I am trying to download the package 'seegSDM' package but keep getting an error despite trying a couple different ways.
I am using Rx64 3.6.2 and have been using the package 'githubinstall' to try and download the package.
library(githubinstall)
gh_install_packages("seegSDM")
When I use this I get the error
"Error: unexpected string constant in:
"suppressPackageStartupMessages(.getRequiredPackages(quietly = TRUE))
tools:::makeLazyLoading("seegSDM", "C:/Users/Laptop'"
Execution halted
ERROR: lazy loading failed for package 'seegSDM'
* removing 'C:/Users/Laptop/Documents/R/win-library/3.6/seegSDM'
Error: Failed to install 'seegSDM' from GitHub:
(converted from warning) installation of package ‘C:/Users/Laptop'~1/AppData/Local/Temp/Rtmpe6YLGi/file26b07cc06130/seegSDM_0.1-9.tar.gz’ had non-zero exit status
In addition: Warning message:
In fread(download_url, sep = "\t", header = FALSE, stringsAsFactors = FALSE, :
Found and resolved improper quoting out-of-sample. First healed line 4848: <<Puriney honfleuR "Evening, honfleuR" by Seurat>>. If the fields are not quoted (e.g. field separator does not appear within any field), try quote="" to avoid this warning.
Any advice? I need to use the function neasrestLand so I can nudge points on a raster to the nearest land.
It think you need to add the organization name (SEEG-Oxford). The package installs fine with
remotes::install_github("SEEG-Oxford/seegSDM"
and I suppose it might also work with
gh_install_packages("SEEG-Oxford/seegSDM")
Related
I'm trying to find a simple way to make install.packages() throw an error if it fails (rather than just a warning).
What I've tried
Setting options(warn=2) converts warnings into errors. Example:
options(warn=2)
warning()
# Error: (converted from warning)
I expected this would now error:
install.packages('thispackagedoesntexist')
# Warning in install.packages :
# package ‘thispackagedoesntexist’ is not available for this version of R
#
# A version of this package for your version of R might be available elsewhere,
# see the ideas at
# https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages
yet it still just gives a warning (no error).
Question
How can install.packages() be made to error (rather than simply warn) on any sort of failure?
Note:
There are a few nice ways of making install.packages() error instead of warning, but I'm scouting for something much more lightweight, preferably without installing other packages, which options() would achieve nicely (if I can get it working).
This is an RStudio "feature".
First I wondered why the warning isn't printed in red. Then I looked at install.packages (in RStudio) and saw this:
> install.packages
function (...)
.rs.callAs(name, hook, original, ...)
<environment: 0x1408432c8>
> getAnywhere(.rs.callAs)
A single object matching ‘.rs.callAs’ was found
It was found in the following places
tools:rstudio
with value
function (name, f, ...)
{
withCallingHandlers(tryCatch(f(...), error = function(e) {
cat("Error in ", name, " : ", e$message, "\n", sep = "")
}), warning = function(w) {
if (getOption("warn") >= 0)
cat("Warning in ", name, " :\n ", w$message, "\n",
sep = "")
invokeRestart("muffleWarning")
})
}
<environment: 0x1181b4928>
See how warnings are handled and how the printed "warning" isn't actually a warning but cat output?
If I run your code in Rgui, I see this:
> options(warn=2)
> install.packages('thispackagedoesntexist')
Error: (converted from warning) package ‘thispackagedoesntexist’ is not available for this version of R
A version of this package for your version of R might be available elsewhere,
see the ideas at
https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages
So, I suggest you go to the RStudio developers and complain that they use cat to misleadingly print "errors" and "warnings".
You can avoid RStudio's masking of install.packages the usual way:
> options(warn=2)
> utils::install.packages('thispackagedoesntexist')
Error: (converted from warning) package ‘thispackagedoesntexist’ is not available for this version of R
A version of this package for your version of R might be available elsewhere,
see the ideas at
https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages
I am trying to push the following package to CRAN, but I keep getting an error on the check.
Error:
✓ checking R/sysdata.rda ...
WARNING
‘qpdf’ is needed for checks on size reduction of PDFs
✓ checking installed files from ‘inst/doc’ ...
✓ checking files in ‘vignettes’ ...
E checking examples (3s)
Running examples in ‘oRus-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: analyseStories
> ### Title: Analysing Stories
> ### Aliases: analyseStories
>
> ### ** Examples
>
> # Transform the stories
> fileUrl <- example_stories()
> stories <- analyseStories(fileUrl, 7)
Joining, by = "word"
Joining, by = "word"
Error in loadNamespace(name) : there is no package called ‘reshape2’
Calls: analyseStories ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Current problems:
The example is in orus::analyseStores(...) function.
The example actually runs and works on the pkgdown website.
The error appears only when doing devtools::check
I have tried multiple things:
This answer base::assign(".ptime", proc.time(), pos = "CheckExEnv") ERROR when using devtools::check suggested using dontrun{...}. It passes CRAN's check, but it was bounced by a person after a couple of days.
This answer R package fails devtools::check, because "could not find function" even though the function is imported in NAMESPACE suggested doing require on the missing library. I did require(reshape2) but the check still does not pass.
This answer "Could not find function" in Roxygen examples during CMD check suggests that I need to make all my functions public (exported). I don't want to do that. I tried doing orus:::some_function(...) to call to the non-exported functions inside analyseStores but it doesn't work either.
According to this one: R package build failed when checking examples the data is working and the function has the #export tag. Also, namespace is properly updated.
I have run out of options. Any idea of what is happening?
