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" 
> To: "Dan Tenenbaum" , "bioc-devel" 
> 
> 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 
> 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" 
>> > To: "Kasper Daniel Hansen" , "bioc-devel"
>> 
>> > 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 
>> >> 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
>> >>>  > roswellpark.org
>> >>> >>
>> 

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" 
> To: "Kasper Daniel Hansen" , "bioc-devel" 
> 
> 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 
>> 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 

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: [Rd] Frames in compiled functions

[luke-tierney]

That's about it. The plan is to modify the interpreter to do the same
so the inconsistency will go away. Code that is affected by this is
making assumptions that it should not.

Best,

luke

On Fri, 11 Nov 2016, Winston Chang wrote:


It looks like the byte compiler is optimizing local() to an
immediately-invoked function, instead of using eval() and substitute(). I
don't know if that's exactly how it's implemented internally, but that's
what it looks like here:

compiler::enableJIT(0)

fun <- function(x) {
  local(sys.calls())
}
fun(1)
## [[1]]
## fun(1)
##
## [[2]]
## local(sys.calls())
##
## [[3]]
## eval.parent(substitute(eval(quote(expr), envir)))
##
## [[4]]
## eval(expr, p)
##
## [[5]]
## eval(expr, envir, enclos)
## call
## [[6]]
## eval(quote(sys.calls()), new.env())
##
## [[7]]
## eval(expr, envir, enclos)


compiler::cmpfun(fun)(1)
## [[1]]
## (compiler::cmpfun(fun))(1)
##
## [[2]]
## (function() sys.calls())()


-Winston


On Fri, Nov 11, 2016 at 1:13 PM, brodie gaslam via R-devel <
r-devel@r-project.org> wrote:


I noticed some problems that cropped in the latest versions of R-devel
(2016-11-08 r71639 in my case) for one of my packages.  I _think_ I have
narrowed it down to the changes to what gets byte-compiled by default.  The
following example run illustrates the problem I'm having:

  compiler::enableJIT(0)
  fun <- function(x) local(as.list(parent.frame(2)))
  fun(1)
  ## $x
  ## [1] 1
  ##



  compiler::cmpfun(fun)(1)
  ## 


Is this considered problematic at all?  If so, might it make sense to
broaden the list of functions that disable JIT compilation beyond
`browser`?  I'm pretty sure I can work around this issue in my specific use
case, but figured it is worth mentioning here since it is a change in
behavior.


Regards,

B.

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--
Luke Tierney
Ralph E. Wareham Professor of Mathematical Sciences
University of Iowa  Phone: 319-335-3386
Department of Statistics andFax:   319-335-3017
   Actuarial Science
241 Schaeffer Hall  email:   luke-tier...@uiowa.edu
Iowa City, IA 52242 WWW:  http://www.stat.uiowa.edu

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Re: [Rd] Frames in compiled functions

[Winston Chang]

It looks like the byte compiler is optimizing local() to an
immediately-invoked function, instead of using eval() and substitute(). I
don't know if that's exactly how it's implemented internally, but that's
what it looks like here:

compiler::enableJIT(0)

fun <- function(x) {
   local(sys.calls())
}
fun(1)
## [[1]]
## fun(1)
##
## [[2]]
## local(sys.calls())
##
## [[3]]
## eval.parent(substitute(eval(quote(expr), envir)))
##
## [[4]]
## eval(expr, p)
##
## [[5]]
## eval(expr, envir, enclos)
## call
## [[6]]
## eval(quote(sys.calls()), new.env())
##
## [[7]]
## eval(expr, envir, enclos)


compiler::cmpfun(fun)(1)
## [[1]]
## (compiler::cmpfun(fun))(1)
##
## [[2]]
## (function() sys.calls())()


-Winston


On Fri, Nov 11, 2016 at 1:13 PM, brodie gaslam via R-devel <
r-devel@r-project.org> wrote:

