
Hi Kasper,

The "GUI" is:
setRepositories() (default launches a tcltk window to select
repositories)
install.packages()  (default launches a tcltk window to select
libraries)


I see now that setRepositories() uses

> tools:::.read_repositories
function (file) 
{
    db <- utils::read.delim(file, header = TRUE, comment.char = "#", 
        colClasses = c(rep.int("character", 3L), rep.int("logical", 
            4L)))
    db[, "URL"] <- .expand_BioC_repository_URLs(db[, "URL"])
    db
}
<environment: namespace:tools>

which provides the incorrect version of Bioc
at .expand_BioC_repository_URLs(db[, "URL"]) I think. The first time I
have encountered that in using the development version for 3 years...

I see now that BiocLite has the bioC version hard-wired so avoids the
issue,  as you have said.

Guess I was unaware that 
setRepositories() 
were unsafe on the development version. I promise not to stray from the
path again ;-)

Versions and platform as per my previous email

Thanks for you help

Best wishes
Paul


 


-----Original Message-----
From: Kasper Daniel Hansen <kasperdanielhansen@gmail.com>
To: Paul Leo <p.leo@uq.edu.au>
Cc: Dan Tenenbaum <dtenenba@fhcrc.org>, BioC
<bioconductor@stat.math.ethz.ch>
Subject: Re: [BioC] Rsamtools from biocLite using R-devel
Date: Tue, 2 Nov 2010 09:19:18 -0400

Hi Paul


A couple of immediate comments on your output below


(1) Yes, upgrading Rsamtools means upgrading IRanges means ..., but that
is unavoidable.  If you are using R-devel, this is what happens.  If you
want stability, you should use R-2.12 and Bioconductor 2.7.


(2) Your GUI (which I have no idea what is, please tell us (and also the
platform)), is broken.  If you look at the URLs below you will see that
it tries to pull tarballs from Bioconductor 2.7 under R-devel, which is
a big no-no.  This is why we have biocLite and why there are thousands
of posts on this email list that says always use biocLite.


If you have packages installed under R-devel from the GUI you should
expect that your entire Bioconductor installation has problems.  Of
course, since we are close to release Biconductor 2.7 is approximately
equal to Bioconductor 2.8, but the discrepancy will increase as times go
on.  You are already experiencing the first big discrepancy.


To be precise, the only way to get Rsamtools to work under current
R-devel is to get the newest version which depends on the newest
IRanges.  There is no way around it.


Now, I would simply do as I said in my previous post (source biocLite,
use update.packages(repos = biocinstallrepos()).  This might update
quite a few packages, but there is no way around it.  And if you are
using a fresh R-devel (as I can see you are), you are on the bleeding
edge anyway.


Trying to deal with this by selectively updating one package at a time
will only lead to frustration.


Kasper

On Tue, Nov 2, 2010 at 1:57 AM, Paul Leo <p.leo@uq.edu.au> wrote:
        
        HI Kasper, 
        Thanks for that info, it seems the mess is not confined to
        Rsamtools
        
        But I have a solution "of sorts"
        
        ---------------------------------
        
        if I use install.packages() and choose packages interactively:
        
        FOR
        
        
        R version 2.13.0 Under development (unstable) (2010-11-01
        r53513)
        
        
        
        I get the following :
        
        trying URL
        'http://www.bioconductor.org/packages/2.7/bioc/src/contrib/IRanges_1.8.2.tar.gz'   (1.9.6 should be used)
        trying URL
        'http://www.bioconductor.org/packages/2.7/bioc/src/contrib/Rsamtools_1.2.0.tar.gz'  (1.3.3 should be used)
        trying URL
        'http://www.bioconductor.org/packages/2.7/bioc/src/contrib/ShortRead_1.8.0.tar.gz'  (1.9.2 ....)
        
        are downloaded with update.packages()
        I can install Rsamtools_1.3.3.tar.gz but needs the latest
        IRanges and I'm then on the dependency treadmill....
        
