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zhengxwen / SeqArray

Data management of large-scale whole-genome sequence variant calls (Development version only)
http://www.bioconductor.org/packages/SeqArray
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SeqArray-1.42.3 build fails with R-4.3.3 and GCC 13.2.0 #89

Open fizwit opened 7 months ago

fizwit commented 7 months ago 
Bioconductor version 3.18 (BiocManager 1.30.22), R 4.3.3 (2024-02-29)
Installing package(s) 'SeqArray'
trying URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/SeqArray_1.42.3.tar.gz'
Content type 'application/x-gzip' length 3594661 bytes (3.4 MB)

downloaded 3.4 MB

* installing *source* package ‘SeqArray’ ...
** using staged installation
** libs
using C compiler: ‘gcc (GCC) 13.2.0’
using C++ compiler: ‘g++ (GCC) 13.2.0’
g++ -std=gnu++17 -I"/app/software/R/4.3.3-gfbf-2023b/lib/R/include" -DNDEBUG -DUSING_R -I'/app/software/fhR/4.3.3-foss-2023b/gdsfmt/include' -I/app/software/FriBidi/1.0.13-GCCcore-13.2.0/include -I/app/software/HarfBuzz/8.2.2-GCCcore-13.2.0/include -I/app/software/Tk/8.6.13-GCCcore-13.2.0/include -I/app/software/cURL/8.3.0-GCCcore-13.2.0/include -I/app/software/OpenSSL/1.1/include -I/app/software/libgit2/1.7.2-GCCcore-13.2.0/include -I/app/software/Java/11.0.2/include -I/app/software/LibTIFF/4.6.0-GCCcore-13.2.0/include -I/app/software/libjpeg-turbo/3.0.1-GCCcore-13.2.0/include -I/app/software/libpng/1.6.40-GCCcore-13.2.0/include -I/app/software/PCRE2/10.42-GCCcore-13.2.0/include -I/app/software/SQLite/3.43.1-GCCcore-13.2.0/include -I/app/software/zlib/1.2.13-GCCcore-13.2.0/include -I/app/software/XZ/5.4.4-GCCcore-13.2.0/include -I/app/software/bzip2/1.0.8-GCCcore-13.2.0/include -I/app/software/ncurses/6.4-GCCcore-13.2.0/include -I/app/software/libreadline/8.2-GCCcore-13.2.0/include -I/app/software/cairo/1.18.0-GCCcore-13.2.0/include -I/app/software/libGLU/9.0.3-GCCcore-13.2.0/include -I/app/software/Mesa/23.1.9-GCCcore-13.2.0/include -I/app/software/X11/20231019-GCCcore-13.2.0/include -I/app/software/pkgconf/2.0.3-GCCcore-13.2.0/include -I/app/software/FFTW/3.3.10-GCC-13.2.0/include -I/app/software/FlexiBLAS/3.3.1-GCC-13.2.0/include -I/app/software/FlexiBLAS/3.3.1-GCC-13.2.0/include/flexiblas    -fpic  -O2 -ftree-vectorize -march=native -fno-math-errno  -c ConvGDS2VCF.cpp -o ConvGDS2VCF.o
g++ -std=gnu++17 -I"/app/software/R/4.3.3-gfbf-2023b/lib/R/include" -DNDEBUG -DUSING_R -I'/app/software/fhR/4.3.3-foss-2023b/gdsfmt/include' -I/app/software/FriBidi/1.0.13-GCCcore-13.2.0/include -I/app/software/HarfBuzz/8.2.2-GCCcore-13.2.0/include -I/app/software/Tk/8.6.13-GCCcore-13.2.0/include -I/app/software/cURL/8.3.0-GCCcore-13.2.0/include -I/app/software/OpenSSL/1.1/include -I/app/software/libgit2/1.7.2-GCCcore-13.2.0/include -I/app/software/Java/11.0.2/include -I/app/software/LibTIFF/4.6.0-GCCcore-13.2.0/include -I/app/software/libjpeg-turbo/3.0.1-GCCcore-13.2.0/include -I/app/software/libpng/1.6.40-GCCcore-13.2.0/include -I/app/software/PCRE2/10.42-GCCcore-13.2.0/include -I/app/software/SQLite/3.43.1-GCCcore-13.2.0/include -I/app/software/zlib/1.2.13-GCCcore-13.2.0/include -I/app/software/XZ/5.4.4-GCCcore-13.2.0/include -I/app/software/bzip2/1.0.8-GCCcore-13.2.0/include -I/app/software/ncurses/6.4-GCCcore-13.2.0/include -I/app/software/libreadline/8.2-GCCcore-13.2.0/include -I/app/software/cairo/1.18.0-GCCcore-13.2.0/include -I/app/software/libGLU/9.0.3-GCCcore-13.2.0/include -I/app/software/Mesa/23.1.9-GCCcore-13.2.0/include -I/app/software/X11/20231019-GCCcore-13.2.0/include -I/app/software/pkgconf/2.0.3-GCCcore-13.2.0/include -I/app/software/FFTW/3.3.10-GCC-13.2.0/include -I/app/software/FlexiBLAS/3.3.1-GCC-13.2.0/include -I/app/software/FlexiBLAS/3.3.1-GCC-13.2.0/include/flexiblas    -fpic  -O2 -ftree-vectorize -march=native -fno-math-errno  -c ConvToGDS.cpp -o ConvToGDS.o
