[MacPorts] #23618: NCBI toolkit not compiling on Snow Leopard

[MacPorts]

#23618: NCBI toolkit not compiling on Snow Leopard
---------------------------------+------------------------------------------
 Reporter:  bkamel@…             |       Owner:  mike.thon@…        
     Type:  defect               |      Status:  new                
 Priority:  Normal               |   Milestone:                     
Component:  ports                |     Version:  1.8.2              
 Keywords:                       |        Port:  ncbi_tools         
---------------------------------+------------------------------------------
Changes (by macsforever2000@…):

  * keywords:  NCBI, Bioinformatics =>
  * owner:  macports-tickets@… => mike.thon@…
  * priority:  High => Normal


Old description:

> sudo port -d install ncbi_tools
> DEBUG: Found port in
> file:///opt/local/var/macports/sources/rsync.macports.org/release/ports/science/ncbi_tools
> DEBUG: Changing to port directory:
> /opt/local/var/macports/sources/rsync.macports.org/release/ports/science/ncbi_tools
> DEBUG: OS Platform: darwin
> DEBUG: OS Version: 10.2.0
> DEBUG: Mac OS X Version: 10.6
> DEBUG: System Arch: i386
> DEBUG: setting option os.universal_supported to yes
> DEBUG: org.macports.load registered provides 'load', a pre-existing
> procedure. Target override will not be provided
> DEBUG: org.macports.unload registered provides 'unload', a pre-existing
> procedure. Target override will not be provided
> DEBUG: org.macports.distfiles registered provides 'distfiles', a pre-
> existing procedure. Target override will not be provided
> DEBUG: not using configure, so not adding the default universal variant
> DEBUG: Requested variant darwin is not provided by port ncbi_tools.
> DEBUG: Requested variant i386 is not provided by port ncbi_tools.
> DEBUG: Requested variant macosx is not provided by port ncbi_tools.
> --->  Computing dependencies for ncbi_tools
> DEBUG: Executing org.macports.main (ncbi_tools)
> DEBUG: Skipping completed org.macports.fetch (ncbi_tools)
> DEBUG: Skipping completed org.macports.checksum (ncbi_tools)
> DEBUG: Skipping completed org.macports.extract (ncbi_tools)
> DEBUG: Skipping completed org.macports.patch (ncbi_tools)
> DEBUG: Skipping completed org.macports.configure (ncbi_tools)
> --->  Building ncbi_tools
> DEBUG: Executing org.macports.build (ncbi_tools)
> DEBUG: Environment: MACOSX_DEPLOYMENT_TARGET='10.6'
> DEBUG: Assembled command: 'cd
> "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_science_ncbi_tools/work/"
> && './ncbi/make/makedis.csh' -j2'
> Unable to find the file -j2
> Error: Target org.macports.build returned: shell command " cd
> "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_science_ncbi_tools/work/"
> && './ncbi/make/makedis.csh' -j2 " returned error 1
> DEBUG: Backtrace: shell command " cd
> "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_science_ncbi_tools/work/"
> && './ncbi/make/makedis.csh' -j2 " returned error 1
>     while executing
> "command_exec build"
>     (procedure "portbuild::build_main" line 9)
>     invoked from within
> "$procedure $targetname"
> Warning: the following items did not execute (for ncbi_tools):
> org.macports.activate org.macports.build org.macports.destroot
> org.macports.install
> Error: Status 1 encountered during processing.
> To report a bug, see <http://guide.macports.org/#project.tickets>

New description:

 {{{
 sudo port -d install ncbi_tools
 DEBUG: Found port in
 file:///opt/local/var/macports/sources/rsync.macports.org/release/ports/science/ncbi_tools
 DEBUG: Changing to port directory:
 /opt/local/var/macports/sources/rsync.macports.org/release/ports/science/ncbi_tools
 DEBUG: OS Platform: darwin
 DEBUG: OS Version: 10.2.0
 DEBUG: Mac OS X Version: 10.6
 DEBUG: System Arch: i386
 DEBUG: setting option os.universal_supported to yes
 DEBUG: org.macports.load registered provides 'load', a pre-existing
 procedure. Target override will not be provided
 DEBUG: org.macports.unload registered provides 'unload', a pre-existing
 procedure. Target override will not be provided
 DEBUG: org.macports.distfiles registered provides 'distfiles', a pre-
 existing procedure. Target override will not be provided
 DEBUG: not using configure, so not adding the default universal variant
 DEBUG: Requested variant darwin is not provided by port ncbi_tools.
 DEBUG: Requested variant i386 is not provided by port ncbi_tools.
 DEBUG: Requested variant macosx is not provided by port ncbi_tools.
 --->  Computing dependencies for ncbi_tools
 DEBUG: Executing org.macports.main (ncbi_tools)
 DEBUG: Skipping completed org.macports.fetch (ncbi_tools)
 DEBUG: Skipping completed org.macports.checksum (ncbi_tools)
 DEBUG: Skipping completed org.macports.extract (ncbi_tools)
 DEBUG: Skipping completed org.macports.patch (ncbi_tools)
 DEBUG: Skipping completed org.macports.configure (ncbi_tools)
 --->  Building ncbi_tools
 DEBUG: Executing org.macports.build (ncbi_tools)
 DEBUG: Environment: MACOSX_DEPLOYMENT_TARGET='10.6'
 DEBUG: Assembled command: 'cd
 "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_science_ncbi_tools/work/"
 && './ncbi/make/makedis.csh' -j2'
 Unable to find the file -j2
 Error: Target org.macports.build returned: shell command " cd
 "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_science_ncbi_tools/work/"
 && './ncbi/make/makedis.csh' -j2 " returned error 1
 DEBUG: Backtrace: shell command " cd
 "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_science_ncbi_tools/work/"
 && './ncbi/make/makedis.csh' -j2 " returned error 1
     while executing
 "command_exec build"
     (procedure "portbuild::build_main" line 9)
     invoked from within
 "$procedure $targetname"
 Warning: the following items did not execute (for ncbi_tools):
 org.macports.activate org.macports.build org.macports.destroot
 org.macports.install
 Error: Status 1 encountered during processing.
 To report a bug, see <http://guide.macports.org/#project.tickets>
 }}}

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Ticket URL: <http://trac.macports.org/ticket/23618#comment:1>
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