Am Dienstag, 25. April 2017, 08:50:34 schrieb Dirk Eddelbuettel:> On 25 April 2017 at 14:58, G?ran Brostr?m wrote: > | hello, > | > | I just installed R-3.4.0 from scratch: > | > | $ sudo apt install r-base > | > | but when I try > | > | > library(survival, lib.loc = "/usr/lib/R/library") > | > fit <- coxph(Surv(exit, event) ~ x, data = mort) > | > | I get > | > | Error in fitter(X, Y, strats, offset, init, control, weights = weights, : > | object 'Ccoxmart' not foundThis looks similar to what I got this morning when I tested my (unreleased) backport of R 3.4.0 to Debian jessie. My test was library(MASS) example(rlm) and there was an object that was not found. I am on a train on the way to a meeting right now, so I can not look into it at the moment. Maybe a side effect of the new registration requirements for compiled objects? Cheers, Johannes
On 2017-04-25 16:11, Johannes Ranke wrote:> Am Dienstag, 25. April 2017, 08:50:34 schrieb Dirk Eddelbuettel: >> On 25 April 2017 at 14:58, G?ran Brostr?m wrote: >> | hello, >> | >> | I just installed R-3.4.0 from scratch: >> | >> | $ sudo apt install r-base >> | >> | but when I try >> | >> | > library(survival, lib.loc = "/usr/lib/R/library") >> | > fit <- coxph(Surv(exit, event) ~ x, data = mort) >> | >> | I get >> | >> | Error in fitter(X, Y, strats, offset, init, control, weights = weights, : >> | object 'Ccoxmart' not found > > This looks similar to what I got this morning when I tested my (unreleased) > backport of R 3.4.0 to Debian jessie. My test was > > library(MASS) > example(rlm) > > and there was an object that was not found. I am on a train on the way to a > meeting right now, so I can not look into it at the moment. Maybe a side effect > of the new registration requirements for compiled objects?Right, you need to run > update.packages(checkBuilt=TRUE) to fix it. Best, G?ran> > > Cheers, > > Johannes >
On 25 April 2017 at 16:11, Johannes Ranke wrote: | This looks similar to what I got this morning when I tested my (unreleased) | backport of R 3.4.0 to Debian jessie. My test was | | library(MASS) | example(rlm) | | and there was an object that was not found. I am on a train on the way to a | meeting right now, so I can not look into it at the moment. Maybe a side effect | of the new registration requirements for compiled objects? I doubt that as it works for me under R 3.4.0 on a current-ish Ubuntu 16.10 box. Dirk -- http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org
> >> | > library(survival, lib.loc = "/usr/lib/R/library") > >> | > fit <- coxph(Surv(exit, event) ~ x, data = mort) > >> | > >> | I get > >> | > >> | Error in fitter(X, Y, strats, offset, init, control, weights = weights,:> >> | object 'Ccoxmart' not found > > > > This looks similar to what I got this morning when I tested my > > (unreleased) > > backport of R 3.4.0 to Debian jessie. My test was > > > > library(MASS) > > example(rlm) > > > > and there was an object that was not found. I am on a train on the way to > > a > > meeting right now, so I can not look into it at the moment. Maybe a side > > effect of the new registration requirements for compiled objects? > > Right, you need to run > > > update.packages(checkBuilt=TRUE) > > to fix it. > > Best, G?ran > > > Cheers, > > > > Johannes-- PD Dr. Johannes Ranke Wissenschaftlicher Berater Kronacher Str. 12 79639 Grenzach-Wyhlen http://jrwb.de/contact
Am Dienstag, 25. April 2017, 11:21:31 schrieb Dirk Eddelbuettel:> On 25 April 2017 at 16:11, Johannes Ranke wrote: > | This looks similar to what I got this morning when I tested my > | (unreleased) > | backport of R 3.4.0 to Debian jessie. My test was > | > | library(MASS) > | example(rlm) > | > | and there was an object that was not found. I am on a train on the way to > | a > | meeting right now, so I can not look into it at the moment. Maybe a side > | effect of the new registration requirements for compiled objects? > > I doubt that as it works for me under R 3.4.0 on a current-ish Ubuntu 16.10 > box.This is because the version of MASS in sid (r-cran-mass) was released on 21 April https://packages.qa.debian.org/r/r-cran-mass.html which is the same day when r-base was released for R 3.4.0, so MASS was obviously built against the current version. I just tried r-cran-spatial on a **fresh Debian sid chroot**, and get> library(spatial) > example(surf.gls)srf.gl> library(MASS) # for eqscplot srf.gl> data(topo, package="MASS") srf.gl> topo.kr <- surf.gls(2, expcov, topo, d=0.7) Error in surf.gls(2, expcov, topo, d = 0.7) : object 'VR_frset' not found so it seems to me this must affect all packages in Debian sid that were built before the release of R 3.4.0! And in fact, nlme, is affected as well:> library(nlme) > example(nlme)nlme> fm1 <- nlme(height ~ SSasymp(age, Asym, R0, lrc), nlme+ data = Loblolly, nlme+ fixed = Asym + R0 + lrc ~ 1, nlme+ random = Asym ~ 1, nlme+ start = c(Asym = 103, R0 = -8.5, lrc = -3.3)) Error in pdFactor.pdLogChol(X[[i]], ...) : object 'logChol_pd' not found So before I start spamming the Debian BTS, what would be the right way to deal with this? Do we need r-api-x here? Cheers, Johannes P.S.: Sorry of the other post, I pressed send before typing and even before thinking ...