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

[Uwe Ligges]

Just FYI: This one slipped through CRAN checks. We are in contact with 
the maintainer.

Best,
Uwe Ligges


On 11.12.2015 22:11, Marc Schwartz wrote:
>
>> 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.
>
> ______________________________________________
> 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.
>