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[NCO]install/make error

Dan_Yan
2013-03-21
2014-08-13
  • Dan_Yan
    Dan_Yan
    2013-03-21

    hello everyone,

    I am new user of NCO and I tried installing nco-4.2.6 in my computer(ubuntu),but when I type `make' to compile the package. it gave me errors:

    make  all-recursive
    make: Entering directory `/tmp/nco-4.2.6'
    Making all in data
    make: Entering directory `/tmp/nco-4.2.6/data'
    make: Nothing to be done for `all'.
    make: Leaving directory `/tmp/nco-4.2.6/data'
    Making all in src
    make: Entering directory `/tmp/nco-4.2.6/src'
    Making all in nco
    make: Entering directory `/tmp/nco-4.2.6/src/nco'
    /bin/bash ../../libtool -tag=CXX -tag=CC   -mode=link gcc -std=gnu99  -g -O2 -std=c99 -D_BSD_SOURCE -D_POSIX_SOURCE  -L/usr/local/netcdf/lib -lnetcdf -L/usr/local/netcdf/lib   -o ncap ncap_utl.o ncap.o ncap_yacc.o ncap_lex.o libnco.la -lm -lnetcdf -lnetcdf  -lcurl
    libtool: link: warning: library `/usr/local/netcdf/lib/libnetcdf.la' was moved.
    libtool: link: warning: library `/usr/local/netcdf/lib/libnetcdf.la' was moved.
    libtool: link: gcc -std=gnu99 -g -O2 -std=c99 -D_BSD_SOURCE -D_POSIX_SOURCE -o .libs/ncap ncap_utl.o ncap.o ncap_yacc.o ncap_lex.o  -L/usr/local/netcdf/lib ./.libs/libnco.so -lm /usr/local/netcdf/lib/libnetcdf.so /usr/lib/libcurl.so -Wl,-rpath -Wl,/usr/local/nco/lib -Wl,-rpath -Wl,/usr/local/netcdf/lib
    ./.libs/libnco.so: undefined reference to `nc_inq_unlimdims'
    ./.libs/libnco.so: undefined reference to `nc_inq_grpname_len'
    ./.libs/libnco.so: undefined reference to `nc_inq_ncid'
    ./.libs/libnco.so: undefined reference to `nc_inq_grp_full_ncid'
    ./.libs/libnco.so: undefined reference to `nc_def_var_chunking'
    ./.libs/libnco.so: undefined reference to `nc_def_var_deflate'
    ./.libs/libnco.so: undefined reference to `nc_inq_dimids'
    ./.libs/libnco.so: undefined reference to `nc_inq_var_chunking'
    ./.libs/libnco.so: undefined reference to `nc_inq_grps'
    ./.libs/libnco.so: undefined reference to `nc_def_grp'
    ./.libs/libnco.so: undefined reference to `nc_inq_grpname_full'
    ./.libs/libnco.so: undefined reference to `nc_inq_var_deflate'
    ./.libs/libnco.so: undefined reference to `nc_inq_grp_parent'
    ./.libs/libnco.so: undefined reference to `nc_inq_grpname'
    ./.libs/libnco.so: undefined reference to `nc_inq_var_fletcher32'
    ./.libs/libnco.so: undefined reference to `nc_inq_grp_ncid'
    ./.libs/libnco.so: undefined reference to `nc_inq_varids'
    collect2: ld returned 1 exit status
    make: ***  Error 1
    make: Leaving directory `/tmp/nco-4.2.6/src/nco'
    make: ***  Error 1
    make: Leaving directory `/tmp/nco-4.2.6/src'
    make: ***  Error 1
    make: Leaving directory `/tmp/nco-4.2.6'
    make: ***  Error 2

    I tried to solve this problem by myself, but i did not make it. hope someone could help me. thank you so much!

    Dan Yan

     
  • Pedro Vicente
    Pedro Vicente
    2013-03-21

    Hi Dan

    Those errors mean that the netCDF library was not found

    Did you install netCDF and to which location?

    To install netCDF in ubuntu the recommended way is to install from a package

    sudo aptitude install libnetcdf6 libnetcdf-dev netcdf-bin # netCDF and DAP

    that installs the library to

    /usr/lib,

    not to the location you have

    /usr/local/netcdf/lib

    you can also set any location you want with environment variables
    for example

    NETCDF_ROOT=/home/pvicente/libs/install/netcdf-4.2
    NETCDF_LIB=/home/pvicente/libs/install/netcdf-4.2/lib
    NETCDF4_ROOT=/home/pvicente/libs/install/netcdf-4.2
    NETCDF_INC=/home/pvicente/libs/install/netcdf-4.2/include

    Pedro

     
  • Dan_Yan
    Dan_Yan
    2013-03-25

    Hi  Pedro,

    Thank you very much for your help. problem solved.

    before install nco, i install all these packages:

    sudo apt-get install antlr libantlr-dev # ANTLR
    sudo apt-get install libcurl4-gnutls-dev libexpat1-dev libxml2-dev # DAP-prereqs
    sudo apt-get install bison flex gcc g++ # GNU toolchain
    sudo apt-get install gsl-bin libgsl0-dev # GSL
    sudo apt-get install libnetcdf6 libnetcdf-dev netcdf-bin # netCDF and DAP
    sudo apt-get install udunits-bin libudunits2-0 libudunits2-dev # UDUnits

    best regards,

    Dan

     
  • Hassan
    Hassan
    2013-08-14

    Dear Dan,
    I try to install nco and have exactly the same error as you mentioned. I try to figure it out by following the instructions as explained by Pedro and installed netcdf library as well. But still I have the same problem.

