Problem bytecompiling an Emacs add-on package
I'm struggling with my first Emacs package, biomode
<http://evolution.bmc.uu.se/~thomas/mol_linux/biomode/>.
Everything works fine if I do not try to bytecompile.
Now, I add a emacsen-install script, which is installed by dh_installemacsen.
When I 'dpkg -i' the resulting package, I see the attempt to bytecompile, a
ton of errors (see the attached file) and the mode no longer works in emacs19
(but it works fine on xemacs20):
File mode specification error: (void-variable bio-gencode-table)
Is it possible that a '.el' file works only when not compiled?
(Reading database ... 45320 files and directories currently installed.)
Preparing to replace biomode 1.002-1 (using ../biomode_1.002-1_i386.deb) ...
remove/biomode: Handling removal of emacsen flavor emacs
remove/biomode: Handling removal of emacsen flavor emacs19
emacsen-common: purging byte-compiled files for emacs19
remove/biomode: Handling removal of emacsen flavor xemacs20
emacsen-common: purging byte-compiled files for xemacs20
Unpacking replacement biomode ...
Setting up biomode (1.002-1) ...
install/biomode: Handling install of emacsen flavor emacs
install/biomode: Handling install of emacsen flavor emacs19
install/biomode: byte-compiling for emacs19
Loading 00debian-vars...
Loading 50dpkg-dev...
Loading 50psgml-init...
Loading 92bio-mode...
While compiling toplevel forms in file /usr/share/emacs19/site-lisp/bio-mode.el:
** reference to free variable bio-gencode-table
** assignment to free variable gene-direction
** assignment to free variable gene-start
** assignment to free variable gene-stop
** assignment to free variable gene-type
** reference to free variable gene-stop
** reference to free variable gene-start
** assignment to free variable gene-length
** reference to free variable gene-type
** reference to free variable gene-direction
** reference to free variable gene-length
While compiling bio-embl-entry-extract:
** assignment to free variable translation-name-tmp
** assignment to free variable gene-direction
** assignment to free variable gene-start
** assignment to free variable gene-stop
** reference to free variable gene-start
** reference to free variable gene-direction
** reference to free variable translation-name-tmp
While compiling bio-embl-extract:
** assignment to free variable buffer-name
** reference to free variable buffer-name
** assignment to free variable entry-counter
** assignment to free variable embl-current-entry
** reference to free variable embl-current-entry
** reference to free variable entry-counter
While compiling bio-blast-on-region:
** assignment to free variable bio-current-seq
** assignment to free variable bio-seq-file
** reference to free variable bio-current-seq
** reference to free variable seq
** assignment to free variable bio-prompt
** reference to free variable bio-prompt
** assignment to free variable buffer-name
** reference to free variable buffer-name
** assignment to free variable bio-temp-file
** reference to free variable bio-seq-file
** reference to free variable bio-temp-file
** assignment to free variable bio-command
** reference to free variable bio-command
** assignment to free variable bio-blastp-res
** reference to free variable bio-blastp-res
While compiling bio-search-forward:
** misplaced interactive spec: (interactive "p
sSearch for oligo: ")
While compiling bio-gccontent-on-region:
** assignment to free variable bio-current-seq
** reference to free variable bio-current-seq
While compiling toplevel forms:
** assignment to free variable bio-current-seq
** reference to free variable bio-current-seq
** assignment to free variable bio-current-seq
** reference to free variable bio-current-seq
While compiling bio-writeseq:
** assignment to free variable bio-current-seq
** reference to free variable bio-current-seq
While compiling bio-get-sequence:
** assignment to free variable bio-current-seq
** assignment to free variable bio-seq-file
** assignment to free variable buffer-name
** reference to free variable buffer-name
** reference to free variable bio-current-seq
While compiling bio-check-seq-type:
** assignment to free variable bio-acgt
** reference to free variable bio-acgt
While compiling bio-translate-codon:
** reference to free variable bio-gencode-table
While compiling bio-translate-string:
** assignment to free variable bio-aa-seq
** reference to free variable bio-aa-seq
While compiling bio-set-genetic-code:
** reference to free variable bio-gencode-table
While compiling bio-translate-region:
** assignment to free variable bio-current-seq
** assignment to free variable bio-seq-file
** assignment to free variable buffer-name
** reference to free variable buffer-name
** reference to free variable bio-gencode-table
** reference to free variable bio-current-seq
** reference to free variable seq
** reference to free variable bio-seq-file
While compiling bio-reverse-region:
** delete-region called with 3 args, but requires 2
While compiling bio-antiparallel-region:
** delete-region called with 3 args, but requires 2
While compiling bio-complement-region:
** delete-region called with 3 args, but requires 2
While compiling the end of the data:
** The following functions are not known to be defined: setf, gethash,
with-output-to-string, make-hash-table, replace-in-string,
exec-to-string, isearch-make-extent, count, loop, return,
char-to-int, substitute, puthash, endp, popup-menu, add-submenu,
add-menu-button
Wrote /usr/share/emacs19/site-lisp/bio-mode.elc
Done
install/biomode: Handling install of emacsen flavor xemacs20
install/biomode: byte-compiling for xemacs20
Loading /usr/share/emacs/site-lisp/debian-startup...
