I downloaded and installed the R-3.3.0 extension for windows. But when i run a netlogo code with extensions [r matrix] (BEFERGYONET MODEL), an error occurs. The error is
Error in R-Extension: Error in runOnce: java.lang.NullPointerException
I read the documentation in the doc folder and various similar posts, then understood that some global environment variables (R_HOME, JRI_HOME and PATH) are need to be changed. But i did not understood how to make these changes and what exactly have to write for these variables. Is there any specific editor and commands to do so.
Related
From the linux console I run a windows console tool using:
wine console_tool.exe ....
The console tool does not involve any windows. It's output is just textual.
Some output is added repeatedly after a given delay time.
However, besides the output of the console_tool.exe I get repeatedly the following error message also interleaved with the other output:
ERROR: ld.so: object 'libgtk3-nocsd.so.0' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
I already tried to export LD_PRELOAD=/usr/lib/x86_64-linux-gnu/libgtk3-nocsd.so.0 but then the only change is that the error message changes:
ERROR: ld.so: object '/usr/lib/x86_64-linux-gnu/libgtk3-nocsd.so.0' from LD_PRELOAD cannot be preloaded (wrong ELF class: ELFCLASS64): ignored.
I also attempted to apt install the :i386 version of the libgtk3-nocsd.so.0 but it doesn't seem to exists.
I don't know why a console application may trigger a gtk error message. This is beyond my knowledge.
My preferred goal would be to tell wine that the .exe does not use windows and it does not need to not use gtk for windows emulation at all. However, as this may not be possible, my second preferred goal would be to solve the gtk issue.
Can you help me achieve at least one of those goals?
I do not know what the error messages mean. However, the wineconsole command runs console executable using wine. Example:
wineconsole console_tool.exe
I tried to load data to my R working directory and receive this error:
Error: bad restore file magic number (file may be corrupted) -- no data loaded
In addition: Warning message:
file ‘classize.RData’ has magic number 'RDX3'
Use of save versions prior to 2 is deprecated
I googled it and tried many options, unsuccessfully.
My Rstudio version is: 1.2.5033 (The error was happening before updating as well)
I create a new project, in the new directory, I put the data file
The data file is "classize.RData"
I have another alternative which is "classize.RDS" with the sugesstion to use readRDS(file = "classize.RDS"). When using this command, I receive that error:
cannot read workspace version 3 written by R 3.6.1; need R 3.5.0 or newer
This is in the context of a statistical course at university and my teacher assistant is unable to help me out, and whitout resolving this issue, I cannot move forward in the resolution of the needed exrecices. So please, couly you help me resolve that problem.
ps: all the students have access to the same data, It's just for me that it's not working, therefore the file should not be corrupted.
I'm building a R package for binary classification and I'm using opencpu to host it. Currently I've saved the h5 file as .RData file(serialized), which is then loaded in the environment using the .onLoad() function in R. This enables the R script to use the environment variable to load keras model using keras::unserialized_model().
I've tried directly using keras::load_model_hdf5() in the code, but after building and deploying on opencpu, when I try to hit the prediction API, I get error
ioerror: unable to open file (unable to open file: name = '/home/modelfile_26feb.h5', errno = 13, error message = 'permission denied', flags = 0, o_flags = 0)
I have changed permission for the file(777) and even the groups but still getting the error.
I even tried putting the file in inst/extdata folder so that it gets in the package but still same error.
Can anyone help on this, or suggest some alternative to load the h5 model directly?
Which OS does OpenCPU run on? Why does it try to write in /home/, this is very unusual? The best solution is to adapt your code to write in getwd() or tempdir(). Even better is to store data in a local database or redis server and let R read it from there, so you don't need disk access at all.
If you run on Ubuntu Server, reading from /home/ is not permitted by default. If you want to allow this, you need to add apparmor rules, see section 3.5 of the server manual.
Some relevant topics from the opencpu mailing list:
write in home dir: https://groups.google.com/d/msg/opencpu/5vRvgSKY-qE/4xMzZCGJBAAJ
keras in opencpu: https://groups.google.com/d/msg/opencpu/HhRzFVVFdaA/n5Nu1sxyFgAJ
write tmp folder: https://groups.google.com/d/msg/opencpu/Y1tYhaQUzwU/ubSEd_CDCgAJ
I have been using roxygen2::roxygenise quite successfully with my package to build exported and imported functions. However, I recently ran into this error which I am unable to resolve:
> roxygen2::roxygenise()
First time using roxygen2. Upgrading automatically...
Error: File file does not exist
This is not the first time I have used roxygen2 with this package. In addition, I am not quite sure what "File file does not exist" means. Has anyone else seen this and been able to resolve it?
I think you have to set the working directory of R to be the package folder
I got the same error when using:
roxygen2::roxygenise("mypackage")
But, I didn't get the error when I instead used:
library(roxygen2)
roxygenise()
I know this is no explanation and I can't comment upon whether this works beyond my case.
When I download files (Windows 7) using
tryCatch(download.file(paste0(url_bv,arq), paste0(dir_bv,arq))
,error=function(cond) message(paste('erro:',arq,'não encontrado'))
,warning=function(cond) message(paste('warning:',arq,'não encontrado')))
I can´t delete files, getting the msg in the question title.
If I just do
download.file(paste0(url_bv,arq), paste0(dir_bv,arq))
there is no problem.
How can I release the folder/file in R?
I think this is likely a bug in R (windows version). I can faithfully reproduce it in R-3.2.5 (win10_64). I suggest you file a bug report (read R FAQ 9.2 for clear direction).
I tried it with several variations:
different url schemes ("http://" and "https://")
different download.file(..., method=...) options ("wininet", "internal", and "auto" all behaved in this manner; "libcurl" did not, but it merely downloaded the 404.html without telling me there was a problem)
triggers whenever warning=... or condition=... clauses are given to tryCatch and something weird happens in expr
does not trigger with error=... or finally=... arguments
32bit and 64bit variants
not in RStudio
as R --vanilla
All attempted on ubuntu-14.04 (R-3.2.3-64bit) as well, it would not trigger.