[Bioc-devel] Fwd: can't install CRAN Packages after installed devel version of R and Bioc 3.4
Dan Tenenbaum
dtenenba at fredhutch.org
Fri Nov 11 22:35:23 CET 2016
Don't do this in RStudio, do it at the command line/terminal. Type in R --vanilla. You won't get the same interface as RStudio but you can see if the problem persists.
Dan
----- Original Message -----
> From: "Jurat Shayidin" <juratbupt at gmail.com>
> To: "Kasper Daniel Hansen" <kasperdanielhansen at gmail.com>, "bioc-devel" <bioc-devel at r-project.org>
> Sent: Friday, November 11, 2016 12:38:57 PM
> Subject: Re: [Bioc-devel] Fwd: can't install CRAN Packages after installed devel version of R and Bioc 3.4
> 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
>>> 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
>>> >>>>
>>> >>>>
>>> >>>
>>> >>> 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
>
> [[alternative HTML version deleted]]
>
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
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