[Bioc-devel] Fwd: can't install CRAN Packages after installed devel version of R and Bioc 3.4
Jurat Shayidin
juratbupt at gmail.com
Fri Nov 11 18:09:09 CET 2016
sorry for this simple question. why use R vanilla ? not familiar enough
with this term.
On Fri, Nov 11, 2016 at 5:51 PM, Martin Morgan <
martin.morgan at roswellpark.org> wrote:
> 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
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> This email message may contain legally privileged and/or
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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
>>> information. If you are not the intended recipient(s), or the employee
>>> or
>>> agent responsible for the delivery of this message to the intended
>>> recipient(s), you are hereby notified that any disclosure, copying,
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>>>
>>>
>>
>>
>>
>
> This email message may contain legally privileged and/or confidential
> information. If you are not the intended recipient(s), or the employee or
> agent responsible for the delivery of this message to the intended
> recipient(s), you are hereby notified that any disclosure, copying,
> distribution, or use of this email message is prohibited. If you have
> received this message in error, please notify the sender immediately by
> e-mail and delete this email message from your computer. Thank you.
>
--
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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