Attachment 1979281 Details for Bug 2226299 – build.log

build.log

build.log (text/plain), 32.00 KB, created by Fedora Release Engineering on 2023-07-25 19:42:21 UTC

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Creator: Fedora Release Engineering

Created: 2023-07-25 19:42:21 UTC

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obsolete

>,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -I/builddir/build/BUILD/pysam-0.19.1/htslib -I/builddir/build/BUILD/pysam-0.19.1/samtools -I/builddir/build/BUILD/pysam-0.19.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.1/bcftools -I/builddir/build/BUILD/pysam-0.19.1/pysam -I/builddir/build/BUILD/pysam-0.19.1 -I/usr/include/python3.12 -c bcftools/version.c.pysam.c -o build/temp.linux-aarch64-cpython-312/bcftools/version.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
>gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -I/builddir/build/BUILD/pysam-0.19.1/htslib -I/builddir/build/BUILD/pysam-0.19.1/samtools -I/builddir/build/BUILD/pysam-0.19.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.1/bcftools -I/builddir/build/BUILD/pysam-0.19.1/pysam -I/builddir/build/BUILD/pysam-0.19.1 -I/usr/include/python3.12 -c pysam/libcbcftools.c -o build/temp.linux-aarch64-cpython-312/pysam/libcbcftools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
>gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer build/temp.linux-aarch64-cpython-312/bcftools/HMM.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/abuf.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/bam2bcf.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/bam2bcf_indel.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/bam_sample.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/bcftools.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/bin.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/ccall.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/cols.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/consensus.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/convert.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/csq.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/dist.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/em.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/extsort.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/filter.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/gvcf.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/hclust.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/kmin.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/main.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/mcall.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/mpileup.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/ploidy.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/prob1.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/regidx.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/reheader.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/smpl_ilist.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/str_finder.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/tabix.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/tsv2vcf.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/vcfannotate.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/vcfbuf.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/vcfcall.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/vcfcnv.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/vcfconcat.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/vcfconvert.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/vcffilter.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/vcfgtcheck.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/vcfhead.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/vcfindex.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/vcfisec.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/vcfmerge.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/vcfnorm.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/vcfplugin.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/vcfquery.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/vcfroh.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/vcfsom.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/vcfsort.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/vcfstats.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/vcfview.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/vcmp.c.pysam.o build/temp.linux-aarch64-cpython-312/bcftools/version.c.pysam.o build/temp.linux-aarch64-cpython-312/pysam/libcbcftools.o -L/builddir/build/BUILD/pysam-0.19.1/pysam -L/builddir/build/BUILD/pysam-0.19.1/pysam -L/builddir/build/BUILD/pysam-0.19.1 -L/builddir/build/BUILD/pysam-0.19.1/build/lib.linux-aarch64-3.12/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-312-aarch64-linux-gnu -o build/lib.linux-aarch64-cpython-312/pysam/libcbcftools.cpython-312-aarch64-linux-gnu.so -Wl,-rpath,$ORIGIN
>bcftools/vcfmerge.c.pysam.c: In function âmaux_initâ:
>bcftools/vcfmerge.c.pysam.c:749:34: warning: argument 1 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
>  749 |         ma->gvcf = (gvcf_aux_t*) calloc(ma->n,sizeof(gvcf_aux_t));  // -Walloc-size-larger-than gives a harmless warning caused by signed integer ma->n
>      |                                  ^
>/usr/include/stdlib.h:675:14: note: in a call to allocation function âcallocâ declared here
>  675 | extern void *calloc (size_t __nmemb, size_t __size)
>      |              ^
>/usr/lib64/python3.12/site-packages/Cython/Compiler/Main.py:381: FutureWarning: Cython directive 'language_level' not set, using '3str' for now (Py3). This has changed from earlier releases! File: /builddir/build/BUILD/pysam-0.19.1/pysam/libcutils.pxd
>  tree = Parsing.p_module(s, pxd, full_module_name)
>Compiling pysam/libcutils.pyx because it changed.
