Mock Version: 2.9 ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target x86_64 --nodeps /builddir/build/SPECS/R-preprocessCore.spec'], chrootPath='/var/lib/mock/fedora-34-x86_64-1614002732.747199/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': 'C.UTF-8'}shell=Falselogger=timeout=0uid=1001gid=135user='mockbuild'nspawn_args=['--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.dmo7rt81:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11']unshare_net=TrueprintOutput=True) Using nspawn with args ['--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.dmo7rt81:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11'] Executing command: ['/usr/bin/systemd-nspawn', '-q', '-M', '2cebd06658e9451eae54dc7afc08dd9c', '-D', '/var/lib/mock/fedora-34-x86_64-1614002732.747199/root', '-a', '-u', 'mockbuild', '--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.dmo7rt81:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11', '--console=pipe', '--setenv=TERM=vt100', '--setenv=SHELL=/bin/bash', '--setenv=HOME=/builddir', '--setenv=HOSTNAME=mock', '--setenv=PATH=/usr/bin:/bin:/usr/sbin:/sbin', '--setenv=PROMPT_COMMAND=printf "\\033]0;\\007"', '--setenv=PS1= \\s-\\v\\$ ', '--setenv=LANG=C.UTF-8', '--resolv-conf=off', 'bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target x86_64 --nodeps /builddir/build/SPECS/R-preprocessCore.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': 'C.UTF-8', 'SYSTEMD_NSPAWN_TMPFS_TMP': '0'} and shell False Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1612396800 Wrote: /builddir/build/SRPMS/R-preprocessCore-1.52.1-1.fc34.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/R-preprocessCore.spec'], chrootPath='/var/lib/mock/fedora-34-x86_64-1614002732.747199/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': 'C.UTF-8'}shell=Falselogger=timeout=0uid=1001gid=135user='mockbuild'nspawn_args=['--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.dmo7rt81:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11']unshare_net=TrueprintOutput=True) Using nspawn with args ['--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.dmo7rt81:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11'] Executing command: ['/usr/bin/systemd-nspawn', '-q', '-M', '7c1a63134fb345648089e0327eb65f2a', '-D', '/var/lib/mock/fedora-34-x86_64-1614002732.747199/root', '-a', '-u', 'mockbuild', '--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.dmo7rt81:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11', '--console=pipe', '--setenv=TERM=vt100', '--setenv=SHELL=/bin/bash', '--setenv=HOME=/builddir', '--setenv=HOSTNAME=mock', '--setenv=PATH=/usr/bin:/bin:/usr/sbin:/sbin', '--setenv=PROMPT_COMMAND=printf "\\033]0;\\007"', '--setenv=PS1= \\s-\\v\\$ ', '--setenv=LANG=C.UTF-8', '--resolv-conf=off', 'bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target x86_64 --nodeps /builddir/build/SPECS/R-preprocessCore.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': 'C.UTF-8', 'SYSTEMD_NSPAWN_TMPFS_TMP': '0'} and shell False Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1612396800 Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.CWBe6Q + umask 022 + cd /builddir/build/BUILD + cd /builddir/build/BUILD + rm -rf preprocessCore + /usr/bin/mkdir -p preprocessCore + cd preprocessCore + /usr/bin/gzip -dc /builddir/build/SOURCES/preprocessCore_1.52.1.tar.gz + /usr/bin/tar -xof - + STATUS=0 + '[' 0 -ne 0 ']' + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w . + echo 'Patch #0 (R-preprocessCore-dlsym-pthread_get_minstack-fix.patch):' Patch #0 (R-preprocessCore-dlsym-pthread_get_minstack-fix.patch): + /usr/bin/patch --no-backup-if-mismatch -p1 -b --suffix .dlsym --fuzz=0 patching file preprocessCore/configure.in patching file preprocessCore/src/qnorm.c Hunk #2 succeeded at 510 (offset 2 lines). Hunk #3 succeeded at 1632 (offset 2 lines). Hunk #4 succeeded at 1935 (offset 2 lines). Hunk #5 succeeded at 2540 (offset 2 lines). Hunk #6 succeeded at 3055 (offset 2 lines). patching file preprocessCore/src/rma_background4.c Hunk #2 succeeded at 370 (offset 2 lines). patching file preprocessCore/src/R_subColSummarize.c Hunk #2 succeeded at 131 (offset 2 lines). Hunk #3 succeeded at 310 (offset 2 lines). Hunk #4 succeeded at 492 (offset 2 lines). Hunk #5 succeeded