[R] Updating Package Fails: Help on How to Fix Needed

[Marc Schwartz]

> On Dec 11, 2015, at 2:40 PM, Duncan Murdoch <murdoch.duncan at gmail.com> wrote:
> 
> On 11/12/2015 2:36 PM, William Dunlap wrote:
>> stats::sigma was added to R recently.  It is is R-devel now, I don't know
>> about yesterday's R-3.2.3.
> 
> As Rich saw, it's not.  pbkrtest should have "Depends: R (>= 3.3.0)" instead of "Depends: R (>= 3.0.0)" in its DESCRIPTION.
> You can see it failed tests on CRAN.
> 
> Duncan Murdoch


Just to confirm, having installed 3.2.3 this morning, stats::sigma is not present.

FWIW, it may, in some fashion, be related to the dependency of pbkrtest on lme4.

The ?sigma for lme4 shows the following in Examples:

  methods(sigma)# from R 3.3.0 on, shows methods from pkgs 'stats' *and* 'lme4'
 
So there may be a package namespace/export issue at play here...

Regards,

Marc Schwartz



>> Bill Dunlap
>> TIBCO Software
>> wdunlap tibco.com
>> 
>> 
>> On Fri, Dec 11, 2015 at 11:05 AM, Duncan Murdoch
>> <murdoch.duncan at gmail.com> wrote:
>> > On 11/12/2015 1:44 PM, Rich Shepard wrote:
>> >>
>> >>     Trying to update package pbkrtest failed because of a missing object
>> >> in
>> >> another namespace. Not having experienced this issue before now I don't
>> >> know
>> >> what to do to fix the problem. Here's the story:
>> >>
>> >> * installing *source* package ‘pbkrtest’ ...
>> >> ** package ‘pbkrtest’ successfully unpacked and MD5 sums checked
>> >> ** R
>> >> ** data
>> >> ** inst
>> >> ** preparing package for lazy loading
>> >> Warning: replacing previous import by ‘stats::sigma’ when loading
>> >> ‘pbkrtest’
>> >> Error : object ‘sigma’ is not exported by 'namespace:stats'
>> >> ERROR: lazy loading failed for package ‘pbkrtest’
>> >> * removing ‘/usr/lib/R/library/pbkrtest’
>> >> * restoring previous ‘/usr/lib/R/library/pbkrtest’
>> >>
>> >> The downloaded source packages are in
>> >>         ‘/tmp/RtmppHtiuJ/downloaded_packages’
>> >> Updating HTML index of packages in '.Library'
>> >> Making 'packages.html' ... done
>> >> Warning message:
>> >> In install.packages(update[instlib == l, "Package"], l, contriburl =
>> >> contriburl,  :
>> >>     installation of package ‘pbkrtest’ had non-zero exit status
>> >>
>> >>     Advice needed.
>> >
>> >
>> > I don't see that.  You need to give more details:  I'd start with
>> > sessionInfo(), and the version number of the pbkrtest package that you're
>> > trying to install.  (If R is downloading it for you,
>> > available.packages()["pbkrtest",]  will give lots of useful information.)
>> >
>> > Duncan Murdoch
>> >
>> > ______________________________________________
>> > R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
>> > https://stat.ethz.ch/mailman/listinfo/r-help
>> > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
>> > and provide commented, minimal, self-contained, reproducible code.
> 
> ______________________________________________
> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.