[Bioc-devel] Fwd: can't install CRAN Packages after installed devel version of R and Bioc 3.4
Dan Tenenbaum
dtenenba at fredhutch.org
Sat Nov 12 02:34:02 CET 2016
You need to figure out where R is installed, probably in
c:\program files\R-3.4\bin
If you go to that directory (you can do it with this command in a command window):
cd c:\progra~1\R-3.4\bin
Then start R like this:
.\R.exe --vanilla
Dan
----- Original Message -----
> From: "Jurat Shayidin" <juratbupt at gmail.com>
> To: "Dan Tenenbaum" <dtenenba at fredhutch.org>, "bioc-devel" <bioc-devel at r-project.org>
> Sent: Friday, November 11, 2016 1:59:32 PM
> Subject: Re: [Bioc-devel] Fwd: can't install CRAN Packages after installed devel version of R and Bioc 3.4
> Dear Dan :
> I tried same command in terminal, but I got an error : 'R' is not
> recognized as internal or external command, operable program or batch
> file. should
> I change the directory under the current package working directory ? How
> can I fix this error ? Any quick solution ? Thanks a lot
>
> Best regards :
> Jurat
>
> On Fri, Nov 11, 2016 at 10:35 PM, Dan Tenenbaum <dtenenba at fredhutch.org>
> wrote:
>
>> 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@
>> 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
>> >>>
>> >>> [[alternative HTML version deleted]]
>> >>>
>> >>> _______________________________________________
>> >>> 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
>>
>
>
>
> --
> 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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