R Installation problem: 'make check' errors
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
dlopen.
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 -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- 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 _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._