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

[Dan Tenenbaum]

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
>
>