From mmokrejs at ribosome.natur.cuni.cz  Mon Nov  1 19:54:28 2004
From: mmokrejs at ribosome.natur.cuni.cz (=?windows-1252?Q?Martin_MOKREJ=8A?=)
Date: Mon Nov  1 19:54:35 2004
Subject: [Rd] R-2.0.0/lib/R/bin/INSTALL (PR#7329)
In-Reply-To: <x2oeihv4t7.fsf@biostat.ku.dk>
References: <20041101171750.C906E11020@slim.kubism.ku.dk>
	<x2oeihv4t7.fsf@biostat.ku.dk>
Message-ID: <41868664.60803@ribosome.natur.cuni.cz>

Dear all,
 I tried to follow http://www.bioconductor.org/faq.html#getBioC to install it,
and that's why I got to the problem.


Using getBioC to obtain Bioconductor packages

         1. From your R session, type:
            source("http://www.bioconductor.org/getBioC.R")
            this will download the getBioC functionality into your R session.
         2. To install Bioconductor packages, use the function "getBioC" as follows. To download and install the default packages, type:
            getBioC()
            For a different subset of packages, use the following  values for the libName argument (or "all" for all packages)
                o "all" - gets all packages (warning: This is a very large set)
                o "affy" - gets packages affy, affycomp, affydata, affyPLM, annaffy, gcrma, makecdfenv, matchprobes, plus "exprs".
                o "cdna" - gets packages marray, vsn, plus "exprs".
                o "default" - gets all packages from "affy", "cdna" and "exprs"
                o "exprs" - gets packages Biobase, annotate, edd, genefilter, geneploter, globaltest,ROC, MAGEML, multtest, limma, pamr, siggenes and vsn.
                o "graph" - gets packages graph, Rgraphviz and RBGL
                o "prog" - gets packages externalVector, graph, hexbin and Ruuid.
                o "widgets" - gets packages tkWidgets, widgetTools and DynDoc.
                o "database"- gets packages AnnBuilder, SAGElyzer, Rdbi, and RdbiPgSQL.
                o "design" - gets packages daMA and factDesign.
                o "annotation" - gets packages annotate, AnnBuilder, humanLLMappings, KEGG, GO, SNPtools, makecdfenv, and ontoTools.
                o "analyses" - gets packages Biobase, ctc, daMA, edd, factDesign, genefilter, geneplotter, globaltest, gpls, limma, RMAGEML, multtest, pamr, ROC, siggenes, and splicegear.
                o "externalData" - gets packages externalVector and rhdf5.
                o "arrayCGH" - gets packages DNAcopy and aCGH.
                o "proteomics" - gets packages gpls, PROcess and apComplex.
              You may also call "getBioC "with other arguments, including
                o "destdir": the directory where the downloaded packages will be stored. The default is the current working directory.
                o "develOK": Can be either TRUE or FALSE. The default value is , which means that only release level software will be installed. If instead it is set to TRUE, developmental software will be preferentially installed.
                o "verbose": TRUE or FALSE, to have any error related to the downloading process printed (TRUE) or not (FALSE). Error messages will still be returned but invisible if verbose is set to FALSE.
                o "bundle": a boolean indicating whether packages will be downloaded as bundles (TRUE) or individual packages (FALSE). Valid bundle (e. g. "all", "exprs") or package ("tkWidgets", "annotate") names have to be used in each case. If "bundle" is FALSE, any packages listed in the "libName" argument will be assumed to be proper package names.
         6. The script will try to install the downloaded packages and print "Installation complete" and TRUE on the screen when the installation was successful. Contact Jeff Gentry (jgentry@jimmy.harvard.edu) if the installation fails.


Maybe, there are items 3-5 lost. The document doesnt even say how to close R.
I doubt thise section is NOT for newbies, this describes how to get the things installed,
right? ;-)

So, typing "quit" at the ">" prompt doesn't help, btw. ^d is better, the only problem
is I've no idea if I should say y or n tot he question if I want to save my temporary image ....




To the INSTALL script actually I got via this problem:

Loading required package: tools 
Welcome to Bioconductor 
         Vignettes contain introductory material.  To view, 
         simply type: openVignette() 
         For details on reading vignettes, see
         the openVignette help page.
[1] TRUE
[1] TRUE
Loading required package: reposTools 

Attaching package 'reposTools':


        The following object(s) are masked from package:base :

         getRversion 

Loading required package: tkWidgets 
Loading required package: widgetTools 
Loading required package: tcltk 
X Error of failed request:  BadAtom (invalid Atom parameter)
  Major opcode of failed request:  18 (X_ChangeProperty)
  Atom id in failed request:  0x26a
  Serial number of failed request:  11
  Current serial number in output stream:  14
/afs/.biomed.cas.cz/i386_linux24/usr/bio/R-2.0.0/lib/R/bin/INSTALL: line 1: 12432 Broken pipe             cat "/afs/.biomed.cas.cz/i386_linux24/usr/bio/R-2.0.0/lib/R/library/AnnBuilder/R/AnnBuilder"
ERROR: execution of package source for 'AnnBuilder' failed



So  I tried to lookup the file and execute it. As is breaks around dcf.sh,
I thought it would help you to make the code die more clearly and more earlier.



Here is another case:

Loading required package: Biobase 
Loading required package: tools 
Welcome to Bioconductor 
         Vignettes contain introductory material.  To view, 
         simply type: openVignette() 
         For details on reading vignettes, see
         the openVignette help page.
[1] TRUE
Loading required package: GO 
Loading required package: annotate 
Loading required package: reposTools 

Attaching package 'reposTools':


        The following object(s) are masked from package:base :

         getRversion 

Loading required package: tkWidgets 
Loading required package: widgetTools 
Loading required package: tcltk 
X Error of failed request:  BadAtom (invalid Atom parameter)
  Major opcode of failed request:  18 (X_ChangeProperty)
  Atom id in failed request:  0x26a
  Serial number of failed request:  11
  Current serial number in output stream:  14
/afs/.biomed.cas.cz/i386_linux24/usr/bio/R-2.0.0/lib/R/bin/INSTALL: line 1: 13475 Broken pipe             cat "/afs/.biomed.cas.cz/i386_linux24/usr/bio/R-2.0.0/lib/R/library/GOstats/R/GOstats"
ERROR: execution of package source for 'GOstats' failed



Actually, as I saw the xauth check in configure, didn't bioconductor screw up my
X-forwarding? It seems so, as I cannot start any X-app right now. It works in a fresh session.
If this is the case, your appas should check first for env variable SSH_TTY, and if not set,
it could run xauth. Otherwise it should rather leave user do take care of X11 output.


Hope this helps
Martin


Peter Dalgaard wrote:
> mmokrejs@ribosome.natur.cuni.cz writes:
> 
> 
>>Hi,
>>  the install script should make sure user has set R_HOME variable.
>>I don't have it as root, and get stupid messages. Anyway, should it be set
>>to $blah/R-2.0.0/lib/R/ or $blah/R-2.0.0 ?
>>Thanks for help
>>Martin
> 
> 
> Please read the R-admin manual. The correct way of calling the INSTALL
> script is via
> 
>    R CMD INSTALL ...
> 
> And that will set automatically set R_HOME appropriately.
> 
> And please try to avoid reporting your own errors as bugs in R...
>


[Rd] R-2.0.0/lib/R/bin/INSTALL (PR#7329)
=?windows-1252?Q?Martin_MOKREJ=8A?=