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 <- call_model()
There is nothing special to the model output, its just a list with slots for betas, VC-matrices, model specification, etc.

Guess: it's not a workspace file, it's a log of the R commands. — Joshua Ulrich, Sep 17 '12 at 16:38
I suspect the same, try loading it with `source(filename)` instead of `load(filename)`. — nograpes, Sep 17 '12 at 17:01
Bummmer - Will have to check. I wish I could claim is was a beginners mistake. — N Brouwer, Sep 18 '12 at 21:01
Similar to what @JoshuaUlrich said, I `load`ed something I had `write.table`ed rather than `save`ed and got this error. Oops. — isomorphismes, Sep 28 '14 at 06:04
Got this error when I load a database with `load`, where `loadDb` should be used. — mt1022, Nov 27 '17 at 11:12
Can you please provide info regarding the type of the file (is this .RData file)? and what exactly function did you use here (`load`?) — David Arenburg, Jan 30 '18 at 09:10

score 122 · Answer 1 · edited May 16 '18 at 21:17

122

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

edited May 16 '18 at 21:17

Laurenz Albe

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answered Feb 02 '14 at 00:57

Chris SH

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So did I, when I accidentally used `load()` instead of `read.csv()`. :p – Waldir Leoncio Feb 12 '14 at 19:31
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So did I, part 2, when I accidentally used `load()` instead of `readRDS()` (yes, 9 months later, I'm back here for pretty much the same mistake). – Waldir Leoncio Nov 13 '14 at 17:35

score 38 · Answer 2 · answered Aug 07 '19 at 17:36

38

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.

answered Aug 07 '19 at 17:36

jhearn

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This is incredibly helpful! – wolfsatthedoor Jan 30 '20 at 04:53
This is the way. – user2961927 Apr 05 '20 at 00:04
Thanks! This helped in my case (had just installed R from ubuntu repository - and tried to open an RData file I had created a few weeks ago on another machine using a slightly newer version of R) – lebatsnok May 13 '20 at 20:55

score 20 · Answer 3 · edited Jan 30 '18 at 08:57

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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")

edited Jan 30 '18 at 08:57

David Arenburg

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answered Aug 01 '13 at 17:43

user2643170

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score 10 · Answer 4 · answered Aug 01 '13 at 17:48

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.

score 6 · Answer 5 · edited Jan 30 '18 at 09:05

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Install the readr package, then use library(readr).

edited Jan 30 '18 at 09:05

zx8754

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answered May 15 '17 at 04:52

Aurelia Aurita

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Nice trick... I had to try a couple of the packs function but with `readr::` it's easy to scan through the functions. `readr::read_rds` is what worked for me in the end. – Matt Bannert Oct 02 '17 at 20:08

score 4 · Answer 6 · answered Apr 04 '18 at 12:47

4

It also occurs when you try to load() an rds object instead of using

object <- readRDS("object.rds")

answered Apr 04 '18 at 12:47

DCZ

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stevec · Answer 7 · 2019-07-16T06:23:05.677

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).

score 1 · Answer 8 · answered Jun 11 '19 at 14:59

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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.

answered Jun 11 '19 at 14:59

Juan Manuel Ortiz de Zarate

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score 0 · Answer 9 · edited Jan 30 '18 at 08:58

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.

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

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