I recently dusted off a script which calls solve.QP from the quadprog package (I currently have version 1.5-5). Now it generates the error "object '.QP_qpgen2' not found". I don't understand why.
This object is not created by me but by the solve.QP function in quadprog.
On Github Quadprog.R has the code (line 117):
res1 <- .Fortran(.QP_qpgen2,
as.double(Dmat), dvec=as.double(dvec),
as.integer(n), as.integer(n),
sol=as.double(sol), lagr=as.double(lagr),
crval=as.double(crval),
as.double(Amat), as.double(bvec), as.integer(n),
as.integer(q), as.integer(meq),
iact=as.integer(iact), nact=as.integer(nact),
iter=as.integer(iter), work=as.double(work),
ierr=as.integer(factorized))
The error can be generated from the code taken from the documentation for solve.QP:
##
## Assume we want to minimize: -(0 5 0) %*% b + 1/2 b^T b
## under the constraints: A^T b >= b0
## with b0 = (-8,2,0)^T
## and (-4 2 0)
## A = (-3 1 -2)
## ( 0 0 1)
## we can use solve.QP as follows:
##
Dmat <- matrix(0,3,3)
diag(Dmat) <- 1
dvec <- c(0,5,0)
Amat <- matrix(c(-4,-3,0,2,1,0,0,-2,1),3,3)
bvec <- c(-8,2,0)
solve.QP(Dmat,dvec,Amat,bvec=bvec)
I am using R v3.4.1 if that helps.
As stated in my comment, R 3.4 has a new method to register external routines. Quadprog relies on Fortran routines.
To solve this, you need to build the package from source in R 3.4 using the current Rtools. You need to have the Rtools installed and setup (A google search will get you to a guide how to set-up Rtools for whatever system you are using). Then, go to CRAN page of the quadprog package and download the source file quadprog.tar.gz. Finally, run the command
install.packages("PATH_TO_FILE/quadprog_1.5-5.tar.gz", repos = NULL, type="source", INSTALL_opts = "--merge-multiarch")
Alternatively, you can wait a few days. I'm sure, the package on CRAN will be updated soon.
As I keep getting e-mails about this issue:
Use packageDescription("quadprog") to see under which version of R your installed package was built.
If the version is R 3.3.x (or earlier), use update.packages(checkBuilt=TRUE) to update your version to a version that was built under R 3.4.x.
Related
I am trying to run the textEmbed function in R.
Set up needed:
require(quanteda)
require(quanteda.textstats)
require(udpipe)
require(reticulate)
#udpipe_download_model(language = "english")
ud_eng <- udpipe_load_model(here::here('english-ewt-ud-2.5-191206.udpipe'))
virtualenv_list()
reticulate::import('torch')
reticulate::import('numpy')
reticulate::import('transformers')
reticulate::import('nltk')
reticulate::import('tokenizers')
require(text)
It runs the following code
tmp1 <- textEmbed(x = 'sofa help',
model = 'roberta-base',
layers = 11)
tmp1$x
However, it does not run the following code
tmp1 <- textEmbed(x = 'sofa help',
model = 'roberta-base',
layers = 11)
tmp1$x
It gives me the following error
Error in x[[1]] : subscript out of bounds
In addition: Warning message:
Unknown or uninitialised column: `words`.
Any suggestions would be highly appreciated
I believe that this error has been fixed with a newer version of the text-package (version .9.50 and above).
(I cannot see any difference in the two code parts – but I think that this error is related to only submitting one token/word to textEmbed, which now works).
Also, see updated instructions for how to install the text-package http://r-text.org/articles/Extended_Installation_Guide.html
library(text)
library(reticulate)
# Install text required python packages in a conda environment (with defaults).
text::textrpp_install()
# Show available conda environments.
reticulate::conda_list()
# Initialize the installed conda environment.
# save_profile = TRUE saves the settings so that you don't have to run textrpp_initialize() after restarting R.
text::textrpp_initialize(save_profile = TRUE)
# Test so that the text package work.
textEmbed("hello")
I'm following the book "Computer-age Calculus with R" but cannot run the function slice_plot( which is the first one used for graphing functions). The library mosaic, mosaicCalc and mosaicModel are installed. I don't know what I'm missing.
