Mock Version: 1.4.9 Mock Version: 1.4.9 ENTER ['do'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target riscv64 --nodeps /builddir/build/SPECS/vcftools.spec'], chrootPath='/var/lib/mock/f29-build-26966-14058/root'env={'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'en_US.UTF-8', 'http_proxy': 'http://192.168.0.254:3128', 'https_proxy': 'http://192.168.0.254:3128'}shell=Falselogger=timeout=345600uid=995gid=135user='mockbuild'nspawn_args=[]unshare_net=FalseprintOutput=False) Executing command: ['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target riscv64 --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;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'en_US.UTF-8', 'http_proxy': 'http://192.168.0.254:3128', 'https_proxy': 'http://192.168.0.254:3128'} and shell False Building target platforms: riscv64 Building for target riscv64 Wrote: /builddir/build/SRPMS/vcftools-0.1.16-1.fc29.src.rpm Child return code was: 0 ENTER ['do'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target riscv64 --nodeps /builddir/build/SPECS/vcftools.spec'], chrootPath='/var/lib/mock/f29-build-26966-14058/root'env={'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'en_US.UTF-8', 'http_proxy': 'http://192.168.0.254:3128', 'https_proxy': 'http://192.168.0.254:3128'}shell=Falselogger=timeout=345600uid=995gid=135user='mockbuild'nspawn_args=[]unshare_net=FalseprintOutput=False) Executing command: ['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target riscv64 --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;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'en_US.UTF-8', 'http_proxy': 'http://192.168.0.254:3128', 'https_proxy': 'http://192.168.0.254:3128'} and shell False Building target platforms: riscv64 Building for target riscv64 Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.xREFCG + umask 022 + cd /builddir/build/BUILD + cd /builddir/build/BUILD + rm -rf vcftools-0.1.16 + /usr/bin/gzip -dc /builddir/build/SOURCES/vcftools-0.1.16.tar.gz + /usr/bin/tar -xof - + STATUS=0 + '[' 0 -ne 0 ']' + cd vcftools-0.1.16 + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w . + exit 0 Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.IQ1cNk + umask 022 + cd /builddir/build/BUILD + cd vcftools-0.1.16 + CFLAGS='-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection' + export CFLAGS + CXXFLAGS='-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection' + export CXXFLAGS + FFLAGS='-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules' + export FFLAGS + FCFLAGS='-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules' + export FCFLAGS + LDFLAGS='-Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld' + export LDFLAGS + '[' 1 = 1 ']' BUILDSTDERR: +++ dirname ./configure BUILDSTDERR: ++ find . -name config.guess -o -name config.sub + '[' 1 = 1 ']' + '[' x '!=' 'x-Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld' ']' BUILDSTDERR: ++ find . -name ltmain.sh + ./configure --build=riscv64-redhat-linux-gnu --host=riscv64-redhat-linux-gnu --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 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 for riscv64-redhat-linux-gnu-g++... no checking for riscv64-redhat-linux-gnu-c++... no checking for riscv64-redhat-linux-gnu-gpp... no checking for riscv64-redhat-linux-gnu-aCC... no checking for riscv64-redhat-linux-gnu-CC... no checking for riscv64-redhat-linux-gnu-cxx... no checking for riscv64-redhat-linux-gnu-cc++... no checking for riscv64-redhat-linux-gnu-cl.exe... no checking for riscv64-redhat-linux-gnu-FCC... no checking for riscv64-redhat-linux-gnu-KCC... no checking for riscv64-redhat-linux-gnu-RCC... no checking for riscv64-redhat-linux-gnu-xlC_r... no checking for riscv64-redhat-linux-gnu-xlC... no checking for g++... g++ 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 riscv64-redhat-linux-gnu-gcc... no checking for 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 riscv64-redhat-linux-gnu-pkg-config... /usr/bin/riscv64-redhat-linux-gnu-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 /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../.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -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' BUILDSTDERR: bgzf.c: In function 'bgzf_check_EOF': BUILDSTDERR: bgzf.c:60:34: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] BUILDSTDERR: #define _bgzf_read(fp, buf, len) fread((buf), 1, (len), (FILE*)(fp)) BUILDSTDERR: ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ BUILDSTDERR: bgzf.c:622:2: note: in expansion of macro '_bgzf_read' BUILDSTDERR: _bgzf_read(fp->fp, buf, 28); BUILDSTDERR: ^~~~~~~~~~ make[3]: Entering directory '/builddir/build/BUILD/vcftools-0.1.16/src/cpp' g++ -DHAVE_CONFIG_H -I. -I../.