As a follow-up to my prior post, if I remove --with-blas
--with-lapack, then the stats test passes:
...
Testing examples for package ?stats?
comparing ?stats-Ex.Rout? to ?stats-Ex.Rout.save? ... OK
...
Perhaps this is now a question about building R with the Intel MKL
libraries instead of one about the make check.
Thanks, -- bennet
On Tue, Aug 21, 2012 at 3:15 PM, Bennet Fauber <bennet at umich.edu>
wrote:> I am installing R 2.15.1 onto RHEL 6, using gcc 4.7.0 with Intel MKL
> 10.3.7 and the following environment:
>
> export BLAS_LIBS="-Wl,--start-group
> /usr/caen/intel-12.1/mkl/lib/intel64/libmkl_gf_lp64.a
> /usr/caen/intel-12.1/mkl/lib/intel64/libmkl_sequential.a
> /usr/caen/intel-12.1/mkl/lib/intel64/libmkl_core.a -Wl,--end-group
> -lpthread"
>
> export LAPACK_LIBS="-Wl,--start-group
> /usr/caen/intel-12.1/mkl/lib/intel64/libmkl_gf_lp64.a
> /usr/caen/intel-12.1/mkl/lib/intel64/libmkl_sequential.a
> /usr/caen/intel-12.1/mkl/lib/intel64/libmkl_core.a -Wl,--end-group
> -lpthread"
>
> ./configure --prefix=/home/software/rhel6/R/2.15.1 \
> -with-x=no --with-blas --with-lapack --enable-R-shlib
>
> Everything compiles OK, but 'make check' shows some differences. I
> tried this first with gcc 4.7.0 and then again with gcc 4.4.6 (RHEL 6
> installed). Same results.
>
> There are differences for the package 'tools', and 'stats'.
The
> first, perhaps, I could ignore because of a change in format, or which
> packages are getting installed with recommended, but the one for
> 'stats' seems not benign because it reverses the sign of all the
> loadings for the third extracted principal component. I would think
> it reasonable that the Grand Means would agree to four decimal places,
> also, no?
>
> Might anyone have a notion why I am seeing these differences?
>
> Copious output follows.
>
> Thanks, -- bennet
>
> Here are the relevant lines copied from the 'make check':
>
> Testing examples for package ?tools?
> comparing ?tools-Ex.Rout? to ?tools-Ex.Rout.save? ...
> files differ in number of lines:
> 811a812,828
>> $Depends
>> [1] "lattice"
>>
>> $Installed
>> [1] "lattice"
>>
>> $Found
>> list()
>>
>> $NotFound
>> character(0)
>>
>> $R
>> [1] "R (>= 2.14.0)"
>>
>> attr(,"class")
>> [1] "DependsList" "list"
>
>
> Testing examples for package ?stats?
> comparing ?stats-Ex.Rout? to ?stats-Ex.Rout.save? ...
> 6325c6325
> < Grand Mean: 291.5937
> ---
>> Grand Mean: 291.5938
> 12674c12674
> < Murder -0.536 0.418 0.341 0.649
> ---
>> Murder -0.536 0.418 -0.341 0.649
> 12675c12675
> < Assault -0.583 0.188 0.268 -0.743
> ---
>> Assault -0.583 0.188 -0.268 -0.743
> 12676c12676
> < UrbanPop -0.278 -0.873 0.378 0.134
> ---
>> UrbanPop -0.278 -0.873 -0.378 0.134
> 12677c12677
> < Rape -0.543 -0.167 -0.818
> ---
>> Rape -0.543 -0.167 0.818
> 14358c14358
> < Grand Mean: 291.5937
> ---
>> Grand Mean: 291.5938
> 15446c15446
> < Murder -0.54 0.42 0.34 0.65
> ---
>> Murder -0.54 0.42 -0.34 0.65
> 15447c15447
> < Assault -0.58 0.27 -0.74
> ---
>> Assault -0.58 -0.27 -0.74
> 15448c15448
> < UrbanPop -0.28 -0.87 0.38
> ---
>> UrbanPop -0.28 -0.87 -0.38
> 15449c15449
> < Rape -0.54 -0.82
> ---
>> Rape -0.54 0.82
>
>
> Here is output of 'diff -c' on the example file and the output file
> generated by this build, edited to remove those that only differ by
> bytecode:
>
> $ diff -c stats-Ex.Rout.save stats-Ex.Rout
> *** stats-Ex.Rout.save 2012-04-23 18:05:02.000000000 -0400