g++ -std=gnu++17 -I"/app/software/R/4.3.3-gfbf-2023b/lib/R/include" -DNDEBUG -DUSING_R -I'/app/software/fhR/4.3.3-foss-2023b/gdsfmt/include' -I/app/software/FriBidi/1.0.13-GCCcore-13.2.0/include -I/app/software/HarfBuzz/8.2.2-GCCcore-13.2.0/include -I/app/software/Tk/8.6.13-GCCcore-13.2.0/include -I/app/software/cURL/8.3.0-GCCcore-13.2.0/include -I/app/software/OpenSSL/1.1/include -I/app/software/libgit2/1.7.2-GCCcore-13.2.0/include -I/app/software/Java/11.0.2/include -I/app/software/LibTIFF/4.6.0-GCCcore-13.2.0/include -I/app/software/libjpeg-turbo/3.0.1-GCCcore-13.2.0/include -I/app/software/libpng/1.6.40-GCCcore-13.2.0/include -I/app/software/PCRE2/10.42-GCCcore-13.2.0/include -I/app/software/SQLite/3.43.1-GCCcore-13.2.0/include -I/app/software/zlib/1.2.13-GCCcore-13.2.0/include -I/app/software/XZ/5.4.4-GCCcore-13.2.0/include -I/app/software/bzip2/1.0.8-GCCcore-13.2.0/include -I/app/software/ncurses/6.4-GCCcore-13.2.0/include -I/app/software/libreadline/8.2-GCCcore-13.2.0/include -I/app/software/cairo/1.18.0-GCCcore-13.2.0/include -I/app/software/libGLU/9.0.3-GCCcore-13.2.0/include -I/app/software/Mesa/23.1.9-GCCcore-13.2.0/include -I/app/software/X11/20231019-GCCcore-13.2.0/include -I/app/software/pkgconf/2.0.3-GCCcore-13.2.0/include -I/app/software/FFTW/3.3.10-GCC-13.2.0/include -I/app/software/FlexiBLAS/3.3.1-GCC-13.2.0/include -I/app/software/FlexiBLAS/3.3.1-GCC-13.2.0/include/flexiblas    -fpic  -O2 -ftree-vectorize -march=native -fno-math-errno  -c ConvVCF2GDS.cpp -o ConvVCF2GDS.o
g++ -std=gnu++17 -I"/app/software/R/4.3.3-gfbf-2023b/lib/R/include" -DNDEBUG -DUSING_R -I'/app/software/fhR/4.3.3-foss-2023b/gdsfmt/include' -I/app/software/FriBidi/1.0.13-GCCcore-13.2.0/include -I/app/software/HarfBuzz/8.2.2-GCCcore-13.2.0/include -I/app/software/Tk/8.6.13-GCCcore-13.2.0/include -I/app/software/cURL/8.3.0-GCCcore-13.2.0/include -I/app/software/OpenSSL/1.1/include -I/app/software/libgit2/1.7.2-GCCcore-13.2.0/include -I/app/software/Java/11.0.2/include -I/app/software/LibTIFF/4.6.0-GCCcore-13.2.0/include -I/app/software/libjpeg-turbo/3.0.1-GCCcore-13.2.0/include -I/app/software/libpng/1.6.40-GCCcore-13.2.0/include -I/app/software/PCRE2/10.42-GCCcore-13.2.0/include -I/app/software/SQLite/3.43.1-GCCcore-13.2.0/include -I/app/software/zlib/1.2.13-GCCcore-13.2.0/include -I/app/software/XZ/5.4.4-GCCcore-13.2.0/include -I/app/software/bzip2/1.0.8-GCCcore-13.2.0/include -I/app/software/ncurses/6.4-GCCcore-13.2.0/include -I/app/software/libreadline/8.2-GCCcore-13.2.0/include -I/app/software/cairo/1.18.0-GCCcore-13.2.0/include -I/app/software/libGLU/9.0.3-GCCcore-13.2.0/include -I/app/software/Mesa/23.1.9-GCCcore-13.2.0/include -I/app/software/X11/20231019-GCCcore-13.2.0/include -I/app/software/pkgconf/2.0.3-GCCcore-13.2.0/include -I/app/software/FFTW/3.3.10-GCC-13.2.0/include -I/app/software/FlexiBLAS/3.3.1-GCC-13.2.0/include -I/app/software/FlexiBLAS/3.3.1-GCC-13.2.0/include/flexiblas    -fpic  -O2 -ftree-vectorize -march=native -fno-math-errno  -c FileMerge.cpp -o FileMerge.o
