I received this error when starting Sublime Text after upgrading to El Capitan. The author of package control is aware of the issue (https://github.com/wbond/package_control/issues/1002) and is working on it but if it annoys you enough to do a workaround, here it is. Remove all of the certificates from your Keychain that are shown when you run the same command: `/usr/bin/security dump-trust-settings -d`
My output looked something like this:
Number of trusted certs = 5 Cert 0: stuff.co Number of trust settings : 1 Trust Setting 0: Policy OID : Apple X509 Basic Allowed Error : CSSMERR_TP_CERT_EXPIRED Result Type : kSecTrustSettingsResultTrustRoot Cert 1: GTE CyberTrust Global Root SecTrustSettingsCopyTrustSettings: The specified item could not be found in the keychain. Cert 2: Class 3 Public Primary Certification Authority SecTrustSettingsCopyTrustSettings: The specified item could not be found in the keychain.
- Open Keychain
- click on your login keychain
- Go to the search box
- Type in the name shown in the Cert <n>: field (in this case stuff.co)
- Select the Certificate entry that is shown in the results
- Right-click -> Delete “…”
- Enter your password (twice for me)
Continue until you run the dump-trust-settings command and get
SecTrustSettingsCopyCertificates: No Trust Settings were found.
Follow Ryan 
Thank you! This has been bugging me for a while.
Thanks
I need that certificate, I can’t just delete it. In any case, how can deleting a certificate from your computer be a fix? Those certificates are there for a reason.
Sorry, I didn’t record information about the specific certificates I deleted so I can’t provide more details. I believe they were all RSA 1024 bit CA certificates which are being phased out and El Capitan doesn’t trust them by default. You could probably force trust them again to get rid of the error and keep the certs. I’ve not come across a site that requires them since deleting them so no harm done for me. Your experience may vary.
In my case it’s a company certificate which I definitely need. I guess I’ll just wait for the official fix.
Thanks