I tried to load my R workspace and received this error:
Error: bad restore file magic number (file may be corrupted) -- no data loaded
In addition: Warning message:
file ‘WORKSPACE_Wedding_Weekend_September’ has magic number '#gets'
Use of save versions prior to 2 is deprecated
I'm not particularly interested in the technical details, but mostly in how I caused it and how I can prevent it in the future. Here's some notes on the situation:
I'm running R 2.15.1 on a MacBook Pro running Windows XP on a bootcamp partition.
There is something obviously wrong this workspace file, since it weighs in at only ~80kb while all my others are usually >10,000
Over the weekend I was running an external modeling program in R and storing its output to different objects. I ran several iterations of the model over the course of several days, eg output_Saturday <- call_model()
There is nothing special to the model output, its just a list with slots for betas, VC-matrices, model specification, etc.
I got that error when I accidentally used load() instead of source() or readRDS().
Also worth noting the following from a document by the R Core Team summarizing changes in versions of R after v3.5.0 (here):
R has new serialization format (version 3) which supports custom serialization of
ALTREP framework objects... Serialized data in format 3 cannot be read by versions of R prior to version 3.5.0.
I encountered this issue when I saved a workspace in v3.6.0, and then shared the file with a colleague that was using v3.4.2. I was able to resolve the issue by adding "version=2" to my save function.
Assuming your file is named "myfile.ext"
If the file you're trying to load is not an R-script, for which you would use
source("myfile.ext")
you might try the readRDSfunction and assign it to a variable-name:
my.data <- readRDS("myfile.ext")
The magic number comes from UNIX-type systems where the first few bytes of a file held a marker indicating the file type.
This error indicates you are trying to load a non-valid file type into R. For some reason, R no longer recognizes this file as an R workspace file.
Install the readr package, then use library(readr).
It also occurs when you try to load() an rds object instead of using
object <- readRDS("object.rds")
I got the error when saved with saveRDS() rather than save(). E.g. save(iris, file="data/iris.RData")
This fixed the issue for me. I found this info here
Also note that with save() / load() the object is loaded in with the same name it is initially saved with (i.e you can't rename it until it's already loaded into the R environment under the name it had when you initially saved it).
I had this problem when I saved the Rdata file in an older version of R and then I tried to open in a new one. I solved by updating my R version to the newest.
If you are working with devtools try to save the files with:
devtools::use_data(x, internal = TRUE)
Then, delete all files saved previously.
From doc:
internal If FALSE, saves each object in individual .rda files in the data directory. These are available whenever the package is loaded. If
TRUE, stores all objects in a single R/sysdata.rda file. These objects
are only available within the package.
This error occured when I updated my R and R Studio versions and loaded files I created under my prior version. So I reinstalled my prior R version and everything worked as it should.
Related
I'm writing a package in R and I'd like to include some sample objects in it that would be easily accessible for users to play with. The problem is they contain non-ASCII characters, and R CMD check won't allow this in .rda files in data. It will, however, allow Unicode in inst/extdata. I could just have these datasets read and wrapped in objects when the package is loaded. I tried assign and <<-, but I couldn't make either work.
Alternately, they could be loaded and saved as .rda files during the installation of the package. This would be preferable, in fact, but from what I read this seemed to be less possible.
Probably irrelevant but possibly interesting bit of history: I started the package on Debian unstable. I saved those datasets as .rda and they passed the check just fine. At one point I made a little correction, resaved them, and got a warning. I saved them again, and the warning disappeared. Then I moved to Debian stable, added some new datasets, resaved them all, and now I can't get rid of the warning in any way. When I save them from r-devel, however, I only get a note, not a warning.
The answer is embarrassingly simple: read the data and prepare the variables in one of the files in the R folder, and #' #export them. No need to assign or anything.
Similar Question
accessing sysdata.rda within package functions
Why This Similar Question Does Not Apply To Me
They were able to actually build it, and apparently it was a Github error for them (not related)
R VERSION
3.4.2 (I tried using 3.4.3 as well but the same problem occurred)
EDIT: I am on Windows 10
Context
I have fully read the following tutorial on R packages and how to include .Rda files in them. I have LazyData in my DESCRIPTION file set as true as well. I have tried both the data/ folder implementation and the R/sysdata.rda implementation using the function devtools::use_data() with the respective options of internal = FALSE and internal = TRUE.
However, when I try to build the package, or use devtools::install (which builds as well I assume), it fails and gives me the following error message:
Error in predict(finalModel, newInput) : object 'finalModel' not found
Where finalModel is stored within my .rda file.
Does anyone know any possible reasons why this might occur?
I also asked a coworker to install the package on his machine, but unfortunately he got the exact same error.
