Bugzilla – Bug 15250
read.dcf reported correctly that it has reached its limit on long lines
Last modified: 2013-07-12 14:25:04 UTC
read.dcf() restricts it's line input to 8192 characters. Neither the Debian or the R documentation reports such limits for instance
cat("test:",paste(sample(letters,8184,TRUE),collapse=""),"\n",file="test.dcf");t <- read.dcf("test.dcf")
While this breaks
cat("test:",paste(sample(letters,8185,TRUE),collapse=""),"\n",file="test.dcf");t <- read.dcf("test.dcf")
Is that expected behavior or a bug?
It isn't a bug, but it's something that could be changed (or should be documented if it is not changed). Do you have an application where DCF files have such long lines? What is it?
Since we've heard no need for a code change, I'll document this limitation.
This message was apparently lost somehow:
On 13-04-06 10:26 AM, Blanchette, Marco wrote:
> Duncan, I did email the bug report list with my need to have read.dcf() read long line... See below. But if you feel it's not worth the effort, just document it... I have a workaround that works for now...
> [Bug 15250] read.dcf crashes on long lines
> I do. I am using H. Pages BSgenome package to read in data. His package
> uses read.dcf() to read a seed file containing chromosome names and for
> some of my applications, the field containing the chromosome names exceeds
> that limit.
I don't believe it did 'crash': it gave an informative error message, which you did not show. I have corrected the mendacious subject line.
It was fairly easy to remove this limit, so I have done so in R-devel.