> I noticed some problems that cropped in the latest versions of R-devel
> (2016-11-08 r71639 in my case) for one of my packages.  I _think_ I have
> narrowed it down to the changes to what gets byte-compiled by default.  The
> following example run illustrates the problem I'm having:
>
>   compiler::enableJIT(0)
>   fun <- function(x) local(as.list(parent.frame(2)))
>   fun(1)
>   ## $x
>   ## [1] 1
>   ##
>
>
>
>   compiler::cmpfun(fun)(1)
>   ## 
>
>
> Is this considered problematic at all?  If so, might it make sense to
> broaden the list of functions that disable JIT compilation beyond
> `browser`?  I'm pretty sure I can work around this issue in my specific use
> case, but figured it is worth mentioning here since it is a change in
> behavior.
>
>
> Regards,
>
> B.
>
> __
> R-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>

[[alternative HTML version deleted]]

__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel

[Rd] Frames in compiled functions

[brodie gaslam via R-devel]

I noticed some problems that cropped in the latest versions of R-devel 
(2016-11-08 r71639 in my case) for one of my packages.  I _think_ I have 
narrowed it down to the changes to what gets byte-compiled by default.  The 
following example run illustrates the problem I'm having:

  compiler::enableJIT(0)
  fun <- function(x) local(as.list(parent.frame(2)))
  fun(1)
  ## $x
  ## [1] 1
  ## 

  

  compiler::cmpfun(fun)(1)
  ## 


Is this considered problematic at all?  If so, might it make sense to broaden 
the list of functions that disable JIT compilation beyond `browser`?  I'm 
pretty sure I can work around this issue in my specific use case, but figured 
it is worth mentioning here since it is a change in behavior.


Regards,

B.

__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel

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







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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,
distribution, or use of this email message is prohibited.  If you have
received this 

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

[Jurat Shayidin]

Thanks for reminding, I'll keep this in mind. I figured out that after
clean R session, problem is solved. But how can I avoid this sort of issue
and facilitate the building package ? How can make R session vanilla ? Any
recommendation for configuration before start building packages ? Could you
elaborate your answer please ? Thanks

Best regards :

Jurat

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,
>> 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
>> building my packages ? Could you elaborate your answer please? Thank you
>> 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

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

[Jurat Shayidin]

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,
>> 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
>> building my packages ? Could you elaborate your answer please? Thank you
>> 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,
> 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 

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

[Martin Morgan]

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









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

[Jurat Shayidin]

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
>

> 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
>



-- 
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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Re: [Rd] Memory leak with tons of closed connections

[Gábor Csárdi]

On Fri, Nov 11, 2016 at 12:46 PM, Gergely Daróczi
 wrote:
[...]
>> I've changed the above to *print* the gc() result every 1000th
>> iteration, and after 100'000 iterations, there is still no
>> memory increase from the point of view of R itself.

Yes, R does not know about it, it does not manage this memory (any
more), but the R process requested this memory from the OS, and never
gave it back, which is basically the definition of a memory leak. No?

I think the leak is because 'stdin' is special and R opens it with fdopen():
https://github.com/wch/r-source/blob/f8cdadb769561970cc42776f563043ea5e12fe05/src/main/connections.c#L561-L579

and then it does not close it:
https://github.com/wch/r-source/blob/f8cdadb769561970cc42776f563043ea5e12fe05/src/main/connections.c#L636

I understand that R cannot fclose the FILE*, because that would also
close the file descriptor, but anyway, this causes a memory leak. I
think.

It seems that you cannot close the FILE* without closing the
descriptor, so maybe a workaround would be to keep one FILE* open,
instead of calling fdopen() to create new ones every time. Another
possible workaround is to use dup(), but I don't know enough about the
details to be sure.

Gabor

[...]

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[Rd] .S3methods: issue in content of info data.frame

[Renaud Gaujoux]

Hi,

I was trying to get a list of S3 method for a given generic, along with the
package in which they are defined, and I came across what looks like an
issue in the data.frame returned in attribute 'info'. The column 'from'
mostly gets the value "registered S3method for ..." except for visible
methods. Is this the expected behavior?
See code and output below.

Thank you.

