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 ----
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