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
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]
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
Hi Steffen,
On 04/12/2017 04:22 AM, Neumann, Steffen wrote:
Hi Martin and malbec2 admin(s):
Some more digging revealed that malbec2
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
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
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
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
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:
