[solved: with timestamp 20180226 there is a new set of packages for gcc@4.9.4 on S11 and OI that has correct settings for directory pkgconfig. Just re-try your update or install now. Thanks for your patience and have fun using the added java compiler "gcj"! edited 20180227-0900-UTC]

A quick note from the workbench..

the last udpate to GCC 4.9.4 and including the java compiler gcj introduced a problem with a conflicting set of attributes to the patch /usr/gnu/lib/pkgconfig and /usr/gnu/lib/amd64/pkgconfig.