[Bioc-devel] R CMD check error on shinytest package

2017-04-12 Thread Samuel Wieczorek 
Hi

For the Prostar package, I began to use the funtionnalities of shinytest 
wich is a package that provides utilities to automatically test shiny apps.

Unfortunately, this package is not available neither on CRAN or 
Bioconductor (it is available on github 
https://github.com/rstudio/shinytest).

Thus, I had a an error on all platforms at the CHECK step.Will it be a 
problem to pass the tests and be in the next release ?


Thanks


Sam



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Re: [Bioc-devel] Iterating over BSgenomeViews returns DNAString instead of BSgenomeViews

2017-04-12 Thread Pariksheet Nanda 
On Fri, Apr 7, 2017 at 1:13 AM, Hervé Pagès  wrote:
>
> This is the expected behavior.
>
> Some background: BSgenomeViews are list-like objects where the *list
> elements* (i.e. the elements one extracts with [[) are the DNA
> sequences from the views
--snip--
> The important difference is that with [[ I get a DNAString object
> (the content of the view) and with [ I get a BSgenomeViews object
> of length 1.

Thank you, Hervé!

I was failing to make the connection with the `[[` accessor.


On Fri, Apr 7, 2017 at 1:16 AM, Michael Lawrence 
wrote:
>
> I'm curious as to why you are looping over the views in the first
> place. Maybe we could arrive at a vectorized solution, which is often
> but not always simpler and faster.

Hi Michael!

Broad background is I'm acculturating an undergraduate student to writing a
bioconductor package and applying software engineering practices of version
control, unit testing, documenting, dependency setup and validation in a
different environment on our university HPC cluster, etc.  The student also
came along to LibrePlanet to better understand the culture of software
freedom :o)  The package goal is to use Biostrings to look for repeating
DNA sequences of a fixed kmer size and subset to portions of the genome
without repeats (an aligner can do this ofc, but the goal is to teach R and
engineering practices).

I appreciate your thoughtfulness for vectorizing the code to best use
BSgenomeViews, but please don't spend more than 10 minutes as I have to
balance changes to the code with the student's learning and coding "voice"
and may not do proper justice for more of your effort.  My slowness to
reply was getting the project further along to be more understandable.
Here was the line which I've updating as Hervé suggested to use seq_along():
https://github.com/coregenomics/kmap/blob/4adaed6b8007e8ea39f39ff57a42a821445d3d46/R/BiostringsProjectNEW.R#L185
(I'm having a hard time thinking of how to summarizing a small example out
of context).
Although in that line ranges_hits() is only operating on single indices,
ranges_hits() was written to process groups of indices to reduce
multi-processor communication.  Generating such sets of indices would
involve applying width() to the views inside mappable() to break in into
chunks of, say, a million bases for matchPDict().  Again, I'm linking to
the code for anything that stands out at you, but I will feel bad if you
spend a lot of time on it.


> H.

> Michael

Pariksheet

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Re: [Bioc-devel] R CMD check without WARNING: g++ and STL issue for xcms and mzR

2017-04-12 Thread Martin Morgan 

On 04/12/2017 11:31 AM, Neumann, Steffen wrote:

Hi,

certainly these are good suggestions, but I would tend
to simply add some whitelisting functionality if the
cause is beyond the package's control.

In this case I doubt it is a handler for SIGABRT,
since that would not go away with -O2, or would it ?

For now, just adding -O2 on Linux would fix this issue.


The code is compiled on the user machine, so twiddling with the build 
system masks the problem from the developer while leaving the user 
vulnerable.


Calling abort() is certainly a serious problem, abruptly ending the user 
session.


Optimization could either eliminate a dead code path, or it could 
compile the call to abort in a way that R no longer recognizes it -- R 
is doing the equivalent of nm *.o |grep abort.


It would be appropriate to ignore the warning about abort() if it were 
never reached; one would only know this by careful code analysis rather 
than adjusting optimization flags.


Rsamtools re-defines abort (before including offending headers), and 
avoids the warning (and crash), with the equivalent of


  PKG_CFLAGS=-D__builtin_abort=_samtools_abort

where _samtools_abort is my own implementation to signal an R error 
telling the user that an unrecoverable error has occurred and they 
should stop what they are doing. Unfortunately this requires 
-U_FORTIFY_SOURCE and doesn't actually address the reason for the abort, 
and is hardly ideal.


I don't think the developer can set the optimization flag in a way that 
overrides the R or user setting (the PKG_CXXFLAGS is inserted before the 
R flags). And it doesn't address the underlying problem anyway.


