Latest revision of lme4 requires 'Matrix' >= 0.995.2 but that version is not available on CRAN

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Latest revision of lme4 requires 'Matrix' >= 0.995.2 but that version is not available on CRAN

Søren Højsgaard
I just updated the packages on my pc (windows xp). When loading lme4 I get
 
 > library(lme4)
Error: package 'Matrix' 0.995-1 was found, but >= 0.995.2 is required by 'lme4'

'Matrix'  0.995-1 is indeed installed on my computer, but update.packages() does not capture a never version; and seemingly for good reasons: When looking at CRAN, the new version of Matrix is available - but only as a .tar.gz archive. Two questions
 
1) How can a new version of lme4 make its way to CRAN when the packages it depends on are not available (that is, in a zip-version)?
 
An answer could be: Buhh, you can just download the .tar.gz archive and then compile it yourself! Surely, that would be possible, but it can not be the intention...
 
2) When actually trying to compile Matrix, I get
 
lmer.o(.text+0x285f):lmer.c: undefined reference to `atanh'
make[3]: *** [Matrix.dll] Error 1
make[2]: *** [srcDynlib] Error 2
make[1]: *** [all] Error 2
make: *** [pkg-Matrix] Error 2
*** Installation of Matrix failed ***
Removing 'c:/programs/R/current/library/Matrix'
Restoring previous 'c:/programs/R/current/library/Matrix'
 
Can anyone help me on what to do???
Thanks / Søren

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Re: Latest revision of lme4 requires 'Matrix' >= 0.995.2 but that version is not available on CRAN

Peter Dalgaard
Søren Højsgaard <[hidden email]> writes:

> I just updated the packages on my pc (windows xp). When loading lme4 I get
>  
>  > library(lme4)
> Error: package 'Matrix' 0.995-1 was found, but >= 0.995.2 is required by 'lme4'
>
> 'Matrix'  0.995-1 is indeed installed on my computer, but
> update.packages() does not capture a never version; and seemingly
> for good reasons: When looking at CRAN, the new version of Matrix is
> available - but only as a .tar.gz archive.

Oh s.....

>Two questions
>  
> 1) How can a new version of lme4 make its way to CRAN when the packages it depends on are not available (that is, in a zip-version)?

Looks like a buglet in Uwe's scripts. He has a check error on Matrix
0.995-2, but presumably it was actually built and loaded by lme4
0.995-2...

And of course the previous version of lme4 goes into the bit bucket
immediately.

lme4 0.995-1 file still exists on the DK mirror. I've put a copy for
you in the usual place, just in case.


 

> An answer could be: Buhh, you can just download the .tar.gz archive and then compile it yourself! Surely, that would be possible, but it can not be the intention...
>  
> 2) When actually trying to compile Matrix, I get
>  
> lmer.o(.text+0x285f):lmer.c: undefined reference to `atanh'
> make[3]: *** [Matrix.dll] Error 1
> make[2]: *** [srcDynlib] Error 2
> make[1]: *** [all] Error 2
> make: *** [pkg-Matrix] Error 2
> *** Installation of Matrix failed ***
> Removing 'c:/programs/R/current/library/Matrix'
> Restoring previous 'c:/programs/R/current/library/Matrix'
>  
> Can anyone help me on what to do???

This is not the same error that Uwe had (that was a clean compile but
error in the check phase), so upgrading to the latest version of the
build tools could be required.

