[R] R Installation problem: 'make check' errors
Fritz Roth
froth at hms.harvard.edu
Sat Sep 15 01:16:15 CEST 2001
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:
>On Fri, Sep 14, 2001 at 05:21:54PM -0400, Fritz Roth wrote:
> > 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
> Hi Fritz,
>
> You should just be able to do
> ./configure --enable-R-shlib ; make
> then I presume it's
> make check
> (rather than make clean)
>
> If tcltk is there it will get found (it might not be in the right
> place etc).
>
> I recommend going:
> make distclean
> ./configure --enable-R-shlib
>
> (now look at what it found -- if it doesn't find either X or tcltk
> you need to either a: install them or b: tell R where they are
> (locate can help).
>
> Next, do
> make
>
> then
> make check
>
> if it still fails then look in tests/Examples/whatevercause the
> first error
>
> in your case it will be in base-Ex.Rout, there should be a file
> called base-Ex.Rout.fail (or something similar).
> look at the last few lines in that, it will tell you what failed and
> then we can proceed from there.
> regards
> Robert
>
>
> > ----------------------------------------------------------------------
> > 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
> > -------------------------------------------------
> >
> >
> -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-
> > 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
> >
> _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._
>
>--
>+---------------------------------------------------------------------------+
>| Robert Gentleman phone : (617) 632-5250 |
>| Associate Professor fax: (617) 632-2444 |
>| Department of Biostatistics office: M1B28
>| Harvard School of Public Health email: rgentlem at jimmy.dfci.harvard.edu |
>+---------------------------------------------------------------------------+
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
-------------------------------------------------
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