Mock Version: 2.12 ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target x86_64 --nodeps /builddir/build/SPECS/R-pbdBASE.spec'], chrootPath='/var/lib/mock/epel-7-x86_64-1629815808.804878/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=1000gid=135user='mockbuild'nspawn_args=['--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.m7s7qo66:/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.m7s7qo66:/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', '54055d7977ad41109422e93181e8205a', '-D', '/var/lib/mock/epel-7-x86_64-1629815808.804878/root', '-a', '-u', 'mockbuild', '--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.m7s7qo66:/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-pbdBASE.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 Wrote: /builddir/build/SRPMS/R-pbdBASE-0.5.3-2.el7.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-pbdBASE.spec'], chrootPath='/var/lib/mock/epel-7-x86_64-1629815808.804878/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=1000gid=135user='mockbuild'nspawn_args=['--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.m7s7qo66:/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.m7s7qo66:/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', 'b0c0d343b7604126b179a51b25b6a41e', '-D', '/var/lib/mock/epel-7-x86_64-1629815808.804878/root', '-a', '-u', 'mockbuild', '--capability=cap_ipc_lock', '--rlimit=RLIMIT_NOFILE=10240', '--capability=cap_ipc_lock', '--bind=/tmp/mock-resolv.m7s7qo66:/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-pbdBASE.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 Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.g9xVOA + umask 022 + cd /builddir/build/BUILD + cd /builddir/build/BUILD + rm -rf pbdBASE + /usr/bin/mkdir -p pbdBASE + cd pbdBASE + /usr/bin/gzip -dc /builddir/build/SOURCES/pbdBASE_0.5-3.tar.gz + /usr/bin/tar -xf - + STATUS=0 + '[' 0 -ne 0 ']' + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w . + unzip /builddir/build/SOURCES/tocbibind.zip Archive: /builddir/build/SOURCES/tocbibind.zip creating: tocbibind/ inflating: tocbibind/README inflating: tocbibind/tocbibind.dtx inflating: tocbibind/tocbibind.ins inflating: tocbibind/tocbibind.pdf + cd tocbibind + latex tocbibind.ins This is pdfTeX, Version 3.1415926-2.5-1.40.14 (TeX Live 2013) restricted \write18 enabled. entering extended mode (./tocbibind.ins LaTeX2e <2011/06/27> Babel and hyphenation patterns for english, dumylang, nohyphenation, lo aded. (/usr/share/texlive/texmf-dist/tex/latex/base/docstrip.tex Utility: `docstrip' 2.5d <2005/07/29> English documentation <1999/03/31> ********************************************************** * This program converts documented macro-files into fast * * loadable files by stripping off (nearly) all comments! * ********************************************************** ******************************************************** * No Configuration file found, using default settings. * ******************************************************** (./tocbibind.ins *** Generating the LaTeX2e package files *** Generating file(s) ./tocbibind.sty Processing file tocbibind.dtx (usc) -> tocbibind.sty File tocbibind.dtx ended by \endinput. Lines processed: 1164 Comments removed: 860 Comments passed: 0 Codelines passed: 300 *********************************************************** * * To finish the installation you have to move the following * file(s) into a directory searched by TeX: * * tocbibind.sty * * * To produce the documentation run the files ending with * `.dtx' through LaTeX. * Process any name.idx file by: * makeindex -s gind.ist name * Process any name.glo file by: * makeindex -s gglo.ist -o name.gls name.glo * * Happy TeXing *********************************************************** ) ) ) No pages of output. Transcript written on tocbibind.log. + exit 0 Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.e0XfBR + umask 022 + cd /builddir/build/BUILD + cd pbdBASE + exit 0 Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.ICy2n8 + umask 022 + cd /builddir/build/BUILD + '[' /builddir/build/BUILDROOT/R-pbdBASE-0.5.3-2.el7.x86_64 '!