Kasper's pragmatic approach (it's a very unlikely situation, and 
difficult to fix, so live with the warning) seems like it would often be 
a reasonable one.


FWIW this little bit of C++ seems to be enough to include abort

tmp.cpp:
---
#include 

int foo(int argc, const char *argv[]) {
std::list l1, l2;
std::list::iterator it;

it = l1.begin();
l1.splice (it, l2); // mylist1: 1 10 20 30 2 3 4

return 0;
}
---

Test with

  rm -f tmp.o && R CMD SHLIB tmp.cpp && nm tmp.o | grep abort

with compiler settings in

~/.R/Makevars
-
CXXFLAGS = -g -O0
-


Martin



Yours,
Steffen


On Mi, 2017-04-12 at 10:07 -0400, Vincent Carey wrote:


Suppose you had a handler for SIGABRT in your code.  Could CMD check
check for that and, if found, refrain from warning?  That is somewhat
involved and goes beyond Bioc but it seems a principled way of
dealing with operations in binary infrastructure whose behavior we
cannot control.  The problem will surely arise in other settings.
Could BiocCheck prototype the approach?

On Wed, Apr 12, 2017 at 9:12 AM, Kasper Daniel Hansen  wrote:


I think "we" have to appreciate that the warning about abort/etc
and others
is really hard to deal with when you're including (large) external
source
as you do in mzR and for example affxparser / Rgraphviz.  Generally
fixing
those in external code requires a lot of effort, and the further
effort to
document that the included sources in the package are different
from the
official sources.  I have had warnings about this in affxparser for
a long,
long time and no-one has bothered me over it.

What might be nice is (somehow) setting a flag saying this should
be
ignored in the check process, but of course we don't want that flag
to be
set by the developer, because usually, these issues should be dealt
with.
So perhaps there is nothing to do and I always have to click on
each build
report to verify that there is only 1 warning from this issues and
not
others.

Best,
Kasper

On Wed, Apr 12, 2017 at 7:22 AM, Neumann, Steffen 
wrote:



Hi Martin and malbec2 admin(s):

Some more digging revealed that malbec2
http://bioconductor.org/checkResults/devel/bioc-
LATEST/malbec2-NodeInfo.html
is using "CFLAGS=-g -O2 -Wall" but only "CXXFLAGS=-Wall"
while e.g. tokay2 uses "CXXFLAGS=-O2 -Wall -mtune=core2"

The -O2 optimisation is getting rid of the abort() symbol,
as shown in https://github.com/sneumann/xcms/issues/150#
issuecomment-293545521

=> Is there a way to get -O2 back on the BioC build machines ?
This should fix our WARNING. Bonus: will fix the same issue
in

mzR :-)



Yours,
Steffen

On So, 2017-04-02 at 10:01 -0400, Martin Morgan wrote:



On 04/02/2017 06:52 AM, Neumann, Steffen wrote:



[...]
in preparation for the release, we are hunting down WARNINGS
"Found ‘abort’, possibly from ‘abort’ (C)" in xcms/mzR.
The abort() call is not coming from XCMS, but rather
from the C++ code in the STL, and we have no idea

[...]






We are tracking this in:
https://github.com/sneumann/xcms/issues/150

[...]



I don't think Bioconductor can help with this; maybe the Rcpp

or R-




devel mailing lists?

--
3rd Leibniz Plant Biochemistry Symposium, 22.-23. of June 2017
http://www.ipb-halle.de/en/public-relations/3rd-leibniz-plant-bio

chemis


try-symposium/

Re: [Bioc-devel] R CMD check without WARNING: g++ and STL issue for xcms and mzR

2017-04-12 Thread Hervé Pagès 

Hi Steffen,

On 04/12/2017 04:22 AM, Neumann, Steffen wrote:

Hi Martin and malbec2 admin(s):

Some more digging revealed that malbec2
https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_checkResults_devel_bioc-2DLATEST_malbec2-2DNodeInfo.html=DwIGaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=V9yGIrMq8w3mmdQPS2JnioJSKNG6iGCu1hurilsGY0I=l35mMJgBfX96wHZ0WjtJoTIFGDvA-IOLXMDy9TVtz6U=
is using "CFLAGS=-g -O2 -Wall" but only "CXXFLAGS=-Wall"
while e.g. tokay2 uses "CXXFLAGS=-O2 -Wall -mtune=core2"

The -O2 optimisation is getting rid of the abort() symbol,
as shown in 
https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_sneumann_xcms_issues_150-23issuecomment-2D293545521=DwIGaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=V9yGIrMq8w3mmdQPS2JnioJSKNG6iGCu1hurilsGY0I=zvwRbtsHJd07tnGbqG5Cnj6SPzEQcadvufl5s_ir9sM=

=> Is there a way to get -O2 back on the BioC build machines ?
   This should fix our WARNING. Bonus: will fix the same issue in mzR :-)


This is apparently the new default for R 3.4 beta. Don't know if that
was an intended change (someone might want to bring this up on R-devel),
but, if it was, then let's assume they had a good reason for it.

So I'm not too keen on touching this on the build machines. Might get
rid of the mzR and xcms warnings, but might also introduce other
problems.

Why not control the compilation flags at the package level?

Thanks,
H.



Yours,
Steffen

On So, 2017-04-02 at 10:01 -0400, Martin Morgan wrote:


On 04/02/2017 06:52 AM, Neumann, Steffen wrote:


[...]
in preparation for the release, we are hunting down WARNINGS
"Found ‘abort’, possibly from ‘abort’ (C)" in xcms/mzR.
The abort() call is not coming from XCMS, but rather
from the C++ code in the STL, and we have no idea

[...]




We are tracking this in:
https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_sneumann_xcms_issues_150=DwIGaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=V9yGIrMq8w3mmdQPS2JnioJSKNG6iGCu1hurilsGY0I=PgXl6YzkPCHh3_1B8D2N15A6-Aftsbr8Wx3bcMTwIQk=

[...]


I don't think Bioconductor can help with this; maybe the Rcpp or R-
devel mailing lists?

--
3rd Leibniz Plant Biochemistry Symposium, 22.-23. of June 2017
https://urldefense.proofpoint.com/v2/url?u=http-3A__www.ipb-2Dhalle.de_en_public-2Drelations_3rd-2Dleibniz-2Dplant-2Dbiochemis=DwIGaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=V9yGIrMq8w3mmdQPS2JnioJSKNG6iGCu1hurilsGY0I=Za8ehpMewAbtvAcr0J0bV8O2S-SsaOwFzIQBfOF80n4=
try-symposium/
--
IPB HalleAG Massenspektrometrie &
Bioinformatik
Dr. Steffen Neumann  
https://urldefense.proofpoint.com/v2/url?u=http-3A__www.IPB-2DHalle.DE=DwIGaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=V9yGIrMq8w3mmdQPS2JnioJSKNG6iGCu1hurilsGY0I=NiMolENKs_yTD3KviDw4AQR5KE4-Zo0wVy34JEO5r7k=
Weinberg 3   Tel. +49 (0) 345 5582 - 1470
06120 Halle   +49 (0) 345 5582 - 0
sneumann(at)IPB-Halle.DE Fax. +49 (0) 345 5582 - 1409



--
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: [Bioc-devel] disable windows build for EiR development

2017-04-12 Thread Hervé Pagès 

Hi Kevin,

Just did that. For the record, it's easy to do this yourself: simply
add a .BBSoptions file in the top-level folder of the package with
the following line in it:

UnsupportedPlatforms: win

If you change your mind, just remove that file.

Cheers,
H.

On 04/12/2017 01:30 PM, Kevin Horan wrote:


Can you please disable the windows build for eiR in the development
branch? Thanks.

Kevin Horan

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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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[Bioc-devel] disable windows build for EiR development

2017-04-12 Thread Kevin Horan 


Can you please disable the windows build for eiR in the development 
branch? Thanks.


Kevin Horan

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Re: [Rd] "table(droplevels(aq)$Month)" in manual page of droplevels

2017-04-12 Thread Rui Barradas 

Hello,

Inline.

Em 12-04-2017 16:40, Henric Winell escreveu:

(Let's keep the discussion on-list -- I've added back R-devel.)

On 2017-04-12 16:39, Ulrich Windl wrote:


Henric Winell  schrieb am 12.04.2017
um 15:35 in

Nachricht :

On 2017-04-12 14:40, Ulrich Windl wrote:


The last line of the example in droplevels' manual page seems to
be incorrect to me. I think it should read:
"table(droplevels(aq$Month))". Amazingly (I don't understand)
both variants seem to produce the same result (R 3.3.3): ---


The manual says that "The function 'droplevels' is used to drop
unused levels from a 'factor' or, more commonly, from factors in a
data frame." and, as documented, the 'droplevels' generic has
methods for objects of class "data.frame" and "factor".  So, your
being amazed is a bit surprising given that 'aq' is a data frame.


The "surprising" thing is the syntax: I was unaware that '$' is a
generic operator that can be applied to the result of a function
(i.e.: droplevels); I thought it's kind of a special variable syntax.


Then your surprise is unrelated to the use of 'droplevels'.

Since the 'droplevels' method for objects of class "data.frame" returns
a data frame, the extraction operator '$' works directly on the
resulting object.  So, 'droplevels(aq)$Month' is essentially the same as

aq <- droplevels(aq)
aq$Month

 > Isn't there also the syntax ``droplevels(aq)["Month"]''?

Sure, and there are even more ways to do subsetting.  But this is basic
stuff and therefore off-topic for R-devel.  Please see the manual
(?Extract) or, e.g., Chapter 3 of Hadley Wickham's "Advanced R".


But note that droplevels(aq)["Month"] and droplevels(aq)$Month are _not_ 
the same. The first returns a data.frame (with just one vector), the 
latter returns a vector. To return just a vector you could also use


droplevels(aq)[["Month"]]

which is preferable for programming, by the way. The '$' operator should 
be reserved for interactive use only.


Hope this helps,

Rui Barradas



Henric Winell





Regards, Ulrich




Henric Winell




aq <- transform(airquality, Month = factor(Month, labels =
month.abb[5:9])) aq <- subset(aq, Month != "Jul")
table(aq$Month)


May Jun Jul Aug Sep 31  30   0  31  30

table(droplevels(aq)$Month)


May Jun Aug Sep 31  30  31  30

table(droplevels(aq$Month))


May Jun Aug Sep 31  30  31  30



--- For the sake of learners, try to keep the examples simple
and useful, even though you experts want to impress the
newbees...

Ulrich

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Re: [Rd] "table(droplevels(aq)$Month)" in manual page of droplevels

2017-04-12 Thread Henric Winell 

(Let's keep the discussion on-list -- I've added back R-devel.)

On 2017-04-12 16:39, Ulrich Windl wrote:


Henric Winell  schrieb am 12.04.2017
um 15:35 in

Nachricht :

On 2017-04-12 14:40, Ulrich Windl wrote:


The last line of the example in droplevels' manual page seems to
be incorrect to me. I think it should read: 
"table(droplevels(aq$Month))". Amazingly (I don't understand)

both variants seem to produce the same result (R 3.3.3): ---


The manual says that "The function 'droplevels' is used to drop
unused levels from a 'factor' or, more commonly, from factors in a
data frame." and, as documented, the 'droplevels' generic has
methods for objects of class "data.frame" and "factor".  So, your
being amazed is a bit surprising given that 'aq' is a data frame.


The "surprising" thing is the syntax: I was unaware that '$' is a
generic operator that can be applied to the result of a function
(i.e.: droplevels); I thought it's kind of a special variable syntax.


Then your surprise is unrelated to the use of 'droplevels'.

Since the 'droplevels' method for objects of class "data.frame" returns 
a data frame, the extraction operator '$' works directly on the 
resulting object.  So, 'droplevels(aq)$Month' is essentially the same as


aq <- droplevels(aq)
aq$Month

> Isn't there also the syntax ``droplevels(aq)["Month"]''?

Sure, and there are even more ways to do subsetting.  But this is basic 
stuff and therefore off-topic for R-devel.  Please see the manual 
(?Extract) or, e.g., Chapter 3 of Hadley Wickham's "Advanced R".



Henric Winell





Regards, Ulrich




Henric Winell



aq <- transform(airquality, Month = factor(Month, labels = 
month.abb[5:9])) aq <- subset(aq, Month != "Jul")

table(aq$Month)


May Jun Jul Aug Sep 31  30   0  31  30

table(droplevels(aq)$Month)


May Jun Aug Sep 31  30  31  30

table(droplevels(aq$Month))


May Jun Aug Sep 31  30  31  30



--- For the sake of learners, try to keep the examples simple
and useful, even though you experts want to impress the
newbees...

Ulrich

__
R-devel@r-project.org mailing list
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Re: [Bioc-devel] R CMD check without WARNING: g++ and STL issue for xcms and mzR

2017-04-12 Thread Neumann, Steffen 
Hi,

certainly these are good suggestions, but I would tend 
to simply add some whitelisting functionality if the 
cause is beyond the package's control. 

In this case I doubt it is a handler for SIGABRT, 
since that would not go away with -O2, or would it ?

For now, just adding -O2 on Linux would fix this issue. 

Yours,
Steffen


On Mi, 2017-04-12 at 10:07 -0400, Vincent Carey wrote:
> 
> Suppose you had a handler for SIGABRT in your code.  Could CMD check
> check for that and, if found, refrain from warning?  That is somewhat
> involved and goes beyond Bioc but it seems a principled way of
> dealing with operations in binary infrastructure whose behavior we
> cannot control.  The problem will surely arise in other settings. 
> Could BiocCheck prototype the approach?
> 
> On Wed, Apr 12, 2017 at 9:12 AM, Kasper Daniel Hansen  n...@gmail.com> wrote:
> > 
> > I think "we" have to appreciate that the warning about abort/etc
> > and others
> > is really hard to deal with when you're including (large) external
> > source
> > as you do in mzR and for example affxparser / Rgraphviz.  Generally
> > fixing
> > those in external code requires a lot of effort, and the further
> > effort to
> > document that the included sources in the package are different
> > from the
> > official sources.  I have had warnings about this in affxparser for
> > a long,
> > long time and no-one has bothered me over it.
> > 
> > What might be nice is (somehow) setting a flag saying this should
> > be
> > ignored in the check process, but of course we don't want that flag
> > to be
> > set by the developer, because usually, these issues should be dealt
> > with.
> > So perhaps there is nothing to do and I always have to click on
> > each build
> > report to verify that there is only 1 warning from this issues and
> > not
> > others.
> > 
> > Best,
> > Kasper
> > 
> > On Wed, Apr 12, 2017 at 7:22 AM, Neumann, Steffen  > le.de>
> > wrote:
> > 
> > > 
> > > Hi Martin and malbec2 admin(s):
> > > 
> > > Some more digging revealed that malbec2
> > > http://bioconductor.org/checkResults/devel/bioc-
> > > LATEST/malbec2-NodeInfo.html
> > > is using "CFLAGS=-g -O2 -Wall" but only "CXXFLAGS=-Wall"
> > > while e.g. tokay2 uses "CXXFLAGS=-O2 -Wall -mtune=core2"
> > > 
> > > The -O2 optimisation is getting rid of the abort() symbol,
> > > as shown in https://github.com/sneumann/xcms/issues/150#
> > > issuecomment-293545521
> > > 
> > > => Is there a way to get -O2 back on the BioC build machines ?
> > >     This should fix our WARNING. Bonus: will fix the same issue
> > > in
> > mzR :-)
> > > 
> > > 
> > > Yours,
> > > Steffen
> > > 
> > > On So, 2017-04-02 at 10:01 -0400, Martin Morgan wrote:
> > > > 
> > > > 
> > > > On 04/02/2017 06:52 AM, Neumann, Steffen wrote:
> > > > > 
> > > > > 
> > > > > [...]
> > > > > in preparation for the release, we are hunting down WARNINGS
> > > > > "Found ‘abort’, possibly from ‘abort’ (C)" in xcms/mzR.
> > > > > The abort() call is not coming from XCMS, but rather
> > > > > from the C++ code in the STL, and we have no idea
> > > [...]
> > > > 
> > > > 
> > > > > 
> > > > > 
> > > > > We are tracking this in:
> > > > > https://github.com/sneumann/xcms/issues/150
> > > [...]
> > > > 
> > > > 
> > > > I don't think Bioconductor can help with this; maybe the Rcpp
> > or R-
> > > 
> > > > 
> > > > devel mailing lists?
> > > --
> > > 3rd Leibniz Plant Biochemistry Symposium, 22.-23. of June 2017
> > > http://www.ipb-halle.de/en/public-relations/3rd-leibniz-plant-bio
> > chemis
> > > 
> > > try-symposium/
> > > --
> > > IPB Halle                    AG Massenspektrometrie &
> > > Bioinformatik
> > > Dr. Steffen Neumann          http://www.IPB-Halle.DE
> > > Weinberg 3                   Tel. +49 (0) 345 5582 - 1470
> > > 06120 Halle                       +49 (0) 345 5582 - 0
> > > sneumann(at)IPB-Halle.DE     Fax. +49 (0) 345 5582 - 1409
> > > 
> > > --
> > > 3rd Leibniz Plant Biochemistry Symposium, 22.-23. of June 2017
> > > http://www.ipb-halle.de/en/public-relations/3rd-leibniz-plant-bio
> > chemis
> > > 
> > > try-symposium/
> > > --
> > > IPB Halle                    AG Massenspektrometrie &
> > > Bioinformatik
> > > Dr. Steffen Neumann          http://www.IPB-Halle.DE
> > > Weinberg 3                   Tel. +49 (0) 345 5582 - 1470
> > > 06120 Halle                       +49 (0) 345 5582 - 0
> > > sneumann(at)IPB-Halle.DE     Fax. +49 (0) 345 5582 - 1409
> > > 
> > > ___
> > > Bioc-devel@r-project.org mailing list
> > > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> > > 
> >         [[alternative HTML version deleted]]
> > 
> > ___
> > Bioc-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> > 
-- 
3rd Leibniz Plant Biochemistry Symposium, 22.-23. of June 2017
http://www.ipb-halle.de/en/public-relations/3rd-leibniz-plant-biochemis
try-symposium/
--
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Re: [Bioc-devel] R CMD check without WARNING: g++ and STL issue for xcms and mzR

2017-04-12 Thread Vincent Carey 
Suppose you had a handler for SIGABRT in your code.  Could CMD check check
for that and, if found, refrain from warning?  That is somewhat involved
and goes beyond Bioc but it seems a principled way of dealing with
operations in binary infrastructure whose behavior we cannot control.  The
problem will surely arise in other settings.  Could BiocCheck prototype the
approach?

On Wed, Apr 12, 2017 at 9:12 AM, Kasper Daniel Hansen <
kasperdanielhan...@gmail.com> wrote:

> I think "we" have to appreciate that the warning about abort/etc and others
> is really hard to deal with when you're including (large) external source
> as you do in mzR and for example affxparser / Rgraphviz.  Generally fixing
> those in external code requires a lot of effort, and the further effort to
> document that the included sources in the package are different from the
> official sources.  I have had warnings about this in affxparser for a long,
> long time and no-one has bothered me over it.
>
> What might be nice is (somehow) setting a flag saying this should be
> ignored in the check process, but of course we don't want that flag to be
> set by the developer, because usually, these issues should be dealt with.
> So perhaps there is nothing to do and I always have to click on each build
> report to verify that there is only 1 warning from this issues and not
> others.
>
> Best,
> Kasper
>
> On Wed, Apr 12, 2017 at 7:22 AM, Neumann, Steffen 
> wrote:
>
> > Hi Martin and malbec2 admin(s):
> >
> > Some more digging revealed that malbec2
> > http://bioconductor.org/checkResults/devel/bioc-
> > LATEST/malbec2-NodeInfo.html
> > is using "CFLAGS=-g -O2 -Wall" but only "CXXFLAGS=-Wall"
> > while e.g. tokay2 uses "CXXFLAGS=-O2 -Wall -mtune=core2"
> >
> > The -O2 optimisation is getting rid of the abort() symbol,
> > as shown in https://github.com/sneumann/xcms/issues/150#
> > issuecomment-293545521
> >
> > => Is there a way to get -O2 back on the BioC build machines ?
> >This should fix our WARNING. Bonus: will fix the same issue in mzR :-)
> >
> > Yours,
> > Steffen
> >
> > On So, 2017-04-02 at 10:01 -0400, Martin Morgan wrote:
> > >
> > > On 04/02/2017 06:52 AM, Neumann, Steffen wrote:
> > > >
> > > > [...]
> > > > in preparation for the release, we are hunting down WARNINGS
> > > > "Found ‘abort’, possibly from ‘abort’ (C)" in xcms/mzR.
> > > > The abort() call is not coming from XCMS, but rather
> > > > from the C++ code in the STL, and we have no idea
> > [...]
> > >
> > > >
> > > > We are tracking this in:
> > > > https://github.com/sneumann/xcms/issues/150
> > [...]
> > >
> > > I don't think Bioconductor can help with this; maybe the Rcpp or R-
> > > devel mailing lists?
> > --
> > 3rd Leibniz Plant Biochemistry Symposium, 22.-23. of June 2017
> > http://www.ipb-halle.de/en/public-relations/3rd-leibniz-plant-biochemis
> > try-symposium/
> > --
> > IPB HalleAG Massenspektrometrie &
> > Bioinformatik
> > Dr. Steffen Neumann  http://www.IPB-Halle.DE
> > Weinberg 3   Tel. +49 (0) 345 5582 - 1470
> > 06120 Halle   +49 (0) 345 5582 - 0
> > sneumann(at)IPB-Halle.DE Fax. +49 (0) 345 5582 - 1409
> >
> > --
> > 3rd Leibniz Plant Biochemistry Symposium, 22.-23. of June 2017
> > http://www.ipb-halle.de/en/public-relations/3rd-leibniz-plant-biochemis
> > try-symposium/
> > --
> > IPB HalleAG Massenspektrometrie &
> > Bioinformatik
> > Dr. Steffen Neumann  http://www.IPB-Halle.DE
> > Weinberg 3   Tel. +49 (0) 345 5582 - 1470
> > 06120 Halle   +49 (0) 345 5582 - 0
> > sneumann(at)IPB-Halle.DE Fax. +49 (0) 345 5582 - 1409
> >
> > ___
> > Bioc-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

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Re: [Rd] "table(droplevels(aq)$Month)" in manual page of droplevels

2017-04-12 Thread Henric Winell 

On 2017-04-12 14:40, Ulrich Windl wrote:


The last line of the example in droplevels' manual page seems to be
incorrect to me. I think it should read:
"table(droplevels(aq$Month))". Amazingly (I don't understand) both
variants seem to produce the same result (R 3.3.3): ---


The manual says that "The function 'droplevels' is used to drop unused 
levels from a 'factor' or, more commonly, from factors in a data frame." 
and, as documented, the 'droplevels' generic has methods for objects of 
class "data.frame" and "factor".  So, your being amazed is a bit 
surprising given that 'aq' is a data frame.



Henric Winell




aq <- transform(airquality, Month = factor(Month, labels =
month.abb[5:9])) aq <- subset(aq, Month != "Jul") table(aq$Month)


May Jun Jul Aug Sep 31  30   0  31  30

table(droplevels(aq)$Month)


May Jun Aug Sep 31  30  31  30

table(droplevels(aq$Month))


May Jun Aug Sep 31  30  31  30



--- For the sake of learners, try to keep the examples simple and
useful, even though you experts want to impress the newbees...

Ulrich

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



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Re: [Bioc-devel] R CMD check without WARNING: g++ and STL issue for xcms and mzR

2017-04-12 Thread Kasper Daniel Hansen 
I think "we" have to appreciate that the warning about abort/etc and others
is really hard to deal with when you're including (large) external source
as you do in mzR and for example affxparser / Rgraphviz.  Generally fixing
those in external code requires a lot of effort, and the further effort to
document that the included sources in the package are different from the
official sources.  I have had warnings about this in affxparser for a long,
long time and no-one has bothered me over it.

What might be nice is (somehow) setting a flag saying this should be
ignored in the check process, but of course we don't want that flag to be
set by the developer, because usually, these issues should be dealt with.
So perhaps there is nothing to do and I always have to click on each build
report to verify that there is only 1 warning from this issues and not
others.

Best,
Kasper

On Wed, Apr 12, 2017 at 7:22 AM, Neumann, Steffen 
wrote:

> Hi Martin and malbec2 admin(s):
>
> Some more digging revealed that malbec2
> http://bioconductor.org/checkResults/devel/bioc-
> LATEST/malbec2-NodeInfo.html
> is using "CFLAGS=-g -O2 -Wall" but only "CXXFLAGS=-Wall"
> while e.g. tokay2 uses "CXXFLAGS=-O2 -Wall -mtune=core2"
>
> The -O2 optimisation is getting rid of the abort() symbol,
> as shown in https://github.com/sneumann/xcms/issues/150#
> issuecomment-293545521
>
> => Is there a way to get -O2 back on the BioC build machines ?
>This should fix our WARNING. Bonus: will fix the same issue in mzR :-)
>
> Yours,
> Steffen
>
> On So, 2017-04-02 at 10:01 -0400, Martin Morgan wrote:
> >
> > On 04/02/2017 06:52 AM, Neumann, Steffen wrote:
> > >
> > > [...]
> > > in preparation for the release, we are hunting down WARNINGS
> > > "Found ‘abort’, possibly from ‘abort’ (C)" in xcms/mzR.
> > > The abort() call is not coming from XCMS, but rather
> > > from the C++ code in the STL, and we have no idea
> [...]
> >
> > >
> > > We are tracking this in:
> > > https://github.com/sneumann/xcms/issues/150
> [...]
> >
> > I don't think Bioconductor can help with this; maybe the Rcpp or R-
> > devel mailing lists?
> --
> 3rd Leibniz Plant Biochemistry Symposium, 22.-23. of June 2017
> http://www.ipb-halle.de/en/public-relations/3rd-leibniz-plant-biochemis
> try-symposium/
> --
> IPB HalleAG Massenspektrometrie &
> Bioinformatik
> Dr. Steffen Neumann  http://www.IPB-Halle.DE
> Weinberg 3   Tel. +49 (0) 345 5582 - 1470
> 06120 Halle   +49 (0) 345 5582 - 0
> sneumann(at)IPB-Halle.DE Fax. +49 (0) 345 5582 - 1409
>
> --
> 3rd Leibniz Plant Biochemistry Symposium, 22.-23. of June 2017
> http://www.ipb-halle.de/en/public-relations/3rd-leibniz-plant-biochemis
> try-symposium/
> --
> IPB HalleAG Massenspektrometrie &
> Bioinformatik
> Dr. Steffen Neumann  http://www.IPB-Halle.DE
> Weinberg 3   Tel. +49 (0) 345 5582 - 1470
> 06120 Halle   +49 (0) 345 5582 - 0
> sneumann(at)IPB-Halle.DE Fax. +49 (0) 345 5582 - 1409
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

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[Rd] "table(droplevels(aq)$Month)" in manual page of droplevels

2017-04-12 Thread Ulrich Windl 
The last line of the example in droplevels' manual page seems to be incorrect 
to me. I think it should read: "table(droplevels(aq$Month))". Amazingly (I 
don't understand) both variants seem to produce the same result (R 3.3.3):
---
> aq <- transform(airquality, Month = factor(Month, labels = month.abb[5:9]))
> aq <- subset(aq, Month != "Jul")
> table(aq$Month)

May Jun Jul Aug Sep 
 31  30   0  31  30 
> table(droplevels(aq)$Month)

May Jun Aug Sep 
 31  30  31  30 
> table(droplevels(aq$Month))

May Jun Aug Sep 
 31  30  31  30 
>
---
For the sake of learners, try to keep the examples simple and useful, even 
though you experts want to impress the newbees...

Ulrich

__
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Re: [Bioc-devel] R CMD check without WARNING: g++ and STL issue for xcms and mzR

2017-04-12 Thread Neumann, Steffen 
Hi Martin and malbec2 admin(s):

Some more digging revealed that malbec2 
http://bioconductor.org/checkResults/devel/bioc-LATEST/malbec2-NodeInfo.html
is using "CFLAGS=-g -O2 -Wall" but only "CXXFLAGS=-Wall"
while e.g. tokay2 uses "CXXFLAGS=-O2 -Wall -mtune=core2"

The -O2 optimisation is getting rid of the abort() symbol,
as shown in https://github.com/sneumann/xcms/issues/150#issuecomment-293545521

=> Is there a way to get -O2 back on the BioC build machines ? 
   This should fix our WARNING. Bonus: will fix the same issue in mzR :-)

Yours,
Steffen

On So, 2017-04-02 at 10:01 -0400, Martin Morgan wrote:
> 
> On 04/02/2017 06:52 AM, Neumann, Steffen wrote:
> > 
> > [...]
> > in preparation for the release, we are hunting down WARNINGS
> > "Found ‘abort’, possibly from ‘abort’ (C)" in xcms/mzR.
> > The abort() call is not coming from XCMS, but rather
> > from the C++ code in the STL, and we have no idea
[...]
> 
> > 
> > We are tracking this in:
> > https://github.com/sneumann/xcms/issues/150
[...]
> 
> I don't think Bioconductor can help with this; maybe the Rcpp or R-
> devel mailing lists?
-- 
3rd Leibniz Plant Biochemistry Symposium, 22.-23. of June 2017
http://www.ipb-halle.de/en/public-relations/3rd-leibniz-plant-biochemis
try-symposium/
--
IPB HalleAG Massenspektrometrie &
Bioinformatik
Dr. Steffen Neumann  http://www.IPB-Halle.DE
Weinberg 3                   Tel. +49 (0) 345 5582 - 1470
06120 Halle                       +49 (0) 345 5582 - 0           
sneumann(at)IPB-Halle.DE Fax. +49 (0) 345 5582 - 1409

-- 
3rd Leibniz Plant Biochemistry Symposium, 22.-23. of June 2017
http://www.ipb-halle.de/en/public-relations/3rd-leibniz-plant-biochemis
try-symposium/
--
IPB HalleAG Massenspektrometrie &
Bioinformatik
Dr. Steffen Neumann  http://www.IPB-Halle.DE
Weinberg 3                   Tel. +49 (0) 345 5582 - 1470
06120 Halle                       +49 (0) 345 5582 - 0           
sneumann(at)IPB-Halle.DE Fax. +49 (0) 345 5582 - 1409

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