[BioC] hcluster crashes R environment

Henrique Proença henrique at est.ipcb.pt
Wed Jul 2 16:40:58 CEST 2008


Thanks for your quickly answer, and for your advice.
The info of my system is:

R version 2.7.0 (2008-04-22)

attached base packages:
[1] tools     stats     graphics  grDevices utils     datasets  methods
[8] base

other attached packages:
[1] amap_0.8-2    Biobase_2.0.1

Henrique Proença

Vincent Carey 525-2265 wrote:
>> Hello,
>> I am trying to apply the function "hcluster" (contained within the
>> "amap" package) to data matrix with no variability between its columns.
>> The example I am using is:
>>   x <- data.frame(col1=c(20,30,45,7,6,5,4,3),col2=c(20,30,45,7,6,5,4,3),
>> stringsAsFactors=FALSE)
>>   hcluster(x, method="correlation", link = "complete")
>> In this case, the error generated is fatal and the application (R
>> environment) stops completely (crashes) without any control of the
>> error. I do understand it in the way one can not apply the correlation
>> to a vector with no variability, but in the following case:
> I can confirm this on R 2.7.0 for macosx; you did not tell us the platform
> you are using; please read the posting guide and supply sessionInfo()
> for such queries.
> amap is contributed by Antoine Lucas, as noted on the CRAN distribution
> point, please notify him.  Clearly there is inadequate error management
> through his call to .C. (Developers are encouraged to use .Call instead.)
>>   x <- data.frame(col1=c(20,30,45,7,6,5,4,3),col2=c(20,30,45,7,6,5,7,7),
>> stringsAsFactors=FALSE)
>>   hcluster(x, method="correlation", link = "complete")
>> There are rows without variability, and others (last two rows)
>> containing some. When I use this example, the R environment does not
>> crash. So, my question is: Why the "hcluster" funcions generates this
>> fatal error when no variability is found in all the matrix rows ?
>> Thanks in advance
>> --
>> Regards
>> Henrique Proen�a
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at stat.math.ethz.ch
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>> ------------------------------------------------------------------------
>> The information transmitted in this electronic communication is intended only
>> for the person or entity to whom it is addressed and may contain confidential
>> and/or privileged material. Any review, retransmission, dissemination or other
>> use of or taking of any action in reliance upon this information by persons or
>> entities other than the intended recipient is prohibited. If you received this
>> information in error, please contact the Compliance HelpLine at 800-856-1983 and
>> properly dispose of this information.

More information about the Bioconductor mailing list