Mock Version: 5.0 Mock Version: 5.0 Mock Version: 5.0 ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --noclean --target riscv64 --nodeps /builddir/build/SPECS/R-Rsolid.spec'], chrootPath='/var/lib/mock/f40-build-789415-135700/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=604800uid=982gid=135user='mockbuild'nspawn_args=['--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.19s3zvt5:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/fuse', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11']unshare_net=TrueprintOutput=False) Using nspawn with args ['--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.19s3zvt5:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/fuse', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11'] Executing command: ['/usr/bin/systemd-nspawn', '-q', '-M', 'd8ab9c6007d44b61b5b2ab48aae743b2', '-D', '/var/lib/mock/f40-build-789415-135700/root', '-a', '-u', 'mockbuild', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.19s3zvt5:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/fuse', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11', '--console=pipe', '--setenv=TERM=vt100', '--setenv=SHELL=/bin/bash', '--setenv=HOME=/builddir', '--setenv=HOSTNAME=mock', '--setenv=PATH=/usr/bin:/bin:/usr/sbin:/sbin', '--setenv=PROMPT_COMMAND=printf "\\033]0;\\007"', '--setenv=PS1= \\s-\\v\\$ ', '--setenv=LANG=C.UTF-8', '--resolv-conf=off', 'bash', '--login', '-c', '/usr/bin/rpmbuild -bs --noclean --target riscv64 --nodeps /builddir/build/SPECS/R-Rsolid.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', 'SYSTEMD_SECCOMP': '0'} and shell False warning: %patchN is deprecated (2 usages found), use %patch N (or %patch -P N) Building target platforms: riscv64 Building for target riscv64 setting SOURCE_DATE_EPOCH=1705881600 Wrote: /builddir/build/SRPMS/R-Rsolid-0.9.31-46.fc40.src.rpm RPM build warnings: %patchN is deprecated (2 usages found), use %patch N (or %patch -P N) Child return code was: 0 ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --noclean --target riscv64 --nodeps /builddir/build/SPECS/R-Rsolid.spec'], chrootPath='/var/lib/mock/f40-build-789415-135700/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=604800uid=982gid=135user='mockbuild'nspawn_args=['--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.19s3zvt5:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/fuse', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11']unshare_net=TrueprintOutput=False) Using nspawn with args ['--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.19s3zvt5:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/fuse', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11'] Executing command: ['/usr/bin/systemd-nspawn', '-q', '-M', 'af4bd18664bc4604be128cbc06c36933', '-D', '/var/lib/mock/f40-build-789415-135700/root', '-a', '-u', 'mockbuild', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.19s3zvt5:/etc/resolv.conf', '--bind=/dev/btrfs-control', '--bind=/dev/mapper/control', '--bind=/dev/fuse', '--bind=/dev/loop-control', '--bind=/dev/loop0', '--bind=/dev/loop1', '--bind=/dev/loop2', '--bind=/dev/loop3', '--bind=/dev/loop4', '--bind=/dev/loop5', '--bind=/dev/loop6', '--bind=/dev/loop7', '--bind=/dev/loop8', '--bind=/dev/loop9', '--bind=/dev/loop10', '--bind=/dev/loop11', '--console=pipe', '--setenv=TERM=vt100', '--setenv=SHELL=/bin/bash', '--setenv=HOME=/builddir', '--setenv=HOSTNAME=mock', '--setenv=PATH=/usr/bin:/bin:/usr/sbin:/sbin', '--setenv=PROMPT_COMMAND=printf "\\033]0;\\007"', '--setenv=PS1= \\s-\\v\\$ ', '--setenv=LANG=C.UTF-8', '--resolv-conf=off', 'bash', '--login', '-c', '/usr/bin/rpmbuild -bb --noclean --target riscv64 --nodeps /builddir/build/SPECS/R-Rsolid.