Trying to load() a file that ends up giving me an error:
load('.RDataTmp', verbose = T)
Loading objects:
object1
object2
object3
object4
object5
Error in load(".RDataTmp", verbose = T) : error reading from connection
when I try to load it. Obviously, I messed up the name when I was saving this originally, but just when messing around I was able to save and load other objects with similarly messed up names. But it's appearing to load some of the objects before failing at loading some later object (secondary question, does this mean it loaded object5 successfully, or that's where the error occurred?). Is there a way to get a list of all the objects in the file? Then, is there a way to try and load only some of the objects?
Related
I am trying to load the state map from the maps package into an R object. I am hoping it is a SpatialPolygonsDataFrame or something I can turn into one after I have inspected it. However I am failing at the first step – getting it into an R object. I do not know the file type.
I first tried to assign the map() output to an R object directly:
st_m <- maps::map(database = "state")
draws the map, but str(st_m) appears to do nothing, unless it is redrawing the same map.
Then I tried loading it as a dataset: st_m <- data("stateMapEnv", package="maps") but this just returns a string:
> str(stateMapEnv)
chr "R_MAP_DATA_DIR"
I opened the maps directory win-library/3.4/maps/mapdata/ and found what I think is the map file, “state.L”.
I tried reading it with scan and got an error message I do not understand:
scan(file = "D:/Documents/R/win-library/3.4/maps/mapdata/state.L")
Error in scan(file = "D:/Documents/R/win-library/3.4/maps/mapdata/state.L") :
scan() expected 'a real', got '#'
I then opened the file with Notepad++. It appears to be a binary or compressed file.
So I thought it might be an R data file with an unusual extension. But my attempt to load it returned a “bad magic number” error:
st_m <- load("D:/Documents/R/win-library/3.4/maps/mapdata/state.L")
Error in load("D:/Documents/R/win-library/3.4/maps/mapdata/state.L") :
bad restore file magic number (file may be corrupted) -- no data loaded
Observing that these responses have progressed from the unhelpful through the incomprehensible to the occult, I thought it best to seek assistance from the wizards of stackoverflow.
This should be able to export the 'state' or any other maps dataset for you:
library(ggplot2)
state_dataset <- map_data("state")
I saved R objects in .Rdata files with save(obj, filename) but now I'm unable to load these objects in my global environment with load(filename).
Files are created in my hard disk with a size around 4.2ko so I guess they contain the data but Rstudio can't load them and load() returns no error.
What can I do to load these data, or at least verify the data are present ?
EDIT: When redirecting load() I can see the data is only a character string and I'm very disappointed of not being able to restore these data. It is true that I should have tested the file restoration earlier, but is there still a hope ? a file of 4.2ko must contain data.
> MYR <- load("/home/R/data/MYR.Rdata")
> MYR
[1] "data"
> class(MYR)
[1] "character"
This is not how load works (see).
It loads the data in the environment and return only a list of names of objects created.
So in your case an object named data has been loaded in the environment. You can confirm with ls() it is there. And of course you can inspect the object data.
I am trying to create a new factor column on an .xdf data set with the rxDataStep function in RevoScaleR:
rxDataStep(nyc_lab1
, nyc_lab1
, transforms = list(RatecodeID_desc = factor(RatecodeID, levels=RatecodeID_Levels, labels=RatecodeID_Labels))
, overwrite=T
)
where nyc_lab1 is a pointer to a .xdf file. I know that the file is fine because I imported it into a data table and successfully created a the new factor column.
However, I get the following error message:
Error in doTryCatch(return(expr), name, parentenv, handler) :
ERROR: The sample data set for the analysis has no variables.
What could be wrong?
First, RevoScaleR has some warts when it comes to replacing data. In particular, overwriting the input file with the output can sometimes causes rxDataStep to fail for unknown reasons.
Even if it works, you probably shouldn't do it anyway. If there is a mistake in your code, you risk destroying your data. Instead, write to a new file each time, and only delete the old file once you've verified you no longer need it.
