R 3.0.0 problems installing flowCore and other packages

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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? ~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.

flowCore flowViz flowQ flowStats flowCore flowViz flowQ flowStats • 2.8k views

ADD COMMENT • link updated 11.1 years ago by Dan Tenenbaum ★ 8.2k • written 11.1 years ago by Guest User ★ 13k

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Dan Tenenbaum ★ 8.2k

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Hi Sisi, ----- Original Message ----- > From: "Sisi Chen [guest]" <guest at="" bioconductor.org=""> > To: bioconductor at r-project.org, sisichen at 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 at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor >

ADD COMMENT • link 11.1 years ago Dan Tenenbaum ★ 8.2k

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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.t gz' 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/Biob ase_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/Bioc Generics_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/grap h_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/flow Core_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/download ed_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 > > > [[alternative HTML version deleted]]

ADD REPLY • link 11.1 years ago Sisi Chen ▴ 20

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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_0.9-1 0.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/Bi obase_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/Bi ocGenerics_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/gr aph_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/fl owCore_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/downlo aded_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 >> > >> > > [[alternative HTML version deleted]]

ADD REPLY • link 11.1 years ago Sisi Chen ▴ 20

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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_0.9-1 0.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_0.9-99 96.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/Bi obase_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/Bi ocGenerics_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/gr aph_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/fl owCore_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/downlo aded_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 > >> > > >> > > > > > > [[alternative HTML version deleted]] > > > _______________________________________________ > 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]]

ADD REPLY • link 11.1 years ago Greg Finak ▴ 240

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