As #stefan suggested in the comments, I had to add reshape2 into the Suggested packages in the description file. I added using:
usethis::usepackage("reshape2", "Suggests")
Followed by regenerating the docs:
devtools:document()
Package is on its way to CRAN!
I am trying to install the dcStockR package from Github, which is an htmlwidgets wrapper around the dc.js dimensional visualization library: devtools::install_github("yutannihilation/dcStockR").
I get the following encoding error:
* installing *source* package 'dcStockR' ...
** R
Error in parse(outFile) :
C:/Users/tirthankarc/AppData/Local/Temp/Rtmpcz8pHX/devtools153839438c/yutannihilation-dcStockR-c6091c8/R/dc.R:11:59: unexpected input
10: #' #export
11: dc <- function(data, chartRecipe = c("yearlyBubbleChart",ã€
^
ERROR: unable to collate and parse R files for package 'dcStockR'
* removing 'C:/Users/tirthankarc/Documents/R/R-3.2.5/library/dcStockR'
Error: Command failed (1)
The offending lines of the file in question can be viewed here: https://github.com/yutannihilation/dcStockR/blob/master/R/dc.R#L11.
Two questions:
Is this error reproducible for others?
If so, is there a way to fix this by passing an explicit encoding option to install.packages? If not, what other options are available to fix this issue?
I am attempting to update the ‘nlme’ package so that I can use great circular distances for the correlation in the gls command. I'm attempting to edit the source code with the changes specified here.
I am unsure about how to proceed in re-compiling the package with the updated source code. I am able to edit the source within the .tar.gz, but when I try to install the package from my local folder, I receive:
Installing package into ‘C:/Users/HSRG1/Documents/R/win-library/3.0’
(as ‘lib’ is unspecified)
* installing *source* package 'nlme' ...
files 'R/corStruct.R', 'R/gls.R', 'R/lme.R' have the wrong MD5 checksums
** libs
*** arch - i386
ERROR: compilation failed for package 'nlme'
* removing 'C:/Users/HSRG1/Documents/R/win-library/3.0/nlme'
Warning messages:
1: running command '"C:/PROGRA~1/R/R-30~1.0/bin/x64/R" CMD INSTALL -l "C:\Users\HSRG1\Documents\R\win-library\3.0" "nlme_3.1-111.tar.gz"' had status 1
2: In install.packages("nlme_3.1-111.tar.gz", repos = NULL, type = "source") :
installation of package ‘nlme_3.1-111.tar.gz’ had non-zero exit status
The functions R/corStruct.R', 'R/gls.R', 'R/lme.R are those which I am trying to edit. I do not know what this error means, particularly the bit about having incorrect checksums (I suspect the other errors follow). I found the following link: http://r.789695.n4.nabble.com/R-3-0-0-wrong-MD5-checksums-for-Windows-td4663348.html which discusses a different linebreak command which is implemented when compiling from Windows, but I do not know how this is relevant (or soluble) as the source has no linebreak declarations.. There is clearly something I'm missing.
I am using a Windows 64 bit computer - please let me know if there is any other information I need to provide.
UPDATE: As suggested I have tried to implement the corRGaus correlation in the ramps package. When I try to use the corRGaus correlation I get the following error:
y = runif(50, 1, 40)
x = runif(50, 1,20)
LC= c(rep(1,25), rep(2,25))
lat = runif(50,-90,90)
long = runif(50,180,180)
fit <- lme(y ~ x,random = ~x|LC, cor = corRGaus(form = ~lat+long))
Error in `coef<-.corSpatial`(`*tmp*`, value = value[parMap[, i]]) :
NA/NaN/Inf in foreign function call (arg 1)
In addition: Warning messages:
1: In nlminb(c(coef(lmeSt)), function(lmePars) -logLik(lmeSt, lmePars), :
NA/NaN function evaluation
2: In nlminb(c(coef(lmeSt)), function(lmePars) -logLik(lmeSt, lmePars), :
NA/NaN function evaluation
3: In nlminb(c(coef(lmeSt)), function(lmePars) -logLik(lmeSt, lmePars), :
NA/NaN function evaluation
4: In nlminb(c(coef(lmeSt)), function(lmePars) -logLik(lmeSt, lmePars), :
I am not sure what this error means, nor how to remedy it.
As a side note, after installing ramps, I am no longer able to use the corGaus correlation until restarting R (even if I detach the ramps package).
I'm having trouble loading the sde package on a clean Debian install running R 2.11.1. I've seen this behavior with some other packages, however, so I don't think it's specific to only this one package. Here's an example of the conundrum:
>install.packages("sde", lib.loc=libPath)
... installs sde, and the packages it's dependent on: zoo, fda
> library(sde, lib=libPath)
Loading required package: fda
Error: package 'fda' could not be loaded
In addition: Warning message:
In library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc = lib.loc) :
there is no package called 'fda'
ok, that's odd. I saw fda being installed. So I manually load the dependencies:
> library(zoo, lib=libPath)
> library(fda, lib=libPath)
Loading required package: splines
ok, that worked. Now let's try sde:
> library(sde, lib=libPath)
To check the errata corrige of the book, type vignette("sde.errata")
WTF? it loaded fine?!?
So why can I manually load the packages but R is not picking them up automagically?
Adding to my confusion, I discovered during debugging that if I don't use the lib=libPath then everything works just fine. So it looks like the use of a custom path for packages is screwing this all up... but why?
You confirmed my suspicions in the comments. You need to do one of two things:
.libPaths(libPath)
or
library(sde, lib=c(libPath,.libPaths()))
I prefer the first method because the second requires you do that for all calls to library.