make check fails two tests on RHEL 6 build

Tue, Aug 21, 2012 12:15 PM

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

Testing examples for package ?stats?
  comparing ?stats-Ex.Rout? to ?stats-Ex.Rout.save? ...
6325c6325
< Grand Mean: 291.5937
---

12674c12674
< Murder   -0.536  0.418  0.341  0.649
---

12675c12675
< Assault  -0.583  0.188  0.268 -0.743
---

12676c12676
< UrbanPop -0.278 -0.873  0.378  0.134
---

12677c12677
< Rape     -0.543 -0.167 -0.818
---

14358c14358
< Grand Mean: 291.5937
---

15446c15446
< Murder   -0.54   0.42   0.34   0.65
---

15447c15447
< Assault  -0.58          0.27  -0.74
---

15448c15448
< UrbanPop -0.28  -0.87   0.38
---

15449c15449
< 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 ----

make check fails two tests on RHEL 6 build

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