I'm trying to code sign a JAR file and am using JDK 1.7u1. We acquired a GoDaddy Code Signing certificate and I followed the instructions (Approach 1) here: http://help.godaddy.com/article/4780
The JAR signs fine, however whenever I try to run the command:
jarsigner -verify on my signed JAR using JDK 1.7u1 I get the following output:  
s        180 Mon Dec 05 10:24:32 EST 2011 META-INF/MANIFEST.MF
      [entry was signed on 12/5/11 10:24 AM]
      X.509, CN=Removed Company Name, O=Removed Company Name, L=Removed City, ST=Removed State, C=US
      [certificate is valid from 12/2/11 4:30 PM to 12/2/13 4:30 PM]
      X.509, SERIALNUMBER=00000000, CN=Go Daddy Secure Certification Authority, OU=http://certificates.godaddy.com/repository, O="GoDaddy.com, Inc.", L=Scottsdale, ST=Arizona, C=US
      [certificate is valid from 11/15/06 8:54 PM to 11/15/26 8:54 PM]
      X.509, OU=Go Daddy Class 2 Certification Authority, O="The Go Daddy Group, Inc.", C=US
      [certificate is valid from 6/29/04 1:06 PM to 6/29/34 1:06 PM]
      [CertPath not validated: null]
         342 Mon Dec 05 10:24:34 EST 2011 META-INF/JAVACSC.SF
        6180 Mon Dec 05 10:24:34 EST 2011 META-INF/JAVACSC.RSA
           0 Mon Dec 05 10:24:30 EST 2011 META-INF/
sm      2161 Wed Nov 30 10:23:20 EST 2011 C:/Users/Seth/Desktop/JAR/RunAppSF.class
      [entry was signed on 12/5/11 10:24 AM]
      X.509, CN=Removed Company Name, O=Removed Company Name, L=Removed City, ST=Removed State, C=US
      [certificate is valid from 12/2/11 4:30 PM to 12/2/13 4:30 PM]
      X.509, SERIALNUMBER=00000000, CN=Go Daddy Secure Certification Authority, OU=http://certificates.godaddy.com/repository, O="GoDaddy.com, Inc.", L=Scottsdale, ST=Arizona, C=US
      [certificate is valid from 11/15/06 8:54 PM to 11/15/26 8:54 PM]
      X.509, OU=Go Daddy Class 2 Certification Authority, O="The Go Daddy Group, Inc.", C=US
      [certificate is valid from 6/29/04 1:06 PM to 6/29/34 1:06 PM]
      [CertPath not validated: null]
  s = signature was verified 
  m = entry is listed in manifest
  k = at least one certificate was found in keystore
  i = at least one certificate was found in identity scope
jar verified.
Warning: 
This jar contains entries whose certificate chain is not validated.
I also tried the jarsigner -verify command using the same JAR as above on JDK 1.6u26 and 1.6u14 and it came back as being fine.  (Output below from 1.6u26).
         180 Mon Dec 05 10:24:32 EST 2011 META-INF/MANIFEST.MF
         342 Mon Dec 05 10:24:34 EST 2011 META-INF/JAVACSC.SF
        6180 Mon Dec 05 10:24:34 EST 2011 META-INF/JAVACSC.RSA
           0 Mon Dec 05 10:24:30 EST 2011 META-INF/
sm      2161 Wed Nov 30 10:23:20 EST 2011 C:/Users/Seth/Desktop/JAR/RunAppSF.class
      [entry was signed on 12/5/11 10:24 AM]
      X.509, CN=Removed Company Name, O=Removed Company Name, L=Removed City, ST=Removed State, C=US
      [certificate is valid from 12/2/11 4:30 PM to 12/2/13 4:30 PM]
      X.509, SERIALNUMBER=00000000, CN=Go Daddy Secure Certification Authority, OU=http://certificates.godaddy.com/repository, O="GoDaddy.com, Inc.", L=Scottsdale, ST=Arizona, C=US
      [certificate is valid from 11/15/06 8:54 PM to 11/15/26 8:54 PM]
      [KeyUsage extension does not support code signing]
      X.509, OU=Go Daddy Class 2 Certification Authority, O="The Go Daddy Group, Inc.", C=US
      [certificate is valid from 6/29/04 1:06 PM to 6/29/34 1:06 PM]
  s = signature was verified 
  m = entry is listed in manifest
  k = at least one certificate was found in keystore
  i = at least one certificate was found in identity scope
jar verified.
Am I missing an extra step I need to take to get the JAR signed properly for JDK 1.7?
I have been having the same issue and if it can help others the problem is in how jarsigner finds the keystore.
In order to fix the issue do:
jarsigner -verify -keystore xxxx.jks mysignedjar.jar
You are not missing anything and you are definitely not alone with this problem. After a struggle of almost 12 hours, I figured out that the root of the problem lies in mixing binaries from JDK 1.7 with an older version of Java such as JRE-1.6. To be more precise, keytool comes with JRE, while JDK ships with both keytool and jarsigner.
So, to resolve the issue, I have completely uninstalled JDK-1.7 from my system and installed JDK-1.6 Update 30. Now, if I would do jarsigner -verify -verbose -certs blah.jar it would produce jar verified without any warning which I believe is what you expect.
It's just a warning you can ignore.
If you really don't want to ignore it then tell jarsigner where your keystore is when you verify.
jarsigner -verbose -verify -keystore ${KEYSTORE_PATH} ${YOUR_JAR_FILE}
This is just a new feature in JDK 7.
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