After upgrade to PHP 5.6 Pear stopped to work properly giving lot's of "Download of "pear/package_name" succeeded, but it is not a valid package archive". To fix this I had to:
# pear upgrade Archive_Tar downloading Archive_Tar-1.4.0.tgz ... Starting to download Archive_Tar-1.4.0.tgz (x bytes) .......done: x bytes could not extract the package.xml file from "/tmp/pear/download/Archive_Tar-1.4.0.tgz" Download of "pear/Archive_Tar" succeeded, but it is not a valid package archive Error: cannot download "pear/Archive_Tar" Download failed upgrade failed # cd /tmp/pear/download/ # tar -zxvf Archive_Tar-1.4.0.tgz package.xml Archive_Tar-1.4.0/Archive/Tar.php Archive_Tar-1.4.0/docs/Archive_Tar.txt # mv /usr/share/pear/Archive/Tar.php /usr/share/pear/Archive/Tar.php.org # cp /tmp/pear/download/Archive_Tar-1.4.0/Archive/Tar.php /usr/share/pear/Archive/
and now I can run 'pear upgrade-all' without any issues.
Alternatviely, after upgrading to PHP 5.6 you can completely remove and re-install PEAR from remi repository:
yum erase php-pear yum install --enablerepo=remi --enablerepo=remi-php56 php-pear