--
   O__  ---- Peter Dalgaard             Øster Farimagsgade 5, Entr.B
  c/ /'_ --- Dept. of Biostatistics     PO Box 2099, 1014 Cph. K
 (*) \(*) -- University of Copenhagen   Denmark          Ph:  (+45) 35327918
~~~~~~~~~~ - ([hidden email])                  FAX: (+45) 35327907

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Re: Latest revision of lme4 requires 'Matrix' >= 0.995.2 but that version is not available on CRAN

Uwe Ligges
Peter Dalgaard wrote:

> Søren Højsgaard <[hidden email]> writes:
>
>
>>I just updated the packages on my pc (windows xp). When loading lme4 I get
>>
>> > library(lme4)
>>Error: package 'Matrix' 0.995-1 was found, but >= 0.995.2 is required by 'lme4'
>>
>>'Matrix'  0.995-1 is indeed installed on my computer, but
>>update.packages() does not capture a never version; and seemingly
>>for good reasons: When looking at CRAN, the new version of Matrix is
>>available - but only as a .tar.gz archive.
>
>
> Oh s.....
>
>
>>Two questions
>>
>>1) How can a new version of lme4 make its way to CRAN when the packages it depends on are not available (that is, in a zip-version)?
>
>
> Looks like a buglet in Uwe's scripts. He has a check error on Matrix
> 0.995-2, but presumably it was actually built and loaded by lme4
> 0.995-2...
>
> And of course the previous version of lme4 goes into the bit bucket
> immediately.
>
> lme4 0.995-1 file still exists on the DK mirror. I've put a copy for
> you in the usual place, just in case.
>
>
>  
>
>>An answer could be: Buhh, you can just download the .tar.gz archive and then compile it yourself! Surely, that would be possible, but it can not be the intention...
>>
>>2) When actually trying to compile Matrix, I get
>>
>>lmer.o(.text+0x285f):lmer.c: undefined reference to `atanh'
>>make[3]: *** [Matrix.dll] Error 1
>>make[2]: *** [srcDynlib] Error 2
>>make[1]: *** [all] Error 2
>>make: *** [pkg-Matrix] Error 2
>>*** Installation of Matrix failed ***
>>Removing 'c:/programs/R/current/library/Matrix'
>>Restoring previous 'c:/programs/R/current/library/Matrix'
>>
>>Can anyone help me on what to do???
>
>
> This is not the same error that Uwe had (that was a clean compile but
> error in the check phase), so upgrading to the latest version of the
> build tools could be required.
>

We (Doug, Martin and I) are trying hard to debug an error in Matrix.
Martin and Doug have ideas for a bugfix and I am checking right now.

The latest version of Matrix that passed the checks was Matrix_0.995-1
which is still available from
http://cran.r-project.org/bin/windows/contrib/2.2/last/

The error was also present in Matrix_0.995-1, but in that case (and by
chance) it did not cause a crash during the examples or tests (what
happens for Matrix_0.995-2 under Windows).

Uwe Ligges

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Re: Latest revision of lme4 requires 'Matrix' >= 0.995.2 but that version is not available on CRAN

Søren Højsgaard

We (Doug, Martin and I) are trying hard to debug an error in Matrix.
Martin and Doug have ideas for a bugfix and I am checking right now.

The latest version of Matrix that passed the checks was Matrix_0.995-1
which is still available from
http://cran.r-project.org/bin/windows/contrib/2.2/last/

The error was also present in Matrix_0.995-1, but in that case (and by
chance) it did not cause a crash during the examples or tests (what
happens for Matrix_0.995-2 under Windows).

Uwe Ligges


----


Dear Uwe,

Thats fine, but what puzzles me is that a new lme4-version can go on CRAN when it can not run under windows... ?

Anyway, that sort of things happen... I've now downloaded the previous version of lme4 as a tar.gz file - and that works. I wonder if it would be an idea to have a function rollback('pkg-name') for that sort of situations???

Best regards

Søren Højsgaard

 

 

Moreover, now that I have updated to the latest release of lme4, I wonder how to get get a version of lme4 that actually works with the version of Matrix which is currently available.

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Re: Latest revision of lme4 requires 'Matrix' >= 0.995.2 but that version is not available on CRAN

Uwe Ligges
Søren Højsgaard wrote:

> We (Doug, Martin and I) are trying hard to debug an error in Matrix.
> Martin and Doug have ideas for a bugfix and I am checking right now.
>
> The latest version of Matrix that passed the checks was
> Matrix_0.995-1 which is still available from
> http://cran.r-project.org/bin/windows/contrib/2.2/last/
>
> The error was also present in Matrix_0.995-1, but in that case (and
> by chance) it did not cause a crash during the examples or tests
> (what happens for Matrix_0.995-2 under Windows).
>
> Uwe Ligges
>
>
> ----
>
>
> Dear Uwe,
>
> Thats fine, but what puzzles me is that a new lme4-version can go on
