Re: [Rd] Debugging tools and practices in Windows?

[Ray Donnelly]

On Thu, Feb 23, 2017 at 7:49 PM, Tomas Kalibera 
wrote:

> The R for Windows FAQ suggests "make DEBUG=T" and has some more hints
> https://cran.r-project.org/bin/windows/base/rw-FAQ.html
>
> Tomas
>
>
>
> On 02/23/2017 08:10 PM, Javier Luraschi wrote:
>
>> Right, I'm talking about C code.
>>
>> Do you remember if you had to set specific CFLAGS or other settings to get
>> gdb working? I wasn't able to get gdb() working with the standard build
>> settings.
>>
>> Otherwise, Rprintf() would work for sure.
>>
>> Thank you!
>>
>>
>>
>> On Thu, Feb 23, 2017 at 10:55 AM, Duncan Murdoch <
>> murdoch.dun...@gmail.com>
>> wrote:
>>
>> On 23/02/2017 1:36 PM, Javier Luraschi wrote:
>>>
>>> Hello r-devel, could someone share the tools and practices they use to
 debug the core R sources in Windows?

 For instance, I would like to set a breakpoint in `gl_loadhistory` and
 troubleshoot from there.

 You're talking about debugging the C code rather than the R code, I
>>> think.
>>>
>>> These days I mostly avoid debugging in Windows, but when I have to do it,
>>> I use gdb.  There used to be a front end for it (Insight) that worked in
>>> Windows, but I don't think it works with our current gdb build.  Google
>>
>> names lots of other front ends, but I haven't tried any of them in
>>> Windows.
>>>
>>>
I feel Qt Creator provides a good enough UI for debugging things on Windows
(it allows you to debug externally-built executables).


> The other choice is the old fashioned method:  add lots of Rprintf()
>>> statements to the source and recompile.
>>>
>>> Duncan Murdoch
>>>
>>>
>>> [[alternative HTML version deleted]]
>>
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Re: [Bioc-devel] BubbleTree devel is not updating

[Martin Morgan]

On 02/23/2017 03:19 PM, Creasy, Todd wrote:

Hi,

I�ve been updating the svn repo with changes to BubbleTree
(https://www.bioconductor.org/packages/devel/bioc/html/BubbleTree.html)
but it doesn�t seem like the nightly builds are picking up the
changes. I�ve changed the version in the description to 2.5.3. Is
there a reason it might not be getting updated?


On the build page for your package, e.g.,


http://bioconductor.org/checkResults/3.5/bioc-LATEST/BubbleTree/malbec2-buildsrc.html

check out to the left the 'Snapshot Date' and 'Last Changed Rev' / 'Last 
Changed Date' and at the top of the page 'This page was generated on...'


Basically, you need to be a little more patient. The builds occur at 
'night' starting at about 5:15, and last until the next day 
mid-afternoon, about 16:12 for the builds that completed today. Your 
initial version bumps on 02-22 were at 16:09 and are reflected in 
today's builds; the bump to 2.5.3 was at 2017-02-23 14:34:46  so in time 
for tonight's build and a report (sometimes things go very wrong and 
there is no build report; this is not happening often these days) at 
tomorrow at around 4pm Eastern.


Martin




Thanks,

-todd To the extent this electronic communication or any of its
attachments contain information that is not in the public domain,
such information is considered by MedImmune to be confidential and
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[Bioc-devel] Question about using R-devel

[Aimin Yan]

When I used R-devel to perform R CMD build on my package, I got the
following errors.

Actually, I put
^packrat/
in PathwaySplice/.Rbuildignore.

Does anyone has idea on this error?

Thank you,

Aimin


cp: PathwaySplice/packrat/lib-R/boot: No such file or directory
cp: PathwaySplice/packrat/lib-R/class: No such file or directory
cp: PathwaySplice/packrat/lib-R/codetools: No such file or directory
cp: PathwaySplice/packrat/lib-R/compiler: No such file or directory
cp: PathwaySplice/packrat/lib-R/datasets: No such file or directory
cp: PathwaySplice/packrat/lib-R/graphics: No such file or directory
cp: PathwaySplice/packrat/lib-R/grDevices: No such file or directory
cp: PathwaySplice/packrat/lib-R/grid: No such file or directory
cp: PathwaySplice/packrat/lib-R/KernSmooth: No such file or directory
cp: PathwaySplice/packrat/lib-R/MASS: No such file or directory
cp: PathwaySplice/packrat/lib-R/methods: No such file or directory
cp: PathwaySplice/packrat/lib-R/nnet: No such file or directory
cp: PathwaySplice/packrat/lib-R/parallel: No such file or directory
cp: PathwaySplice/packrat/lib-R/rpart: No such file or directory
cp: PathwaySplice/packrat/lib-R/spatial: No such file or directory
cp: PathwaySplice/packrat/lib-R/splines: No such file or directory
cp: PathwaySplice/packrat/lib-R/stats: No such file or directory
cp: PathwaySplice/packrat/lib-R/stats4: No such file or directory
cp: PathwaySplice/packrat/lib-R/tcltk: No such file or directory
cp: PathwaySplice/packrat/lib-R/tools: No such file or directory
cp: PathwaySplice/packrat/lib-R/utils: No such file or directory
 ERROR
copying to build directory failed
Error: Command failed (1)
In addition: Warning message:
`cleanup` is deprecated
Execution halted

