[R] R Installation problem: 'make check' errors

Peter Dalgaard BSA p.dalgaard at biostat.ku.dk
Sat Sep 15 12:03:14 CEST 2001

Fritz Roth <froth at hms.harvard.edu> writes:

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

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).

> ../../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]$

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.

> [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.

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

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

   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
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