g++ -std=gnu++17 -I"/app/software/R/4.3.3-gfbf-2023b/lib/R/include" -DNDEBUG -DUSING_R -I'/app/software/fhR/4.3.3-foss-2023b/gdsfmt/include' -I/app/software/FriBidi/1.0.13-GCCcore-13.2.0/include -I/app/software/HarfBuzz/8.2.2-GCCcore-13.2.0/include -I/app/software/Tk/8.6.13-GCCcore-13.2.0/include -I/app/software/cURL/8.3.0-GCCcore-13.2.0/include -I/app/software/OpenSSL/1.1/include -I/app/software/libgit2/1.7.2-GCCcore-13.2.0/include -I/app/software/Java/11.0.2/include -I/app/software/LibTIFF/4.6.0-GCCcore-13.2.0/include -I/app/software/libjpeg-turbo/3.0.1-GCCcore-13.2.0/include -I/app/software/libpng/1.6.40-GCCcore-13.2.0/include -I/app/software/PCRE2/10.42-GCCcore-13.2.0/include -I/app/software/SQLite/3.43.1-GCCcore-13.2.0/include -I/app/software/zlib/1.2.13-GCCcore-13.2.0/include -I/app/software/XZ/5.4.4-GCCcore-13.2.0/include -I/app/software/bzip2/1.0.8-GCCcore-13.2.0/include -I/app/software/ncurses/6.4-GCCcore-13.2.0/include -I/app/software/libreadline/8.2-GCCcore-13.2.0/include -I/app/software/cairo/1.18.0-GCCcore-13.2.0/include -I/app/software/libGLU/9.0.3-GCCcore-13.2.0/include -I/app/software/Mesa/23.1.9-GCCcore-13.2.0/include -I/app/software/X11/20231019-GCCcore-13.2.0/include -I/app/software/pkgconf/2.0.3-GCCcore-13.2.0/include -I/app/software/FFTW/3.3.10-GCC-13.2.0/include -I/app/software/FlexiBLAS/3.3.1-GCC-13.2.0/include -I/app/software/FlexiBLAS/3.3.1-GCC-13.2.0/include/flexiblas    -fpic  -O2 -ftree-vectorize -march=native -fno-math-errno  -c GetData.cpp -o GetData.o
g++ -std=gnu++17 -I"/app/software/R/4.3.3-gfbf-2023b/lib/R/include" -DNDEBUG -DUSING_R -I'/app/software/fhR/4.3.3-foss-2023b/gdsfmt/include' -I/app/software/FriBidi/1.0.13-GCCcore-13.2.0/include -I/app/software/HarfBuzz/8.2.2-GCCcore-13.2.0/include -I/app/software/Tk/8.6.13-GCCcore-13.2.0/include -I/app/software/cURL/8.3.0-GCCcore-13.2.0/include -I/app/software/OpenSSL/1.1/include -I/app/software/libgit2/1.7.2-GCCcore-13.2.0/include -I/app/software/Java/11.0.2/include -I/app/software/LibTIFF/4.6.0-GCCcore-13.2.0/include -I/app/software/libjpeg-turbo/3.0.1-GCCcore-13.2.0/include -I/app/software/libpng/1.6.40-GCCcore-13.2.0/include -I/app/software/PCRE2/10.42-GCCcore-13.2.0/include -I/app/software/SQLite/3.43.1-GCCcore-13.2.0/include -I/app/software/zlib/1.2.13-GCCcore-13.2.0/include -I/app/software/XZ/5.4.4-GCCcore-13.2.0/include -I/app/software/bzip2/1.0.8-GCCcore-13.2.0/include -I/app/software/ncurses/6.4-GCCcore-13.2.0/include -I/app/software/libreadline/8.2-GCCcore-13.2.0/include -I/app/software/cairo/1.18.0-GCCcore-13.2.0/include -I/app/software/libGLU/9.0.3-GCCcore-13.2.0/include -I/app/software/Mesa/23.1.9-GCCcore-13.2.0/include -I/app/software/X11/20231019-GCCcore-13.2.0/include -I/app/software/pkgconf/2.0.3-GCCcore-13.2.0/include -I/app/software/FFTW/3.3.10-GCC-13.2.0/include -I/app/software/FlexiBLAS/3.3.1-GCC-13.2.0/include -I/app/software/FlexiBLAS/3.3.1-GCC-13.2.0/include/flexiblas    -fpic  -O2 -ftree-vectorize -march=native -fno-math-errno  -c Index.cpp -o Index.o
g++ -std=gnu++17 -I"/app/software/R/4.3.3-gfbf-2023b/lib/R/include" -DNDEBUG -DUSING_R -I'/app/software/fhR/4.3.3-foss-2023b/gdsfmt/include' -I/app/software/FriBidi/1.0.13-GCCcore-13.2.0/include -I/app/software/HarfBuzz/8.2.2-GCCcore-13.2.0/include -I/app/software/Tk/8.6.13-GCCcore-13.2.0/include -I/app/software/cURL/8.3.0-GCCcore-13.2.0/include -I/app/software/OpenSSL/1.1/include -I/app/software/libgit2/1.7.2-GCCcore-13.2.0/include -I/app/software/Java/11.0.2/include -I/app/software/LibTIFF/4.6.0-GCCcore-13.2.0/include -I/app/software/libjpeg-turbo/3.0.1-GCCcore-13.2.0/include -I/app/software/libpng/1.6.40-GCCcore-13.2.0/include -I/app/software/PCRE2/10.42-GCCcore-13.2.0/include -I/app/software/SQLite/3.43.1-GCCcore-13.2.0/include -I/app/software/zlib/1.2.13-GCCcore-13.2.0/include -I/app/software/XZ/5.4.4-GCCcore-13.2.0/include -I/app/software/bzip2/1.0.8-GCCcore-13.2.0/include -I/app/software/ncurses/6.4-GCCcore-13.2.0/include -I/app/software/libreadline/8.2-GCCcore-13.2.0/include -I/app/software/cairo/1.18.0-GCCcore-13.2.0/include -I/app/software/libGLU/9.0.3-GCCcore-13.2.0/include -I/app/software/Mesa/23.1.9-GCCcore-13.2.0/include -I/app/software/X11/20231019-GCCcore-13.2.0/include -I/app/software/pkgconf/2.0.3-GCCcore-13.2.0/include -I/app/software/FFTW/3.3.10-GCC-13.2.0/include -I/app/software/FlexiBLAS/3.3.1-GCC-13.2.0/include -I/app/software/FlexiBLAS/3.3.1-GCC-13.2.0/include/flexiblas    -fpic  -O2 -ftree-vectorize -march=native -fno-math-errno  -c LinkSNPRelate.cpp -o LinkSNPRelate.o
