emerge glpk fails. It seems that some header files are missing or something: /usr/include/mysql/my_global.h:361:24: asm/atomic.h: No such file or directory i686-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I../include -I/usr/include/mysql -I/usr/include/iodbc -march=pentium4 -O2 -pipe -fomit-frame-pointer -MT glpssx02.lo -MD -MP -MF .deps/glpssx02.Tpo -c glpssx02.c -fPIC -DPIC -o .libs/glpssx02.o i686-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I../include -I/usr/include/mysql -I/usr/include/iodbc -march=pentium4 -O2 -pipe -fomit-frame-pointer -MT glptsp.lo -MD -MP -MF .deps/glptsp.Tpo -c glptsp.c -fPIC -DPIC -o .libs/glptsp.o i686-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I../include -I/usr/include/mysql -I/usr/include/iodbc -march=pentium4 -O2 -pipe -fomit-frame-pointer -MT glpssx02.lo -MD -MP -MF .deps/glpssx02.Tpo -c glpssx02.c -o glpssx02.o >/dev/null 2>&1 In file included from glpsql.c:957: /usr/include/mysql/my_global.h:361:24: asm/atomic.h: No such file or directory mv -f .deps/glpssx02.Tpo .deps/glpssx02.Plo make[2]: *** [glpsql.lo] Error 1 make[2]: *** Waiting for unfinished jobs.... i686-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I../include -I/usr/include/mysql -I/usr/include/iodbc -march=pentium4 -O2 -pipe -fomit-frame-pointer -MT glptsp.lo -MD -MP -MF .deps/glptsp.Tpo -c glptsp.c -o glptsp.o >/dev/null 2>&1 mv -f .deps/glptsp.Tpo .deps/glptsp.Plo make[2]: Leaving directory `/var/tmp/portage/sci-mathematics/glpk-4.32/work/glpk-4.32/src' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory `/var/tmp/portage/sci-mathematics/glpk-4.32/work/glpk-4.32' make: *** [all] Error 2 Reproducible: Always Steps to Reproduce: 1.unmask glpk 4.32 2.emerge glpk-4.32 Actual Results: Compilation stop due to: /usr/include/mysql/my_global.h:361:24: asm/atomic.h: No such file or directory dev-db/mysql-5.0.60-r1 installed locate atomic.h /usr/lib/klibc/include/asm-x86/atomic.h /usr/lib/klibc/include/asm-generic/atomic.h /usr/lib/klibc/include/asm-generic/bitops/atomic.h /usr/lib/klibc/include/asm-generic/bitops/ext2-atomic.h /usr/lib/klibc/include/asm-generic/bitops/ext2-non-atomic.h /usr/lib/klibc/include/asm-generic/bitops/non-atomic.h /usr/share/doc/sqlite-3.5.9/html/c3ref/c_iocap_atomic.html /usr/include/isc/atomic.h /usr/include/qt4/Qt/qatomic.h /usr/include/qt4/QtCore/qatomic.h /usr/include/alsa/iatomic.h /usr/include/apr-1/apr_atomic.h /usr/include/glib-2.0/glib/gatomic.h /usr/include/stlport/stl/_sparc_atomic.h /usr/include/mono-1.0/mono/io-layer/atomic.h
Try unmerging mysql and emerging it again (NOTE: don't skip the unmerge part and try to install on top of the old mysql). It should fix this problem, which seems to stem from using a mysql that was built against old kernel headers that have since been upgraded (see bug 163151) *** This bug has been marked as a duplicate of bug 163151 ***
That solved the problem. Thanks! Daniel
