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

From: Fernando Mayer <fernandomayer_at_gmail.com>
Date: Thu 29 Sep 2005 - 02:19:03 EST

Dear Peter Dalgaard,

first, sorry for my delay to this reply, but I only have acces to this machine in the morning (consider also the time it takes to run make and make check)...

It seems that the problem was really with some missing -devel packages. I followed your suggestions and installed libjpeg-devel, tk-devel and tcl-devel. The readline-devel and xorg-x11-devel packages were already installed. After this, I also re-built R, now as 'normal' user to my home folder (/home/fernando/programs/R-2.1.1). So I re-run again make check, make check-devel and make check-all. Everything seems OK now. No more those warnings in tcltk package and in any other.

Now going to installation...

Thank you very much for your (and Prof Brian Ripley) help! Fernando Mayer.

Peter Dalgaard escreveu:

>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
>>>>
>>>>

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