at 675 (offset 2 lines). Hunk #6 succeeded at 857 (offset 2 lines). Hunk #7 succeeded at 1040 (offset 2 lines). Hunk #8 succeeded at 1221 (offset 2 lines). Hunk #9 succeeded at 1401 (offset 2 lines). Hunk #10 succeeded at 1586 (offset 2 lines). Hunk #11 succeeded at 1772 (offset 2 lines). patching file preprocessCore/src/R_subrcModel_interfaces.c Hunk #2 succeeded at 187 (offset 2 lines). Hunk #3 succeeded at 513 (offset 2 lines). ~/build/BUILD/preprocessCore/preprocessCore ~/build/BUILD/preprocessCore + pushd preprocessCore + autoreconf -ifv . autoreconf: export WARNINGS= autoreconf: warning: autoconf input should be named 'configure.ac', not 'configure.in' autoreconf: Entering directory '.' autoreconf: configure.in: not using Gettext autoreconf: running: aclocal --force aclocal: warning: autoconf input should be named 'configure.ac', not 'configure.in' configure.in:34: warning: The macro `AC_HEADER_STDC' is obsolete. configure.in:34: You should run autoupdate. ./lib/autoconf/headers.m4:704: AC_HEADER_STDC is expanded from... configure.in:34: the top level configure.in:88: warning: AC_OUTPUT should be used without arguments. configure.in:88: You should run autoupdate. autoreconf: configure.in: tracing autoreconf: configure.in: not using Libtool autoreconf: configure.in: not using Intltool autoreconf: configure.in: not using Gtkdoc autoreconf: running: /usr/bin/autoconf --force configure.in:34: warning: The macro `AC_HEADER_STDC' is obsolete. configure.in:34: You should run autoupdate. ./lib/autoconf/headers.m4:704: AC_HEADER_STDC is expanded from... configure.in:34: the top level configure.in:88: warning: AC_OUTPUT should be used without arguments. configure.in:88: You should run autoupdate. autoreconf: configure.in: not using Autoheader autoreconf: configure.in: not using Automake autoreconf: Leaving directory '.' + popd ~/build/BUILD/preprocessCore + RPM_EC=0 ++ jobs -p + exit 0 Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.cFUbuZ + umask 022 + cd /builddir/build/BUILD + cd preprocessCore + RPM_EC=0 ++ jobs -p + exit 0 Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.MjF63f + umask 022 + cd /builddir/build/BUILD + '[' /builddir/build/BUILDROOT/R-preprocessCore-1.52.1-1.fc34.x86_64 '!=' / ']' + rm -rf /builddir/build/BUILDROOT/R-preprocessCore-1.52.1-1.fc34.x86_64 ++ dirname /builddir/build/BUILDROOT/R-preprocessCore-1.52.1-1.fc34.x86_64 + mkdir -p /builddir/build/BUILDROOT + mkdir /builddir/build/BUILDROOT/R-preprocessCore-1.52.1-1.fc34.x86_64 + cd preprocessCore + mkdir -p /builddir/build/BUILDROOT/R-preprocessCore-1.52.1-1.fc34.x86_64/usr/lib64/R/library + R CMD INSTALL preprocessCore -l /builddir/build/BUILDROOT/R-preprocessCore-1.52.1-1.fc34.x86_64/usr/lib64/R/library * installing *source* package 'preprocessCore' ... ** using staged installation 'config' variable 'CPP' is deprecated checking for gcc... gcc -m64 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 the compiler supports GNU C... yes checking whether gcc -m64 accepts -g... yes checking for gcc -m64 option to enable C11 features... none needed checking how to run the C preprocessor... gcc -m64 -E checking for library containing pthread_create... -lpthread checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for stdlib.h... (cached) yes checking if PTHREAD_STACK_MIN is defined... yes checking for dlfcn.h... yes checking for library containing dlsym... -ldl configure: Enabling threading for preprocessCore configure: creating ./config.status config.status: creating src/Makevars ** libs gcc -m64 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -I/usr/local/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_STDLIB_H=1 -DHAVE_DLFCN_H=1 -DHAS_DLSYM=1 -DUSE_PTHREADS=1 -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c R_colSummarize.c -o R_colSummarize.o gcc -m64 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -I/usr/local/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_STDLIB_H=1 -DHAVE_DLFCN_H=1 -DHAS_DLSYM=1 -DUSE_PTHREADS=1 -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c R_plmd_interfaces.c -o R_plmd_interfaces.o gcc -m64 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -I/usr/local/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_STDLIB_H=1 -DHAVE_DLFCN_H=1 -DHAS_DLSYM=1 -DUSE_PTHREADS=1 -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c R_plmr_interfaces.c -o R_plmr_interfaces.o gcc -m64 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -I/usr/local/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_STDLIB_H=1 -DHAVE_DLFCN_H=1 -DHAS_DLSYM=1 -DUSE_PTHREADS=1 -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c R_rlm_interfaces.c -o R_rlm_interfaces.o gcc -m64 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -I/usr/local/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_STDLIB_H=1 -DHAVE_DLFCN_H=1 -DHAS_DLSYM=1 -DUSE_PTHREADS=1 -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c R_subColSummarize.c -o R_subColSummarize.o R_subColSummarize.c: In function 'R_subColSummarize_avg_log': R_subColSummarize.c:121:9: warning: unused variable 'j' [-Wunused-variable] 121 | int i,j; | ^ R_subColSummarize.c:119:7: warning: unused variable 'ncur_rows' [-Wunused-variable] 119 | int ncur_rows; | ^~~~~~~~~ R_subColSummarize.c:115:8: warning: unused variable 'cur_rows' [-Wunused-variable] 115 | int *cur_rows; | ^~~~~~~~ R_subColSummarize.c:113:21: warning: unused variable 'buffer' [-Wunused-variable] 113 | double *results, *buffer; | ^~~~~~ R_subColSummarize.c: In function 'R_subColSummarize_log_avg': R_subColSummarize.c:300:9: warning: unused variable 'j' [-Wunused-variable] 300 | int i,j; | ^ R_subColSummarize.c:298:7: warning: unused variable 'ncur_rows' [-Wunused-variable] 298 | int ncur_rows; | ^~~~~~~~~ R_subColSummarize.c:294:8: warning: unused variable 'cur_rows' [-Wunused-variable] 294 | int *cur_rows; | ^~~~~~~~ R_subColSummarize.c:292:21: warning: unused variable 'buffer' [-Wunused-variable] 292 | double *results, *buffer; | ^~~~~~ R_subColSummarize.c: In function 'R_subColSummarize_avg': R_subColSummarize.c:482:9: warning: unused variable 'j' [-Wunused-variable] 482 | int i,j; | ^ R_subColSummarize.c:480:7: warning: unused variable 'ncur_rows' [-Wunused-variable] 480 | int ncur_rows; | ^~~~~~~~~ R_subColSummarize.c:476:8: warning: unused variable 'cur_rows' [-Wunused-variable] 476 | int *cur_rows; | ^~~~~~~~ R_subColSummarize.c:474:21: warning: unused variable 'buffer' [-Wunused-variable] 474 | double *results, *buffer; | ^~~~~~ R_subColSummarize.c: In function 'R_subColSummarize_biweight_log': R_subColSummarize.c:665:9: warning: unused variable 'j' [-Wunused-variable] 665 | int i,j; | ^ R_subColSummarize.c:663:7: warning: unused variable 'ncur_rows' [-Wunused-variable] 663 | int ncur_rows; | ^~~~~~~~~ R_subColSummarize.c:659:8: warning: unused variable 'cur_rows' [-Wunused-variable] 659 | int *cur_rows; | ^~~~~~~~ R_subColSummarize.c:657:21: warning: unused variable 'buffer' [-Wunused-variable] 657 | double *results, *buffer; | ^~~~~~ R_subColSummarize.c: In function 'R_subColSummarize_biweight': R_subColSummarize.c:847:9: warning: unused variable 'j' [-Wunused-variable] 847 | int i,j; | ^ R_subColSummarize.c:845:7: warning: unused variable 'ncur_rows' [-Wunused-variable] 845 | int ncur_rows; | ^~~~~~~~~ R_subColSummarize.c:841:8: warning: unused variable 'cur_rows' [-Wunused-variable] 841 | int *cur_rows; | ^~~~~~~~ R_subColSummarize.c:839:21: warning: unused variable 'buffer' [-Wunused-variable] 839 | double *results, *buffer; | ^~~~~~ R_subColSummarize.c: In function 'R_subColSummarize_median_log': R_subColSummarize.c:1030:9: warning: unused variable 'j' [-Wunused-variable] 1030 | int i,j; | ^ R_subColSummarize.c:1028:7: warning: unused variable 'ncur_rows' [-Wunused-variable] 1028 | int ncur_rows; | ^~~~~~~~~ R_subColSummarize.c:1024:8: warning: unused variable 'cur_rows' [-Wunused-variable] 1024 | int *cur_rows; | ^~~~~~~~ R_subColSummarize.c:1022:21: warning: unused variable 'buffer' [-Wunused-variable] 1022 | double *results, *buffer; | ^~~~~~ R_subColSummarize.c: In function 'R_subColSummarize_log_median': R_subColSummarize.c:1211:9: warning: unused variable 'j' [-Wunused-variable] 1211 | int i,j; | ^ R_subColSummarize.c:1209:7: warning: unused variable 'ncur_rows' [-Wunused-variable] 1209 | int ncur_rows; | ^~~~~~~~~ R_subColSummarize.c:1205:8: warning: unused variable 'cur_rows' [-Wunused-variable] 1205 | int *cur_rows; | ^~~~~~~~ R_subColSummarize.c:1203:21: warning: unused variable 'buffer' [-Wunused-variable] 1203 | double *results, *buffer; | ^~~~~~ R_subColSummarize.c: In function 'R_subColSummarize_median': R_subColSummarize.c:1391:9: warning: unused variable 'j' [-Wunused-variable] 1391 | int i,j; | ^ R_subColSummarize.c:1389:7: warning: unused variable 'ncur_rows' [-Wunused-variable] 1389 | int ncur_rows; | ^~~~~~~~~ R_subColSummarize.c:1385:8: warning: unused variable 'cur_rows' [-Wunused-variable] 1385 | int *cur_rows; | ^~~~~~~~ R_subColSummarize.c:1383:21: warning: unused variable 'buffer' [-Wunused-variable] 1383 | double *results, *buffer; | ^~~~~~ R_subColSummarize.c: In function 'R_subColSummarize_medianpolish_log': R_subColSummarize.c:1576:9: warning: unused variable 'j' [-Wunused-variable] 1576 | int i,j; | ^ R_subColSummarize.c:1574:7: warning: unused variable 'ncur_rows' [-Wunused-variable] 1574 | int ncur_rows; | ^~~~~~~~~ R_subColSummarize.c:1570:8: warning: unused variable 'cur_rows' [-Wunused-variable] 1570 | int *cur_rows; | ^~~~~~~~ R_subColSummarize.c:1568:30: warning: variable 'buffer2' set but not used [-Wunused-but-set-variable] 1568 | double *results, *buffer, *buffer2; | ^~~~~~~ R_subColSummarize.c:1568:21: warning: variable 'buffer' set but not used [-Wunused-but-set-variable] 1568 | double *results, *buffer, *buffer2; | ^~~~~~ R_subColSummarize.c: In function 'R_subColSummarize_medianpolish': R_subColSummarize.c:1762:9: warning: unused variable 'j' [-Wunused-variable] 1762 | int i,j; | ^ R_subColSummarize.c:1760:7: warning: unused variable 'ncur_rows' [-Wunused-variable] 1760 | int ncur_rows; | ^~~~~~~~~ R_subColSummarize.c:1756:8: warning: unused variable 'cur_rows' [-Wunused-variable] 1756 | int *cur_rows; | ^~~~~~~~ R_subColSummarize.c:1754:30: warning: unused variable 'buffer2' [-Wunused-variable] 1754 | double *results, *buffer, *buffer2; | ^~~~~~~ R_subColSummarize.c:1754:21: warning: unused variable 'buffer' [-Wunused-variable] 1754 | double *results, *buffer, *buffer2; | ^~~~~~ At top level: R_subColSummarize.c:1718:14: warning: 'subColSummarize_medianpolish_group' defined but not used [-Wunused-function] 1718 | static void *subColSummarize_medianpolish_group(void *data){ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -m64 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -I/usr/local/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_STDLIB_H=1 -DHAVE_DLFCN_H=1 -DHAS_DLSYM=1 -DUSE_PTHREADS=1 -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c R_subrcModel_interfaces.c -o R_subrcModel_interfaces.o R_subrcModel_interfaces.c: In function 'sub_rcModelSummarize_medianpolish_group': R_subrcModel_interfaces.c:95:11: warning: unused variable 'se' [-Wunused-variable] 95 | double *se; | ^~ R_subrcModel_interfaces.c:94:11: warning: unused variable 'weights' [-Wunused-variable] 94 | double *weights; | ^~~~~~~ R_subrcModel_interfaces.c:79:20: warning: unused variable 'buffer2' [-Wunused-variable] 79 | double *buffer, *buffer2; | ^~~~~~~ R_subrcModel_interfaces.c:79:11: warning: unused variable 'buffer' [-Wunused-variable] 79 | double *buffer, *buffer2; | ^~~~~~ R_subrcModel_interfaces.c: In function 'R_sub_rcModelSummarize_medianpolish': R_subrcModel_interfaces.c:177:9: warning: unused variable 'j' [-Wunused-variable] 177 | int i,j; | ^ R_subrcModel_interfaces.c:175:7: warning: unused variable 'ncur_rows' [-Wunused-variable] 175 | int ncur_rows; | ^~~~~~~~~ R_subrcModel_interfaces.c:171:8: warning: unused variable 'cur_rows' [-Wunused-variable] 171 | int *cur_rows; | ^~~~~~~~ R_subrcModel_interfaces.c:169:30: warning: unused variable 'buffer2' [-Wunused-variable] 169 | double *results, *buffer, *buffer2; | ^~~~~~~ R_subrcModel_interfaces.c:169:21: warning: unused variable 'buffer' [-Wunused-variable] 169 | double *results, *buffer, *buffer2; | ^~~~~~ R_subrcModel_interfaces.c:169:11: warning: unused variable 'results' [-Wunused-variable] 169 | double *results, *buffer, *buffer2; | ^~~~~~~ R_subrcModel_interfaces.c: In function 'sub_rcModelSummarize_plm_group': R_subrcModel_interfaces.c:408:10: warning: unused variable 'scale' [-Wunused-variable] 408 | double scale=-1.0; | ^~~~~ R_subrcModel_interfaces.c:387:20: warning: unused variable 'buffer2' [-Wunused-variable] 387 | double *buffer, *buffer2; | ^~~~~~~ R_subrcModel_interfaces.c:387:11: warning: unused variable 