[BioC] Building BioC 2.2 with R 2.7.0

[Groot, Philip de]

Hello all,
 
I encountered the same problem with genefilter. Genefilter depends on tkWidgets which in turn depends on access to the x-server (stupid, but this is true for several Bioconductor packages now; it's rather annoying). So: use the xhost command to properly arrange your X display properties and the genefilter problem might be solved.
 
Regards,
 
Dr. Philip de Groot
Wageningen University

________________________________

From: Robert Gentleman [mailto:rgentlem at fhcrc.org]
Sent: Mon 26/05/2008 10:36 PM
To: Kasper Daniel Hansen
Cc: Atro.Tossavainen at helsinki.fi; bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] Building BioC 2.2 with R 2.7.0



Hi all,

Kasper Daniel Hansen wrote:
> The first thing to understand is that in some case R CMD INSTALL can
> seem sucessful, but when you to to do the librray command from within R
> it fails, ie.
>
> R> library(SOMEPACKAGE)
>
> This typically happens when a package is dynamically linked to something
> that R cannot find when it tries to load the package. Now, the slightly
> confusing issue that may happen is that when package XX depends on
> package YY, R will try to load the YY package when it tries to install
> XX. So if YY has the problem I just mention you will not discover it
> when you install YY but rather when you install something that depends
> on YY.
>
> See below for rest of comments
>
> On May 26, 2008, at 4:03 AM, Atro Tossavainen wrote:
>
>> I've successfully built R 2.7.0 for x86 Linux (RHEL4), x86_64 Linux
>> (RHEL4), Solaris 8 SPARC and IRIX 6.5.  The Bioconductor installation
>> process works fine on x86_64 Linux and IRIX.
>>
>> Building annaffy fails on x86 Linux, and building annaffy and simpleaffy
>> fail on Solaris 8.  In both cases, the annaffy error message is as
>> follows:
>>
>> Loading required package: GO.db
>> Loading required package: AnnotationDbi
>> Loading required package: DBI
>> Loading required package: RSQLite
>> Error in sqliteExecStatement(con, statement, bind.data) :
>>  RS-DBI driver: (error in statement: no such table: metadata)

   My guess is that Kasper is pretty close, but that the real culprit is
RSQLite. But without a complete log of what did and did not install we
won't know.

   So, if you could, please try
  library(RSQLite)

   and

  library(GO)

  and let us know which of them fails?
  Depending on the outcome of that, you might then try to install as
described on the download instructions - via biocLite (as you may also
have version mismatches, which we can't know about from the output given).

   If you did not use biocLite please do, it is intended to help avoid
just these issues.

>> Error : .onLoad failed in 'loadNamespace' for 'GO.db'
>> Error: package 'GO.db' could not be loaded
>> Execution halted
>> ERROR: lazy loading failed for package 'annaffy'
>> ** Removing '/.../R/2.7.0/lib/R/library/annaffy'
>
> Here it seems like you GO.db installation is wrong. This is not a
> dynamically linked issue, but something else. My guess is that you have
> some version mismatch.
>
>>
>> The simpleaffy installation attempt ends with:
>>
>> Loading required package: splines
>> Error in dyn.load(file, DLLpath = DLLpath, ...) :
>>  unable to load shared library
>> '/.../R/2.7.0/lib/R/library/genefilter/libs/genefilter.so':
>>  ld.so.1: /.../R/2.7.0/lib. at sys/R/bin/exec/R: fatal: relocation error:
>> file /.../R/2.7.0/lib/R/library/genefilter/libs/genefilter.so: symbol
>> __1cDstdJexceptionG__vtbl_: referenced symbol not found
>> Error: package 'genefilter' could not be loaded
>> Execution halted
>> ERROR: lazy loading failed for package 'simpleaffy'
>> ** Removing '/.../R/2.7.0/lib/R/library/simpleaffy'

   This looks a lot like you did not reinstall genefilter, or if you
did, then perhaps you did not use biocLite.
   Using ldd on
R/2.7.0/lib/R/library/genefilter/libs/genefilter.so
   might reveal what library is missing - but it is typically hard to
get this kind of failure, without doing fairly odd things, and the best
advice is to do something like:

  biocLite("genefilter")

  and then see if it fails to install properly - report back if it
fails, with complete details of what you typed and what you got - and we
might be able to help.

  best wishes
    Robert

>
> Looking at the error, it happens when you try to load genefilter. I will
> bet that if you open up R and do
> R> library(genefilter)
> you will get the same error.
>
> Now, why genefilter does not install properly, I have no idea about.
>
>
>> All help appreciated.
>>
>> --
>> Atro Tossavainen (Mr.)               / The Institute of Biotechnology at
>> Systems Analyst, Techno-Amish &     / the University of Helsinki,
>> Finland,
>> +358-9-19158939  UNIX Dinosaur     / employs me, but my opinions are
>> my own.
>> < URL : http : / / www . helsinki . fi / %7E atossava / > NO FILE
>> ATTACHMENTS
>>
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>
> _______________________________________________
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>

--
Robert Gentleman, PhD
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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206-667-7700
rgentlem at fhcrc.org