Hi, Sisi
FYI, the error message is from rgl failing to install, which is not a flow
package.

Greg
 On Oct 4, 2013 11:36 PM, "Sisi Chen" <sisichen@berkeley.edu> wrote:

> I think I fixed it by installing R3.0.1. I experimented with 3.0.2 and
> 3.0.0, but I think that 3.0.1 is the only one that works for me. It looks
> like the 3.0.2 compatible flow packages will not be released until Oct 15.
>
> ~Sisi
>
>
> On Fri, Oct 4, 2013 at 11:17 PM, Sisi Chen <sisichen@berkeley.edu> wrote:
>
> > Hi Dan!
> >
> > Okay, I changed my R version to 3.0.1 and this is the message I get when
> > installing flowCore:
> >
> > BioC_mirror: http://bioconductor.org
> > Using Bioconductor version 2.12 (BiocInstaller 1.10.3), R version 3.0.1.
> > Installing package(s) 'flowCore'
> > also installing the dependencies ‘rgl’, ‘misc3d’, ‘robustbase’, ‘pcaPP’,
> > ‘mvtnorm’, ‘ks’, ‘Biobase’, ‘rrcov’, ‘BiocGenerics’, ‘feature’, ‘graph’
> >
> > trying URL '
> > http://cran.cnr.Berkeley.edu/bin/macosx/contrib/3.0/rgl_0.93.963.tgz'
> > Content type 'application/x-gzip' length 4635832 bytes (4.4 Mb)
> > opened URL
> > =
> > downloaded 94 Kb
> >
> > trying URL '
> > http://cran.cnr.Berkeley.edu/bin/macosx/contrib/3.0/misc3d_0.8-4.tgz'
> > Content type 'application/x-gzip' length 150245 bytes (146 Kb)
> > opened URL
> > ==================================================
> > downloaded 146 Kb
> >
> > trying URL '
> >
> http://cran.cnr.Berkeley.edu/bin/macosx/contrib/3.0/robustbase_0.9-10.tgz'
> > Content type 'application/x-gzip' length 2303844 bytes (2.2 Mb)
> > opened URL
> > ==================================
> > downloaded 1.5 Mb
> >
> > trying URL '
> > http://cran.cnr.Berkeley.edu/bin/macosx/contrib/3.0/pcaPP_1.9-49.tgz'
> > Content type 'application/x-gzip' length 459941 bytes (449 Kb)
> > opened URL
> > ==================================================
> > downloaded 449 Kb
> >
> > trying URL '
> > http://cran.cnr.Berkeley.edu/bin/macosx/contrib/3.0/mvtnorm_0.9-9996.tgz
> '
> > Content type 'application/x-gzip' length 206552 bytes (201 Kb)
> > opened URL
> > ==================================================
> > downloaded 201 Kb
> >
> > trying URL '
> > http://cran.cnr.Berkeley.edu/bin/macosx/contrib/3.0/ks_1.8.13.tgz'
> > Content type 'application/x-gzip' length 596821 bytes (582 Kb)
> > opened URL
> > ==================================================
> > downloaded 582 Kb
> >
> > trying URL '
> >
> http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/Biobase_2.20.1.tgz
> > '
> > Content type 'application/x-gzip' length 2354463 bytes (2.2 Mb)
> > opened URL
> > ==================================================
> > downloaded 2.2 Mb
> >
> > trying URL '
> > http://cran.cnr.Berkeley.edu/bin/macosx/contrib/3.0/rrcov_1.3-4.tgz'
> > Content type 'application/x-gzip' length 1297823 bytes (1.2 Mb)
> > opened URL
> > ==================================================
> > downloaded 1.2 Mb
> >
> > trying URL '
> >
> http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/BiocGenerics_0.6.0.tgz
> > '
> > Content type 'application/x-gzip' length 333465 bytes (325 Kb)
> > opened URL
> > ==================================================
> > downloaded 325 Kb
> >
> > trying URL '
> > http://cran.cnr.Berkeley.edu/bin/macosx/contrib/3.0/feature_1.2.9.tgz'
> > Content type 'application/x-gzip' length 235771 bytes (230 Kb)
> > opened URL
> > ==================================================
> > downloaded 230 Kb
> >
> > trying URL '
> >
> http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/graph_1.38.3.tgz
> > '
> > Content type 'application/x-gzip' length 1327243 bytes (1.3 Mb)
> > opened URL
> > ==================================================
> > downloaded 1.3 Mb
> >
> > trying URL '
> >
> http://bioconductor.org/packages/2.12/bioc/bin/macosx/contrib/3.0/flowCore_1.26.3.tgz
> > '
> > Content type 'application/x-gzip' length 7808292 bytes (7.4 Mb)
> > opened URL
> > ==================================================
> > downloaded 7.4 Mb
> >
> > Error: file
> >
> ‘/var/folders/3c/dqj_pwz15jx7byqfqftmn_n00000gp/T//Rtmp8ln5bp/downloaded_packages/rgl_0.93.963.tgz’
> > is not an OS X binary package
> > In addition: Warning messages:
> > 1: In download.file(url, destfile, method, mode = "wb", ...) :
> >   downloaded length 96856 != reported length 4635832
> > 2: In download.file(url, destfile, method, mode = "wb", ...) :
> >   downloaded length 1577032 != reported length 2303844
> > 3: 'tar' returned non-zero exit code 1
> > rgl/textures/nightfire.png: (Empty error message)
> > tar: Error exit delayed from previous errors.
> >
> >
> >
> > On Fri, Oct 4, 2013 at 8:41 PM, Dan Tenenbaum <dtenenba@fhcrc.org>
> wrote:
> >
> >> Hi Sisi,
> >>
> >> ----- Original Message -----
> >> > From: "Sisi Chen [guest]" <guest@bioconductor.org>
> >> > To: bioconductor@r-project.org, sisichen@berkeley.edu
> >> > Sent: Friday, October 4, 2013 8:36:48 PM
> >> > Subject: [BioC] R 3.0.0 problems installing flowCore and other
> packages
> >> >
> >> >
> >> > Hi there,
> >> >
> >> > I recently upgraded my version of R to 3.0.2 because I was having
> >> > trouble installing packages. But now I can't install any of the main
> >> > flowcytometry packages: flowCore, flowQ, flowStats, flowViz etc
> >> > using bioclite().
> >> >
> >> > Some of the dependencies seem to download incompletely and also the
> >> > packages don't attach automatically. Is anyone else having this
> >> > problem?
> >> >
> >>
> >> Can you please post the complete output of the biocLite() and library()
> >> commands you tried?
> >>
> >> Dan
> >>
> >>
> >> > ~Sisi Chen
> >> > UC-Berkeley
> >> >
> >> >  -- output of sessionInfo():
> >> >
> >> >
> >> > R version 3.0.0 (2013-04-03)
> >> > Platform: x86_64-apple-darwin10.8.0 (64-bit)
> >> >
> >> > locale:
> >> > [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
> >> >
> >> > attached base packages:
> >> > [1] stats     graphics  grDevices utils     datasets  methods   base
> >> >
> >> > loaded via a namespace (and not attached):
> >> > [1] tools_3.0.0
> >> >
> >> > --
> >> > Sent via the guest posting facility at bioconductor.org.
> >> >
> >> > _______________________________________________
> >> > 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
> >> >
> >>
> >
> >
>
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>
>
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