You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
I was trying to follow the tutorials and wanted to look at the data shared on Zenodo but I get an error when I try to load the file. Here's a reproducible example:
Title: PBMC datasets for harmony
Keywords:
Publication date: 2023-07-19
DOI: 10.5281/zenodo.8164711
Total size: 132.5 MB
Link: https://zenodo.org/api/records/8164711/files/pbmc_stim.RData/content size: 30.5 MB
100% [........................................................................] 31973441 / 31973441
Checksum is correct. (dab7de4203a0f5bec3ba67d5c1e614c4)
Link: https://zenodo.org/api/records/8164711/files/pbmc.RData/content size: 102.0 MB
100% [......................................................................] 106968050 / 106968050
Checksum is correct. (23b2f9e77a602de4d4bd9c69c1024db0)
All files have been downloaded.
Try to load pbmc.RData.
docker run --rm -it -v $(pwd):$(pwd) rocker/verse:4.3.2 R -q -e 'load("/home/dtang/tmp/pbmc.RData")'
> load("/home/dtang/tmp/pbmc.RData")
Error in load("/home/dtang/tmp/pbmc.RData") :
bad restore file magic number (file may be corrupted) -- no data loaded
In addition: Warning messages:
1: In readChar(con, 5L, useBytes = TRUE) :
truncating string with embedded nuls
2: file ‘pbmc.RData’ has magic number 'X'
Use of save versions prior to 2 is deprecated
Execution halted
pbmc_stim.RData loads fine.
docker run --rm -it -v $(pwd):$(pwd) rocker/verse:4.3.2 R -q -e 'load("/home/dtang/tmp/pbmc_stim.RData")'
The text was updated successfully, but these errors were encountered:
Thanks for reporting this. I can reproduce the bug in my environment, also R 4.3.3. It is because R deprecated the old serialization scheme. The files are not corrupt.
There is a workaround.
Error: Please run UpdateSeuratObject on your object
Error during wrapup: no slot of name "images" for this object of class "Seurat"
Error: no more error handlers available (recursive errors?); invoking 'abort' restart
Hi there,
I was trying to follow the tutorials and wanted to look at the data shared on Zenodo but I get an error when I try to load the file. Here's a reproducible example:
Download the data.
Try to load
pbmc.RData
.docker run --rm -it -v $(pwd):$(pwd) rocker/verse:4.3.2 R -q -e 'load("/home/dtang/tmp/pbmc.RData")'
pbmc_stim.RData
loads fine.docker run --rm -it -v $(pwd):$(pwd) rocker/verse:4.3.2 R -q -e 'load("/home/dtang/tmp/pbmc_stim.RData")'
The text was updated successfully, but these errors were encountered: