Bug 518731

Note that both gcc _AND_ sage have the version number of '4.4.1'!

Created attachment 358290 [details]
sage-4.1.1/spkg/build/pari-2.3.3.p1/src/src/language/init.c

$ wc /home/gavin/AAA/updates/sage/sage-4.1.1/spkg/build/pari-2.3.3.p1/src/src/language/init.c
 2078  6920 52634 /home/gavin/AAA/updates/sage/sage-4.1.1/spkg/build/pari-2.3.3.p1/src/src/language/init.c
$ 


This is the file that cc! chokes on.

You need to provide preprocessed source for it, otherwise it can't be reproduced without all the included headers.

How do I provide preprocessed source?


All the included headers are part of the source tar I downloaded.

See http://gcc.gnu.org/bugs.html for details, or just use -E instead of -c on the command line, or add -save-temps to the command line.

I can't simply add a flag to the command line, as there are some very complicated scripts which generate makefiles on the fly.

I've spent over 2 hours trying to figure out a way to get the file you need without success.

Created attachment 359611 [details]
Assembly of "my" view to this problem (maybe another bug)

If the build aborts, you could go to the directory spkg/build/pari-2.3.3.p1/src/Olinux-x86_64 and run your command from above:
gcc  -c -O3 -Wall -fno-strict-aliasing -fomit-frame-pointer    -I.
-I../src/headers -fPIC -o init.o ../src/language/init.c


I just wanted to try so, but this file builds fine here.
gcc  -c -O3 -Wall -fno-strict-aliasing -fomit-frame-pointer    -I. -I../src/headers -fPIC -o base3.o ../src/basemath/base3.c

results in an infinite loop. With -E instead of -c nothing happens.

Even there is a infinite loop, the base3.o is created.

The only thing I can supply is the .s file...

From man gcc...

 -E  Stop after the preprocessing stage; do not run the compiler proper.  The output is in the form of preprocessed source code, which is sent to the standard output.

I'll have another go tomorrow based on the suggestion of Comment #7, but using -save-temps on the command line as per Comment #5.

You just copy the command line and paste it into shell and add -save-temps in the right directory, no need to use the makefiles.

cd ../src/desc && /usr/bin/perl gen_proto basic pari.desc > init-linux-x86_64-6448.tmp
gcc  -c -O3 -Wall -fno-strict-aliasing -fomit-frame-pointer    -I. -I../src/headers -I../src/graph -o gp_init.o ../src/gp/gp_init.c
gcc  -c -O3 -Wall -fno-strict-aliasing -fomit-frame-pointer    -I. -I../src/headers -DDL_DFLT_NAME=NULL -o highlvl.o ../src/gp/highlvl.c
mv ../src/desc/init-linux-x86_64-6448.tmp ../src/language/init.h
gcc  -c -O3 -Wall -fno-strict-aliasing -fomit-frame-pointer    -I. -I../src/headers -fPIC -o anal.o ../src/language/anal.c
gcc  -c -O3 -Wall -fno-strict-aliasing -fomit-frame-pointer    -I. -I../src/headers -fPIC -o init.o ../src/language/init.c
^Cmake: *** [all] Error 130

$ gcc  -E -O3 -Wall -fno-strict-aliasing -fomit-frame-pointer    -I. -I../src/headers -fPIC -o init.o ../src/language/init.c
gcc: ../src/language/init.c: No such file or directory
gcc: no input files
$ pwd
/home/gavin/AAA/updates/sage/sage-4.1.1

[...
    some mucking about trying to ascertain the correct directory to run gcc in
...]

