Mock Version: 5.5
ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bs  --target x86_64 --nodeps /builddir/build/SPECS/vcftools.spec'], chrootPath='/var/lib/mock/fedorarebuild-x86_64-0fcyoPKj8N/root'env={'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;<mock-chroot>\\007"', 'PS1': '<mock-chroot> \\s-\\v\\$ ', 'LANG': 'C.UTF-8'}shell=Falselogger=<mockbuild.trace_decorator.getLog object at 0x7fe6b4aaeb50>timeout=0uid=11527gid=900user='mockbuild'nspawn_args=['--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.s19l3o8_:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/fuse', '--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']unshare_net=TrueprintOutput=False)
Using nspawn with args ['--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.s19l3o8_:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/fuse', '--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']
Executing command: ['/usr/bin/systemd-nspawn', '-q', '-M', '5cca568781414f118af1d69876e15e99', '-D', '/var/lib/mock/fedorarebuild-x86_64-0fcyoPKj8N/root', '-a', '-u', 'mockbuild', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.s19l3o8_:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/fuse', '--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 -bs  --target x86_64 --nodeps /builddir/build/SPECS/vcftools.spec'] with env {'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;<mock-chroot>\\007"', 'PS1': '<mock-chroot> \\s-\\v\\$ ', 'LANG': 'C.UTF-8', 'SYSTEMD_NSPAWN_TMPFS_TMP': '0', 'SYSTEMD_SECCOMP': '0'} and shell False
sh: line 1: perl: command not found
Building target platforms: x86_64
Building for target x86_64
setting SOURCE_DATE_EPOCH=1713830400
Wrote: /builddir/build/SRPMS/vcftools-0.1.16-19.fc41.src.rpm
Child return code was: 0
ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bb  --target x86_64 --nodeps /builddir/build/SPECS/vcftools.spec'], chrootPath='/var/lib/mock/fedorarebuild-x86_64-0fcyoPKj8N/root'env={'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;<mock-chroot>\\007"', 'PS1': '<mock-chroot> \\s-\\v\\$ ', 'LANG': 'C.UTF-8'}shell=Falselogger=<mockbuild.trace_decorator.getLog object at 0x7fe6b4aaeb50>timeout=0uid=11527gid=900user='mockbuild'nspawn_args=['--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.s19l3o8_:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/fuse', '--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']unshare_net=TrueprintOutput=False)
Using nspawn with args ['--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.s19l3o8_:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/fuse', '--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']
Executing command: ['/usr/bin/systemd-nspawn', '-q', '-M', 'ba2a4bf3efd748dba8a104c441f320af', '-D', '/var/lib/mock/fedorarebuild-x86_64-0fcyoPKj8N/root', '-a', '-u', 'mockbuild', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.s19l3o8_:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/fuse', '--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  --target x86_64 --nodeps /builddir/build/SPECS/vcftools.spec'] with env {'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;<mock-chroot>\\007"', 'PS1': '<mock-chroot> \\s-\\v\\$ ', 'LANG': 'C.UTF-8', 'SYSTEMD_NSPAWN_TMPFS_TMP': '0', 'SYSTEMD_SECCOMP': '0'} and shell False
Building target platforms: x86_64
Building for target x86_64
setting SOURCE_DATE_EPOCH=1713830400
Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.jSYQt1
+ umask 022
+ cd /builddir/build/BUILD
+ cd /builddir/build/BUILD
+ rm -rf vcftools-0.1.16
+ /usr/lib/rpm/rpmuncompress -x /builddir/build/SOURCES/vcftools-0.1.16.tar.gz
+ STATUS=0
+ '[' 0 -ne 0 ']'
+ cd vcftools-0.1.16
+ rm -rf /builddir/build/BUILD/vcftools-0.1.16-SPECPARTS
+ /usr/bin/mkdir -p /builddir/build/BUILD/vcftools-0.1.16-SPECPARTS
+ /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w .
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.hqYpIG
+ umask 022
+ cd /builddir/build/BUILD
+ CFLAGS='-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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ export CFLAGS
+ CXXFLAGS='-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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules '
+ export FFLAGS
+ FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules '
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn'
+ export RUSTFLAGS
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -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 '
+ export LDFLAGS
+ LT_SYS_LIBRARY_PATH=/usr/lib64:
+ export LT_SYS_LIBRARY_PATH
+ CC=gcc
+ export CC
+ CXX=g++
+ export CXX
+ cd vcftools-0.1.16
+ CFLAGS='-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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ export CFLAGS
+ CXXFLAGS='-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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules '
+ export FFLAGS
+ FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules '
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn'
+ export RUSTFLAGS
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -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 '
+ export LDFLAGS
+ LT_SYS_LIBRARY_PATH=/usr/lib64:
+ export LT_SYS_LIBRARY_PATH
+ CC=gcc
+ export CC
+ CXX=g++
+ export CXX
+ '[' '-flto=auto -ffat-lto-objectsx' '!=' x ']'
++ find . -type f -name configure -print
+ for file in $(find . -type f -name configure -print)
+ /usr/bin/sed -r --in-place=.backup 's/^char \(\*f\) \(\) = /__attribute__ ((used)) char (*f) () = /g' ./configure
+ diff -u ./configure.backup ./configure
+ mv ./configure.backup ./configure
+ /usr/bin/sed -r --in-place=.backup 's/^char \(\*f\) \(\);/__attribute__ ((used)) char (*f) ();/g' ./configure
