[Debian-med-packaging] Bug#976567: libhmsbeagle: FTBFS: GPUInterface.h:221:27: error: there are no arguments to ‘malloc’ that depend on a template parameter, so a declaration of ‘malloc’ must be available [-fpermissive]

[Lucas Nussbaum]

Source: libhmsbeagle
Version: 3.1.2+dfsg-8
Severity: serious
Justification: FTBFS on arm64
Tags: bullseye sid ftbfs
Usertags: ftbfs-20201205 ftbfs-bullseye

Hi,

During a rebuild of all packages in sid, your package failed to build
on arm64 (I don't know if it also fails on amd64).

Relevant part (hopefully):
> /bin/bash ../../libtool  --tag=CXX   --mode=compile g++ -DHAVE_CONFIG_H -I. -I../../libhmsbeagle  -I/<<PKGBUILDDIR>> -I/<<PKGBUILDDIR>> -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/lib/jvm/java-11-openjdk-arm64/include -I/usr/lib/jvm/java-11-openjdk-arm64/include/linux -O3 -std=c++11 -D FW_OPENCL -I/usr/include/CL/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libhmsbeagle_opencl_la-OpenCLPlugin.lo `test -f 'OpenCLPlugin.cpp' || echo './'`OpenCLPlugin.cpp
> libtool: compile:  g++ -DHAVE_CONFIG_H -I. -I../../libhmsbeagle -I/<<PKGBUILDDIR>> -I/<<PKGBUILDDIR>> -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/lib/jvm/java-11-openjdk-arm64/include -I/usr/lib/jvm/java-11-openjdk-arm64/include/linux -O3 -std=c++11 -D FW_OPENCL -I/usr/include/CL/include -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c OpenCLPlugin.cpp  -fPIC -DPIC -o .libs/libhmsbeagle_opencl_la-OpenCLPlugin.o
> In file included from /usr/include/CL/cl.h:20,
>                  from /usr/include/CL/opencl.h:24,
>                  from /<<PKGBUILDDIR>>/libhmsbeagle/GPU/GPUInterface.h:60,
>                  from /<<PKGBUILDDIR>>/libhmsbeagle/GPU/BeagleGPUImpl.h:39,
>                  from OpenCLPlugin.cpp:8:
> /usr/include/CL/cl_version.h:22:104: note: ‘#pragma message: cl_version.h: CL_TARGET_OPENCL_VERSION is not defined. Defaulting to 300 (OpenCL 3.0)’
>    22 | #pragma message("cl_version.h: CL_TARGET_OPENCL_VERSION is not defined. Defaulting to 300 (OpenCL 3.0)")
>       |                                                                                                        ^
> In file included from /<<PKGBUILDDIR>>/libhmsbeagle/GPU/BeagleGPUImpl.h:39,
>                  from OpenCLPlugin.cpp:8:
> /<<PKGBUILDDIR>>/libhmsbeagle/GPU/GPUInterface.h: In member function ‘void opencl_device::GPUInterface::PrintfDeviceVector(GPUPtr, int, double, int*, Real)’:
> /<<PKGBUILDDIR>>/libhmsbeagle/GPU/GPUInterface.h:221:27: error: there are no arguments to ‘malloc’ that depend on a template parameter, so a declaration of ‘malloc’ must be available [-fpermissive]
>   221 |      Real* hPtr = (Real*) malloc(sizeof(Real) * length);
>       |                           ^~~~~~
> /<<PKGBUILDDIR>>/libhmsbeagle/GPU/GPUInterface.h:221:27: note: (if you use ‘-fpermissive’, G++ will accept your code, but allowing the use of an undeclared name is deprecated)
> make[6]: *** [Makefile:701: libhmsbeagle_opencl_la-OpenCLPlugin.lo] Error 1

The full build log is available from:
   http://qa-logs.debian.net/2020/12/05/libhmsbeagle_3.1.2+dfsg-8_unstable.log

A list of current common problems and possible solutions is available at
http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute!

If you reassign this bug to another package, please marking it as 'affects'-ing
this package. See https://www.debian.org/Bugs/server-control#affects

If you fail to reproduce this, please provide a build log and diff it with me
so that we can identify if something relevant changed in the meantime.

About the archive rebuild: The rebuild was done on EC2 VM instances from
Amazon Web Services, using a clean, minimal and up-to-date chroot. Every
failed build was retried once to eliminate random failures.