     
  • Pedro Vicente
    Pedro Vicente
    2013-08-14

    You can find the location of the netcdf library by typing

    which ncdump

    in ubuntu this is

    /usr/bin/ncdump

    make sure that your $PATH environment variable contains this location

    PATH=/usr/bin:$PATH
    export PATH

    Pedro

     
  • Hassan
    Hassan
    2013-08-15

    Dear Pedro
    Problem was with the path environment and now Its OK.
    Thanks for your guidance,
    Best Regards

     
  • Hassan
    Hassan
    2013-11-09

    Dear Pedro
    This time I am trying to instal NCO on my HP PC.
    After successful configuration, I have the following error while ruining the "make" command .
    [dupf@ln0 nco-4.3.7]$ make
    make all-recursive
    make[1]: Entering directory /home/dupf/nco-4.3.7' Making all in data make[2]: Entering directory/home/dupf/nco-4.3.7/data'
    /home/dupf/netcdf/bin/ncgen -o big.nc big.cdl
    /home/dupf/netcdf/bin/ncgen -o in_rec_zero.nc in_rec_zero.cdl
    /home/dupf/netcdf/bin/ncgen -k netCDF-4 -o in_grp.nc in_grp.cdl
    Undefined name: g1v1
    make[2]: [in_grp.nc] Error 1 (ignored)
    /home/dupf/netcdf/bin/ncgen -k netCDF-4 -o in_grp_1.nc in_grp_1.cdl
    Undefined name: var1
    make[2]: [in_grp_1.nc] Error 1 (ignored)
    /home/dupf/netcdf/bin/ncgen -k netCDF-4 -o in_grp_2.nc in_grp_2.cdl
    Undefined name: var1
    make[2]: [in_grp_2.nc] Error 1 (ignored)
    /home/dupf/netcdf/bin/ncgen -k netCDF-4 -o in_grp_3.nc in_grp_3.cdl
    Undefined or forward referenced dimension: rlev
    make[2]: [in_grp_3.nc] Error 1 (ignored)
    /home/dupf/netcdf/bin/ncgen -k netCDF-4 -o cmip5.nc cmip5.cdl
    Undefined or forward referenced dimension: time
    make[2]: [cmip5.nc] Error 1 (ignored)
    /home/dupf/netcdf/bin/ncgen -k netCDF-4 -o obs.nc obs.cdl
    ncgen: NetCDF: Unknown file format
    (genbin.c:59)
    make[2]: [obs.nc] Error 1 (ignored)
    /home/dupf/netcdf/bin/ncgen -k netCDF-4 -o mdl.nc mdl.cdl
    Undefined or forward referenced dimension: time
    make[2]: [mdl.nc] Error 1 (ignored)
    make[2]: Leaving directory /home/dupf/nco-4.3.7/data' Making all in src make[2]: Entering directory/home/dupf/nco-4.3.7/src'
    Making all in nco
    make[3]: Entering directory /home/dupf/nco-4.3.7/src/nco' /bin/sh ../../libtool --tag=CXX --tag=CC --mode=compile gcc -std=gnu99 -DHAVE_CONFIG_H -I. -I../.. -I/home/dupf/netcdf/include -I/home/dupf/netcdf/include -UNEED_NC_INQ_FORMAT -fPIC -std=c99 -D_BSD_SOURCE -D_POSIX_SOURCE -MT nco_att_utl.lo -MD -MP -MF .deps/nco_att_utl.Tpo -c -o nco_att_utl.lo nco_att_utl.c libtool: compile: gcc -std=gnu99 -DHAVE_CONFIG_H -I. -I../.. -I/home/dupf/netcdf/include -I/home/dupf/netcdf/include -UNEED_NC_INQ_FORMAT -fPIC -std=c99 -D_BSD_SOURCE -D_POSIX_SOURCE -MT nco_att_utl.lo -MD -MP -MF .deps/nco_att_utl.Tpo -c nco_att_utl.c -o nco_att_utl.o mv -f .deps/nco_att_utl.Tpo .deps/nco_att_utl.Plo /bin/sh ../../libtool --tag=CXX --tag=CC --mode=compile gcc -std=gnu99 -DHAVE_CONFIG_H -I. -I../.. -I/home/dupf/netcdf/include -I/home/dupf/netcdf/include -UNEED_NC_INQ_FORMAT -fPIC -std=c99 -D_BSD_SOURCE -D_POSIX_SOURCE -MT nco_aux.lo -MD -MP -MF .deps/nco_aux.Tpo -c -o nco_aux.lo nco_aux.c libtool: compile: gcc -std=gnu99 -DHAVE_CONFIG_H -I. -I../.. -I/home/dupf/netcdf/include -I/home/dupf/netcdf/include -UNEED_NC_INQ_FORMAT -fPIC -std=c99 -D_BSD_SOURCE -D_POSIX_SOURCE -MT nco_aux.lo -MD -MP -MF .deps/nco_aux.Tpo -c nco_aux.c -o nco_aux.o mv -f .deps/nco_aux.Tpo .deps/nco_aux.Plo /bin/sh ../../libtool --tag=CXX --tag=CC --mode=compile gcc -std=gnu99 -DHAVE_CONFIG_H -I. -I../.. -I/home/dupf/netcdf/include -I/home/dupf/netcdf/include -UNEED_NC_INQ_FORMAT -fPIC -std=c99 -D_BSD_SOURCE -D_POSIX_SOURCE -MT nco_bnr.lo -MD -MP -MF .deps/nco_bnr.Tpo -c -o nco_bnr.lo nco_bnr.c libtool: compile: gcc -std=gnu99 -DHAVE_CONFIG_H -I. -I../.. -I/home/dupf/netcdf/include -I/home/dupf/netcdf/include -UNEED_NC_INQ_FORMAT -fPIC -std=c99 -D_BSD_SOURCE -D_POSIX_SOURCE -MT nco_bnr.lo -MD -MP -MF .deps/nco_bnr.Tpo -c nco_bnr.c -o nco_bnr.o mv -f .deps/nco_bnr.Tpo .deps/nco_bnr.Plo /bin/sh ../../libtool --tag=CXX --tag=CC --mode=compile gcc -std=gnu99 -DHAVE_CONFIG_H -I. -I../.. -I/home/dupf/netcdf/include -I/home/dupf/netcdf/include -UNEED_NC_INQ_FORMAT -fPIC -std=c99 -D_BSD_SOURCE -D_POSIX_SOURCE -MT nco_cln_utl.lo -MD -MP -MF .deps/nco_cln_utl.Tpo -c -o nco_cln_utl.lo nco_cln_utl.c libtool: compile: gcc -std=gnu99 -DHAVE_CONFIG_H -I. -I../.. -I/home/dupf/netcdf/include -I/home/dupf/netcdf/include -UNEED_NC_INQ_FORMAT -fPIC -std=c99 -D_BSD_SOURCE -D_POSIX_SOURCE -MT nco_cln_utl.lo -MD -MP -MF .deps/nco_cln_utl.Tpo -c nco_cln_utl.c -o nco_cln_utl.o mv -f .deps/nco_cln_utl.Tpo .deps/nco_cln_utl.Plo /bin/sh ../../libtool --tag=CXX --tag=CC --mode=compile gcc -std=gnu99 -DHAVE_CONFIG_H -I. -I../.. -I/home/dupf/netcdf/include -I/home/dupf/netcdf/include -UNEED_NC_INQ_FORMAT -fPIC -std=c99 -D_BSD_SOURCE -D_POSIX_SOURCE -MT nco_cnf_dmn.lo -MD -MP -MF .deps/nco_cnf_dmn.Tpo -c -o nco_cnf_dmn.lo nco_cnf_dmn.c libtool: compile: gcc -std=gnu99 -DHAVE_CONFIG_H -I. -I../.. -I/home/dupf/netcdf/include -I/home/dupf/netcdf/include -UNEED_NC_INQ_FORMAT -fPIC -std=c99 -D_BSD_SOURCE -D_POSIX_SOURCE -MT nco_cnf_dmn.lo -MD -MP -MF .deps/nco_cnf_dmn.Tpo -c nco_cnf_dmn.c -o nco_cnf_dmn.o mv -f .deps/nco_cnf_dmn.Tpo .deps/nco_cnf_dmn.Plo /bin/sh ../../libtool --tag=CXX --tag=CC --mode=compile gcc -std=gnu99 -DHAVE_CONFIG_H -I. -I../.. -I/home/dupf/netcdf/include -I/home/dupf/netcdf/include -UNEED_NC_INQ_FORMAT -fPIC -std=c99 -D_BSD_SOURCE -D_POSIX_SOURCE -MT nco_cnf_typ.lo -MD -MP -MF .deps/nco_cnf_typ.Tpo -c -o nco_cnf_typ.lo nco_cnf_typ.c libtool: compile: gcc -std=gnu99 -DHAVE_CONFIG_H -I. -I../.. -I/home/dupf/netcdf/include -I/home/dupf/netcdf/include -UNEED_NC_INQ_FORMAT -fPIC -std=c99 -D_BSD_SOURCE -D_POSIX_SOURCE -MT nco_cnf_typ.lo -MD -MP -MF .deps/nco_cnf_typ.Tpo -c nco_cnf_typ.c -o nco_cnf_typ.o mv -f .deps/nco_cnf_typ.Tpo .deps/nco_cnf_typ.Plo /bin/sh ../../libtool --tag=CXX --tag=CC --mode=compile gcc -std=gnu99 -DHAVE_CONFIG_H -I. -I../.. -I/home/dupf/netcdf/include -I/home/dupf/netcdf/include -UNEED_NC_INQ_FORMAT -fPIC -std=c99 -D_BSD_SOURCE -D_POSIX_SOURCE -MT nco_cnk.lo -MD -MP -MF .deps/nco_cnk.Tpo -c -o nco_cnk.lo nco_cnk.c libtool: compile: gcc -std=gnu99 -DHAVE_CONFIG_H -I. -I../.. -I/home/dupf/netcdf/include -I/home/dupf/netcdf/include -UNEED_NC_INQ_FORMAT -fPIC -std=c99 -D_BSD_SOURCE -D_POSIX_SOURCE -MT nco_cnk.lo -MD -MP -MF .deps/nco_cnk.Tpo -c nco_cnk.c -o nco_cnk.o mv -f .deps/nco_cnk.Tpo .deps/nco_cnk.Plo /bin/sh ../../libtool --tag=CXX --tag=CC --mode=compile gcc -std=gnu99 -DHAVE_CONFIG_H -I. -I../.. -I/home/dupf/netcdf/include -I/home/dupf/netcdf/include -UNEED_NC_INQ_FORMAT -fPIC -std=c99 -D_BSD_SOURCE -D_POSIX_SOURCE -MT nco_cnv_arm.lo -MD -MP -MF .deps/nco_cnv_arm.Tpo -c -o nco_cnv_arm.lo nco_cnv_arm.c libtool: compile: gcc -std=gnu99 -DHAVE_CONFIG_H -I. -I../.. -I/home/dupf/netcdf/include -I/home/dupf/netcdf/include -UNEED_NC_INQ_FORMAT -fPIC -std=c99 -D_BSD_SOURCE -D_POSIX_SOURCE -MT nco_cnv_arm.lo -MD -MP -MF .deps/nco_cnv_arm.Tpo -c nco_cnv_arm.c -o nco_cnv_arm.o mv -f .deps/nco_cnv_arm.Tpo 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-I../.. -I/home/dupf/netcdf/include -I/home/dupf/netcdf/include -UNEED_NC_INQ_FORMAT -fPIC -std=c99 -D_BSD_SOURCE -D_POSIX_SOURCE -MT nco_ctl.lo -MD -MP -MF .deps/nco_ctl.Tpo -c nco_ctl.c -o nco_ctl.o mv -f .deps/nco_ctl.Tpo .deps/nco_ctl.Plo /bin/sh ../../libtool --tag=CXX --tag=CC --mode=compile gcc -std=gnu99 -DHAVE_CONFIG_H -I. -I../.. -I/home/dupf/netcdf/include -I/home/dupf/netcdf/include -UNEED_NC_INQ_FORMAT -fPIC -std=c99 -D_BSD_SOURCE -D_POSIX_SOURCE -MT nco_dbg.lo -MD -MP -MF .deps/nco_dbg.Tpo -c -o nco_dbg.lo nco_dbg.c libtool: compile: gcc -std=gnu99 -DHAVE_CONFIG_H -I. -I../.. -I/home/dupf/netcdf/include -I/home/dupf/netcdf/include -UNEED_NC_INQ_FORMAT -fPIC -std=c99 -D_BSD_SOURCE -D_POSIX_SOURCE -MT nco_dbg.lo -MD -MP -MF .deps/nco_dbg.Tpo -c nco_dbg.c -o nco_dbg.o mv -f .deps/nco_dbg.Tpo .deps/nco_dbg.Plo /bin/sh ../../libtool --tag=CXX --tag=CC --mode=compile gcc -std=gnu99 -DHAVE_CONFIG_H -I. -I../.. -I/home/dupf/netcdf/include -I/home/dupf/netcdf/include -UNEED_NC_INQ_FORMAT -fPIC -std=c99 -D_BSD_SOURCE -D_POSIX_SOURCE -MT nco_dmn_utl.lo -MD -MP -MF .deps/nco_dmn_utl.Tpo -c -o nco_dmn_utl.lo nco_dmn_utl.c libtool: compile: gcc -std=gnu99 -DHAVE_CONFIG_H -I. -I../.. -I/home/dupf/netcdf/include -I/home/dupf/netcdf/include -UNEED_NC_INQ_FORMAT -fPIC -std=c99 -D_BSD_SOURCE -D_POSIX_SOURCE -MT nco_dmn_utl.lo -MD -MP -MF .deps/nco_dmn_utl.Tpo -c nco_dmn_utl.c -o nco_dmn_utl.o mv -f .deps/nco_dmn_utl.Tpo .deps/nco_dmn_utl.Plo /bin/sh ../../libtool --tag=CXX --tag=CC --mode=compile gcc -std=gnu99 -DHAVE_CONFIG_H -I. -I../.. -I/home/dupf/netcdf/include -I/home/dupf/netcdf/include -UNEED_NC_INQ_FORMAT -fPIC -std=c99 -D_BSD_SOURCE -D_POSIX_SOURCE -MT nco_fl_utl.lo -MD -MP -MF .deps/nco_fl_utl.Tpo -c -o nco_fl_utl.lo nco_fl_utl.c libtool: compile: gcc -std=gnu99 -DHAVE_CONFIG_H -I. -I../.. -I/home/dupf/netcdf/include -I/home/dupf/netcdf/include -UNEED_NC_INQ_FORMAT -fPIC -std=c99 -D_BSD_SOURCE -D_POSIX_SOURCE -MT nco_fl_utl.lo -MD -MP -MF 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-I/home/dupf/netcdf/include -UNEED_NC_INQ_FORMAT -fPIC -std=c99 -D_BSD_SOURCE -D_POSIX_SOURCE -MT nco_var_rth.lo -MD -MP -MF .deps/nco_var_rth.Tpo -c nco_var_rth.c -o nco_var_rth.o mv -f .deps/nco_var_rth.Tpo .deps/nco_var_rth.Plo /bin/sh ../../libtool --tag=CXX --tag=CC --mode=compile gcc -std=gnu99 -DHAVE_CONFIG_H -I. -I../.. -I/home/dupf/netcdf/include -I/home/dupf/netcdf/include -UNEED_NC_INQ_FORMAT -fPIC -std=c99 -D_BSD_SOURCE -D_POSIX_SOURCE -MT nco_var_scv.lo -MD -MP -MF .deps/nco_var_scv.Tpo -c -o nco_var_scv.lo nco_var_scv.c libtool: compile: gcc -std=gnu99 -DHAVE_CONFIG_H -I. -I../.. -I/home/dupf/netcdf/include -I/home/dupf/netcdf/include -UNEED_NC_INQ_FORMAT -fPIC -std=c99 -D_BSD_SOURCE -D_POSIX_SOURCE -MT nco_var_scv.lo -MD -MP -MF .deps/nco_var_scv.Tpo -c nco_var_scv.c -o nco_var_scv.o mv -f .deps/nco_var_scv.Tpo .deps/nco_var_scv.Plo /bin/sh ../../libtool --tag=CXX --tag=CC --mode=compile gcc -std=gnu99 -DHAVE_CONFIG_H -I. -I../.. -I/home/dupf/netcdf/include -I/home/dupf/netcdf/include -UNEED_NC_INQ_FORMAT -fPIC -std=c99 -D_BSD_SOURCE -D_POSIX_SOURCE -MT nco_var_utl.lo -MD -MP -MF .deps/nco_var_utl.Tpo -c -o nco_var_utl.lo nco_var_utl.c libtool: compile: gcc -std=gnu99 -DHAVE_CONFIG_H -I. -I../.. -I/home/dupf/netcdf/include -I/home/dupf/netcdf/include -UNEED_NC_INQ_FORMAT -fPIC -std=c99 -D_BSD_SOURCE -D_POSIX_SOURCE -MT nco_var_utl.lo -MD -MP -MF .deps/nco_var_utl.Tpo -c nco_var_utl.c -o nco_var_utl.o mv -f .deps/nco_var_utl.Tpo .deps/nco_var_utl.Plo /bin/sh ../../libtool --tag=CXX --tag=CC --mode=link gcc -std=gnu99 -fPIC -std=c99 -D_BSD_SOURCE -D_POSIX_SOURCE -release 4.3.6 -L/home/dupf/netcdf/lib -lnetcdf -L/home/dupf/netcdf/lib -o libnco.la -rpath /home/dupf/nco/lib nco_att_utl.lo nco_aux.lo nco_bnr.lo nco_cln_utl.lo nco_cnf_dmn.lo nco_cnf_typ.lo nco_cnk.lo nco_cnv_arm.lo nco_cnv_csm.lo nco_ctl.lo nco_dbg.lo nco_dmn_utl.lo nco_fl_utl.lo nco_grp_utl.lo nco_grp_trv.lo nco_lmt.lo nco_lst_utl.lo nco_md5.lo nco_mmr.lo nco_msa.lo nco_mss_val.lo nco_netcdf.lo nco_omp.lo nco_pck.lo nco_prn.lo nco_rec_var.lo nco_rth_flt.lo nco_rth_utl.lo nco_scl_utl.lo nco_scm.lo nco_sng_utl.lo nco_var_avg.lo nco_var_lst.lo nco_var_rth.lo nco_var_scv.lo nco_var_utl.lo -lexpat -lm -lnetcdf libtool: link: ar cru .libs/libnco.a nco_att_utl.o nco_aux.o nco_bnr.o nco_cln_utl.o nco_cnf_dmn.o nco_cnf_typ.o nco_cnk.o nco_cnv_arm.o nco_cnv_csm.o nco_ctl.o nco_dbg.o nco_dmn_utl.o nco_fl_utl.o nco_grp_utl.o nco_grp_trv.o nco_lmt.o nco_lst_utl.o nco_md5.o nco_mmr.o nco_msa.o nco_mss_val.o nco_netcdf.o nco_omp.o nco_pck.o nco_prn.o nco_rec_var.o nco_rth_flt.o nco_rth_utl.o nco_scl_utl.o nco_scm.o nco_sng_utl.o nco_var_avg.o nco_var_lst.o nco_var_rth.o nco_var_scv.o nco_var_utl.o libtool: link: ranlib .libs/libnco.a libtool: link: ( cd ".libs" && rm -f "libnco.la" && ln -s "../libnco.la" "libnco.la" ) gcc -std=gnu99 -DHAVE_CONFIG_H -I. -I../.. -I/home/dupf/netcdf/include -I/home/dupf/netcdf/include -UNEED_NC_INQ_FORMAT -fPIC -std=c99 -D_BSD_SOURCE -D_POSIX_SOURCE -MT ncap_utl.o -MD -MP -MF .deps/ncap_utl.Tpo -c -o ncap_utl.o ncap_utl.c mv -f .deps/ncap_utl.Tpo .deps/ncap_utl.Po gcc -std=gnu99 -DHAVE_CONFIG_H -I. -I../.. -I/home/dupf/netcdf/include -I/home/dupf/netcdf/include -UNEED_NC_INQ_FORMAT -fPIC -std=c99 -D_BSD_SOURCE -D_POSIX_SOURCE -MT ncap.o -MD -MP -MF .deps/ncap.Tpo -c -o ncap.o ncap.c mv -f .deps/ncap.Tpo .deps/ncap.Po gcc -std=gnu99 -DHAVE_CONFIG_H -I. -I../.. -I/home/dupf/netcdf/include -I/home/dupf/netcdf/include -UNEED_NC_INQ_FORMAT -fPIC -std=c99 -D_BSD_SOURCE -D_POSIX_SOURCE -MT ncap_yacc.o -MD -MP -MF .deps/ncap_yacc.Tpo -c -o ncap_yacc.o