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
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
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
I installed devel version of R, I removed R released version, while
keep devel version instead. Is this correct ? I didn't clean R
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
open a Windows shell ('cmd') and type
R --vanilla
or perhaps
Rgui --vanilla
building my packages ? Could you elaborate your answer please? Thank you
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
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
devel
version of Bioc and R, so I did it. But can't installl
from CRAN
like dplyr. How can I overcome this issue ? Any quick
? 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
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
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Jurat Shahidin
Dipartimento di Elettronica, Informazione e Bioingegneria
Politecnico di Milano
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Mobile : +39 3279366608
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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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