Second, any object you reference that isn't part of the dataset itself, has to be passed in via the transformObjects argument. See ?rxTransform. Basically the rx* functions are meant to be portable to distributed computing contexts, where the R session that runs the code isn't be the same as your local session. In this scenario, you can't assume that objects in your global environment will exist in the session where the code executes.
Try something like this:
nyc_lab2 <- RxXdfData("nyc_lab2.xdf")
nyc_lab2 <- rxDataStep(nyc_lab1, nyc_lab2,
transforms=list(
RatecodeID_desc=factor(RatecodeID, levels=.levs, labels=.labs)
),
rxTransformObjects=list(
.levs=RatecodeID_Levels,
.labs=RatecodeID_Labels
)
)
Or, you could use dplyrXdf which will handle all this file management business for you:
nyc_lab2 <- nyc_lab1 %>% factorise(RatecodeID)
I have received a bunch of data saved with the save function of R.
When I try to load it, I got a Warning about the namespace and so finally an error. Is there a way to sort that out and to recover the data ?
> load('mydata')
Warning: namespace ‘BMP’ is not available and has been replaced
by .GlobalEnv when processing object ‘res’
Error: ReadItem: unknown type 0, perhaps written by later version of R
I know that BMP is a function used to generate the data, and that res is one of the elements contained in mydata.
I am trying to load an .rda file in r which was a saved dataframe. I do not remember the name of it though.
I have tried
a<-load("al.rda")
which then does not let me do anything with a. I get the error
Error:object 'a' not found
I have also tried to use the = sign.
How do I load this .rda file so I can use it?
I restared R with load("al.rda) and I know get the following error
Error: C stack usage is too close to the limit
Use 'attach' and then 'ls' with a name argument. Something like:
attach("al.rda")
ls("file:al.rda")
The data file is now on your search path in position 2, most likely. Do:
search()
ls(pos=2)
for enlightenment. Typing the name of any object saved in al.rda will now get it, unless you have something in search path position 1, but R will probably warn you with some message about a thing masking another thing if there is.
However I now suspect you've saved nothing in your RData file. Two reasons:
You say you don't get an error message
load says there's nothing loaded
I can duplicate this situation. If you do save(file="foo.RData") then you'll get an empty RData file - what you probably meant to do was save.image(file="foo.RData") which saves all your objects.
How big is this .rda file of yours? If its under 100 bytes (my empty RData files are 42 bytes long) then I suspect that's what's happened.
I had to reinstall R...somehow it was corrupt. The simple command which I expected of
load("al.rda")
finally worked.
I had a similar issue, and it was solved without reinstall R. for example doing
load("al.rda) works fine, however if you do
a <- load("al.rda") will not work.
The load function does return the list of variables that it loaded. I suspect you actually get an error when you load "al.rda". What exactly does R output when you load?
Example of how it should work:
d <- data.frame(a=11:13, b=letters[1:3])
save(d, file='foo.rda')
a <- load('foo.rda')
a # prints "d"
Just to be sure, check that the load function you actually call is the original one:
find("load") # should print "package:base"
EDIT Since you now get an error when you load the file, it is probably corrupt in some way. Try this and say what it prints:
file.info("a1.rda") # Prints the file size etc...
readBin("a1.rda", "raw", 50) # reads first 50 bytes from the file
Without having access to the file, it's hard to investigate more... Maybe you could share the file somehow (http://www.filedropper.com or similar)?
I usually use save to save only a single object, and I then use the following utility method to retrieve that object into a given variable name using load, but into a temporary namespace to avoid overwriting existing objects. Maybe it will be helpful for others as well:
load_first_object <- function(fname){
e <- new.env(parent = parent.frame())
load(fname, e)
return(e[[ls(e)[1]]])
}
The method can of course be extended to also return named objects and lists of objects, but this simple version is for me the most useful.