        Problem is for both 2010-10-26 r53428 and r53513 installed from 
        
        svn checkout
        https://svn.r-project.org/R/trunk/ /media/Bioinform-D/Research/R_latest_install etc ...
        
        BOTH
        
        source("http://bioconductor.org/biocLite.R")
        update.packages(repos=biocinstallRepos(), ask=FALSE)
        
        OR
        
        source("http://bioconductor.org/biocLite.R")
        pkgs <- rownames(installed.packages())
        biocLite(pkgs)
        
        Do not help it all otherwise appears up-to date
        
        $$$$$$$$ HOWEVER  
        
        if I use 
        > biocLite("Rsamtools")
        
        I get
        trying URL
        'http://www.bioconductor.org/packages/2.8/bioc/src/contrib/Rsamtools_1.3.3.tar.gz' 
        
        and the correct version  of ShortRead etc etc
        
        So its just install.packages() and using the Tcl/Tk interface to install that is causing the problem....?
        Not sure how that gets fixed....
        
        Cheers
        Paul
        
        
        
        
        -----Original Message-----
        From: Kasper Daniel Hansen <kasperdanielhansen@gmail.com>
        To: Paul Leo <p.leo@uq.edu.au>
        Cc: Dan Tenenbaum <dtenenba@fhcrc.org>, BioC
        <bioconductor@stat.math.ethz.ch>
        Subject: Re: [BioC] Rsamtools from biocLite using R-devel
        
        
        Date: Mon, 1 Nov 2010 23:00:46 -0400
        
        Hi Paul 
        
        The issue was (on my end at least) fixed this afternoon (EST
        time).  I now get the new version of Rsamtools (and a lot of
        other core packages) when I use biocLite under R-devel.  But
        earlier today the source tarball was broken.  
        
        I have no idea why a svn checkout would not work.  As far as I
        know, that has been working for some days.  Did you remember to
        rebuild the source tarball before installing, like   R-devel CMD
        build Rsamtools   R-devel CMD INSTALL Rsamtools_1.3.3.tar.gz
        Note that your svn checkout version should certainly be 1.3.3. 
        
        I would recommend  R>
        source("http://www.bioconductor.org/biocLite.R") R>
        update.packages(repos = biocinstallrepos()) in a fresh R-devel
        session. 
        
        Double-check that the version of Rsamtools it is downloading is
        something like 1.3.3 (and not 1.1.17). 
        
        Given the problems there has been the last couple of days it
        might be nice if you report back whether or not you got this
        fixed. 
        
        Kasper 
        
        On Mon, Nov 1, 2010 at 9:43 PM, Paul Leo <p.leo@uq.edu.au>
        wrote: 
        
                It appears this is a known issue, was the fix time just
                optimistic?
                
                
                I did a svn checkout today abs R and Rsamtools do not
                play nice.
                ShortRead will not load without Rsamtools either....
                
                
                
                
                
                
                
                ** preparing package for lazy loading Attaching package:
                'IRanges' The following object(s) are masked from
                'package:base':     Map, cbind, eval, mapply, order,
                paste, pmax, pmax.int, pmin,     pmin.int, rbind,
                rep.int 
                
                , table
                
                Error : object ‘normalizePath’ is not exported by 'namespace:utils'
                ERROR: lazy loading failed for package ‘Rsamtools’
                * removing ‘/home/pleo/R_latest/library/Rsamtools’
                
                The downloaded packages are in
                	‘/tmp/RtmpuHAod7/downloaded_packages’
                Updating HTML index of packages in '.Library'
                Warning message:
                In install.packages() :
                  installation of package 'Rsamtools' had non-zero exit status
                
