[Bioc-devel] C++ compiler error on kunpeng2 ?

[Katja Danielzik]

Hi Martin,

thank you! The installation now runs error free, but the build report 
returns warnings (only on kungpen2 and at least for packages 
MetaboDynamics, ClustIRR and IgGeneUsage):

Found the following significant warnings:
   /home/biocbuild/R/R-devel_2025-02-19/site-library/RcppEigen/include/Eigen/src/Core/arch/NEON/PacketMath.h:1671:9:
  warning: ‘void* memcpy(void*, const void*, size_t)’ copying an object of non-trivial type ‘Eigen::internal::Packet4c’
  {aka ‘struct Eigen::internal::eigen_packet_wrapper<int, 2>’} from an array of ‘const int8_t’ {aka ‘const signed char’} [-Wclass-memaccess]
   /home/biocbuild/R/R-devel_2025-02-19/site-library/RcppEigen/include/Eigen/src/Core/arch/NEON/PacketMath.h:1716:9:
warning: ‘void* memcpy(void*, const void*, size_t)’ copying an object of non-trivial type ‘Eigen::internal::Packet4c’
{aka ‘struct Eigen::internal::eigen_packet_wrapper<int, 2>’} from an array of ‘const int8_t’ {aka ‘const signed char’} [-Wclass-memaccess]
See ‘/home/biocbuild/bbs-3.21-bioc/meat/MetaboDynamics.Rcheck/00install.out’ for details.

 From what I got from https://gitlab.com/libeigen/eigen/-/issues/2546 
there might be still something up with the C++ compiler on kungpeng2.

Best,

Katja


On 10.03.25 13:58, Martin Grigorov wrote:
> Hi,
>
> Installed the tbb-devel package!
> The next build should be fine!
>
> Thanks for the report!
>
> Regards,
> Martin
>
> On Mon, Mar 10, 2025 at 1:39 PM Martin Grigorov<mgrigorov using apache.org>
> wrote:
>
>> Hi,
>>
>> I’ll check which package needs to be installed to provide libtbbmalloc!
>>
>> On Mon, 10 Mar 2025 at 13:19, Katja Danielzik <
>> katja.danielzik using stud.uni-due.de> wrote:
>>
>>> Dear all,
>>>
>>> i have noticed that my package "MetaboDynamics" which employs stan
>>> models ,that are pre-compiled to C++ during installation, fails to
>>> install on kunpeng2 (and only there) with the following error message:
>>>
>>> /usr/bin/ld: cannot find -ltbbmalloc: No such file or directory
>>> collect2: error: ld returned 1 exit status
>>> make: *** [/home/biocbuild/R/R/share/make/shlib.mk:10:
>>> MetaboDynamics.so] Error 1
>>> ERROR: compilation failed for package ‘MetaboDynamics’
>>> * removing
>>> ‘/home/biocbuild/R/R-devel_2025-02-19/site-library/MetaboDynamics’
>>>
>>> The same error exists for the packages "IgGeneUsage" and "ClustIRR"
>>> which also contain stan models that are compiled to C++.
>>>
>>> Might it be that the C++ compiler has an error or something is not
>>> installed properly on the kunpeng2 VM?
>>>
>>> Best,
>>>
>>> Katja Danielzik
>>>
>>> --
>>> PhD Student
>>> AG Bioinformatics and Computational Biophysics
>>> University of Duisburg-Essen
>>> Tel: +49 201 183 4265
>>> e-mail:katja.danielzik using uni-due.de
>>>
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>>>
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