this is the code with the libraries required by the book:
library(mosaic)
library(mosaicCalc)
library(mosaicModel)
library(akima)
drug_remaining <- function(dose, duration, time_constant){
dose * exp(-duration / time_constant)
}
slice_plot(
drug_remaining(dose = 100, time_constant = 4, duration = t) ~ t,
domain(t = 0:20))
I've found the function slice_plot() and countour_plot() are still in development in a beta version of the mosaicCalc package, to use them we need to install the beta version running this code:
remotes::install_github("ProjectMOSAIC/mosaicCalc", ref="beta")
https://github.com/ProjectMOSAIC/mosaicCalc/issues/4
I installed 'caTools' R package through the command line:
$ R
$ install.packages("caTools", lib="~/R/library")
Then, did this command:
INPUT=/home/user/file.bam
OUTPUT=/home/user/file_cor.bam
Rscript run_spp_nodups.R -c=$INPUT -savp -out=$OUTPUT
And got the error:
Error: could not find function "runmean"
Execution halted
The function 'runmean' belongs to package I installed, 'caTools'.
The R version is appropriate, as R in my machine is version 3.3.2 and 'caTools' depends on R (≥ 2.2.0).
The R code of 'run_spp_nodups.R' is to big to paste here. I show only the part with runmean:
# Smooth the cross-correlation curve if required
cc <- crosscorr$cross.correlation
crosscorr$min.cc <- crosscorr$cross.correlation[ length(crosscorr$cross.correlation$y) , ] # minimum value and shift of cross-correlation
cat("Minimum cross-correlation value", crosscorr$min.cc$y,"\n",file=stdout())
cat("Minimum cross-correlation shift", crosscorr$min.cc$x,"\n",file=stdout())
sbw <- 2*floor(ceiling(5/iparams$sep.range[2]) / 2) + 1 # smoothing bandwidth
cc$y <- runmean(cc$y,sbw,alg="fast")
What's happening and how to solve it?
I have recently run into a problem running a GAM model from a previously working code. I believe it is related to an updated R-Version and an updated Version of the mgcv package. It would be great to know if anyone has the same problem or has a solution to it.
I am currently running R version 3.2.2 (2015-08-14) -- "Fire Safety"
on Windows. I am using the mgcv Package 1.8-7. Below is an example code that re-produces the error message, when run on my computer.
###Load package
library(mgcv)
This is mgcv 1.8-7.
###Simulate some example data
set.seed(2) ## simulate some data...
dat <- gamSim(1,n=400,dist="normal",scale=2)
###Run normal model
b <- gam(y~s(x0)+s(x1)+s(x2)+s(x3),data=dat, family=gaussian())
This works.
###change the smoothness selection method to REML
b0 <- gam(y~s(x0)+s(x1)+s(x2)+s(x3),data=dat,method="REML")
Gives the following error message:
Error in .C(C_gdi1, X = as.double(x[good, ]), E = as.double(Sr), Eb = as.double(Eb), : Incorrect number of arguments (48), expecting 47 for 'gdi1'
Thanks for your help!
I have re-installed R and the mgcv package and it seems as if this has resolved the issue.
I am using the "BMA" package in R 3.1.0, and get an error when running one of the functions in the package, iBMA.glm. When running the example in the package documentation:
## Not run:
############ iBMA.glm
library("MASS")
library("BMA")
data(birthwt)
y<- birthwt$lo
x<- data.frame(birthwt[,-1])
x$race<- as.factor(x$race)
x$ht<- (x$ht>=1)+0
x<- x[,-9]
x$smoke <- as.factor(x$smoke)
x$ptl<- as.factor(x$ptl)
x$ht <- as.factor(x$ht)
x$ui <- as.factor(x$ui)
### add 41 columns of noise
noise<- matrix(rnorm(41*nrow(x)), ncol=41)
colnames(noise)<- paste('noise', 1:41, sep='')
x<- cbind(x, noise)
iBMA.glm.out<- iBMA.glm( x, y, glm.family="binomial",
factor.type=FALSE, verbose = TRUE,
thresProbne0 = 5 )
summary(iBMA.glm.out)
I get the error:
Error in registerNames(names, package, ".__global__", add) :
The namespace for package "BMA" is locked; no changes in the global variables list may be made.
I get the error in RStudio running R 3.1.0 on Ubuntu.
on Windows 7, from RStudio and the R console I get a similar error:
Error in utils::globalVariables(c("nastyHack_glm.family", "nastyHack_x.df")) :
The namespace for package "BMA" is locked; no changes in the global variables list may be made.
I also get the same error when running my own data in the function. I'm not clear on what this error means and how to work around the error to be actually able to use the function. Any advice would be appreciated!