Bests,
Renaud

$ Rscript -e "library(xtable); attr(.S3methods('plot'), 'info');
sessionInfo()"
   visible from generic  isS4
plot.acf FALSE registered S3method for plotplot FALSE
plot.data.frame  FALSE registered S3method for plotplot FALSE
plot.decomposed.ts   FALSE registered S3method for plotplot FALSE
plot.default  TRUE graphicsplot FALSE
plot.dendrogram  FALSE registered S3method for plotplot FALSE
plot.density FALSE registered S3method for plotplot FALSE
plot.ecdf TRUEstatsplot FALSE
plot.factor  FALSE registered S3method for plotplot FALSE
plot.formula FALSE registered S3method for plotplot FALSE
plot.function TRUE graphicsplot FALSE
plot.hclust  FALSE registered S3method for plotplot FALSE
plot.histogram   FALSE registered S3method for plotplot FALSE
plot.HoltWinters FALSE registered S3method for plotplot FALSE
plot.isoreg  FALSE registered S3method for plotplot FALSE
plot.lm  FALSE registered S3method for plotplot FALSE
plot.medpolish   FALSE registered S3method for plotplot FALSE
plot.mlm FALSE registered S3method for plotplot FALSE
plot.ppr FALSE registered S3method for plotplot FALSE
plot.prcomp  FALSE registered S3method for plotplot FALSE
plot.princompFALSE registered S3method for plotplot FALSE
plot.profile.nls FALSE registered S3method for plotplot FALSE
plot.raster  FALSE registered S3method for plotplot FALSE
plot.specFALSE registered S3method for plotplot FALSE
plot.stepfun  TRUEstatsplot FALSE
plot.stl FALSE registered S3method for plotplot FALSE
plot.table   FALSE registered S3method for plotplot FALSE
plot.ts   TRUEstatsplot FALSE
plot.tskernelFALSE registered S3method for plotplot FALSE
plot.TukeyHSDFALSE registered S3method for plotplot FALSE
R version 3.3.2 (2016-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.1 LTS

locale:
 [1] LC_CTYPE=en_ZA.UTF-8   LC_NUMERIC=C
LC_TIME=en_ZA.UTF-8LC_COLLATE=en_ZA.UTF-8
LC_MONETARY=en_ZA.UTF-8
 [6] LC_MESSAGES=en_ZA.UTF-8LC_PAPER=en_ZA.UTF-8
LC_NAME=C  LC_ADDRESS=C
LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_ZA.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats graphics  grDevices utils datasets  base

other attached packages:
[1] xtable_1.8-2

loaded via a namespace (and not attached):
[1] tools_3.3.2

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Re: [Rd] Memory leak with tons of closed connections

[Gergely Daróczi]

