Filename seems to cause errors.

[averaart]

While running some tests, I've come across several files that make quip crash. The errors seem to be dependent on the name of the files, although I haven't been able to determine a pattern for what could cause the crash. Renaming the files works, but some names need more drastic change than others.

The crash occurs almost immediately after starting quip.

Here's the error message:

quip: malloc.c:2451: sYSMALLOc: Assertion `(old_top == (((mbinptr) (((char *) &((av)->bins[((1) - 1) * 2])) - __builtin_offsetof (struct malloc_chunk, fd)))) && old_size == 0) || ((unsigned long) (old_size) >= (unsigned long)((((__builtin_offsetof (struct malloc_chunk, fd_nextsize))+((2 * (sizeof(size_t))) - 1)) & ~((2 * (sizeof(size_t))) - 1))) && ((old_top)->size & 0x1) && ((unsigned long)old_end & pagemask) == 0)' failed.

The tests were conducted on a Dell Precision M6600 with an Intel® Core™ i5-2520M CPU @ 2.50GHz and 4GB of system memory. The operating system was Ubuntu 12.04.2 LTS, configured with a 4GB swap volume. The version of quip was 1.1.6.

These are the files that crash during compression: SRR062634_1.filt.fastq SRR062634_2.filt.fastq SRR062635_1.filt.fastq SRR062635_2.filt.fastq SRR062641_1.filt.fastq SRR062641_2.filt.fastq SRR077487_1.filt.fastq SRR077487_2.filt.fastq SRR081241_1.filt.fastq SRR081241_2.filt.fastq SRR227337_second.fastq SRR340194_second.fastq SRR353483_second.fastq wgEncodeCshlShortRnaSeqMonocd14CellTapRawDataRep2.fastq

These are publicly available files, so you should be able to download them yourself if you'd like to test any of them. The files with "_second" in their names were originally named without that string, e.g. SRR340194.fastq (they are the smallest files, so the easiest to test).

Renaming the files using these names resolved the problem: SRR0626341.fastq SRR0626342.fastq SRR0626351.fastq SRR0626352.fastq SRR0626411.fastq SRR0626412.fastq SRR0774871.fastq SRR0774872.fastq SRR0812411.fastq SRR0812412.fastq SRR227337con.fastq SRR340194con.fastq SRR353483con.fastq wgEncodeCshlShortRnaSeqMonocd14CellTapRawDataRe.fastq

Do you have any ideas on what could be causing this error?

[dcjones]

Thanks for the detailed description! I release 1.1.7 a few days ago to fix a bug that sounds like it could be this one.

Could you give that a try and see if it persists: http://homes.cs.washington.edu/~dcjones/quip/quip-1.1.7.tar.gz

[averaart]

Release 1.1.7 solves this problem.

Thanks for the quick response, and sorry I took a while to test it. I've only tried it with the smallest files, but given that file size didn't seem to influence the problem I'm convinced the new release solves it.