Trouble installing rgdal --- libcurl.4.dylib

Hello everyone,

I have trouble installing the rgdal package.
I run R 2.15.0 on Mac OS 10.6.8.

I followed the instructions given by Roger Bivand, who develops rgdal and ran:
> library(sp);
> setRepositories(ind=1:2)
> install.packages("rgdal")
--- SVP sélectionner un miroir CRAN pour cette session ---
essai de l'URL 'http://www.stats.ox.ac.uk/pub/RWin/bin/macosx/leopard/contrib/2.15/rgdal_0.7-8.tgz'
Content type 'application/x-gzip' length 13810017 bytes (13.2 Mb)
URL ouverte
==================================================
downloaded 13.2 Mb

It seemed to be OK, but when I try to call rgdal, I get:
> library(rgdal)
Error in dyn.load(file, DLLpath = DLLpath, ...) :
  impossible de charger l'objet partagé '/Library/Frameworks/R.framework/Versions/2.15/Resources/library/rgdal/libs/i386/rgdal.so':

dlopen(/Library/Frameworks/R.framework/Versions/2.15/Resources/library/rgdal/libs/i386/rgdal.so,
6): Library not loaded: /usr/lib/libcurl.4.dylib
  Referenced from: /Library/Frameworks/R.framework/Versions/2.15/Resources/library/rgdal/libs/i386/rgdal.so
  Reason: Incompatible library version: rgdal.so requires version 7.0.0 or later, but libcurl.4.dylib
provides version 6.0.0
Erreur : le chargement du package / espace de noms a échoué pour ‘rgdal’

It seems that the problem comes from libcurl.4.dylib.

.First for R.app called twice?

Suppose I have the following very simple ~/.Rprofile

.First <- function(){
    assign("e", exp(1), .GlobalEnv)
    lockBinding("e", .GlobalEnv)
}

If I start R from the terminal, all is fine, but if I use R.app this
throws an error about not being able to change the assigned value of a
locked binding on "e". This makes me think that R.app hits .First()
twice -- is that the intended behavior? [You can demonstrate this with
cat() statements more directly, but I figured I'd show a use case]

I don't have access to another computer right now to confirm, but the
difference between Terminal and R.app seems funny. If it seems to be a
problem with my machine, I'll hunt further.

Thanks,
Michael

R.app ''crashing'' when trying to install bioconductor packages

Hi,

on a R64 R.app [R.app GUI 1.52 (6153) x86_64-apple-darwin9.8.0] the R.app stops responding and has to be
force quit if I try to install any Bioconductor package.

sessionInfo()
R version 2.15.0 (2012-03-30)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
[1] tools_2.15.0

BW

F

--
Federico C. F. Calboli
Neuroepidemiology and Ageing Research
Imperial College, St. Mary's Campus
Norfolk Place, London W2 1PG

Tel +44 (0)20 75941602   Fax +44 (0)20 75943193

More FastRWeb questions

Hello all,

I am in the process of installing the latest CRAN repository versions
of Rserve (0.6-8) and FastRWeb (1.0-1) on MacOS 10.6.8 machine. I have
installed Rserve and verified that it can start up just fine on its
own both by using the following commands in the R GUI:

library(Rserve)
Rserve(args="--no-save")

and by running "R CMD Rserve" from the command line. After doing
either of those methods I can telnet to my localhost port 6311 and
verify that Rserve is running. However, when I try to start Rserve
(after killing any existing processes) by using the FastRWeb
code/start script, I get the following error:

##> SOCK_ERROR: bind error #13(access denied)

When I go into R GUI and run this under debug mode I get the same end
result. Here is the session transcript from R:

# START SESSION TRANSCRIPT
> Rserve(TRUE, args="--RS-conf /var/FastRWeb/code/rserve.conf --vanilla --no-save")
Starting Rserve on port 6311 :
 /Library/Frameworks/R.framework/Resources/bin/R CMD
/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rserve/libs/x86_64/Rserve-dbg.so
--RS-conf /var/FastRWeb/code/rserve.conf --vanilla --no-save

Note: debug version of Rserve doesn't daemonize so your R session will
be blocked until you shut down Rserve.

