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

[Jurat Shayidin]

Thanks for reminding, I'll keep this in mind. I figured out that after
clean R session, problem is solved. But how can I avoid this sort of issue
and facilitate the building package ? How can make R session vanilla ? Any
recommendation for configuration before start building packages ? Could you
elaborate your answer please ? Thanks

Best regards :

Jurat

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,
>> 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
>> building my packages ? Could you elaborate your answer please? Thank you
>> 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
>>
>
>
> This email message may contain legally privileged and/or confidential
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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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