Re: [Rd] Fresh build from source of R-3.2.5 failing "make check" under 64-bit Ubuntu [SOLVED]

Testing for an NFS effect on the failure of 'make check': Try first on /usr/local/ 9:42cd /usr/local/src/ 9:42sudo mkdir R 9:43 sudo chown mdalphin:mdalphin R 9:43 cd R 9:43 gunzip -c /opt/apps/x86_64/R/Archive/R-3.2.5.tar.gz | tar xf -

Re: [Bioc-devel] linking stage excessive runtime issue on windows (was: New package submission)

Great! Thank you. Tom On Thu, Apr 21, 2016 at 9:41 PM, Dan Tenenbaum wrote: > > > - Original Message - > > From: "Thomas Lawson" > > To: "Dan Tenenbaum" > > Cc: "Steffen Neumann" ,

Re: [Bioc-devel] linking stage excessive runtime issue on windows (was: New package submission)

- Original Message - > From: "Thomas Lawson" > To: "Dan Tenenbaum" > Cc: "Steffen Neumann" , "bioc-devel" > > Sent: Thursday, April 21, 2016 1:37:15 PM > Subject: Re: [Bioc-devel]

Re: [Bioc-devel] linking stage excessive runtime issue on windows (was: New package submission)

Hi Steffen/Dan Thank you both for your quick responses and help. I have just submitted another job and it looks like moscato2 is passing now. Which is great! However, I am now missing the mac morelia build completely, which is a bit strange -

Re: [Rd] locked environments

Ideally they should all work. What is happening is that the current implementation of complex assignment wants to use a temporary variable named *tmp*, which it can't when the evaluation environment is locked. Assignments in compiled code use a different mechanism that I hope will eventually be

Re: [Rd] "cophenetic" function for objects of class "dendrogram"

Note that cophenetic.default (which works on the output of hclust(dist(X))) uses the row names of X as labels. as.dendrogram.hclust does not retain those row names so cophenetic.dendrogram cannot use them (so it orders them based on the topology of the dendrogram). Bill Dunlap TIBCO Software

Re: [Bioc-devel] linking stage excessive runtime issue on windows (was: New package submission)

- Original Message - > From: "Steffen Neumann" > To: "Thomas Lawson" , "bioc-devel" > > Sent: Thursday, April 21, 2016 7:29:50 AM > Subject: Re: [Bioc-devel] linking stage excessive runtime issue on

Re: [Rd] "cophenetic" function for objects of class "dendrogram"

I think the results differ only in the order of the labels. The following function puts the labels in a standard order and then the results are the same: canonicalize.dist <- function (distObject) { o <- order(labels(distObject)) as.matrix(distObject)[o, o, drop = FALSE] }

Re: [Bioc-devel] linking stage excessive runtime issue on windows (was: New package submission)

Hi Thomas,  mzR has been in stormy waters since the new Windows toolchain  was used. While now all compile errors are gone: http://bioconductor.org/checkResults/devel/bioc-LATEST/mzR/ The build still timeouts on windows, because for reasons completely  unknown to me the linking step into mzR.dll

[Bioc-devel] New package submission

Hi BioConductor community, I have recently submitted my new R package into BioConductor tracker (issue 1455) that carries out some data pre-processing for MS/MS spectra. I seem to be having trouble with the moscato2 Windows build though. The package is fine on Linux and Mac but I get an error

Re: [Bioc-devel] Bioc-devel Digest, Vol 145, Issue 60

On 04/20/2016 11:15 PM, Aedin Culhane wrote: Hi Vince Agreed, I agree fData is over-simplification. But if data have an associated "annotation", the feature annotation associated with it should be available. I was recently trying to map between one of the hugene st1.0 and primeview arrays.

Re: [Rd] Fresh build from source of R-3.2.5 failing "make check" under 64-bit Ubuntu

Hmm. I don't think this has been seen by other Ubuntu users, or other Linuxen for that matter. You have a gratuitous use of "&", but I don't really see how that would give these symptoms, unless you accidentally run a command twice, creating a race condition between two background processes.

[Rd] "cophenetic" function for objects of class "dendrogram"

Hello, I have been using the "cophenetic" function for objects of class "dendrogram" and I have realised that it gives different results when it is used with objects of class "hclust". For instance, running the first example in the help file of the "cophenetic" function, d1 <-

Re: [Rd] Benchmarks for R

make check-all ? On 21 Apr 2016, at 10:23 , Francisco Banha wrote: > Hello, > > I'm currently working on a project where I have to make chages to the source > code of R itself. By doing this it's possible that I mess something up and > make R stop working

[Rd] Benchmarks for R

Hello, I'm currently working on a project where I have to make chages to the source code of R itself. By doing this it's possible that I mess something up and make R stop working correctly. Can anyone tell me if there are some benchmarks that test the whole R language or at least the most