> source("http://bioconductor.org/biocLite.R")Bioconductor version 2.11 (BiocInstaller 1.8.3), ?biocLite for help> biocLite("goseq")'BiocInstaller' package not in repository http://bioconductor.org/packages/2.11/bioc, using 'http://bioconductor.org/packages/2.11/bioc'Error: 'BiocInstaller' package not in repository http://bioconductor.org/packages/2.11/bioc === sessionInfo()R version 2.15.2 (2012-10-26) 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=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] splines grid stats graphics grDevices utils datasets [8] methods base other attached packages: [1] BiocInstaller_1.8.3 gplots_2.11.0 MASS_7.3-22 [4] KernSmooth_2.23-8 caTools_1.13 bitops_1.0-5 [7] gdata_2.12.0 gtools_2.7.0 Hmisc_3.10-1 [10] survival_2.36-14 cluster_1.14.3 cummeRbund_2.0.0 [13] Gviz_1.2.0 rtracklayer_1.18.0 GenomicRanges_1.10.5 [16] IRanges_1.16.3 fastcluster_1.1.7 reshape2_1.2.1 [19] ggplot2_0.9.2.1 RSQLite_0.11.2 DBI_0.2-5 [22] BiocGenerics_0.4.0 loaded via a namespace (and not attached): [1] AnnotationDbi_1.20.2 Biobase_2.18.0 biomaRt_2.14.0 [4] Biostrings_2.26.2 biovizBase_1.6.0 BSgenome_1.26.1 [7] colorspace_1.2-0 dichromat_1.2-4 digest_0.5.2 [10] GenomicFeatures_1.10.0 gtable_0.1.1 labeling_0.1 [13] lattice_0.20-10 memoise_0.1 munsell_0.4 [16] parallel_2.15.2 plyr_1.7.1 proto_0.3-9.2 [19] RColorBrewer_1.0-5 RCurl_1.95-3 Rsamtools_1.10.2 [22] scales_0.2.2 stats4_2.15.2 stringr_0.6.1 [25] tools_2.15.2 XML_3.95-0.1 zlibbioc_1.4.0 [[alternative HTML version deleted]]

Hi Abhishek, On Thu, Dec 13, 2012 at 9:26 AM, Abhishek Pratap <apratap at="" lbl.gov=""> wrote: >> source("http://bioconductor.org/biocLite.R")Bioconductor version 2.11 (BiocInstaller 1.8.3), ?biocLite for help> biocLite("goseq")'BiocInstaller' package not in repository > http://bioconductor.org/packages/2.11/bioc, using > 'http://bioconductor.org/packages/2.11/bioc'Error: 'BiocInstaller' > package not in repository > http://bioconductor.org/packages/2.11/bioc > > It isn't clear to me what's going on. I can't reproduce this situation. Since you already have BiocInstaller installed, you can just do this: library(BiocInstaller) biocLite("goseq") If that fails, try this: install.packages("goseq", repos="http://bioconductor.org/packages/2.11/bioc") Please report if you continue to have problems. Dan > > === > > sessionInfo()R version 2.15.2 (2012-10-26) > 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=C LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] splines grid stats graphics grDevices utils datasets > [8] methods base > > other attached packages: > [1] BiocInstaller_1.8.3 gplots_2.11.0 MASS_7.3-22 > [4] KernSmooth_2.23-8 caTools_1.13 bitops_1.0-5 > [7] gdata_2.12.0 gtools_2.7.0 Hmisc_3.10-1 > [10] survival_2.36-14 cluster_1.14.3 cummeRbund_2.0.0 > [13] Gviz_1.2.0 rtracklayer_1.18.0 GenomicRanges_1.10.5 > [16] IRanges_1.16.3 fastcluster_1.1.7 reshape2_1.2.1 > [19] ggplot2_0.9.2.1 RSQLite_0.11.2 DBI_0.2-5 > [22] BiocGenerics_0.4.0 > > loaded via a namespace (and not attached): > [1] AnnotationDbi_1.20.2 Biobase_2.18.0 biomaRt_2.14.0 > [4] Biostrings_2.26.2 biovizBase_1.6.0 BSgenome_1.26.1 > [7] colorspace_1.2-0 dichromat_1.2-4 digest_0.5.2 > [10] GenomicFeatures_1.10.0 gtable_0.1.1 labeling_0.1 > [13] lattice_0.20-10 memoise_0.1 munsell_0.4 > [16] parallel_2.15.2 plyr_1.7.1 proto_0.3-9.2 > [19] RColorBrewer_1.0-5 RCurl_1.95-3 Rsamtools_1.10.2 > [22] scales_0.2.2 stats4_2.15.2 stringr_0.6.1 > [25] tools_2.15.2 XML_3.95-0.1 zlibbioc_1.4.0 > > [[alternative HTML version deleted]] > > _______________________________________________ > 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

