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R Installation problem: 'make check' errors

4 messages · Fritz Roth, Peter Dalgaard

Fritz Roth
# 
Hi All,

I'm trying to install R from source on an Intel machine running Linux 
(RedHat 6.2) and I am getting errors (Error 139, Error 2, and Error 1) on 
'make check'.  Perhaps I've forgotten something basic?

---------------------------------------------------------------------
Here's what I've done:
/configure --prefix=/home1/froth/R --enable-R-shlib --with-tcltk --with-x
make
make clean
----------------------------------------------------------------------
The output from 'make clean' is as follows:
[froth at lama R-1.3.1]$ make check
make[1]: Entering directory `/home1/froth/R/src/R-1.3.1/tests'
make[2]: Entering directory `/home1/froth/R/src/R-1.3.1/tests'
make[3]: Entering directory `/home1/froth/R/src/R-1.3.1/tests/Examples'
make[4]: Entering directory `/home1/froth/R/src/R-1.3.1/tests/Examples'
make[4]: Leaving directory `/home1/froth/R/src/R-1.3.1/tests/Examples'
make[4]: Entering directory `/home1/froth/R/src/R-1.3.1/tests/Examples'
collecting examples for package `base' ...
make[5]: Entering directory `/home1/froth/R/src/R-1.3.1/src/library'
  >>> Building/Updating help pages for package `base'
      Formats: text example
make[5]: Leaving directory `/home1/froth/R/src/R-1.3.1/src/library'
running code in base-Ex.R ...
../../bin/R --vanilla < base-Ex.R > base-Ex.Rout
make[4]: *** [base-Ex.Rout] Error 139
make[4]: Leaving directory `/home1/froth/R/src/R-1.3.1/tests/Examples'
make[3]: *** [test-Examples] Error 2
make[3]: Leaving directory `/home1/froth/R/src/R-1.3.1/tests/Examples'
make[2]: *** [test-Examples] Error 2
make[2]: Leaving directory `/home1/froth/R/src/R-1.3.1/tests'
make[1]: *** [test-all-basics] Error 1
make[1]: Leaving directory `/home1/froth/R/src/R-1.3.1/tests'
make: *** [check] Error 2
[froth at lama R-1.3.1]$

Any advice would be greatly appreciated.

Thanks!
Fritz Roth

-------------------------------------------------
Frederick P. Roth, Asst. Professor
Harvard Medical School
Dept. of Biological Chemistry and Molecular Pharmacology
250 Longwood Avenue, SGMB-322, Boston, MA 02115
(617) 432-3551 phone            (617) 432-3557 FAX
froth at hms.harvard.edu           http://llama.med.harvard.edu
-------------------------------------------------

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Peter Dalgaard
# 
Fritz Roth <froth at hms.harvard.edu> writes:
Hmm. The compilers of 6.2 aren't all that hot (and are known to break
the next R version) but I thought that 1.3.x would work.

The clue to what might be wrong comes at the end of the base-Ex.Rout
file  (except if file buffering causes the output to be lost, but I
think the error looks different then), so that's what you should show
us.
Fritz Roth
# 
Robert and Peter,

Thanks for the quick feedback.

As you both supposed, I did actually use 'make check' previously even 
though I said 'make clean' in my email for some strange reason.

OK.. so I used "./configure --enable-R-shlib" as suggested by Robert, and 
it did find tcl/tk and X libraries.

I get the same 'make check' output as before (Error 139 on 
'base-Ex.Rout').  Also I noticed there was a core dump in ./tests/Examples.

Per your suggestions I looked at the file "base-Ex.Rout" to get a clue 
about the first error (there wasn't any file called 
"base-Ex.Rout.fail").  The tail end of 'base-Ex.Rout' is below:
-------------------------------------------------------------------------------------------------------------
[froth at lama Examples]$
[froth at lama Examples]$ tail --lines=40 base-Ex.Rout
lm(formula = Employed ~ . - Population - GNP.deflator, data = longley)

Residuals:
      Min       1Q   Median       3Q      Max
-0.42165 -0.12457 -0.02416  0.08369  0.45268

Coefficients:
                Estimate Std. Error t value Pr(>|t|)
(Intercept)  -3.599e+03  7.406e+02  -4.859 0.000503 ***
GNP          -4.019e-02  1.647e-02  -2.440 0.032833 *
Unemployed   -2.088e-02  2.900e-03  -7.202 1.75e-05 ***
Armed.Forces -1.015e-02  1.837e-03  -5.522 0.000180 ***
Year          1.887e+00  3.828e-01   4.931 0.000449 ***
---
Signif. codes:  0 `***' 0.001 `**' 0.01 `*' 0.05 `.' 0.1 ` ' 1

