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 I was told on R-help that I need to > update.packages(checkBuilt = TRUE) (and it works), but 1. I get two versions of recommended packages, one in /usr/lib/R/library, and one in ~/R/x86_64-pc-linux-gnu-library/3.4 I could fix a write permission in /usr/lib/R or run R as root. 2. Installing from scratch should have this fixed automatically, right? Thanks, G?ran
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 | | I was told on R-help that I need to | | > update.packages(checkBuilt = TRUE) | | (and it works), but | | 1. I get two versions of recommended packages, one in | /usr/lib/R/library, and one in That is from apt / dpkg -- ie pre-packaged. | ~/R/x86_64-pc-linux-gnu-library/3.4 | I could fix a write permission in /usr/lib/R or run R as root. That is from you. The two have ALWAYS been independent. | 2. Installing from scratch should have this fixed automatically, right? False. Dirk -- http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org
On 2017-04-25 15:50, Dirk Eddelbuettel wrote:> > 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 > | > | I was told on R-help that I need to > | > | > update.packages(checkBuilt = TRUE) > | > | (and it works), but > | > | 1. I get two versions of recommended packages, one in > | /usr/lib/R/library, and one in > > That is from apt / dpkg -- ie pre-packaged. > > | ~/R/x86_64-pc-linux-gnu-library/3.4 > | I could fix a write permission in /usr/lib/R or run R as root. > > That is from you. > > The two have ALWAYS been independent.I understand that, but what is then the best practice to avoid having duplicates of the recommended packages? I tried running R as root and > update.packages(checkBuilt=TRUE) --- Please select a CRAN mirror for use in this session --- Warning: package 'class' in library '/usr/lib/R/library' will not be updated Warning: package 'cluster' in library '/usr/lib/R/library' will not be updated Warning: package 'codetools' in library '/usr/lib/R/library' will not be updated Warning: package 'foreign' in library '/usr/lib/R/library' will not be updated Warning: package 'KernSmooth' in library '/usr/lib/R/library' will not be updated Warning: package 'lattice' in library '/usr/lib/R/library' will not be updated Warning: package 'Matrix' in library '/usr/lib/R/library' will not be updated Warning: package 'nlme' in library '/usr/lib/R/library' will not be updated Warning: package 'nnet' in library '/usr/lib/R/library' will not be updated Warning: package 'spatial' in library '/usr/lib/R/library' will not be updated Warning: package 'survival' in library '/usr/lib/R/library' will not be updated > Not possible? I also tried $ sudo apt install --reinstall r-cran-survival to no avail.> > | 2. Installing from scratch should have this fixed automatically, right? > > False.Thanks. Maybe better to install R from source then. G?ran
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