Solved suitesparse - portmaster

fernandel

fernandel

I got an error when I try to update ports with portmaster which I am using it about one month without problems on FreeBSD 11.1-RELEASE (amd64):

Code: 
fstack-protector -Wl,-rpath=/usr/local/lib/gcc6 -L/usr/local/lib/gcc6]
gmake[5]: Leaving directory
'/usr/ports/math/suitesparse/work/SuiteSparse'
( cd ../../SuiteSparse_config ; gmake )
gmake[5]: Entering directory
'/usr/ports/math/suitesparse/work/SuiteSparse/SuiteSparse_config'
gmake install INSTALL=/usr/ports/math/suitesparse/work/SuiteSparse
gmake[6]: Entering directory
'/usr/ports/math/suitesparse/work/SuiteSparse/SuiteSparse_config'
gmake[6]: Nothing to be done for 'install'.
gmake[6]: Leaving directory
'/usr/ports/math/suitesparse/work/SuiteSparse/SuiteSparse_config'
gmake[5]: Leaving directory
'/usr/ports/math/suitesparse/work/SuiteSparse/SuiteSparse_config'
( cd ../../AMD ; gmake library )
gmake[5]: Entering directory
'/usr/ports/math/suitesparse/work/SuiteSparse/AMD'
( cd Lib    ; gmake )
gmake[6]: Entering directory
'/usr/ports/math/suitesparse/work/SuiteSparse/AMD/Lib'
gmake install INSTALL=/usr/ports/math/suitesparse/work/SuiteSparse
gmake[7]: Entering directory
'/usr/ports/math/suitesparse/work/SuiteSparse/AMD/Lib'
gmake[7]: Nothing to be done for 'install'.
gmake[7]: Leaving directory
'/usr/ports/math/suitesparse/work/SuiteSparse/AMD/Lib'
gmake[6]: Leaving directory
'/usr/ports/math/suitesparse/work/SuiteSparse/AMD/Lib'
gmake[5]: Leaving directory
'/usr/ports/math/suitesparse/work/SuiteSparse/AMD'
( cd ../Lib ; gmake )
gmake[5]: Entering directory
'/usr/ports/math/suitesparse/work/SuiteSparse/UMFPACK/Lib'
gmake install INSTALL=/usr/ports/math/suitesparse/work/SuiteSparse
gmake[6]: Entering directory
'/usr/ports/math/suitesparse/work/SuiteSparse/UMFPACK/Lib'
gmake[6]: Nothing to be done for 'install'.
gmake[6]: Leaving directory
'/usr/ports/math/suitesparse/work/SuiteSparse/UMFPACK/Lib'
gmake[5]: Leaving directory
'/usr/ports/math/suitesparse/work/SuiteSparse/UMFPACK/Lib'
( cd ../../CHOLMOD && gmake library )
gmake[5]: Entering directory
'/usr/ports/math/suitesparse/work/SuiteSparse/CHOLMOD'
( cd Lib ; gmake )
gmake[6]: Entering directory
'/usr/ports/math/suitesparse/work/SuiteSparse/CHOLMOD/Lib'
gmake install INSTALL=/usr/ports/math/suitesparse/work/SuiteSparse
gmake[7]: Entering directory
'/usr/ports/math/suitesparse/work/SuiteSparse/CHOLMOD/Lib'
gmake[7]: Nothing to be done for 'install'.
gmake[7]: Leaving directory
'/usr/ports/math/suitesparse/work/SuiteSparse/CHOLMOD/Lib'
gmake[6]: Leaving directory