+ diff -u ./configure.backup ./configure
+ mv ./configure.backup ./configure
+ /usr/bin/sed -r --in-place=.backup 's/^char \$2 \(\);/__attribute__ ((used)) char \$2 ();/g' ./configure
+ diff -u ./configure.backup ./configure
--- ./configure.backup	2018-08-02 19:46:48.000000000 +0200
+++ ./configure	2024-04-24 16:04:24.382013846 +0200
@@ -2020,7 +2020,7 @@
 #ifdef __cplusplus
 extern "C"
 #endif
-char $2 ();
+__attribute__ ((used)) char $2 ();
 /* The GNU C library defines this for functions which it implements
     to always fail with ENOSYS.  Some functions are actually named
     something starting with __ and the normal name is an alias.  */
+ /usr/bin/sed --in-place=.backup '1{$!N;$!N};$!N;s/int x = 1;\nint y = 0;\nint z;\nint nan;/volatile int x = 1; volatile int y = 0; volatile int z, nan;/;P;D' ./configure
+ diff -u ./configure.backup ./configure
+ mv ./configure.backup ./configure
+ /usr/bin/sed --in-place=.backup 's#^lt_cv_sys_global_symbol_to_cdecl=.*#lt_cv_sys_global_symbol_to_cdecl="sed -n -e '\''s/^T .* \\(.*\\)$/extern int \\1();/p'\'' -e '\''s/^$symcode* .* \\(.*\\)$/extern char \\1;/p'\''"#' ./configure
+ diff -u ./configure.backup ./configure
+ mv ./configure.backup ./configure
+ '[' 1 = 1 ']'
+++ dirname ./configure
++ find . -name config.guess -o -name config.sub
+ '[' 1 = 1 ']'
+ '[' x '!=' 'x-Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld' ']'
++ find . -name ltmain.sh
++ grep -q runstatedir=DIR ./configure
+ ./configure --build=x86_64-redhat-linux --host=x86_64-redhat-linux --program-prefix= --disable-dependency-tracking --prefix=/usr --exec-prefix=/usr --bindir=/usr/bin --sbindir=/usr/sbin --sysconfdir=/etc --datadir=/usr/share --includedir=/usr/include --libdir=/usr/lib64 --libexecdir=/usr/libexec --localstatedir=/var --sharedstatedir=/var/lib --mandir=/usr/share/man --infodir=/usr/share/info --with-pmdir=share/perl5/vendor_perl
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /usr/bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking for style of include used by make... GNU
checking dependency style of g++... none
checking for x86_64-redhat-linux-gcc... gcc
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking whether gcc understands -c and -o together... yes
checking dependency style of gcc... none
checking how to run the C preprocessor... gcc -E
checking for perl... /usr/bin/perl
checking for x86_64-redhat-linux-pkg-config... no
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for ZLIB... yes
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking arpa/inet.h usability... yes
checking arpa/inet.h presence... yes
checking for arpa/inet.h... yes
checking fcntl.h usability... yes
checking fcntl.h presence... yes
checking for fcntl.h... yes
checking limits.h usability... yes
checking limits.h presence... yes
checking for limits.h... yes
checking netdb.h usability... yes
checking netdb.h presence... yes
checking for netdb.h... yes
checking for stdint.h... (cached) yes
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking sys/socket.h usability... yes
checking sys/socket.h presence... yes
checking for sys/socket.h... yes
checking for unistd.h... (cached) yes
checking for stdbool.h that conforms to C99... yes
checking for _Bool... yes
checking for inline... inline
checking for int16_t... yes
checking for int32_t... yes
checking for int64_t... yes
checking for int8_t... yes
checking for off_t... yes
checking for size_t... yes
checking for ssize_t... yes
checking for uint16_t... yes
checking for uint32_t... yes
checking for uint8_t... yes
checking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... no
checking for error_at_line... yes
checking for stdlib.h... (cached) yes
checking for GNU libc compatible malloc... yes
checking for stdlib.h... (cached) yes
checking for GNU libc compatible realloc... yes
checking for gethostbyaddr... yes
checking for gethostbyname... yes
checking for memset... yes
checking for pow... no
checking for select... yes
checking for socket... yes
checking for sqrt... no
checking for strchr... yes
checking for strdup... yes
checking for strerror... yes
checking for strstr... yes
checking for strtol... yes
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating src/cpp/Makefile
config.status: creating src/perl/Makefile
config.status: creating config.h
config.status: executing depfiles commands
+ /usr/bin/make -O -j4 V=1 VERBOSE=1
/usr/bin/make  all-recursive
Making all in src
Making all in cpp
make[3]: Entering directory '/builddir/build/BUILD/vcftools-0.1.16/src/cpp'
gcc -DHAVE_CONFIG_H -I. -I../..  -DWITH_GZFILEOP   -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  -c -o vcftools-bgzf.o `test -f 'bgzf.c' || echo './'`bgzf.c
make[3]: Leaving directory '/builddir/build/BUILD/vcftools-0.1.16/src/cpp'
bgzf.c: In function ‘bgzf_check_EOF’:
bgzf.c:60:34: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
   60 | #define _bgzf_read(fp, buf, len) fread((buf), 1, (len), (FILE*)(fp))
      |                                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
bgzf.c:622:9: note: in expansion of macro ‘_bgzf_read’
  622 |         _bgzf_read(fp->fp, buf, 28);
      |         ^~~~~~~~~~
make[3]: Entering directory '/builddir/build/BUILD/vcftools-0.1.16/src/cpp'
g++ -DHAVE_CONFIG_H -I. -I../..  -DWITH_GZFILEOP   -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  -c -o vcftools-dgeev.o `test -f 'dgeev.cpp' || echo './'`dgeev.cpp
make[3]: Leaving directory '/builddir/build/BUILD/vcftools-0.1.16/src/cpp'
make[3]: Entering directory '/builddir/build/BUILD/vcftools-0.1.16/src/cpp'