>[1/1] Cythonizing pysam/libcutils.pyx
>building 'pysam.libcutils' extension
>gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -I/builddir/build/BUILD/pysam-0.19.1/htslib -I/builddir/build/BUILD/pysam-0.19.1/samtools -I/builddir/build/BUILD/pysam-0.19.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.1/bcftools -I/builddir/build/BUILD/pysam-0.19.1/pysam -I/builddir/build/BUILD/pysam-0.19.1 -I/usr/include/python3.12 -c pysam/libcutils.c -o build/temp.linux-aarch64-cpython-312/pysam/libcutils.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
>gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -I/builddir/build/BUILD/pysam-0.19.1/htslib -I/builddir/build/BUILD/pysam-0.19.1/samtools -I/builddir/build/BUILD/pysam-0.19.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.1/bcftools -I/builddir/build/BUILD/pysam-0.19.1/pysam -I/builddir/build/BUILD/pysam-0.19.1 -I/usr/include/python3.12 -c pysam/pysam_util.c -o build/temp.linux-aarch64-cpython-312/pysam/pysam_util.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
>gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer build/temp.linux-aarch64-cpython-312/pysam/libcutils.o build/temp.linux-aarch64-cpython-312/pysam/pysam_util.o -L/builddir/build/BUILD/pysam-0.19.1/pysam -L/builddir/build/BUILD/pysam-0.19.1/pysam -L/builddir/build/BUILD/pysam-0.19.1 -L/builddir/build/BUILD/pysam-0.19.1/build/lib.linux-aarch64-3.12/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-312-aarch64-linux-gnu -lcsamtools.cpython-312-aarch64-linux-gnu -lcbcftools.cpython-312-aarch64-linux-gnu -o build/lib.linux-aarch64-cpython-312/pysam/libcutils.cpython-312-aarch64-linux-gnu.so -Wl,-rpath,$ORIGIN
>/usr/lib64/python3.12/site-packages/Cython/Compiler/Main.py:381: FutureWarning: Cython directive 'language_level' not set, using '3str' for now (Py3). This has changed from earlier releases! File: /builddir/build/BUILD/pysam-0.19.1/pysam/libcalignmentfile.pxd
>  tree = Parsing.p_module(s, pxd, full_module_name)
>warning: pysam/libcalignmentfile.pyx:2573:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation
>warning: pysam/libcalignmentfile.pyx:2578:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation
>warning: pysam/libcalignmentfile.pyx:2583:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation
>warning: pysam/libcalignmentfile.pyx:2622:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation
>warning: pysam/libcalignmentfile.pyx:2627:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation
>warning: pysam/libcalignmentfile.pyx:2632:49: Casting a GIL-requiring function into a nogil function circumvents GIL validation
>Compiling pysam/libcalignmentfile.pyx because it changed.
>[1/1] Cythonizing pysam/libcalignmentfile.pyx
>building 'pysam.libcalignmentfile' extension
>gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -I/builddir/build/BUILD/pysam-0.19.1/htslib -I/builddir/build/BUILD/pysam-0.19.1/samtools -I/builddir/build/BUILD/pysam-0.19.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.1/bcftools -I/builddir/build/BUILD/pysam-0.19.1/pysam -I/builddir/build/BUILD/pysam-0.19.1 -I/usr/include/python3.12 -c pysam/libcalignmentfile.c -o build/temp.linux-aarch64-cpython-312/pysam/libcalignmentfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
>pysam/libcalignmentfile.c: In function â__pyx_pf_5pysam_17libcalignmentfile_13AlignmentFile_6_openâ:
>pysam/libcalignmentfile.c:19510:20: warning: ignoring return value of âsam_hdr_writeâ declared with attribute âwarn_unused_resultâ [-Wunused-result]
>19510 |             (void)(sam_hdr_write(__pyx_v_self->__pyx_base.htsfile, __pyx_v_hdr));
>      |                   ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>pysam/libcalignmentfile.c: In function â__pyx_f_5pysam_17libcalignmentfile_20IteratorRowSelection_cnextâ:
>pysam/libcalignmentfile.c:35202:16: warning: ignoring return value of âbgzf_seekâ declared with attribute âwarn_unused_resultâ [-Wunused-result]
>35202 |         (void)(bgzf_seek(hts_get_bgzfp(__pyx_v_self->__pyx_base.htsfile), __pyx_v_pos, 0));
>      |               ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer build/temp.linux-aarch64-cpython-312/pysam/libcalignmentfile.o -L/builddir/build/BUILD/pysam-0.19.1/pysam -L/builddir/build/BUILD/pysam-0.19.1/pysam -L/builddir/build/BUILD/pysam-0.19.1 -L/builddir/build/BUILD/pysam-0.19.1/build/lib.linux-aarch64-3.12/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-312-aarch64-linux-gnu -lcutils.cpython-312-aarch64-linux-gnu -o build/lib.linux-aarch64-cpython-312/pysam/libcalignmentfile.cpython-312-aarch64-linux-gnu.so -Wl,-rpath,$ORIGIN
>/usr/lib64/python3.12/site-packages/Cython/Compiler/Main.py:381: FutureWarning: Cython directive 'language_level' not set, using '3str' for now (Py3). This has changed from earlier releases! File: /builddir/build/BUILD/pysam-0.19.1/pysam/libcsamfile.pxd
>  tree = Parsing.p_module(s, pxd, full_module_name)
>Compiling pysam/libcsamfile.pyx because it changed.