$ ll ../src/language/init.c
-rw-r--r-- 1 gavin gavin 52634 2007-12-27 18:36 ../src/language/init.c
$ pwd
/home/gavin/AAA/updates/sage/sage-4.1.1/spkg/build/pari-2.3.3.p1/src/src
$ gcc  -E -O3 -Wall -fno-strict-aliasing -fomit-frame-pointer    -I. -I../src/headers -fPIC -o init.o ../src/language/init.c
In file included from ../src/language/init.c:22:
../src/headers/pari.h:18:21: error: paricfg.h: No such file or directory
../src/headers/pari.h:76:21: error: pariinl.h: No such file or directory
$

That means you are in a wrong directory.  Try the one which contains paricfg.h and pariinl.h, assuming ../src/language/init.c still exist.
Or, do:
mkdir ~/wrapper
echo '#!/bin/sh' > ~/wrapper/gcc
echo 'exec /usr/bin/gcc -save-temps "$@"' >> ~/wrapper/gcc
chmod 755 ~/wrapper/gcc
and build sage with
PATH=~/wrapper/gcc:$PATH make
and then just look for init.i in the sage tree.

I have applied all the updates offerred, including:

Linux saturn 2.6.30.5-43.fc11.x86_64 #1 SMP Thu Aug 27 21:39:52 EDT 2009 x86_64 x86_64 x86_64 GNU/Linux

glibc.x86_64 0:2.10.1-5 etc.

I then deleted the sage 4.1.1 directory and restarted.  The sage compile failed in the same place wity the same symptoms.

I ran the wrapper code as per the above comment.

N.B. I ran an updatedb in another terminal, after I had aborted the compile, but before I used locate init.i.  However, I did not find the init.i for sage.

I will leave the /home/gavin/AAA/updates/sage/sage-4.1.1 directory structure as is, and await further instructions...


[...]
make[1]: *** [installed/pari-2.3.3.p1] Error 1
make[1]: Leaving directory `/home/gavin/AAA/updates/sage/sage-4.1.1/spkg'

real	9m53.807s
user	11m2.338s
sys	2m8.698s
Error building Sage.

real	9m54.318s
user	11m2.581s
sys	2m9.439s
$ mkdir ~/wrapper
$ echo '#!/bin/sh' > ~/wrapper/gcc
$ echo 'exec /usr/bin/gcc -save-temps "$@"' >> ~/wrapper/gc
$ chmod 755 ~/wrapper/gcc
$ ll ~/wrapper/gc
-rw-rw-r-- 1 gavin gavin 35 2009-09-10 09:13 /home/gavin/wrapper/gc
$ PATH=~/wrapper/gcc:$PATH make
cd spkg && ./install all 2>&1 | tee -a ../install.log
make[1]: Entering directory `/home/gavin/AAA/updates/sage/sage-4.1.1/spkg'
sage-spkg pari-2.3.3.p1 2>&1
You must set the SAGE_ROOT environment variable or
run this script from the SAGE_ROOT or 
SAGE_ROOT/local/bin/ directory.
pari-2.3.3.p1
Machine:
Linux saturn 2.6.30.5-43.fc11.x86_64 #1 SMP Thu Aug 27 21:39:52 EDT 2009 x86_64 x86_64 x86_64 GNU/Linux
Deleting directories from past builds of previous/current versions of pari-2.3.3.p1
Extracting package /home/gavin/AAA/updates/sage/sage-4.1.1/spkg/standard/pari-2.3.3.p1.spkg ...
-rw-r--r-- 1 gavin gavin 1868037 2009-08-01 09:45 /home/gavin/AAA/updates/sage/sage-4.1.1/spkg/standard/pari-2.3.3.p1.spkg
pari-2.3.3.p1/
[...]
cd ../src/desc && /usr/bin/perl gen_proto basic pari.desc > init-linux-x86_64-1891.tmp
mv ../src/desc/members-linux-x86_64-1891.tmp ../src/language/members.h
mv ../src/desc/init-linux-x86_64-1891.tmp ../src/language/init.h
gcc  -c -O3 -Wall -fno-strict-aliasing -fomit-frame-pointer    -I. -I../src/headers -I../src/graph -o gp_init.o ../src/gp/gp_init.c
gcc  -c -O3 -Wall -fno-strict-aliasing -fomit-frame-pointer    -I. -I../src/headers -DDL_DFLT_NAME=NULL -o highlvl.o ../src/gp/highlvl.c
gcc  -c -O3 -Wall -fno-strict-aliasing -fomit-frame-pointer    -I. -I../src/headers -fPIC -o anal.o ../src/language/anal.c
gcc  -c -O3 -Wall -fno-strict-aliasing -fomit-frame-pointer    -I. -I../src/headers -fPIC -o init.o ../src/language/init.c
gcc: Internal error: Terminated (program cc1)
Please submit a full bug report.
See <http://bugzilla.redhat.com/bugzilla> for instructions.
make[3]: *** [base3.o] Error 1
make[3]: Leaving directory `/home/gavin/AAA/updates/sage/sage-4.1.1/spkg/build/pari-2.3.3.p1/src/Olinux-x86_64'
make[2]: *** [gp] Error 2
make[2]: Leaving directory `/home/gavin/AAA/updates/sage/sage-4.1.1/spkg/build/pari-2.3.3.p1/src'
Error building GP

