Mock Version: 1.4.14 Mock Version: 1.4.14 ENTER ['do'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target aarch64 --nodeps /builddir/build/SPECS/R-ncdf4.spec'], chrootPath='/var/lib/mock/f30-build-15482643-1115265/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=172800uid=1000gid=425user='mockbuild'nspawn_args=[]unshare_net=TrueprintOutput=False) Executing command: ['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target aarch64 --nodeps /builddir/build/SPECS/R-ncdf4.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'} and shell False Building target platforms: aarch64 Building for target aarch64 Wrote: /builddir/build/SRPMS/R-ncdf4-1.16-2.fc30.src.rpm Child return code was: 0 ENTER ['do'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target aarch64 --nodeps /builddir/build/SPECS/R-ncdf4.spec'], chrootPath='/var/lib/mock/f30-build-15482643-1115265/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=172800uid=1000gid=425user='mockbuild'nspawn_args=[]unshare_net=TrueprintOutput=False) Executing command: ['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target aarch64 --nodeps /builddir/build/SPECS/R-ncdf4.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'} and shell False Building target platforms: aarch64 Building for target aarch64 Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.jvG2TV + umask 022 + cd /builddir/build/BUILD + cd /builddir/build/BUILD + rm -rf ncdf4 + /usr/bin/mkdir -p ncdf4 + cd ncdf4 + /usr/bin/tar -xof - + /usr/bin/gzip -dc /builddir/build/SOURCES/ncdf4_1.16.tar.gz + STATUS=0 + '[' 0 -ne 0 ']' + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w . + rm ncdf4/inst/HDF5_COPYING Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.OlTLGN + exit 0 + umask 022 + cd /builddir/build/BUILD + cd ncdf4 + exit 0 Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.hfgvHD + umask 022 + cd /builddir/build/BUILD + '[' /builddir/build/BUILDROOT/R-ncdf4-1.16-2.fc30.aarch64 '!=' / ']' + rm -rf /builddir/build/BUILDROOT/R-ncdf4-1.16-2.fc30.aarch64 BUILDSTDERR: ++ dirname /builddir/build/BUILDROOT/R-ncdf4-1.16-2.fc30.aarch64 + mkdir -p /builddir/build/BUILDROOT + mkdir /builddir/build/BUILDROOT/R-ncdf4-1.16-2.fc30.aarch64 + cd ncdf4 + mkdir -p /builddir/build/BUILDROOT/R-ncdf4-1.16-2.fc30.aarch64/usr/lib64/R/library + /usr/bin/R CMD INSTALL -l /builddir/build/BUILDROOT/R-ncdf4-1.16-2.fc30.aarch64/usr/lib64/R/library ncdf4 BUILDSTDERR: * installing *source* package 'ncdf4' ... file 'inst/HDF5_COPYING' is missing configure.ac: starting checking for nc-config... yes Using nc-config: nc-config Output of nc-config --all: This netCDF 4.4.1.1 has been built with the following features: --cc -> gcc --cflags -> -I/usr/include -I/usr/include/hdf --libs -> -L/usr/lib64 -lnetcdf --has-c++ -> no --cxx -> --has-c++4 -> no --cxx4 -> --has-fortran-> no --has-dap -> yes --has-nc2 -> yes --has-nc4 -> yes --has-hdf5 -> yes --has-hdf4 -> yes --has-logging-> no --has-pnetcdf-> no --has-szlib -> --prefix -> /usr --includedir-> /usr/include --libdir -> /usr/lib64 --version -> netCDF 4.4.1.1 --- netcdf.m4: about to set rpath, here is source string: >-L/usr/lib64 -lnetcdf< netcdf.m4: final rpath: -Wl,-rpath,/usr/lib64 Netcdf library version: netCDF 4.4.1.1 Netcdf library has version 4 interface present: yes Netcdf library was compiled with C compiler: gcc configure: creating ./config.status config.status: creating src/Makevars ********************** Results of ncdf4 package configure ******************* netCDF v4 CPP flags = -I/usr/include -I/usr/include/hdf netCDF v4 LD flags = -Wl,-rpath,/usr/lib64 -L/usr/lib64 -lnetcdf netCDF v4 runtime path = -Wl,-rpath,/usr/lib64 netCDF C compiler used = gcc R C compiler used = gcc -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection ****************************************************************************** BUILDSTDERR: ** libs gcc -I"/usr/include/R" -DNDEBUG -I/usr/include -I/usr/include/hdf -I/usr/local/include -fpic -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -c ncdf.c -o ncdf.o BUILDSTDERR: ncdf.c:113:27: warning: missing braces around initializer [-Wmissing-braces] BUILDSTDERR: 113 | R_CMethodDef cMethods[] = { BUILDSTDERR: | ^ BUILDSTDERR: ncdf.c:186:33: warning: missing braces around initializer [-Wmissing-braces] BUILDSTDERR: 186 | R_CallMethodDef callMethods[] = { BUILDSTDERR: | ^ BUILDSTDERR: ncdf.c: In function 'R_nc4_put_att_text': BUILDSTDERR: ncdf.c:1008:10: warning: variable 'ttc' set but not used [-Wunused-but-set-variable] BUILDSTDERR: 1008 | nc_type ttc; BUILDSTDERR: | ^~~ BUILDSTDERR: ncdf.c: In function 'R_nc4_get_vara_numvarid': BUILDSTDERR: ncdf.c:2300:42: warning: variable 'sx_ncdf_var' set but not used [-Wunused-but-set-variable] BUILDSTDERR: 2300 | SEXP rv_data = R_NilValue /* -Wall */, sx_ncdf_var, sx_dim; BUILDSTDERR: | ^~~~~~~~~~~ BUILDSTDERR: ncdf.c: In function 'R_nc4_get_vara_string': BUILDSTDERR: ncdf.c:2548:15: warning: variable 'nchar' set but not used [-Wunused-but-set-variable] BUILDSTDERR: 2548 | int i, ierr, nchar, varid, ncid, ndims, count_int[MAX_NC_DIMS], start_int[MAX_NC_DIMS], len_count, len_start; BUILDSTDERR: | ^~~~~ gcc -shared -L/usr/lib64/R/lib -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -o ncdf4.so ncdf.o -Wl,-rpath,/usr/lib64 -L/usr/lib64 -lnetcdf -L/usr/lib64/R/lib -lR BUILDSTDERR: installing to /builddir/build/BUILDROOT/R-ncdf4-1.16-2.fc30.aarch64/usr/lib64/R/library/ncdf4/libs BUILDSTDERR: ** R BUILDSTDERR: ** byte-compile and prepare package for lazy loading BUILDSTDERR: ** help BUILDSTDERR: *** installing help indices converting help for package 'ncdf4' BUILDSTDERR: finding HTML links ... done ancvar_put html nc_close html nc_create html nc_enddef html nc_open html nc_redef html nc_sync html nc_version html ncatt_get html ncatt_put html ncdf4-internal html ncdf4-package html Rd warning: /builddir/build/BUILD/ncdf4/ncdf4/man/ncdf4-package.Rd:57: file link 'ncvar_put' in package 'ncdf4' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/ncdf4/ncdf4/man/ncdf4-package.Rd:74: file link 'ncvar_put' in package 'ncdf4' does not exist and so has been treated as a topic ncdim_def html ncvar_add html ncvar_change_missval html ncvar_def html Rd warning: /builddir/build/BUILD/ncdf4/ncdf4/man/ncvar_def.Rd:67: file link 'ncvar_put' in package 'ncdf4' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/ncdf4/ncdf4/man/ncvar_def.Rd:108: file link 'ncvar_put' in package 'ncdf4' does not exist and so has been treated as a topic Rd warning: /builddir/build/BUILD/ncdf4/ncdf4/man/ncvar_def.Rd:114: file link 'ncvar_put' in package 'ncdf4' does not exist and so has been treated as a topic ncvar_get html Rd warning: /builddir/build/BUILD/ncdf4/ncdf4/man/ncvar_get.Rd:80: file link 'ncvar_put' in package 'ncdf4' does not exist and so has been treated as a topic ncvar_rename html print.ncdf4 html BUILDSTDERR: ** building package indices BUILDSTDERR: ** testing if installed package can be loaded BUILDSTDERR: * DONE (ncdf4) + test -d ncdf4/src + cd ncdf4/src + rm -f ncdf.o ncdf4.so + rm -f /builddir/build/BUILDROOT/R-ncdf4-1.16-2.fc30.aarch64/usr/lib64/R/library/R.css + chrpath -d /builddir/build/BUILDROOT/R-ncdf4-1.16-2.fc30.aarch64/usr/lib64/R/library/ncdf4/libs/ncdf4.so + /usr/lib/rpm/find-debuginfo.sh -j4 --strict-build-id -m -i --build-id-seed 1.16-2.fc30 --unique-debug-suffix -1.16-2.fc30.aarch64 --unique-debug-src-base R-ncdf4-1.16-2.fc30.aarch64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 50000000 -S debugsourcefiles.list /builddir/build/BUILD/ncdf4 explicitly decompress any DWARF compressed ELF sections in /builddir/build/BUILDROOT/R-ncdf4-1.16-2.fc30.aarch64/usr/lib64/R/library/ncdf4/libs/ncdf4.so extracting debug info from /builddir/build/BUILDROOT/R-ncdf4-1.16-2.fc30.aarch64/usr/lib64/R/library/ncdf4/libs/ncdf4.so /usr/lib/rpm/sepdebugcrcfix: Updated 1 CRC32s, 0 CRC32s did match. BUILDSTDERR: 176 blocks + /usr/lib/rpm/check-buildroot + /usr/lib/rpm/redhat/brp-ldconfig + /usr/lib/rpm/brp-compress + /usr/lib/rpm/brp-strip-static-archive /usr/bin/strip + /usr/lib/rpm/brp-python-bytecompile /usr/bin/python 1 0 + /usr/lib/rpm/brp-python-hardlink + /usr/lib/rpm/redhat/brp-mangle-shebangs Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.oCuUpZ + umask 022 + cd /builddir/build/BUILD + cd ncdf4 + /usr/bin/R CMD check ncdf4 * using log directory '/builddir/build/BUILD/ncdf4/ncdf4.Rcheck' * using R version 3.5.2 (2018-12-20) * using platform: aarch64-redhat-linux-gnu (64-bit) * using session charset: ASCII * checking for file 'ncdf4/DESCRIPTION' ... OK * this is package 'ncdf4' version '1.16' * checking package namespace information ... OK BUILDSTDERR: * checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib: BUILDSTDERR: cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES' BUILDSTDERR: Warning: unable to access index for repository https://bioconductor.org/packages/3.8/bioc/src/contrib: BUILDSTDERR: cannot open URL 'https://bioconductor.org/packages/3.8/bioc/src/contrib/PACKAGES' BUILDSTDERR: Warning: unable to access index for repository https://bioconductor.org/packages/3.8/data/annotation/src/contrib: BUILDSTDERR: cannot open URL 'https://bioconductor.org/packages/3.8/data/annotation/src/contrib/PACKAGES' BUILDSTDERR: Warning: unable to access index for repository https://bioconductor.org/packages/3.8/data/experiment/src/contrib: BUILDSTDERR: cannot open URL 'https://bioconductor.org/packages/3.8/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 ... OK * checking whether package 'ncdf4' can be installed ... OK * 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 ... WARNING Subdirectory 'inst' contains no files. * 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 ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... 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 compiled code ... OK * checking examples ... OK * checking PDF version of manual ... OK * DONE Status: 1 WARNING, 1 NOTE BUILDSTDERR: See BUILDSTDERR: '/builddir/build/BUILD/ncdf4/ncdf4.Rcheck/00check.log' BUILDSTDERR: for details. + exit 0 Processing files: R-ncdf4-1.16-2.fc30.aarch64 Provides: R-ncdf4 = 1.16-2.fc30 R-ncdf4(aarch-64) = 1.16-2.fc30 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: ld-linux-aarch64.so.1()(64bit) ld-linux-aarch64.so.1(GLIBC_2.17)(64bit) libR.so()(64bit) libc.so.6()(64bit) libc.so.6(GLIBC_2.17)(64bit) libnetcdf.so.11()(64bit) rtld(GNU_HASH) Processing files: R-ncdf4-debugsource-1.16-2.fc30.aarch64 Provides: R-ncdf4-debugsource = 1.16-2.fc30 R-ncdf4-debugsource(aarch-64) = 1.16-2.fc30 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: R-ncdf4-debuginfo-1.16-2.fc30.aarch64 Provides: R-ncdf4-debuginfo = 1.16-2.fc30 R-ncdf4-debuginfo(aarch-64) = 1.16-2.fc30 debuginfo(build-id) = 5c3b8bbb05ba14deda2d32b4b7568aa89c3fd57a Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: R-ncdf4-debugsource(aarch-64) = 1.16-2.fc30 Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/R-ncdf4-1.16-2.fc30.aarch64 Wrote: /builddir/build/RPMS/R-ncdf4-1.16-2.fc30.aarch64.rpm Wrote: /builddir/build/RPMS/R-ncdf4-debugsource-1.16-2.fc30.aarch64.rpm Wrote: /builddir/build/RPMS/R-ncdf4-debuginfo-1.16-2.fc30.aarch64.rpm Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.98OKgu + umask 022 + cd /builddir/build/BUILD + cd ncdf4 + /usr/bin/rm -rf /builddir/build/BUILDROOT/R-ncdf4-1.16-2.fc30.aarch64 + exit 0 Child return code was: 0