g++ -std=gnu++17 -I"/app/software/R/4.3.3-gfbf-2023b/lib/R/include" -DNDEBUG -DUSING_R -I'/app/software/fhR/4.3.3-foss-2023b/gdsfmt/include' -I/app/software/FriBidi/1.0.13-GCCcore-13.2.0/include -I/app/software/HarfBuzz/8.2.2-GCCcore-13.2.0/include -I/app/software/Tk/8.6.13-GCCcore-13.2.0/include -I/app/software/cURL/8.3.0-GCCcore-13.2.0/include -I/app/software/OpenSSL/1.1/include -I/app/software/libgit2/1.7.2-GCCcore-13.2.0/include -I/app/software/Java/11.0.2/include -I/app/software/LibTIFF/4.6.0-GCCcore-13.2.0/include -I/app/software/libjpeg-turbo/3.0.1-GCCcore-13.2.0/include -I/app/software/libpng/1.6.40-GCCcore-13.2.0/include -I/app/software/PCRE2/10.42-GCCcore-13.2.0/include -I/app/software/SQLite/3.43.1-GCCcore-13.2.0/include -I/app/software/zlib/1.2.13-GCCcore-13.2.0/include -I/app/software/XZ/5.4.4-GCCcore-13.2.0/include -I/app/software/bzip2/1.0.8-GCCcore-13.2.0/include -I/app/software/ncurses/6.4-GCCcore-13.2.0/include -I/app/software/libreadline/8.2-GCCcore-13.2.0/include -I/app/software/cairo/1.18.0-GCCcore-13.2.0/include -I/app/software/libGLU/9.0.3-GCCcore-13.2.0/include -I/app/software/Mesa/23.1.9-GCCcore-13.2.0/include -I/app/software/X11/20231019-GCCcore-13.2.0/include -I/app/software/pkgconf/2.0.3-GCCcore-13.2.0/include -I/app/software/FFTW/3.3.10-GCC-13.2.0/include -I/app/software/FlexiBLAS/3.3.1-GCC-13.2.0/include -I/app/software/FlexiBLAS/3.3.1-GCC-13.2.0/include/flexiblas    -fpic  -O2 -ftree-vectorize -march=native -fno-math-errno  -c Methods.cpp -o Methods.o
gcc -I"/app/software/R/4.3.3-gfbf-2023b/lib/R/include" -DNDEBUG -DUSING_R -I'/app/software/fhR/4.3.3-foss-2023b/gdsfmt/include' -I/app/software/FriBidi/1.0.13-GCCcore-13.2.0/include -I/app/software/HarfBuzz/8.2.2-GCCcore-13.2.0/include -I/app/software/Tk/8.6.13-GCCcore-13.2.0/include -I/app/software/cURL/8.3.0-GCCcore-13.2.0/include -I/app/software/OpenSSL/1.1/include -I/app/software/libgit2/1.7.2-GCCcore-13.2.0/include -I/app/software/Java/11.0.2/include -I/app/software/LibTIFF/4.6.0-GCCcore-13.2.0/include -I/app/software/libjpeg-turbo/3.0.1-GCCcore-13.2.0/include -I/app/software/libpng/1.6.40-GCCcore-13.2.0/include -I/app/software/PCRE2/10.42-GCCcore-13.2.0/include -I/app/software/SQLite/3.43.1-GCCcore-13.2.0/include -I/app/software/zlib/1.2.13-GCCcore-13.2.0/include -I/app/software/XZ/5.4.4-GCCcore-13.2.0/include -I/app/software/bzip2/1.0.8-GCCcore-13.2.0/include -I/app/software/ncurses/6.4-GCCcore-13.2.0/include -I/app/software/libreadline/8.2-GCCcore-13.2.0/include -I/app/software/cairo/1.18.0-GCCcore-13.2.0/include -I/app/software/libGLU/9.0.3-GCCcore-13.2.0/include -I/app/software/Mesa/23.1.9-GCCcore-13.2.0/include -I/app/software/X11/20231019-GCCcore-13.2.0/include -I/app/software/pkgconf/2.0.3-GCCcore-13.2.0/include -I/app/software/FFTW/3.3.10-GCC-13.2.0/include -I/app/software/FlexiBLAS/3.3.1-GCC-13.2.0/include -I/app/software/FlexiBLAS/3.3.1-GCC-13.2.0/include/flexiblas    -fpic  -O2 -ftree-vectorize -march=native -fno-math-errno  -c R_SeqArray.c -o R_SeqArray.o