>[1/1] Cythonizing pysam/libcsamfile.pyx
>building 'pysam.libcsamfile' extension
>gcc -fno-strict-overflow -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fPIC -I/builddir/build/BUILD/pysam-0.19.1/htslib -I/builddir/build/BUILD/pysam-0.19.1/samtools -I/builddir/build/BUILD/pysam-0.19.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.19.1/bcftools -I/builddir/build/BUILD/pysam-0.19.1/pysam -I/builddir/build/BUILD/pysam-0.19.1 -I/usr/include/python3.12 -c pysam/libcsamfile.c -o build/temp.linux-aarch64-cpython-312/pysam/libcsamfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
>gcc -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -Wl,--build-id=sha1 -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -mbranch-protection=standard -fasynchronous-unwind-tables -fstack-clash-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer build/temp.linux-aarch64-cpython-312/pysam/libcsamfile.o -L/builddir/build/BUILD/pysam-0.19.1/pysam -L/builddir/build/BUILD/pysam-0.19.1/pysam -L/builddir/build/BUILD/pysam-0.19.1 -L/builddir/build/BUILD/pysam-0.19.1/build/lib.linux-aarch64-3.12/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -Lbuild/lib.linux-aarch64-cpython-312/pysam -L/usr/lib64 -lz -llzma -lbz2 -lz -lm -lchtslib.cpython-312-aarch64-linux-gnu -lcutils.cpython-312-aarch64-linux-gnu -o build/lib.linux-aarch64-cpython-312/pysam/libcsamfile.cpython-312-aarch64-linux-gnu.so -Wl,-rpath,$ORIGIN
>/usr/lib64/python3.12/site-packages/Cython/Compiler/Main.py:381: FutureWarning: Cython directive 'language_level' not set, using '3str' for now (Py3). This has changed from earlier releases! File: /builddir/build/BUILD/pysam-0.19.1/pysam/libcalignedsegment.pxd
>  tree = Parsing.p_module(s, pxd, full_module_name)
>Error compiling Cython file:
>------------------------------------------------------------
>...
>    p   = pysam_bam_get_seq(src)
>    for k from start <= k < end:
>        # equivalent to seq_nt16_str[bam1_seqi(s, i)] (see bam.c)
>        # note: do not use string literal as it will be a python string
>        s[k-start] = seq_nt16_str[p[k/2] >> 4 * (1 - k%2) & 0xf]
>                                   ^
>------------------------------------------------------------
>pysam/libcalignedsegment.pyx:570:35: Invalid index type 'double'
>Error compiling Cython file:
>------------------------------------------------------------
>...
>            src = self._delegate
>            # as the sequence is stored in half-bytes, the total length (sequence
>            # plus quality scores) is (l+1)/2 + l
>            nbytes_new = (l + 1) / 2 + l
>                                     ^
>------------------------------------------------------------
>pysam/libcalignedsegment.pyx:1426:37: Cannot assign type 'double' to 'Py_ssize_t'
>Error compiling Cython file:
>------------------------------------------------------------
>...