I made another test package as a 'sanity-check' by creating a simple linear model using the lm() function on datasets::swiss, and then made a test package with this newly created model as a .rda file. When I referenced this test model in a function within this test package, it eerily worked, despite the fact that (to the best of my knowledge) I used the exact same steps to create this new R package.
Also, I unfortunately cannot share the code for the package I am creating, but I am willing to share the code for the test package that uses the swiss dataset.
Thank you in advance.
EDIT: My .rda file I am putting in the package was created last year, if that has anything to do with it.
I just solved a similar issue of having object 'objectName' not found that arose during package management. In my case, the issue related to losing the context of variables when working with parallelization.
When using parallel::clusterExport(cl, varlist=c("function-name")), clusterExport looks at .GlobalEnv for variable definitions. This wouldn't come up during debugging, as I always the variables defined in .GlobalEnv. The solution was to state the environment explicitly: parallel::clusterExport(cl, varlist=c("function-name"), envir=environment()). This ensures that the parallel processes have context of the variables within the data/ folder and R/sysdata.rda.
Source
If you have more than one internal file, you must save them together:
usethis::use_data(file_1,
file_2,
file_3,
internal = TRUE,
overwrite = TRUE)
I have written an R package in which the names of the functions are in Turkish.
I wanna take that package to CRAN with internalization. I changed all of the Turkish names (of functions, of data sets) to English so that everybody can easily use the package. After that, I followed regular "library(roxygen2); library(devtools); library(digest); roxygenize("causfinder"); build("causfinder"); install("causfinder"); library(causfinder)" way in process.
At the end, all of the functions appear with their English names this time in the Object Browser of Revolution R (version 7.1.0 Academic License). So, for the conversion of the names of the functions, all are OK.
Problem:
But, interestingly, not all of the names of data files in the package are not converted to English.
What I did to solve the problem till now:
I tried every sort of trick I know:
1. I deleted package from library location (I have only 1 such location: "C:\Revolution\R-Enterprise-7.1\R-3.0.2\library") completely and rebuild package and install again.
2. I deleted package from working directory "C:\Users\erdogan\Documents\Revolution", and triggered "library(roxygen2); library(devtools); library(digest); roxygenize("causfinder"); build("causfinder"); install("causfinder"); library(causfinder)" process
3. By giving possibility to Buffer effects, I deleted "C:\Users\erdogan\Documents\Revolution\32_7.1" so that "PackageXMLs\causfinder.xml" in that folder does not meddle in improperly. I had R created "32_7.1" folder by restarting Revo R.
4. I applied tricks suggested by "Dirk Eddelbuettel" here:
Update the dataset in an installed package
"updating the source and re-installing with a new distinctive version number": Not worked.
"by forcefully overwriting it, possibly. Not the proper way to do it.": How to apply that force?
My findings that may perhaps give an idea to professionals to solve the problem:
Only one of the data files correctly got renamed, and at the end of that data file in object browser "[Package causfinder version 1.0 Index]" appears. The names of all the other data files are still in Turkish and at the end of those data files, the phrase "[Package causfinder version 1.0 Index]" does not appear! I did not do anything peculiar to that data file whose internalization was done correctly.
Any help will be greatly appreciated.
Step by Step Solution: (Notebook with 32-bit Windows; GUI: Revolution R Enterprise (32-bit))
1. Prepare the environment by cleaning related folders:
1a. Delete the package folder in R's library location via Windows Explorer:
(I have only 1 such location: I deleted "C:\Revolution\R-Enterprise-7.1\R-3.0.2\library\causfinder" folder)
(Run ".libPaths()" to see R's library locations and delete the package's folder from all R's library locations)
1b. Delete the package folder in R's working directory via Windows Explorer:
(I have only 1 such location: I deleted "C:\Users\erdogan\Documents\Revolution\causfinder" folder)
(Run "getwd()" to see R's working directory and delete the package's folder from all R's working directories)
1c. Delete the "32_7.1" or "64_7.1" folder (32bit, 64 bit R, whichever you use) from R's working directory via Windows Explorer:
The .xml file of the package in discussion in this folder may sometimes meddle in and affect the results of R commands, and gives unexpected results.
Delete "C:\Users\erdogan\Documents\Revolution\32_7.1" folder where "PackageXMLs\causfinder.xml" is located.
(When Revolution R restarted, 32_7.1 (or 64_7.1) folder is created automatically if it doesn't exist)
Restart Revolution R now.
