The cause of bad magic number error when loading a workspace and how to avoid it

Question

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  lt - call model   There is nothing special to the model output  its just a list with slots for betas  VC-matrices  model specification  etc

User · Answer

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  lt - readRDS  myfile ext

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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

User · Answer

It also occurs when you try to load   an rds object instead of using   object  lt - readRDS  object rds

User · Answer

I got the error when building an R package  using roxygen2   The cause in my case was that I had saved data mydata RData 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

User · Answer

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

User · Answer

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

User · Answer

I got that error when I accidentally used load   instead of source   or readRDS

User · Answer

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

User · Answer

Install the readr package  then use library readr

[r] The cause of "bad magic number" error when loading a workspace and how to avoid it?

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