Re: [Rd] R-2.15 compile error: fatal error: internal consistency failure
On 18/04/2012 00:51, Duncan Murdoch wrote: On 12-04-17 5:24 PM, andre zege wrote: I am unable to compile R-2.15.0 source. I configured it without problems with options that i used many times before ./configure --prefix=/home/andre/R-2.15.0 --enable-byte-compiled-packages=no --with-tcltk --enable-R-shlib=yes Then when i started making it, it died while making lapack, particularly on the line gfortran -fopenmp -fpic -g -O2 -c dlapack3.f -o dlapack3.o dlapack3.f: In function ‘dsbgst’: dlapack3.f:12097: fatal error: internal consistency failure compilation terminated. make[4]: *** [dlapack3.o] Error 1 Could anyone give me a clue what is going wrong and how could i fix that? I am running Centos 5.5, in particular, the following $ more /proc/version Linux version 2.6.18-194.el5 (mockbu...@builder10.centos.org) (gcc version 4.1.2 20080704 (Red Hat 4.1.2-48)) #1 SMP Fri Apr 2 14:58:14 EDT 2010 That looks like a message from your compiler. I think gcc 4.1.2 is fairly old (Windows builds are using gcc 4.6.3). Perhaps it's time to upgrade. Correct, it is very old (the date shows 2008). But then so are the lapack sources, and that file is unchanged since 2006 (and R compiled on Linux perfectly well over those years). So if R compiled on this system before, the system has changed Your first port of call is to see if there are missing patches on your OS, then report to the vendor. I might see if a lower optimization level would work. Duncan Murdoch __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel -- Brian D. Ripley, rip...@stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Method=df for coxph in survival package
In that particular example the value of "4" was pulled out of the air. There is no particular justification. There is a strong relationship between the "effective" degrees of freedom and the variance of the random effect, and I often find the df scale easier to interpret. See the Hodges and Sargent paper in Biometrika (2001) for a nice explanation of the connection in linear models. Terry T. === begin included message = I've been following the example in the R help page: http://stat.ethz.ch/R-manual/R-devel/library/survival/html/frailty.html library(survival); coxph(Surv(time, status) ~ age + frailty(inst, df=4), lung) Here, in this particular example they fixed the degrees of freedom for the random institution effects to be 4. But, how did they decide? __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] url, readLines, source behind a proxy
Hi Renaud, On Wed, Apr 18, 2012 at 12:22 AM, Renaud Gaujoux wrote: > Hi Henrik, > > > Could anybody behind a proxy check if the issue can be reproduced? > My proxy is in fact provided by cntml, which acts as a local proxy that > takes care of tricky authentication protocols with the actual university > proxy, not natively supported by my system (Ubuntu). Anybody in this case? > I can replicate this on a WinXP system, where I normally have to use the --internet2 flag to get internet access through a proxy. ?download.file has a section on "Setting Proxies", which describes how to use environment variables to set proxy information. Setting http_proxy='http://my.proxy.com/' was enough for me to get R CMD check to run successfully with the --as-cran flag. > Thanks. > Renaud > Best, -- Joshua Ulrich | FOSS Trading: www.fosstrading.com R/Finance 2012: Applied Finance with R www.RinFinance.com > On Tue, 17 Apr 2012, Henrik Bengtsson wrote: > >> On Tue, Apr 17, 2012 at 1:01 AM, Renaud Gaujoux >> wrote: >> > Hi, >> > >> > when I run R CMD check with flag --as-cran, the process hangs at stage: >> > >> > * checking CRAN incoming feasibility ... >> >> Doesn't it time-out eventually? I'm not behind a proxy but when I've >> been running 'R CMD check' whenon very poor 3G connection, it had >> eventually timed out. >> >> /Henrik >> >> > >> > I am pretty sure it is a proxy issue. >> > I looked at the check code in the tools package and it seems that the issue >> > is in the local function `.repository_db()` (defined in >> > `tools:::.check_package_CRAN_incoming()`), which eventually calls `url()` >> > with argument open="rb", that hangs probably because it does not use the >> > proxy settings. >> > I had a similar issue with `source()`, which apparently uses internal >> > network functions (not as download.file), but is supposed to work behind a >> > proxy (correct?). >> > Does anybody else have this problem? >> > >> > I was wondering if there is a way around, as I would like to be able to use >> > --as-cran for my checks. >> > Thank you. >> > >> > Renaud >> > >> > -- >> > Renaud Gaujoux >> > Computational Biology - University of Cape Town >> > South Africa >> > >> > __ >> > R-devel@r-project.org mailing list >> > https://stat.ethz.ch/mailman/listinfo/r-devel >> > > __ > R-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