g++ -std=gnu++17 -I"/app/software/R/4.3.3-gfbf-2023b/lib/R/include" -DNDEBUG -DUSING_R -I'/app/software/fhR/4.3.3-foss-2023b/gdsfmt/include' -I/app/software/FriBidi/1.0.13-GCCcore-13.2.0/include -I/app/software/HarfBuzz/8.2.2-GCCcore-13.2.0/include -I/app/software/Tk/8.6.13-GCCcore-13.2.0/include -I/app/software/cURL/8.3.0-GCCcore-13.2.0/include -I/app/software/OpenSSL/1.1/include -I/app/software/libgit2/1.7.2-GCCcore-13.2.0/include -I/app/software/Java/11.0.2/include -I/app/software/LibTIFF/4.6.0-GCCcore-13.2.0/include -I/app/software/libjpeg-turbo/3.0.1-GCCcore-13.2.0/include -I/app/software/libpng/1.6.40-GCCcore-13.2.0/include -I/app/software/PCRE2/10.42-GCCcore-13.2.0/include -I/app/software/SQLite/3.43.1-GCCcore-13.2.0/include -I/app/software/zlib/1.2.13-GCCcore-13.2.0/include -I/app/software/XZ/5.4.4-GCCcore-13.2.0/include -I/app/software/bzip2/1.0.8-GCCcore-13.2.0/include -I/app/software/ncurses/6.4-GCCcore-13.2.0/include -I/app/software/libreadline/8.2-GCCcore-13.2.0/include -I/app/software/cairo/1.18.0-GCCcore-13.2.0/include -I/app/software/libGLU/9.0.3-GCCcore-13.2.0/include -I/app/software/Mesa/23.1.9-GCCcore-13.2.0/include -I/app/software/X11/20231019-GCCcore-13.2.0/include -I/app/software/pkgconf/2.0.3-GCCcore-13.2.0/include -I/app/software/FFTW/3.3.10-GCC-13.2.0/include -I/app/software/FlexiBLAS/3.3.1-GCC-13.2.0/include -I/app/software/FlexiBLAS/3.3.1-GCC-13.2.0/include/flexiblas    -fpic  -O2 -ftree-vectorize -march=native -fno-math-errno  -c ReadBySample.cpp -o ReadBySample.o
g++ -std=gnu++17 -I"/app/software/R/4.3.3-gfbf-2023b/lib/R/include" -DNDEBUG -DUSING_R -I'/app/software/fhR/4.3.3-foss-2023b/gdsfmt/include' -I/app/software/FriBidi/1.0.13-GCCcore-13.2.0/include -I/app/software/HarfBuzz/8.2.2-GCCcore-13.2.0/include -I/app/software/Tk/8.6.13-GCCcore-13.2.0/include -I/app/software/cURL/8.3.0-GCCcore-13.2.0/include -I/app/software/OpenSSL/1.1/include -I/app/software/libgit2/1.7.2-GCCcore-13.2.0/include -I/app/software/Java/11.0.2/include -I/app/software/LibTIFF/4.6.0-GCCcore-13.2.0/include -I/app/software/libjpeg-turbo/3.0.1-GCCcore-13.2.0/include -I/app/software/libpng/1.6.40-GCCcore-13.2.0/include -I/app/software/PCRE2/10.42-GCCcore-13.2.0/include -I/app/software/SQLite/3.43.1-GCCcore-13.2.0/include -I/app/software/zlib/1.2.13-GCCcore-13.2.0/include -I/app/software/XZ/5.4.4-GCCcore-13.2.0/include -I/app/software/bzip2/1.0.8-GCCcore-13.2.0/include -I/app/software/ncurses/6.4-GCCcore-13.2.0/include -I/app/software/libreadline/8.2-GCCcore-13.2.0/include -I/app/software/cairo/1.18.0-GCCcore-13.2.0/include -I/app/software/libGLU/9.0.3-GCCcore-13.2.0/include -I/app/software/Mesa/23.1.9-GCCcore-13.2.0/include -I/app/software/X11/20231019-GCCcore-13.2.0/include -I/app/software/pkgconf/2.0.3-GCCcore-13.2.0/include -I/app/software/FFTW/3.3.10-GCC-13.2.0/include -I/app/software/FlexiBLAS/3.3.1-GCC-13.2.0/include -I/app/software/FlexiBLAS/3.3.1-GCC-13.2.0/include/flexiblas    -fpic  -O2 -ftree-vectorize -march=native -fno-math-errno  -c ReadByUnit.cpp -o ReadByUnit.o
g++ -std=gnu++17 -I"/app/software/R/4.3.3-gfbf-2023b/lib/R/include" -DNDEBUG -DUSING_R -I'/app/software/fhR/4.3.3-foss-2023b/gdsfmt/include' -I/app/software/FriBidi/1.0.13-GCCcore-13.2.0/include -I/app/software/HarfBuzz/8.2.2-GCCcore-13.2.0/include -I/app/software/Tk/8.6.13-GCCcore-13.2.0/include -I/app/software/cURL/8.3.0-GCCcore-13.2.0/include -I/app/software/OpenSSL/1.1/include -I/app/software/libgit2/1.7.2-GCCcore-13.2.0/include -I/app/software/Java/11.0.2/include -I/app/software/LibTIFF/4.6.0-GCCcore-13.2.0/include -I/app/software/libjpeg-turbo/3.0.1-GCCcore-13.2.0/include -I/app/software/libpng/1.6.40-GCCcore-13.2.0/include -I/app/software/PCRE2/10.42-GCCcore-13.2.0/include -I/app/software/SQLite/3.43.1-GCCcore-13.2.0/include -I/app/software/zlib/1.2.13-GCCcore-13.2.0/include -I/app/software/XZ/5.4.4-GCCcore-13.2.0/include -I/app/software/bzip2/1.0.8-GCCcore-13.2.0/include -I/app/software/ncurses/6.4-GCCcore-13.2.0/include -I/app/software/libreadline/8.2-GCCcore-13.2.0/include -I/app/software/cairo/1.18.0-GCCcore-13.2.0/include -I/app/software/libGLU/9.0.3-GCCcore-13.2.0/include -I/app/software/Mesa/23.1.9-GCCcore-13.2.0/include -I/app/software/X11/20231019-GCCcore-13.2.0/include -I/app/software/pkgconf/2.0.3-GCCcore-13.2.0/include -I/app/software/FFTW/3.3.10-GCC-13.2.0/include -I/app/software/FlexiBLAS/3.3.1-GCC-13.2.0/include -I/app/software/FlexiBLAS/3.3.1-GCC-13.2.0/include/flexiblas    -fpic  -O2 -ftree-vectorize -march=native -fno-math-errno  -c ReadByVariant.cpp -o ReadByVariant.o