g++ -DHAVE_CONFIG_H -I. -I../..  -DWITH_GZFILEOP   -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  -c -o vcftools-entry.o `test -f 'entry.cpp' || echo './'`entry.cpp
make[3]: Leaving directory '/builddir/build/BUILD/vcftools-0.1.16/src/cpp'
make[3]: Entering directory '/builddir/build/BUILD/vcftools-0.1.16/src/cpp'
g++ -DHAVE_CONFIG_H -I. -I../..  -DWITH_GZFILEOP   -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  -c -o vcftools-bcf_file.o `test -f 'bcf_file.cpp' || echo './'`bcf_file.cpp
make[3]: Leaving directory '/builddir/build/BUILD/vcftools-0.1.16/src/cpp'
make[3]: Entering directory '/builddir/build/BUILD/vcftools-0.1.16/src/cpp'
g++ -DHAVE_CONFIG_H -I. -I../..  -DWITH_GZFILEOP   -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  -c -o vcftools-bcf_entry_setters.o `test -f 'bcf_entry_setters.cpp' || echo './'`bcf_entry_setters.cpp
make[3]: Leaving directory '/builddir/build/BUILD/vcftools-0.1.16/src/cpp'
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g++ -DHAVE_CONFIG_H -I. -I../..  -DWITH_GZFILEOP   -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  -c -o vcftools-bcf_entry.o `test -f 'bcf_entry.cpp' || echo './'`bcf_entry.cpp
make[3]: Leaving directory '/builddir/build/BUILD/vcftools-0.1.16/src/cpp'
make[3]: Entering directory '/builddir/build/BUILD/vcftools-0.1.16/src/cpp'
g++ -DHAVE_CONFIG_H -I. -I../..  -DWITH_GZFILEOP   -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  -c -o vcftools-gamma.o `test -f 'gamma.cpp' || echo './'`gamma.cpp
make[3]: Leaving directory '/builddir/build/BUILD/vcftools-0.1.16/src/cpp'
make[3]: Entering directory '/builddir/build/BUILD/vcftools-0.1.16/src/cpp'
g++ -DHAVE_CONFIG_H -I. -I../..  -DWITH_GZFILEOP   -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  -c -o vcftools-entry_setters.o `test -f 'entry_setters.cpp' || echo './'`entry_setters.cpp
make[3]: Leaving directory '/builddir/build/BUILD/vcftools-0.1.16/src/cpp'
make[3]: Entering directory '/builddir/build/BUILD/vcftools-0.1.16/src/cpp'
g++ -DHAVE_CONFIG_H -I. -I../..  -DWITH_GZFILEOP   -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  -c -o vcftools-entry_getters.o `test -f 'entry_getters.cpp' || echo './'`entry_getters.cpp
make[3]: Leaving directory '/builddir/build/BUILD/vcftools-0.1.16/src/cpp'
make[3]: Entering directory '/builddir/build/BUILD/vcftools-0.1.16/src/cpp'
gcc -DHAVE_CONFIG_H -I. -I../..  -DWITH_GZFILEOP   -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  -c -o vcftools-knetfile.o `test -f 'knetfile.c' || echo './'`knetfile.c
make[3]: Leaving directory '/builddir/build/BUILD/vcftools-0.1.16/src/cpp'
In file included from knetfile.c:46:
knetfile.c: In function ‘kftp_send_cmd’:
knetfile.h:9:32: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
    9 | #define netwrite(fd, ptr, len) write(fd, ptr, len)
      |                                ^~~~~~~~~~~~~~~~~~~
knetfile.c:236:9: note: in expansion of macro ‘netwrite’
  236 |         netwrite(ftp->ctrl_fd, cmd, strlen(cmd));
      |         ^~~~~~~~
knetfile.c: In function ‘khttp_connect_file’:
knetfile.h:9:32: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
    9 | #define netwrite(fd, ptr, len) write(fd, ptr, len)
      |                                ^~~~~~~~~~~~~~~~~~~
knetfile.c:415:9: note: in expansion of macro ‘netwrite’
  415 |         netwrite(fp->fd, buf, l);
      |         ^~~~~~~~
make[3]: Entering directory '/builddir/build/BUILD/vcftools-0.1.16/src/cpp'
g++ -DHAVE_CONFIG_H -I. -I../..  -DWITH_GZFILEOP   -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  -c -o vcftools-output_log.o `test -f 'output_log.cpp' || echo './'`output_log.cpp
output_log.cpp: In member function ‘void output_log::printLOG(std::string)’:
output_log.cpp:42:9: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
   42 |         if (output_to_file)
      |         ^~
output_log.cpp:43:27: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
   43 |                 LOG << s; LOG.flush();
      |                           ^~~
output_log.cpp:44:9: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
   44 |         if (output_to_screen)
      |         ^~
output_log.cpp:45:28: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
   45 |                 cerr << s; cerr.flush();
      |                            ^~~~
make[3]: Leaving directory '/builddir/build/BUILD/vcftools-0.1.16/src/cpp'
make[3]: Entering directory '/builddir/build/BUILD/vcftools-0.1.16/src/cpp'
g++ -DHAVE_CONFIG_H -I. -I../..  -DWITH_GZFILEOP   -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  -c -o vcftools-entry_filters.o `test -f 'entry_filters.cpp' || echo './'`entry_filters.cpp
make[3]: Leaving directory '/builddir/build/BUILD/vcftools-0.1.16/src/cpp'
entry_filters.cpp: In member function ‘void entry::filter_sites_by_overlap_positions(const std::string&, const std::string&)’:
entry_filters.cpp:540:25: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
  540 |                         for (unsigned int ui=POS; ui<(POS+REF.size()); ui++)
      |                         ^~~
entry_filters.cpp:544:33: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
  544 |                                 if (found == true)
      |                                 ^~
entry_filters.cpp: In member function ‘void entry::filter_sites_by_frequency_and_call_rate(double, double, double, double, double, double, double)’:
entry_filters.cpp:814:77: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
  814 |         if (((min_non_ref_af > 0.0) || (max_non_ref_af < 1.0)) && (N_failed == (N_alleles-1)))
      |                                                                    ~~~~~~~~~^~~~~~~~~~~~~~~~