> CRAN when it can not run under windows... ?

Yes, but implementing this would require an even higher computational
effort to build and check Windows binary packages.

Since it looks like the Matrix problems are persisting, I will play back
the "old" versions of both packages to CRAN shortly.

Uwe



> Anyway, that sort of things happen... I've now downloaded the
> previous version of lme4 as a tar.gz file - and that works. I wonder
> if it would be an idea to have a function rollback('pkg-name') for
> that sort of situations???
>
> Best regards
>
> Søren Højsgaard
>
>
>
>
>
> Moreover, now that I have updated to the latest release of lme4, I
> wonder how to get get a version of lme4 that actually works with the
> version of Matrix which is currently available.
>
>
>
>
>
>

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Re: Latest revision of lme4 requires 'Matrix' >= 0.995.2 but that version is not available on CRAN

Prof Brian Ripley
In reply to this post by Peter Dalgaard
On Sat, 21 Jan 2006, Peter Dalgaard wrote:

> Søren Højsgaard <[hidden email]> writes:
>
>> I just updated the packages on my pc (windows xp). When loading lme4 I get
>>
>> > library(lme4)
>> Error: package 'Matrix' 0.995-1 was found, but >= 0.995.2 is required by 'lme4'

[...]

>> 2) When actually trying to compile Matrix, I get
>>
>> lmer.o(.text+0x285f):lmer.c: undefined reference to `atanh'
>> make[3]: *** [Matrix.dll] Error 1
>> make[2]: *** [srcDynlib] Error 2
>> make[1]: *** [all] Error 2
>> make: *** [pkg-Matrix] Error 2
>> *** Installation of Matrix failed ***
>> Removing 'c:/programs/R/current/library/Matrix'
>> Restoring previous 'c:/programs/R/current/library/Matrix'
>>
>> Can anyone help me on what to do???
Your toolset is out of date (well out of date, I suspect).  Please do
ensure you have the versions listed in the R 2.2.1 R-admin manual.  I
think this issue is an old mingw-runtime, but have not checked.

I can build Matrix 0.995.2 on Windows and have once checked it under
R-devel.  However, it segfaults in its checks for me on almost all
platforms, not always in the same test and not even in the same place on
repeated runs.  I think the maintainers need to consider testing under
valgrind.

--
Brian D. Ripley,                  [hidden email]
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595
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Re: Latest revision of lme4 requires 'Matrix' >= 0.995.2 but that version is not available on CRAN

Søren Højsgaard
In reply to this post by Uwe Ligges
I see that Matrix, lme4 and SASmixed in zip format have been 'rolled back' to the previous versions - which I have now installed. Running
 
library(SASmixed)
data(Demand)
example(Demand)
 
gives
....
 
Demand> fm1Demand <- lmer(log(d) ~ log(y) + log(rd) + log(rt) +
    log(rs) + (1 | State) + (1 | Year), Demand)
Error: object "d" not found
Error in log(d) : unable to find the argument 'x' in selecting a method for function 'log'

- so it is not a complete 'roll back' - unless I've misunderstood something? Help will be appreciated...
 
/ Søren

 

[...]


Yes, but implementing this would require an even higher computational
effort to build and check Windows binary packages.

Since it looks like the Matrix problems are persisting, I will play back
the "old" versions of both packages to CRAN shortly.

Uwe



> Anyway, that sort of things happen... I've now downloaded the
> previous version of lme4 as a tar.gz file - and that works. I wonder
> if it would be an idea to have a function rollback('pkg-name') for
> that sort of situations???
>
> Best regards
>
> Søren Højsgaard
>
>
>
>
>
> Moreover, now that I have updated to the latest release of lme4, I
> wonder how to get get a version of lme4 that actually works with the
> version of Matrix which is currently available.
>
>
>
>
>
>

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Re: Latest revision of lme4 requires 'Matrix' >= 0.995.2 but that version is not available on CRAN

John Logsdon-2
In reply to this post by Søren Højsgaard
I've just hit this problem as well and as I am slumming it on XP at the
moment, I don't have the compilation tools to use the .tar.gz version.

I also notice that the numbering format has changed.  Is this intentional?

Best wishes

John

John Logsdon                               "Try to make things as simple
Quantex Research Ltd, Manchester UK         as possible but not simpler"
[hidden email]              [hidden email]
+44(0)161 445 4951/G:+44(0)7717758675       www.quantex-research.com


On Sat, 21 Jan 2006, Søren Højsgaard wrote:

> I just updated the packages on my pc (windows xp). When loading lme4 I get
>  
>  > library(lme4)
> Error: package 'Matrix' 0.995-1 was found, but >= 0.995.2 is required by 'lme4'
>
