Malformed database schema

Hello, can you help me on my Sqlite issue? I used RStudio 2023.12.1 with R 4.3.3 and SqliteStudio 3.2.2. Following the R tutorial available at Express Analyst R Tutorial ([ExpressAnalyst]),




dataName ← “endotoxin_data.txt”;

dataSets ← ReadTabExpressData(dataName);

dataSets ← PerformDataAnnot(dataName, “hsa”, “array”, “refseq”, “mean”);

I encountered the following error message:

“trying URL ‘
Content type ‘unknown’ length 32493568 bytes (31.0 MB)
downloaded 31.0 MB
Error: malformed database schema (?)
In addition: Warning message:
Couldn’t set synchronous mode: malformed database schema (?)
Use synchronous = NULL to turn off this warning.”

Furthermore, attempting to load the “hsa_genes.sqlite” file into the SQLite database resulted in the error message “malformed database schema (?)”.
I am seeking your expertise and guidance on how to resolve these issues. If you have encountered similar problems or have any suggestions on how to navigate these obstacles, your advice would be immensely appreciated.


I am unable to reproduce the error, one possible issue is a mismatch in sqlite version. The one I am using is: sqlite_version()
1 3.44.2