entry_filters.cpp: In member function ‘void entry::filter_sites_by_allele_count(double, double, double, double, double, double, double)’:
entry_filters.cpp:912:106: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
  912 |         if (((min_non_ref_ac_any > 0) || (max_non_ref_ac_any < numeric_limits<int>::max())) && (N_failed == (N_alleles-1)))
      |                                                                                                 ~~~~~~~~~^~~~~~~~~~~~~~~~
make[3]: Entering directory '/builddir/build/BUILD/vcftools-0.1.16/src/cpp'
g++ -DHAVE_CONFIG_H -I. -I../..  -DWITH_GZFILEOP   -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  -c -o vcftools-variant_file.o `test -f 'variant_file.cpp' || echo './'`variant_file.cpp
make[3]: Leaving directory '/builddir/build/BUILD/vcftools-0.1.16/src/cpp'
make[3]: Entering directory '/builddir/build/BUILD/vcftools-0.1.16/src/cpp'
g++ -DHAVE_CONFIG_H -I. -I../..  -DWITH_GZFILEOP   -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  -c -o vcftools-header.o `test -f 'header.cpp' || echo './'`header.cpp
make[3]: Leaving directory '/builddir/build/BUILD/vcftools-0.1.16/src/cpp'
header.cpp: In static member function ‘static void header::split(const std::string&, char, std::vector<std::__cxx11::basic_string<char> >&)’:
header.cpp:477:46: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const std::__cxx11::basic_string<char>::size_type’ {aka ‘const long unsigned int’} [-Wsign-compare]
  477 |         while ((end = text.find(sep, start)) != string::npos)
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
make[3]: Entering directory '/builddir/build/BUILD/vcftools-0.1.16/src/cpp'
g++ -DHAVE_CONFIG_H -I. -I../..  -DWITH_GZFILEOP   -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  -c -o vcftools-variant_file_filters.o `test -f 'variant_file_filters.cpp' || echo './'`variant_file_filters.cpp
make[3]: Leaving directory '/builddir/build/BUILD/vcftools-0.1.16/src/cpp'
variant_file_filters.cpp: In member function ‘void variant_file::filter_individuals_randomly(int)’:
variant_file_filters.cpp:129:23: warning: ‘void std::random_shuffle(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<unsigned int*, vector<unsigned int> >]’ is deprecated: use 'std::shuffle' instead [-Wdeprecated-declarations]
  129 |         random_shuffle(keep_index.begin(), keep_index.end());                   // Get a random order
      |         ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/algorithm:61,
                 from variant_file.h:15,
                 from variant_file_filters.cpp:7:
/usr/include/c++/14/bits/stl_algo.h:4491:5: note: declared here
 4491 |     random_shuffle(_RandomAccessIterator __first, _RandomAccessIterator __last)
      |     ^~~~~~~~~~~~~~
make[3]: Entering directory '/builddir/build/BUILD/vcftools-0.1.16/src/cpp'
g++ -DHAVE_CONFIG_H -I. -I../..  -DWITH_GZFILEOP   -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  -c -o vcftools-parameters.o `test -f 'parameters.cpp' || echo './'`parameters.cpp
make[3]: Leaving directory '/builddir/build/BUILD/vcftools-0.1.16/src/cpp'
parameters.cpp: In member function ‘void parameters::print_params()’:
parameters.cpp:491:5: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  491 |     if (output_N_PCA_SNP_loadings != defaults.output_N_PCA_SNP_loadings)
      |     ^~
parameters.cpp:493:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
  493 |         if (output_prefix != defaults.output_prefix) LOG.printLOG("\t--out " + output_prefix + "\n");
      |         ^~
make[3]: Entering directory '/builddir/build/BUILD/vcftools-0.1.16/src/cpp'
g++ -DHAVE_CONFIG_H -I. -I../..  -DWITH_GZFILEOP   -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  -c -o vcftools-variant_file_diff.o `test -f 'variant_file_diff.cpp' || echo './'`variant_file_diff.cpp
variant_file_diff.cpp: In member function ‘void variant_file::output_sites_in_files(const parameters&, variant_file&)’:
variant_file_diff.cpp:219:42: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  219 |                                 if (POS2 < (POS1+REF1.size()))
      |                                     ~~~~~^~~~~~~~~~~~~~~~~~~~
variant_file_diff.cpp:235:42: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  235 |                                 if (POS1 < (POS2+REF2.size()))
      |                                     ~~~~~^~~~~~~~~~~~~~~~~~~~
make[3]: Leaving directory '/builddir/build/BUILD/vcftools-0.1.16/src/cpp'
make[3]: Entering directory '/builddir/build/BUILD/vcftools-0.1.16/src/cpp'
g++ -DHAVE_CONFIG_H -I. -I../..  -DWITH_GZFILEOP   -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  -c -o vcftools-variant_file_format_convert.o `test -f 'variant_file_format_convert.cpp' || echo './'`variant_file_format_convert.cpp
variant_file_format_convert.cpp: In member function ‘void variant_file::output_as_LDhelmet(const parameters&)’:
variant_file_format_convert.cpp:1015:22: warning: unused variable ‘n_indv’ [-Wunused-variable]
 1015 |         unsigned int n_indv = N_kept_individuals();
      |                      ^~~~~~
make[3]: Leaving directory '/builddir/build/BUILD/vcftools-0.1.16/src/cpp'
make[3]: Entering directory '/builddir/build/BUILD/vcftools-0.1.16/src/cpp'
g++ -DHAVE_CONFIG_H -I. -I../..  -DWITH_GZFILEOP   -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  -c -o vcftools-vcf_entry.o `test -f 'vcf_entry.cpp' || echo './'`vcf_entry.cpp
vcf_entry.cpp: In member function ‘virtual void vcf_entry::parse_genotype_entry(unsigned int, bool, bool, bool, bool)’:
vcf_entry.cpp:135:59: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const std::__cxx11::basic_string<char>::size_type’ {aka ‘const long unsigned int’} [-Wsign-compare]
