I am seeing a failure both when using --setup-ca in ipa-replica-install and
running ipa-ca-install separately when --setup-ca not used.

From an ipa-ca-install:

Configuring certificate server (pki-tomcatd). Estimated time: 3 minutes 30
seconds
[1/22]: creating certificate server user
[2/22]: configuring certificate server instance
ipa.ipaserver.install.cainstance.CAInstance: CRITICAL Failed to configure CA
instance: Command /usr/sbin/pkispawn' '-s' 'CA' '-f' '/tmp/tmp4raVhy
returned non-zero exit status 1
ipa.ipaserver.install.cainstance.CAInstance: CRITICAL See the installation logs
and the following files/directories for more information:
ipa.ipaserver.install.cainstance.CAInstance: CRITICAL
/var/log/pki-ca-install.log
ipa.ipaserver.install.cainstance.CAInstance: CRITICAL /var/log/pki/pki-tomcat
[error] RuntimeError: CA configuration failed.

Your system may be partly configured.
Run /usr/sbin/ipa-server-install --uninstall to clean up.

CA configuration failed.

Then at the end of the /var/log/pki/pki-tomcat/ca/debug, I see this:

[01/Apr/2016:20:49:37]http-bio-8443-exec-3: SystemConfigService: clone does
not have all the certificates.
[01/Apr/2016:20:49:37]http-bio-8443-exec-3: Clone does not have all the
required certificates

Steps to Reproduce:

1.  Install IPA master
2.  Install IPA replica
3.  Install CA on replica using:
ipa-ca-install -p Password -w Password /var/lib/ipa/replica-file.gpg

Problem was also seen with 2 steps:
1.  Install IPA master
2.  Install IPA replica with CA
include --setup-ca in ipa-replica-install command.

Actual results:

Fails as mentioned above.

Expected results:

No failure and CA properly installed.

Additional info:

While this particular problem might be caused by environment issue, invalid certificate could happen due to various reasons (e.g. expired certificate, future certificate validity, missing extension). To help troubleshooting the installation code should be fixed to show which specific certificate is missing/invalid.