real	6m20.110s
user	7m29.360s
sys	0m5.283s
sage: An error occurred while installing pari-2.3.3.p1
Please email sage-devel http://groups.google.com/group/sage-devel
explaining the problem and send the relevant part of
of /home/gavin/AAA/updates/sage/sage-4.1.1/install.log.  Describe your computer, operating system, etc.
If you want to try to fix the problem, yourself *don't* just cd to
/home/gavin/AAA/updates/sage/sage-4.1.1/spkg/build/pari-2.3.3.p1 and type 'make'.
Instead type "/home/gavin/AAA/updates/sage/sage-4.1.1/sage -sh"
in order to set all environment variables correctly, then cd to
/home/gavin/AAA/updates/sage/sage-4.1.1/spkg/build/pari-2.3.3.p1
(When you are done debugging, you can type "exit" to leave the
subshell.)
make[1]: *** [installed/pari-2.3.3.p1] Error 1
make[1]: Leaving directory `/home/gavin/AAA/updates/sage/sage-4.1.1/spkg'

real	6m20.908s
user	7m30.077s
sys	0m5.400s
Error building Sage.
$ locate init.i
/etc/sysconfig/network-scripts/init.ipv6-global
/usr/include/wine/windows/dbinit.idl
/usr/share/selinux/devel/include/system/init.if
/usr/share/xemacs-21.5-b29/etc/gdbinit.in
$

You've used ~/wrapper/gc instead of ~/wrapper/gcc, note the missing c at the end.
Also, the PATH should be
PATH=~/wrapper/:$PATH make
(not ~/wrapper/gcc, that's my pasto, but it ought to be rather obvious).

I ran an updatedb in another terminal, after I had aborted the compile,
but before I used locate init.i.  However, I did not find the init.i for sage.


$ pwd
/home/gavin/wrapper
$ ll
total 4
-rwxr-xr-x 1 gavin gavin 46 2009-09-10 11:16 gcc*
$ cat gcc
#!/bin/sh
exec /usr/bin/gcc -save-temps "$@"

$ cd /home/gavin/AAA/updates/sage/sage-4.1.1/spkg/build/pari-2.3.3.p1/src/Olinux-x86_64
$ PATH=~/wrapper/:$PATH make
File ../src/funclist not changed.
gcc  -c -O3 -Wall -fno-strict-aliasing -fomit-frame-pointer    -I. -I../src/headers -fPIC -o base3.o ../src/basemath/base3.c
gcc: Internal error: Terminated (program cc1)
Please submit a full bug report.
See <http://bugzilla.redhat.com/bugzilla> for instructions.
make: *** [base3.o] Error 1
$ locate init.i
/etc/sysconfig/network-scripts/init.ipv6-global
/usr/include/wine/windows/dbinit.idl
/usr/share/selinux/devel/include/system/init.if
/usr/share/xemacs-21.5-b29/etc/gdbinit.in
$

Just in case there was something funny with the configuration of updatedb, I tried find...

$ cd /home/gavin/AAA/updates/sage/sage-4.1.1
$ find . -name 'init.i'
$ find . -name 'init.c'
./spkg/build/pari-2.3.3.p1/src/src/language/init.c
$

Correcting silly typo in heading: had sage 4.4.1 instead of 4.1.1.

Same bug was reported in Debian and is fixed in Debian gcc 4.4.1-4
See http://bugs.debian.org/541816

PR41101 is now fixed in gcc-4.4.1-15.