IssuesPage202407

Known Issues in the 20240710 BUSTER (including also Pipedream, Grade2 and Rhofit) release:

• Perl messages about "Use of uninitialized value in numeric eq ..."

• Problem with the "qm" and "force_field" options

• See also the Grade2 known issues page

Perl messages about "Use of uninitialized value in numeric eq ..."

There is a buglet in the core Perl interpreter distributed with many OS versions, that produces warning messages of the type

Use of uninitialized value in numeric eq (==) at /usr/lib/x86_64-linux-gnu/perl-base/IO/Select.pm line 68.

Although without effect on the functionality of a "pipedream", "buster-report", "rhofit" or "grade" job, they can still be disconcerting and plain ugly. The easiest solution is to surpress all warning messages from our perl scripts by adding "-X" to the perl invocation. This can be done e.g. by adding

  export KeepFromEnv_BDG_perl="yes"
  export BDG_perl="/usr/bin/perl -X"

to $BDG_home/setup_local.sh and/or

  setenv KeepFromEnv_BDG_perl "yes"
  setenv BDG_perl_arg "-X"

to $BDG_home/setup_local.csh. Another option is to point to a local (distributed) version of Perl by adding

  export KeepFromEnv_BDG_perl="yes"
  case `uname` in
    Linux) export BDG_perl="$BDG_home/.mc/linux64/3.9/bin/perl";;
    Darwin) export BDG_perl="$BDG_home/.mc/darwin/3.9/bin/perl";;
  esac

to $BDG_home/setup_local.sh and/or

  setenv KeepFromEnv_BDG_perl "yes"
  if ( `uname` == "Linux" ) then
    setenv BDG_perl "$BDG_home/.mc/linux64/3.9/bin/perl"
  else
    setenv BDG_perl "$BDG_home/.mc/darwin/3.9/bin/perl"
  endif

to $BDG_home/setup_local.csh.

Alternatively, one could run the above commands also via e.g.

  KeepFromEnv_BDG_perl="yes" BDG_perl_arg="-X" pipedream ...      # bash/sh/zsh
- or -
  env KeepFromEnv_BDG_perl="yes" BDG_perl_arg="-X" pipedream ...  # tcsh/csh

To see if your particular perl version (as used by our programs) is affected by this issue, you can use the attached test_perl.sh script. Running

  ./test_perl.sh

could return something like

##
## Testing perl environment/setup for BUSTER (Pipedream, buster-report etc)
## (for helpc contact us at buster-develop@GlobalPhasing.com)
##


  BDG_home = /home/software/GPhL/BUSTER/20240710
  BDG_perl = /usr/bin/perl (v5.34.0 - see "/usr/bin/perl -V" for more details)


### see: https://github.com/Perl/perl5/issues/18238

 interaction with IPC::Cmd::run (GH 18238) =  >>> WARNING <<< 

 $IO::Select::VERSION = 1.46
 $IPC::Cmd::VERSION   = 1.04
 Perl version         = 5.034000
                      = 5.34.0

(showing vulnerability of Ubuntu 22.04 LTS) or

##
## Testing perl environment/setup for BUSTER (Pipedream, buster-report etc)
## (for helpc contact us at buster-develop@GlobalPhasing.com)
##


  BDG_home = /home/software/GPhL/BUSTER/20240710
  BDG_perl = /bin/perl (v5.36.0 - see "/bin/perl -V" for more details)


### see: https://github.com/Perl/perl5/issues/18238

 interaction with IPC::Cmd::run (GH 18238) = OK

 $IO::Select::VERSION = 1.49
 $IPC::Cmd::VERSION   = 1.04
 Perl version         = 5.036000
                      = 5.36.0

(showing Debian 12 bookworm being fixed).

The bug was introduced (it seems) at v1.42 of Perl's IO::Select and fixed at v1.48 with this bug report.

Problem with the qm and forcefield options

For both BUSTER and gelly_refine the two options: "qm" and "force_field" are not working as expected. This will be fixed in the next release.

Until then a work around exists if there is only a single uncharged ligand. Simply append an underscore to the three-letter code i.e.

gelly_refine -qm I0G_ ...

and it should work.