g++ -std=gnu++17 -I"/app/software/R/4.3.3-gfbf-2023b/lib/R/include" -DNDEBUG -DUSING_R -I'/app/software/fhR/4.3.3-foss-2023b/gdsfmt/include' -I/app/software/FriBidi/1.0.13-GCCcore-13.2.0/include -I/app/software/HarfBuzz/8.2.2-GCCcore-13.2.0/include -I/app/software/Tk/8.6.13-GCCcore-13.2.0/include -I/app/software/cURL/8.3.0-GCCcore-13.2.0/include -I/app/software/OpenSSL/1.1/include -I/app/software/libgit2/1.7.2-GCCcore-13.2.0/include -I/app/software/Java/11.0.2/include -I/app/software/LibTIFF/4.6.0-GCCcore-13.2.0/include -I/app/software/libjpeg-turbo/3.0.1-GCCcore-13.2.0/include -I/app/software/libpng/1.6.40-GCCcore-13.2.0/include -I/app/software/PCRE2/10.42-GCCcore-13.2.0/include -I/app/software/SQLite/3.43.1-GCCcore-13.2.0/include -I/app/software/zlib/1.2.13-GCCcore-13.2.0/include -I/app/software/XZ/5.4.4-GCCcore-13.2.0/include -I/app/software/bzip2/1.0.8-GCCcore-13.2.0/include -I/app/software/ncurses/6.4-GCCcore-13.2.0/include -I/app/software/libreadline/8.2-GCCcore-13.2.0/include -I/app/software/cairo/1.18.0-GCCcore-13.2.0/include -I/app/software/libGLU/9.0.3-GCCcore-13.2.0/include -I/app/software/Mesa/23.1.9-GCCcore-13.2.0/include -I/app/software/X11/20231019-GCCcore-13.2.0/include -I/app/software/pkgconf/2.0.3-GCCcore-13.2.0/include -I/app/software/FFTW/3.3.10-GCC-13.2.0/include -I/app/software/FlexiBLAS/3.3.1-GCC-13.2.0/include -I/app/software/FlexiBLAS/3.3.1-GCC-13.2.0/include/flexiblas    -fpic  -O2 -ftree-vectorize -march=native -fno-math-errno  -c SeqArray.cpp -o SeqArray.o
g++ -std=gnu++17 -I"/app/software/R/4.3.3-gfbf-2023b/lib/R/include" -DNDEBUG -DUSING_R -I'/app/software/fhR/4.3.3-foss-2023b/gdsfmt/include' -I/app/software/FriBidi/1.0.13-GCCcore-13.2.0/include -I/app/software/HarfBuzz/8.2.2-GCCcore-13.2.0/include -I/app/software/Tk/8.6.13-GCCcore-13.2.0/include -I/app/software/cURL/8.3.0-GCCcore-13.2.0/include -I/app/software/OpenSSL/1.1/include -I/app/software/libgit2/1.7.2-GCCcore-13.2.0/include -I/app/software/Java/11.0.2/include -I/app/software/LibTIFF/4.6.0-GCCcore-13.2.0/include -I/app/software/libjpeg-turbo/3.0.1-GCCcore-13.2.0/include -I/app/software/libpng/1.6.40-GCCcore-13.2.0/include -I/app/software/PCRE2/10.42-GCCcore-13.2.0/include -I/app/software/SQLite/3.43.1-GCCcore-13.2.0/include -I/app/software/zlib/1.2.13-GCCcore-13.2.0/include -I/app/software/XZ/5.4.4-GCCcore-13.2.0/include -I/app/software/bzip2/1.0.8-GCCcore-13.2.0/include -I/app/software/ncurses/6.4-GCCcore-13.2.0/include -I/app/software/libreadline/8.2-GCCcore-13.2.0/include -I/app/software/cairo/1.18.0-GCCcore-13.2.0/include -I/app/software/libGLU/9.0.3-GCCcore-13.2.0/include -I/app/software/Mesa/23.1.9-GCCcore-13.2.0/include -I/app/software/X11/20231019-GCCcore-13.2.0/include -I/app/software/pkgconf/2.0.3-GCCcore-13.2.0/include -I/app/software/FFTW/3.3.10-GCC-13.2.0/include -I/app/software/FlexiBLAS/3.3.1-GCC-13.2.0/include -I/app/software/FlexiBLAS/3.3.1-GCC-13.2.0/include/flexiblas    -fpic  -O2 -ftree-vectorize -march=native -fno-math-errno  -c pkg_test.cpp -o pkg_test.o