'buffer' [-Wunused-variable] 387 | double *buffer, *buffer2; | ^~~~~~ R_subrcModel_interfaces.c: In function 'R_sub_rcModelSummarize_plm': R_subrcModel_interfaces.c:503:9: warning: unused variable 'j' [-Wunused-variable] 503 | int i,j; | ^ R_subrcModel_interfaces.c:501:7: warning: unused variable 'ncur_rows' [-Wunused-variable] 501 | int ncur_rows; | ^~~~~~~~~ R_subrcModel_interfaces.c:497:8: warning: unused variable 'cur_rows' [-Wunused-variable] 497 | int *cur_rows; | ^~~~~~~~ R_subrcModel_interfaces.c:495:30: warning: unused variable 'buffer2' [-Wunused-variable] 495 | double *results, *buffer, *buffer2; | ^~~~~~~ R_subrcModel_interfaces.c:495:21: warning: unused variable 'buffer' [-Wunused-variable] 495 | double *results, *buffer, *buffer2; | ^~~~~~ R_subrcModel_interfaces.c:495:11: warning: unused variable 'results' [-Wunused-variable] 495 | double *results, *buffer, *buffer2; | ^~~~~~~ gcc -m64 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -I/usr/local/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_STDLIB_H=1 -DHAVE_DLFCN_H=1 -DHAS_DLSYM=1 -DUSE_PTHREADS=1 -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c avg.c -o avg.o gcc -m64 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -I/usr/local/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_STDLIB_H=1 -DHAVE_DLFCN_H=1 -DHAS_DLSYM=1 -DUSE_PTHREADS=1 -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c avg_log.c -o avg_log.o gcc -m64 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -I/usr/local/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_STDLIB_H=1 -DHAVE_DLFCN_H=1 -DHAS_DLSYM=1 -DUSE_PTHREADS=1 -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c biweight.c -o biweight.o gcc -m64 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -I/usr/local/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_STDLIB_H=1 -DHAVE_DLFCN_H=1 -DHAS_DLSYM=1 -DUSE_PTHREADS=1 -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c init_package.c -o init_package.o gcc -m64 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -I/usr/local/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_STDLIB_H=1 -DHAVE_DLFCN_H=1 -DHAS_DLSYM=1 -DUSE_PTHREADS=1 -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c lm.c -o lm.o gcc -m64 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -I/usr/local/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_STDLIB_H=1 -DHAVE_DLFCN_H=1 -DHAS_DLSYM=1 -DUSE_PTHREADS=1 -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c log_avg.c -o log_avg.o gcc -m64 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -I/usr/local/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_STDLIB_H=1 -DHAVE_DLFCN_H=1 -DHAS_DLSYM=1 -DUSE_PTHREADS=1 -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c log_median.c -o log_median.o gcc -m64 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -I/usr/local/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_STDLIB_H=1 -DHAVE_DLFCN_H=1 -DHAS_DLSYM=1 -DUSE_PTHREADS=1 -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c matrix_functions.c -o matrix_functions.o gcc -m64 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -I/usr/local/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_STDLIB_H=1 -DHAVE_DLFCN_H=1 -DHAS_DLSYM=1 -DUSE_PTHREADS=1 -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c median.c -o median.o gcc -m64 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -I/usr/local/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_STDLIB_H=1 -DHAVE_DLFCN_H=1 -DHAS_DLSYM=1 -DUSE_PTHREADS=1 -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c median_log.c -o median_log.o gcc -m64 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -I/usr/local/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_STDLIB_H=1 -DHAVE_DLFCN_H=1 -DHAS_DLSYM=1 -DUSE_PTHREADS=1 -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c medianpolish.c -o medianpolish.o gcc -m64 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -I/usr/local/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_STDLIB_H=1 -DHAVE_DLFCN_H=1 -DHAS_DLSYM=1 -DUSE_PTHREADS=1 -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c plmd.c -o plmd.o gcc -m64 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -I/usr/local/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_STDLIB_H=1 -DHAVE_DLFCN_H=1 -DHAS_DLSYM=1 -DUSE_PTHREADS=1 -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c plmr.c -o plmr.o plmr.c:279:13: warning: 'XTWX_R_inv' defined but not used [-Wunused-function] 279 | static void XTWX_R_inv(int *rows, int *cols, double *xtwx){ | ^~~~~~~~~~ plmr.c:152:13: warning: 'XTWX_R' defined but not used [-Wunused-function] 152 | static void XTWX_R(int *rows, int *cols, double *out_weights, double *xtwx){ | ^~~~~~ plmr.c:82:13: warning: 'XTWY_R' defined but not used [-Wunused-function] 82 | static void XTWY_R(int *rows, int *cols, double *out_weights, double *y,double *xtwy){ | ^~~~~~ gcc -m64 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -I/usr/local/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_STDLIB_H=1 -DHAVE_DLFCN_H=1 -DHAS_DLSYM=1 -DUSE_PTHREADS=1 -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c psi_fns.c -o psi_fns.o gcc -m64 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -I/usr/local/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_STDLIB_H=1 -DHAVE_DLFCN_H=1 -DHAS_DLSYM=1 -DUSE_PTHREADS=1 -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c qnorm.c -o qnorm.o qnorm.c: In function 'qnorm_c_determine_target_l': qnorm.c:1925:7: warning: unused variable 'non_na' [-Wunused-variable] 1925 | int non_na; | ^~~~~~ qnorm.c:1920:12: warning: unused variable 'j' [-Wunused-variable] 1920 | size_t i,j,row_mean_ind; | ^ qnorm.c: In function 'qnorm_c_determine_target_via_subset_l': qnorm.c:2530:7: warning: unused variable 'non_na' [-Wunused-variable] 2530 | int non_na; | ^~~~~~ qnorm.c:2525:12: warning: unused variable 'j' [-Wunused-variable] 2525 | size_t i,j,row_mean_ind; | ^ qnorm.c: In function 'using_target_via_subset_part1': qnorm.c:2752:14: warning: variable 'ind' set but not used [-Wunused-but-set-variable] 2752 | size_t i,j,ind,target_ind; | ^~~ qnorm.c: In function 'using_target_via_subset_part2': qnorm.c:2851:11: warning: unused variable 'datvec' [-Wunused-variable] 2851 | double *datvec; | ^~~~~~ qnorm.c:2850:11: warning: unused variable 'sample_percentiles' [-Wunused-variable] 2850 | double *sample_percentiles; | ^~~~~~~~~~~~~~~~~~ qnorm.c: In function 'using_target_via_subset': qnorm.c:3000:11: warning: unused variable 'datvec' [-Wunused-variable] 3000 | double *datvec; | ^~~~~~ qnorm.c:2999:11: warning: unused variable 'sample_percentiles' [-Wunused-variable] 2999 | double *sample_percentiles; | ^~~~~~~~~~~~~~~~~~ qnorm.c:2995:7: warning: unused variable 'non_na' [-Wunused-variable] 2995 | int non_na = 0; | ^~~~~~ qnorm.c:2994:7: warning: unused variable 'targetnon_na' [-Wunused-variable] 2994 | int targetnon_na = targetrows; | ^~~~~~~~~~~~ qnorm.c:2992:28: warning: unused variable 'target_ind_double_floor' [-Wunused-variable] 2992 | double target_ind_double,target_ind_double_floor; | ^~~~~~~~~~~~~~~~~~~~~~~ qnorm.c:2992:10: warning: unused variable 'target_ind_double' [-Wunused-variable] 2992 | double target_ind_double,target_ind_double_floor; | ^~~~~~~~~~~~~~~~~ qnorm.c:2991:10: warning: unused variable 'samplepercentile' [-Wunused-variable] 2991 | double samplepercentile; | ^~~~~~~~~~~~~~~~ qnorm.c:2990:11: warning: unused variable 'ranks' [-Wunused-variable] 2990 | double *ranks = (double *)Calloc((rows),double); | ^~~~~ qnorm.c:2988:11: warning: unused variable 'row_mean' [-Wunused-variable] 2988 | double *row_mean = target; | ^~~~~~~~ qnorm.c:2986:14: warning: unused variable 'dimat' [-Wunused-variable] 2986 | dataitem **dimat; | ^~~~~ qnorm.c:2984:18: warning: unused variable 'target_ind' [-Wunused-variable] 2984 | size_t i,j,ind,target_ind; | ^~~~~~~~~~ qnorm.c:2984:14: warning: unused variable 'ind' [-Wunused-variable] 2984 | size_t i,j,ind,target_ind; | ^~~ qnorm.c:2984:12: warning: unused variable 'j' [-Wunused-variable] 2984 | size_t i,j,ind,target_ind; | ^ qnorm.c: In function 'R_qnorm_using_target': qnorm.c:2136:3: warning: 'target_rows' may be used uninitialized in this function [-Wmaybe-uninitialized] 2136 | qnorm_c_using_target_l(Xptr, rows, cols ,targetptr, target_rows); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ qnorm.c: In function 'R_qnorm_using_target_via_subset': qnorm.c:3275:3: warning: 'target_rows' may be used uninitialized in this function [-Wmaybe-uninitialized] 3275 | qnorm_c_using_target_via_subset_l(Xptr, rows, cols, subsetptr, targetptr, target_rows); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -m64 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -I/usr/local/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_STDLIB_H=1 -DHAVE_DLFCN_H=1 -DHAS_DLSYM=1 -DUSE_PTHREADS=1 -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c rlm.c -o rlm.o gcc -m64 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -I/usr/local/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_STDLIB_H=1 -DHAVE_DLFCN_H=1 -DHAS_DLSYM=1 -DUSE_PTHREADS=1 -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c rlm_anova.c -o rlm_anova.o rlm_anova.c: In function 'rlm_fit_anova_given_probe_effects_engine': rlm_anova.c:1235:10: warning: unused variable 'endprobe' [-Wunused-variable] 1235 | double endprobe; | ^~~~~~~~ rlm_anova.c: In function 'rlm_compute_se_anova_given_probe_effects': rlm_anova.c:1426:19: warning: unused variable 'varderivpsi' [-Wunused-variable] 1426 | double vs=0.0,m,varderivpsi=0.0; | ^~~~~~~~~~~ rlm_anova.c:1426:17: warning: unused variable 'm' [-Wunused-variable] 1426 | double vs=0.0,m,varderivpsi=0.0; | ^ rlm_anova.c:1426:10: warning: unused variable 'vs' [-Wunused-variable] 1426 | double vs=0.0,m,varderivpsi=0.0; | ^~ rlm_anova.c:1419:10: warning: unused variable 'scale' [-Wunused-variable] 1419 | double scale=0.0; | ^~~~~ rlm_anova.c:1418:10: warning: unused variable 'Kappa' [-Wunused-variable] 1418 | double Kappa=0.0; /* A correction factor */ | ^~~~~ rlm_anova.c:1417:10: warning: unused variable 'sumderivpsi' [-Wunused-variable] 1417 | double sumderivpsi=0.0; /* sum of psi'(r_i) */ | ^~~~~~~~~~~ rlm_anova.c:1415:10: warning: unused variable 'sumpsi2' [-Wunused-variable] 1415 | double sumpsi2=0.0; /* sum of psi(r_i)^2 */ | ^~~~~~~ rlm_anova.c:1414:10: warning: unused variable 'k1' [-Wunused-variable] 1414 | double k1 = psi_k; /* was 1.345; */ | ^~ rlm_anova.c: In function 'rlm_wfit_anova_given_probe_effects_engine': rlm_anova.c:1505:10: warning: unused variable 'endprobe' [-Wunused-variable] 1505 | double endprobe; | ^~~~~~~~ gcc -m64 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -I/usr/local/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_STDLIB_H=1 -DHAVE_DLFCN_H=1 -DHAS_DLSYM=1 -DUSE_PTHREADS=1 -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c rlm_se.c -o rlm_se.o gcc -m64 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -I/usr/local/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_STDLIB_H=1 -DHAVE_DLFCN_H=1 -DHAS_DLSYM=1 -DUSE_PTHREADS=1 -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c rma_background4.c -o rma_background4.o rma_background4.c: In function 'rma_bg_correct': rma_background4.c:359:10: warning: unused variable 'param' [-Wunused-variable] 359 | double param[3]; | ^~~~~ rma_background4.c:358:10: warning: unused variable 'j' [-Wunused-variable] 358 | size_t j; | ^ rma_background4.c: In function 'R_rma_bg_correct': rma_background4.c:519:12: warning: 'PMcopy' may be used uninitialized in this function [-Wmaybe-uninitialized] 519 | return PMcopy; | ^~~~~~ gcc -m64 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -I/usr/local/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_STDLIB_H=1 -DHAVE_DLFCN_H=1 -DHAS_DLSYM=1 -DUSE_PTHREADS=1 -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c rma_common.c -o rma_common.o gcc -m64 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -I/usr/local/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_STDLIB_H=1 -DHAVE_DLFCN_H=1 -DHAS_DLSYM=1 -DUSE_PTHREADS=1 -fpic -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -c weightedkerneldensity.c -o weightedkerneldensity.o gcc -m64 -shared -L/usr/lib64/R/lib -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o preprocessCore.so R_colSummarize.o R_plmd_interfaces.o R_plmr_interfaces.o R_rlm_interfaces.o R_subColSummarize.o R_subrcModel_interfaces.o avg.o avg_log.o biweight.o init_package.o lm.o log_avg.o log_median.o matrix_functions.o median.o median_log.o medianpolish.o plmd.o plmr.o psi_fns.o qnorm.o rlm.o rlm_anova.o rlm_se.o rma_background4.o rma_common.o weightedkerneldensity.o -ldl -lpthread -lflexiblas -lgfortran -lm -lquadmath -L/usr/lib64/R/lib -lR installing to /builddir/build/BUILDROOT/R-preprocessCore-1.52.1-1.fc34.x86_64/usr/lib64/R/library/00LOCK-preprocessCore/00new/preprocessCore/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'preprocessCore' finding HTML links ... done colSummarize html normalize.quantiles html normalize.quantiles.in.blocks html normalize.quantiles.robust html normalize.quantiles.target html rcModelPLMd html rcModelPLMr html rcModels html rma.background.correct html subColSummarize html subrcModels html ** building package indices ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (preprocessCore) + test -d preprocessCore/src + cd preprocessCore/src + rm -f R_colSummarize.o R_plmd_interfaces.o R_plmr_interfaces.o R_rlm_interfaces.o R_subColSummarize.o R_subrcModel_interfaces.o avg.o avg_log.o biweight.o init_package.o lm.o log_avg.o log_median.o matrix_functions.o median.o median_log.o medianpolish.o plmd.o plmr.o psi_fns.o qnorm.o rlm.o rlm_anova.o rlm_se.o rma_background4.o rma_common.o weightedkerneldensity.o preprocessCore.so + rm -rf /builddir/build/BUILDROOT/R-preprocessCore-1.52.1-1.fc34.x86_64/usr/lib64/R/library/R.css + install -m 664 -p /builddir/build/SOURCES/preprocessCore_license /builddir/build/BUILDROOT/R-preprocessCore-1.52.1-1.fc34.x86_64/usr/lib64/R/library/preprocessCore + /usr/lib/rpm/find-debuginfo.sh -j2 --strict-build-id -m -i --build-id-seed 1.52.1-1.fc34 --unique-debug-suffix -1.52.1-1.fc34.x86_64 --unique-debug-src-base R-preprocessCore-1.52.1-1.fc34.x86_64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 110000000 -S debugsourcefiles.list /builddir/build/BUILD/preprocessCore explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/R-preprocessCore-1.52.1-1.fc34.x86_64/usr/lib64/R/library/preprocessCore/libs/preprocessCore.so extracting debug info from /builddir/build/BUILDROOT/R-preprocessCore-1.52.1-1.fc34.x86_64/usr/lib64/R/library/preprocessCore/libs/preprocessCore.so original debug info size: 512kB, size after compression: 484kB /usr/lib/rpm/sepdebugcrcfix: Updated 1 CRC32s, 0 CRC32s did match. 959 blocks + /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/redhat/brp-python-bytecompile '' 1 0 + /usr/lib/rpm/brp-python-hardlink + /usr/lib/rpm/redhat/brp-mangle-shebangs Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.d9aTJw + umask 022 + cd /builddir/build/BUILD + cd preprocessCore + RPM_EC=0 ++ jobs -p + exit 0 Processing files: R-preprocessCore-1.52.1-1.fc34.x86_64 Provides: R(preprocessCore) = 1.52.1 R-preprocessCore = 1.52.1-1.fc34 R-preprocessCore(x86-64) = 1.52.1-1.fc34 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: R(ABI) = 4.0 R(stats) R-core libR.so()(64bit) libc.so.6()(64bit) libc.so.6(GLIBC_2.14)(64bit) libc.so.6(GLIBC_2.2.5)(64bit) libc.so.6(GLIBC_2.4)(64bit) libflexiblas.so.3()(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.2.5)(64bit) libm.so.6(GLIBC_2.29)(64bit) libpthread.so.0()(64bit) libpthread.so.0(GLIBC_2.2.5)(64bit) rtld(GNU_HASH) Processing files: R-preprocessCore-devel-1.52.1-1.fc34.x86_64 Provides: R-preprocessCore-devel = 1.52.1-1.fc34 R-preprocessCore-devel(x86-64) = 1.52.1-1.fc34 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: R-preprocessCore-debugsource-1.52.1-1.fc34.x86_64 Provides: R-preprocessCore-debugsource = 1.52.1-1.fc34 R-preprocessCore-debugsource(x86-64) = 1.52.1-1.fc34 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: R-preprocessCore-debuginfo-1.52.1-1.fc34.x86_64 Provides: R-preprocessCore-debuginfo = 1.52.1-1.fc34 R-preprocessCore-debuginfo(x86-64) = 1.52.1-1.fc34 debuginfo(build-id) = 28f22d33f81f9fa205f4e70e90fc18f7a569b417 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: R-preprocessCore-debugsource(x86-64) = 1.52.1-1.fc34 Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/R-preprocessCore-1.52.1-1.fc34.x86_64 Wrote: /builddir/build/RPMS/R-preprocessCore-debuginfo-1.52.1-1.fc34.x86_64.rpm Wrote: /builddir/build/RPMS/R-preprocessCore-debugsource-1.52.1-1.fc34.x86_64.rpm Wrote: /builddir/build/RPMS/R-preprocessCore-1.52.1-1.fc34.x86_64.rpm Wrote: /builddir/build/RPMS/R-preprocessCore-devel-1.52.1-1.fc34.x86_64.rpm Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.ThetZn + umask 022 + cd /builddir/build/BUILD + cd preprocessCore + /usr/bin/rm -rf /builddir/build/BUILDROOT/R-preprocessCore-1.52.1-1.fc34.x86_64 + RPM_EC=0 ++ jobs -p + exit 0 Child return code was: 0