[Bioc-devel] Fwd: can't install CRAN Packages after installed devel version of R and Bioc 3.4

On 11/11/2016 11:42 AM, Jurat Shayidin wrote:

I'll keep this in mind. Thanks for reminding. Could you please elaborate
your answer on my doubt ? Thanks

On Fri, Nov 11, 2016 at 5:27 PM, Martin Morgan <
martin.morgan at roswellpark.org> wrote:

Please respond on the mailing list, so that others in similar situations

can benefit / contribute.

On 11/11/2016 10:39 AM, Jurat Shayidin wrote:

Dear Martin :

Thanks for your prompt hit . I used to have R release version, so after
I installed devel version of R, I removed R released version, while only
keep devel version instead. Is this correct ? I didn't clean R session,

this is not related to your original question. I personally need both a
release and devel version of R and have both installed.

how can I make it happen on windows?  Plus, How to make R session

vanilla ? What's right configuration both R devel and Bioc devel before

open a Windows shell ('cmd') and type

  R --vanilla

or perhaps

  Rgui --vanilla

building my packages ? Could you elaborate your answer please? Thank you

again, this isn't related to your original question. See the section
'Which version of R?' in

  http://bioconductor.org/developers/how-to/useDevel/

Martin


very much

Best regards :

On Fri, Nov 11, 2016 at 4:04 PM, Martin Morgan
<martin.morgan at roswellpark.org <mailto:martin.morgan at roswellpark.org>>

wrote:

    On 11/11/2016 09:44 AM, Jurat Shayidin wrote:

        Dear BiocDevel:

        I ran into the issue after installed devel version of R and Bioc
        3.4.
        Because my packages depends on some packages from CRAN
        repository, now I
        failed to installed paclages from CRAN. I don't have problem
        when I used
        released version of R. Because new packages must coordinate with
        devel
        version of Bioc and R, so I did it. But can't installl packages
        from CRAN
        like dplyr. How can I overcome this issue ? Any quick solution
        ?  I got
        error as follow:


            BiocInstaller::useDevel()

        Error: 'devel' version already in use

            install.packages("dplyr")

        Error in install.packages : missing value where TRUE/FALSE
needed


    this does not happen for me; you'll need to debug on your end,
    minimally, reporting the output of traceback() after the error
occurs.

    are you in a clean R session with no .RData or other objects loaded
    that might interfere with R?

      R --vanilla

    Martin

    PS -- please do not 'close' questions that have been answered on
    support.bioconductor.org <http://support.bioconductor.org>.





            sessionInfo()

        R Under development (unstable) (2016-11-09 r71642)
        Platform: x86_64-w64-mingw32/x64 (64-bit)
        Running under: Windows >= 8 x64 (build 9200)

        locale:
        [1] LC_COLLATE=English_United States.1252
        [2] LC_CTYPE=English_United States.1252
        [3] LC_MONETARY=English_United States.1252
        [4] LC_NUMERIC=C
        [5] LC_TIME=English_United States.1252

        attached base packages:
        [1] parallel  stats4    stats     graphics  grDevices
        [6] utils     datasets  methods   base

        other attached packages:
         [1] SummarizedExperiment_1.5.2 Biobase_2.35.0
         [3] XVector_0.15.0             rtracklayer_1.35.1
         [5] GenomicRanges_1.27.5       GenomeInfoDb_1.11.3
         [7] IRanges_2.9.7              S4Vectors_0.13.2
         [9] BiocGenerics_0.21.0        BiocInstaller_1.25.2

        loaded via a namespace (and not attached):
         [1] lattice_0.20-34          XML_3.98-1.5
         [3] Rsamtools_1.27.2         Biostrings_2.43.0
         [5] GenomicAlignments_1.11.0 bitops_1.0-6
         [7] grid_3.4.0               zlibbioc_1.21.0
         [9] Matrix_1.2-7.1           BiocParallel_1.9.1
        [11] tools_3.4.0              RCurl_1.95-4.8
        [13] compiler_3.4.0







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--
Jurat Shahidin

Dipartimento di Elettronica, Informazione e Bioingegneria
Politecnico di Milano
Piazza Leonardo da Vinci 32 - 20133 Milano, Italy
Mobile : +39 3279366608

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