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 = > 1132,1147,1326,1540,1654,1831,1917,2058,2289,3301,3305,3310,3312,331 3,3320,3326,3376,3476,3551,4790,4791,4792,4793,4794,5151,5495,5537,564 6,5917,5966,5970,5971,5977,6885,7098,7128,7132,7185,7278,7763,8517,851 8,8717,8737,8767,8915,9020,9253,9532,9701,9755,10010,10293,10318,10382 ,10454,10758,10848,10892,11035,11140,22870,23085,23118,23243,23291,234 74,26133,26610,28511,28512,29110,29775,54765,55140,55250,55291,55728,5 7805,64170,64332,64343,79092,79155,81030,84433,89891,92609,113457,1363 19,148022,150684,203068,257397,347733,387521,387522 > > 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. > [[alternative HTML version deleted]]