Note: This is a historical reference, not a current security baseline. Magento 1 is end-of-life.

During Magento upgrade via Magento Connect Manager or from ./mage upgrade-all CLI command there is the following or similar message reported in console:

package community/lib_linlibertinefont 2.8.14.17 conflicts with: community/mage_core_adminhtml 1.9.3.10

Cause

Most likely cause of this dependency issue is the following:
upgrade-all: Failed to delete files: ./pkginfo/Mage_All_Latest.txt Check permissions

The actual error message is just masked in long output from ./mage upgrade-all

Solution

The solution is to locate actual error message and correct it, i.e. delete pkginfo/Mage_All_Latest.txt

If you have any difficulties with solving this problem or got a similar one, please let us know in comments below, so we can find the solution together.