[BioC] GLAD crashes when built with gcc-4.8

[Ramon Diaz-Uriarte]

Dear All,

At least one function (daglad) from the GLAD package crashes with a
segfault when compiled with gcc-4.8 but not with gcc-4.7. I am not sure if
this is a problem with GLAD or, more unlikely, with R. (Details below)


Has anybody seen something similar?

Best,

R.


Details:
========

- How to reproduce the error

  ## make sure you are using gcc-4.8 and g++-4.8
  biocLite("GLAD")
  library(GLAD)
  example(daglad)


- Errors: there are several; these are some

*** Error in `/home/ramon/Sources/R-3.1.0-64488/bin/exec/R': free(): invalid next size (fast): 0x0000000014144d70 ***
======= Backtrace: =========
/lib/x86_64-linux-gnu/libc.so.6(+0x7aa16)[0x7f2ff0f04a16]
/lib/x86_64-linux-gnu/libc.so.6(+0x7b793)[0x7f2ff0f05793]
/home/ramon/Sources/R-3.1.0-64488/library/GLAD/libs/GLAD.so(mad_vector_double+0x184)[0x7f2fed753bc4]


[1] "Optimization of the Breakpoints and DNA copy number calling"
*** Error in `/usr/lib/R/bin/exec/R': corrupted double-linked list: 0x00000000010f24a0 ***


 *** caught segfault ***
address 0x140000000a, cause 'memory not mapped'

Traceback:
 1: gc(FALSE)
 2: system.time(BP <- merge(BP, profileCGH$SigmaC))
 3: BkpInfo.profileCGH(profileCGH)
 4: BkpInfo(profileCGH)


- OS: Debian GNU/Linux, a mixture of testing and unstable

- version of gcc/g++: 4.8.2-1 and 4.7.3-9 (for Debian)

- version of GLAD: 2.26.0 (for R-3.0.2) and 2.27.1 (for R-3.1.0)

- versions of R: several from R-3.0.2 and R-3.1.0. For instance

  ## the current Debian version
  > version
               _                           
platform       x86_64-pc-linux-gnu         
arch           x86_64                      
os             linux-gnu                   
system         x86_64, linux-gnu           
status                                     
major          3                           
minor          0.2                         
year           2013                        
month          09                          
day            25                          
svn rev        63987                       
language       R                           
version.string R version 3.0.2 (2013-09-25)
nickname       Frisbee Sailing   

## the R-devel that seems to be used in the testing of BioC packages
> version
               _                                                 
platform       x86_64-pc-linux-gnu                               
arch           x86_64                                            
os             linux-gnu                                         
system         x86_64, linux-gnu                                 
status         Under development (unstable)                      
major          3                                                 
minor          1.0                                               
year           2013                                              
month          12                                                
day            19                                                
svn rev        64488                                             
language       R                                                 
version.string R Under development (unstable) (2013-12-19 r64488)
nickname       Unsuffered Consequences      

## the latest R-devel
> version        
               _                                                 
platform       x86_64-pc-linux-gnu                               
arch           x86_64                                            
os             linux-gnu                                         
system         x86_64, linux-gnu                                 
status         Under development (unstable)                      
major          3                                                 
minor          1.0                                               
year           2013                                              
month          12                                                
day            27                                                
svn rev        64562                                             
language       R                                                 
version.string R Under development (unstable) (2013-12-27 r64562)
nickname       Unsuffered Consequences  


- version of GSL: crashes happen with the two available versions in Debian
  for libgsl0ldbl and libgsl0-dev: 1.16+dfsg-1 and 1.15+dfsg.2-2








-- 
Ramon Diaz-Uriarte
Department of Biochemistry, Lab B-25
Facultad de Medicina 
Universidad Autónoma de Madrid 
Arzobispo Morcillo, 4
28029 Madrid
Spain

Phone: +34-91-497-2412

Email: rdiaz02 at gmail.com
       ramon.diaz at iib.uam.es

http://ligarto.org/rdiaz