[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 21:38:57 CET 2016
Dear Kasper :
Thanks for your explanation. However, I opened the shell from Rstudio and
type the command R --vanilla, seems it works fine, but still not sure about
efficiency of using R -vanilla. I am not confident about using R commands,
so is there any quick example that I can practice and understand this in
depth ? Thanks a lot
Best regards:
Jurat
On Fri, Nov 11, 2016 at 7:22 PM, Kasper Daniel Hansen <
kasperdanielhansen at gmail.com> wrote:
> You're bing asked to use
> R --vanilla
> because you have a non-standard problem, exemplified by the fact that what
> you have problems with (installing CRAN packages) works for thousands of
> users of Bioconductor (certainly for me). This suggests that there is
> something wrong with something on your computer. Starting R with R
> --vanilla disables loading of some user-specific component. If it works
> with R --vanilla the conclusion is that whatever made it fail was something
> loaded by R but not R --vanilla. If it doesn't work with R --vanilla the
> conclusion is that your problem is elsewhere.
>
> Best,
> Kasper
>
> On Fri, Nov 11, 2016 at 12:09 PM, Jurat Shayidin <juratbupt at gmail.com>
> wrote:
>
>> 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
>> >>>> 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
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>> >>>> any disclosure, copying, distribution, or use of this email
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>> >>>> is prohibited. If you have received this message in error,
>> please
>> >>>> notify the sender immediately by e-mail and delete this email
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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,
>> >>> 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.
>> >>>
>> >>>
>> >>
>> >>
>> >>
>> >
>> > 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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>>
>> _______________________________________________
>> Bioc-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>
>
--
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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