> 'Matrix'  0.995-1 is indeed installed on my computer, but update.packages() does not capture a never version; and seemingly for good reasons: When looking at CRAN, the new version of Matrix is available - but only as a .tar.gz archive. Two questions
>  
> 1) How can a new version of lme4 make its way to CRAN when the packages it depends on are not available (that is, in a zip-version)?
>  
> An answer could be: Buhh, you can just download the .tar.gz archive and then compile it yourself! Surely, that would be possible, but it can not be the intention...
>  
> 2) When actually trying to compile Matrix, I get
>  
> lmer.o(.text+0x285f):lmer.c: undefined reference to `atanh'
> make[3]: *** [Matrix.dll] Error 1
> make[2]: *** [srcDynlib] Error 2
> make[1]: *** [all] Error 2
> make: *** [pkg-Matrix] Error 2
> *** Installation of Matrix failed ***
> Removing 'c:/programs/R/current/library/Matrix'
> Restoring previous 'c:/programs/R/current/library/Matrix'
>  
> Can anyone help me on what to do???
> Thanks / Søren
>
> ______________________________________________
> [hidden email] mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
>

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Re: Latest revision of lme4 requires 'Matrix' >= 0.995.2 but that version is not available on CRAN

Uwe Ligges
In reply to this post by Søren Højsgaard
Søren Højsgaard wrote:

> I see that Matrix, lme4 and SASmixed in zip format have been 'rolled back' to the previous versions - which I have now installed. Running
>  
> library(SASmixed)
> data(Demand)
> example(Demand)
>  
> gives
> ....
>  
> Demand> fm1Demand <- lmer(log(d) ~ log(y) + log(rd) + log(rt) +
>     log(rs) + (1 | State) + (1 | Year), Demand)
> Error: object "d" not found
> Error in log(d) : unable to find the argument 'x' in selecting a method for function 'log'
>
> - so it is not a complete 'roll back' - unless I've misunderstood something? Help will be appreciated...

Yes, I rolled back one version. This is another error in the former
version. But since Matrix 0.995-3 is on its way to CRAN, there are
hopefully completely working versions available within 24 hours.

Uwe Ligges


> / Søren
>
>  
>
> [...]
>
>
> Yes, but implementing this would require an even higher computational
> effort to build and check Windows binary packages.
>
> Since it looks like the Matrix problems are persisting, I will play back
> the "old" versions of both packages to CRAN shortly.
>
> Uwe
>
>
>
>
>>Anyway, that sort of things happen... I've now downloaded the
>>previous version of lme4 as a tar.gz file - and that works. I wonder
>>if it would be an idea to have a function rollback('pkg-name') for
>>that sort of situations???
>>
>>Best regards
>>
>>Søren Højsgaard
>>
>>
>>
>>
>>
>>Moreover, now that I have updated to the latest release of lme4, I
>>wonder how to get get a version of lme4 that actually works with the
>>version of Matrix which is currently available.
>>
>>
>>
>>
>>
>>
>
>
>

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Re: Latest revision of lme4 requires 'Matrix' >= 0.995.2 but that version is not available on CRAN

Uwe Ligges
In reply to this post by John Logsdon-2
John Logsdon wrote:

> I've just hit this problem as well and as I am slumming it on XP at the
> moment, I don't have the compilation tools to use the .tar.gz version.

So please follow that thread and note that people were already working
on it for you during the whole weekend!
In this case, it does not help to have the tools. The Windows binary
package maintainer has had his reasons not to publish the most recent
Matrix version.

> I also notice that the numbering format has changed.  Is this intentional?

Yes.

Uwe Ligges


> Best wishes
>
> John
>
> John Logsdon                               "Try to make things as simple
> Quantex Research Ltd, Manchester UK         as possible but not simpler"
> [hidden email]              [hidden email]
> +44(0)161 445 4951/G:+44(0)7717758675       www.quantex-research.com
>
>
> On Sat, 21 Jan 2006, Søren Højsgaard wrote:
>
>
>>I just updated the packages on my pc (windows xp). When loading lme4 I get
>>
>> > library(lme4)
>>Error: package 'Matrix' 0.995-1 was found, but >= 0.995.2 is required by 'lme4'
>>
>>'Matrix'  0.995-1 is indeed installed on my computer, but update.packages() does not capture a never version; and seemingly for good reasons: When looking at CRAN, the new version of Matrix is available - but only as a .tar.gz archive. Two questions
>>
>>1) How can a new version of lme4 make its way to CRAN when the packages it depends on are not available (that is, in a zip-version)?
>>
>>An answer could be: Buhh, you can just download the .tar.gz archive and then compile it yourself! Surely, that would be possible, but it can not be the intention...
>>
>>2) When actually trying to compile Matrix, I get
>>
>>lmer.o(.text+0x285f):lmer.c: undefined reference to `atanh'
