Hi,

I've optimized the code for the next release.

If you would like to have a try, please install GOSemSim (version >= 1.5.3)
and re-run your script.

You can use the following command to install the devel version of BioC:

install.packages("GOSemSim", repos = "
http://www.bioconductor.org/packages/devel/bioc")

This devel version of GOSemSim will officially release in Oct 2 within BioC
2.11 release.

Bests,
Guangchuang Yu
--~--~---------~--~----~------------~-------~--~----~
Department of Biochemistry & Molecular Biology
College of Life Science and Technology
Jinan University, 601 Huangpu Ave. W.
Guangzhou 510632,  P.R. China
Tel: +86-20-85222677
Email: guangchuangyu@gmail.com
          guangchuangyu@jnu.edu.cn
Publications: http://bit.ly/IpzxpH
-~----------~----~----~----~------~----~------~--~---


On Wed, Aug 22, 2012 at 6:35 PM, Sandeep Amberkar [guest] <
guest@bioconductor.org> wrote:

>
> Dear All,
>
> I am using GOSemSim package to calculate semantic similarity of genes
> within a cluster, for all clusters derived from a clustering algorithm. I
> use the mgeneSim function to carry out these calculations. The function
> works fine for GO.MF and GO.CC ontologies but it seems to fail for GO.BP.
> When given a list of Entrez identifiers, the function seems to be stuck for
> a long time, thus requiring the R session to be terminated. No warning or
> error messages are produced. I don't seem to understand this behaviour of
> this function for GO.BP.. What could be wrong here? I would appreciate any
> help in this regard. Thanks a lot in advance.
>
> Please find attached sample Entrez IDs used for the calculation and my R
> session info.
>
>  -- output of sessionInfo():
>
> Entrez ids =
> 1132,1147,1326,1540,1654,1831,1917,2058,2289,3301,3305,3310,3312,3313,3320,3326,3376,3476,3551,4790,4791,4792,4793,4794,5151,5495,5537,5646,5917,5966,5970,5971,5977,6885,7098,7128,7132,7185,7278,7763,8517,8518,8717,8737,8767,8915,9020,9253,9532,9701,9755,10010,10293,10318,10382,10454,10758,10848,10892,11035,11140,22870,23085,23118,23243,23291,23474,26133,26610,28511,28512,29110,29775,54765,55140,55250,55291,55728,57805,64170,64332,64343,79092,79155,81030,84433,89891,92609,113457,136319,148022,150684,203068,257397,347733,387521,387522
>
> OS -- opensuse 12.1
> > sessionInfo()
> R version 2.15.1 (2012-06-22)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
>  [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C
> LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8
>  [5] LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.UTF-8    LC_PAPER=C
>             LC_NAME=C
>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
> LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] org.Hs.eg.db_2.7.1   igraph_0.6-2         GOSemSim_1.14.0
>  BiocInstaller_1.4.7  AnnotationDbi_1.18.1
> [6] Biobase_2.16.0       BiocGenerics_0.2.0   RSQLite_0.11.1
> DBI_0.2-5
>
> loaded via a namespace (and not attached):
> [1] GO.db_2.7.1    IRanges_1.14.4 stats4_2.15.1  tools_2.15.1
>
> --
> Sent via the guest posting facility at bioconductor.org.
>

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