2. Create .rda and .Rd files via R and put them in relevant location.
((For English ones, I created .rda and .Rd files like this:
V6Stationary43Obs.df <-
read.csv("C:/Users/erdogan/Documents/Revolution/V6Stationary43ObsWithoutX.csv", header = TRUE, stringsAsFactors = FALSE)
# create V6Stationary43Obs.df.rda dataset file; df to denote data frame
save(V6Stationary43Obs.df, file="V6Stationary43Obs.df.rda")
prompt(V6Stationary43Obs.df) # creates V6Stationary43Obs.df.Rd help file))
((For Turkish ones, I performed the followings once upon a time
D6Duragan43Gozlem.dvc<- read.csv("C:/Users/erdogan/Documents/Revolution/D6Duragan43GozlemXsiz.csv", header = TRUE, stringsAsFactors = FALSE)
# create D6Duragan43Gozlem.vc.rda dataset file; df to denote data frame
save(D6Duragan43Gozlem.vc, file="D6Duragan43Gozlem.vc.rda")
prompt(D6Duragan43Gozlem.vc) # create D6Duragan43Gozlem.vc.Rd help file))
3. Take the .rda and .Rd files (created in Step2) to the "data" and "man" folder in R's working directory via Windows Explorer:
V6Stationary43Obs.df.rda dataset file --> C:\Users\erdogan\Documents\Revolution\causfinder\data
V6Stationary43Obs.df.Rd help file --> C:\Users\erdogan\Documents\Revolution\causfinder\man
4. Fill at least the "Title" and "Description" tags of .Rd files (created in Step3) via R:
"File - Open - File... - V6Stationary43Obs.df.Rd"
\title{
V6Stationary43Obs is..... .
}
\description{
V6Stationary43Obs does..... .
}
5. Apply roxygenization:
library(roxygen2)
library(devtools)
library(digest)
roxygenize("causfinder")
build("causfinder")
install("causfinder")
library(causfinder)
Solution: (Notebook with 64-bit Windows; GUI: Revolution R Enterprise (32-bit))
The above process is performed with the following additional actions:
1. The datasets are created as usual (for example; ".df" to denote data frame):
X.df <- read.csv("C:/Users/erdogan/Documents/Revolution/X.csv", header = TRUE, stringsAsFactors = FALSE)
save(X.df, file="X.df.rda") # X.df.rda dataset is created
prompt(X.df) #X.df.Rd help file is created.
2. Revolution R is closed, and in the working directory, the folder "32_7.3" is deleted. We delete this folder because: The information (functions, data sets, etc.) of our package (here: causfinder) are stored as .xml file in 32_7.3. However, this .xml file cannot update itself once we add our data sets one by one.
3. Revolution R is opened (the folder "32_7.3" is re-created). At this point, Step 5 above (Applying roxygenization) is performed. Once we do this, the datasets are visible in Revolution R's Object Browser.
4. The control of everything realized seamlessly: Go to the "data" folder of package's library location. Here, you must see only ".rdb, .rds, .rdx" files.
Solution: (Notebook with 64-bit Windows; GUI: Revolution R Enterprise (64-bit))
Apply the steps for 32-bits. If everything is OK, then fine: you are done. If not OK (i.e. datasets are not visible in Object Browser of Revo R and data folder of the package in the library location does not include only the .rdb, .rds, .rdx files), then do not panic:
You can still work with the datasets you created that are seen as .rda files in the package's library location: Use "data" command:
data(YourDatasetName, package = causfinder, lib.loc = YourLibraryLocation)
Learn about data command more. Upon using this command, you get the dataset in the Object Browser as an object of Global Environment.
I am trying to read a matlab file into R using R.matlab but am encountering this error:
require(R.matlab)
r <- readMat("file.mat", verbose=T)
Trying to read MAT v5 file stream...
Error in readTag(this) : Unknown data type. Not in range [1,19]: 18569
In addition: Warning message:
In readMat5Header(this, firstFourBytes = firstFourBytes) :
Unknown MAT version tag: 512. Will assume version 5.
How can this issue be solved or is there an alternative way to load matlab files? I can use hdf5load but have heard this can mess with the data. Thanks!
This is a bit late on the response, but I've recently been running into the same issues. For me, the issue was that I was saving matlab files by default using the '-v7.3' option. After extensive searching, the R.matlab source documentation (http://cran.r-project.org/web/packages/R.matlab/R.matlab.pdf) indicates the following:
Reading compressed MAT files
From MATLAB v7, compressed MAT version 5 files are used by default
[3,4]. This function supports reading such
files, if running R v2.10.0 or newer. For older versions of R, the
Rcompression package is used. To install that package, please see
instructions at http://www.omegahat.org/ cranRepository.html. As a
last resort, use save -V6 in MATLAB to write MAT files that are
compatible with MATLAB v6, that is, to write non-compressed MAT
version 5 files.
