search

lifebit-ai / gwas

GWAS pipeline using SAIGE
5 stars 2 forks source link

address (nil), cause 'memory not mapped' [rmarkdown issue] #13

Closed cgpu closed 4 years ago

cgpu commented 4 years ago

The error happens when plotting with cairo.

An example failed log can be found here: https://cloudos.lifebit.ai/public/jobs/5f3a4698170414011206d7f3

 *** caught segfault ***
address (nil), cause 'memory not mapped'

Traceback:
 1: cairoVersion()
 2: grSoftVersion()
 3: symbolType1support()
 4: optionSymbolFont(d$symbolfamily)
 5: png(filename = paste0(output_tag, "_", "manhattan", ".png"))
An irrecoverable exception occurred. R is aborting now ...
Segmentation fault

ToDo:

Inspect heavier containers with full dependencies for rmarkdown and examine what lib is misisng.

cgpu commented 4 years ago

https://github.com/cgpu/gel-gwas/commit/2c5a4e5e216478c4a0cbe869c8b4e437b333b787 fixed it 🎉