FastRWeb Questions

I have gotten FastRWeb working on Mac OS X 10.5 but I have a few of questions.  Is it possible to send more than
one argument to run(...)?  How would I parse a range sent as an argument (i.e. run(x=1:20))?  Finally,
what is the syntax to call the R script from within a PERL script?  I have read Simon's paper at:
http://urbanek.info/research/pub/urbanek-iasc08.pdf and it has helped, but I didn't see these
particular items addressed.  FastRWeb looks very promising, my current implementation initializes R
each time and is a bit slow, I am hopeful this will speed things up a lot. 

-Carl
	[[alternative HTML version deleted]]

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Re: R-SIG-Mac Digest, Vol 111, Issue 6

Simon's response may have misled some folks:

Naive Windows users (redundant?)  don't understand either icon 
relationships or how to display full file names.  Those "bad" zip files 
are actually "sneakyname.zip.exe" .

AFAIK none of the more common unzipping utilities will launch an 
executable after unpacking the archive.  It may well be that some idiot 
(at Microsoft) set things up so that a new, say, .img file gets 
automounted sort of like what Windows does with an inserted audio CD. 
Otherwise, unpacking a true zip, or gzip, or tar.gz file will not lead 
to any autoexec.

On 5/3/12 11:56 AM, r-sig-mac-request <at> r-project.org wrote:
-- DWin wrote:
>
> So I'm now wondering if there are two components to my misunderstanding:
>
> 1) My experience with Windows is that zip files are sometimes delivery
> vehicles for executable files and htat the OS can be configure to auto-
> execute such files on decompression without further intervention. I
> worried that MacOS might have the same potential.
>
Simon wrote:
On Windows, yes, executables can be masqueraded as zip files with 
interesting consequences if the tools on the machine are broken enough

--

-- 

Sent from my Cray XK6

Crash on pasting large amounts of text.

Hi,

I'm getting a repeatable crash with R64:

R version 2.15.0 (2012-03-30)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
[R.app GUI 1.51 (6148) x86_64-apple-darwin9.8.0]

I have two (admittedly long) lines of values where I am creating two arrays. When I have them both in my clipboard and paste them into the console, things work without a problem. If I open a new text document in R and paste the lines, R crashes. The precision in the data is ridiculous, yes (they are output from another program as double precision), but the program probably shouldn't crash in any event. I don't know if a buffer is being exceeded or if it's another problem, but since it's trivially repeatable I thought I'd report it.

To reproduce, copy the entire text block below the divider at the bottom of this email, create a new text document, and paste.

