[BioC] GLAD crashes when built with gcc-4.8

[Martin Morgan]

If possible run as. 

  R -d valgrind -f script.R

Where script.R is the minimal commands to produce the problem ( eg no need for biocLite). Compare the output with one less than the minimal script, looking in particular for 'invalid write' errors. 

-- 
Martin Morgan

On Dec 28, 2013, at 8:32 AM, Ramon Diaz-Uriarte <rdiaz02 at gmail.com> wrote:

> 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
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor