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 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 wrote: > >> Hi Sisi, >> >> ----- Original Message ----- >> > From: "Sisi Chen [guest]" >> > 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 >> > >> > > [[alternative HTML version deleted]]