[BioC] installing flowDensity

Dan Tenenbaum dtenenba at fhcrc.org
Thu Apr 10 16:27:16 CEST 2014


Please see my subsequent email, quoted here:

---
Martin points out that there is no package called flowDensity. Looks like there is something called the "flowDensity gating plugin" for openCyto but I don't know how you install it. You should contact the maintainer of openCyto (maintainer email address available at http://bioconductor.org/packages/release/bioc/html/openCyto.html).
---

Dan


----- Original Message -----
> From: "Raghu" <eraghu at mpi-muenster.mpg.de>
> To: "Dan Tenenbaum" <dtenenba at fhcrc.org>
> Cc: bioconductor at r-project.org
> Sent: Thursday, April 10, 2014 12:29:45 AM
> Subject: Re: [BioC] installing flowDensity
> 
> This is the output when installing in R v3.1 beta (ubuntu 12.04)
> =================================================
> > source('http://bioconductor.org/biocLite.R')
> Bioconductor version 2.13 (BiocInstaller 1.12.0), ?biocLite for help
> > biocLite('flowDensity')
> 
> BioC_mirror: http://bioconductor.org
> Using Bioconductor version 2.13 (BiocInstaller 1.12.0), R version
> 3.1.0.
> Installing package(s) 'flowDensity'
> Warning message:
> package ‘flowDensity’ is not available (for R version 3.1.0 beta)
> > sessionInfo()
> R version 3.1.0 beta (2014-03-28 r65330)
> Platform: x86_64-pc-linux-gnu (64-bit)
> 
> locale:
>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
>  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
> 
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
> 
> other attached packages:
> [1] BiocInstaller_1.12.0
> 
> loaded via a namespace (and not attached):
> [1] tools_3.1.0
> > biocinstallRepos()
>                                                BioCsoft
>            "http://bioconductor.org/packages/2.13/bioc"
>                                                 BioCann
> "http://bioconductor.org/packages/2.13/data/annotation"
>                                                 BioCexp
> "http://bioconductor.org/packages/2.13/data/experiment"
>                                               BioCextra
>           "http://bioconductor.org/packages/2.13/extra"
>                                                    CRAN
>                                 "http://cran.fhcrc.org"
> 
> when trying to install in R v3.0 (this is in windows -7)
> =================================================
> 
> 
> > source('http://bioconductor.org/biocLite.R')
> Bioconductor version 2.13 (BiocInstaller 1.12.0), ?biocLite for help
> > biocLite('flowDensity')
> BioC_mirror: http://bioconductor.org
> Using Bioconductor version 2.13 (BiocInstaller 1.12.0), R version
> 3.0.3.
> Installing package(s) 'flowDensity'
> Warning message:
> package ‘flowDensity’ is not available (for R version 3.0.3)
> > sessionInfo()
> R version 3.0.3 (2014-03-06)
> Platform: i386-w64-mingw32/i386 (32-bit)
> 
> locale:
> [1] LC_COLLATE=German_Germany.1252  LC_CTYPE=German_Germany.1252
> [3] LC_MONETARY=German_Germany.1252 LC_NUMERIC=C
> [5] LC_TIME=German_Germany.1252
> 
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
> 
> other attached packages:
> [1] BiocInstaller_1.12.0
> 
> loaded via a namespace (and not attached):
> [1] tools_3.0.3
> > biocinstallRepos()
>                                                BioCsoft
>            "http://bioconductor.org/packages/2.13/bioc"
>                                                 BioCann
> "http://bioconductor.org/packages/2.13/data/annotation"
>                                                 BioCexp
> "http://bioconductor.org/packages/2.13/data/experiment"
>                                               BioCextra
>           "http://bioconductor.org/packages/2.13/extra"
>                                                    CRAN
>                                 "http://cran.fhcrc.org"
>                                               CRANextra
>                    "http://www.stats.ox.ac.uk/pub/RWin"
> 
> 
> 
> regards,
> Raghu
> 
> 
> 
> On Thu 10 Apr 2014 07:31:13 AM CEST, Dan Tenenbaum wrote:
> >
> >
> > ----- Original Message -----
> >> From: "Raghu" <eraghu at mpi-muenster.mpg.de>
> >> To: bioconductor at r-project.org
> >> Sent: Wednesday, April 9, 2014 12:17:46 PM
> >> Subject: [BioC] installing flowDensity
> >>
> >> Dear all,
> >>
> >> I am unable to install flowDensity package for cytometry analysis.
> >> The
> >> error in both 3.0 and 3.1 versions of R (ubuntu 12.04) shows
> >>
> >> using normal install.packages('flowDensity') and bioconductor
> >> installtion, the error message is
> >> Warning message:
> >> package ‘flowDensity’ is not available (for R version 3.1.0 beta)
> >
> > Please show us how you tried to install the package.
> >
> > The recommended way is:
> >
> > source('http://bioconductor.org/biocLite.R')
> > biocLite('flowDensity')
> >
> > In order to help us diagnose your problem, please also send the
> > output of
> > the sessionInfo() and biocinstallRepos() commands.
> >
> > Dan
> >
> >
> >
> >
> >>
> >> Thanks,
> >> Raghu
> >>
> >> _______________________________________________
> >> Bioconductor mailing list
> >> Bioconductor at r-project.org
> >> https://stat.ethz.ch/mailman/listinfo/bioconductor
> >> Search the archives:
> >> http://news.gmane.org/gmane.science.biology.informatics.conductor
> >>
> 
> 
> 
> --
> Raghu Erapaneedi
> Max Planck Institute for Molecular Biomedicine
> Mammalian Cell Signalling Laboratory
> Department of Vascular Cell Biology
> Roentgenstr-20
> D-48149 Muenster
> Germany
> Tel:+49(0)251-70365-223
> 



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