[BioC] Problem running summarizeOverlaps()

[Jessica Perry Hekman]

On 05/20/2014 02:20 PM, Jessica Perry Hekman wrote:
>>> Error: C stack usage is too close to the limit

>> You might then try adding a 'yieldSize' argument to the following line,
>> starting small (e.g., 100000) and moving toward the default (1000000) if
>> the small size works when calling summarizeOverlaps, or perhaps smaller
>> if it fails.
>>
>>    bamfls <- BamFileList(fls, yieldSize=100000)

So, this is perplexing. Is 1000000 really the default? Because I can set 
yieldSize to much larger OR smaller than that and the command will 
succeed (or at least complete without errors). But when I do not specify 
yieldSize at all, there is an error!

 > bamfls <- BamFileList(fls, yieldSize=100000)
 > gnCnt <- summarizeOverlaps(exByGn, bamfls, mode="Union",
+          ignore.strand=TRUE, single.end=TRUE, param=param)
 > bamfls <- BamFileList(fls, yieldSize=500000)
 > gnCnt <- summarizeOverlaps(exByGn, bamfls, mode="Union",
+          ignore.strand=TRUE, single.end=TRUE, param=param)
 > bamfls <- BamFileList(fls, yieldSize=1000000)
 > gnCnt <- summarizeOverlaps(exByGn, bamfls, mode="Union",
+          ignore.strand=TRUE, single.end=TRUE, param=param)
 > bamfls <- BamFileList(fls, yieldSize=10000000)
 > gnCnt <- summarizeOverlaps(exByGn, bamfls, mode="Union",
+          ignore.strand=TRUE, single.end=TRUE, param=param)
 > bamfls <- BamFileList(fls, yieldSize=1000000000)
 > gnCnt <- summarizeOverlaps(exByGn, bamfls, mode="Union",
+          ignore.strand=TRUE, single.end=TRUE, param=param)


BUT:

 > bamfls <- BamFileList(fls)
 > gnCnt <- summarizeOverlaps(exByGn, bamfls, mode="Union",
+          ignore.strand=TRUE, single.end=TRUE, param=param)
Error: C stack usage is too close to the limit

?!

Jessica