>            src = self._delegate
>            # as the sequence is stored in half-bytes, the total length (sequence
>            # plus quality scores) is (l+1)/2 + l
>            nbytes_new = (l + 1) / 2 + l
>            nbytes_old = (src.core.l_qseq + 1) / 2 + src.core.l_qseq
>                                                   ^
>------------------------------------------------------------
>pysam/libcalignedsegment.pyx:1427:51: Cannot assign type 'double' to 'Py_ssize_t'
>Error compiling Cython file:
>------------------------------------------------------------
>...
>                for k from 0 <= k < nbytes_new:
>                    p[k] = 0
>                # convert to C string
>                s = seq
>                for k from 0 <= k < l:
>                    p[k/2] |= seq_nt16_table[<unsigned char>s[k]] << 4 * (1 - k % 2)
>                     ^
>------------------------------------------------------------
>pysam/libcalignedsegment.pyx:1451:21: Invalid index type 'double'
>Error compiling Cython file:
>------------------------------------------------------------
>...
>                for k from 0 <= k < nbytes_new:
>                    p[k] = 0
>                # convert to C string
>                s = seq
>                for k from 0 <= k < l:
>                    p[k/2] |= seq_nt16_table[<unsigned char>s[k]] << 4 * (1 - k % 2)
>                     ^
>------------------------------------------------------------
>pysam/libcalignedsegment.pyx:1451:21: Invalid index type 'double'
>Error compiling Cython file:
>------------------------------------------------------------
>...
>                for k from 0 <= k < nbytes_new:
>                    p[k] = 0
>                # convert to C string
>                s = seq
>                for k from 0 <= k < l:
>                    p[k/2] |= seq_nt16_table[<unsigned char>s[k]] << 4 * (1 - k % 2)
>                     ^
>------------------------------------------------------------
>pysam/libcalignedsegment.pyx:1451:21: Invalid index type 'double'
>Compiling pysam/libcalignedsegment.pyx because it changed.
>[1/1] Cythonizing pysam/libcalignedsegment.pyx
>Traceback (most recent call last):
>  File "/builddir/build/BUILD/pysam-0.19.1/setup.py", line 602, in <module>
>    dist = setup(**metadata)
>           ^^^^^^^^^^^^^^^^^
>  File "/usr/lib/python3.12/site-packages/setuptools/__init__.py", line 107, in setup
>    return distutils.core.setup(**attrs)
>           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
>  File "/usr/lib/python3.12/site-packages/setuptools/_distutils/core.py", line 185, in setup
>    return run_commands(dist)
>           ^^^^^^^^^^^^^^^^^^
>  File "/usr/lib/python3.12/site-packages/setuptools/_distutils/core.py", line 201, in run_commands
>    dist.run_commands()
>  File "/usr/lib/python3.12/site-packages/setuptools/_distutils/dist.py", line 969, in run_commands
>    self.run_command(cmd)
>  File "/usr/lib/python3.12/site-packages/setuptools/dist.py", line 1244, in run_command
>    super().run_command(command)
>  File "/usr/lib/python3.12/site-packages/setuptools/_distutils/dist.py", line 988, in run_command
>    cmd_obj.run()
>  File "/builddir/build/BUILD/pysam-0.19.1/setup.py", line 261, in run
>    build.run(self)
>  File "/usr/lib/python3.12/site-packages/setuptools/_distutils/command/build.py", line 131, in run
>    self.run_command(cmd_name)
>  File "/usr/lib/python3.12/site-packages/setuptools/_distutils/cmd.py", line 318, in run_command
>    self.distribution.run_command(command)
>  File "/usr/lib/python3.12/site-packages/setuptools/dist.py", line 1244, in run_command
>    super().run_command(command)
