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

[Martin Morgan]

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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>
>
>


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