gcc -I"/app/software/R/4.3.3-gfbf-2023b/lib/R/include" -DNDEBUG -DUSING_R -I'/app/software/fhR/4.3.3-foss-2023b/gdsfmt/include' -I/app/software/FriBidi/1.0.13-GCCcore-13.2.0/include -I/app/software/HarfBuzz/8.2.2-GCCcore-13.2.0/include -I/app/software/Tk/8.6.13-GCCcore-13.2.0/include -I/app/software/cURL/8.3.0-GCCcore-13.2.0/include -I/app/software/OpenSSL/1.1/include -I/app/software/libgit2/1.7.2-GCCcore-13.2.0/include -I/app/software/Java/11.0.2/include -I/app/software/LibTIFF/4.6.0-GCCcore-13.2.0/include -I/app/software/libjpeg-turbo/3.0.1-GCCcore-13.2.0/include -I/app/software/libpng/1.6.40-GCCcore-13.2.0/include -I/app/software/PCRE2/10.42-GCCcore-13.2.0/include -I/app/software/SQLite/3.43.1-GCCcore-13.2.0/include -I/app/software/zlib/1.2.13-GCCcore-13.2.0/include -I/app/software/XZ/5.4.4-GCCcore-13.2.0/include -I/app/software/bzip2/1.0.8-GCCcore-13.2.0/include -I/app/software/ncurses/6.4-GCCcore-13.2.0/include -I/app/software/libreadline/8.2-GCCcore-13.2.0/include -I/app/software/cairo/1.18.0-GCCcore-13.2.0/include -I/app/software/libGLU/9.0.3-GCCcore-13.2.0/include -I/app/software/Mesa/23.1.9-GCCcore-13.2.0/include -I/app/software/X11/20231019-GCCcore-13.2.0/include -I/app/software/pkgconf/2.0.3-GCCcore-13.2.0/include -I/app/software/FFTW/3.3.10-GCC-13.2.0/include -I/app/software/FlexiBLAS/3.3.1-GCC-13.2.0/include -I/app/software/FlexiBLAS/3.3.1-GCC-13.2.0/include/flexiblas    -fpic  -O2 -ftree-vectorize -march=native -fno-math-errno  -c samtools_ext.c -o samtools_ext.o
g++ -std=gnu++17 -I"/app/software/R/4.3.3-gfbf-2023b/lib/R/include" -DNDEBUG -DUSING_R -I'/app/software/fhR/4.3.3-foss-2023b/gdsfmt/include' -I/app/software/FriBidi/1.0.13-GCCcore-13.2.0/include -I/app/software/HarfBuzz/8.2.2-GCCcore-13.2.0/include -I/app/software/Tk/8.6.13-GCCcore-13.2.0/include -I/app/software/cURL/8.3.0-GCCcore-13.2.0/include -I/app/software/OpenSSL/1.1/include -I/app/software/libgit2/1.7.2-GCCcore-13.2.0/include -I/app/software/Java/11.0.2/include -I/app/software/LibTIFF/4.6.0-GCCcore-13.2.0/include -I/app/software/libjpeg-turbo/3.0.1-GCCcore-13.2.0/include -I/app/software/libpng/1.6.40-GCCcore-13.2.0/include -I/app/software/PCRE2/10.42-GCCcore-13.2.0/include -I/app/software/SQLite/3.43.1-GCCcore-13.2.0/include -I/app/software/zlib/1.2.13-GCCcore-13.2.0/include -I/app/software/XZ/5.4.4-GCCcore-13.2.0/include -I/app/software/bzip2/1.0.8-GCCcore-13.2.0/include -I/app/software/ncurses/6.4-GCCcore-13.2.0/include -I/app/software/libreadline/8.2-GCCcore-13.2.0/include -I/app/software/cairo/1.18.0-GCCcore-13.2.0/include -I/app/software/libGLU/9.0.3-GCCcore-13.2.0/include -I/app/software/Mesa/23.1.9-GCCcore-13.2.0/include -I/app/software/X11/20231019-GCCcore-13.2.0/include -I/app/software/pkgconf/2.0.3-GCCcore-13.2.0/include -I/app/software/FFTW/3.3.10-GCC-13.2.0/include -I/app/software/FlexiBLAS/3.3.1-GCC-13.2.0/include -I/app/software/FlexiBLAS/3.3.1-GCC-13.2.0/include/flexiblas    -fpic  -O2 -ftree-vectorize -march=native -fno-math-errno  -c vectorization.cpp -o vectorization.o
vectorization.cpp: In function ‘const char* vec_char_find_CRLF(const char*, size_t)’:
vectorization.cpp:1878:1: error: jump to label ‘tail’
 1878 | tail:
      | ^~~~
vectorization.cpp:1849:30: note:   from here
 1849 |                         goto tail;
      |                              ^~~~
vectorization.cpp:1855:23: note:   crosses initialization of ‘const __m256i mask4’
 1855 |         const __m256i mask4 = _mm256_set1_epi8('\r');
      |                       ^~~~~
vectorization.cpp:1854:23: note:   crosses initialization of ‘const __m256i mask3’
 1854 |         const __m256i mask3 = _mm256_set1_epi8('\n');
      |                       ^~~~~
/app/software/R/4.3.3-gfbf-2023b/lib64/R/etc/Makeconf:200: recipe for target 'vectorization.o' failed
make: *** [vectorization.o] Error 1
ERROR: compilation failed for package ‘SeqArray’
* removing ‘/app/software/fhR/4.3.3-foss-2023b/SeqArray’
zhengxwen commented 7 months ago