  135 |         while ((end = GENOTYPE_str[indv].find(':',start)) != string::npos)
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
make[3]: Leaving directory '/builddir/build/BUILD/vcftools-0.1.16/src/cpp'
make[3]: Entering directory '/builddir/build/BUILD/vcftools-0.1.16/src/cpp'
g++ -DHAVE_CONFIG_H -I. -I../..  -DWITH_GZFILEOP   -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  -c -o vcftools-vcf_entry_setters.o `test -f 'vcf_entry_setters.cpp' || echo './'`vcf_entry_setters.cpp
make[3]: Leaving directory '/builddir/build/BUILD/vcftools-0.1.16/src/cpp'
make[3]: Entering directory '/builddir/build/BUILD/vcftools-0.1.16/src/cpp'
g++ -DHAVE_CONFIG_H -I. -I../..  -DWITH_GZFILEOP   -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  -c -o vcftools-vcf_file.o `test -f 'vcf_file.cpp' || echo './'`vcf_file.cpp
make[3]: Leaving directory '/builddir/build/BUILD/vcftools-0.1.16/src/cpp'
make[3]: Entering directory '/builddir/build/BUILD/vcftools-0.1.16/src/cpp'
g++ -DHAVE_CONFIG_H -I. -I../..  -DWITH_GZFILEOP   -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  -c -o vcftools-vcftools.o `test -f 'vcftools.cpp' || echo './'`vcftools.cpp
make[3]: Leaving directory '/builddir/build/BUILD/vcftools-0.1.16/src/cpp'
make[3]: Entering directory '/builddir/build/BUILD/vcftools-0.1.16/src/cpp'
g++ -DHAVE_CONFIG_H -I. -I../..  -DWITH_GZFILEOP   -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  -c -o vcftools-variant_file_output.o `test -f 'variant_file_output.cpp' || echo './'`variant_file_output.cpp
make[3]: Leaving directory '/builddir/build/BUILD/vcftools-0.1.16/src/cpp'
variant_file_output.cpp: In member function ‘void variant_file::output_haplotype_r2(const parameters&)’:
variant_file_output.cpp:1540:34: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
 1540 |         for(unsigned int ui=0; ui<site_count-1; ui++)
      |                                ~~^~~~~~~~~~~~~
variant_file_output.cpp:1547:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
 1547 |                 for(uj=ui+1; uj<site_count; uj++)
      |                              ~~^~~~~~~~~~~
variant_file_output.cpp: In member function ‘void variant_file::output_genotype_r2(const parameters&)’:
variant_file_output.cpp:1713:34: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
 1713 |         for(unsigned int ui=0; ui<count-1; ui++)
      |                                ~~^~~~~~~~
variant_file_output.cpp:1720:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
 1720 |                 for(uj=ui+1; uj<count; uj++)
      |                              ~~^~~~~~
variant_file_output.cpp: In member function ‘void variant_file::output_interchromosomal_genotype_r2(const parameters&)’:
variant_file_output.cpp:2050:34: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
 2050 |         for(unsigned int ui=0; ui<count-1; ui++)
      |                                ~~^~~~~~~~
variant_file_output.cpp:2057:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
 2057 |                 for(uj=ui+1; uj<count; uj++)
      |                              ~~^~~~~~
variant_file_output.cpp: In member function ‘void variant_file::output_interchromosomal_haplotype_r2(const parameters&)’:
variant_file_output.cpp:2211:34: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
 2211 |         for(unsigned int ui=0; ui<site_count-1; ui++)
      |                                ~~^~~~~~~~~~~~~
variant_file_output.cpp:2218:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
 2218 |                 for(uj=ui+1; uj<site_count; uj++)
      |                              ~~^~~~~~~~~~~
variant_file_output.cpp: In member function ‘void variant_file::output_haplotype_r2_of_SNP_list_vs_all_others(const parameters&)’:
variant_file_output.cpp:2442:34: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
 2442 |         for(unsigned int ui=0; ui<nlist; ui++)
      |                                ~~^~~~~~
variant_file_output.cpp: In member function ‘void variant_file::output_genotype_r2_of_SNP_list_vs_all_others(const parameters&)’:
variant_file_output.cpp:2675:34: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
 2675 |         for(unsigned int ui=0; ui<nlist; ui++)
      |                                ~~^~~~~~
variant_file_output.cpp: In member function ‘variant_file::output_haplotype_count(parameters const&)’:
variant_file_output.cpp:1372:9: warning: ‘idx’ may be used uninitialized [-Wmaybe-uninitialized]
 1372 |         if (idx == prev_idx)
      |         ^~
variant_file_output.cpp:1181:43: note: ‘idx’ was declared here
 1181 |         string CHROM; int POS1, POS2; int idx;
      |                                           ^~~
make[3]: Entering directory '/builddir/build/BUILD/vcftools-0.1.16/src/cpp'
g++  -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer   -Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -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  -o vcftools vcftools-bcf_entry.o vcftools-bcf_entry_setters.o vcftools-bcf_file.o vcftools-bgzf.o vcftools-dgeev.o vcftools-entry.o vcftools-entry_filters.o vcftools-entry_getters.o vcftools-entry_setters.o vcftools-gamma.o vcftools-header.o vcftools-knetfile.o vcftools-output_log.o vcftools-parameters.o vcftools-variant_file.o vcftools-variant_file_diff.o vcftools-variant_file_filters.o vcftools-variant_file_format_convert.o vcftools-variant_file_output.o vcftools-vcf_entry.o vcftools-vcf_entry_setters.o vcftools-vcf_file.o vcftools-vcftools.o -lz 
make[3]: Leaving directory '/builddir/build/BUILD/vcftools-0.1.16/src/cpp'
Making all in perl
make[3]: Nothing to be done for 'all'.
make[3]: Nothing to be done for 'all-am'.
