Re: installation problem with octave-octcdf

[Marius Schamschula]

On Feb 8, 2016, at 2:03 AM, Chaitanya v.s <address@hidden> wrote:

> 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

This looks like your problem. What did 

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

say?

I currently have the following active:

netcdf @4.3.3.1_4+dap+netcdf4

in other words w/o +openmpi, which I haven’t tested.

The best approach is to clean netcdf

sudo port clean netcdf

then install netcdf

sudo port install netcdf

with the appropriate variants.

> 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
> 
> 
> 
> 
> 

Marius
--
Marius Schamschula