[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 22:59:32 CET 2016
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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