From pgilbert902 at gmail.com  Wed Apr  3 18:10:17 2013
From: pgilbert902 at gmail.com (Paul Gilbert)
Date: Wed, 03 Apr 2013 12:10:17 -0400
Subject: [Rd] R-3.0.0  reg-tests-3.R / survival
In-Reply-To: <1CFE4B7A-7D3E-4507-924B-6D61956E568E@gmail.com>
References: <515C43F9.60303@gmail.com>
	<1CFE4B7A-7D3E-4507-924B-6D61956E568E@gmail.com>
Message-ID: <515C5469.9060200@gmail.com>


"make check" seems to be picking up the setting of my  R_LIBS_SITE which 
is still set for 2.15.3 and had survival in it. At least, when I set 
that to empty then the check passes.  I'm not sure if checking worked 
like that before, I don't think so. I have not usually had base packages 
in my site-library. In any case, it seems like a bad idea for "make 
check" to use an existing setting of R_LIBS_SITE. At least, I think the 
idea is that it should be checking the just built library.

Paul


On 13-04-03 11:36 AM, peter dalgaard wrote:
> Any chance that you might have a personal library, which isn't versioned? If you do and you for some reason installed survival into it, it would explain it.
>
> E.g., I have, with the system-wide R
>
>> .libPaths()
> [1] "/Users/pd/Library/R/2.15/library"
> [2] "/opt/local/Library/Frameworks/R.framework/Versions/2.15/Resources/library"
>> lapply(.libPaths(), list.files)
> [[1]]
>   [1] "abind"      "aplpack"    "car"        "colorspace" "e1071"
>   [6] "effects"    "ellipse"    "Hmisc"      "ISwR"       "leaps"
> [11] "lmtest"     "matrixcalc" "mclust"     "multcomp"   "mvtnorm"
> [16] "pcaPP"      "Rcmdr"      "relimp"     "represent"  "rgl"
> [21] "robustbase" "rrcov"      "sem"        "xtable"     "zoo"
>
> [[2]]
>   [1] "base"       "boot"       "class"      "cluster"    "codetools"
>   [6] "compiler"   "datasets"   "foreign"    "graphics"   "grDevices"
> [11] "grid"       "KernSmooth" "lattice"    "MASS"       "Matrix"
> [16] "methods"    "mgcv"       "nlme"       "nnet"       "parallel"
> [21] "rpart"      "spatial"    "splines"    "stats"      "stats4"
> [26] "survival"   "tcltk"      "tools"      "utils"
>
> but the one in my development build tree of 3.0.0 has
>
>> .libPaths()
> [1] "/Users/pd/r-release-branch/BUILD-dist/library"
>
> If I explicitly set R_LIBS, I can easily reproduce your error.
>
>
> On Apr 3, 2013, at 17:00 , Paul Gilbert wrote:
>
>>
>> "make check" is failing on reg-test3.R with a message that survival was built with an older version of R.  (On my Ubuntu 32 bit and Ubuntu 64 bit machines). Why would "make check" be looking anywhere that it would find something built with an older version of R?
>>
>> ~/RoboAdmin/R-3.0.0/tests$ tail reg-tests-3.Rout.fail
>>> print(1.001, digits=16)
>> [1] 1.001
>>> ## 2.4.1 gave  1.001000000000000
>>> ## 2.5.0 errs on the side of caution.
>>>
>>>
>>> ## as.matrix.data.frame with coercion
>>> library(survival)
>> Error: package 'survival' was built before R 3.0.0: please re-install it
>> Execution halted
>>
>> ______________________________________________
>> R-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
>



[Rd] R-3.0.0 reg-tests-3.R / survival
Paul Gilbert