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.Uk3FiR
+ umask 022
+ cd /builddir/build/BUILD
+ '[' /builddir/build/BUILDROOT/vcftools-0.1.16-19.fc41.x86_64 '!=' / ']'
+ rm -rf /builddir/build/BUILDROOT/vcftools-0.1.16-19.fc41.x86_64
++ dirname /builddir/build/BUILDROOT/vcftools-0.1.16-19.fc41.x86_64
+ mkdir -p /builddir/build/BUILDROOT
+ mkdir /builddir/build/BUILDROOT/vcftools-0.1.16-19.fc41.x86_64
+ CFLAGS='-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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ export CFLAGS
+ CXXFLAGS='-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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules '
+ export FFLAGS
+ FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules '
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn'
+ export RUSTFLAGS
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -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 '
+ export LDFLAGS
+ LT_SYS_LIBRARY_PATH=/usr/lib64:
+ export LT_SYS_LIBRARY_PATH
+ CC=gcc
+ export CC
+ CXX=g++
+ export CXX
+ cd vcftools-0.1.16
+ /usr/bin/make install DESTDIR=/builddir/build/BUILDROOT/vcftools-0.1.16-19.fc41.x86_64 'INSTALL=/usr/bin/install -p'
Making install in src
make[1]: Entering directory '/builddir/build/BUILD/vcftools-0.1.16/src'
Making install in cpp
make[2]: Entering directory '/builddir/build/BUILD/vcftools-0.1.16/src/cpp'
make[3]: Entering directory '/builddir/build/BUILD/vcftools-0.1.16/src/cpp'
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/vcftools-0.1.16-19.fc41.x86_64/usr/bin'
  /usr/bin/install -p vcftools '/builddir/build/BUILDROOT/vcftools-0.1.16-19.fc41.x86_64/usr/bin'
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/vcftools-0.1.16-19.fc41.x86_64/usr/share/man/man1'
 /usr/bin/install -p -m 644 vcftools.1 '/builddir/build/BUILDROOT/vcftools-0.1.16-19.fc41.x86_64/usr/share/man/man1'
make[3]: Leaving directory '/builddir/build/BUILD/vcftools-0.1.16/src/cpp'
make[2]: Leaving directory '/builddir/build/BUILD/vcftools-0.1.16/src/cpp'
Making install in perl
make[2]: Entering directory '/builddir/build/BUILD/vcftools-0.1.16/src/perl'
make[3]: Entering directory '/builddir/build/BUILD/vcftools-0.1.16/src/perl'
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/vcftools-0.1.16-19.fc41.x86_64/usr/bin'
 /usr/bin/install -p fill-aa fill-an-ac fill-fs fill-ref-md5 vcf-annotate vcf-compare vcf-concat vcf-consensus vcf-contrast vcf-convert vcf-fix-newlines vcf-fix-ploidy vcf-indel-stats vcf-isec vcf-merge vcf-phased-join vcf-query vcf-shuffle-cols vcf-sort vcf-stats vcf-subset vcf-to-tab vcf-tstv vcf-validator '/builddir/build/BUILDROOT/vcftools-0.1.16-19.fc41.x86_64/usr/bin'
 /usr/bin/mkdir -p '/builddir/build/BUILDROOT/vcftools-0.1.16-19.fc41.x86_64/usr/share/perl5/vendor_perl'
 /usr/bin/install -p -m 644 FaSlice.pm Vcf.pm VcfStats.pm '/builddir/build/BUILDROOT/vcftools-0.1.16-19.fc41.x86_64/usr/share/perl5/vendor_perl'
make[3]: Leaving directory '/builddir/build/BUILD/vcftools-0.1.16/src/perl'
make[2]: Leaving directory '/builddir/build/BUILD/vcftools-0.1.16/src/perl'
make[2]: Entering directory '/builddir/build/BUILD/vcftools-0.1.16/src'
make[3]: Entering directory '/builddir/build/BUILD/vcftools-0.1.16/src'
make[3]: Nothing to be done for 'install-exec-am'.
make[3]: Nothing to be done for 'install-data-am'.
make[3]: Leaving directory '/builddir/build/BUILD/vcftools-0.1.16/src'
make[2]: Leaving directory '/builddir/build/BUILD/vcftools-0.1.16/src'
make[1]: Leaving directory '/builddir/build/BUILD/vcftools-0.1.16/src'
make[1]: Entering directory '/builddir/build/BUILD/vcftools-0.1.16'
make[2]: Entering directory '/builddir/build/BUILD/vcftools-0.1.16'
make[2]: Nothing to be done for 'install-exec-am'.
make[2]: Nothing to be done for 'install-data-am'.
make[2]: Leaving directory '/builddir/build/BUILD/vcftools-0.1.16'
make[1]: Leaving directory '/builddir/build/BUILD/vcftools-0.1.16'
+ /usr/bin/find-debuginfo -j4 --strict-build-id -m -i --build-id-seed 0.1.16-19.fc41 --unique-debug-suffix -0.1.16-19.fc41.x86_64 --unique-debug-src-base vcftools-0.1.16-19.fc41.x86_64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 110000000 -S debugsourcefiles.list /builddir/build/BUILD/vcftools-0.1.16
find-debuginfo: starting
Extracting debug info from 1 files
DWARF-compressing 1 files
sepdebugcrcfix: Updated 1 CRC32s, 0 CRC32s did match.
Creating .debug symlinks for symlinks to ELF files
Copying sources found by 'debugedit -l' to /usr/src/debug/vcftools-0.1.16-19.fc41.x86_64
1005 blocks
find-debuginfo: done
+ /usr/lib/rpm/check-buildroot
+ /usr/lib/rpm/redhat/brp-ldconfig
+ /usr/lib/rpm/brp-compress
+ /usr/lib/rpm/redhat/brp-strip-lto /usr/bin/strip
+ /usr/lib/rpm/brp-strip-static-archive /usr/bin/strip
+ /usr/lib/rpm/check-rpaths
+ /usr/lib/rpm/redhat/brp-mangle-shebangs
mangling shebang in /usr/bin/vcf-phased-join from /usr/bin/env perl to #!/usr/bin/perl
mangling shebang in /usr/bin/vcf-sort from /usr/bin/env perl to #!/usr/bin/perl
mangling shebang in /usr/bin/vcf-annotate from /usr/bin/env perl to #!/usr/bin/perl
mangling shebang in /usr/bin/vcf-stats from /usr/bin/env perl to #!/usr/bin/perl
mangling shebang in /usr/bin/vcf-subset from /usr/bin/env perl to #!/usr/bin/perl
mangling shebang in /usr/bin/vcf-merge from /usr/bin/env perl to #!/usr/bin/perl
mangling shebang in /usr/bin/vcf-convert from /usr/bin/env perl to #!/usr/bin/perl
mangling shebang in /usr/bin/fill-aa from /usr/bin/env perl to #!/usr/bin/perl
mangling shebang in /usr/bin/vcf-contrast from /usr/bin/env perl to #!/usr/bin/perl
mangling shebang in /usr/bin/fill-fs from /usr/bin/env perl to #!/usr/bin/perl
mangling shebang in /usr/bin/vcf-fix-newlines from /usr/bin/env perl to #!/usr/bin/perl
mangling shebang in /usr/bin/vcf-to-tab from /usr/bin/env perl to #!/usr/bin/perl
mangling shebang in /usr/bin/fill-ref-md5 from /usr/bin/env perl to #!/usr/bin/perl
mangling shebang in /usr/bin/vcf-indel-stats from /usr/bin/env perl to #!/usr/bin/perl
mangling shebang in /usr/bin/vcf-fix-ploidy from /usr/bin/env perl to #!/usr/bin/perl
mangling shebang in /usr/bin/vcf-validator from /usr/bin/env perl to #!/usr/bin/perl