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[Bioc-devel] BubbleTree devel is not updating

[Creasy, Todd]

Hi,

I�ve been updating the svn repo with changes to BubbleTree 
(https://www.bioconductor.org/packages/devel/bioc/html/BubbleTree.html) but it 
doesn�t seem like the nightly builds are picking up the changes. I�ve changed 
the version in the description to 2.5.3. Is there a reason it might not be 
getting updated?

Thanks,

-todd
To the extent this electronic communication or any of its attachments contain 
information that is not in the public domain, such information is considered by 
MedImmune to be confidential and proprietary. This communication is expected to 
be read and/or used only by the individual(s) for whom it is intended. If you 
have received this electronic communication in error, please reply to the 
sender advising of the error in transmission and delete the original message 
and any accompanying documents from your system immediately, without copying, 
reviewing or otherwise using them for any purpose. Thank you for your 
cooperation.

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Re: [Rd] Debugging tools and practices in Windows?

[Tomas Kalibera]

The R for Windows FAQ suggests "make DEBUG=T" and has some more hints
https://cran.r-project.org/bin/windows/base/rw-FAQ.html

Tomas


On 02/23/2017 08:10 PM, Javier Luraschi wrote:

Right, I'm talking about C code.

Do you remember if you had to set specific CFLAGS or other settings to get
gdb working? I wasn't able to get gdb() working with the standard build
settings.

Otherwise, Rprintf() would work for sure.

Thank you!



On Thu, Feb 23, 2017 at 10:55 AM, Duncan Murdoch 
wrote:


On 23/02/2017 1:36 PM, Javier Luraschi wrote:


Hello r-devel, could someone share the tools and practices they use to
debug the core R sources in Windows?

For instance, I would like to set a breakpoint in `gl_loadhistory` and
troubleshoot from there.


You're talking about debugging the C code rather than the R code, I think.

These days I mostly avoid debugging in Windows, but when I have to do it,
I use gdb.  There used to be a front end for it (Insight) that worked in
Windows, but I don't think it works with our current gdb build.  Google
names lots of other front ends, but I haven't tried any of them in Windows.

The other choice is the old fashioned method:  add lots of Rprintf()
statements to the source and recompile.

Duncan Murdoch



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Re: [Rd] Debugging tools and practices in Windows?

[Javier Luraschi]

Right, I'm talking about C code.

Do you remember if you had to set specific CFLAGS or other settings to get
gdb working? I wasn't able to get gdb() working with the standard build
settings.

Otherwise, Rprintf() would work for sure.

Thank you!



On Thu, Feb 23, 2017 at 10:55 AM, Duncan Murdoch 
wrote:

> On 23/02/2017 1:36 PM, Javier Luraschi wrote:
>
>> Hello r-devel, could someone share the tools and practices they use to
>> debug the core R sources in Windows?
>>
>> For instance, I would like to set a breakpoint in `gl_loadhistory` and
>> troubleshoot from there.
>>
>
> You're talking about debugging the C code rather than the R code, I think.
>
> These days I mostly avoid debugging in Windows, but when I have to do it,
> I use gdb.  There used to be a front end for it (Insight) that worked in
> Windows, but I don't think it works with our current gdb build.  Google
> names lots of other front ends, but I haven't tried any of them in Windows.
>
> The other choice is the old fashioned method:  add lots of Rprintf()
> statements to the source and recompile.
>
> Duncan Murdoch
>
>

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Re: [Rd] Debugging tools and practices in Windows?

[Duncan Murdoch]

On 23/02/2017 1:36 PM, Javier Luraschi wrote:

Hello r-devel, could someone share the tools and practices they use to
debug the core R sources in Windows?

For instance, I would like to set a breakpoint in `gl_loadhistory` and
troubleshoot from there.


You're talking about debugging the C code rather than the R code, I think.

These days I mostly avoid debugging in Windows, but when I have to do 
it, I use gdb.  There used to be a front end for it (Insight) that 
worked in Windows, but I don't think it works with our current gdb 
build.  Google names lots of other front ends, but I haven't tried any 
of them in Windows.


The other choice is the old fashioned method:  add lots of Rprintf() 
statements to the source and recompile.