Loading 00debian...
Loading 00debian-vars...
Loading 50dpkg-dev...
Loading 92bio-mode...
Compiling /usr/share/xemacs20/site-lisp/bio-mode.el...
While compiling toplevel forms in file /usr/share/xemacs20/site-lisp/bio-mode.el:
** assignment to free variable bio-gencode-table
While compiling bio-embl-entry-gtf:
** assignment to free variable gene-direction
** assignment to free variable gene-start
** assignment to free variable gene-stop
** assignment to free variable gene-type
** reference to free variable gene-stop
** reference to free variable gene-start
** assignment to free variable gene-length
** reference to free variable gene-type
** reference to free variable gene-direction
** reference to free variable gene-length
While compiling bio-embl-entry-extract:
** assignment to free variable translation-name-tmp
** assignment to free variable gene-direction
** assignment to free variable gene-start
** assignment to free variable gene-stop
** reference to free variable gene-start
** reference to free variable gene-direction
** reference to free variable translation-name-tmp
** variable translation-name bound but not referenced
While compiling bio-embl-extract:
** assignment to free variable buffer-name
** reference to free variable buffer-name
** assignment to free variable entry-counter
** assignment to free variable embl-current-entry
** reference to free variable embl-current-entry
** reference to free variable entry-counter
While compiling bio-blast-on-region:
** assignment to free variable bio-current-seq
** assignment to free variable bio-seq-file
** reference to free variable bio-current-seq
** reference to free variable seq
** assignment to free variable bio-prompt
** reference to free variable bio-prompt
** assignment to free variable buffer-name
** reference to free variable buffer-name
** assignment to free variable bio-temp-file
** reference to free variable bio-seq-file
** reference to free variable bio-temp-file
** assignment to free variable bio-command
** reference to free variable bio-command
** assignment to free variable bio-blastp-res
** reference to free variable bio-blastp-res
While compiling bio-search-forward:
** misplaced interactive spec: (interactive "p
sSearch for oligo: ")
While compiling bio-gccontent-on-region:
** assignment to free variable bio-current-seq
** reference to free variable bio-current-seq
While compiling toplevel forms:
** assignment to free variable bio-current-seq
** reference to free variable bio-current-seq
While compiling bio-seqinfo:
** assignment to free variable bio-current-seq
** reference to free variable bio-current-seq
While compiling bio-writeseq:
** assignment to free variable bio-current-seq
** reference to free variable bio-current-seq
** variable buffer-name bound but not referenced
While compiling bio-get-sequence:
** assignment to free variable bio-current-seq
** assignment to free variable bio-seq-file
** assignment to free variable buffer-name
** reference to free variable buffer-name
** reference to free variable bio-current-seq
While compiling bio-check-seq-type:
** assignment to free variable bio-acgt
** reference to free variable bio-acgt
While compiling bio-translate-codon:
** reference to free variable bio-gencode-table
While compiling bio-translate-string:
** assignment to free variable bio-aa-seq
** reference to free variable bio-aa-seq
While compiling bio-set-genetic-code:
** reference to free variable bio-gencode-table
While compiling bio-translate-region:
** assignment to free variable bio-current-seq
** assignment to free variable bio-seq-file
** assignment to free variable buffer-name
** reference to free variable buffer-name
** reference to free variable bio-gencode-table
** reference to free variable bio-current-seq
** reference to free variable seq
** reference to free variable bio-seq-file
Wrote /usr/share/xemacs20/site-lisp/bio-mode.elc
Done
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