On Fri, Nov 11, 2016 at 12:08 PM, Martin Maechler
 wrote:
>> Gergely Daróczi 
>> on Thu, 10 Nov 2016 16:48:12 +0100 writes:
>
> > Dear All,
> > I'm developing an R application running inside of a Java daemon on
> > multiple threads, and interacting with the parent daemon via stdin and
> > stdout.
>
> > Everything works perfectly fine except for having some memory leaks
> > somewhere. Simplified version of the R app:
>
> > while (TRUE) {
> > con <- file('stdin', open = 'r', blocking = TRUE)
> > line <- scan(con, what = character(0), nlines = 1, quiet = TRUE)
> > close(con)
> > }
>
> > This loop uses more and more RAM as time passes (see more on this
> > below), not sure why, and I have no idea currently on how to debug
> > this further. Can someone please try to reproduce it and give me some
> > hints on what is the problem?
>
> > Sample bash script to trigger an R process with such memory leak:
>
> > Rscript --vanilla -e "while(TRUE)cat(runif(1),'\n')" | Rscript
> > --vanilla -e 
> "cat(Sys.getpid(),'\n');while(TRUE){con<-file('stdin',open='r',blocking=TRUE);line<-scan(con,what=character(0),nlines=1,quiet=TRUE);close(con);rm(con);gc()}"
>
> > Maybe you have to escape '\n' depending on your shell.
>
> > Thanks for reading this and any hints would be highly appreciated!
>
> I have no hints, sorry... but give some more "data":
>
> I've changed the above to *print* the gc() result every 1000th
> iteration, and after 100'000 iterations, there is still no
> memory increase from the point of view of R itself.
>
> However, monitoring the process (via 'htop', e.g.) shows about
> 1 MB per second increase in memory foot print of the process.
>
> One could argue that the error is with the OS / pipe / bash
> rather than with R itself... but I'm not expert enough to do
> argue  here at all.
>
> Here's my version of your sample bash script and its output:
>
> $  Rscript --vanilla -e "while(TRUE)cat(runif(1),'\n')" | Rscript --vanilla 
> -e "cat(Sys.getpid(),'\n');i <- 0; 
> while(TRUE){con<-file('stdin',open='r',blocking=TRUE);line<-scan(con,what=character(0),nlines=1,quiet=TRUE);close(con);rm(con);a
>  <- gc(); i <- i+1; if(i %% 1000 == 1) {cat('i=',i,'\\n'); print(a)} }"
>
> 11059
> i= 1
>  used (Mb) gc trigger  (Mb) max used (Mb)
> Ncells  83216  4.5   1000 534.1   213529 11.5
> Vcells 172923  1.4   16777216 128.0   562476  4.3
> i= 1001
>  used (Mb) gc trigger  (Mb) max used (Mb)
> Ncells  83255  4.5   1000 534.1   213529 11.5
> Vcells 172958  1.4   16777216 128.0   562476  4.3
> ...
> ...
> ...
> ...
> i= 80001
>  used (Mb) gc trigger  (Mb) max used (Mb)
> Ncells  83255  4.5   1000 534.1   213529 11.5
> Vcells 172958  1.4   16777216 128.0   562476  4.3
> i= 81001
>  used (Mb) gc trigger  (Mb) max used (Mb)
> Ncells  83255  4.5   1000 534.1   213529 11.5
> Vcells 172959  1.4   16777216 128.0   562476  4.3
> i= 82001
>  used (Mb) gc trigger  (Mb) max used (Mb)
> Ncells  83255  4.5   1000 534.1   213529 11.5
> Vcells 172959  1.4   16777216 128.0   562476  4.3
> i= 83001
>  used (Mb) gc trigger  (Mb) max used (Mb)
> Ncells  83255  4.5   1000 534.1   213529 11.5
> Vcells 172958  1.4   16777216 128.0   562476  4.3
> i= 84001
>  used (Mb) gc trigger  (Mb) max used (Mb)
> Ncells  83255  4.5   1000 534.1   213529 11.5
> Vcells 172958  1.4   16777216 128.0   562476  4.3
>

Thank you very much, this was very useful!

I tried to do some more research on this, as Gabor Csardi also
suspected that the memory grow might be due to the writer being faster
than the reader, so data is simply accumulating in the input buffer of
the reader. I double checked this via:

Rscript --vanilla -e
"i<-1;while(TRUE){cat(runif(1),'\n');i<-i+1;if(i==1e6){Sys.sleep(15);i<-1}}"
| Rscript --vanilla -e
"cat(Sys.getpid(),'\n');i<-0;while(TRUE){con<-file('stdin',open='r',blocking=TRUE);line<-scan(con,what=character(0),nlines=1,quiet=TRUE);close(con);rm(con);a<-gc();i<-i+1;if(i%%1e3==1){cat('i=',i,'\\n');print(a)}}"scan(con,what=character(0),nlines=1,quiet=TRUE);close(con);rm(con);gc()}"

So the writer generates a good number of lines, but sleeps for 15
seconds after a while so that the reader can catch up. Monitoring the
memory footprint of the process (by the way gc reported no memory
increase in the reader, just like in Martin's output) shows that the
memory grows when the writer sends data, and it's constant when the
writer is sleeping, but it never decreases: http://imgur.com/r7T02pK

Maybe it's more like an OS-specific question based on this, you are
absolutely right, but I was not able to reproduce the same memory
issue in plain bash via:

while :;do echo '1';done | bash -c "while 

Re: [Rd] Memory leak with tons of closed connections

[Martin Maechler]

> Gergely Daróczi 
> on Thu, 10 Nov 2016 16:48:12 +0100 writes:

> Dear All,
> I'm developing an R application running inside of a Java daemon on
> multiple threads, and interacting with the parent daemon via stdin and
> stdout.

