Re: installation problem with octave-octcdf

[Chaitanya v.s]

Dear Marius,

I installed GNU Octave, version 3.8.2

I uninstalled octave and i reinstalled using the command 

sudo port -v install octave

and I ended with the following error

====================

--->  Cleaning octave

--->  Removing work directory for octave

--->  Updating database of binaries

--->  Scanning binaries for linking errors               

Could not open /opt/local/lib/libnettle.4.dylib: Error opening or reading file (referenced from /opt/local/bin/wget)

Could not open /opt/local/lib/openmpi-mp/libmpi.1.dylib: Error opening or reading file (referenced from /opt/local/bin/cdo)

Could not open /opt/local/lib/libhdf5.8.dylib: Error opening or reading file (referenced from /opt/local/bin/cdo)

Could not open /opt/local/lib/openmpi-gcc45/libmpi.1.dylib: Error opening or reading file (referenced from /opt/local/bin/nccopy)

Could not open /opt/local/lib/libicudata.53.dylib: Error opening or reading file (referenced from /opt/local/libexec/slapd)

Could not open /opt/local/lib/libicuuc.53.dylib: Error opening or reading file (referenced from /opt/local/libexec/slapd)

Could not open /opt/local/lib/libncurses.5.dylib: Error opening or reading file (referenced from /opt/local/bin/sftp)

--->  Found 16 broken file(s), matching files to ports   

--->  Found 5 broken port(s), determining rebuild order

--->  Rebuilding in order

     netcdf @4.3.2 +dap+gcc45+netcdf4+openmpi

     cdo @1.6.4 +openmpi

     openssh @6.6p1 +kerberos5+xauth

     wget @1.15 +ssl

     openldap @2.4.39 

--->  Computing dependencies for netcdf.

--->  Fetching distfiles for netcdf

Error: Install hdf5 +openmpi

Error: org.macports.fetch for port netcdf returned: hdf5 +openmpi not installed

Warning: targets not executed for netcdf: org.macports.install org.macports.fetch org.macports.checksum org.macports.extract org.macports.patch org.macports.configure org.macports.build org.macports.destroot

Please see the log file for port netcdf for details:

    /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_netcdf/netcdf/main.log

Error: Unable to upgrade port: 1

Error rebuilding netcdf

    while executing

"error "Error rebuilding $portname""

    (procedure "revupgrade_scanandrebuild" line 395)

    invoked from within

"revupgrade_scanandrebuild broken_port_counts $opts"

    (procedure "macports::revupgrade" line 5)

    invoked from within

"macports::revupgrade $opts"

    (procedure "action_revupgrade" line 2)

    invoked from within

"action_revupgrade $action $portlist $opts"

    (procedure "action_target" line 96)

    invoked from within

"$action_proc $action $portlist [array get global_options]"

    (procedure "process_cmd" line 103)

    invoked from within

"process_cmd $remaining_args"

    invoked from within

"if { [llength $remaining_args] > 0 } {

    # If there are remaining arguments, process those as a command

    set exit_status [process_cmd $remaining..."

    (file "/opt/local/bin/port" line 5268)

==================================

can you please let me know what to do with this error.

with warm regards

Chaitanya

On Fri, Feb 5, 2016 at 8:14 PM, Marius Schamschula <address@hidden> wrote:

Chaitanya,

On Feb 5, 2016, at 6:52 AM, Chaitanya v.s <address@hidden> wrote:

Hi....this is chaitanya,

I am using Macbook pro with OS X 10.9.5.

I was trying to install octave and its tool boxes in this mac.

I successfully installed octave through macports but when i am trying to install octave-octcdf , octave-netcdf and octave-ncarray facing some problem with installation errors.

seriously i don't understand what it is and why it is.....

please any one can help me in this regards....

Here I added the contents from log file which is generated while installation.

========================================

version:1

:debug:main changing euid/egid - current euid: 0 - current egid: 0

:debug:main egid changed to: 501

:debug:main euid changed to: 502

:debug:main Executing org.macports.main (octave-netcdf)

:debug:main Privilege de-escalation not attempted as not running as root.

:debug:main Skipping completed org.macports.archivefetch (octave-netcdf)

:debug:main Privilege de-escalation not attempted as not running as root.

:debug:main Skipping completed org.macports.fetch (octave-netcdf)

:debug:main Privilege de-escalation not attempted as not running as root.

:debug:main Skipping completed org.macports.checksum (octave-netcdf)

:debug:main Privilege de-escalation not attempted as not running as root.

:debug:main Skipping completed org.macports.extract (octave-netcdf)

:debug:main Privilege de-escalation not attempted as not running as root.

:debug:main Skipping completed org.macports.patch (octave-netcdf)

:debug:main Privilege de-escalation not attempted as not running as root.

:debug:configure configure phase started at Fri Feb  5 17:37:26 IST 2016

:notice:configure --->  Configuring octave-netcdf

:debug:configure Using compiler 'Xcode Clang'

:debug:configure Executing proc-pre-org.macports.configure-configure-0

:info:configure --->  Patching DESCRIPTION: /Autoload/address@hidden@address@hidden

:debug:configure Executing reinplace: /usr/bin/sed /Autoload/address@hidden@address@hidden < /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_octave-netcdf/octave-netcdf/work/netcdf/DESCRIPTION >@ file11 2>@stderr

:debug:configure couldn't read file "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_octave-netcdf/octave-netcdf/work/netcdf/DESCRIPTION": no such file or directory

    while executing

"exec /usr/bin/sed /Autoload/address@hidden@address@hidden < /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_..."

    ("eval" body line 1)

    invoked from within

"eval exec $cmdline"

===================================

thanks in advance....

with regards

Chaitanya

First of all which version of octave did you install? (i.e. octave, octave-devel, octave-devel-rc, octave-devel-release)

Second try running

sudo port clean octave-netcdf

before

sudo port -v install octave-netcdf

What you are seeing is an artifact of the way the octave port group installs octave packages under MacPorts. You likely are trying to resume an interrupted build.

Marius

--

Marius Schamschula