Entering edit mode
Don Maszle
▴
10
@don-maszle-3135
Last seen 10.2 years ago
I just upgraded from R-2.3.0 / BioC 2.? (Biobase version 1.10.1 from
June 2006)
to R-2.8.0 / BioC 2.3 and cannot rebuild my cdf environments for two
binary CDFs.
A number of plain text CDFs rebuilt without a problem. System
information and
a backtrace are provided below. I'm hoping that this is due to
something like
the comments in read_cdf_xda.c which foretells of a future problem.
Note, I have cleaned some names from this trace as this is a
proprietary chip
design. This of course means that I cannot pass the CDF to you for
testing,
however I am happy to do what I can on this end. The chip is an
Affymetrix
oligonucleotide array with 1.3 million features for 84000 probeset
using a
slide dimension of 1162x1162.
Please let me know what else I can provide.
Sincerely,
Don Maszle
Sr. Computational Biologist, Manager
Mendel Biotechnology, Inc.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+++++++++
# uname -a
Linux ray 2.6.9-42.ELsmp #1 SMP Wed Jul 12 23:32:02 EDT 2006 x86_64
x86_64 x86_64 GNU/Linux
# R -d gdb
GNU gdb Red Hat Linux (6.3.0.0-1.132.EL4rh)
...
This GDB was configured as "x86_64-redhat-linux-gnu"...
Using host libthread_db library "/lib64/tls/libthread_db.so.1".
(gdb) run
Starting program: /usr/local/lib64/R/bin/exec/R
R version 2.8.0 (2008-10-20)
Copyright (C) 2008 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
...
> version
_
platform x86_64-unknown-linux-gnu
arch x86_64
os linux-gnu
system x86_64, linux-gnu
status
major 2
minor 8.0
year 2008
month 10
day 20
svn rev 46754
language R
version.string R version 2.8.0 (2008-10-20)
> dirLib <- 'path-to-lib';
> dirPkg <- 'path-to-packages';
> library(makecdfenv)
Loading required package: Biobase
Loading required package: tools
...
Loading required package: affy
[Thread debugging using libthread_db enabled]
[New Thread 182895468000 (LWP 5281)]
Loading required package: affyio
> fn <- 'file.cdf';
> make.cdf.package(cdf.path=dirLib,
+ package.path=dirPkg,
+ compress=TRUE,
+ species='species',
+ filename=fn,
+ author='D.R.Maszle',
+ maintainer='D.R.Maszle <dmaszle at="" mendelbio.com="">')
*** glibc detected *** malloc(): memory corruption: 0x0000000001f9cbd0
***
Program received signal SIGABRT, Aborted.
[Switching to Thread 182895468000 (LWP 7083)]
0x00000035cdf2e21d in raise () from /lib64/tls/libc.so.6
(gdb) backtrace
#0 0x00000035cdf2e21d in raise () from /lib64/tls/libc.so.6
#1 0x00000035cdf2fa1e in abort () from /lib64/tls/libc.so.6
#2 0x00000035cdf63291 in __libc_message () from /lib64/tls/libc.so.6
#3 0x00000035cdf69881 in _int_malloc () from /lib64/tls/libc.so.6
#4 0x00000035cdf6b272 in malloc () from /lib64/tls/libc.so.6
#5 0x0000000000418748 in Rf_allocVector (type=14, length=40) at
memory.c:1999
#6 0x00000000004c5a61 in Rf_allocMatrix (mode=14, nrow=20, ncol=2)
at array.c:171
#7 0x0000002a992bdd57 in ReadCDFFile (filename=Variable "filename" is
not available.
) at read_cdf_xda.c:738
#8 0x000000000050e47a in do_dotcall (call=0x21730e0, op=Variable "op"
is not available.
) at dotcode.c:856
#9 0x000000000053b5c3 in Rf_eval (e=0x21730e0, rho=0x2174b10) at
eval.c:487
#10 0x000000000053d316 in do_set (call=0x2172220, op=0x825858,
args=0x21721e8,
rho=0x2174b10) at eval.c:1422
#11 0x000000000053b487 in Rf_eval (e=0x2172220, rho=0x2174b10) at
eval.c:461
#12 0x000000000053d39c in do_begin (call=0x2172290, op=0x825660,
args=0x2172258, rho=0x2174b10) at eval.c:1174
#13 0x000000000053b487 in Rf_eval (e=0x2172290, rho=0x2174b10) at
eval.c:461
#14 0x000000000053b487 in Rf_eval (e=0x216c268, rho=0x2174b10) at
eval.c:461
#15 0x000000000053d39c in do_begin (call=0x216b2e8, op=0x825660,
args=0x216c2a0, rho=0x2174b10) at eval.c:1174
#16 0x000000000053b487 in Rf_eval (e=0x216b2e8, rho=0x2174b10) at
eval.c:461
#17 0x000000000053ea74 in Rf_applyClosure (call=0x20efb58,
op=0x21671b8,
arglist=0x2174db0, rho=0x20f3438, suppliedenv=0x8478b0) at
eval.c:667
#18 0x000000000053b39b in Rf_eval (e=0x20efb58, rho=0x20f3438) at
eval.c:505
#19 0x000000000053d316 in do_set (call=0x20efc70, op=0x825858,
args=0x20efc38,
rho=0x20f3438) at eval.c:1422
#20 0x000000000053b487 in Rf_eval (e=0x20efc70, rho=0x20f3438) at
eval.c:461
#21 0x000000000053d39c in do_begin (call=0x20ef4e8, op=0x825660,
args=0x20efca8, rho=0x20f3438) at eval.c:1174
#22 0x000000000053b487 in Rf_eval (e=0x20ef4e8, rho=0x20f3438) at
eval.c:461
#23 0x000000000053ea74 in Rf_applyClosure (call=0x20ecf88,
op=0x20ecdc8,
arglist=0x20f2a10, rho=0x847878, suppliedenv=0x8478b0) at
eval.c:667
#24 0x000000000053b39b in Rf_eval (e=0x20ecf88, rho=0x847878) at
eval.c:505
#25 0x0000000000414109 in Rf_ReplIteration (rho=0x847878, savestack=0,
browselevel=0, state=0x7fbfffe770) at main.c:257
#26 0x0000000000414238 in R_ReplConsole (rho=0x847878, savestack=0,
browselevel=0) at main.c:306
#27 0x00000000004144e2 in run_Rmainloop () at main.c:966
#28 0x00000000004125f8 in main (ac=Variable "ac" is not available.
) at Rmain.c:33
(gdb)
