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Support for Linux ARM64 #4

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martin-g opened this issue Feb 16, 2023 · 0 comments · May be fixed by #5
Open

Support for Linux ARM64 #4

martin-g opened this issue Feb 16, 2023 · 0 comments · May be fixed by #5

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@martin-g
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Hi,

We are working on adding support for Linux ARM64 for Bioconductor and we faced the following build problem:

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### Running command:
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###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL Rbec
###
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* installing *source* package ‘Rbec’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
g++ -std=gnu++14  -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c RcppExports.cpp -o RcppExports.o
In file included from ../inst/include/Rbec.h:7,
                 from RcppExports.cpp:4:
../inst/include/Rbec_RcppExports.h:14:14: warning: ‘void Rbec::{anonymous}::validateSignature(const char*)’ defined but not used [-Wunused-function]
   14 |         void validateSignature(const char* sig) {
      |              ^~~~~~~~~~~~~~~~~
g++ -std=gnu++14  -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c kmer_dist.cpp -o kmer_dist.o
kmer_dist.cpp: In function ‘Rcpp::NumericVector kmer_dist(std::vector<std::__cxx11::basic_string<char> >, std::vector<std::__cxx11::basic_string<char> >, int)’:
kmer_dist.cpp:33:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
   33 |   for(int i=0;i<nseqs;i++) {
      |               ~^~~~~~
g++ -std=gnu++14  -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c rcpp_test.cpp -o rcpp_test.o
rcpp_test.cpp:3:10: fatal error: emmintrin.h: No such file or directory
    3 | #include "emmintrin.h"
      |          ^~~~~~~~~~~~~
compilation terminated.
make: *** [/home/biocbuild/bbs-3.17-bioc/R/etc/Makeconf:198: rcpp_test.o] Error 1
ERROR: compilation failed for package ‘Rbec’
* removing ‘/home/biocbuild/bbs-3.17-bioc/R/library/Rbec’

It fails compiling the test due to usage of x86_64 specific import: emmintrin.h.

I'll try to provide a PR with a fix !

martin-g added a commit to martin-g/Rbec that referenced this issue Feb 16, 2023
Signed-off-by: Martin Tzvetanov Grigorov <[email protected]>
@martin-g martin-g linked a pull request Feb 16, 2023 that will close this issue
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