Re: [Bioc-devel] Fwd: can't install CRAN Packages after installed devel version of R and Bioc 3.4

[Dan Tenenbaum]

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" <juratb...@gmail.com>
> To: "Dan Tenenbaum" <dtene...@fredhutch.org>, "bioc-devel" 
> <bioc-devel@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 <dtene...@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" <juratb...@gmail.com>
>> > To: "Kasper Daniel Hansen" <kasperdanielhan...@gmail.com>, "bioc-devel"
>> <bioc-devel@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 <
>> > kasperdanielhan...@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 <juratb...@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.mor...@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.mor...@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
>> >

Re: [Bioc-devel] Fwd: can't install CRAN Packages after installed devel version of R and Bioc 3.4

[Dan Tenenbaum]

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" <juratb...@gmail.com>
> To: "Kasper Daniel Hansen" <kasperdanielhan...@gmail.com>, "bioc-devel" 
> <bioc-devel@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 <
> kasperdanielhan...@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 <juratb...@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.mor...@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.mor...@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.mor...@roswellpark.org <mailto:martin.mor...@roswellpark.org
>>> >>
>>> >>>>
>>> >>>> wrote:
>>> >>>>
>>> >>>> On 11/11/2016 09:44 AM, Jurat Sh

Re: [Bioc-devel] Fwd: can't install CRAN Packages after installed devel version of R and Bioc 3.4

[Jurat Shayidin]

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 <
kasperdanielhan...@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 
> 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.mor...@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.mor...@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
>>  > >>
>> 
>>  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 .
>> 
>> 
>> 
>> 
>> 
>>  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 

Re: [Bioc-devel] Fwd: can't install CRAN Packages after installed devel version of R and Bioc 3.4

[Jurat Shayidin]

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.mor...@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.mor...@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
 >

 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 .





 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  stats4stats 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_0.21.0BiocInstaller_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 

Re: [Bioc-devel] Fwd: can't install CRAN Packages after installed devel version of R and Bioc 3.4

[Martin Morgan]

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.mor...@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
>

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 .





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  stats4stats 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_0.21.0BiocInstaller_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,
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