I guess I'll step in since I haven't seen a response from Jafar yet...
It
is my understanding that flowDensity has been submitted to
BioConductor
quite a while ago, but there is some disagreement about certain design
aspects between the main package developer (Jafar) and the package
reviewer
on the BioConductor side. So this went back and forth a few times,
plus
Jafar just came back from (a rather long :-) vacation, which means
that
this still hasn't been resolved. So the package is not in BioConductor
(yet), but it is available from the author if someone wants to use it
right
now. The best way is to email Jafar directly (Jafar Taghiyar, <
jafar.taghiyar@gmail.com>). Alternatively (e.g., if he does not
respond
fast enough), please feel free to email me offline and I can grab the
latest version from our internal SVN and just give it to you. We are
using
flowDensity routinely in our lab so I would say it is ready for
production
in that sense.
Cheers,
Josef
--
Josef Spidlen, Ph.D.
Staff Scientist, Terry Fox Laboratory, BC Cancer Agency, Cancer
Research
Centre
675 West 10th Avenue, Vancouver, BC, V5Z1L3, Canada
Tel. +1 604-675-8000, ex. 7755
>
> Message: 1
> Date: Thu, 10 Apr 2014 09:29:45 +0200
> From: Raghu <eraghu@mpi-muenster.mpg.de>
> To: Dan Tenenbaum <dtenenba@fhcrc.org>
> Cc: bioconductor@r-project.org
> Subject: Re: [BioC] installing flowDensity
> Message-ID: <53464869.8050306@mpi-muenster.mpg.de>
> Content-Type: text/plain; charset=UTF-8; format=flowed
> 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@mpi-muenster.mpg.de>
> >> To: bioconductor@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@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
>
>
> ------------------------------
> Message: 2
> Date: Thu, 10 Apr 2014 07:27:16 -0700 (PDT)
> From: Dan Tenenbaum <dtenenba@fhcrc.org>
> To: Raghu <eraghu@mpi-muenster.mpg.de>
> Cc: bioconductor@r-project.org
> Subject: Re: [BioC] installing flowDensity
> Message-ID:
<830338663.1497875.1397140036758.JavaMail.root@fhcrc.org>
> Content-Type: text/plain; charset=utf-8
> 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@mpi-muenster.mpg.de>
> > To: "Dan Tenenbaum" <dtenenba@fhcrc.org>
> > Cc: bioconductor@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@mpi-muenster.mpg.de>
> > >> To: bioconductor@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@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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