I have no idea if it relates to what you describe with cask and dependencies, but I had the same error and found several old threads stating that it's caused by installing org when it's already initialized.
I solved it by Emacs -q and reinstalling from elpa. If you search for the old threads there was a link to documentation that explains why this occurs which may be of some help addressing with cask.
Good afternoon,
Just upgraded to 8.2.7 and was surprised to get the
"org-with-silent-modifications" error. Here is what happened.
The first time that I set up my Emacs libraries, using Cask, which
uses the Emacs package manager, it install org2blog which has org
8.2.6 as a dependency. Then, Cask installed org-plus-contrib 8.2.6 and
life went on. Then I can cask update to get the 8.2.7 release (Cask
just pulls from the org repo).
Started up Emacs and got that aforementioned error. The issue seemed
to revolve around load-path or
load-order, and I didn't understand any further than that. It was very
strange because my whole approach
had been to automate everything so it would "just work".
Poking around, I eventually saw that org2blog depends on "org" (yes
now I admit that I didn't know this when
at first, but that is not relevant here I believe). That just didn't
look right to have both orgs in there, so I deleted plain old "org"
and commented out the org2blog load. Now Emacs works again.
The issue seems to be that org-plus-contrib doesn't satisfy "org" from
a package manager perspective.
This surprised me because the former is a superset.
My next step now is to figure out what to do from a package
perspective, because I would like to keep
org2blog in there.
Anyone else encountered this and want to share the solution?
I'm going to think about this some more and see.
Kind regards,
Grant Rettke | AAAS, ACM, ASA, FSF, IEEE, SIAM, Sigma Xi
gcr@wisdomandwonder.com | http://www.wisdomandwonder.com/
“Wisdom begins in wonder.” --Socrates
((λ (x) (x x)) (λ (x) (x x)))
“Life has become immeasurably better since I have been forced to stop
taking it seriously.” --Thompson