Re: [R] Rtools virus
Thanks Jeff, It was downloaded from https://cran.r-project.org/bin/windows/Rtools/ Kind Regards, Gavan Dr Gavan McGrath, PhD, B.E. Research Scientist Biodiversity and Conservation Science Department of Biodiversity, Conservation and Attractions Street Address: 17 Dick Perry Avenue, Kensington, Postal Address Locked Bag 104, Bentley Delivery Centre, WA 6983 Phone: +618 9219 9447 Mobile: +61 458 559 765 Email: gavan.mcgr...@dbca.wa.gov.au From: Jeff Newmiller Sent: Friday, May 8, 2020 10:58:34 PM To: r-help@r-project.org ; Gavan McGrath ; r-help@R-project.org Subject: Re: [R] Rtools virus [External Email] This email was sent from outside the department � be cautious, particularly with links and attachments. Sorry to hear that. It is most likely a false positive (antivirus software has little incentive to minimise false positives), but no one here can follow up on your report because you did not say precisely which website you downloaded it from. On May 5, 2020 8:50:12 PM PDT, Gavan McGrath wrote: >Hi, >My IT department instructed me to uninstall Windows 64-bit: >rtools40-x86_64.exe as it contained a virus which they identified at > >https://aus01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.virustotal.com%2Fgui%2Ffile%2F5c10d60e73dd0186e8f886ef0b9388bb7dbdfdc17366c14c16183edb08fdb58a%2Fdetectiondata=02%7C01%7Cgavan.mcgrath%40dbca.wa.gov.au%7Cd11b1d11755f4072370108d7f3604a58%7C7b934664cdcf4e28a3ee1a5bcca0a1b6%7C1%7C0%7C637245467257277714sdata=KQOX0z8gqcwhZaR9CUNpDMN1WCMTOFeqzafAoiQEYIw%3Dreserved=0 > >Kind Regards, > >Dr Gavan McGrath, PhD, B.E. > >Research Scientist >Biodiversity and Conservation Science >Department of Biodiversity, Conservation and Attractions >Street Address: 17 Dick Perry Avenue, Kensington, WA 6151, Australia >Postal Address Locked Bag 104, Bentley Delivery Centre, WA 6983, >Australia >Phone: +618 9219 9447 Mobile: +61 458 559 765 >Email: gavan.mcgr...@dbca.wa.gov.au > >Adjunct Research Fellow >School of Agriculture and Environment >The University of Western Australia >Perth, Western Australia >Email: gavan.mcgr...@uwa.edu.au > > >This message is confidential and is intended for the recipient named >above. If you are not the intended recipient, you must not disclose, >use or copy the message or any part of it. If you received this message >in error, please notify the sender immediately by replying to this >message, then delete it from your system. > >__ >R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see >https://aus01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fr-helpdata=02%7C01%7Cgavan.mcgrath%40dbca.wa.gov.au%7Cd11b1d11755f4072370108d7f3604a58%7C7b934664cdcf4e28a3ee1a5bcca0a1b6%7C1%7C0%7C637245467257287711sdata=GDLcw1UMHpiVcfAWoqdNaloY1phY%2FI0mMPaiX8TaJr8%3Dreserved=0 >PLEASE do read the posting guide >https://aus01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.r-project.org%2Fposting-guide.htmldata=02%7C01%7Cgavan.mcgrath%40dbca.wa.gov.au%7Cd11b1d11755f4072370108d7f3604a58%7C7b934664cdcf4e28a3ee1a5bcca0a1b6%7C1%7C0%7C637245467257287711sdata=isvQYq8ImiPnxS0OoMae5eGCzx6M9EXs85iVpEQ52uk%3Dreserved=0 >and provide commented, minimal, self-contained, reproducible code. -- Sent from my phone. Please excuse my brevity. This message is confidential and is intended for the recipient named above. If you are not the intended recipient, you must not disclose, use or copy the message or any part of it. If you received this message in error, please notify the sender immediately by replying to this message, then delete it from your system. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Rtools virus
