Hi, I get a warning when I try to install a bioc package. http://brainarray.mbni.med.umich.edu/bioc/bin/macosx/leopard/contrib/2 .15 is not accessible. But I don't understand why it is accessed. Does anybody know how to fix this problem? source("http://bioconductor.org/biocLite.R") biocLite("ALL") BiocInstaller version 1.4.7, ?biocLite for help BioC_mirror: http://bioconductor.org Using R version 2.15, BiocInstaller version 1.4.7. Warning: unable to access index for repository http://brainarray.mbni.med.umich.edu/bioc/bin/macosx/leopard/contrib/2 .15 Installing package(s) 'ALL' Warning: unable to access index for repository http://brainarray.mbni.med.umich.edu/bioc/bin/macosx/leopard/contrib/2 .15 trying URL 'http://www.bioconductor.org/packages/2.10/data/experiment/ bin/macosx/leopard/contrib/2.15/ALL_1.4.12.tgz' Content type 'application/x-gzip' length 11426100 bytes (10.9 Mb) opened URL ================================================== downloaded 10.9 Mb The downloaded binary packages are in /var/folders/ok/okxjw3HGEsyvIrMaKBkHhE+++TI/-Tmp-//RtmpCArm2G/ downloaded_packages Warning: unable to access index for repository http://brainarray.mbni.med.umich.edu/bioc/bin/macosx/leopard/contrib/2 .15 Old packages: 'agricolae', 'animation', 'aplpack', 'aroma.affymetrix', 'aroma.apd', 'aroma.core', 'aroma.light', 'ca', 'Cairo', 'cairoDevice', 'Category', 'compositions', 'copula', 'depmixS4', 'diagram', 'dichromat', 'digest', 'doBy', 'drc', 'ellipse', 'elliptic', 'emulator', 'energy', 'Fahrmeir', 'filehash', 'fitdistrplus', 'gamlss', 'gamlss.data', 'gamlss.dist', 'geometry', 'glmnet', 'gmodels', 'GO.db', 'GOstats', 'GPArotation', 'graph', 'gridBase', 'gridExtra', 'grImport', 'GSEABase', 'gWidgets', 'gWidgetsRGtk2', 'gWidgetstcltk', 'HiddenMarkov', 'hmm.discnp', 'igraph', 'KEGG.db', 'lars', 'latticist', 'lavaan', 'mapdata', 'marray', 'matrixStats', 'mc2d', 'mcmc', 'MCMCpack', 'mouse.db0', 'msm', 'openair', 'org.Mm.eg.db', 'partitions', 'princurve', 'psych', 'qgraph', 'R.cache', 'R.filesets', 'R.huge', 'R.matlab', 'R.methodsS3', 'R.oo', 'R.rsp', 'R.utils', 'R2jags', 'raster', 'RBGL', 'Rcmdr', 'ReadImages', 'rggobi', 'RgoogleMaps', 'RGtk2', 'rJava', 'Rmpfr', 'RMySQL', 'Rsolnp', 'RSVGTipsDevice', 'sfsmisc', 'soiltexture', 'sos', 'splus2R', 'timecourse', 'topGO', 'TTR', 'vcdExtra', 'vrmlgen', 'WriteXLS', 'pasilla', 'rtracklayer' -- Regards, Peng

On Tue, Jul 17, 2012 at 5:43 PM, Peng Yu <pengyu.ut at="" gmail.com=""> wrote: > Hi, > > I get a warning when I try to install a bioc package. > http://brainarray.mbni.med.umich.edu/bioc/bin/macosx/leopard/contrib /2.15 > is not accessible. But I don't understand why it is accessed. Does > anybody know how to fix this problem? > This is just a warning. You can ignore it. Dan > source("http://bioconductor.org/biocLite.R") > biocLite("ALL") > BiocInstaller version 1.4.7, ?biocLite for help > BioC_mirror: http://bioconductor.org > Using R version 2.15, BiocInstaller version 1.4.7. > Warning: unable to access index for repository > http://brainarray.mbni.med.umich.edu/bioc/bin/macosx/leopard/contrib /2.15 > Installing package(s) 'ALL' > Warning: unable to access index for repository > http://brainarray.mbni.med.umich.edu/bioc/bin/macosx/leopard/contrib /2.15 > trying URL 'http://www.bioconductor.org/packages/2.10/data/experimen t/bin/macosx/leopard/contrib/2.15/ALL_1.4.12.tgz' > Content type 'application/x-gzip' length 11426100 bytes (10.9 Mb) > opened URL > ================================================== > downloaded 10.9 Mb > > > The downloaded binary packages are in > /var/folders/ok/okxjw3HGEsyvIrMaKBkHhE+++TI/-Tmp-//RtmpCArm2 G/downloaded_packages > Warning: unable to access index for repository > http://brainarray.mbni.med.umich.edu/bioc/bin/macosx/leopard/contrib /2.15 > Old packages: 'agricolae', 'animation', 'aplpack', 'aroma.affymetrix', > 'aroma.apd', 'aroma.core', 'aroma.light', 'ca', 'Cairo', 'cairoDevice', > 'Category', 'compositions', 'copula', 