'/usr/ports/math/suitesparse/work/SuiteSparse/CHOLMOD/Lib'
gmake[5]: Leaving directory
'/usr/ports/math/suitesparse/work/SuiteSparse/CHOLMOD'
( cd ../../COLAMD && gmake library )
gmake[5]: Entering directory
'/usr/ports/math/suitesparse/work/SuiteSparse/COLAMD'
( cd Lib    ; gmake )
gmake[6]: Entering directory
'/usr/ports/math/suitesparse/work/SuiteSparse/COLAMD/Lib'
gmake install INSTALL=/usr/ports/math/suitesparse/work/SuiteSparse
gmake[7]: Entering directory
'/usr/ports/math/suitesparse/work/SuiteSparse/COLAMD/Lib'
gmake[7]: Nothing to be done for 'install'.
gmake[7]: Leaving directory
'/usr/ports/math/suitesparse/work/SuiteSparse/COLAMD/Lib'
gmake[6]: Leaving directory
'/usr/ports/math/suitesparse/work/SuiteSparse/COLAMD/Lib'
gmake[5]: Leaving directory
'/usr/ports/math/suitesparse/work/SuiteSparse/COLAMD'
( cd ../../CCOLAMD ; gmake library )
gmake[5]: Entering directory
'/usr/ports/math/suitesparse/work/SuiteSparse/CCOLAMD'
( cd Lib    ; gmake )
gmake[6]: Entering directory
'/usr/ports/math/suitesparse/work/SuiteSparse/CCOLAMD/Lib'
gmake install INSTALL=/usr/ports/math/suitesparse/work/SuiteSparse
gmake[7]: Entering directory
'/usr/ports/math/suitesparse/work/SuiteSparse/CCOLAMD/Lib'
gmake[7]: Nothing to be done for 'install'.
gmake[7]: Leaving directory
'/usr/ports/math/suitesparse/work/SuiteSparse/CCOLAMD/Lib'
gmake[6]: Leaving directory
'/usr/ports/math/suitesparse/work/SuiteSparse/CCOLAMD/Lib'
gmake[5]: Leaving directory
'/usr/ports/math/suitesparse/work/SuiteSparse/CCOLAMD'
( cd ../../CAMD ; gmake library )
gmake[5]: Entering directory
'/usr/ports/math/suitesparse/work/SuiteSparse/CAMD'
( cd Lib    ; gmake )
gmake[6]: Entering directory
'/usr/ports/math/suitesparse/work/SuiteSparse/CAMD/Lib'
gmake install INSTALL=/usr/ports/math/suitesparse/work/SuiteSparse
gmake[7]: Entering directory
'/usr/ports/math/suitesparse/work/SuiteSparse/CAMD/Lib'
gmake[7]: Nothing to be done for 'install'.
gmake[7]: Leaving directory
'/usr/ports/math/suitesparse/work/SuiteSparse/CAMD/Lib'
gmake[6]: Leaving directory
'/usr/ports/math/suitesparse/work/SuiteSparse/CAMD/Lib'
gmake[5]: Leaving directory
'/usr/ports/math/suitesparse/work/SuiteSparse/CAMD'
./umfpack_simple
gmake[4]: *** [Makefile:95: run] Segmentation fault (core dumped)
gmake[4]: Leaving directory
'/usr/ports/math/suitesparse/work/SuiteSparse/UMFPACK/Demo'
gmake[3]: *** [Makefile:15: all] Error 2
gmake[3]: Leaving directory
'/usr/ports/math/suitesparse/work/SuiteSparse/UMFPACK'
gmake[2]: *** [Makefile:26: go] Error 2
gmake[2]: Leaving directory
'/usr/ports/math/suitesparse/work/SuiteSparse'
*** Error code 2

