Re: [R] Error in "make check-all"

From: Peter Dalgaard <p.dalgaard_at_biostat.ku.dk>
Date: Wed 28 Sep 2005 - 20:06:21 EST

Fernando Mayer <fernandomayer@gmail.com> writes:

> Dear Prof. Ripley, that was exactly what i did. Should i login on the
> system as root, instead of login as user and became root via console?
> What should i do to have X11 usable?

I don't actually think that this is the problem. You shouldn't generally trust me rather than Brian, but I'm sitting at a SUSE 9.3 system, and he's not... If I "su -" to root, I can happily run "xterm" etc. from the root shell with display on the console, and also run make check on the current r-devel. So go look for missing RPM packages.

That said, it is not generally a good idea to build as root. I prefer to build things as myself and only do the final install step as root if necessary.

        -pd

(PS: I had a powercut when I was either 99.99% or 100.01% done with writing this before. Apologies if it went out twice...)  

> Thanks,
> Fernando Mayer.
>
>
> Prof Brian Ripley escreveu:
>
> >This is what happens if you don't have a usable X11 display. Did you
> >perhaps use a root account on a console owned by a normal user?
> >
> >On Tue, 27 Sep 2005, Fernando Mayer wrote:
> >
> >
> >
> >>Dear R-users,
> >>
> >>i'm a very newbie in linux, but decided to build R from source.
> >>Following the "R Installation and Administration" manual, i did this:
> >>
> >>./configure --enable-R-shlib # this option is here because i intend to
> >>build the GNOME console after...
> >>make
> >>make check
> >>
> >>no problems in make check, but:
> >>
> >>make check-devel #and also
> >>make check-all
> >>
> >>indicated some WARNINGs in the log file:
> >>
> >>/usr/local/R-2.1.1/tests/tcltk.Rcheck/00check.Rcheck
> >>
> >>Right below is the content of this log file (I translated some words):
> >>
> >>[start log file]
> >>
> >>* using log directory '/usr/local/R-2.1.1/tests/tcltk.Rcheck'
> >>* using R version 2.1.1, 2005-06-20
> >>* looks like 'tcltk' is a base package
> >>* skipping installation test
> >>* checking package directory ... OK
> >>* checking for portable file names ... OK
> >>* checking for sufficient/correct file permissions ... OK
> >>* checking DESCRIPTION meta-information ... OK
> >>* checking package dependencies ... OK
> >>* checking index information ... OK
> >>* checking package subdirectories ... OK
> >>* checking S3 generic/method consistency ... WARNING
> >>Erro: .First.lib failed for 'tcltk'
> >>Call sequence:
> >>2: stop(gettextf(".First.lib failed for '%s'", libraryPkgName(package)),
> >> domain = NA)
> >>1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose =
> >>FALSE)
> >>Interrupted execution
> >>See section 'Generic functions and methods' of the 'Writing R Extensions'
> >>manual.
> >>* checking replacement functions ... WARNING
> >>Error: .First.lib failed for 'tcltk'
> >>Call sequence:
> >>2: stop(gettextf(".First.lib failed for '%s'", libraryPkgName(package)),
> >> domain = NA)
> >>1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose =
> >>FALSE)
> >>Interrupted execution
> >>In R, the argument of a replacement function which corresponds to the right
> >>hand side must be named 'value'.
> >>* checking foreign function calls ... WARNING
> >>Error: .First.lib failed for 'tcltk'
> >>Call sequence:
> >>2: stop(gettextf(".First.lib failed for '%s'", libraryPkgName(package)),
> >> domain = NA)
> >>1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose =
> >>FALSE)
> >>Interrupted execution
> >>See section 'System and foreign language interfaces' of the 'Writing R
> >>Extensions' manual.
> >>* checking Rd files ... OK
> >>* checking for missing documentation entries ... WARNING
> >>Error: .First.lib failed for 'tcltk'
> >>Call sequence:
> >>2: stop(gettextf(".First.lib failed for '%s'", libraryPkgName(package)),
> >> domain = NA)
> >>1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose =
> >>FALSE)
> >>Interrupted execution
> >>All user-level objects in a package should have documentation entries.
> >>See chapter 'Writing R documentation files' in manual 'Writing R
> >>Extensions'.
> >>* checking for code/documentation mismatches ... WARNING
> >>Error: .First.lib failed for 'tcltk'
> >>Call sequence:
> >>2: stop(gettextf(".First.lib failed for '%s'", libraryPkgName(package)),
> >> domain = NA)
> >>1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose =
> >>FALSE)
> >>Interrupted execution
> >>Error: .First.lib failed for 'tcltk'
> >>Call sequence:
> >>2: stop(gettextf(".First.lib failed for '%s'", libraryPkgName(package)),
> >> domain = NA)
> >>1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose =
> >>FALSE)
> >>Interrupted execution
> >>Error: .First.lib failed for 'tcltk'
> >>Call sequence:
> >>2: stop(gettextf(".First.lib failed for '%s'", libraryPkgName(package)),
> >> domain = NA)
> >>1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose =
> >>FALSE)
> >>Interrupted execution
> >>* checking Rd \usage sections ... OK
> >>* checking DVI version of manual ... OK
> >>
> >>[end log file]
> >>
> >>The problem is in the tcltk package. I have searched in the archives,
> >>but didin't find anything similar to this problem (maybe there is, but i
> >>was not able to identify it). I really don't know what all the warnings
> >>means. What i need to know is what am i missing, and if there is
> >>something i can fix it. Also, are there any problems if i continue the
> >>installation without fix something?
> >>
> >>P.S.: actually R is running already from where it was buit, but i want
> >>to install it. So i want to avoid future problems, if this warnings
> >>really make some.
> >>
> >>Any help is appreciated. Thanks!
> >>
> >>Fernando Mayer.
> >>
> >>version
> >> _
> >>platform i686-pc-linux-gnu
> >>arch i686
> >>os linux-gnu [SuSE 9.3]
> >>system i686, linux-gnu
> >>status
> >>major 2
> >>minor 1.1
> >>year 2005
> >>month 06
> >>day 20
> >>language R
> >>
> >>
> >> [[alternative HTML version deleted]]
> >>
> >>______________________________________________
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> >>https://stat.ethz.ch/mailman/listinfo/r-help
> >>PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
> >>
> >>
> >>
> >
> >
> >
>
> [[alternative HTML version deleted]]
>
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-- 
   O__  ---- Peter Dalgaard             ุster Farimagsgade 5, Entr.B
  c/ /'_ --- Dept. of Biostatistics     PO Box 2099, 1014 Cph. K
 (*) \(*) -- University of Copenhagen   Denmark          Ph:  (+45) 35327918
~~~~~~~~~~ - (p.dalgaard@biostat.ku.dk)                  FAX: (+45) 35327907

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Received on Wed Sep 28 20:21:34 2005

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