[BioC] Installing problems of Flow Cytometry on Ubuntu Karmic

[Vincent Carey]

sorry, I am not reading carefully enough at such odd hours.  anyway,
indeed one needs to use R 2.11 to get iFlow to install via biocLite,
and there are numerous dependencies as with flowMerge

On Mon, Feb 8, 2010 at 8:50 AM, Philipp Meng
<philipp.meng at meduniwien.ac.at> wrote:
> Hi Vincent,
>
> Sorry for giving not adequate information.
> I am using R version 2.10 and i am trying to install "iFlow" with the
> command
> "biocLite("iFlow")" as described in the installation instructions.
>
> The installation stops with:
> ####begin msg
>> biocLite("iFlow")
> Using R version 2.10.1, biocinstall version 2.5.10.
> Installing Bioconductor version 2.5 packages:
> [1] "iFlow"
> Please wait...
>
> Warnung in install.packages(pkgs = pkgs, repos = repos, ...) :
>  argument 'lib' is missing: using '/usr/local/lib/R/site-library'
> Warnmeldung:
> In getDependencies(pkgs, dependencies, available, lib) :
>  package ‘iFlow’ is not available
>>
> ####end msg
>
> flowMerge is installed already - the broken installation has been
> resolved by upgrading to R v.2.10.
>
> Sorry for the confusion,
>
> Philipp
>
> Am Montag, den 08.02.2010, 06:01 -0500 schrieb Vincent Carey:
>> you are not giving adequate information, please read the posting
>> guide.  "not installable" can mean any number of things.  i have a
>> reasonably well-equipped linux machine with R 2.10 and i tried
>> biocLite("flowMerge") -- it chunked along, finding deficiencies in my
>> tcltk support, unable to load rpanel,
>> and then
>>
>> checking for gcc -std=gnu99 option to accept ISO C89... none needed
>> checking for gsl-config... no
>> checking for GSL - version >= 1.6... no
>> *** The gsl-config script installed by GSL could not be found
>> *** If GSL was installed in PREFIX, make sure PREFIX/bin is in
>> *** your path, or set the GSL_CONFIG environment variable to the
>> *** full path to gsl-config.
>> configure: error: Cannot find Gnu Scientific Library >=1.6
>> ERROR: configuration failed for package 'flowClust'
>> * removing '/mnt/data/stvjc/ExternalSoft/R-2-10-branch/library/flowClust'
>> Loading required package: utils
>> * installing *source* package 'flowMerge' ...
>>
>> so if i want to install flowMerge, i'll have to improve my
>> infrastructure.  please report detailed error messages if you need
>> additional assistance ... flowMerge has numerous dependencies and the
>> chain could break at any one of them
>>
>> On Mon, Feb 8, 2010 at 5:52 AM, Philipp Meng
>> <philipp.meng at meduniwien.ac.at> wrote:
>> > Hi Martin,
>> >
>> > Thanks for your fast response. I updated R now to version 2.10.2 from
>> > the repositories directly from the R project.
>> > Now i can install flowMerge without problems.
>> > THANK YOU!
>> > But still, iFlow is not installable. Does it need the development
>> > version of R? Do you have an idea where i could get this?
>> >
>> > Thanks,
>> >
>> > Philipp
>> >
>> > Am Sonntag, den 07.02.2010, 16:27 -0800 schrieb Martin Morgan:
>> >> Hi Philipp --
>> >>
>> >> On 02/07/2010 02:19 PM, Philipp Meng wrote:
>> >> > Dear All,
>> >> >
>> >> >
>> >> > I experience installation problems of the Flow Cytometry Packages on
>> >> > Ubuntu Karmic 9.10.
>> >> > My R version is 2.9.2
>> >> >
>> >> > I can only install parts of the packages mentioned on the following
>> >> > page:
>> >> > http://bioconductor.org/docs/workflows/flowoverview/
>> >> >
>> >> > I always get errormessages like this one:
>> >> > ####begin error msg
>> >> >> biocLite("flowMerge")
>> >> > Using R version 2.9.2, biocinstall version 2.4.13.
>> >> > Installing Bioconductor version 2.4 packages:
>> >> > [1] "flowMerge"
>> >> > Please wait...
>> >> >
>> >> > Warnung in install.packages(pkgs = pkgs, repos = repos, dependencies =
>> >> > dependencies,  :
>> >> >   argument 'lib' is missing: using '/usr/local/lib/R/site-library'
>> >> > Warnmeldung:
>> >> > In getDependencies(pkgs, dependencies, available, lib) :
>> >> >   package ‘flowMerge’ is not available
>> >> > ####end error msg
>> >>
>> >> flowMerge wasn't introduced until Bioc 2.5 / R-2.10; you'll need to
>> >> update your R before being able to install flowMerge. To find out about
>> >> packages available for your release, visit http://bioconductor.org,
>> >> follow Software > Downloads and then Past BioC Releases on the left
>> >> navigation panel.
>> >>
>> >> Martin
>> >>
>> >> >
>> >> > I really appreciate your help!
>> >> > Thanks in advance!
>> >> >
>> >> > Greetings,
>> >> >
>> >> > Philipp
>> >> >
>> >> > _______________________________________________
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>> >>
>> >>
>> >
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>
>