Residual standard error: 0.2794 on 11 degrees of freedom
Multiple R-Squared: 0.9954,     Adjusted R-squared: 0.9937
F-statistic: 589.8 on 4 and 11 DF,  p-value: 9.5e-13

 >  for(wh in 1:4) plot(lm.fm2, which = wh)
 >
 >
 > ## Keywords: 'hplot', 'regression'.
 >
 >
 > par(get("par.postscript", env = .CheckExEnv))
 > rm(list = ls(all = TRUE)); .Random.seed <- c(0,rep(7654,3))
 > ..nameEx <- "plot.table"
 > ###--- >>> `plot.table' <<<----- Plot Methods for `table' Objects
 >
 >       ## alias         help(plot.table)
 >
 > ##___ Examples ___:
 >
 > ## 1-d tables
 > (Poiss.tab <- table(N = rpois(200, lam= 5)))
N
  0  1  2  3  4  5  6  7  8  9 10 11 18
  1  4 14 21 46 40 24 14 19 11  3  2  1
[froth at lama Examples]$


------------------------------------------------------------------------------------------

Just for kicks I ran make check again, and got farther along before another 
Error 139:

------------------------------------------------------------------



[froth at lama R-1.3.1]$ make check
make[1]: Entering directory `/home1/froth/R/src/R-1.3.1/tests'
make[2]: Entering directory `/home1/froth/R/src/R-1.3.1/tests'
make[3]: Entering directory `/home1/froth/R/src/R-1.3.1/tests/Examples'
make[4]: Entering directory `/home1/froth/R/src/R-1.3.1/tests/Examples'
make[4]: `Makedeps' is up to date.
make[4]: Leaving directory `/home1/froth/R/src/R-1.3.1/tests/Examples'
make[4]: Entering directory `/home1/froth/R/src/R-1.3.1/tests/Examples'
collecting examples for package `ctest' ...
make[5]: Entering directory `/home1/froth/R/src/R-1.3.1/src/library'
  >>> Building/Updating help pages for package `ctest'
      Formats: text example
make[5]: Leaving directory `/home1/froth/R/src/R-1.3.1/src/library'
running code in ctest-Ex.R ...
./../bin/R --vanilla < ctest-Ex.R > ctest-Ex.Rout
collecting examples for package `eda' ...
make[5]: Entering directory `/home1/froth/R/src/R-1.3.1/src/library'
  >>> Building/Updating help pages for package `eda'
      Formats: text example
make[5]: Leaving directory `/home1/froth/R/src/R-1.3.1/src/library'
running code in eda-Ex.R ...
../../bin/R --vanilla < eda-Ex.R > eda-Ex.Rout
collecting examples for package `lqs' ...
make[5]: Entering directory `/home1/froth/R/src/R-1.3.1/src/library'
  >>> Building/Updating help pages for package `lqs'
      Formats: text example
make[5]: Leaving directory `/home1/froth/R/src/R-1.3.1/src/library'
running code in lqs-Ex.R ...
../../bin/R --vanilla < lqs-Ex.R > lqs-Ex.Rout
collecting examples for package `modreg' ...
make[5]: Entering directory `/home1/froth/R/src/R-1.3.1/src/library'
  >>> Building/Updating help pages for package `modreg'
      Formats: text example
make[5]: Leaving directory `/home1/froth/R/src/R-1.3.1/src/library'
running code in modreg-Ex.R ...
../../bin/R --vanilla < modreg-Ex.R > modreg-Ex.Rout
collecting examples for package `mva' ...
make[5]: Entering directory `/home1/froth/R/src/R-1.3.1/src/library'
  >>> Building/Updating help pages for package `mva'
      Formats: text example
make[5]: Leaving directory `/home1/froth/R/src/R-1.3.1/src/library'
running code in mva-Ex.R ...
../../bin/R --vanilla < mva-Ex.R > mva-Ex.Rout
make[4]: *** [mva-Ex.Rout] Error 139
make[4]: Leaving directory `/home1/froth/R/src/R-1.3.1/tests/Examples'
make[3]: *** [test-Examples] Error 2
make[3]: Leaving directory `/home1/froth/R/src/R-1.3.1/tests/Examples'
make[2]: *** [test-Examples] Error 2
make[2]: Leaving directory `/home1/froth/R/src/R-1.3.1/tests'
make[1]: *** [test-all-basics] Error 1
make[1]: Leaving directory `/home1/froth/R/src/R-1.3.1/tests'
make: *** [check] Error 2
[froth at lama R-1.3.1]$



------------------------------------------------------------------------------------------------

Here's a look at 'mva-Ex.Rout':

------------------------------------------------------------------------------------------------



[froth at lama Examples]$ tail -n 40 mva-Ex.Rout

R : Copyright 2001, The R Development Core Team
Version 1.3.1  (2001-08-31)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type `license()' or `licence()' for distribution details.

R is a collaborative project with many contributors.
Type `contributors()' for more information.