mangling shebang in /usr/bin/vcf-isec from /usr/bin/env perl to #!/usr/bin/perl
mangling shebang in /usr/bin/vcf-consensus from /usr/bin/env perl to #!/usr/bin/perl
mangling shebang in /usr/bin/vcf-shuffle-cols from /usr/bin/env perl to #!/usr/bin/perl
mangling shebang in /usr/bin/fill-an-ac from /usr/bin/env perl to #!/usr/bin/perl
mangling shebang in /usr/bin/vcf-concat from /usr/bin/env perl to #!/usr/bin/perl
mangling shebang in /usr/bin/vcf-query from /usr/bin/env perl to #!/usr/bin/perl
mangling shebang in /usr/bin/vcf-tstv from /usr/bin/env perl to #!/usr/bin/perl
mangling shebang in /usr/bin/vcf-compare from /usr/bin/env perl to #!/usr/bin/perl
*** WARNING: ./usr/src/debug/vcftools-0.1.16-19.fc41.x86_64/src/cpp/bgzf.c is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/vcftools-0.1.16-19.fc41.x86_64/src/cpp/entry_filters.cpp is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/vcftools-0.1.16-19.fc41.x86_64/src/cpp/vcf_entry_setters.cpp is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/vcftools-0.1.16-19.fc41.x86_64/src/cpp/variant_file.cpp is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/vcftools-0.1.16-19.fc41.x86_64/src/cpp/bcf_entry.cpp is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/vcftools-0.1.16-19.fc41.x86_64/src/cpp/parameters.cpp is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/vcftools-0.1.16-19.fc41.x86_64/src/cpp/header.cpp is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/vcftools-0.1.16-19.fc41.x86_64/src/cpp/vcf_file.h is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/vcftools-0.1.16-19.fc41.x86_64/src/cpp/bcf_file.cpp is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/vcftools-0.1.16-19.fc41.x86_64/src/cpp/header.h is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/vcftools-0.1.16-19.fc41.x86_64/src/cpp/gamma.cpp is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/vcftools-0.1.16-19.fc41.x86_64/src/cpp/bcf_entry.h is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/vcftools-0.1.16-19.fc41.x86_64/src/cpp/bcf_entry_setters.cpp is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/vcftools-0.1.16-19.fc41.x86_64/src/cpp/entry.cpp is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/vcftools-0.1.16-19.fc41.x86_64/src/cpp/variant_file_diff.cpp is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/vcftools-0.1.16-19.fc41.x86_64/src/cpp/variant_file_output.cpp is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/vcftools-0.1.16-19.fc41.x86_64/src/cpp/output_log.cpp is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/vcftools-0.1.16-19.fc41.x86_64/src/cpp/knetfile.c is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/vcftools-0.1.16-19.fc41.x86_64/src/cpp/gamma.h is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/vcftools-0.1.16-19.fc41.x86_64/src/cpp/entry_getters.cpp is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/vcftools-0.1.16-19.fc41.x86_64/src/cpp/variant_file_filters.cpp is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/vcftools-0.1.16-19.fc41.x86_64/src/cpp/knetfile.h is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/vcftools-0.1.16-19.fc41.x86_64/src/cpp/vcf_file.cpp is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/vcftools-0.1.16-19.fc41.x86_64/src/cpp/output_log.h is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/vcftools-0.1.16-19.fc41.x86_64/src/cpp/parameters.h is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/vcftools-0.1.16-19.fc41.x86_64/src/cpp/bcf_file.h is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/vcftools-0.1.16-19.fc41.x86_64/src/cpp/variant_file.h is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/vcftools-0.1.16-19.fc41.x86_64/src/cpp/dgeev.cpp is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/vcftools-0.1.16-19.fc41.x86_64/src/cpp/vcftools.cpp is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/vcftools-0.1.16-19.fc41.x86_64/src/cpp/entry_setters.cpp is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/vcftools-0.1.16-19.fc41.x86_64/src/cpp/vcf_entry.cpp is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/vcftools-0.1.16-19.fc41.x86_64/src/cpp/entry.h is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/vcftools-0.1.16-19.fc41.x86_64/src/cpp/variant_file_format_convert.cpp is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/vcftools-0.1.16-19.fc41.x86_64/src/cpp/bgzf.h is executable but has no shebang, removing executable bit
*** WARNING: ./usr/src/debug/vcftools-0.1.16-19.fc41.x86_64/src/cpp/vcf_entry.h is executable but has no shebang, removing executable bit
+ /usr/lib/rpm/brp-remove-la-files
+ env /usr/lib/rpm/redhat/brp-python-bytecompile '' 1 0 -j4
+ /usr/lib/rpm/redhat/brp-python-hardlink
Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.ZPCSol
+ umask 022
+ cd /builddir/build/BUILD
+ CFLAGS='-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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ export CFLAGS
+ CXXFLAGS='-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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules '
+ export FFLAGS
+ FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -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  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules '
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn'
+ export RUSTFLAGS
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -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 '
+ export LDFLAGS
+ LT_SYS_LIBRARY_PATH=/usr/lib64:
+ export LT_SYS_LIBRARY_PATH
+ CC=gcc
+ export CC
+ CXX=g++
+ export CXX
+ cd vcftools-0.1.16
+ make check
Making check in src
make[1]: Entering directory '/builddir/build/BUILD/vcftools-0.1.16/src'
Making check in cpp
make[2]: Entering directory '/builddir/build/BUILD/vcftools-0.1.16/src/cpp'
make[2]: Nothing to be done for 'check'.
make[2]: Leaving directory '/builddir/build/BUILD/vcftools-0.1.16/src/cpp'
Making check in perl
make[2]: Entering directory '/builddir/build/BUILD/vcftools-0.1.16/src/perl'
make[2]: Nothing to be done for 'check'.
make[2]: Leaving directory '/builddir/build/BUILD/vcftools-0.1.16/src/perl'
make[2]: Entering directory '/builddir/build/BUILD/vcftools-0.1.16/src'
make[2]: Nothing to be done for 'check-am'.