ncap_yacc.c mv -f .deps/ncap_yacc.Tpo .deps/ncap_yacc.Po gcc -std=gnu99 -DHAVE_CONFIG_H -I. -I../.. -I/home/dupf/netcdf/include -I/home/dupf/netcdf/include -UNEED_NC_INQ_FORMAT -fPIC -std=c99 -D_BSD_SOURCE -D_POSIX_SOURCE -MT ncap_lex.o -MD -MP -MF .deps/ncap_lex.Tpo -c -o ncap_lex.o ncap_lex.c mv -f .deps/ncap_lex.Tpo .deps/ncap_lex.Po /bin/sh ../../libtool --tag=CXX --tag=CC --mode=link gcc -std=gnu99 -fPIC -std=c99 -D_BSD_SOURCE -D_POSIX_SOURCE -L/home/dupf/netcdf/lib -lnetcdf -L/home/dupf/netcdf/lib -o ncap ncap_utl.o ncap.o ncap_yacc.o ncap_lex.o libnco.la -lexpat -lm -lnetcdf libtool: link: gcc -std=gnu99 -fPIC -std=c99 -D_BSD_SOURCE -D_POSIX_SOURCE -o ncap ncap_utl.o ncap.o ncap_yacc.o ncap_lex.o -L/home/dupf/netcdf/lib ./.libs/libnco.a /usr/lib64/libexpat.so /home/dupf/netcdf/lib/libnetcdf.so -lm -Wl,-rpath -Wl,/usr/lib64 -Wl,-rpath -Wl,/home/dupf/netcdf/lib -Wl,-rpath -Wl,/usr/lib64 -Wl,-rpath -Wl,/home/dupf/netcdf/lib ./.libs/libnco.a(nco_netcdf.o): In functionnco_inq_ncid':
    nco_netcdf.c:(.text+0x102a): undefined reference to nc_inq_ncid' ./.libs/libnco.a(nco_netcdf.o): In functionnco_inq_ncid_flg':
    nco_netcdf.c:(.text+0x106a): undefined reference to nc_inq_ncid' ./.libs/libnco.a(nco_netcdf.o): In functionnco_def_grp':
    nco_netcdf.c:(.text+0x11ea): undefined reference to nc_def_grp' ./.libs/libnco.a(nco_netcdf.o): In functionnco_def_grp_flg':
    nco_netcdf.c:(.text+0x122a): undefined reference to nc_def_grp' ./.libs/libnco.a(nco_netcdf.o): In functionnco_inq_dimids':
    nco_netcdf.c:(.text+0x1350): undefined reference to nc_inq_dimids' ./.libs/libnco.a(nco_netcdf.o): In functionnco_inq_grpname':
    nco_netcdf.c:(.text+0x1388): undefined reference to nc_inq_grpname' ./.libs/libnco.a(nco_netcdf.o): In functionnco_inq_grpname_full':
    nco_netcdf.c:(.text+0x13c8): undefined reference to nc_inq_grpname_full' ./.libs/libnco.a(nco_netcdf.o): In functionnco_inq_grpname_len':
    nco_netcdf.c:(.text+0x1400): undefined reference to nc_inq_grpname_len' ./.libs/libnco.a(nco_netcdf.o): In functionnco_inq_grps':
    nco_netcdf.c:(.text+0x1440): undefined reference to nc_inq_grps' ./.libs/libnco.a(nco_netcdf.o): In functionnco_inq_grp_ncid':
    nco_netcdf.c:(.text+0x1480): undefined reference to nc_inq_grp_ncid' ./.libs/libnco.a(nco_netcdf.o): In functionnco_inq_grp_ncid_flg':
    nco_netcdf.c:(.text+0x14c0): undefined reference to nc_inq_grp_ncid' ./.libs/libnco.a(nco_netcdf.o): In functionnco_inq_grp_full_ncid':
    nco_netcdf.c:(.text+0x1533): undefined reference to nc_inq_grp_full_ncid' ./.libs/libnco.a(nco_netcdf.o): In functionnco_inq_grp_full_ncid_flg':
    nco_netcdf.c:(.text+0x159d): undefined reference to nc_inq_grp_full_ncid' ./.libs/libnco.a(nco_netcdf.o): In functionnco_inq_grp_parent':
    nco_netcdf.c:(.text+0x15f4): undefined reference to nc_inq_grp_parent' ./.libs/libnco.a(nco_netcdf.o): In functionnco_inq_grp_parent_flg':
    nco_netcdf.c:(.text+0x162c): undefined reference to nc_inq_grp_parent' ./.libs/libnco.a(nco_netcdf.o): In functionnco_inq_varids':
    nco_netcdf.c:(.text+0x1680): undefined reference to nc_inq_varids' ./.libs/libnco.a(nco_netcdf.o): In functionnco_inq_unlimdims':
    nco_netcdf.c:(.text+0x16c0): undefined reference to nc_inq_unlimdims' ./.libs/libnco.a(nco_netcdf.o): In functionnco_def_var_chunking':
    nco_netcdf.c:(.text+0x1a21): undefined reference to nc_def_var_chunking' ./.libs/libnco.a(nco_netcdf.o): In functionnco_def_var_deflate':
    nco_netcdf.c:(.text+0x1a6d): undefined reference to nc_def_var_deflate' ./.libs/libnco.a(nco_netcdf.o): In functionnco_inq_var_chunking':
    nco_netcdf.c:(.text+0x1b44): undefined reference to nc_inq_var_chunking' ./.libs/libnco.a(nco_netcdf.o): In functionnco_inq_var_deflate':
    nco_netcdf.c:(.text+0x1bc0): undefined reference to nc_inq_var_deflate' ./.libs/libnco.a(nco_netcdf.o): In functionnco_inq_var_fletcher32':
    nco_netcdf.c:(.text+0x1c52): undefined reference to nc_inq_var_fletcher32' collect2: ld returned 1 exit status make[3]: *** [ncap] Error 1 make[3]: Leaving directory/home/dupf/nco-4.3.7/src/nco'
    make[2]: [all-recursive] Error 1
    make[2]: Leaving directory /home/dupf/nco-4.3.7/src' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory/home/dupf/nco-4.3.7'
    make:
    [all] Error 2

