Dear all,
My package has Depends: lme4.0 in the DESCRIPTION. I need to extract the fixed
effect of a model and their standard errors. I use coef(summary(model)) inside
a function to do that. Model is the output of a call to glmer() from the lme4.0
package.
coef(summary(model)) throws an error:
Dear Thierry,
You have lme4.0_0.99-4 attached and lme4_1.1-5 loaded via a namespace.
I wonder if changes between the versions and which was getting called when
are making the difference. In particular, when you source it, I would
assume methods from the attached package are used. When you
For what it's worth, this issue persists in R-rc_2014-04-02_r65358.
Regards,
Jon
On 24 March 2014 10:40, Jon Clayden wrote:
> Dear all,
>
> As of the current R alpha release, I'm seeing timezone-related warnings on
> installing any package (including the recommended ones), which I haven't
> se
On 03/27/2014 06:31 PM, Hervé Pagès wrote:
On 03/27/2014 02:13 AM, Ulrich Bodenhofer wrote:
[...]
For the time being, it seems I have three options:
1) not supplying the sort() function yet (it is not yet in the release,
but only in my internal devel version)
2) including a dependency to BiocG
Dear Joshua,
Thank you for quick reply.
Note that my package has Depends: lme4.0 in DESCRIPTION. It imports and
suggests other packages but not lme4. lme4_1.1-5 is attached because my package
imports (via Imports: in DESCRIPTION) functions from package A, which imports
(via Imports: in DESCRIP
On Thu, Apr 3, 2014 at 4:33 AM, Ulrich Bodenhofer
wrote:
> On 03/27/2014 06:31 PM, Hervé Pagès wrote:
>
>> On 03/27/2014 02:13 AM, Ulrich Bodenhofer wrote:
>>
>>> [...]
>>>
>>>
>>> For the time being, it seems I have three options:
>>>
>>> 1) not supplying the sort() function yet (it is not yet in
I'm seeing nothing of the sort with the nightly build of 3.1.0RC, also on
10.9.2. This is a plain-vanilla Xcode+ancillaries build as per Simon's
instructions (I think):
pd$ more config.site
r_arch=${r_arch:=x86_64}
CC="gcc -arch $r_arch"
CXX="g++ -arch $r_arch"
F77="gfortran -arch $r_arch"
FC="
On 3 April 2014 at 12:24, Jon Clayden wrote:
| For what it's worth, this issue persists in R-rc_2014-04-02_r65358.
I'm running a beta version on Ubuntu and do not see this, neither on INSTALL
or check during package development nor during normal use:
R> R.version
_
On 03/04/2014 13:27, peter dalgaard wrote:
I'm seeing nothing of the sort with the nightly build of 3.1.0RC, also on
10.9.2. This is a plain-vanilla Xcode+ancillaries build as per Simon's
instructions (I think):
pd$ more config.site
r_arch=${r_arch:=x86_64}
CC="gcc -arch $r_arch"
CXX="g++ -arc
Many thanks, Prof Ripley. The "--without-internal-tzcode" option does
indeed resolve the problem.
Regards,
Jon
On 3 April 2014 13:38, Prof Brian Ripley wrote:
> On 03/04/2014 13:27, peter dalgaard wrote:
>
>> I'm seeing nothing of the sort with the nightly build of 3.1.0RC, also on
>> 10.9.2.
An update: I copied the functions from package A into MyPackage instead of
importing them. This avoids lme4_1.1-5 to be loaded via namespace (see
sessionInfo). However, the error remains. Nlme is loaded via namespace by lme4.0
R version 3.0.2 (2013-09-25)
Platform: i386-w64-mingw32/i386 (32-bit)
Thierry,
did you try to importFrom() in the namespace file? That way you know for
sure you have the correct summary function in the namespace of your
package. Since namespaces are available, I personally found that using them
whenever possible/suitable can prevent a lot of conflicts due to similar
Thanks to Brian. Yet another thing that zoomed by without me really noticing.
However, I'd like to be sure that it isn't a "make dist" issue. We do seem to
ship the correct files in src/extra/tzone, but could you please check Brian's
suggestion about TZDIR possibly being set incorrectly?
-pd
O
That doesn't seem to be the case. After rebuilding using the old configure
options, I see
> Sys.getenv("TZDIR")
[1] ""
Jon
On 3 April 2014 14:39, peter dalgaard wrote:
> Thanks to Brian. Yet another thing that zoomed by without me really
> noticing.
>
> However, I'd like to be sure that it is
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