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', 'SYSTEMD_SECCOMP': '0'} and shell False warning: %patchN is deprecated (2 usages found), use %patch N (or %patch -P N) Building target platforms: riscv64 Building for target riscv64 setting SOURCE_DATE_EPOCH=1705881600 Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.VKNDiz + umask 022 + cd /builddir/build/BUILD + cd /builddir/build/BUILD + rm -rf Rsolid + /usr/bin/mkdir -p Rsolid + cd Rsolid + /usr/lib/rpm/rpmuncompress -x /builddir/build/SOURCES/Rsolid_0.9-31.tar.gz + STATUS=0 + '[' 0 -ne 0 ']' + rm -rf /builddir/build/BUILD/Rsolid-SPECPARTS + /usr/bin/mkdir -p /builddir/build/BUILD/Rsolid-SPECPARTS + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w . + echo 'Patch #0 (R-Rsolid-R3.patch):' Patch #0 (R-Rsolid-R3.patch): + /usr/bin/patch --no-backup-if-mismatch -f -p1 -b --suffix .fixed --fuzz=0 patching file Rsolid/NAMESPACE patching file Rsolid/src/util.c Patch #1 (R-Rsolid-configure-c99.patch): + echo 'Patch #1 (R-Rsolid-configure-c99.patch):' + /usr/bin/patch --no-backup-if-mismatch -f -p1 -b --suffix .configure-c99 --fuzz=0 patching file Rsolid/configure + RPM_EC=0 ++ jobs -p + exit 0 Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.mYyoKx + umask 022 + cd /builddir/build/BUILD + CFLAGS='-O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer ' + export CFLAGS + CXXFLAGS='-O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer ' + export CXXFLAGS + FFLAGS='-O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + cd Rsolid + RPM_EC=0 ++ jobs -p + exit 0 Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.oBUvbm + umask 022 + cd /builddir/build/BUILD + '[' /builddir/build/BUILDROOT/R-Rsolid-0.9.31-46.fc40.riscv64 '!=' / ']' + rm -rf /builddir/build/BUILDROOT/R-Rsolid-0.9.31-46.fc40.riscv64 ++ dirname /builddir/build/BUILDROOT/R-Rsolid-0.9.31-46.fc40.riscv64 + mkdir -p /builddir/build/BUILDROOT + mkdir /builddir/build/BUILDROOT/R-Rsolid-0.9.31-46.fc40.riscv64 + CFLAGS='-O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer ' + export CFLAGS + CXXFLAGS='-O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer ' + export CXXFLAGS + FFLAGS='-O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + cd Rsolid + mkdir -p /builddir/build/BUILDROOT/R-Rsolid-0.9.31-46.fc40.riscv64/usr/lib64/R/library + R CMD INSTALL Rsolid --configure-args=--with-hdf5=/usr -l /builddir/build/BUILDROOT/R-Rsolid-0.9.31-46.fc40.riscv64/usr/lib64/R/library * installing *source* package ‘Rsolid’ ... ** using staged installation checking for gcc... gcc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ANSI C... none needed checking how to run the C preprocessor... gcc -E checking for egrep... 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 hdf5.h usability... yes checking hdf5.h presence... yes checking for hdf5.h... yes configure: creating ./config.status config.status: creating src/Makevars ** libs using C compiler: ‘gcc (GCC) 14.0.1 20240217 (Red Hat 14.0.1-0)’ gcc -I"/usr/include/R" -DNDEBUG -I/usr/include -I/usr/local/include -fpic -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -c Rdriver.c -o Rdriver.o Rdriver.c: In function ‘rdriver’: Rdriver.c:271:8: warning: unused variable ‘p_yxloc’ [-Wunused-variable] 271 | SEXP p_yxloc; | ^~~~~~~ Rdriver.c:270:8: warning: unused variable ‘p_intensities’ [-Wunused-variable] 270 | SEXP p_intensities; | ^~~~~~~~~~~~~ Rdriver.c:269:8: warning: unused variable ‘ligation_names’ [-Wunused-variable] 269 | SEXP ligation_names; | ^~~~~~~~~~~~~~ Rdriver.c:268:8: warning: unused variable ‘primer_names’ [-Wunused-variable] 268 | SEXP primer_names; | ^~~~~~~~~~~~ Rdriver.c:266:15: warning: unused variable ‘i’ [-Wunused-variable] 266 | int status, i; | ^ Rdriver.c:264:13: warning: unused variable ‘panel_info’ [-Wunused-variable] 264 | panelInfo panel_info; | ^~~~~~~~~~ gcc -I"/usr/include/R" -DNDEBUG -I/usr/include -I/usr/local/include -fpic -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -c reader.c -o reader.o reader.c: In function ‘ligationIter_data’: reader.c:315:7: warning: unused variable ‘offset’ [-Wunused-variable] 315 | int offset; | ^~~~~~ gcc -I"/usr/include/R" -DNDEBUG -I/usr/include -I/usr/local/include -fpic -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -c reader_util.c -o reader_util.o gcc -I"/usr/include/R" -DNDEBUG -I/usr/include -I/usr/local/include -fpic -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -c util.c -o util.o util.c: In function ‘callBases’: util.c:163:41: warning: unused variable ‘dscore’ [-Wunused-variable] 163 | double *input=REAL(mat), dtmp, dtmp2, dscore; | ^~~~~~ util.c:240:7: warning: ‘quals’ may be used uninitialized [-Wmaybe-uninitialized] 240 | SET_STRING_ELT(quals, iread, mkChar(tmpscore)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util.c:178:15: note: ‘quals’ was declared here 178 | SEXP calls, quals, res; | ^~~~~ util.c:169:19: warning: ‘tmpscore’ may be used uninitialized [-Wmaybe-uninitialized] 169 | char *tmpchar, *tmpscore; | ^~~~~~~~ util.c:245:5: warning: ‘res’ may be used uninitialized [-Wmaybe-uninitialized] 245 | SET_VECTOR_ELT(res, 1, quals); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ util.c:178:22: note: ‘res’ was declared here 178 | SEXP calls, quals, res; | ^~~ gcc -shared -L/usr/lib64/R/lib -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -o Rsolid.so Rdriver.o reader.o reader_util.o util.o -L/usr/lib -lhdf5 -L/usr/lib64/R/lib -lR installing to /builddir/build/BUILDROOT/R-Rsolid-0.9.31-46.fc40.riscv64/usr/lib64/R/library/00LOCK-Rsolid/00new/Rsolid/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package ‘Rsolid’ finding HTML links ... done Rsolid html finding level-2 HTML links ... done Rd warning: Rsolid.Rd:44: missing link ‘snow’ Rd warning: Rsolid.Rd:45: missing link ‘Rmpi’ ** 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 (Rsolid) + test -d Rsolid/src + cd Rsolid/src + rm -f Rdriver.o reader.o reader_util.o util.o Rsolid.so + rm -rf /builddir/build/BUILDROOT/R-Rsolid-0.9.31-46.fc40.riscv64/usr/lib64/R/library/R.css + rm -rf Rsolid/src/hdf5-1.8.3 + rm -rf Rsolid/config.status + rm -rf Rsolid/configure + /usr/bin/find-debuginfo -j64 --strict-build-id -m -i --build-id-seed 0.9.31-46.fc40 --unique-debug-suffix -0.9.31-46.fc40.riscv64 --unique-debug-src-base R-Rsolid-0.9.31-46.fc40.riscv64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 50000000 -S debugsourcefiles.list /builddir/build/BUILD/Rsolid find-debuginfo: starting Extracting debug info from 1 files DWARF-compressing 1 files sepdebugcrcfix: Updated 1 CRC32s, 0 CRC32s did match. Creating .debug symlinks for symlinks to ELF files Copying sources found by 'debugedit -l' to /usr/src/debug/R-Rsolid-0.9.31-46.fc40.riscv64 72 blocks find-debuginfo: done + /usr/lib/rpm/check-buildroot + /usr/lib/rpm/redhat/brp-ldconfig + /usr/lib/rpm/brp-compress + /usr/lib/rpm/redhat/brp-strip-lto /usr/bin/strip + /usr/lib/rpm/brp-strip-static-archive /usr/bin/strip + /usr/lib/rpm/check-rpaths + /usr/lib/rpm/redhat/brp-mangle-shebangs + /usr/lib/rpm/brp-remove-la-files + env /usr/lib/rpm/redhat/brp-python-bytecompile '' 1 0 -j64 + /usr/lib/rpm/redhat/brp-python-hardlink Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.6ZYtcc + umask 022 + cd /builddir/build/BUILD + CFLAGS='-O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer ' + export CFLAGS + CXXFLAGS='-O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer ' + export CXXFLAGS + FFLAGS='-O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fno-omit-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + cd Rsolid + /usr/bin/R CMD check Rsolid * using log directory ‘/builddir/build/BUILD/Rsolid/Rsolid.Rcheck’ * using R version 4.3.3 (2024-02-29) * using platform: riscv64-redhat-linux-gnu (64-bit) * R was compiled by gcc (GCC) 14.0.1 20240217 (Red Hat 14.0.1-0) GNU Fortran (GCC) 14.0.1 20240217 (Red Hat 14.0.1-0) * running under: Fedora Linux 40 (Rawhide Prerelease) * using session charset: UTF-8 * checking for file ‘Rsolid/DESCRIPTION’ ... OK * this is package ‘Rsolid’ version ‘0.9-31’ * checking package namespace information ... OK * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' Warning: unable to access index for repository https://bioconductor.org/packages/3.18/bioc/src/contrib: cannot open URL 'https://bioconductor.org/packages/3.18/bioc/src/contrib/PACKAGES' Warning: unable to access index for repository https://bioconductor.org/packages/3.18/data/annotation/src/contrib: cannot open URL 'https://bioconductor.org/packages/3.18/data/annotation/src/contrib/PACKAGES' Warning: unable to access index for repository https://bioconductor.org/packages/3.18/data/experiment/src/contrib: cannot open URL 'https://bioconductor.org/packages/3.18/data/experiment/src/contrib/PACKAGES' OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for executable files ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... WARNING The following files should most likely be executable (for the owner): cleanup Please fix their permissions * checking whether package ‘Rsolid’ can be installed ... OK * used C compiler: ‘gcc (GCC) 14.0.1 20240217 (Red Hat 14.0.1-0)’ * checking installed package size ... OK * checking package directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... WARNING Foreign function calls without 'PACKAGE' argument: .Call("callBases", ...) .Call("callBases", ...) .Call("rowMaxPos", ...) .Call("rdriver", ...) See chapter ‘System and foreign language interfaces’ in the ‘Writing R Extensions’ manual. * checking R code for possible problems ... NOTE NB: .First.lib is obsolete and will not be used in R >= 3.0.0 readspch: warning in matrix(0, nr = nbeads, nc = total.nligation.cycles): partial argument match of 'nr' to 'nrow' readspch: warning in matrix(0, nr = nbeads, nc = total.nligation.cycles): partial argument match of 'nc' to 'ncol' readspch: warning in matrix(NA, nr = max.ligation.cycles, nc = max.primer.cycles): partial argument match of 'nr' to 'nrow' readspch: warning in matrix(NA, nr = max.ligation.cycles, nc = max.primer.cycles): partial argument match of 'nc' to 'ncol' Rsolid: no visible global function definition for ‘write.table’ Undefined global functions or variables: write.table Consider adding importFrom("utils", "write.table") to your NAMESPACE file. * checking Rd files ... NOTE prepare_Rd: Rsolid.Rd:61-63: Dropping empty section \seealso * checking Rd metadata ... OK * checking Rd cross-references ... WARNING Missing link or links in documentation object 'Rsolid.Rd': ‘snow’ ‘Rmpi’ See section 'Cross-references' in the 'Writing R Extensions' manual. * checking for missing documentation entries ... WARNING Undocumented code objects: ‘makeTarget’ ‘quantile.norm’ ‘readspch’ Undocumented data sets: ‘prop.Hs’ All user-level objects in a package should have documentation entries. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking line endings in shell scripts ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... NOTE Package has both ‘src/Makevars.in’ and ‘src/Makevars’. Installation with --no-configure' is unlikely to work. If you intended ‘src/Makevars’ to be used on Windows, rename it to ‘src/Makevars.win’ otherwise remove it. If ‘configure’ created ‘src/Makevars’, you need a ‘cleanup’ script. * checking for GNU extensions in Makefiles ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking compiled code ... NOTE File ‘Rsolid/libs/Rsolid.so’: Found ‘__printf_chk’, possibly from ‘printf’ (C) Objects: ‘reader.o’, ‘reader_util.o’ Found ‘putchar’, possibly from ‘putchar’ (C) Object: ‘reader_util.o’ Found ‘puts’, possibly from ‘printf’ (C), ‘puts’ (C) Objects: ‘reader.o’, ‘reader_util.o’ Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs nor [v]sprintf. See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual. * checking examples ... OK * checking PDF version of manual ... WARNING LaTeX errors when creating PDF version. This typically indicates Rd problems. LaTeX errors found: ! LaTeX Error: File `inconsolata.sty' not found. Type X to quit or to proceed, or enter new name. (Default extension: sty) ! Emergency stop. l.303 ^^M ! ==> Fatal error occurred, no output PDF file produced! * checking PDF version of manual without index ... OK * DONE Status: 5 WARNINGs, 4 NOTEs See ‘/builddir/build/BUILD/Rsolid/Rsolid.Rcheck/00check.log’ for details. + RPM_EC=0 ++ jobs -p + exit 0 Processing files: R-Rsolid-0.9.31-46.fc40.riscv64 Provides: R(Rsolid) = 0.9.31 R-Rsolid = 0.9.31-46.fc40 R-Rsolid(riscv-64) = 0.9.31-46.fc40 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: R(ABI) = 4.3 R-core ld-linux-riscv64-lp64d.so.1()(64bit) ld-linux-riscv64-lp64d.so.1(GLIBC_2.27)(64bit) libR.so()(64bit) libc.so.6()(64bit) libc.so.6(GLIBC_2.27)(64bit) libhdf5.so.200()(64bit) rtld(GNU_HASH) Processing files: R-Rsolid-devel-0.9.31-46.fc40.riscv64 Provides: R-Rsolid-devel = 0.9.31-46.fc40 R-Rsolid-devel(riscv-64) = 0.9.31-46.fc40 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: R-Rsolid-debugsource-0.9.31-46.fc40.riscv64 Provides: R-Rsolid-debugsource = 0.9.31-46.fc40 R-Rsolid-debugsource(riscv-64) = 0.9.31-46.fc40 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: R-Rsolid-debuginfo-0.9.31-46.fc40.riscv64 Provides: R-Rsolid-debuginfo = 0.9.31-46.fc40 R-Rsolid-debuginfo(riscv-64) = 0.9.31-46.fc40 debuginfo(build-id) = f209b61d16b9fea302a818e04257c3de4c5da0ed Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: R-Rsolid-debugsource(riscv-64) = 0.9.31-46.fc40 Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/R-Rsolid-0.9.31-46.fc40.riscv64 Wrote: /builddir/build/RPMS/R-Rsolid-0.9.31-46.fc40.riscv64.rpm Wrote: /builddir/build/RPMS/R-Rsolid-debugsource-0.9.31-46.fc40.riscv64.rpm Wrote: /builddir/build/RPMS/R-Rsolid-debuginfo-0.9.31-46.fc40.riscv64.rpm Wrote: /builddir/build/RPMS/R-Rsolid-devel-0.9.31-46.fc40.riscv64.rpm RPM build warnings: %patchN is deprecated (2 usages found), use %patch N (or %patch -P N) Child return code was: 0