    Waiting for your reply.
    Thanks in advance

     
  • Pedro Vicente
    Pedro Vicente
    2013-11-09

    @Hassan

    That error shows that the netCDF library was not found.

    What OS are you running?
    Can you send the file config.log located at the source root to pvicente@uci.edu?

    Also, for some OSs, NCO provides binary builds, so there is no need to build from source.

    They are listed here

    http://nco.sourceforge.net/#Binaries

    Pedro

     
  • Pedro Vicente
    Pedro Vicente
    2013-11-09

    configure: error: cannot find netCDF header

    this message , from the output of ./configure tells that the file netcdf.h was not found.

    posts #2 and #3 above show 2 ways to install netCDF, the recommended is to install from a package

    http://nco.sourceforge.net/#bld

    Pedro

     
  • Hassan
    Hassan
    2013-11-10

    Dear Pedro
    Thanks for your reply.
    I am using x86_64 GNU/Linux Red Hat Enterprise release 5.5 (Tikanga)
    Kernel.
    I have sent the config.log file at pvicente@uci.edu.
    I will also try it from binaries.
    Thanks

     
  • Hassan
    Hassan
    2013-11-17

    @Zender
    I re-installed netCDF along with the required libraries (ANTLR 2.7.x, GSL, UDUnits) and also bison.
    The problem is still ncap error,

