The cause of "bad magic number" error when loading a workspace and how to avoid it?
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 readRDS
function 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.