'depmixS4', 'diagram', 'dichromat', > 'digest', 'doBy', 'drc', 'ellipse', 'elliptic', 'emulator', 'energy', > 'Fahrmeir', 'filehash', 'fitdistrplus', 'gamlss', 'gamlss.data', > 'gamlss.dist', 'geometry', 'glmnet', 'gmodels', 'GO.db', 'GOstats', > 'GPArotation', 'graph', 'gridBase', 'gridExtra', 'grImport', 'GSEABase', > 'gWidgets', 'gWidgetsRGtk2', 'gWidgetstcltk', 'HiddenMarkov', 'hmm.discnp', > 'igraph', 'KEGG.db', 'lars', 'latticist', 'lavaan', 'mapdata', 'marray', > 'matrixStats', 'mc2d', 'mcmc', 'MCMCpack', 'mouse.db0', 'msm', 'openair', > 'org.Mm.eg.db', 'partitions', 'princurve', 'psych', 'qgraph', 'R.cache', > 'R.filesets', 'R.huge', 'R.matlab', 'R.methodsS3', 'R.oo', 'R.rsp', > 'R.utils', 'R2jags', 'raster', 'RBGL', 'Rcmdr', 'ReadImages', 'rggobi', > 'RgoogleMaps', 'RGtk2', 'rJava', 'Rmpfr', 'RMySQL', 'Rsolnp', > 'RSVGTipsDevice', 'sfsmisc', 'soiltexture', 'sos', 'splus2R', 'timecourse', > 'topGO', 'TTR', 'vcdExtra', 'vrmlgen', 'WriteXLS', 'pasilla', 'rtracklayer' > > > -- > Regards, > Peng > > _______________________________________________ > 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

Hi, I never try to install all packages at one time. If you can install individual package? If you can, then your problem is unlikely of connection problem or access limitation. Wen On Jul 17, 2012 8:44 PM, "Peng Yu" <pengyu.ut@gmail.com> wrote: > Hi, > > I get a warning when I try to install a bioc package. > http://brainarray.mbni.med.umich.edu/bioc/bin/macosx/leopard/contrib /2.15 > is not accessible. But I don't understand why it is accessed. Does > anybody know how to fix this problem? > > source("http://bioconductor.org/biocLite.R") > biocLite("ALL") > > BiocInstaller version 1.4.7, ?biocLite for help > BioC_mirror: http://bioconductor.org > Using R version 2.15, BiocInstaller version 1.4.7. > Warning: unable to access index for repository > http://brainarray.mbni.med.umich.edu/bioc/bin/macosx/leopard/contrib /2.15 > Installing package(s) 'ALL' > Warning: unable to access index for repository > http://brainarray.mbni.med.umich.edu/bioc/bin/macosx/leopard/contrib /2.15 > trying URL ' > http://www.bioconductor.org/packages/2.10/data/experiment/bin/macosx /leopard/contrib/2.15/ALL_1.4.12.tgz > ' > Content type 'application/x-gzip' length 11426100 bytes (10.9 Mb) > opened URL > ================================================== > downloaded 10.9 Mb > > > The downloaded binary packages are in > > /var/folders/ok/okxjw3HGEsyvIrMaKBkHhE+++TI/-Tmp-//RtmpCArm2G/downlo aded_packages > Warning: unable to access index for repository > http://brainarray.mbni.med.umich.edu/bioc/bin/macosx/leopard/contrib /2.15 > Old packages: 'agricolae', 'animation', 'aplpack', 'aroma.affymetrix', > 'aroma.apd', 'aroma.core', 'aroma.light', 'ca', 'Cairo', 'cairoDevice', > 'Category', 'compositions', 'copula', 'depmixS4', 'diagram', 'dichromat', > 'digest', 'doBy', 'drc', 'ellipse', 'elliptic', 'emulator', 'energy', > 'Fahrmeir', 'filehash', 'fitdistrplus', 'gamlss', 'gamlss.data', > 'gamlss.dist', 'geometry', 'glmnet', 'gmodels', 'GO.db', 'GOstats', > 'GPArotation', 'graph', 'gridBase', 'gridExtra', 'grImport', 'GSEABase', > 'gWidgets', 'gWidgetsRGtk2', 'gWidgetstcltk', 'HiddenMarkov', > 'hmm.discnp', > 'igraph', 'KEGG.db', 'lars', 'latticist', 'lavaan', 'mapdata', 'marray', > 'matrixStats', 'mc2d', 'mcmc', 'MCMCpack', 'mouse.db0', 'msm', 'openair', > 'org.Mm.eg.db', 'partitions', 'princurve', 'psych', 'qgraph', 'R.cache', > 'R.filesets', 'R.huge', 'R.matlab', 'R.methodsS3', 'R.oo', 'R.rsp', > 'R.utils', 'R2jags', 'raster', 'RBGL', 'Rcmdr', 'ReadImages', 'rggobi', > 'RgoogleMaps', 'RGtk2', 'rJava', 'Rmpfr', 'RMySQL', 'Rsolnp', > 'RSVGTipsDevice', 'sfsmisc', 'soiltexture', 'sos', 'splus2R', > 'timecourse', > 'topGO', 'TTR', 'vcdExtra', 'vrmlgen', 'WriteXLS', 'pasilla', > 'rtracklayer' > > > -- > Regards, > Peng > > _______________________________________________ > 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]]