    ./.libs/libnco.so: undefined reference to nc_def_var_deflate' ./.libs/libnco.so: undefined reference tonc_inq_ncid'
    ./.libs/libnco.so: undefined reference to nc_inq_var_fletcher32' ./.libs/libnco.so: undefined reference tonc_inq_grp_parent'
    ./.libs/libnco.so: undefined reference to nc_inq_unlimdims' ./.libs/libnco.so: undefined reference tonc_inq_grpname_len'
    ./.libs/libnco.so: undefined reference to nc_inq_grps' ./.libs/libnco.so: undefined reference tonc_def_var_chunking'
    ./.libs/libnco.so: undefined reference to nc_inq_var_chunking' ./.libs/libnco.so: undefined reference tonc_inq_var_deflate'
    ./.libs/libnco.so: undefined reference to nc_inq_grp_ncid' ./.libs/libnco.so: undefined reference tonc_inq_grpname'
    ./.libs/libnco.so: undefined reference to nc_inq_grpname_full' ./.libs/libnco.so: undefined reference tonc_def_grp'
    ./.libs/libnco.so: undefined reference to nc_inq_dimids' ./.libs/libnco.so: undefined reference tonc_inq_grp_full_ncid'
    ./.libs/libnco.so: undefined reference to nc_inq_varids' collect2: ld returned 1 exit status make[3]: *** [ncap] Error 1 make[3]: Leaving directory/home/dupf/nco-4.3.7/src/nco'
    make[2]: [all-recursive] Error 1
    make[2]: Leaving directory /home/dupf/nco-4.3.7/src' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory/home/dupf/nco-4.3.7'
    make:
    [all] Error 2

    I tried too much but unable to solve.

     
  • Hi every body
    I want to install nco on ubuntu-14.04.1 and I am very bigineer in linux
    after changing direction to nco-4.4.4 by command: "cd /home/nghajarnia/nco/nco-4.4.4", I configured by command: "sh ./configure"

    following the installation text file. now I have write the command: "Make" but i encounter this error:
    Make: *** No target specified and no makefile found. stop.
    while in all folders of the nco software that I have downloaded, there exist makefile or/and makefile.am and makefile.in

    can you please help me?
    thank you so much in advanced

     
  • Charlie Zender
    Charlie Zender
    2014-08-12

    Run the command "./configure" in the top-level directory (nco-4.4.4).
    After it completes there should be a file name Makefile.
    Now type "make".
    Does this work?
    cz

     
  • Hi charlie

    no it didnt work. the command "./configure" worked but the makefile is not made and I am again encountering with the same error after writing "make". as bellow:

    nghajarnia@Navid:~/nco/nco-4.4.4$ ./configure
    checking build system type... x86_64-unknown-linux-gnu
    checking host system type... x86_64-unknown-linux-gnu
    checking target system type... x86_64-unknown-linux-gnu
    checking for grep that handles long lines and -e... /bin/grep
    checking for egrep... /bin/grep -E
    checking for a BSD-compatible install... /usr/bin/install -c
    checking whether build environment is sane... yes
    checking for a thread-safe mkdir -p... /bin/mkdir -p
    checking for gawk... no
    checking for mawk... mawk
    checking whether make sets $(MAKE)... yes
    checking whether make supports nested variables... yes
    checking for gcc... gcc
    checking whether the C compiler works... yes
    checking for C compiler default output file name... a.out
    checking for suffix of executables...
    checking whether we are cross compiling... no
    checking for suffix of object files... o
    checking whether we are using the GNU C compiler... yes
    checking whether gcc accepts -g... yes
    checking for gcc option to accept ISO C89... none needed
    checking for style of include used by make... GNU
    checking dependency style of gcc... gcc3
    checking for g++... no
    checking for c++... no
    checking for gpp... no
    checking for aCC... no
    checking for CC... no
    checking for cxx... no
    checking for cc++... no
    checking for cl.exe... no
    checking for FCC... no
    checking for KCC... no
    checking for RCC... no
    checking for xlC_r... no
    checking for xlC... no
    checking whether we are using the GNU C++ compiler... no
    checking whether g++ accepts -g... no
    checking dependency style of g++... none
    checking how to run the C preprocessor... gcc -E
    checking how to run the C++ preprocessor... /lib/cpp
    configure: error: in /home/nghajarnia/nco/nco-4.4.4': configure: error: C++ preprocessor "/lib/cpp" fails sanity check Seeconfig.log' for more details
    nghajarnia@Navid:~/nco/nco-4.4.4$ make
    make: *** No targets specified and no makefile found. Stop.

    thank you for your helps, and I am waiting again. thanks

     
  • Hi Charlie again

    I tried to install ANTLR, I do not exactly know how much I was succsfull but I guess I did some works. this time the printed comments in terminal after the command "./configure" are much more as bellow. but still the "make" problems remains.