Stop.
make[1]: stopped in /usr/ports/math/suitesparse
*** Error code 1

Stop.
make: stopped in /usr/ports/math/suitesparse

===>>> make build failed for math/suitesparse
===>>> Aborting update

===>>> Update for math/suitesparse failed
===>>> Aborting update

===>>> Update for math/py-numpy@py36 failed
===>>> Aborting update

Thank you.
 
I assume you don't mix ports and packages? This could be just about anything, from a problem with the port to a small hiccup somewhere. What I usually do in situations like those is to reinstall any build dependencies for the port. Sometimes that can do the trick: where a library should have been updated because of another library update which didn't happen for some reason (it wouldn't be the first time that some updates aren't mentioned in /usr/ports/UPDATING).

Which is another suggestion in itself: always pay close attention to UPDATING.

Anyway: portmaster `make build-depends-list | sed -e 's/\/usr\/ports\///g'`

This would tell portmaster to (re)install any build dependencies this port might have. You can even use -x pkg if you want to save some time: portmaster -x pkg `make build-depends-list | sed -e 's/\/usr\/ports\///g'`. I prefer using this over the regular -t option because that would basically re-install half the system due to its full dependency follow-up.

Hope this can help.
 
This is most likely because it picks old headers, and they aren't compatible. Try using the poudriere build, or uninstalling suitesparse first.

I'll notify the upstream about this, but there's not much more that can be done about this at this time.
 
ShelLuser said:
I assume you don't mix ports and packages? This could be just about anything, from a problem with the port to a small hiccup somewhere. What I usually do in situations like those is to reinstall any build dependencies for the port. Sometimes that can do the trick: where a library should have been updated because of another library update which didn't happen for some reason (it wouldn't be the first time that some updates aren't mentioned in /usr/ports/UPDATING).

Which is another suggestion in itself: always pay close attention to UPDATING.

Anyway: portmaster `make build-depends-list | sed -e 's/\/usr\/ports\///g'`

This would tell portmaster to (re)install any build dependencies this port might have. You can even use -x pkg if you want to save some time: portmaster -x pkg `make build-depends-list | sed -e 's/\/usr\/ports\///g'`. I prefer using this over the regular -t option because that would basically re-install half the system due to its full dependency follow-up.

Hope this can help.
Click to expand...
No, it didn't help. It rebuilt some ports and one of them was gcc6 but the problem exist.
I do not mixing ports and packages and I use also pkg -n -d and was okay and the same with pkg_libchk -o.
I like to update graphics/blender which needs math/py-numpy which needs math/suitesparse and I am here.
I am using devel/ccache.
Thank you.
 
talsamon said:
/usr/local/lib/libamd.a causes the error. Deinstall the math/suitesparse before you build the update (if it is the same error I had. I can't see it in your post. The error was before the lines you show).
Btw, portmaster builds devel/py-numpy and math/suitesparse in the wrong order.
Click to expand...
I tried to build just suitesparse and I got:
Code: 
gmake[6]: Entering directory '/usr/ports/math/suitesparse/work/SuiteSparse/CCOLAMD/Lib'
gmake install INSTALL=/usr/ports/math/suitesparse/work/SuiteSparse
gmake[7]: Entering directory '/usr/ports/math/suitesparse/work/SuiteSparse/CCOLAMD/Lib'
gmake[7]: Nothing to be done for 'install'.
gmake[7]: Leaving directory '/usr/ports/math/suitesparse/work/SuiteSparse/CCOLAMD/Lib'
gmake[6]: Leaving directory '/usr/ports/math/suitesparse/work/SuiteSparse/CCOLAMD/Lib'
gmake[5]: Leaving directory '/usr/ports/math/suitesparse/work/SuiteSparse/CCOLAMD'
( cd ../../CAMD ; gmake library )
gmake[5]: Entering directory '/usr/ports/math/suitesparse/work/SuiteSparse/CAMD'
( cd Lib    ; gmake )
gmake[6]: Entering directory '/usr/ports/math/suitesparse/work/SuiteSparse/CAMD/Lib'
gmake install INSTALL=/usr/ports/math/suitesparse/work/SuiteSparse
./umfpack_simple
gmake[7]: Entering directory '/usr/ports/math/suitesparse/work/SuiteSparse/CAMD/Lib'
gmake[7]: Nothing to be done for 'install'.
gmake[7]: Leaving directory '/usr/ports/math/suitesparse/work/SuiteSparse/CAMD/Lib'
gmake[6]: Leaving directory '/usr/ports/math/suitesparse/work/SuiteSparse/CAMD/Lib'
gmake[5]: Leaving directory '/usr/ports/math/suitesparse/work/SuiteSparse/CAMD'
gmake[4]: *** [Makefile:95: run] Segmentation fault (core dumped)
gmake[4]: Leaving directory '/usr/ports/math/suitesparse/work/SuiteSparse/UMFPACK/Demo'
gmake[3]: *** [Makefile:15: all] Error 2
gmake[3]: Leaving directory '/usr/ports/math/suitesparse/work/SuiteSparse/UMFPACK'
gmake[2]: *** [Makefile:26: go] Error 2
gmake[2]: Leaving directory '/usr/ports/math/suitesparse/work/SuiteSparse'
*** Error code 2

Stop.
make[1]: stopped in /usr/ports/math/suitesparse
*** Error code 1

Stop.
make: stopped in /usr/ports/math/suitesparse

===>>> make build failed for math/suitesparse
===>>> Aborting update
 
In the mean time I've ran into the same issue.