Cheers,
Demitri

---

x = c(2300.2654319061871320,2300.7951485790772495,2301.3249872377800784,2301.8549479103917292,2302.3850306250055837,2302.9152354097309399,2303.4455622926739125,2303.9760113019560777,2304.5065824656971927,2305.0372758120324761,2305.5680913690957823,2306.0990291650282416,2306.6300892279846266,2307.1612715861160723,2307.6925762675905389,2308.2240033005723490,2308.7555527132417410,2309.2872245337762251,2309.8190187903692276,2310.3509355112119010,2310.8829747245094950,2311.4151364584663497,2311.9474207413013573,2312.4798276012311362,2313.0123570664882209,2313.5450091653019626,2314.0777839259180837,2314.6106813765782135,2315.1437015455412620,2315.6768444610625011,2316.2101101514140282,2316.7434986448656673,2317.2770099696954276,2317.8106441541945060,2318.3444012266500067,2318.8782812153663144,23
 19.4122841486450852,2319.9464100548025272,2320.4806589621530293,2321.0150308990268968,2321.5495258937507970,2322.0841439746677679,2322.6188851701185740,2323.1537495084589864,2323.6887370180!
 425023,2324.2238477272380806,2324.7590816644119514,2325.2944388579467159,2325.8299193362217920,2326.3655231276320592,2326.9012502605723967,2327.4371007634445050,2327.9730746646632724,2328.5091719926408587,2329.0453927758048849,2329.5817370425806985,2330.1182048214095630,2330.6547961407300136,2331.1915110289955919,2331.7283495146580208,2332.2653116261849391,2332.8023973920403478,2333.3396068407050734,2333.8769400006563046,2334.4143969003880557,2334.9519775683902481,2335.4896820331705385,2336.0275103232324909,2336.5654624670955855,2337.1035384932770285,2337.6417384303094877,2338.1800623067260858,2338.7185101510649474,2339.2570819918796587,2339.7957778577192585,2340.3345977771500657,2340.8735417787347615,2341.4126098910523979,2341.9518021426792984,2342.4911185622077028,2343.0305591782262127,
 2343.5701240193407102,2344.1098131141534395,2344.6496264912830156,2345.1895641793453251,2345.7296262069712611,2346.2698126027903527,2346.8101233954471354,2347.3505586135838712,2347.89111828!
 58582833,2348.4318024409258214,2348.9726111074573964,2349.513544314124
3741,2350.0546020896035770,2350.5957844625859252,2351.1370914617605195,2351.6785231158305578,2352.2200794534983288,2352.7617605034806729,2353.3035662944926116,2353.8454968552650826,2354.3875522145253854,2354.9297324010176453,2355.4720374434832593,2356.0144673706790854,2356.5570222113597083,2357.0997019942956285,2357.6425067482541635,2358.1854365020190016,2358.7284912843711027,2359.2716711241077974,2359.8149760500250522,2360.3584060909261098,2360.9019612756278548,2361.4456416329439890,2361.9894471917050396,2362.5333779807383507,2363.0774340288867279,2363.6216153649916123,2364.1659220179085423,2364.7103540164926017,2365.2549113896129711,2365.7995941661365578,2366.3444023749475491,2366.8893360449260399,2367.4343952049680411,2367.9795798839677445,2368.5248901108352584,2369.0703259144770527,236
 9.6158873238164233,2370.1615743677743922,2370.7073870752869880,2371.2533254752897847,2371.7993895967265416,2372.3455794685532965,2372.8918951197233582,2373.4383365792068616,2373.98490387597!
 12130,2374.5315970389988252,2375.0784160972707468,2375.6253610797834881,2376.1724320155303758,2376.7196289335211077,2377.2669518627635625,2377.8144008322801710,2378.3619758710919996,2378.9096770082355761,2379.4575042727442451,2380.0054576936686317,2380.5535373000552681,2381.1017431209679671,2381.6500751854696318,2382.1985335226295319,2382.7471181615319438,2383.2958291312565962,2383.8446664609009531,2384.3936301795583859,2384.9427203163400009,2385.4919369003523570,2386.0412799607202032,2386.5907495265632861,2387.1403456270190873,2387.6900682912223601,2388.2399175483228646,2388.7898934274689964,2389.3399959578237031,2389.8902251685490228,2390.4405810888220003,2390.9910637478174067,2391.5416731747254744,2392.0924093987341621,2392.6432724490487089,2393.1942623548720803,2393.7453791454145176,2
 394.2966228499017234,2394.8479934975539436,2395.3994911176096139,2395.9511157393039866,2396.5028673918882305,2397.0547461046107856,2397.6067519067369176,2398.1588848275282544,2398.711144896!
 2627946,2399.2635321422162633,2399.8160465946812110,2400.3686882829456
408,2400.9214572363148363,2401.4743534840918073,2402.0273770555954798,2402.5805279801406869,2403.1338062870609065,2403.6872120056850690,2404.2407451653593853,2404.7944057954287018,2405.3481939252451411,2405.9021095841753777,2406.4561528015819931,2407.0103236068448496,2407.5646220293406259,2408.1190480984628266,2408.6736018436013183,2409.2282832941632478,2409.7830924795516694,2410.3380294291878272,2410.8930941724884178,2411.4482867388874183,2412.0036071578151677,2412.5590554587201950,2413.1146316710460269,2413.6703358242543800,2414.2261679478024234,2414.7821280711650616,2415.3382162238162891,2415.8944324352369222,2416.4507767349218739,2417.0072491523628742,2417.5638497170689334,2418.1205784585449692,2418.6774354063131796,2419.2344205898925793,2419.7915340388194636,2420.3487757826255802,2420
 .9061458508613214,2421.4636442730720773,2422.0212710788209733,2422.5790262976679514,2423.1369099591897793,2423.6949220929595867,2424.2530627285677838,2424.8113318956015974,2425.369729623664!
 1705,2425.9282559423568273,2426.4869108812972627,2427.0456944701018074,2427.6046067383940681,2428.1636477158122034,2428.7228174319911886,2429.2821159165823701,2429.8415431992339109,2430.4010993096117090,2430.9607842773771154,2431.5205981322101252,2432.0805409037852769,2432.6406126217962083,2433.2008133159315548,2433.7611430158981420,2434.3216017513987026,2434.8821895521532497,2435.4429064478786131,2436.0037524683089032,2436.5647276431736827,2437.1258320022211592,2437.6870655751972663,2438.2484283918565779,2438.8099204819654915,2439.3715418752904043,2439.9332926016113561,2440.4951726907079319,2441.0571821723747235,2441.6193210764045034,2442.1815894326059606,2442.7439872707850554,2443.3065146207641192,2443.8691715123636641,2444.4319579754196639,2444.9948740397653637,2445.5579197352512892,24

Check for R updates… (doesn't visit CRAN)

hi,
selected Check for R updates from R.app’s Application menu

get:

This version of R is 2.14.1
There is a newer version of R on CRAN which is 2.15.0 
> 
Do you want to visit CRAN now? Y

> 

So, no opening of browser...should this be giving an informative error?

