On 10/25/2010 01:40 AM, Alberto Goldoni wrote: > Yes i use the version 2.2.0 but with revolution R... > > So when i type "R" the system doesn't load "R base", but the > "revolution-r" version 3.0.0 that is the last release on ubuntu 10.04 > 64 bit. > > Please try to re-run you analysis with revolution-r and tell me if in > your computer all works fine. Hi Alberto -- I believe that Revolution R lags release R at least by months, perhaps longer; please correct me if I am wrong. Use a current R with current Bioconductor packages, or seek technical support from Revolution. Martin > > Best regards. > > 2010/10/25 Richard Pearson <richard.pearson at="" well.ox.ac.uk="">: >> Hi Alberto >> >> I have just run this same command, also on 64 bit ubuntu, with no problems. >> I think you didn't paste the full output of sessionInfo() - e.g. there are >> no attached packages shown. You do have version 2.2.0 of puma, right? >> >> Here's my full sessionInfo: >> >>> sessionInfo() >> R version 2.12.0 (2010-10-15) >> 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 LC_MONETARY=C >> LC_MESSAGES=en_GB.UTF-8 LC_PAPER=en_GB.UTF-8 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 datasets grid utils methods >> base >> >> other attached packages: >> [1] pumadata_1.0.3 puma_2.2.0 mclust_3.4.6 affy_1.28.0 >> Biobase_2.10.0 xtable_1.5-6 ggplot2_0.8.8 proto_0.3-8 reshape_0.8.3 >> plyr_1.2.1 t2d_0.0.1 GWAS_0.0.1 abind_1.1-0 >> >> loaded via a namespace (and not attached): >> [1] affyio_1.18.0 preprocessCore_1.12.0 tools_2.12.0 >> >> Best wishes >> >> Richard >> >> On 21/10/2010 09:02, Alberto Goldoni wrote: >>> >>> sorry i forget >>> >>> my sessionInfo >>> >>>> sessionInfo() >>> >>> R version 2.12.0 (2010-10-15) >>> Platform: x86_64-pc-linux-gnu (64-bit) >>> >>> locale: >>> [1] LC_CTYPE=en_US.utf8 LC_NUMERIC=C >>> [3] LC_TIME=en_US.utf8 LC_COLLATE=en_US.utf8 >>> [5] LC_MONETARY=C LC_MESSAGES=en_US.utf8 >>> [7] LC_PAPER=en_US.utf8 LC_NAME=C >>> [9] LC_ADDRESS=C LC_TELEPHONE=C >>> [11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C >>> >>> attached base packages: >>> [1] stats graphics grDevices utils datasets methods base >>> >>> ---------- Forwarded message ---------- >>> From: Alberto Goldoni<alberto.goldoni1975 at="" gmail.com=""> >>> Date: 2010/10/21 >>> Subject: *** caught segfault *** ....cause 'invalid permissions' with >>> PUMA pachage >>> To: BioC<bioconductor at="" stat.math.ethz.ch=""> >>> >>> >>> Dear all, >>> today i have installed "puma" package in my second computer with >>> ubuntu 64 bit and when i try to run this command: >>> >>> eset_estrogen_mmgmos<- mmgmos(affybatch.estrogen, gsnorm="none") >>> >>> it return this error: >>> >>> Model optimising >>> *** caught segfault *** >>> address 0x7f307c7102ec, cause 'invalid permissions' >>> >>> Traceback: >>> 1: .Call("mmgmos_c", pm(object), mm(object), genes, >>> probeNames(object), phis, prctiles, length(prctiles), savepar, >>> eps, PACKAGE = "puma") >>> 2: mmgmos(data, gsnorm = "none") >>> >>> Possible actions: >>> 1: abort (with core dump, if enabled) >>> 2: normal R exit >>> 3: exit R without saving workspace >>> 4: exit R saving workspace >>> >>> IT'S VERY STRANGE!!!!! because yesterday with the other computer with >>> ubuntu 32 bit puma was able to perform this type of calculation... >>> >>> it seems an error due to the R 64 bit version.... >>> >>> someone can help me because in internet i was not able to find a trick! >>> >>> best regards >>> >>> -- >>> ----------------------------------------------------- >>> Dr. Alberto Goldoni >>> Parma, Italy >>> ----------------------------------------------------- >>> >>> >>> >> >> -- >> Dr Richard D Pearson richard.pearson at well.ox.ac.uk >> Wellcome Trust Centre for Human Genetics >> http://www.well.ox.ac.uk/~rpearson >> University of Oxford Tel: +44 (0)1865 617890 >> Roosevelt Drive Mob: +44 (0)7971 221181 >> Oxford OX3 7BN, UK Fax: +44 (0)1865 287664 >> > > > -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793