make check fails two tests on RHEL 6 build
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 ---- ***************