OS X 10.7 Lion "Gotchas"

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png() segfaults inside a parallel::mclapply loop?

Hi,

I can't figure this out -- I have to (slightly different) OSX boxes
running the same version of R that I grabbed from r.research.att.com a
little while ago:

R version 2.15.0 Patched (2012-04-18 r59079)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

Simply calling png() w/in a parallel loop always crashed the
subprocesses on one machine. This code, for example:

library(parallel)
mclapply(1:10, function(i) {
  png(paste("~/tmp/p", i, "png", sep="."))
  plot(1:10)
  dev.off()
}, mc.cores=8)

The error (from each subprocess) is pasted below, however swapping out
the png() call to pdf() works on both.

The machine that png() fails on is a ~ 2008 2x4-core mac pro. The one
that doesn't have a problem is a late 2010 core2duo macbook pro 13"

Both are running OSX.6.8

Anybody else have this problem?

-steve

Error from one process:

 *** caught segfault ***
address 0x108, cause 'memory not mapped'

Traceback:
 1: png(paste("~/tmp/p", i, "png", sep = "."))
 2: FUN(7L[[1L]], ...)
 3: lapply(X = S, FUN = FUN, ...)
 4: doTryCatch(return(expr), name, parentenv, handler)
 5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
 6: tryCatchList(expr, classes, parentenv, handlers)
 7: tryCatch(expr, error = function(e) {    call <- conditionCall(e)
 if (!is.null(call)) {        if (identical(call[[1L]],
quote(doTryCatch)))             call <- sys.call(-4L)        dcall <-
deparse(call)[1L]        prefix <- paste("Error in", dcall, ": ")
  LO
NG <- 75L        msg <- conditionMessage(e)        sm <- strsplit(msg,
"\n")[[1L]]        w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L],
type = "w")        if (is.na(w))             w <- 14L + nchar(dcall,
type = "b") + nchar(sm[1L],                 type = "b")
  if (w > LONG)             prefix <- paste0(prefix, "\n  ")    }
else prefix <- "Error : "    msg <- paste0(prefix,
conditionMessage(e), "\n")    .Internal(seterrmessage(msg[1L]))    if
(!silent && identical(getOption("show.error.messages"),         TRUE))
{        ca
t(msg, file = stderr())        .Internal(printDeferredWarnings())    }
   invisible(structure(msg, class = "try-error", condition = e))})
 8: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
 9: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
10: FUN(1:8[[7L]], ...)
11: lapply(seq_len(cores), inner.do)
12: mclapply(1:10, function(i) {    png(paste("~/tmp/p", i, "png", sep
= "."))    plot(1:10)    dev.off()}, mc.cores = 8)

--

-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact

clearing plot / over plotting of points

Hello,

points are not completely erased if overplotted in the background color, using points from base graphics.
Instead, they leave a faint grey trace, both if running R.app and R in Terminal. Is this intended? What is
the proper way to erase a plot if one does not want to create a new plot, which presumably has some overhead in
an animation?

Example,  using points:

A <- matrix(rnorm(1000), 500, 2)
plot(range(A), range(A), type="n")
points(A)
points(A[1:250, 1:2], col="white", bg="white")

I'm posting to this list because I have not tested under a different OS.

Jochen

> sessionInfo()
R version 2.15.0 (2012-03-30)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] lattice_0.20-6 MASS_7.3-17   

loaded via a namespace (and not attached):
[1] grid_2.15.0  tools_2.15.0

PS: Points *are* erased if using image

# using image
A <- matrix(0, 100, 100)
ix <- runif(1000, 0, 10000)
A[ix] <- 1
image(seq(0,1,length=100), seq(0,1,length=100), A, col=c("white", "black"))
A[ix[1:500]] <- 0
image(seq(0,1,length=100), seq(0,1,length=100), A, col=c("white", "black"))