Hmm, I see that the delete in modify-phases doesn't "actually" delete what you tell it to, but rather just adds (delete _) to the end of the list:
(apologies for the long text; just notice that move-gui, for example isn't actually removed from the output, and that (delete (quote move-gui)) is added at the end) --8<---------------cut here---------------start------------->8--- scheme@(guix-user)> (substitute-keyword-arguments transmission-args ((#:phases phases) #~(modify-phases #$phases (delete 'move-gui) (delete 'glib-or-gtk-wrap) (delete 'wrap-program)))) $30 = (#:imported-modules ((guix build glib-or-gtk-build-system) (guix build cmake-build-system) (guix build gnu-build-system) (guix build utils) (guix build gremlin) (guix elf)) #:modules (((guix build glib-or-gtk-build-system) #:prefix glib-or-gtk:) (guix build cmake-build-system) (guix build utils)) #:phases #<gexp (modify-phases #<gexp-input #<gexp (modify-phases %standard-phases (add-after (quote unpack) (quote remove-kernel-version) (lambda _ (substitute* "third-party/miniupnp/miniupnpc/updateminiupnpcstrings.sh" (("OS_VERSION=`uname -r`") "OS_VERSION=Guix")))) (replace (quote check) (lambda* (#:key tests? parallel-tests? #:allow-other-keys) (if tests? (invoke "ctest" "-E" "usesBootstrapFile" "-j" (if parallel-tests? (number->string (parallel-job-count)) "1")) (format #t "test suite not run~%")))) (add-after (quote install) (quote move-gui) (lambda* (#:key outputs #:allow-other-keys) (mkdir-p (string-append #<gexp-output gui> "/bin")) (mkdir-p (string-append #<gexp-output gui> "/share/man/man1")) (rename-file (string-append #<gexp-output out> "/bin/transmission-gtk") (string-append #<gexp-output gui> "/bin/transmission-gtk")) (for-each (lambda (dir) (rename-file (string-append #<gexp-output out> "/share/" dir) (string-append #<gexp-output gui> "/share/" dir))) (quote ("applications" "icons" "metainfo"))) (rename-file (string-append #<gexp-output out> "/share/man/man1/transmission-gtk.1") (string-append #<gexp-output gui> "/share/man/man1/transmission-gtk.1")))) (add-after (quote move-gui) (quote glib-or-gtk-wrap) (lambda* (#:key outputs #:allow-other-keys #:rest args) (apply (assoc-ref glib-or-gtk:%standard-phases (quote glib-or-gtk-wrap)) #:glib-or-gtk-wrap-excluded-outputs (list "out") args))) (add-after (quote glib-or-gtk-wrap) (quote wrap-program) (lambda* (#:key outputs #:allow-other-keys) (wrap-program (string-append #<gexp-output gui> "/bin/transmission-gtk") (quasiquote ("GDK_PIXBUF_MODULE_FILE" = ((unquote (getenv "GDK_PIXBUF_MODULE_FILE"))))))))) gnu/packages/bittorrent.scm:113:8 7f08847bfcc0>:out> (delete (quote move-gui)) (delete (quote glib-or-gtk-wrap)) (delete (quote wrap-program))) 7f088c309bd0>) --8<---------------cut here---------------end--------------->8--- Is this the problem? Is there some way to "actually" delete the offending entries that mention #<gexp-output gui>?