5129 Work, & Mobile & VoiceMail (317) 663-0513 Home (no voice mail please) ** [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] error with R-patched (2008-05-02 r45591)
Just installed the latest R-patched and get the error seen at the end of the output below. Don't know what to make of this but thought I should report it. In general, when installing the latest version of R, should one use R-latest or R-patched? R-latest is stable, but one would assume that R-patched includes the latest bug fixes. Mark mkimpel-m90 ~/R_HOME/R-patched/R-build/bin: ./R R version 2.7.0 Patched (2008-05-02 r45591) Copyright (C) 2008 The R Foundation for Statistical Computing ISBN 3-900051-07-0 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. Loading required package: utils [1] "packages do not need updated" Error in source(source.files[i]) : invalid multibyte character in mbcs_get_next at line 17 [Previously saved workspace restored] > sessionInfo() R version 2.7.0 Patched (2008-05-02 r45591) x86_64-unknown-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices datasets utils methods base -- Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry Indiana University School of Medicine 15032 Hunter Court, Westfield, IN 46074 (317) 490-5129 Work, & Mobile & VoiceMail (317) 663-0513 Home (no voice mail please) ** [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