Hi, My IT department instructed me to uninstall Windows 64-bit: rtools40-x86_64.exe as it contained a virus which they identified at https://www.virustotal.com/gui/file/5c10d60e73dd0186e8f886ef0b9388bb7dbdfdc17366c14c16183edb08fdb58a/detection Kind Regards, Dr Gavan McGrath, PhD, B.E. Research Scientist Biodiversity and Conservation Science Department of Biodiversity, Conservation and Attractions Street Address: 17 Dick Perry Avenue, Kensington, WA 6151, Australia Postal Address Locked Bag 104, Bentley Delivery Centre, WA 6983, Australia Phone: +618 9219 9447 Mobile: +61 458 559 765 Email: gavan.mcgr...@dbca.wa.gov.au Adjunct Research Fellow School of Agriculture and Environment The University of Western Australia Perth, Western Australia Email: gavan.mcgr...@uwa.edu.au This message is confidential and is intended for the recipient named above. If you are not the intended recipient, you must not disclose, use or copy the message or any part of it. If you received this message in error, please notify the sender immediately by replying to this message, then delete it from your system. __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] BayesianTools update prior
Hi,
Using the example in ?VSEM in the package BayesianTools I'm attempting to
iteratively update the prior but find the plotTimeSeriesResults produces the
following errors when I extend the VSEM example in BayesianTools. With the
Code below (the errors) I get:
" Error in quantile.default(x, probs = quantiles[i]) :
missing values and NaN's not allowed if 'na.rm' is FALSE"
The error appears to come from the function getPredictiveIntervals,
specifically the lines:
for (i in 1:nrow(predDistr)) {
predDistr[i, ] = error(mean = pred[i, ], par = parMatrix[i,
])
}
predInt = getCredibleIntervals(sampleMatrix = predDistr,
quantiles = quantiles)
I suspect lower and upper bounds on the parameters are not being enforced
leading to a negative standard deviation being passed to rnorm?.
Any suggestions on how to proceed would be welcome.
Code:
#run the example in ?VSEM first then:
newPrior = createPriorDensity(out, method = "multivariate",
eps = 1e-10,
lower = refPars$lower[parSel],
upper = refPars$upper[parSel])
bayesianSetup <- createBayesianSetup(likelihood = likelihood,
prior = newPrior,
names = rownames(refPars)[parSel] )
out <- runMCMC(bayesianSetup = bayesianSetup, settings = settings)
plotTimeSeriesResults(sampler = out,
model = createPredictions,
observed = obs,
error = createError,
prior = TRUE,
main = "Prior predictive")
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[R] How to make new predictions from a GAM with a spline forced through the origin
Hi, I’m followed an example to fit a GAM with a spline forced through a point, i.e. (0,0). This works fine from one of Simon’s examples however when it comes to making a prediction from a new set of x values I’m a bit stumped. In the example below a smooth term is constructed and the basis and penalties at x=0 are removed then the gam is fitted to a spline basis matrix X using spline penalties. Can someone suggest a way that I can make predictions at new x values based on the gam b below. Here is Simon Wood's example: library(mgcv) set.seed(0) n - 100 x - runif(n)*4-1;x - sort(x); f - exp(4*x)/(1+exp(4*x));y - f+rnorm(100)*0.1;plot(x,y) dat - data.frame(x=x,y=y) ## Create a spline basis and penalty, making sure there is a knot ## at the constraint point, (0 here, but could be anywhere) knots - data.frame(x=seq(-1,3,length=9)) ## create knots ## set up smoother... sm - smoothCon(s(x,k=9,bs=cr),dat,knots=knots)[[1]] ## 3rd parameter is value of spline at knot location 0, ## set it to 0 by dropping... X - sm$X[,-3]## spline basis S - sm$S[[1]][-3,-3] ## spline penalty off - y*0 + .6 ## offset term to force curve through (0, .6) ## fit spline constrained through (0, .6)... b - gam(y ~ X - 1 + offset(off),paraPen=list(X=list(S))) lines(x,predict(b)) [[alternative HTML version deleted]] __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Bigalgebra and irlba error
When running irlba on a big.matrix as in the example from the vignette (on
Windows R 2.15.2 64 bit) it returns with an error (see below). irlba works
fine on a regular R matrix
library(bigalgebra)
library(irlba)
Loading required package: Matrix
Loading required package: lattice
matmul - function(A, x, transpose=FALSE)
+ {
+ if(transpose) {return(t( t(x) %*% A))}# i.e., t(A) %*% x
+ return (A %*% x)
+ }
set.seed(1)
A - matrix(rnorm(100),10)
a - as.big.matrix(A)
La - irlba(a, nu=2, nv=2, matmul=matmul)
Error in W[, j] - matmul(A, V[, j, drop = FALSE]) :
number of items to replace is not a multiple of replacement length
LA - irlba(A, nu=2, nv=2, matmul=matmul)
LA$d
[1] 5.154081 4.816501
Any clues or is this a bug with the package integration?