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -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../.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -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../.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -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../.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -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' make[3]: Entering directory '/builddir/build/BUILD/vcftools-0.1.16/src/cpp' g++ -DHAVE_CONFIG_H -I. -I../.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -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../.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -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' g++ -DHAVE_CONFIG_H -I. -I../.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -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../.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -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' gcc -DHAVE_CONFIG_H -I. -I../.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -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' BUILDSTDERR: In file included from knetfile.c:46: BUILDSTDERR: knetfile.c: In function 'kftp_send_cmd': BUILDSTDERR: knetfile.h:9:32: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] BUILDSTDERR: #define netwrite(fd, ptr, len) write(fd, ptr, len) BUILDSTDERR: ^~~~~~~~~~~~~~~~~~~ BUILDSTDERR: knetfile.c:236:2: note: in expansion of macro 'netwrite' BUILDSTDERR: netwrite(ftp->ctrl_fd, cmd, strlen(cmd)); BUILDSTDERR: ^~~~~~~~ BUILDSTDERR: knetfile.c: In function 'khttp_connect_file': BUILDSTDERR: knetfile.h:9:32: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result] BUILDSTDERR: #define netwrite(fd, ptr, len) write(fd, ptr, len) BUILDSTDERR: ^~~~~~~~~~~~~~~~~~~ BUILDSTDERR: knetfile.c:415:2: note: in expansion of macro 'netwrite' BUILDSTDERR: netwrite(fp->fd, buf, l); BUILDSTDERR: ^~~~~~~~ make[3]: Entering directory '/builddir/build/BUILD/vcftools-0.1.16/src/cpp' g++ -DHAVE_CONFIG_H -I. -I../.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c -o vcftools-output_log.o `test -f 'output_log.cpp' || echo './'`output_log.cpp make[3]: Leaving directory '/builddir/build/BUILD/vcftools-0.1.16/src/cpp' BUILDSTDERR: output_log.cpp: In member function 'void output_log::printLOG(std::__cxx11::string)': BUILDSTDERR: output_log.cpp:42:2: warning: this 'if' clause does not guard... [-Wmisleading-indentation] BUILDSTDERR: if (output_to_file) BUILDSTDERR: ^~ BUILDSTDERR: output_log.cpp:43:13: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' BUILDSTDERR: LOG << s; LOG.flush(); BUILDSTDERR: ^~~ BUILDSTDERR: output_log.cpp:44:2: warning: this 'if' clause does not guard... [-Wmisleading-indentation] BUILDSTDERR: if (output_to_screen) BUILDSTDERR: ^~ BUILDSTDERR: output_log.cpp:45:14: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' BUILDSTDERR: cerr << s; cerr.flush(); BUILDSTDERR: ^~~~ make[3]: Entering directory '/builddir/build/BUILD/vcftools-0.1.16/src/cpp' g++ -DHAVE_CONFIG_H -I. -I../.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -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' BUILDSTDERR: entry_filters.cpp: In member function 'void entry::filter_sites_by_overlap_positions(const string&, const string&)': BUILDSTDERR: entry_filters.cpp:540:4: warning: this 'for' clause does not guard... [-Wmisleading-indentation] BUILDSTDERR: for (unsigned int ui=POS; ui<(POS+REF.size()); ui++) BUILDSTDERR: ^~~ BUILDSTDERR: entry_filters.cpp:544:5: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for' BUILDSTDERR: if (found == true) BUILDSTDERR: ^~ BUILDSTDERR: entry_filters.cpp: In member function 'void entry::filter_sites_by_frequency_and_call_rate(double, double, double, double, double, double, double)': BUILDSTDERR: entry_filters.cpp:814:70: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] BUILDSTDERR: if (((min_non_ref_af > 0.0) || (max_non_ref_af < 1.0)) && (N_failed == (N_alleles-1))) BUILDSTDERR: ~~~~~~~~~^~~~~~~~~~~~~~~~ BUILDSTDERR: entry_filters.cpp: In member function 'void entry::filter_sites_by_allele_count(double, double, double, double, double, double, double)': BUILDSTDERR: entry_filters.cpp:912:99: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] BUILDSTDERR: if (((min_non_ref_ac_any > 0) || (max_non_ref_ac_any < numeric_limits::max())) && (N_failed == (N_alleles-1))) BUILDSTDERR: ~~~~~~~~~^~~~~~~~~~~~~~~~ make[3]: Entering directory '/builddir/build/BUILD/vcftools-0.1.16/src/cpp' g++ -DHAVE_CONFIG_H -I. -I../.