Hi,
I am using R (v4.1) in my Linux server with Ubuntu 22.04.2. I want to use the function processBismarkAln from the package MethylKit to read my .sam files (output from BisMark). The bam files are ~8 GB in size. The server has a RAM of ~250 GB. When the running the function, an output file is created but is incomplete and is only of 100 kb.
After that this error message is displayed:
free(): invalid next size (fast) Aborted (core dumped)
At first there was already some issue related to .sam file sorting but the error is persists even after this is rectified. If ran properly the function is supposed to output CpG reports of more than ~1 GB.
When I browsed about this error in Google I understood that is something related to memory corruption. Since I am using an R package and didn't write my own code I don't understand how to rectify this error.
Hope someone would help me solve this.
Thank you.
The error is in
c, I would try to upgrade the package (and maybe R) to the latest version.I updated both R and package but error persists.