Duncan Murdoch

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[Rd] Debugging tools and practices in Windows?

[Javier Luraschi]

Hello r-devel, could someone share the tools and practices they use to
debug the core R sources in Windows?

For instance, I would like to set a breakpoint in `gl_loadhistory` and
troubleshoot from there.

Thanks in advance - Javier Luraschi

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Re: [Bioc-devel] covr

[Estefania Mancini]

Thanks Herve! 

I will try to include test code in the next version of the package. 

By the way, I am a little lost with changes in the package. I want to modify 
the code of the accepted package and  I want to add people to my project in 
GitHub so I think is better for us continuing using it repository. What do you 
suggest? I have a version in GitHub, linked to Bioconductor repository. Does 
commit impact on my devel version of the package? I dont understand clearly 
where I should commit. 

Thanks in advance,

Estefania


De: Hervé Pagès [hpa...@fredhutch.org]
Enviado: lunes, 13 de febrero de 2017 03:15 p.m.
Para: Estefania Mancini; bioc-devel@r-project.org
Asunto: Re: [Bioc-devel] covr

Hi Estefania,

See here

   https://bioconductor.org/developers/how-to/unitTesting-guidelines/

for our guidelines to how to add unit tests to your package.

Cheers,
H.

On 02/13/2017 04:17 AM, Estefania Mancini wrote:
> Hi,
> I would like to add coverage test to my package. What should I do? Thanks in 
> advance
>
> Estefania
>
>   [[alternative HTML version deleted]]
>
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--
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpa...@fredhutch.org
Phone:  (206) 667-5791
Fax:(206) 667-1319

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Re: [Rd] Registration of native routines

[Avraham Adler]

I believe Dr. Ripley said that the UseDynLib doesn't address the
middle two points of the list.

I experimented with the Delaporte package timing calls using both
methods, and they were within 1~2 microseconds of each other using
microbenchmark. Since the more complicated way is now expressly
preferred, it isn't a big deal for me personally to change so the next
version of Delaporte will use CallMethod/useDynLib(foo,
.registration=TRUE) etc. I can see how in more complicated packages
that could become more burdensome.

Thanks,

Avi

On Wed, Feb 22, 2017 at 9:34 AM, Jeroen Ooms  wrote:
> On Tue, Feb 14, 2017 at 5:25 PM, Prof Brian Ripley
>  wrote:
>>
>> Registration has similar benefits to name spaces in R code:
>>
>> - it ensures that the routines used by .C, .Call etc are those in your 
>> package (without needing a PACKAGE argument).
>> - it avoids polluting the search space for native routines with those from 
>> your package.
>> - it checks the number of arguments passed to .Call/.External, and the 
>> number and optionally the type for .C/.Fortran.
>> - it finds native routines faster, especially if 10s of name spaces are 
>> loaded.
>
> Do these benefits also hold for packages that currently use useDynLib
> exclusively in combination symbol names? E.g for the example from WRE:
>
>useDynLib(foo, myRoutine, myOtherRoutine)
>
> Which is invoked via:
>
>   .Call(myRoutine, x, y)
>
> What ambiguity or pollution is introduced by foo:::myRoutine? Should
> manually registering 'myRoutine' in C still be mandatory in this case?
>
> It was nice having the NAMESPACE as the central declaration of
> callable C routines. The "R_registerRoutines" system will require
> maintaining additional C code which re-declares all callable C
> functions from other compilation units. This introduces additional
> complexity for package authors and might become a source of bugs when
> we forget to update the registrations when C functions have changed.
>
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Re: [Rd] Update copyright year in manuals

[Martin Maechler]

> Mikko Korpela 
> on Thu, 23 Feb 2017 14:02:58 +0200 writes:

> With new R releases soon to come, I suggest updating the
> Rcopyright macro in "doc/manual/R-defs.texi" to use year
> 2017.

Now this is an e-mail that *REALLY* does not fit to the R-devel
mailing list ... even though it is very very slightly related to
the R sources.

We do *not* want noise on R-devel, please.

(and let's continue this issue in private if you want)
Martin

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[Bioc-devel] Mac devel builds: oaxaca update

[Obenchain, Valerie]

Hi,

oaxaca has been in and out of the build report the past couple of days
because it was not completing on time. The machine has been rebooted and
should be back in today's report (Feb 23). Transitioning to toluca2 as
the primary Mac devel builder is a priority for us over the next couple
of weeks. We'll announce when the switch is complete and oaxaca will be
taken off-line.

Valerie



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[Rd] Update copyright year in manuals

[Mikko Korpela]

With new R releases soon to come, I suggest updating the Rcopyright 
macro in "doc/manual/R-defs.texi" to use year 2017.


--
Mikko Korpela
Department of Geosciences and Geography
University of Helsinki

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