Bug 232959

Summary:	sci-mathematics/glpk-4.29 fails (mysql-5.0.60-r1 header problem)
Product:	Gentoo Linux	Reporter:	Patrizio Bassi <patrizio.bassi>
Component:	New packages	Assignee:	Gentoo Linux MySQL bugs team <mysql-bugs>
Status:	RESOLVED WORKSFORME
Severity:	normal	CC:	cbm
Priority:	High
Version:	2008.0
Hardware:	All
OS:	Linux
Whiteboard:
Package list:		Runtime testing required:	---

Description Patrizio Bassi 2008-07-25 19:38:03 UTC

/bin/sh ../libtool --tag=CC   --mode=compile x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I../include  -I/usr/include/mysql  -I/usr/include/iodbc  -O3 -pipe -mtune=core2 -march=core2 -fomit-frame-pointer -mmmx -msse -msse2 -msse3 -mfpmath=sse -MT glpssx02.lo -MD -MP -MF .deps/glpssx02.Tpo -c -o glpssx02.lo glpssx02.c
 x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I../include -I/usr/include/mysql -I/usr/include/iodbc -O3 -pipe -mtune=core2 -march=core2 -fomit-frame-pointer -mmmx -msse -msse2 -msse3 -mfpmath=sse -MT glpsql.lo -MD -MP -MF .deps/glpsql.Tpo -c glpsql.c  -fPIC -DPIC -o .libs/glpsql.o
 x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I../include -I/usr/include/mysql -I/usr/include/iodbc -O3 -pipe -mtune=core2 -march=core2 -fomit-frame-pointer -mmmx -msse -msse2 -msse3 -mfpmath=sse -MT glpssx02.lo -MD -MP -MF .deps/glpssx02.Tpo -c glpssx02.c  -fPIC -DPIC -o .libs/glpssx02.o
glpsql.c: In function '_glp_db_iodbc_open':
glpsql.c:700: warning: passing argument 6 of 'dl_SQLBindCol' from incompatible pointer type
In file included from glpsql.c:956:
/usr/include/mysql/my_global.h:361:24: error: asm/atomic.h: No such file or directory
make[2]: *** [glpsql.lo] Error 1
make[2]: *** Waiting for unfinished jobs....
 x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I../include -I/usr/include/mysql -I/usr/include/iodbc -O3 -pipe -mtune=core2 -march=core2 -fomit-frame-pointer -mmmx -msse -msse2 -msse3 -mfpmath=sse -MT glpssx02.lo -MD -MP -MF .deps/glpssx02.Tpo -c glpssx02.c -o glpssx02.o >/dev/null 2>&1
 x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I../include -I/usr/include/mysql -I/usr/include/iodbc -O3 -pipe -mtune=core2 -march=core2 -fomit-frame-pointer -mmmx -msse -msse2 -msse3 -mfpmath=sse -MT glpssx01.lo -MD -MP -MF .deps/glpssx01.Tpo -c glpssx01.c  -fPIC -DPIC -o .libs/glpssx01.o
mv -f .deps/glpssx02.Tpo .deps/glpssx02.Plo
 x86_64-pc-linux-gnu-gcc -DHAVE_CONFIG_H -I. -I.. -I../include -I/usr/include/mysql -I/usr/include/iodbc -O3 -pipe -mtune=core2 -march=core2 -fomit-frame-pointer -mmmx -msse -msse2 -msse3 -mfpmath=sse -MT glpssx01.lo -MD -MP -MF .deps/glpssx01.Tpo -c glpssx01.c -o glpssx01.o >/dev/null 2>&1
mv -f .deps/glpspx01.Tpo .deps/glpspx01.Plo
mv -f .deps/glpssx01.Tpo .deps/glpssx01.Plo
make[2]: Leaving directory `/mnt/Dati/Gentoo/tmp/portage/sci-mathematics/glpk-4.29/work/glpk-4.29/src'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/mnt/Dati/Gentoo/tmp/portage/sci-mathematics/glpk-4.29/work/glpk-4.29'
make: *** [all] Error 2

Comment 1 Carsten Lohrke (RETIRED) gentoo-dev

2008-07-25 19:44:37 UTC

This seems to be a dupe of bug 168931. Which MySQL ebuild are you using exactly?

Comment 2 Patrizio Bassi 2008-07-25 21:25:48 UTC

[ebuild   R   ] dev-db/mysql-5.0.60-r1  USE="berkdb extraengine perl ssl
-big-tables -cluster -debug -embedded -latin1 -max-idx-128 -minimal (-selinux)
-static" 27,369 kB

Comment 3 Wormo (RETIRED) gentoo-dev

2008-07-25 23:04:10 UTC

Maybe the same bug was reintroduced in later versions... try this test to see if behavior is same as in bug 168931:

>As a test, I moved the old /usr/include/mysql/my_config.h file to a temporary
location, then re-emerged dev-db/mysql-5.0.32 again, and this time it did
install the newly generated my_config.h file into /usr/include/mysql. However,
at the same time, I observed the following error towards the end of the build,
either immediately before or during the install phase:
>
>install: cannot stat `/usr/include/mysql/my_config.h': No such file or directory
 
Also, tell us what happens if you unmerge mysql and then install it, since the old issue happened when reinstalling over an existing mysql.

Comment 4 Patrizio Bassi 2008-07-26 08:21:29 UTC

it has been enough to delete the my_config.h, reemerge mysql then this one.

so it's an error in the update procedure of mysql.

for me, we can close this bug, but the other must be reopen.

It's up to you now.

Comment 5 Wormo (RETIRED) gentoo-dev

2008-07-26 19:38:21 UTC

Thanks for the clarification. I'll assign this to mysql guys and let them decide whether to keep this one open or reopen the other.

Comment 6 Chad A. Simmons 2008-08-07 16:22:10 UTC

verified here. Fix of deleting file and reemerging mysql fixed.

Comment 7 Patrizio Bassi 2008-09-09 16:43:01 UTC

i would like to close it, as it's mysql issue only.