Thanks. Copying the BioC list. Dan On Thu, Dec 13, 2012 at 11:22 AM, Shreyartha Mukherjee <shreyartha at="" gmail.com=""> wrote: > Hi, > > I was having the same weird problem a few days ago, I uninstalled/installed > R and then installed goseq successfully. > Hope this helps. > > Thanks, > Shreyartha > > > > > > On Thu, Dec 13, 2012 at 11:53 AM, Dan Tenenbaum <dtenenba at="" fhcrc.org=""> wrote: >> >> Hi Abhishek, >> >> On Thu, Dec 13, 2012 at 9:26 AM, Abhishek Pratap <apratap at="" lbl.gov=""> wrote: >> >> source("http://bioconductor.org/biocLite.R")Bioconductor version 2.11 >> >> (BiocInstaller 1.8.3), ?biocLite for help> biocLite("goseq")'BiocInstaller' >> >> package not in repository >> > http://bioconductor.org/packages/2.11/bioc, using >> > 'http://bioconductor.org/packages/2.11/bioc'Error: 'BiocInstaller' >> > package not in repository >> > http://bioconductor.org/packages/2.11/bioc >> > >> > >> >> It isn't clear to me what's going on. I can't reproduce this situation. >> >> Since you already have BiocInstaller installed, you can just do this: >> library(BiocInstaller) >> biocLite("goseq") >> If that fails, try this: >> install.packages("goseq", >> repos="http://bioconductor.org/packages/2.11/bioc") >> >> Please report if you continue to have problems. >> >> Dan >> >> >> >> >> > >> > === >> > >> > sessionInfo()R version 2.15.2 (2012-10-26) >> > 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=C LC_NAME=C >> > [9] LC_ADDRESS=C LC_TELEPHONE=C >> > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >> > >> > attached base packages: >> > [1] splines grid stats graphics grDevices utils datasets >> > [8] methods base >> > >> > other attached packages: >> > [1] BiocInstaller_1.8.3 gplots_2.11.0 MASS_7.3-22 >> > [4] KernSmooth_2.23-8 caTools_1.13 bitops_1.0-5 >> > [7] gdata_2.12.0 gtools_2.7.0 Hmisc_3.10-1 >> > [10] survival_2.36-14 cluster_1.14.3 cummeRbund_2.0.0 >> > [13] Gviz_1.2.0 rtracklayer_1.18.0 GenomicRanges_1.10.5 >> > [16] IRanges_1.16.3 fastcluster_1.1.7 reshape2_1.2.1 >> > [19] ggplot2_0.9.2.1 RSQLite_0.11.2 DBI_0.2-5 >> > [22] BiocGenerics_0.4.0 >> > >> > loaded via a namespace (and not attached): >> > [1] AnnotationDbi_1.20.2 Biobase_2.18.0 biomaRt_2.14.0 >> > [4] Biostrings_2.26.2 biovizBase_1.6.0 BSgenome_1.26.1 >> > [7] colorspace_1.2-0 dichromat_1.2-4 digest_0.5.2 >> > [10] GenomicFeatures_1.10.0 gtable_0.1.1 labeling_0.1 >> > [13] lattice_0.20-10 memoise_0.1 munsell_0.4 >> > [16] parallel_2.15.2 plyr_1.7.1 proto_0.3-9.2 >> > [19] RColorBrewer_1.0-5 RCurl_1.95-3 Rsamtools_1.10.2 >> > [22] scales_0.2.2 stats4_2.15.2 stringr_0.6.1 >> > [25] tools_2.15.2 XML_3.95-0.1 zlibbioc_1.4.0 >> > >> > [[alternative HTML version deleted]] >> > >> > _______________________________________________ >> > 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 >> >> _______________________________________________ >> 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 > >