[Bioc-devel] Fwd: can't install CRAN Packages after installed devel version of R and Bioc 3.4
Martin Morgan
martin.morgan at roswellpark.org
Fri Nov 11 18:16:01 CET 2016
On 11/11/2016 12:09 PM, Jurat Shayidin wrote:
> sorry for this simple question. why use R vanilla ? not familiar enough
> with this term.
It's not R vanilla, but R --vanilla; see
R --help
>
> 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
>>>>> confidential information. If you are not the intended recipient(s),
>>>>> or the employee or agent responsible for the delivery of this
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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
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>>>>
>>>>
>>>
>>>
>>>
>>
>> This email message may contain legally privileged and/or confidential
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>>
>
>
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