                > sessionInfo()
                R version 2.13.0 Under development (unstable) (2010-11-01 r53513)
                Platform: x86_64-unknown-linux-gnu (64-bit)
                
                locale:
                 [1] LC_CTYPE=en_AU.UTF-8       LC_NUMERIC=C              
                 [3] LC_TIME=en_AU.UTF-8        LC_COLLATE=en_AU.UTF-8    
                 [5] LC_MONETARY=C              LC_MESSAGES=en_AU.UTF-8   
                 [7] LC_PAPER=en_AU.UTF-8       LC_NAME=C                 
                 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
                [11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C       
                
                attached base packages:
                [1] stats     graphics  grDevices utils     datasets  methods   base     
                
                loaded via a namespace (and not attached):
                [1] tcltk_2.13.0 tools_2.13.0
                
                
                
                
                
                -----Original Message-----
                From: Dan Tenenbaum <dtenenba@fhcrc.org>
                To: Kasper Daniel Hansen <kasperdanielhansen@gmail.com>
                Cc: BioC <bioconductor@stat.math.ethz.ch>
                Subject: Re: [BioC] Rsamtools from biocLite using
                R-devel
                Date: Thu, 28 Oct 2010 07:41:22 -0700
                
                
                
                On Thu, Oct 28, 2010 at 7:06 AM, Kasper Daniel Hansen <
                kasperdanielhansen@gmail.com> wrote: > Just a note about
                this: so far I have not seen any resolution. And >
                according to the devel build logs the R-devel on lamb2
                (which I assume > is being used for generating the
                source tarballs, but I could be > completely wrong) is
                from 9-30 which is almost a month old (which kind > of
                surprised me) (pelham is 1.5 months old). > > Kasper, R
                and Rsamtools should play well together now on lamb2. R
                2.13 has been updated on all build nodes in the last
                couple of days. The build report is out of date due to
                other issues which will be resolved today. Thanks Dan >
                Kasper > > On Tue, Oct 26, 2010 at 4:11 PM, Martin
                Morgan <mtmorgan@fhcrc.org> wrote: > > On 10/26/2010
                12:47 PM, Kasper Daniel Hansen wrote: > >> When I try to
                use biocLite to upgrade my Rsamtools under R-devel, > >>
                biocLite reports that it tries to use the 2.8 repository
                (correct), > >> but it tries to download Rsamtools
                1.1.17 whereas the version of > >> Rsamtools installed
                using R-2.12 is version 1.2.0 (later than 1.1.17) > >>
                and the version accessible from subversion is version
                1.3.2. > >> > >> I suspect this has something to do with
                the recent problem with > >> R-devel and biocLite and
                also by the fact that Rsamtools currently > >> does not
                seem to build under any platform. > >> > >> Besides the
                obvious problem, I am running into problems with my > >>
                existing Rsamtools because normalizePath has been moved
                from utils to > >> base (which is commented on in
                NAMESPACE). Coincidently, it seems > >> that the issue
                that makes Rsamtools 1.3.2 fail to build is also > >>
                related to the use of normalizePath that may have its
                arguments > >> changed, > > > > yes you and I are ahead
                of the build system -- Rsamtools wants > > normalizePath
                to be in base, but R-devel on the build system was not
                (it > > has been updated very recently) current enough
                for that. So you were > > getting the last Rsamtools
                that the 'devel' portion of the build system > >
                correctly built, v. 1.1.17. > > > > This is being
                straightened out, and should be back to normal over the
                > > next day or so. The short-term solution is to
                install Rsamtools from > > source, from an svn checkout
                > > > >
                http://bioconductor.org/developers/source-control/ > > >
                > Martin > > > >> > >> Kasper > >> > >>
                _______________________________________________ > >>
                Bioconductor mailing list > >>
                Bioconductor@stat.math.ethz.ch > >>
                https://stat.ethz.ch/mailman/listinfo/bioconductor > >>
                Search the archives: >
                http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > > > -- > > Computational Biology > > Fred Hutchinson Cancer Research Center > > 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 > > > > Location: M1-B861 > > Telephone: 206 667-2793 > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor
                
                >
                >
                
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