Type `demo()' for some demos, `help()' for on-line help, or
`help.start()' for a HTML browser interface to help.
Type `q()' to quit R.

[froth at lama Examples]$
------------------------------------------------------------------------------------
At 05:40 PM 9/14/2001 -0400, Robert Gentleman wrote:
Fritz Roth <froth at hms.harvard.edu> writes:

 > Hi All,
 >
 > I'm trying to install R from source on an Intel machine running Linux
 > (RedHat 6.2) and I am getting errors (Error 139, Error 2, and Error 1)
 > on 'make check'.  Perhaps I've forgotten something basic?
 >
 > ---------------------------------------------------------------------
 > Here's what I've done:
 > /configure --prefix=/home1/froth/R --enable-R-shlib --with-tcltk --with-x
 > make
 > make clean
 > ----------------------------------------------------------------------
 > The output from 'make clean' is as follows:
 > [froth at lama R-1.3.1]$ make check
 > make[1]: Entering directory `/home1/froth/R/src/R-1.3.1/tests'
 > make[2]: Entering directory `/home1/froth/R/src/R-1.3.1/tests'
 > make[3]: Entering directory `/home1/froth/R/src/R-1.3.1/tests/Examples'
 > make[4]: Entering directory `/home1/froth/R/src/R-1.3.1/tests/Examples'
 > make[4]: Leaving directory `/home1/froth/R/src/R-1.3.1/tests/Examples'
 > make[4]: Entering directory `/home1/froth/R/src/R-1.3.1/tests/Examples'
 > collecting examples for package `base' ...
 > make[5]: Entering directory `/home1/froth/R/src/R-1.3.1/src/library'
 >   >>> Building/Updating help pages for package `base'
 >       Formats: text example
 > make[5]: Leaving directory `/home1/froth/R/src/R-1.3.1/src/library'
 > running code in base-Ex.R ...
 > ../../bin/R --vanilla < base-Ex.R > base-Ex.Rout
 > make[4]: *** [base-Ex.Rout] Error 139
 > make[4]: Leaving directory `/home1/froth/R/src/R-1.3.1/tests/Examples'
 > make[3]: *** [test-Examples] Error 2
 > make[3]: Leaving directory `/home1/froth/R/src/R-1.3.1/tests/Examples'
 > make[2]: *** [test-Examples] Error 2
 > make[2]: Leaving directory `/home1/froth/R/src/R-1.3.1/tests'
 > make[1]: *** [test-all-basics] Error 1
 > make[1]: Leaving directory `/home1/froth/R/src/R-1.3.1/tests'
 > make: *** [check] Error 2
 > [froth at lama R-1.3.1]$
 >
 > Any advice would be greatly appreciated.

Hmm. The compilers of 6.2 aren't all that hot (and are known to break
the next R version) but I thought that 1.3.x would work.

The clue to what might be wrong comes at the end of the base-Ex.Rout
file  (except if file buffering causes the output to be lost, but I
think the error looks different then), so that's what you should show
us.

--
    O__  ---- Peter Dalgaard             Blegdamsvej 3
   c/ /'_ --- Dept. of Biostatistics     2200 Cph. N
  (*) \(*) -- University of Copenhagen   Denmark      Ph: (+45) 35327918
~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk)             FAX: (+45) 35327907
-------------------------------------------------
Frederick P. Roth, Asst. Professor
Harvard Medical School
Dept. of Biological Chemistry and Molecular Pharmacology
250 Longwood Avenue, SGMB-322, Boston, MA 02115
(617) 432-3551 phone            (617) 432-3557 FAX
froth at hms.harvard.edu           http://llama.med.harvard.edu
-------------------------------------------------

-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-
r-help mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html
Send "info", "help", or "[un]subscribe"
(in the "body", not the subject !)  To: r-help-request at stat.math.ethz.ch
_._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._
Peter Dalgaard
# 
Fritz Roth <froth at hms.harvard.edu> writes:
....
Yes, that is a bug in the make process. It is not re-running the
failed check of base-Ex.R. I think we got that fixed in 1.4(-pre).
Hmmmm. Is mva the first of those packages that use Fortran? There are
known issues with Fortran dynamic libraries and 6.2, and the
--enable-shlib might trigger a problem where it normally doesn't.
This is incomplete because you get a fatal error (triggering the core
dump). What happens if you go to the tests/Examples directory and type

../../bin/R --vanilla < mva-Ex.R

?

My guess is that you get as far as library('mva'), and if you do the
same with base-Ex.R you'll see the crash happening at a similar spot.

You can also try running under gdb ("../../bin/R -d gdb" then "run
--vanilla < mva-Ex.R") and see if the crash doesn't happen inside
dlopen.  

Either way, you should probably upgrade the compiler suite (or the OS)
or maybe try using f2c.