Could you please show me sessionInfo()?

fizwit commented 7 months ago 
> sessionInfo()
R version 4.3.3 (2024-02-29)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.6 LTS

Matrix products: default
BLAS/LAPACK: FlexiBLAS OPENBLAS;  LAPACK version 3.11.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

time zone: America/Los_Angeles
tzcode source: system (glibc)

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

loaded via a namespace (and not attached):
[1] compiler_4.3.3
idavydov commented 6 months ago

I am experiencing a similar problem on R-4.3.2 and GCC:

g++ -std=gnu++17 <...>    -fpic  -O2 -ftree-vectorize -march=cascadelake -fno-math-errno  -c vectorization.cpp -o vectorization.o
vectorization.cpp: In function ‘const char* vec_char_find_CRLF(const char*, size_t)’:
vectorization.cpp:1878:1: error: jump to label ‘tail’
 1878 | tail:
      | ^~~~
vectorization.cpp:1849:9: note:   from here
 1849 |    goto tail;
      |         ^~~~
vectorization.cpp:1855:16: note:   crosses initialization of ‘const __m256i mask4’
 1855 |  const __m256i mask4 = _mm256_set1_epi8('\r');
      |                ^~~~~
vectorization.cpp:1854:16: note:   crosses initialization of ‘const __m256i mask3’
 1854 |  const __m256i mask3 = _mm256_set1_epi8('\n');
      |                ^~~~~
make: *** [<...>/R/4.3.2-foss-2020a/lib64/R/etc/Makeconf:200: vectorization.o] Error 1
ERROR: compilation failed for package ‘SeqArray’
> sessionInfo()
R version 4.3.2 (2023-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux 8.6 (Ootpa)

Matrix products: default
BLAS/LAPACK: <...>/OpenBLAS/0.3.9-GCC-9.3.0/lib/libopenblas_skylakexp-r0.3.9.so;  LAPACK version 3.9.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

time zone: Europe/Amsterdam
tzcode source: system (glibc)

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
[1] compiler_4.3.2      BiocManager_1.30.22
zhengxwen commented 6 months ago

The latest commit should fix this issue: https://github.com/zhengxwen/SeqArray/commit/16bba1eba7e4935f13c72026974e9c12720aa23a

Install SeqArray_1.44.0 from Bioconductor or install from GitHub.

Best,

Xiuwen