Gettin Parser Error while installing Package in Julia 1.0.1 - julia

When I tried to run Pkg.add('BenchmarkTools") I got the following error.
ERROR: Pkg.TOML.ParserError(3, 4, "expected `=`, but found `\x90`")

It seems to be a general problem. The only solution for this is to close julia or coding environment, delete the TOML file in
C:\Users<USER>.julia\logs
and restart Julia

Related

Error when trying to Pkg.add("Playground") in Julia

I am trying to install Playground in Julia 1.7.2 in order to make a virtual environment. However, when I go about julia> Pkg.add("Playground") the following error appears:
ERROR: The following package names could not be resolved:
* Playground (not found in project, manifest or registry)
I am not sure what is happening and how to properly resolve this issue in the most convenient way. Could it be a version incompatibility issue?

Unable to install package Sleuth in R

I've been trying to install the Sleuth package in R all morning and it keeps giving me errors. This is how I tried to install it:
if(!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("DESeq2")
BiocManager::install ("rhdf5")
install.packages("devtools")
devtools:: install_github("pachterlab/sleuth")
I did use the library() command.
I get the following error messages:
Error: object 'h5write.default' is not exported by 'namespace:rhdf5'
Execution halted
ERROR: lazy loading failed for package 'sleuth'
removing 'C:/Users/31625/OneDrive/Documents/R/win-library/4.1/sleuth'
I was having the same issue and found that there's current an open issue on Github discussing this problem.
Currently there is a workaround which was shared in the same issue on Github:
Run git clone https://github.com/pachterlab/sleuth
Remove the last line in ./sleuth/NAMESPACE which is the h5write.default that raises the error during installation - ignore the warning in the first line
Then in R: devtools::install('./sleuth/')
It worked for me while using Linux - ZorinOS and R 4.1.2 but it should work on Windows as well.
Someone also opened a PR to fix the whole issue but it seems they are not updating the package anymore (unfortunately).

Run Pkg.instantiate() error when importing julia package

I have added a package Relief.jl to my environment. I have also checked if it's available by typing stand it's listed under available packages for the environment. However when I type using Relief I get the following error,
ERROR: ArgumentError: Package Relief [e59a39ae-ffc4-11ea-35a5-2b2996f35250] is required but does not seem to be installed:
- Run Pkg.instantiate() to install all recorded dependencies.
Any ideas what I should do to resolve this?
You need to run the command: ] build "name of package" in the terminal. This should fix the problem.
(Without the speech marks. That is just to highlight its a name)

Fail to install RCall - Julia package

Following RCall's documentation, I ran Pkg.add("RCall") which looked to be working. Then, running using RCall gave:
WARNING: could not import StatsModels.Formula into RCall
ERROR: LoadError: RCall not properly installed. Please run Pkg.build("RCall")
#... few lines later
ERROR: Failed to precompile RCall [6f49c342-dc21-5d91-9882-a32aef131414] to C:\Users\jke4\.julia\compiled\v1.1\RCall\8GFyb.ji.
That's why I ran Pkg.build("RCall"):
┌ Error: Error building `RCall`:
│ ERROR: LoadError: R cannot be found. Set the "R_HOME" environment variable to re-run Pkg.build("RCall").
I believe, accordingly to RCall's documentation that I have to do a custom installation, but why can't am I able to simply install by Pkg.add("RCall") like it's suppose to be done?
RCall.jl can simply be installed with
Pkg.add("RCall")
Note:
Julia version is 1.1.0.
using Conda does work.
There is no R version installed in my Windows computer
I do understand what is my error message and how I can deal with it. My question is why do I have it whereas I wasn't suppose to, quoting RCall's documentation:
RCall.jl will automatically install R for you using Conda if it doesn't detect that you have R 3.4.0 or later installed already.
Update
Alright, I've done what #Cameron Bieganek suggests: pkg> pin StatsModels#0.5
And it seems to work for a moment. However, after doing ] up, accordingly with the issue I had in this question.
using RCall now gives:
ERROR: LoadError: RCall not properly installed. Please run Pkg.build("RCall")
and Pkg.build("RCall"):
┌ Error: Error building `RCall`:
│ ERROR: LoadError: IOError: stat: invalid argument (EINVAL)
This time I can't get what's the error.
GitHub
Please note that this question is also referenced on GitHub RCall.jl.

How to install 'XLConnect'-package in R correctly

I am very new to this community.
My aim is to use R for statistical analysis but some errors occurred.
In the first step, I want to load the "XLConnect"-package, in order to open an xlsx-data file, with this code:
install.packages('XLConnect')
library(XLConnect)
Answer was "package ‘XLConnect’ successfully unpacked and MD5 sums checked", after which the following error was given:
Error in library(XLConnect) : the package ‘XLConnect’ doesn't exist.
I also tried the xlsx package, but in this case always got:
Error in -library('openxlsx') : invalid argument to unary operator
or, that the package openxlsx, doesn't exist but some line before it told me the download, installation and check sums were correct!
Additionally, when I try to change the directory in a script, using
getwd(), the following error occurs:
Error in -getwd() : invalid argument to unary operator
When I type it in the console it works.
I downloaded R here: https://cran.r-project.org/bin/windows/base, installed R version 3.4.3 as well as R Studio.
I already looked in the community for some hints but neither could solve my problem:
XLConnect function is not passing argument to system.file
Error when installing XLConnect in RStudio
MY OS is Windows 10, I tried the 32-bit as well as the 64-bit version of R and installed fitting Java-Versions for both verisons( that was the first error that occured but now isn't there anymore).
I tried to load the packages from several CRAN-Mirrors but always the same error occurs (e.g. Germany(Göttingen),Germany(Münster), Belgium(Ghent) or Switzerland ).
Maybe I missed some very basic setting. Is the information I provided enough or do you need more?
Thanks a lot in advance for your support!
Thanks a lot! I installed java 32-bit and 64-bit versions the way it is recommended here: https://www.r-statistics.com/2012/08/how-to-load-the-rjava-package-after-the-error-java_home-cannot-be-determined-from-the-registry/ and I installed the rJava package like this: install.packages("rJava")
library(rJava) and here: https://askubuntu.com/questions/176115/what-is-the-best-way-of-installing-the-r-package-xlconnect I found that this here should work to register R correctly: sudo R CMD javareconf but then I get the error that the console got an unexpected symbol. Or Do you know how to register Java Development Kit in R correctly. I installed jdk-8u161-windows-x64.
Make sure you have Java Development Kit installed and correctly registered in R.

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