About MAT files saved in MATLAB using ’-v7.3’
This function does not
support MAT files saved in MATLAB as save('foo.mat',
'-v7.3'). Such MAT files are of a completely different file format
[5,6] compared to those saved with, say, '-v7'."
adding the '-v7' option at the end of my save command fixed this issue.
i.e.: save('filename', 'variable', '-v7')
i had a very similar problem until i pointed the function to an actual .mat file that existed. before that i'd been specifying two files of the same name, but one was .mat and the other was .txt, so it may have been trying to open the other.
i realize this may not directly solve your issue (the only difference i saw in my error message was the absence of that first line "Trying ..." and the specific numbers thereafter as well as the presence of another couple similar warnings with odd numbers), but it might point to some simple filename problem as the issue.
i use the latest matlab on 64 bit vista and the latest R on 32 bit xp.
I want to find the location of the script .R files which are used for computation in R.
I know that by typing the object function, I will get the code which is running and then I can copy and edit and save it as a new script file and use that.
The reason for asking to find the foo.R file is
Curiosity
Know what is the algorithm used in the numerical computations
More immedietly, the function from stats package I am using, is running results for two of the arguments and not the others and have to figure out how to make it work.
Error shown by R implies that there might be some modification required in the script file.
I am looking for a more general answer, if its possible.
Edit: As per the comments so far, here is the code to compute spectrum of a time series using autoregressive methods. The data input is a univariate series.
x = ts(data)
spec.ar(x, method = "yule-walker") 1
spec.ar(x, method = "burg") 2
command 1 is running ok.
command 2 gives the following error.
Error in ar.burg.default(x, aic = aic, order.max = order.max, na.action = na.action, :
Burg's algorithm only implemented for univariate series
I did try specify all the arguments correctly like na.action=na.fail, order.max = NULL etc but the message is the same.
Kindly suggest possible solutions.
P.S. (This question is posted after searching the library folder where R is installed and zip files which come with packages, manuals, and opening .rdb, .rdx files)
See FAQ 7.40 How do I access the source code for a function?
In most cases, typing the name of the function will print its source
code. However, code is sometimes hidden in a namespace, or compiled.
For a complete overview on how to access source code, see Uwe Ligges
(2006), “Help Desk: Accessing the sources”, R News, 6/4, 43–45
(http://cran.r-project.org/doc/Rnews/Rnews_2006-4.pdf).
When R installs a package, it evaluates all the ".R" source files and re-saves them into a binary format for faster loading. Therefore you typically cannot easily find the source file.
As has been suggested elsewhere, you can simply type the function name and see the source code, or download the source package and find the source there.
library(plyr)
ddply # prints the source for ddply
# See the content of the R directory for plyr,
# but it's only binary files:
dir(file.path(find.package("plyr"), "R"))
# [1] "plyr" "plyr.rdb" "plyr.rdx"
# Get the source for the package:
download.packages("plyr", "~", type="source")
# ...then unpack and inspect the R directory...
.libPaths() should tell you all of your current library locations. It's possible to have more than one installation of a package if there are two libraries but only the one that is in the first library will be used. Unless you offer the code and the exact error message, it's not likely that anyone will be able to offer better advice.
I think you are asking to see what I call the source code for a function in a package. If so, the way I do it is as follows, which has worked successfully for me on the three times I have tried. I keep these instructions handy in a few places and just copied and pasted them here:
To see the source code for a function in Program R download the package containing the function. Specifically, download the file that ends in "tar.gz". This is a compressed file. Expand the compressed file using, for example, "WinZip". Now you need to open the uncompressed file that ends in ".tar". Download the free software "7-Zip". Click on the file "7zFM.exe" and navigate to the directory containing the ".tar" file. You can extract the contents of that ".tar" file into a new folder. The contents consist of R files showing the source code for the functions in the R package.
EDIT:
Today (July 8, 2012) I was able to open the 'tar.gz' file using the latest version of 'WinZIP' and could copy the contents (the source code) from there without having to use '7-Zip'.
EDIT:
Today (January 19, 2013) I viewed the source code for functions in base R by downloading the file
'R-2.15.2.tar.gz'
To download that file go to the http://cran.at.r-project.org/ webpage and click on that file in this line:
"The latest release (2012-10-26, Trick or Treat): R-2.15.2.tar.gz, read what's new in the latest version."
Unzip the file. WinZip will work, or it did for me. Then search your computer for readtable.r or another base R function.
agstudy noted here https://stackoverflow.com/questions/14417214/source-file-for-r-function that source code for read.csv is located in the file readtable.r, so do not expect every base R function to have its own file.