I always update my servers on Monday and today I noticed that this port is also part of my update cycle. And during the process it did indeed fail with several errors, from what I can tell the same as the OP. I already confirmed that the port used the default settings on my end so right now I'm testing this in my Jail (a clean environment which is solely used for testing software ( pkg build and then pkg delete) and of course sometimes building ports).

If I stumble upon something new I'll share.
 
I never use pkg for update my system but I downloaded suitesparse package and installed it because I had some ports broken.
BTW downgraded version of math/suitesparse is not a problem to build.
 
Fix for me was what talsamon described above:
Code: 
# pkg delete -f suitesparse
# cd /usr/ports/math/suitesparse
# make all install clean

Port builds and installs without any issues.
 
pboehmer said:
Fix for me was what talsamon described above:
Code: 
# pkg delete -f suitesparse
# cd /usr/ports/math/suitesparse
# make all install clean

Port builds and installs without any issues.
Click to expand...

I am glad that works for you but doesn't work for me also doesn't built with Synth as I wrote before and attached file is from Synth log.
 
I filed PR 227791 because I got undefined references. But there seem to be more problems with math/suitesparse than the undefined references alone.
Also, math/suitesparse was installed on my system as a dependency, but after deleting it it didn't got reinstalled with a portupgrade -a, so I don't know which port installed it in the first place. I just leave it deinstalled for now.
 
garry said:
As do I..... on amd64 11.2-RELEASE with current ports suitesparse does not build (in a clean jail). I'll drop the dependency on suitesparse in numpy for now; just wanted to confirm the existence of a problem.
Click to expand...

The previous error was due to pre-installed older version of suitesparse. This is impossible in a clean jail. What's the error message?
 
yurivict said:
The previous error was due to pre-installed older version of suitesparse. This is impossible in a clean jail. What's the error message?
Click to expand...

At the end of the log I have
Code: 
6031 gmake[3]: Leaving directory '/construction/xports/math/suitesparse/work/SuiteSparse/UMFPACK/Demo'
6032 gmake[2]: *** [Makefile:15: all] Error 2
6033 gmake[2]: Leaving directory '/construction/xports/math/suitesparse/work/SuiteSparse/UMFPACK'
6034 gmake[1]: *** [Makefile:26: go] Error 2
6035 gmake[1]: Leaving directory '/construction/xports/math/suitesparse/work/SuiteSparse'
6036 *** Error code 2
6037 
6038 Stop.
6039 make: stopped in /xports/math/suitesparse
much further up I see messages about demos not being found
Code: 
gmake[3]: Leaving directory '/construction/xports/math/suitesparse/work/SuiteSparse/GraphBLAS/build'
 389 ./demo: ../build/simple_demo: not found
 390 ./demo: ../build/complex_demo: not found
 391 ./demo: ../build/wildtype_demo: not found
 392 ./demo: ../build/mis_demo: not found
...
 450 ./demo: ../build/tri_demo: not found
 451 ./demo: ../build/tri_demo: not found
It appears to me that in GraphBLAS/Demo the demo script encounters some error in building. The demo source files that are present are these
Code: 
cd GraphBLAS/Demo
 echo */*.c
Program/bfs_demo.c Program/complex_demo.c Program/kron_demo.c Program/mis_demo.c Program/simple_demo.c Program/tri_demo.c Program/wildtype_demo.c Source/bfs_level.c Source/bfs5m_check.c Source/bfs5m.c Source/bfs6_check.c Source/bfs6.c Source/get_matrix.c Source/mis_check.c Source/mis_score.c Source/mis.c Source/random_matrix.c Source/read_matrix.c Source/simple_rand.c Source/simple_timer.c Source/tricount.c Source/usercomplex.c Source/wathen.c
so at least it seems that it is failing to building some demos for which source code is present. Is this error silently ignored in other build environments? I'm using synth.
 
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