>>make[3]: *** [Matrix.dll] Error 1
>>make[2]: *** [srcDynlib] Error 2
>>make[1]: *** [all] Error 2
>>make: *** [pkg-Matrix] Error 2
>>*** Installation of Matrix failed ***
>>Removing 'c:/programs/R/current/library/Matrix'
>>Restoring previous 'c:/programs/R/current/library/Matrix'
>>
>>Can anyone help me on what to do???
>>Thanks / Søren
>>
>>______________________________________________
>>[hidden email] mailing list
>>https://stat.ethz.ch/mailman/listinfo/r-help
>>PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
>>
>
>
> ______________________________________________
> [hidden email] mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html

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Re: Latest revision of lme4 requires 'Matrix' >= 0.995.2 but that version is not available on CRAN

Douglas Bates
In reply to this post by John Logsdon-2
On 1/22/06, John Logsdon <[hidden email]> wrote:
> I've just hit this problem as well and as I am slumming it on XP at the
> moment, I don't have the compilation tools to use the .tar.gz version.
>
> I also notice that the numbering format has changed.  Is this intentional?

Which numbering format?  If you mean the use of 0.995 rather than 0.99
it is because I keep finding changes that need to be made in the
underlying format for mixed-effects representations (i.e. mer objects)
before a 1.0 release.  The current sequence of numbers is 0.99 (99%),
0.995 (99 1/2%), 0.9975 (99 3/4%), 0.99875 (99 7/8%), ...

It is a pattern like, but not as inventive as, Donald Knuth's
numbering sequence for TeX releases.  It has the desirable property of
allowing for an infinite number of releases before you need to declare
the package to be at release 1.0

There will be at least a 0.9975 series of minor releases (I need to
add another two slots to the mer object).

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Re: Latest revision of lme4 requires 'Matrix' >= 0.995.2 but that version is not available on CRAN

John Logsdon-2
Doug and list

No, the change as reported on my XP PC was Matrix package 0.995-1 was
found but lme4 requires >= 0.995.2.

The format change was from a dash to a dot.  

Maybe a few more would spell SOS!

But it's the sort of thing where sometimes even the geniuses very close to
the work may read the string they think they wrote by gestalt.  As long as
it is what was intended and works, it doesn't matter.

But what about working in logits.  Each new mini-version would have a
constant amount of logit added, ultimately to be changed to the next
release...:-))

Best wishes to all

John

John Logsdon                               "Try to make things as simple
Quantex Research Ltd, Manchester UK         as possible but not simpler"
[hidden email]              [hidden email]
+44(0)161 445 4951/G:+44(0)7717758675       www.quantex-research.com


On Mon, 23 Jan 2006, Douglas Bates wrote:

> On 1/22/06, John Logsdon <[hidden email]> wrote:
> > I've just hit this problem as well and as I am slumming it on XP at the
> > moment, I don't have the compilation tools to use the .tar.gz version.
> >
> > I also notice that the numbering format has changed.  Is this intentional?
>
> Which numbering format?  If you mean the use of 0.995 rather than 0.99
> it is because I keep finding changes that need to be made in the
> underlying format for mixed-effects representations (i.e. mer objects)
> before a 1.0 release.  The current sequence of numbers is 0.99 (99%),
> 0.995 (99 1/2%), 0.9975 (99 3/4%), 0.99875 (99 7/8%), ...
>
> It is a pattern like, but not as inventive as, Donald Knuth's
> numbering sequence for TeX releases.  It has the desirable property of
> allowing for an infinite number of releases before you need to declare
> the package to be at release 1.0
>
> There will be at least a 0.9975 series of minor releases (I need to
> add another two slots to the mer object).
>

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Re: Latest revision of lme4 requires 'Matrix' >= 0.995.2 but that version is not available on CRAN

Peter Dalgaard
John Logsdon <[hidden email]> writes:

> Doug and list
>
> No, the change as reported on my XP PC was Matrix package 0.995-1 was
> found but lme4 requires >= 0.995.2.
>
> The format change was from a dash to a dot.  

As far as I remember, the version comparison logic is
separator-agnostic, so it's purely a cosmetic issue.
 
> Maybe a few more would spell SOS!

Some of the users are already going ... --- ... / .... . .-.. .--.

--
   O__  ---- Peter Dalgaard             Øster Farimagsgade 5, Entr.B
  c/ /'_ --- Dept. of Biostatistics     PO Box 2099, 1014 Cph. K
 (*) \(*) -- University of Copenhagen   Denmark          Ph:  (+45) 35327918
~~~~~~~~~~ - ([hidden email])                  FAX: (+45) 35327907

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