[Bioc-devel] Fwd: can't install CRAN Packages after installed devel version of R and Bioc 3.4
Kasper Daniel Hansen
kasperdanielhansen at gmail.com
Fri Nov 11 19:22:21 CET 2016
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
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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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>
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