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -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../.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -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' make[3]: Entering directory '/builddir/build/BUILD/vcftools-0.1.16/src/cpp' g++ -DHAVE_CONFIG_H -I. -I../.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -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' BUILDSTDERR: header.cpp: In static member function 'static void header::split(const string&, char, std::vector >&)': BUILDSTDERR: header.cpp:477:39: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} [-Wsign-compare] BUILDSTDERR: while ((end = text.find(sep, start)) != string::npos) BUILDSTDERR: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~ make[3]: Entering directory '/builddir/build/BUILD/vcftools-0.1.16/src/cpp' g++ -DHAVE_CONFIG_H -I. -I../.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -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' BUILDSTDERR: parameters.cpp: In member function 'void parameters::print_params()': BUILDSTDERR: parameters.cpp:491:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation] BUILDSTDERR: if (output_N_PCA_SNP_loadings != defaults.output_N_PCA_SNP_loadings) BUILDSTDERR: ^~ BUILDSTDERR: parameters.cpp:493:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' BUILDSTDERR: if (output_prefix != defaults.output_prefix) LOG.printLOG("\t--out " + output_prefix + "\n"); BUILDSTDERR: ^~ make[3]: Entering directory '/builddir/build/BUILD/vcftools-0.1.16/src/cpp' g++ -DHAVE_CONFIG_H -I. -I../.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c -o vcftools-variant_file_diff.o `test -f 'variant_file_diff.cpp' || echo './'`variant_file_diff.cpp make[3]: Leaving directory '/builddir/build/BUILD/vcftools-0.1.16/src/cpp' BUILDSTDERR: variant_file_diff.cpp: In member function 'void variant_file::output_sites_in_files(const parameters&, variant_file&)': BUILDSTDERR: variant_file_diff.cpp:219:14: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} [-Wsign-compare] BUILDSTDERR: if (POS2 < (POS1+REF1.size())) BUILDSTDERR: ~~~~~^~~~~~~~~~~~~~~~~~~~ BUILDSTDERR: variant_file_diff.cpp:235:14: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} [-Wsign-compare] BUILDSTDERR: if (POS1 < (POS2+REF2.size())) BUILDSTDERR: ~~~~~^~~~~~~~~~~~~~~~~~~~ make[3]: Entering directory '/builddir/build/BUILD/vcftools-0.1.16/src/cpp' g++ -DHAVE_CONFIG_H -I. -I../.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c -o vcftools-variant_file_format_convert.o `test -f 'variant_file_format_convert.cpp' || echo './'`variant_file_format_convert.cpp make[3]: Leaving directory '/builddir/build/BUILD/vcftools-0.1.16/src/cpp' BUILDSTDERR: variant_file_format_convert.cpp: In member function 'void variant_file::output_as_LDhelmet(const parameters&)': BUILDSTDERR: variant_file_format_convert.cpp:1015:15: warning: unused variable 'n_indv' [-Wunused-variable] BUILDSTDERR: unsigned int n_indv = N_kept_individuals(); BUILDSTDERR: ^~~~~~ make[3]: Entering directory '/builddir/build/BUILD/vcftools-0.1.16/src/cpp' g++ -DHAVE_CONFIG_H -I. -I../.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -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../.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -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../.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c -o vcftools-vcf_entry.o `test -f 'vcf_entry.cpp' || echo './'`vcf_entry.cpp make[3]: Leaving directory '/builddir/build/BUILD/vcftools-0.1.16/src/cpp' BUILDSTDERR: vcf_entry.cpp: In member function 'virtual void vcf_entry::parse_genotype_entry(unsigned int, bool, bool, bool, bool)': BUILDSTDERR: vcf_entry.cpp:135:52: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} [-Wsign-compare] BUILDSTDERR: while ((end = GENOTYPE_str[indv].find(':',start)) != string::npos) BUILDSTDERR: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~ make[3]: Entering directory '/builddir/build/BUILD/vcftools-0.1.16/src/cpp' g++ -DHAVE_CONFIG_H -I. -I../.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -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../.. -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -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' BUILDSTDERR: variant_file_output.cpp: In member function 'void variant_file::output_haplotype_r2(const parameters&)': BUILDSTDERR: variant_file_output.cpp:1540:27: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare] BUILDSTDERR: for(unsigned int ui=0; ui