User: Atro Tossavainen

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Posts by Atro Tossavainen

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Comment: C: Network install of packages
... > Has anyone done any benchmarking on accessing the annotation packages > over a network vs. a local drive? I can image (guess) that for some > annotation packages that are frequently used, it may pay of to have > the on a local drive, especially the SQLite based ones. Correct me if &g ...
written 10.7 years ago by Atro Tossavainen160
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Comment: C: Building BioC 2.2 with R 2.7.0
... Robert, > Thanks for all your efforts in trouble shooting. If I understand, > the GO issue is now resolved but genefilter is still problematic. Yes indeed. > Could you try using gcc to compile rather than sunperf? As the Bioconductor packages are built with whatever was used to c ...
written 11.2 years ago by Atro Tossavainen160
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Comment: C: Building BioC 2.2 with R 2.7.0
... Here's the line that generated genefilter.so: (I'm using Sun's Studio 11 compilers and enabled the use of the sunperf library while building R.) CC -G -o genefilter.so half_range_mode.o init.o nd.o pAUC.o rowPAUCs.o rowttests.o ttest.o -R/opt/SUNWspro/lib/v8plus:/opt/SUNWspro/lib:/opt/ SUNWspro/li ...
written 11.2 years ago by Atro Tossavainen160
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Comment: C: Building BioC 2.2 with R 2.7.0
... > I encountered the same problem with genefilter. Genefilter depends on > tkWidgets which in turn depends on access to the x-server (stupid, but > this is true for several Bioconductor packages now; it's rather annoying). > So: use the xhost command to properly arrange your X display pro ...
written 11.2 years ago by Atro Tossavainen160
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Comment: C: Building BioC 2.2 with R 2.7.0
... Thanks all for your help so far. > My guess is that Kasper is pretty close, but that the real culprit is > RSQLite. But without a complete log of what did and did not install we > won't know. > > So, if you could, please try > library(RSQLite) Loading RSQLite on both Sola ...
written 11.2 years ago by Atro Tossavainen160
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Building BioC 2.2 with R 2.7.0
... I've successfully built R 2.7.0 for x86 Linux (RHEL4), x86_64 Linux (RHEL4), Solaris 8 SPARC and IRIX 6.5. The Bioconductor installation process works fine on x86_64 Linux and IRIX. Building annaffy fails on x86 Linux, and building annaffy and simpleaffy fail on Solaris 8. In both cases, the anna ...
go annaffy simpleaffy written 11.2 years ago by Atro Tossavainen160 • updated 11.2 years ago by Groot, Philip de630
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Comment: C: Installation on a cluster
... Sean Davis wrote: > I agree that I/O can be an issue. There are file systems that are > specifically designed with some of these issues in mind (see AFS, as > an example). In most use cases of AFS, the cluster nodes would not see AFS any more than any other part of the public Internet. ...
written 11.3 years ago by Atro Tossavainen160
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Comment: C: R help with large matrices
... Ian, >> Unless you have a pretty big machine, you will probably not be able to >> fit a 19,300 x 19,300 member matrix into memory. > > The work is being undertaken on CamGrid. > http://www.escience.cam.ac.uk/projects/camgrid/ The problem is if you can't split the task, which y ...
written 11.3 years ago by Atro Tossavainen160
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Comment: C: Running Pumacomb on both cores of dual-core machine
... > makeCluster is a function from the snow package, and I also can't find > much information about setting up "socket" clusters. However, I think > the fundamental problem here is that you can't ssh to localhost without > a password. Of course this begs the question of why does one need ...
written 11.4 years ago by Atro Tossavainen160
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Comment: C: Wannt new PPorshe or BMW?
... > Are you serious? I think the bigger issue is that the Bioconductor list has recently been seeing a fairly large amount of mails that the filters at phil*.ethz.ch have analysed as spam but nonetheless allowed to pass through. Has something changed @ ETH? In the list configuration perhaps? -- ...
written 11.6 years ago by Atro Tossavainen160

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