[BioC] can't install "goseq" through BioC

[Dan Tenenbaum]

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]]
>
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