Question: GO.db/GOSim bugged or my bad?
0
gravatar for lejeczek
4.3 years ago by
lejeczek0
United Kingdom
lejeczek0 wrote:

hi everybody,

I'm trying something seemingly simple but it segfaults and I wonder it this might be a bug?

I run:

"

library(GOSim)
library(org.Hs.eg.db)
library(org.Mm.eg.db)
library(GO.db)
setEvidenceLevel(evidences = "all", organism=org.Hs.egORGANISM, gomap=org.Hs.egGO)
calc.diffusion.kernel(method="diffKernelLLE", m=5, normalization.method="sqrt", DIR="/tmp")

"

and it fails:

"

initializing GOSim package ...
-> retrieving GO information for all available genes for organism 'human' in GO database
-> filtering GO terms according to evidence levels 'all'
-> loading files with information content for corresponding GO category (human)
finished.
-> retrieving GO information for all available genes for organism 'Homo sapiens' in GO database
-> filtering GO terms according to evidence levels 'all'
calculating diffusion kernel 'diffKernelLLE' for ontology BP using evidence codes 'all' (Homo sapiens) ...
Note: method with signature ‘Matrix#matrix’ chosen for function ‘-’,
 target signature ‘ddiMatrix#matrix’.
 "ddiMatrix#ANY" would also be valid

 *** caught segfault ***
address 0x7ffefe409dc8, cause 'memory not mapped'

Traceback:
 1: E %*% K %*% E
 2: E %*% K %*% E
 3: calc.diffusion.kernel(method = "diffKernelLLE", m = 5, normalization.method = "sqrt",     DIR = "/tmp")


"

Could this be a bug?

many thanks

 

 

 

software error bug go.db • 706 views
ADD COMMENTlink modified 4.3 years ago by Hervé Pagès ♦♦ 14k • written 4.3 years ago by lejeczek0
Answer: GO.db/GOSim bugged or my bad?
0
gravatar for Hervé Pagès
4.3 years ago by
Hervé Pagès ♦♦ 14k
United States
Hervé Pagès ♦♦ 14k wrote:

Hi peljasz,

When misused, software is expected to either (from best to worse): (a) raise an error, (b) raise a warning, or (c) silently return a wrong result. But not to crash. So yes, clearly a bug. I tried to reproduce this but the call to calc.diffusion.kernel() is still running after 10 minutes...

No answer from the maintainer of GOSim so far. Maybe it would have helped if you had included the gosim tag to your post as it was suggested to you when you filled the Post Form. Anyway, you might have better luck trying to contact the maintainer directly:

> maintainer("GOSim")
[1] "Holger Froehlich <frohlich@bit.uni-bonn.de>"

Don't forget to provide the output of your sessionInfo() (call it right before you call the command causing the crash i.e. calc.diffusion.kernel in your case).

H.

ADD COMMENTlink modified 4.3 years ago • written 4.3 years ago by Hervé Pagès ♦♦ 14k
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