Running update.packages on R 3.1 for Mavericks complains that some CRAN packages do not have binary builds available. For example lme4 is missing from http://cran.r-project.org/bin/macosx/mavericks/contrib/3.1/. Is there any reason for this, or do I just need some patience? I installed lme4 from source and it seems to build without problems.
Missing binary packages for Mavericks
5 messages · Jeroen Ooms, Simon Urbanek, Steve Walker
On Apr 11, 2014, at 12:54 AM, Jeroen Ooms <jeroen.ooms at stat.ucla.edu> wrote:
Running update.packages on R 3.1 for Mavericks complains that some CRAN packages do not have binary builds available. For example lme4 is missing from http://cran.r-project.org/bin/macosx/mavericks/contrib/3.1/. Is there any reason for this,
Yes, only packages that pass make check are present.
or do I just need some patience? I installed lme4 from source and it seems to build without problems.
It fails make check with * checking for unstated dependencies in tests ... OK * checking tests ... ERROR Running the tests in ?tests/priorWeights.R? failed. Last 13 lines of output: > sleepLmer <- lmer(Reaction ~ Days + (Days|Subject), + sleepstudy, weights = w, + REML = FALSE) > sleepComp <- compFunc(sleepLme, sleepLmer) > stopifnot(do.call(all.equal, sleepComp)) > ## look at relative differences: > sleepComp$tolerance <- 0 > do.call(all.equal, sleepComp) [1] "Mean relative difference: 0.000818191" > > library(mlmRev) Error in library(mlmRev) : there is no package called 'mlmRev' Execution halted * elapsed time (check, wall clock): 7:57 However, mlmRev itself depends on lme4, so it's not available. It seems like a bug in the tests which should not fail if mlmRev is not available since it's only suggested, not required. Cheers, Simon
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Thank you Jeroen for this report. We (the lme4 authors) apologize for this inconvenience. Thank you Simon. Your diagnosis is correct. The test in question should only run if mlmRev is available. This bug is now fixed in the development version. Ben and I just discussed the matter, and we will be submitting a patch to cran within 24 hours. We would also like to include some other back compatibility fixes within the patch, but are still deliberating about which of these to include. Steve Walker
On 2014-04-11, 10:43 AM, Simon Urbanek wrote:
On Apr 11, 2014, at 12:54 AM, Jeroen Ooms <jeroen.ooms at stat.ucla.edu> wrote:
Running update.packages on R 3.1 for Mavericks complains that some CRAN packages do not have binary builds available. For example lme4 is missing from http://cran.r-project.org/bin/macosx/mavericks/contrib/3.1/. Is there any reason for this,
Yes, only packages that pass make check are present.
or do I just need some patience? I installed lme4 from source and it seems to build without problems.
It fails make check with * checking for unstated dependencies in tests ... OK * checking tests ... ERROR Running the tests in ?tests/priorWeights.R? failed. Last 13 lines of output:
> sleepLmer <- lmer(Reaction ~ Days + (Days|Subject),
+ sleepstudy, weights = w, + REML = FALSE)
> sleepComp <- compFunc(sleepLme, sleepLmer) > stopifnot(do.call(all.equal, sleepComp)) > ## look at relative differences: > sleepComp$tolerance <- 0 > do.call(all.equal, sleepComp)
[1] "Mean relative difference: 0.000818191"
> > library(mlmRev)
Error in library(mlmRev) : there is no package called 'mlmRev' Execution halted * elapsed time (check, wall clock): 7:57 However, mlmRev itself depends on lme4, so it's not available. It seems like a bug in the tests which should not fail if mlmRev is not available since it's only suggested, not required. Cheers, Simon
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On Apr 11, 2014, at 11:11 PM, Jeroen Ooms <jeroen.ooms at stat.ucla.edu> wrote:
There are actually over 500 packages that do not have a mavericks build.
That's only a small fraction, it's not many more than the failures for the regular build.
Maybe send some auto generated emails to maintainers?
Some 3rd party library dependencies are not currently available on the Mavericks build machine since they need to be rebuilt for 10.9. I'll try to build those in the near future so the number should go down over time. Given the fairly recent introduction of the Mavericks build, there are still things to iron out. People that don't want to be living on the edge can use the regular build instead. Cheers, Simon
mav <- read.dcf(url("
http://cran.r-project.org/bin/macosx/mavericks/contrib/3.1/PACKAGES"))
osx <- read.dcf(url("
http://cran.r-project.org/bin/macosx/contrib/3.1/PACKAGES"))
mav <- as.data.frame(mav, stringsAsFactors=FALSE)
osx <- as.data.frame(osx, stringsAsFactors=FALSE)
mav$Package[!(mav$Package %in% osx$Package)]
osx$Package[!(osx$Package %in% mav$Package)]
FWIW there's available.packages() that does the job of pulling what you need.
On Thu, Apr 10, 2014 at 9:54 PM, Jeroen Ooms <jeroen.ooms at stat.ucla.edu>wrote:
Running update.packages on R 3.1 for Mavericks complains that some CRAN packages do not have binary builds available. For example lme4 is missing from http://cran.r-project.org/bin/macosx/mavericks/contrib/3.1/. Is there any reason for this, or do I just need some patience? I installed lme4 from source and it seems to build without problems.
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