[Rd] Cluster: Various GCC, how important is consistency?

On a cluster that is based on RedHat 6.2, we are updating to R-3.3.1. I have, from time to time, run into problems with various R packages and some older versions of GCC. I wish we had newer Linux in the cluster, but with 1000s of nodes running 1000s of jobs, well, they don't want a restart.

Re: [Rd] Cluster: Various GCC, how important is consistency?

There are many issues with different gcc versions, but they can at least be minimized by using static linking, i.e. you should at the very least use -static-libstdc++ -static-libgcc to make sure you don't mix runtime versions. We run into the same problem since C++11 compilers are rare on

Re: [Rd] Cluster: Various GCC, how important is consistency?

This absolutely causes it's own problems (and they may be bad enough that you shouldnt do it) but you can also install an older version of rcpparmadillo. My switchr package makes this more convenient from within r but grabbing tarballs from the crank Web archive also works (in fact that's what

Re: [R-pkg-devel] using optimx in a package

You are calling an optimizer that wants gradients without specifying the gradient method. I've not done any work on optimx for a couple of years -- on R-forge I've put optimrx which has a more maintainable design and allows more solvers to be called using the optim() syntax, including parameter

[R-pkg-devel] Makevar file issue.

Dear R package developers, I have developed an R package and its working locally on my system ( mac os x El Capitan, Xcode 7, gfortran 6.1) with ~/.R/Makevars. The Makevar file in the home directory contains: F77 = gfortran FC = gfortran FLIBS = -L/usr/local/gfortran/lib Now I'm trying

Re: [Bioc-devel] A bug in TxDb.Hsapiens.UCSC.hg38.knownGene?

Hi Shilin, I answered this on the support site: https://support.bioconductor.org/p/88232/#88347 Cheers, H. On 10/16/2016 08:35 PM, zhao shilin wrote: Dear BioC team, I think I found something incorrect in TxDb.Hsapiens.UCSC.hg38.knownGene, and reported in

Re: [Bioc-devel] BioC 3.4: several package failures traceable to vsn req. R >= 3.4.0?

Hi all, I would like to add also metaseqR in the list of packages failing to build in malbec1 and morelia because of vsn. What would be the most appropriate course of action for the maintainers? Wait for vsn to be correctly built? Best regards, Panagiotis On 10/17/2016 11:34 AM, Ramon

Re: [Bioc-devel] BioC 3.4: several package failures traceable to vsn req. R >= 3.4.0?

Hi Ramon, Yes the issue is known. The vsn maintainers have fixed the problem yesterday in svn, right before the builds started. All the failures due to vsn not installing on the build machines should be gone in today's report. Cheers, H. On 10/17/2016 01:34 AM, Ramon Diaz-Uriarte wrote: Dear

[Bioc-devel] BioC 3.4: several package failures traceable to vsn req. R >= 3.4.0?

Dear All, Several packages (at least ADaCGH2, snapCGH, tilingArray, cellHTS2) are now (last 24 to 48 hours?) failing to build in BioC 3.4 in Linux (malbec1) and Mac OSX (morelia). Looking at the error reports they seem to be due to vsn not being available. Checking the vsn report

[Bioc-devel] Bioconductor 3.4 branch to be created in about 1 hour - do not commit during this time

Hello BioC developers, We will be creating the Bioconductor 3.4 branch today in about one hour (around 2:30pm EST). Please stop all commits to trunk before 2:30pm EST (18:30 UTC) and do not resume until further notice. We will send another email when it is OK to resume commits. The process

Re: [Bioc-devel] A bug in TxDb.Hsapiens.UCSC.hg38.knownGene?

Thanks Hervé! 2016-10-17 2:18 GMT-05:00 Hervé Pagès : > Hi Shilin, > > I answered this on the support site: > > https://support.bioconductor.org/p/88232/#88347 > > Cheers, > H. > > > On 10/16/2016 08:35 PM, zhao shilin wrote: > >> Dear BioC team, >> >> I think I found

[Bioc-devel] 3.4 branch created in svn

The BioC 3.4 branch is now ready. Remember, you always have access to 2 versions of your package in svn: the "release" and "devel" versions. Right now the "release" version of your package (which is not officially released yet but will be tomorrow if everything goes well) is in the 3.4 branch