I am trying to install the 32 bits staden-1.7.0 on a 32 bits chroot environment running on a 64 bits Ubuntu 7.04.
I think that I set up all the paths correctly:
$ ls $STADENROOT
course demo doc lib linux-bin staden.login staden.profile tables userdata Version
$ echo $MACHINE
$ ls $LD_LIBRARY_PATH
libcopy_reads.so libitcl3.3.so libpng12.so libprimer3.so libtcl8.4.so
libgap.so libitk3.3.so libpng12.so.0 libread.so libtext_utils.so
libg.so libmisc.so libpng12.so.0.1.2.7 libseq_utils.so libtk8.4.so
libhaplo.so libmutlib.so libprefinish.so libspin.so libtk_utils.so
$ ls $STADTABL
2bars_h.bmp eia.wts gaprc_menu_mito m13mp18_primers prokprom_35.wts spin2rc
2bars_v.bmp emboss_menu gaprc_menu_viewer niprc README spin_embossrc
align_lib_nuc_matrix fak2rc gcodes NOTEDB RENZYM.4 spinrc
alus FEATCOLDB GTAGDB nuc_matrix RENZYM.6 tk_utilsrc
blast_data FEATQUALDB haplorc pam250 RENZYM.ALL trevrc
cap2rc FEATUREDB help_config perceptron.wts renzyme_bairoch unchecked.gif
cap3rc follow.bitmap ied.wts phraprc seqedrc vector_primer
checked.gif gaprc itcl3.3rc prefinishrc shlib.conf vectors
config.prefinish gaprc_menu_demo itk3.3rc pregap4rc siprc
copy_readsrc gaprc_menu_full iwidgetsrc prokprom_10.wts spin2_embossrc
$ ls $STADLIB
cap2 fak2 itcl3.3 linux-binaries pregap4 spin_emboss tk
cap3 gap itk3.3 phrap spin tablelist3.4 tk_utils
copy_reads haplo iwidgets prefinish spin2_emboss tcl trev
$ echo $PATH
$ ls $TCL_LIBRARY
auto.tcl http1.0 init.tcl.02.10.02 ldAout.tcl opt0.4 safe.tcl tcltest2.2
encoding http2.4 init.tcl.orig license.terms package.tcl tclAppInit.c word.tcl
history.tcl init.tcl ldAix msgcat1.3 parray.tcl tclIndex
$ ls $TK_LIBRARY
bgerror.tcl entry.tcl mkpsenc.tcl panedwindow.tcl scrlbar.tcl.orig tkfbox.tcl.orig
button.tcl focus.tcl msgbox.tcl pkgIndex.tcl spinbox.tcl tk.tcl
choosedir.tcl images msgs pkgIndex.tcl.orig tclIndex unsupported.tcl
clrpick.tcl license.terms obsolete.tcl prolog.ps tearoff.tcl xmfbox.tcl
comdlg.tcl listbox.tcl optMenu.tcl safetk.tcl text.tcl xmfbox.tcl.orig
console.tcl listbox.tcl.orig palette.tcl scale.tcl tkAppInit.c
dialog.tcl menu.tcl palette.tcl.orig scrlbar.tcl tkfbox.tcl
But when I try to run any executable I have the following error:
invalid command name "load_package"
(file "/home/nas/pignatelli/download/staden-linux-x86-1-7-0/lib/trev/trev.tcl" line 1468)
Does anyone have any idea on how to solve this?
Thank you very much in advance,
My first question is why if you launch 'pregap4' ('pregap' is not in 1.7.0) do you get a message from 'trev.tcl'?
'pregap4' is a script and at its end it has 'stash' run 'pregap4.tcl', which is in 'lib/pregap4'. About two thirds down that tcl file is 'load_package tk_utils'. So the error you're getting seems to be a second instance of that command ('load_package tk_utils'). 'Trev' is called by one of pregap4's modules, 'interactive_clip.p4m', but when you launch 'trev', 'spin' or 'gap4' do you get similar error messages?
This seems to be an usual error even for 'staden'.
You should check (although this probably isn't an issue) that your Staden' libraries are completely compatible with your OS environment. Go into $STADENROOT/lib/linux-binaries and do a 'file libxxxx.so' on each library there (so 'file libread.so', 'file libtk_utils.so' and so on) and then try 'ldd libtk_utils.so' and so on. You should be worried if 'ldd' returns a "not found" for any of the referenced libraries, or if it gives the even more cryptic (and unreliable) error "file or directory not found" which would indicate that you have a conflict between 32 bit and 64 bit libraries.
load_package is in $STADLIB/tk_utils/user_defaults.tcl
The "stash" shell is basically Tcl with a few tweaks. Try starting stash and doing "puts $auto_path". Eg:
% puts $auto_path
/software/badger/opt/staden_test/lib/tcl /software/badger/opt/staden_test/lib /usr/local/lib /software/badger/opt/staden_test/lib/tk_utils
Here we see the tk_utils directory listed. Make sure you have a tclIndex file in the tk_utils directory you've installed as this is used by the Tcl auto-loading system to provide the mapping of currently unloaded procedures to the files that provide them. Eg the auto-loading can be seen in use here:
% info args load_package
"load_package" isn't a procedure
wrong # args: should be "load_package tcldir ?libdir? ?name? ?init?"
% info args load_package
tcldir libdir name init
Finally, sometimes setting the STADEN_DEBUG environment variable can track down library issues. Some of the warnings issues are harmless (failure to find a .so file for a library which is pure-tcl and doesn't even need a C .so file) while others may be indicative of missing system components (libg2c perhaps seems quite common).
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