Cheers,
Gavan
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[R] Compiling R extension: undefined reference to `__mingw_vsprintf'
I'm trying to link a hydrological model in FORTRAN with R. I have a subroutine inside wetall.f90 which calls two contained functions. When I try rcmd SHLIB -o wetall.dll wetall.f90 I get a bunch of errors stating undefined reference to `__mingw_vsprintf' from dos (see below). When the same is run from cygwin the dll is compiled but hangs R when dyn.load(ed) The code does not do any I/O so the errors seem unusual. Any suggestions? Microsoft Windows [Version 6.0.6002] Copyright (c) 2006 Microsoft Corporation. All rights reserved. C: \wetland_testrcmd SHLIB -o wetall2.dll wetall.f90 gfortran -shared -s -static-libgcc -o wetall2.dll tmp.def wetall.o -LC:/PROGRA~1/R/R-212~1.1/bin/i386 -lR c:/rtools/mingw/bin/../lib/gcc/mingw32/4.5.0/libgfortran.a(unix.o):(.text$sprintf+0x1b): undefined reference to `__mingw_vsprintf' c:/rtools/mingw/bin/../lib/gcc/mingw32/4.5.0/libgfortran.a(main.o):(.text$sprintf+0x1b): undefined reference to `__mingw_vsprintf' c:/rtools/mingw/bin/../lib/gcc/mingw32/4.5.0/libgfortran.a(format.o):(.text$sprintf+0x1b): undefined reference to `__mingw_vsprintf' c:/rtools/mingw/bin/../lib/gcc/mingw32/4.5.0/libgfortran.a(transfer.o):(.text$sprintf+0x1b): undefined reference to `__mingw_vsprintf' c:/rtools/mingw/bin/../lib/gcc/mingw32/4.5.0/libgfortran.a(list_read.o):(.text$sprintf+0x1b): undefined reference to `__mingw_vsprintf' c:/rtools/mingw/bin/../lib/gcc/mingw32/4.5.0/libgfortran.a(list_read.o):(.text$nml_read_obj.clone.1+0x199): undefined reference to `__mingw_snprintf' c:/rtools/mingw/bin/../lib/gcc/mingw32/4.5.0/libgfortran.a(list_read.o):(.text$nml_read_obj.clone.1+0x345): undefined reference to `__mingw_snprintf' c:/rtools/mingw/bin/../lib/gcc/mingw32/4.5.0/libgfortran.a(list_read.o):(.text$nml_get_obj_data.clone.0+0x4ab): undefined reference to `__mingw_snprintf' c:/rtools/mingw/bin/../lib/gcc/mingw32/4.5.0/libgfortran.a(list_read.o):(.text$nml_get_obj_data.clone.0+0x56b): undefined reference to `__mingw_snprintf' c:/rtools/mingw/bin/../lib/gcc/mingw32/4.5.0/libgfortran.a(list_read.o):(.text$nml_get_obj_data.clone.0+0x602): undefined reference to `__mingw_snprintf' c:/rtools/mingw/bin/../lib/gcc/mingw32/4.5.0/libgfortran.a(list_read.o):(.text$nml_get_obj_data.clone.0+0x69c): more undefined references to `__mingw_snprintf' follow c:/rtools/mingw/bin/../lib/gcc/mingw32/4.5.0/libgfortran.a(write.o):(.text$sprintf+0x1b): undefined reference to `__mingw_vsprintf' c:/rtools/mingw/bin/../lib/gcc/mingw32/4.5.0/libgfortran.a(write.o):(.text$output_float.clone.5+0x536): undefined reference to `__mingw_snprintf' c:/rtools/mingw/bin/../lib/gcc/mingw32/4.5.0/libgfortran.a(write.o):(.text$write_float+0xf9): undefined reference to `__mingw_snprintf' c:/rtools/mingw/bin/../lib/gcc/mingw32/4.5.0/libgfortran.a(write.o):(.text$write_float+0x18d): undefined reference to `__mingw_snprintf' c:/rtools/mingw/bin/../lib/gcc/mingw32/4.5.0/libgfortran.a(write.o):(.text$write_float+0x36e): undefined reference to `__mingw_snprintf' c:/rtools/mingw/bin/../lib/gcc/mingw32/4.5.0/libgfortran.a(open.o):(.text$sprintf+0x1b): undefined reference to `__mingw_vsprintf' c:/rtools/mingw/bin/../lib/gcc/mingw32/4.5.0/libgfortran.a(open.o):(.text$__gfortrani_new_unit+0x560): undefined reference to `__mingw_snprintf' collect2: ld returned 1 exit status [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
