When running CNS it cannot find its files because the "sed" commands in the ebuild that edit the cns_solve_env files do not seem to set the actual location of the files. Reproducible: Always Steps to Reproduce: 1.emerge cns 2.try to run cns (I tried to run the anneal.inp and accept.inp module and can give you the files I used for the run on request) Actual Results: cns does not run and gives an error message about not being able to find the location of the "toppar" files. After manually correcting the locations in /etc/profile.d/cns_solve_env.sh it runs nicely. Expected Results: It should have run. I did not check the cns_solve_env.csh script, but maybe it also contains the wrong locations.
It would be helpful if you could attach a diff (diff -u originalfile newfile > cns.diff) between the original file and the fixed file, or at least the fixed version.
Here is the diff that that works for me (note that I changed the filenames to .ORIGINAL and .EDITED) I do not know if it fixes the locations for all of the cns possibilities, but it fixes mine. It would be good to check what the variables are supposed to point to exactly, because this is just a quick (egoistic) fix. In the weekend I may have some time to check this fix and make a better one if necessary. --- cns_solve_env.sh.ORIGINAL 2008-02-12 19:39:45.000000000 +0100 +++ cns_solve_env.sh.EDITED 2008-02-12 19:50:12.000000000 +0100 @@ -18,7 +18,7 @@ export _POSIX2_VERSION; _POSIX2_VERSION=199209 CNS_SOLVE=/usr export CNS_ROOT=/usr -export CNS_DATA=$CNS_ROOT/share/data +export CNS_DATA=$CNS_ROOT/share/cns export CNS_DOC=$CNS_ROOT/share/doc/cns-1.2-r1 # @@ -39,9 +39,9 @@ # # general environmental variables # -export CNS_LIB; CNS_LIB=$CNS_SOLVE/libraries +export CNS_LIB; CNS_LIB=$CNS_DATA/libraries export CNS_MODULE; CNS_MODULE=$CNS_DATA/modules -export CNS_TOPPAR; CNS_TOPPAR=$CNS_DATA/toppar +export CNS_TOPPAR; CNS_TOPPAR=$CNS_LIB/toppar export CNS_CONFDB; CNS_CONFDB=$CNS_DATA/confdb export CNS_XTALLIB; CNS_XTALLIB=$CNS_DATA/xtal export CNS_NMRLIB; CNS_NMRLIB=$CNS_DATA/nmr
I checked the locations of all cns files and corrected them in /etc/profile.d/cns_solve_env.sh The diff-file is given below. I think this is what still needs to be done: - double check the changes I made - make similar corrections to /etc/profile.d/cns_solve.csh - edit the sed-stuff in the ebuild so that it puts the correct locations in the two files mentioned after emerging diff follows (again with changed filenames): --- cns_solve_env.sh.ORIGINAL 2008-02-12 19:39:45.000000000 +0100 +++ cns_solve_env.sh.EDITED 2008-02-13 09:33:15.000000000 +0100 @@ -18,7 +18,7 @@ export _POSIX2_VERSION; _POSIX2_VERSION=199209 CNS_SOLVE=/usr export CNS_ROOT=/usr -export CNS_DATA=$CNS_ROOT/share/data +export CNS_DATA=$CNS_ROOT/share/cns export CNS_DOC=$CNS_ROOT/share/doc/cns-1.2-r1 # @@ -39,13 +39,13 @@ # # general environmental variables # -export CNS_LIB; CNS_LIB=$CNS_SOLVE/libraries +export CNS_LIB; CNS_LIB=$CNS_DATA/libraries export CNS_MODULE; CNS_MODULE=$CNS_DATA/modules -export CNS_TOPPAR; CNS_TOPPAR=$CNS_DATA/toppar -export CNS_CONFDB; CNS_CONFDB=$CNS_DATA/confdb -export CNS_XTALLIB; CNS_XTALLIB=$CNS_DATA/xtal -export CNS_NMRLIB; CNS_NMRLIB=$CNS_DATA/nmr -export CNS_XRAYLIB; CNS_XRAYLIB=$CNS_DATA/xray +export CNS_TOPPAR; CNS_TOPPAR=$CNS_LIB/toppar +export CNS_CONFDB; CNS_CONFDB=$CNS_LIB/confdb +export CNS_XTALLIB; CNS_XTALLIB=$CNS_LIB/xtal +export CNS_NMRLIB; CNS_NMRLIB=$CNS_LIB/nmr +export CNS_XRAYLIB; CNS_XRAYLIB=$CNS_LIB/xray export CNS_XTALMODULE; CNS_XTALMODULE=$CNS_MODULE/xtal export CNS_NMRMODULE; CNS_NMRMODULE=$CNS_MODULE/nmr export CNS_HELPLIB; CNS_HELPLIB=$CNS_DATA/helplib @@ -54,8 +54,8 @@ # cns_web () { $CNS_SOLVE/bin/cns_web; } cns_header () { $CNS_SOLVE/bin/cns_header; } -cns_info () { cat $CNS_DATA/bin/cns_info; } -cns_transfer () { $CNS_SOLVE/bin/cns_transfer; } +cns_info () { cat $CNS_DATA/cns_info; } +cns_transfer () { $CNS_ROOT/bin/cns_transfer; } if [ -x $CNS_SOLVE/bin/cns_edit_local ]; then cns_edit () { $CNS_SOLVE/bin/cns_edit_local; } else
Fixed in 1.2.1, finally. Thanks for your patience in this.
(In reply to comment #4) >Thanks for your patience in this. Thanks for the fix :)