=' / ']' + rm -rf /builddir/build/BUILDROOT/R-pbdBASE-0.5.3-2.el7.x86_64 ++ dirname /builddir/build/BUILDROOT/R-pbdBASE-0.5.3-2.el7.x86_64 + mkdir -p /builddir/build/BUILDROOT + mkdir /builddir/build/BUILDROOT/R-pbdBASE-0.5.3-2.el7.x86_64 + cd pbdBASE + mkdir -p /builddir/build/BUILDROOT/R-pbdBASE-0.5.3-2.el7.x86_64/usr/lib64/R/library + . /etc/profile.d/modules.sh ++++ /bin/ps -p 36 -ocomm= +++ /bin/basename sh ++ shell=sh ++ '[' -f /usr/share/Modules/init/sh ']' ++ . /usr/share/Modules/init/sh +++ MODULESHOME=/usr/share/Modules +++ export MODULESHOME +++ '[' '' = '' ']' +++ LOADEDMODULES= +++ export LOADEDMODULES +++ '[' /usr/share/Modules/modulefiles:/etc/modulefiles = '' ']' + module load mpi/openmpi-x86_64 ++ /usr/bin/modulecmd sh load mpi/openmpi-x86_64 + eval LD_LIBRARY_PATH=/usr/lib64/openmpi/lib ';export' 'LD_LIBRARY_PATH;LOADEDMODULES=mpi/openmpi-x86_64' ';export' 'LOADEDMODULES;MANPATH=/usr/share/man/openmpi-x86_64:/usr/share/man:/usr/local/share/man' ';export' 'MANPATH;MPI_BIN=/usr/lib64/openmpi/bin' ';export' 'MPI_BIN;MPI_COMPILER=openmpi-x86_64' ';export' 'MPI_COMPILER;MPI_FORTRAN_MOD_DIR=/usr/lib64/gfortran/modules/openmpi-x86_64' ';export' 'MPI_FORTRAN_MOD_DIR;MPI_HOME=/usr/lib64/openmpi' ';export' 'MPI_HOME;MPI_INCLUDE=/usr/include/openmpi-x86_64' ';export' 'MPI_INCLUDE;MPI_LIB=/usr/lib64/openmpi/lib' ';export' 'MPI_LIB;MPI_MAN=/usr/share/man/openmpi-x86_64' ';export' 'MPI_MAN;MPI_PYTHON_SITEARCH=/usr/lib64/python2.7/site-packages/openmpi' ';export' 'MPI_PYTHON_SITEARCH;MPI_SUFFIX=_openmpi' ';export' 'MPI_SUFFIX;MPI_SYSCONFIG=/etc/openmpi-x86_64' ';export' 'MPI_SYSCONFIG;PATH=/usr/lib64/openmpi/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin:/builddir/.local/bin:/builddir/bin' ';export' 'PATH;PYTHONPATH=/usr/lib64/python2.7/site-packages/openmpi' ';export' 'PYTHONPATH;_LMFILES_=/etc/modulefiles/mpi/openmpi-x86_64' ';export' '_LMFILES_;' ++ LD_LIBRARY_PATH=/usr/lib64/openmpi/lib ++ export LD_LIBRARY_PATH ++ LOADEDMODULES=mpi/openmpi-x86_64 ++ export LOADEDMODULES ++ MANPATH=/usr/share/man/openmpi-x86_64:/usr/share/man:/usr/local/share/man ++ export MANPATH ++ MPI_BIN=/usr/lib64/openmpi/bin ++ export MPI_BIN ++ MPI_COMPILER=openmpi-x86_64 ++ export MPI_COMPILER ++ MPI_FORTRAN_MOD_DIR=/usr/lib64/gfortran/modules/openmpi-x86_64 ++ export MPI_FORTRAN_MOD_DIR ++ MPI_HOME=/usr/lib64/openmpi ++ export MPI_HOME ++ MPI_INCLUDE=/usr/include/openmpi-x86_64 ++ export MPI_INCLUDE ++ MPI_LIB=/usr/lib64/openmpi/lib ++ export MPI_LIB ++ MPI_MAN=/usr/share/man/openmpi-x86_64 ++ export MPI_MAN ++ MPI_PYTHON_SITEARCH=/usr/lib64/python2.7/site-packages/openmpi ++ export MPI_PYTHON_SITEARCH ++ MPI_SUFFIX=_openmpi ++ export MPI_SUFFIX ++ MPI_SYSCONFIG=/etc/openmpi-x86_64 ++ export MPI_SYSCONFIG ++ PATH=/usr/lib64/openmpi/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin:/builddir/.local/bin:/builddir/bin ++ export PATH ++ PYTHONPATH=/usr/lib64/python2.7/site-packages/openmpi ++ export PYTHONPATH ++ _LMFILES_=/etc/modulefiles/mpi/openmpi-x86_64 ++ export _LMFILES_ + export 'CFLAGS= -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic' + CFLAGS=' -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic' + OMPI_MCA_rmaps_base_oversubscribe=1 + OMPI_MCA_orte_rsh_agent=/bin/false ++ pwd + TEXINPUTS=.:/builddir/build/BUILD/pbdBASE/tocbibind: + R CMD INSTALL -l /builddir/build/BUILDROOT/R-pbdBASE-0.5.3-2.el7.x86_64/usr/lib64/R/library pbdBASE * installing *source* package 'pbdBASE' ... ** package 'pbdBASE' successfully unpacked and MD5 sums checked ** using staged installation checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for gcc option to accept ISO C99... -std=gnu99 Error in tools::file_path_as_absolute(system.file(lib.file, package = package)) : file '' does not exist Calls: get.lib -> Execution halted ****************** Results of pbdBASE package configure ***************** >> EXT_LDFLAGS = -lscalapack -lmpiblacs -lopenblas >> EXPORT_BLACS = export_blacs/pkg_tools.o >> R_SLAP = >> SLAP_LDFLAGS = -lscalapack -lmpiblacs -lopenblas >> SPMD_CPPFLAGS = -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI >> SPMD_LDFLAGS = -L/usr/lib64/openmpi/lib -lmpi -lutil -lpthread ************************************************************************* configure: creating ./config.status config.status: creating src/Makevars ** libs echo "SLAP_LDFLAGS = -lscalapack -lmpiblacs -lopenblas" >> Makeconf echo "SPMD_CPPFLAGS = -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI" >> Makeconf echo "SPMD_LDFLAGS = -L/usr/lib64/openmpi/lib -lmpi -lutil -lpthread" >> Makeconf echo "GFORTRAN_FLAGS = -DUSE_FC_LEN_T" >> Makeconf echo "PKG_CPPFLAGS = -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -I../inst/RNACI -DUSE_FC_LEN_T" >> Makeconf echo "PKG_CFLAGS = " >> Makeconf echo "PKG_FFLAGS = " >> Makeconf echo "PKG_LIBS = -lscalapack -lmpiblacs -lopenblas -lgfortran -lm -lquadmath -L/usr/lib64/openmpi/lib -lmpi -lutil -lpthread" >> Makeconf gfortran -m64 -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -I/usr/lib64/gfortran/modules -c base/bprnt.f -o base/bprnt.o base/bprnt.f:13.39: $ CMATNM, NOUT, WORK ) 1 Warning: Unused dummy argument 'nout' at (1) gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -I../inst/RNACI -DUSE_FC_LEN_T -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c base/bprnt_c.c -o base/bprnt_c.o gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -I../inst/RNACI -DUSE_FC_LEN_T -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c base/expm/pade_coefs.c -o base/expm/pade_coefs.o gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -I../inst/RNACI -DUSE_FC_LEN_T -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c base/expm/matexp.c -o base/expm/matexp.o gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -I../inst/RNACI -DUSE_FC_LEN_T -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c base/expm/p_matexp.c -o base/expm/p_matexp.o gfortran -m64 -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c base/linalg/norms.f90 -o base/linalg/norms.o gfortran -m64 -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c base/linalg/pcrossprod.f90 -o base/linalg/pcrossprod.o gfortran -m64 -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c base/linalg/pinverse.f90 -o base/linalg/pinverse.o gfortran -m64 -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c base/linalg/prblas.f90 -o base/linalg/prblas.o gfortran -m64 -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -I/usr/lib64/gfortran/modules -c base/linalg/plm.f -o base/linalg/plm.o base/linalg/plm.f: In function 'rpdgeqpf': base/linalg/plm.f:450:0: warning: 'jb' may be used uninitialized in this function [-Wmaybe-uninitialized] DO 60 KK = 0, JB-1 ^ base/linalg/plm.f:447:0: warning: 'nq0' may be used uninitialized in this function [-Wmaybe-uninitialized] IPW = IPN + NQ0 + NQ ^ base/linalg/plm.f:401:0: warning: 'nq' may be used uninitialized in this function [-Wmaybe-uninitialized] $ NQ = NQ - ICOFF ^ base/linalg/plm.f:708:0: warning: 'lwmin' may be used uninitialized in this function [-Wmaybe-uninitialized] WORK( 1 ) = DBLE( LWMIN ) ^ base/linalg/plm.f:387:0: warning: 'lquery' may be used uninitialized in this function [-Wmaybe-uninitialized] ELSE IF( LQUERY ) THEN ^ base/linalg/plm.f:399:0: warning: 'iroff' may be used uninitialized in this function [-Wmaybe-uninitialized] $ MP = MP - IROFF ^ base/linalg/plm.f:401:0: warning: 'icoff' may be used uninitialized in this function [-Wmaybe-uninitialized] $ NQ = NQ - ICOFF ^ base/linalg/plm.f: In function 'rpdormqr': base/linalg/plm.f:264:0: warning: 'lwmin' may be used uninitialized in this function [-Wmaybe-uninitialized] WORK( 1 ) = DBLE( LWMIN ) ^ base/linalg/plm.f:180:0: warning: 'lquery' may be used uninitialized in this function [-Wmaybe-uninitialized] ELSE IF( LQUERY ) THEN ^ base/linalg/plm.f: In function 'rpdgels': base/linalg/plm.f:954:0: warning: 'tpsd' may be used uninitialized in this function [-Wmaybe-uninitialized] IF( TPSD ) ^ base/linalg/plm.f:1052:0: warning: 'lwmin' may be used uninitialized in this function [-Wmaybe-uninitialized] WORK( 1 ) = DBLE( LWMIN ) ^ base/linalg/plm.f:987:0: warning: 'ltau' may be used uninitialized in this function [-Wmaybe-uninitialized] $ TAU, WORK( IPW ), LWORK-LTAU, RANK, INFO) ^ base/linalg/plm.f:907:0: warning: 'lquery' may be used uninitialized in this function [-Wmaybe-uninitialized] ELSE IF( LQUERY ) THEN ^ gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -I../inst/RNACI -DUSE_FC_LEN_T -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c coords.c -o coords.o gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -I../inst/RNACI -DUSE_FC_LEN_T -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c comm_utils.c -o comm_utils.o gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -I../inst/RNACI -DUSE_FC_LEN_T -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c export_blacs/pkg_tools.c -o export_blacs/pkg_tools.o gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -I../inst/RNACI -DUSE_FC_LEN_T -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c base_mpi_blacs.c -o base_mpi_blacs.o gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -I../inst/RNACI -DUSE_FC_LEN_T -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c base_mpi_blacs_reductions.c -o base_mpi_blacs_reductions.o gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -I../inst/RNACI -DUSE_FC_LEN_T -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c base_pblas_level3.c -o base_pblas_level3.o gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -I../inst/RNACI -DUSE_FC_LEN_T -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c base_plinalg.c -o base_plinalg.o gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -I../inst/RNACI -DUSE_FC_LEN_T -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c base_prblas.c -o base_prblas.o gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -I../inst/RNACI -DUSE_FC_LEN_T -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c base_putil.c -o base_putil.o gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -I../inst/RNACI -DUSE_FC_LEN_T -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c base_scalapack.c -o base_scalapack.o gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -I../inst/RNACI -DUSE_FC_LEN_T -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c base_variance.c -o base_variance.o gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -I../inst/RNACI -DUSE_FC_LEN_T -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c dims.c -o dims.o gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -I../inst/RNACI -DUSE_FC_LEN_T -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c lm.c -o lm.o gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -I../inst/RNACI -DUSE_FC_LEN_T -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c matexp.c -o matexp.o gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -I../inst/RNACI -DUSE_FC_LEN_T -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c pbdBASE_native.c -o pbdBASE_native.o gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -I../inst/RNACI -DUSE_FC_LEN_T -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c qr.c -o qr.o gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -I../inst/RNACI -DUSE_FC_LEN_T -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c redist.c -o redist.o gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -I../inst/RNACI -DUSE_FC_LEN_T -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c svd.c -o svd.o gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -I../inst/RNACI -DUSE_FC_LEN_T -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c utility.c -o utility.o gfortran -m64 -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c base/stats/variance.f90 -o base/stats/variance.o gfortran -m64 -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c utils/fpmod.f90 -o utils/fpmod.o utils/fpmod.f90: In function 'fpmod': utils/fpmod.f90:10:0: warning: 'nan' may be used uninitialized in this function [-Wmaybe-uninitialized] ret = nan !ieee_value(1.0d0, ieee_quiet_nan) ^ gfortran -m64 -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c utils/swaps.f90 -o utils/swaps.o gfortran -m64 -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c utils/quicksort_utils.f90 -o utils/quicksort_utils.o gfortran -m64 -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c utils/signs.f90 -o utils/signs.o gfortran -m64 -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c utils/sorts.f90 -o utils/sorts.o gfortran -m64 -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c utils/strings.f90 -o utils/strings.o gfortran -m64 -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c base/utils/blacs_util.f90 -o base/utils/blacs_util.o gfortran -m64 -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -I/usr/lib64/gfortran/modules -c base/utils/dmat_redist.f -o base/utils/dmat_redist.o gfortran -m64 -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c base/utils/indices.f90 -o base/utils/indices.o gfortran -m64 -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -I/usr/lib64/gfortran/modules -c base/utils/putil.f -o base/utils/putil.o base/utils/putil.f:307.30: SUBROUTINE PDGDGTK(X, IX, JX, DESCX, DIAG, RDEST, CDEST) 1 Warning: Unused dummy argument 'ix' at (1) base/utils/putil.f:307.34: SUBROUTINE PDGDGTK(X, IX, JX, DESCX, DIAG, RDEST, CDEST) 1 Warning: Unused dummy argument 'jx' at (1) base/utils/putil.f:357.31: SUBROUTINE PDDIAGMK(X, IX, JX, DESCX, DIAG, LDIAG) 1 Warning: Unused dummy argument 'ix' at (1) base/utils/putil.f:357.35: SUBROUTINE PDDIAGMK(X, IX, JX, DESCX, DIAG, LDIAG) 1 Warning: Unused dummy argument 'jx' at (1) gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -I../inst/RNACI -DUSE_FC_LEN_T -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c base/utils/redist.c -o base/utils/redist.o gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I/usr/include/openmpi-x86_64 -DMPI2 -DOPENMPI -I../inst/RNACI -DUSE_FC_LEN_T -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c base/utils/scale.c -o base/utils/scale.o gfortran -m64 -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c base/utils/special.f90 -o base/utils/special.o gcc -m64 -std=gnu99 -shared -L/usr/lib64/R/lib -Wl,-z,relro -o pbdBASE.so base/bprnt.o base/bprnt_c.o base/expm/pade_coefs.o