    nghajarnia@Navid:~/nco/nco-4.4.4$ ./configure
    checking build system type... x86_64-unknown-linux-gnu
    checking host system type... x86_64-unknown-linux-gnu
    checking target system type... x86_64-unknown-linux-gnu
    checking for grep that handles long lines and -e... /bin/grep
    checking for egrep... /bin/grep -E
    checking for a BSD-compatible install... /usr/bin/install -c
    checking whether build environment is sane... yes
    checking for a thread-safe mkdir -p... /bin/mkdir -p
    checking for gawk... no
    checking for mawk... mawk
    checking whether make sets $(MAKE)... yes
    checking whether make supports nested variables... yes
    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 style of include used by make... GNU
    checking dependency style of gcc... gcc3
    checking for g++... g++
    checking whether we are using the GNU C++ compiler... yes
    checking whether g++ accepts -g... yes
    checking dependency style of g++... gcc3
    checking how to run the C preprocessor... gcc -E
    checking how to run the C++ preprocessor... g++ -E
    checking for gcc option to accept ISO C99... -std=gnu99
    checking for gcc -std=gnu99 option to accept ISO Standard C... (cached) -std=gnu99
    checking for flex... no
    checking for lex... no
    checking for bison... no
    checking for byacc... no
    checking whether ln -s works... yes
    checking how to print strings... printf
    checking for a sed that does not truncate output... /bin/sed
    checking for fgrep... /bin/grep -F
    checking for ld used by gcc -std=gnu99... /usr/bin/ld
    checking if the linker (/usr/bin/ld) is GNU ld... yes
    checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
    checking the name lister (/usr/bin/nm -B) interface... BSD nm
    checking the maximum length of command line arguments... 1572864
    checking whether the shell understands some XSI constructs... yes
    checking whether the shell understands "+="... yes
    checking how to convert x86_64-unknown-linux-gnu file names to x86_64-unknown-linux-gnu format... func_convert_file_noop
    checking how to convert x86_64-unknown-linux-gnu file names to toolchain format... func_convert_file_noop
    checking for /usr/bin/ld option to reload object files... -r
    checking for objdump... objdump
    checking how to recognize dependent libraries... pass_all
    checking for dlltool... no
    checking how to associate runtime and link libraries... printf %s\n
    checking for ar... ar
    checking for archiver @FILE support... @
    checking for strip... strip
    checking for ranlib... ranlib
    checking command to parse /usr/bin/nm -B output from gcc -std=gnu99 object... ok
    checking for sysroot... no
    checking for mt... mt
    checking if mt is a manifest tool... no
    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 for dlfcn.h... yes
    checking for objdir... .libs
    checking if gcc -std=gnu99 supports -fno-rtti -fno-exceptions... no
    checking for gcc -std=gnu99 option to produce PIC... -fPIC -DPIC
    checking if gcc -std=gnu99 PIC flag -fPIC -DPIC works... yes
    checking if gcc -std=gnu99 static flag -static works... yes
    checking if gcc -std=gnu99 supports -c -o file.o... yes
    checking if gcc -std=gnu99 supports -c -o file.o... (cached) yes
    checking whether the gcc -std=gnu99 linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
    checking whether -lc should be explicitly linked in... no
    checking dynamic linker characteristics... GNU/Linux ld.so
    checking how to hardcode library paths into programs... immediate
    checking whether stripping libraries is possible... yes
    checking if libtool supports shared libraries... yes
    checking whether to build shared libraries... yes
    checking whether to build static libraries... yes
    checking how to run the C++ preprocessor... g++ -E
    checking for ld used by g++... /usr/bin/ld -m elf_x86_64
    checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes
    checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
    checking for g++ option to produce PIC... -fPIC -DPIC
    checking if g++ PIC flag -fPIC -DPIC works... yes
    checking if g++ static flag -static works... yes
    checking if g++ supports -c -o file.o... yes
    checking if g++ supports -c -o file.o... (cached) yes
    checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
    checking dynamic linker characteristics... (cached) GNU/Linux ld.so
    checking how to hardcode library paths into programs... immediate
    checking whether to enable maintainer-specific portions of Makefiles... no
    checking for working memcmp... yes
    checking whether lstat correctly handles trailing slash... yes
    checking whether stat accepts an empty string... no
    checking for working strtod... yes
    checking for canonicalize_file_name... yes
    checking for floor... no
    checking for gethostname... yes
    checking for getpagesize... yes
    checking for getrusage... yes
    checking for memchr... yes
    checking for memmove... yes
    checking for memset... yes
    checking for mkstemp... yes
    checking for pow... no
    checking for readlink... yes
    checking for realpath... yes
    checking for regcomp... yes
    checking for setlocale... yes
    checking for sqrt... no
    checking for strchr... yes
    checking for strerror... yes
    checking for strpbrk... yes
    checking for strrchr... yes
    checking for strstr... yes
    checking for strtol... yes
    checking for ANSI C header files... (cached) yes
    checking getopt.h usability... yes
    checking getopt.h presence... yes
    checking for getopt.h... yes
    checking libintl.h usability... yes
    checking libintl.h presence... yes
    checking for libintl.h... yes
    checking limits.h usability... yes
    checking limits.h presence... yes
    checking for limits.h... yes
    checking locale.h usability... yes
    checking locale.h presence... yes
    checking for locale.h... yes
    checking netinet/in.h usability... yes
    checking netinet/in.h presence... yes
    checking for netinet/in.h... yes
    checking for stdlib.h... (cached) yes
    checking for string.h... (cached) yes
    checking for strings.h... (cached) yes
    checking for unistd.h... (cached) yes
    checking cstdlib usability... yes
    checking cstdlib presence... yes
    checking for cstdlib... yes
    checking for an ANSI C-conforming const... yes
    checking for inline... inline
    checking for pid_t... yes
    checking for size_t... yes
    checking whether struct tm is in sys/time.h or time.h... time.h
    checking for uid_t in sys/types.h... yes
    checking for ptrdiff_t... yes
    checking size of int*... 8
    checking whether C++ compiler implements namespaces... yes
    checking whether C++ compiler has working valarray<T>... yes
    checking for special C compiler options needed for large files... no
    checking for _FILE_OFFSET_BITS value needed for large files... no

    Test for netCDF

    checking for /opt/local/include/netcdf.h... no
    checking for /opt/local/lib/libnetcdf.a... no
    checking for /sopt/netcdf/netcdf411-gcc-serial/include/netcdf.h... no
    checking for /sopt/netcdf/netcdf411-gcc-serial/lib/libnetcdf.a... no
    checking netcdf.h usability... no
    checking netcdf.h presence... no
    checking for netcdf.h... no
    configure: error: in /home/nghajarnia/nco/nco-4.4.4': configure: error: cannot find netCDF header Seeconfig.log' for more details
    nghajarnia@Navid:~/nco/nco-4.4.4$ make
    make: *** No targets specified and no makefile found. Stop.
    nghajarnia@Navid:~/nco/nco-4.4.4$

    thanks
    navid

     
  • Charlie Zender
    Charlie Zender
    2014-08-13

    Read the NCO homepage until you get to the part about "bonobo". Then you'll know what to do next.
    cz

     
  • bonobo

    sorry, my apology