>  File "/usr/lib/python3.12/site-packages/setuptools/_distutils/dist.py", line 988, in run_command
>    cmd_obj.run()
>  File "/usr/lib/python3.12/site-packages/setuptools/_distutils/command/build_ext.py", line 345, in run
>    self.build_extensions()
>  File "/usr/lib/python3.12/site-packages/setuptools/_distutils/command/build_ext.py", line 467, in build_extensions
>    self._build_extensions_serial()
>  File "/usr/lib/python3.12/site-packages/setuptools/_distutils/command/build_ext.py", line 493, in _build_extensions_serial
>    self.build_extension(ext)
>  File "/builddir/build/BUILD/pysam-0.19.1/cy_build.py", line 90, in build_extension
>    build_ext.build_extension(self, ext)
>  File "/usr/lib64/python3.12/site-packages/Cython/Distutils/build_ext.py", line 122, in build_extension
>    new_ext = cythonize(
>              ^^^^^^^^^^
>  File "/usr/lib64/python3.12/site-packages/Cython/Build/Dependencies.py", line 1134, in cythonize
>    cythonize_one(*args)
>  File "/usr/lib64/python3.12/site-packages/Cython/Build/Dependencies.py", line 1301, in cythonize_one
>    raise CompileError(None, pyx_file)
>Cython.Compiler.Errors.CompileError: pysam/libcalignedsegment.pyx
>RPM build errors:
>error: Bad exit status from /var/tmp/rpm-tmp.tIihKm (%build)
>    Bad exit status from /var/tmp/rpm-tmp.tIihKm (%build)
>Child return code was: 1
>EXCEPTION: [Error('Command failed: \n # /usr/bin/systemd-nspawn -q -M 160159cad758432991932a6f02f29d3d -D /var/lib/mock/f39-build-44340668-5276606/root -a -u mockbuild --capability=cap_ipc_lock --bind=/tmp/mock-resolv.8vmewapc:/etc/resolv.conf --bind=/dev/btrfs-control --bind=/dev/mapper/control --bind=/dev/loop-control --bind=/dev/loop0 --bind=/dev/loop1 --bind=/dev/loop2 --bind=/dev/loop3 --bind=/dev/loop4 --bind=/dev/loop5 --bind=/dev/loop6 --bind=/dev/loop7 --bind=/dev/loop8 --bind=/dev/loop9 --bind=/dev/loop10 --bind=/dev/loop11 --console=pipe --setenv=TERM=vt100 --setenv=SHELL=/bin/bash --setenv=HOME=/builddir --setenv=HOSTNAME=mock --setenv=PATH=/usr/bin:/bin:/usr/sbin:/sbin --setenv=PROMPT_COMMAND=printf "\\033]0;<mock-chroot>\\007" --setenv=PS1=<mock-chroot> \\s-\\v\\$  --setenv=LANG=C.UTF-8 --resolv-conf=off bash --login -c /usr/bin/rpmbuild -bb --noclean --target aarch64 --nodeps /builddir/build/SPECS/python-pysam.spec\n', 1)]
>Traceback (most recent call last):
>  File "/usr/lib/python3.11/site-packages/mockbuild/trace_decorator.py", line 93, in trace
>    result = func(*args, **kw)
>             ^^^^^^^^^^^^^^^^^
>  File "/usr/lib/python3.11/site-packages/mockbuild/util.py", line 597, in do_with_status
>    raise exception.Error("Command failed: \n # %s\n%s" % (command, output), child.returncode)
>mockbuild.exception.Error: Command failed: 
> # /usr/bin/systemd-nspawn -q -M 160159cad758432991932a6f02f29d3d -D /var/lib/mock/f39-build-44340668-5276606/root -a -u mockbuild --capability=cap_ipc_lock --bind=/tmp/mock-resolv.8vmewapc:/etc/resolv.conf --bind=/dev/btrfs-control --bind=/dev/mapper/control --bind=/dev/loop-control --bind=/dev/loop0 --bind=/dev/loop1 --bind=/dev/loop2 --bind=/dev/loop3 --bind=/dev/loop4 --bind=/dev/loop5 --bind=/dev/loop6 --bind=/dev/loop7 --bind=/dev/loop8 --bind=/dev/loop9 --bind=/dev/loop10 --bind=/dev/loop11 --console=pipe --setenv=TERM=vt100 --setenv=SHELL=/bin/bash --setenv=HOME=/builddir --setenv=HOSTNAME=mock --setenv=PATH=/usr/bin:/bin:/usr/sbin:/sbin --setenv=PROMPT_COMMAND=printf "\033]0;<mock-chroot>\007" --setenv=PS1=<mock-chroot> \s-\v\$  --setenv=LANG=C.UTF-8 --resolv-conf=off bash --login -c /usr/bin/rpmbuild -bb --noclean --target aarch64 --nodeps /builddir/build/SPECS/python-pysam.spec
>

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Attachments on bug 2226299: 1979281 | 1979282 | 1979283