base/expm/matexp.o base/expm/p_matexp.o base/linalg/norms.o base/linalg/pcrossprod.o base/linalg/pinverse.o base/linalg/prblas.o base/linalg/plm.o coords.o comm_utils.o export_blacs/pkg_tools.o base_mpi_blacs.o base_mpi_blacs_reductions.o base_pblas_level3.o base_plinalg.o base_prblas.o base_putil.o base_scalapack.o base_variance.o dims.o lm.o matexp.o pbdBASE_native.o qr.o redist.o svd.o utility.o base/stats/variance.o utils/fpmod.o utils/quicksort_utils.o utils/signs.o utils/sorts.o utils/strings.o utils/swaps.o base/utils/blacs_util.o base/utils/dmat_redist.o base/utils/indices.o base/utils/putil.o base/utils/redist.o base/utils/scale.o base/utils/special.o -lscalapack -lmpiblacs -lopenblas -lgfortran -lm -lquadmath -L/usr/lib64/openmpi/lib -lmpi -lutil -lpthread -L/usr/lib64/R/lib -lR installing via 'install.libs.R' to /builddir/build/BUILDROOT/R-pbdBASE-0.5.3-2.el7.x86_64/usr/lib64/R/library/00LOCK-pbdBASE/00new/pbdBASE ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'pbdBASE' finding HTML links ... done BASE-Global-Environment html base.blacs_gridinit html base.crossprod html base.descinit html base.det html base.dhilbmk html base.dim0 html base.free_blacs_system_handle html base.indxg2p html base.matexp html base.maxdim html base.minctxt html base.nbd html base.numroc html base.ownany html base.p_matexp_pade_wrap html base.p_matpow_by_squaring_wrap html base.pdchtri html base.pdclvar html base.pdhilbmk html base.pdmkcpn1 html base.pdmvsum html base.pdsweep html base.procgrid html base.rcolcpy html base.rcolcpy2 html base.redist html base.rl2blas html base.rl2insert html base.rpdgecon html base.rpdgelqf html base.rpdgels html base.rpdgemm html base.rpdgemr2d html base.rpdgeqpf html base.rpdgesv html base.rpdgesvd html base.rpdgetrf html base.rpdgetri html base.rpdlange html base.rpdlaprnt html base.rpdorglq html base.rpdorgqr html base.rpdormqr html base.rpdpotrf html base.rpdsyevr html base.rpdsyevx html base.rpdtran html base.rpdtrcon html base.rrowcpy html base.rrowcpy2 html base.tri2zero html base.valid_context html blacs-max html blacs-min html blacs-p2p html blacs-sums html blacs_apts html blacsexit html coords html coordspair html diag html finalizer html g2l_coord html g2lcoord html get.comm.from.ICTXT html gridexit html gridinfo html gridinit html init.grid html l2g_coord html lclgblmat html numroc2 html pbdBASE-package html pcoords html sys2blacs.handle html ** building package indices ** installing vignettes 'pbdBASE-guide.Rnw' ** 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 (pbdBASE) + test -d pbdBASE/src + cd pbdBASE/src + rm -f base_mpi_blacs.o base_mpi_blacs_reductions.o base_pblas_level3.o base_plinalg.o base_prblas.o base_putil.o base_scalapack.o base_variance.o comm_utils.o coords.o dims.o lm.o matexp.o pbdBASE_native.o qr.o redist.o svd.o utility.o pbdBASE.so + rm -f /builddir/build/BUILDROOT/R-pbdBASE-0.5.3-2.el7.x86_64/usr/lib64/R/library/R.css + /usr/lib/rpm/find-debuginfo.sh --strict-build-id -m --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 110000000 /builddir/build/BUILD/pbdBASE extracting debug info from /builddir/build/BUILDROOT/R-pbdBASE-0.5.3-2.el7.x86_64/usr/lib64/R/library/pbdBASE/libs/pbdBASE.so dwz: Too few files for multifile optimization /usr/lib/rpm/sepdebugcrcfix: Updated 1 CRC32s, 0 CRC32s did match. cpio: pbdBASE/pbdBASE/src/include/insertionsort_generic.inc: Cannot stat: No such file or directory cpio: pbdBASE/pbdBASE/src/include/quicksort_median_of_3_generic.inc: Cannot stat: No such file or directory cpio: pbdBASE/pbdBASE/src/include/quicksort_partition_generic.inc: Cannot stat: No such file or directory cpio: pbdBASE/pbdBASE/src/include/quicksort_r_generic.inc: Cannot stat: No such file or directory cpio: pbdBASE/pbdBASE/src/include/swap_generic.inc: Cannot stat: No such file or directory 486 blocks + /usr/lib/rpm/check-buildroot + /usr/lib/rpm/redhat/brp-compress + /usr/lib/rpm/redhat/brp-strip-static-archive /usr/bin/strip + /usr/lib/rpm/brp-python-bytecompile /usr/bin/python 1 + /usr/lib/rpm/redhat/brp-python-hardlink + /usr/lib/rpm/redhat/brp-java-repack-jars Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.yfamUN + umask 022 + cd /builddir/build/BUILD + cd pbdBASE + . /etc/profile.d/modules.sh ++++ /bin/ps -p 718 -ocomm= +++ /bin/basename sh ++ shell=sh ++ '[' -f /usr/share/Modules/init/sh ']' ++ . /usr/share/Modules/init/sh +++ MODULESHOME=/usr/share/Modules +++ export MODULESHOME +++ '[' '' = '' ']' +++ LOADEDMODULES= +++ export LOADEDMODULES +++ '[' /usr/share/Modules/modulefiles:/etc/modulefiles = '' ']' + module load mpi/openmpi-x86_64 ++ /usr/bin/modulecmd sh load mpi/openmpi-x86_64 + eval LD_LIBRARY_PATH=/usr/lib64/openmpi/lib ';export' 'LD_LIBRARY_PATH;LOADEDMODULES=mpi/openmpi-x86_64' ';export' 'LOADEDMODULES;MANPATH=/usr/share/man/openmpi-x86_64:/usr/share/man:/usr/local/share/man' ';export' 'MANPATH;MPI_BIN=/usr/lib64/openmpi/bin' ';export' 'MPI_BIN;MPI_COMPILER=openmpi-x86_64' ';export' 'MPI_COMPILER;MPI_FORTRAN_MOD_DIR=/usr/lib64/gfortran/modules/openmpi-x86_64' ';export' 'MPI_FORTRAN_MOD_DIR;MPI_HOME=/usr/lib64/openmpi' ';export' 'MPI_HOME;MPI_INCLUDE=/usr/include/openmpi-x86_64' ';export' 'MPI_INCLUDE;MPI_LIB=/usr/lib64/openmpi/lib' ';export' 'MPI_LIB;MPI_MAN=/usr/share/man/openmpi-x86_64' ';export' 'MPI_MAN;MPI_PYTHON_SITEARCH=/usr/lib64/python2.7/site-packages/openmpi' ';export' 'MPI_PYTHON_SITEARCH;MPI_SUFFIX=_openmpi' ';export' 'MPI_SUFFIX;MPI_SYSCONFIG=/etc/openmpi-x86_64' ';export' 'MPI_SYSCONFIG;PATH=/usr/lib64/openmpi/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin:/builddir/.local/bin:/builddir/bin' ';export' 'PATH;PYTHONPATH=/usr/lib64/python2.7/site-packages/openmpi' ';export' 'PYTHONPATH;_LMFILES_=/etc/modulefiles/mpi/openmpi-x86_64' ';export' '_LMFILES_;' ++ LD_LIBRARY_PATH=/usr/lib64/openmpi/lib ++ export LD_LIBRARY_PATH ++ LOADEDMODULES=mpi/openmpi-x86_64 ++ export LOADEDMODULES ++ MANPATH=/usr/share/man/openmpi-x86_64:/usr/share/man:/usr/local/share/man ++ export MANPATH ++ MPI_BIN=/usr/lib64/openmpi/bin ++ export MPI_BIN ++ MPI_COMPILER=openmpi-x86_64 ++ export MPI_COMPILER ++ MPI_FORTRAN_MOD_DIR=/usr/lib64/gfortran/modules/openmpi-x86_64 ++ export MPI_FORTRAN_MOD_DIR ++ MPI_HOME=/usr/lib64/openmpi ++ export MPI_HOME ++ MPI_INCLUDE=/usr/include/openmpi-x86_64 ++ export MPI_INCLUDE ++ MPI_LIB=/usr/lib64/openmpi/lib ++ export MPI_LIB ++ MPI_MAN=/usr/share/man/openmpi-x86_64 ++ export MPI_MAN ++ MPI_PYTHON_SITEARCH=/usr/lib64/python2.7/site-packages/openmpi ++ export MPI_PYTHON_SITEARCH ++ MPI_SUFFIX=_openmpi ++ export MPI_SUFFIX ++ MPI_SYSCONFIG=/etc/openmpi-x86_64 ++ export MPI_SYSCONFIG ++ PATH=/usr/lib64/openmpi/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/sbin:/builddir/.local/bin:/builddir/bin ++ export PATH ++ PYTHONPATH=/usr/lib64/python2.7/site-packages/openmpi ++ export PYTHONPATH ++ _LMFILES_=/etc/modulefiles/mpi/openmpi-x86_64 ++ export _LMFILES_ + export 'CFLAGS= -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic' + CFLAGS=' -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic' + OMPI_MCA_rmaps_base_oversubscribe=1 + OMPI_MCA_orte_rsh_agent=/bin/false ++ pwd + TEXINPUTS=.:/builddir/build/BUILD/pbdBASE/tocbibind: + R CMD check pbdBASE * using log directory '/builddir/build/BUILD/pbdBASE/pbdBASE.Rcheck' * using R version 3.6.0 (2019-04-26) * using platform: x86_64-redhat-linux-gnu (64-bit) * using session charset: ASCII * checking for file 'pbdBASE/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'pbdBASE' version '0.5-3' * 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/3.9/bioc/src/contrib: cannot open URL 'https://bioconductor.org/packages/3.9/bioc/src/contrib/PACKAGES' Warning: unable to access index for repository https://bioconductor.org/packages/3.9/data/annotation/src/contrib: cannot open URL 'https://bioconductor.org/packages/3.9/data/annotation/src/contrib/PACKAGES' Warning: unable to access index for repository https://bioconductor.org/packages/3.9/data/experiment/src/contrib: cannot open URL 'https://bioconductor.org/packages/3.9/data/experiment/src/contrib/PACKAGES' OK * checking if this is a source package ... NOTE Found the following apparent object files/libraries: src/base/bprnt.o src/base/bprnt_c.o src/base/expm/matexp.o src/base/expm/p_matexp.o src/base/expm/pade_coefs.o src/base/linalg/norms.o src/base/linalg/pcrossprod.o src/base/linalg/pinverse.o src/base/linalg/plm.o src/base/linalg/prblas.o src/base/stats/variance.o src/base/utils/blacs_util.o src/base/utils/dmat_redist.o src/base/utils/indices.o src/base/utils/putil.o src/base/utils/redist.o src/base/utils/scale.o src/base/utils/special.o src/export_blacs/pkg_tools.o src/utils/fpmod.o src/utils/quicksort_utils.o src/utils/signs.o src/utils/sorts.o src/utils/strings.o src/utils/swaps.o Object files/libraries should not be included in a source package. * 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 'pbdBASE' 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 ... 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 ... 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 installed files from 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in 'inst/doc' ... OK * checking running R code from vignettes ... 'pbdBASE-guide.Rnw' ... OK NONE * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 2 NOTEs See '/builddir/build/BUILD/pbdBASE/pbdBASE.Rcheck/00check.log' for details. + exit 0 Processing files: R-pbdBASE-0.5.3-2.el7.x86_64 Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.kW1xCH + umask 022 + cd /builddir/build/BUILD + cd pbdBASE + LICENSEDIR=/builddir/build/BUILDROOT/R-pbdBASE-0.5.3-2.el7.x86_64/usr/share/licenses/R-pbdBASE-0.5.3 + export LICENSEDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/R-pbdBASE-0.5.3-2.el7.x86_64/usr/share/licenses/R-pbdBASE-0.5.3 + cp -pr pbdBASE/COPYING /builddir/build/BUILDROOT/R-pbdBASE-0.5.3-2.el7.x86_64/usr/share/licenses/R-pbdBASE-0.5.3 + exit 0 Provides: R-pbdBASE = 0.5.3-2.el7 R-pbdBASE(x86-64) = 0.5.3-2.el7 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: 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) libgfortran.so.3()(64bit) libgfortran.so.3(GFORTRAN_1.0)(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.2.5)(64bit) libopenblas.so.0()(64bit) libpthread.so.0()(64bit) libquadmath.so.0()(64bit) libutil.so.1()(64bit) rtld(GNU_HASH) Processing files: R-pbdBASE-debuginfo-0.5.3-2.el7.x86_64 Provides: R-pbdBASE-debuginfo = 0.5.3-2.el7 R-pbdBASE-debuginfo(x86-64) = 0.5.3-2.el7 Requires(rpmlib): rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 rpmlib(CompressedFileNames) <= 3.0.4-1 Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/R-pbdBASE-0.5.3-2.el7.x86_64 Wrote: /builddir/build/RPMS/R-pbdBASE-0.5.3-2.el7.x86_64.rpm Wrote: /builddir/build/RPMS/R-pbdBASE-debuginfo-0.5.3-2.el7.x86_64.rpm Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.CRremq + umask 022 + cd /builddir/build/BUILD + cd pbdBASE + /usr/bin/rm -rf /builddir/build/BUILDROOT/R-pbdBASE-0.5.3-2.el7.x86_64 + exit 0 Child return code was: 0