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...] lattice_0.18-5 custom_1.1 loaded via a namespace (and not attached): [1] grid_2.11.0 -- Nicolas STRANSKY, Ph.D. Computational Biologist, Cancer Program Broad Institute of MIT and Harvard 5CC-1339 | 7 Cambridge Center | Cambridge, MA 02142, USA Phone: +1 617 714 7564 | nico at BroadInstitute.org

CentOS, I'm not sure where to ask this, please let me know if there is a more appropriate place. On CentOS 7, I'm building a large C++ package with rpmbuild. Arachne (https://www.broadinstitute.org/crd/wiki/index.php/Arachne_Main_Page). During the debuginfo extraction stage, I get the following error: + /usr/lib/rpm/find-debuginfo.sh --strict-build-id -m --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 110000000 /home/andrew/rpmbuild/BUILD/arachne-46233 dwz: Multifile te...

Am 21.08.2015 um 21:08 schrieb ????????? ???????? <nevis2us at infoline.su>: >> On CentOS 7, I'm building a large C++ package with rpmbuild. Arachne >> (https://www.broadinstitute.org/crd/wiki/index.php/Arachne_Main_Page). >> During the debuginfo extraction stage, I get the following error: >> + /usr/lib/rpm/find-debuginfo.sh --strict-build-id -m --run-dwz >> --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 110000000 >> /home/andrew/rpmbuild/BUILD...

...to distribute, but which the user can easily download manually. Moreover, it is not possible to download this file automatically from R: downloading requires a (free) registration that seems to work only through a browser. (I'm talking here about the MSigDB from the Broad Institute, http://www.broadinstitute.org/gsea/msigdb/index.jsp). In the vignette, I tell the user to download the file and then show how it can be parsed and used in R. Thus, I can compile the vignette only if this file is present in the vignettes/ directory of the package. However, it would then get included in the package -- which...

...an easily download manually. Moreover, it >> is not possible to download this file automatically from R: downloading >> requires a (free) registration that seems to work only through a browser. >> (I'm talking here about the MSigDB from the Broad Institute, >> http://www.broadinstitute.org/gsea/msigdb/index.jsp). >> >> In the vignette, I tell the user to download the file and then show how it >> can be parsed and used in R. Thus, I can compile the vignette only if this >> file is present in the vignettes/ directory of the package. However, it >> woul...

> On CentOS 7, I'm building a large C++ package with rpmbuild. Arachne > (https://www.broadinstitute.org/crd/wiki/index.php/Arachne_Main_Page). > > During the debuginfo extraction stage, I get the following error: > > + /usr/lib/rpm/find-debuginfo.sh --strict-build-id -m --run-dwz > --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 110000000 > /home/andrew/rpmbuild/BUILD/ara...

On 08/21/2015 02:04 PM, Leon Fauster wrote: > Am 21.08.2015 um 21:08 schrieb ????????? ???????? <nevis2us at infoline.su>: >>> On CentOS 7, I'm building a large C++ package with rpmbuild. Arachne >>> (https://www.broadinstitute.org/crd/wiki/index.php/Arachne_Main_Page). >>> During the debuginfo extraction stage, I get the following error: >>> + /usr/lib/rpm/find-debuginfo.sh --strict-build-id -m --run-dwz >>> --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 110000000 >>> /home/andre...

...which the user can easily download manually. Moreover, it > is not possible to download this file automatically from R: downloading > requires a (free) registration that seems to work only through a browser. > (I'm talking here about the MSigDB from the Broad Institute, > http://www.broadinstitute.org/gsea/msigdb/index.jsp). > > In the vignette, I tell the user to download the file and then show how it > can be parsed and used in R. Thus, I can compile the vignette only if this > file is present in the vignettes/ directory of the package. However, it > would then get included...

...8/15 22:46, Andrew Neuschwander wrote: > On 08/21/2015 02:04 PM, Leon Fauster wrote: >> Am 21.08.2015 um 21:08 schrieb ????????? ???????? <nevis2us at infoline.su>: >>>> On CentOS 7, I'm building a large C++ package with rpmbuild. Arachne >>>> (https://www.broadinstitute.org/crd/wiki/index.php/Arachne_Main_Page). >>>> During the debuginfo extraction stage, I get the following error: >>>> + /usr/lib/rpm/find-debuginfo.sh --strict-build-id -m --run-dwz >>>> --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 110000000 >>>...

...===================================================================================| 100% Starting to add information to samples => Add clinical information to samples Add FFPE information. More information at: => https://cancergenome.nih.gov/cancersselected/biospeccriteria => http://gdac.broadinstitute.org/runs/sampleReports/latest/FPPP_FFPE_Cases.html => Adding subtype information to samples luad subtype information from:doi:10.1038/nature13385 Request to BioMart web service failed. The BioMart web service you're accessing may be down. Check the following URL and see if this website is a...

Is there any way to force a slice of a matrix to stay a matrix? R tends to convert a single row of a matrix into a vector. Example: z<-matrix (rnorm(20), ncol=5) zz<-z[1,] is.matrix(zz) #FALSE I usually resort to: zz<-matrix(z[1,], ncol=dim(z)[2], dimnames=list(rownames(z)[1], colnames(z))) But that seems horribly kludgy. Thanks! -Jim

Hi all, I have a rather peculiar dataset that I'm not sure how to model properly. This is data from an instrument that measures the size of particles but instead of giving a continuous value, it generates a "histogram" of the counts for a particular bin size. So the data looks like this: Condition 1 Condition 2 Dimension Rep1.A Rep1.B

Hello, I am working from a linux 64 machine on a server with R-2.12 (I can't update to 2.13). I am iterating through many linear mixed models for longitudinal data and I occasionally receive the following convergence error: > BI.lme <- lme(cd4 ~ time + genBI + genBI:time + C1 + C2 + C11 + C12, random =~ 1 + time | IID, data = d) Error in lme.formula(cd4 ~ time + genBI + genBI:time +