> --- stats-Ex.Rout 2012-08-21 14:45:12.204670303 -0400
> ***************
> *** 1,5 ****
>
> ! R version 2.15.0 Patched (2012-04-22 r59138) -- "Easter Beagle"
> Copyright (C) 2012 The R Foundation for Statistical Computing
> ISBN 3-900051-07-0
> Platform: x86_64-unknown-linux-gnu (64-bit)
> --- 1,5 ----
>
> ! R version 2.15.1 (2012-06-22) -- "Roasted Marshmallows"
> Copyright (C) 2012 The R Foundation for Statistical Computing
> ISBN 3-900051-07-0
> Platform: x86_64-unknown-linux-gnu (64-bit)
> ***************
> *** 6356,6362 ****
> Call:
> aov(formula = Yield ~ A * B * C + Error(Block), data = aovdat)
>
> ! Grand Mean: 291.5938
>
> Stratum 1: Block
>
> --- 6356,6362 ----
> Call:
> aov(formula = Yield ~ A * B * C + Error(Block), data = aovdat)
>
> ! Grand Mean: 291.5937
>
> Stratum 1: Block
>
> ***************
> *** 12728,12737 ****
>
> Loadings:
> Comp.1 Comp.2 Comp.3 Comp.4
> ! Murder -0.536 0.418 -0.341 0.649
> ! Assault -0.583 0.188 -0.268 -0.743
> ! UrbanPop -0.278 -0.873 -0.378 0.134
> ! Rape -0.543 -0.167 0.818
>
> Comp.1 Comp.2 Comp.3 Comp.4
> SS loadings 1.00 1.00 1.00 1.00
> --- 12728,12737 ----
>
> Loadings:
> Comp.1 Comp.2 Comp.3 Comp.4
> ! Murder -0.536 0.418 0.341 0.649
> ! Assault -0.583 0.188 0.268 -0.743
> ! UrbanPop -0.278 -0.873 0.378 0.134
> ! Rape -0.543 -0.167 -0.818
>
> Comp.1 Comp.2 Comp.3 Comp.4
> SS loadings 1.00 1.00 1.00 1.00
> ***************
> *** 14412,14418 ****
> Call:
> aov(formula = Yield ~ A * B * C + Error(Block), data = aovdat)
>
> ! Grand Mean: 291.5938
>
> Stratum 1: Block
>
> --- 14412,14418 ----
> Call:
> aov(formula = Yield ~ A * B * C + Error(Block), data = aovdat)
>
> ! Grand Mean: 291.5937
>
> Stratum 1: Block
>
> ***************
> *** 15502,15511 ****
>
> Loadings:
> Comp.1 Comp.2 Comp.3 Comp.4
> ! Murder -0.54 0.42 -0.34 0.65
> ! Assault -0.58 -0.27 -0.74
> ! UrbanPop -0.28 -0.87 -0.38
> ! Rape -0.54 0.82
> >
> >
> >
> --- 15502,15511 ----
>
> Loadings:
> Comp.1 Comp.2 Comp.3 Comp.4
> ! Murder -0.54 0.42 0.34 0.65
> ! Assault -0.58 0.27 -0.74
> ! UrbanPop -0.28 -0.87 0.38
> ! Rape -0.54 -0.82
> >
> >
> >
> ***************
>
>
> $ diff -c tools-Ex.Rout.save tools-Ex.Rout
> *** tools-Ex.Rout.save 2012-04-15 18:05:38.000000000 -0400
> --- tools-Ex.Rout 2012-08-21 14:43:48.578067277 -0400
> ***************
> *** 1,8 ****
>
> ! R version 2.15.0 Patched (2012-04-15 r59036) -- "Easter Beagle"
> Copyright (C) 2012 The R Foundation for Statistical Computing
> ISBN 3-900051-07-0
> ! Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
>
> R is free software and comes with ABSOLUTELY NO WARRANTY.
> You are welcome to redistribute it under certain conditions.
> --- 1,8 ----
>
> ! R version 2.15.1 (2012-06-22) -- "Roasted Marshmallows"
> Copyright (C) 2012 The R Foundation for Statistical Computing
> ISBN 3-900051-07-0
> ! Platform: x86_64-unknown-linux-gnu (64-bit)
>
> R is free software and comes with ABSOLUTELY NO WARRANTY.
> You are welcome to redistribute it under certain conditions.
> ***************
> *** 831,853 ****
> > ## This may not be installed
> > gridEx <- system.file("doc", "grid.Rnw",
package = "grid")
> > vignetteDepends(gridEx)
> - $Depends
> - [1] "lattice"
> -
> - $Installed
> - [1] "lattice"
> -
> - $Found
> - list()
> -
> - $NotFound
> - character(0)
> -
> - $R
> - [1] "R (>= 2.14.0)"
> -
> - attr(,"class")
> - [1] "DependsList" "list"
> >
> >
> >
> --- 831,836 ----
> ***************