make[2]: Leaving directory '/builddir/build/BUILD/vcftools-0.1.16/src'
make[1]: Leaving directory '/builddir/build/BUILD/vcftools-0.1.16/src'
make[1]: Entering directory '/builddir/build/BUILD/vcftools-0.1.16'
make[1]: Leaving directory '/builddir/build/BUILD/vcftools-0.1.16'
+ RPM_EC=0
++ jobs -p
+ exit 0
Processing files: vcftools-0.1.16-19.fc41.x86_64
Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.FMSgPE
+ umask 022
+ cd /builddir/build/BUILD
+ cd vcftools-0.1.16
+ DOCDIR=/builddir/build/BUILDROOT/vcftools-0.1.16-19.fc41.x86_64/usr/share/doc/vcftools
+ export LC_ALL=
+ LC_ALL=
+ export DOCDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/vcftools-0.1.16-19.fc41.x86_64/usr/share/doc/vcftools
+ cp -pr /builddir/build/BUILD/vcftools-0.1.16/README.md /builddir/build/BUILDROOT/vcftools-0.1.16-19.fc41.x86_64/usr/share/doc/vcftools
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.i0SMnI
+ umask 022
+ cd /builddir/build/BUILD
+ cd vcftools-0.1.16
+ LICENSEDIR=/builddir/build/BUILDROOT/vcftools-0.1.16-19.fc41.x86_64/usr/share/licenses/vcftools
+ export LC_ALL=
+ LC_ALL=
+ export LICENSEDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/vcftools-0.1.16-19.fc41.x86_64/usr/share/licenses/vcftools
+ cp -pr /builddir/build/BUILD/vcftools-0.1.16/LICENSE /builddir/build/BUILDROOT/vcftools-0.1.16-19.fc41.x86_64/usr/share/licenses/vcftools
+ RPM_EC=0
++ jobs -p
+ exit 0
Provides: perl(FaSlice) perl(Vcf) = 0.1.14 perl(Vcf3_2) perl(Vcf3_3) perl(Vcf4_0) perl(Vcf4_1) perl(Vcf4_2) perl(Vcf4_3) perl(VcfReader) perl(VcfStats) vcftools = 0.1.16-19.fc41 vcftools(x86-64) = 0.1.16-19.fc41
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Requires: /usr/bin/perl libc.so.6()(64bit) libc.so.6(GLIBC_2.14)(64bit) libc.so.6(GLIBC_2.2.5)(64bit) libc.so.6(GLIBC_2.3.4)(64bit) libc.so.6(GLIBC_2.33)(64bit) libc.so.6(GLIBC_2.34)(64bit) libc.so.6(GLIBC_2.38)(64bit) libc.so.6(GLIBC_2.4)(64bit) libc.so.6(GLIBC_ABI_DT_RELR)(64bit) libgcc_s.so.1()(64bit) libgcc_s.so.1(GCC_3.0)(64bit) libgcc_s.so.1(GCC_3.3.1)(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.2.5)(64bit) libm.so.6(GLIBC_2.29)(64bit) libstdc++.so.6()(64bit) libstdc++.so.6(CXXABI_1.3)(64bit) libstdc++.so.6(CXXABI_1.3.9)(64bit) libstdc++.so.6(GLIBCXX_3.4)(64bit) libstdc++.so.6(GLIBCXX_3.4.11)(64bit) libstdc++.so.6(GLIBCXX_3.4.20)(64bit) libstdc++.so.6(GLIBCXX_3.4.21)(64bit) libstdc++.so.6(GLIBCXX_3.4.26)(64bit) libstdc++.so.6(GLIBCXX_3.4.29)(64bit) libstdc++.so.6(GLIBCXX_3.4.30)(64bit) libstdc++.so.6(GLIBCXX_3.4.32)(64bit) libstdc++.so.6(GLIBCXX_3.4.9)(64bit) libz.so.1()(64bit) libz.so.1(ZLIB_1.2.0)(64bit) libz.so.1(ZLIB_1.2.3.5)(64bit) perl(Carp) perl(Data::Dumper) perl(Exporter) perl(FaSlice) perl(FindBin) perl(IO::Select) perl(IPC::Open2) perl(IPC::Open3) perl(List::Util) perl(POSIX) perl(Vcf) perl(VcfStats) perl(base) perl(lib) perl(strict) perl(vars) perl(warnings) perl-libs rtld(GNU_HASH)
Processing files: vcftools-debugsource-0.1.16-19.fc41.x86_64
Provides: vcftools-debugsource = 0.1.16-19.fc41 vcftools-debugsource(x86-64) = 0.1.16-19.fc41
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Processing files: vcftools-debuginfo-0.1.16-19.fc41.x86_64
Provides: debuginfo(build-id) = 16128116fd08ddf57861e21a07a00a7eecb67c60 vcftools-debuginfo = 0.1.16-19.fc41 vcftools-debuginfo(x86-64) = 0.1.16-19.fc41
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Recommends: vcftools-debugsource(x86-64) = 0.1.16-19.fc41
Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/vcftools-0.1.16-19.fc41.x86_64
Wrote: /builddir/build/RPMS/vcftools-debugsource-0.1.16-19.fc41.x86_64.rpm
Wrote: /builddir/build/RPMS/vcftools-0.1.16-19.fc41.x86_64.rpm
Wrote: /builddir/build/RPMS/vcftools-debuginfo-0.1.16-19.fc41.x86_64.rpm
Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.FFU0dr
+ umask 022
+ cd /builddir/build/BUILD
+ cd vcftools-0.1.16
+ /usr/bin/rm -rf /builddir/build/BUILDROOT/vcftools-0.1.16-19.fc41.x86_64
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(rmbuild): /bin/sh -e /var/tmp/rpm-tmp.1Xoy05
+ umask 022
+ cd /builddir/build/BUILD
+ rm -rf /builddir/build/BUILD/vcftools-0.1.16-SPECPARTS
+ rm -rf vcftools-0.1.16 vcftools-0.1.16.gemspec
+ RPM_EC=0
++ jobs -p
+ exit 0
Child return code was: 0