I tried to update my org-mode using make up2 but got an error that looks similar.
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install -m 755 -d /tmp/tmp-orgtest
TMPDIR=/tmp/tmp-orgtest emacs -Q -batch --eval '(setq vc-handled-backends nil org-startup-folded nil)' --eval '(add-to-list '"'"'load-path (concat default-directory "lisp"))' --eval '(add-to-list '"'"'load-path (concat default-directory "testing"))' -l org-batch-test-init --eval '(setq org-batch-test t org-babel-load-languages (quote ( (awk . t) (C . t) (fortran . t) (maxima . t) (lilypond . t) (octave . t) (python . t) (sh . t) (perl . t) (emacs-lisp . t) (shell . t) (org . t))) org-test-select-re "\\(org\\|ob\\)" )' -l org-loaddefs.el -l cl -l testing/org-test.el -l ert -l org -l ox --eval '(org-test-run-batch-tests org-test-select-re)'
`flet' is an obsolete macro (as of 24.3); use either `cl-flet' or `cl-letf'.
Cannot open load file: ob-sh
make[1]: *** [test-dirty] Error 255
make: *** [up2] Error 2
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Where does it load the list of babel languages from?
Vikas