[BioC] Installing problems of Flow Cytometry on Ubuntu Karmic

[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
>> >
>> > _______________________________________________
>> > Bioconductor mailing list
>> > Bioconductor at stat.math.ethz.ch
>> > https://stat.ethz.ch/mailman/listinfo/bioconductor
>> > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>>
>>
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor