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

[Hervé Pagès]

Thanks Steffen for bringing this to the R-devel list. I only
see the fix in trunk for now. They'll need to port it to the 3.4
branch if we want to see it propagate to our BioC 3.5 builds.

Just to clarify, by default R doesn't use the -Wall flag to
compile packages on Linux. It's something we add on our Linux
builders.

Cheers,
H.


On 04/19/2017 11:52 AM, Neumann, Steffen wrote:

Hi,

just a quick report, I followed this up to r-devel,
and a fix adding -O2 back to default CXXFLAGS
has been committed (r72549, see [1]) to R by Martyn Plummer,
thus "fixing" the abort() related WARNING in mzR/xcms
once this gets into the R version used on malbec2.

Yours,
Steffen

[1] 
https://urldefense.proofpoint.com/v2/url?u=http-3A__developer.r-2Dproject.org_R-5Fsvnlog-5F2013=DwIGaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=YE8GxLGaWhq-2Zt3n3yIFSqX3K1hSlEQgyUpXjLaYPg=nRu69QAXHm0lBKf9Al-8KvSvfGAqLrzp1uWirvd6XF0=

On Mi, 2017-04-12 at 22:07 -0400, Martin Morgan wrote:

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

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

[Neumann, Steffen]

Hi,

just a quick report, I followed this up to r-devel,
and a fix adding -O2 back to default CXXFLAGS 
has been committed (r72549, see [1]) to R by Martyn Plummer, 
thus "fixing" the abort() related WARNING in mzR/xcms 
once this gets into the R version used on malbec2.

Yours,
Steffen

[1] http://developer.r-project.org/R_svnlog_2013

On Mi, 2017-04-12 at 22:07 -0400, Martin Morgan wrote:
> 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
> > >  > > 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  > > > -hal
> > > > le.de>
> > > > wrote:
> > > > 
> > > > > 
> > > > > 
> > > > > Hi Martin and malbec2 admin(s):
> > > > > 
> > > > > Some more digging revealed that malbec2
> > > > > 

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

[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

[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

___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

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

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

[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
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>

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

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

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

[Neumann, Steffen]

Hi,

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 
how to get rid of it.

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

In a nutshell, the standard tenplate library (STL) that comes 
with g++-5.4.0 has a snippet:

https://github.com/gcc-mirror/gcc/blob/1cb6c2eb3b8361d850be8e8270c59727
0a1a7967/libstdc%2B%2B-v3/include/bits/stl_list.h#L1825

...
# 1770 "/usr/include/c++/5/bits/stl_list.h"
void _M_check_equal_allocators(list& __x) {
 if (_M_get_Node_allocator())
   __builtin_abort();
}

You can also check this by looking at the compiler output 
after the preprocess step:

g++ -I/usr/share/R/include -DNDEBUG  -fpic  -g -O2 -fstack-
protector-strong -Wformat -Werror=format-security -Wdate-time
-D_FORTIFY_SOURCE=2 -g  -c massifquant/TrMgr.cpp -E | less

The same applies to mzR, where the same stl_list.h is included
in two files (Found ‘abort’, possibly from ‘abort’ (C)
Objects: ‘./boost/libs/regex/src/instances.o’,
  ‘./boost/libs/regex/src/winstances.o’)

=> Since we don't want to patch the STL, we have no idea 
   how to fix that WARNING. Is there a way to get an exception, 
   or patch/whitelist this call in R CMD check ?

Yours, 
Steffen Neumann

-- 
Current job opportunities @ IPB Halle:
For details, see: http://www.ipb-halle.de/en/career/job-vacancies/

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--
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Dr. Steffen Neumann  http://www.IPB-Halle.DE
Weinberg 3                   Tel. +49 (0) 345 5582 - 1470
06120 Halle                       +49 (0) 345 5582 - 0           
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