> Everything works perfectly fine except for having some memory leaks
> somewhere. Simplified version of the R app:

> while (TRUE) {
> con <- file('stdin', open = 'r', blocking = TRUE)
> line <- scan(con, what = character(0), nlines = 1, quiet = TRUE)
> close(con)
> }

> This loop uses more and more RAM as time passes (see more on this
> below), not sure why, and I have no idea currently on how to debug
> this further. Can someone please try to reproduce it and give me some
> hints on what is the problem?

> Sample bash script to trigger an R process with such memory leak:

> Rscript --vanilla -e "while(TRUE)cat(runif(1),'\n')" | Rscript
> --vanilla -e 
"cat(Sys.getpid(),'\n');while(TRUE){con<-file('stdin',open='r',blocking=TRUE);line<-scan(con,what=character(0),nlines=1,quiet=TRUE);close(con);rm(con);gc()}"

> Maybe you have to escape '\n' depending on your shell.

> Thanks for reading this and any hints would be highly appreciated!

I have no hints, sorry... but give some more "data":

I've changed the above to *print* the gc() result every 1000th
iteration, and after 100'000 iterations, there is still no
memory increase from the point of view of R itself.

However, monitoring the process (via 'htop', e.g.) shows about
1 MB per second increase in memory foot print of the process.

One could argue that the error is with the OS / pipe / bash
rather than with R itself... but I'm not expert enough to do
argue  here at all.

Here's my version of your sample bash script and its output:

$  Rscript --vanilla -e "while(TRUE)cat(runif(1),'\n')" | Rscript --vanilla -e 
"cat(Sys.getpid(),'\n');i <- 0; 
while(TRUE){con<-file('stdin',open='r',blocking=TRUE);line<-scan(con,what=character(0),nlines=1,quiet=TRUE);close(con);rm(con);a
 <- gc(); i <- i+1; if(i %% 1000 == 1) {cat('i=',i,'\\n'); print(a)} }"

11059 
i= 1 
 used (Mb) gc trigger  (Mb) max used (Mb)
Ncells  83216  4.5   1000 534.1   213529 11.5
Vcells 172923  1.4   16777216 128.0   562476  4.3
i= 1001 
 used (Mb) gc trigger  (Mb) max used (Mb)
Ncells  83255  4.5   1000 534.1   213529 11.5
Vcells 172958  1.4   16777216 128.0   562476  4.3
...
...
...
...
i= 80001 
 used (Mb) gc trigger  (Mb) max used (Mb)
Ncells  83255  4.5   1000 534.1   213529 11.5
Vcells 172958  1.4   16777216 128.0   562476  4.3
i= 81001 
 used (Mb) gc trigger  (Mb) max used (Mb)
Ncells  83255  4.5   1000 534.1   213529 11.5
Vcells 172959  1.4   16777216 128.0   562476  4.3
i= 82001 
 used (Mb) gc trigger  (Mb) max used (Mb)
Ncells  83255  4.5   1000 534.1   213529 11.5
Vcells 172959  1.4   16777216 128.0   562476  4.3
i= 83001 
 used (Mb) gc trigger  (Mb) max used (Mb)
Ncells  83255  4.5   1000 534.1   213529 11.5
Vcells 172958  1.4   16777216 128.0   562476  4.3
i= 84001 
 used (Mb) gc trigger  (Mb) max used (Mb)
Ncells  83255  4.5   1000 534.1   213529 11.5
Vcells 172958  1.4   16777216 128.0   562476  4.3


> Best,
> Gergely

> PS1 see the image posted at
> 
http://stackoverflow.com/questions/40522584/memory-leak-with-closed-connections
> on memory usage over time
> PS2 the issue doesn't seem to be due to writing more data in the first
> R app compared to what the second R app can handle, as I tried the
> same with adding a Sys.sleep(0.01) in the first app and that's not an
> issue at all in the real application
> PS3 I also tried using stdin() instead of file('stdin'), but that did
> not work well for the stream running on multiple threads started by
> the same parent Java daemon
> PS4 I've tried this on Linux using R 3.2.3 and 3.3.2

For me, it's Linux, too (Fedora 24), using  'R 3.3.2 patched'..

Martin

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