Opened 11 years ago

Closed 11 years ago

Last modified 11 years ago

#38776 closed defect (fixed)

SuiteSparse @4.0.0 Linking error: no such file or directory: 'libcholmod.a'

Reported by: gregmainland@… Owned by: macports-tickets@…
Priority: Normal Milestone:
Component: ports Version: 2.1.3
Keywords: Cc: michaelld (Michael Dickens), sebastien@…, stromnov (Andrey Stromnov), cooljeanius (Eric Gallager), harris.snyder@…, robitaille@…, fabrizio.giuliano@…, mndavidoff (Monte Davidoff), jrhope, meyumer@…, jasimpson@…, jdgleeson, casey.l.kiernan@…
Port: SuiteSparse

Description

This is the end of the output of "sudo port -v install SuiteSparse":

clang: error: no such file or directory: 'libcholmod.a'
Command failed:  /usr/bin/clang++ -Wall -O2 -arch x86_64 -dynamiclib -Wl,-all_load  -L/opt/local/lib -framework Accelerate  libamd.a libbtf.a libcamd.a libccolamd.a libcholmod.a libcolamd.a libcxsparse.a libklu.a libldl.a librbio.a libspqr.a libsuitesparseconfig.a libumfpack.a -o libSuiteSparse.4.1.0.dylib  -compatibility_version 4 -current_version 4.1.0  -install_name /opt/local/lib/libSuiteSparse.4.1.0.dylib
Exit code: 1
Error: org.macports.destroot for port SuiteSparse returned: command execution failed
Warning: targets not executed for SuiteSparse: org.macports.activate org.macports.destroot org.macports.install
Please see the log file for port SuiteSparse for details:
    /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_math_SuiteSparse/SuiteSparse/main.log
To report a bug, follow the instructions in the guide:
    http://guide.macports.org/#project.tickets
Error: Processing of port SuiteSparse failed

Attachments (5)

main.log (24.3 KB) - added by gregmainland@… 11 years ago.
log file
main-ptch-CHOLMOD.log (383.3 KB) - added by jdgleeson 11 years ago.
PPC failure with patch-CHOLMOD_Lib_Makefile.diff applied
main.2.log (226.6 KB) - added by casey.l.kiernan@… 11 years ago.
consolelog.txt (47.3 KB) - added by casey.l.kiernan@… 11 years ago.
patch-CHOLMOD_Lib_Makefile.diff (557 bytes) - added by jdgleeson 11 years ago.

Download all attachments as: .zip

Change History (43)

comment:1 Changed 11 years ago by gregmainland@…

Cc: gregmainland@… added

Cc Me!

comment:2 Changed 11 years ago by sebastien@…

Cc: sebastien@… added

Cc Me!

comment:3 Changed 11 years ago by ryandesign (Ryan Carsten Schmidt)

Cc: gregmainland@… removed

Please attach the main.log file.

comment:4 Changed 11 years ago by stromnov (Andrey Stromnov)

Cc: stromnov@… added

Cc Me!

comment:5 Changed 11 years ago by stromnov (Andrey Stromnov)

The same error (with SuiteSparse 4.1.0) at buildbot: http://build.macports.org/builders/buildports-snowleopard-x86_64/builds/16663

comment:6 Changed 11 years ago by cooljeanius (Eric Gallager)

Cc: egall@… added

Cc Me!

comment:7 Changed 11 years ago by jmroot (Joshua Root)

Cc: michaelld@… added

comment:8 Changed 11 years ago by harris.snyder@…

Cc: harris.snyder@… added

Cc Me!

Changed 11 years ago by gregmainland@…

Attachment: main.log added

log file

comment:9 Changed 11 years ago by robitaille@…

Cc: robitaille@… added

Cc Me!

comment:10 Changed 11 years ago by michaelld (Michael Dickens)

!@#$ build system doesn't stop when there are errors. Let me see what I can do.

comment:11 Changed 11 years ago by fabrizio.giuliano@…

Cc: fabrizio.giuliano@… added

Cc Me!

comment:12 Changed 11 years ago by mndavidoff (Monte Davidoff)

Cc: md14-macports@… added

Cc Me!

comment:13 Changed 11 years ago by jrhope

Cc: jrh@… added

Cc Me!

comment:14 Changed 11 years ago by meyumer@…

Cc: meyumer@… added

Cc Me!

comment:15 Changed 11 years ago by nathanfriday@…

Cc Me!

comment:16 in reply to:  15 Changed 11 years ago by larryv (Lawrence Velázquez)

Cc: nathanfriday@… added

Replying to nathanfriday@…:

Cc Me!

To be Cc’d on ticket updates, you actually need to click the “CcMe!” button next to the Cc list. I’ve added you manually.

comment:17 Changed 11 years ago by jasimpson@…

Cc: jasimpson@… added

Cc Me!

comment:18 Changed 11 years ago by jdgleeson

Cc: jdgleeson@… added

Cc Me!

comment:19 Changed 11 years ago by michaelld (Michael Dickens)

Should be fixed in r105225. Please do a "sudo port selfupdate", "sudo port clean SuiteSparse", and then try again. Also please report back successes or failures!

comment:20 in reply to:  19 Changed 11 years ago by mndavidoff (Monte Davidoff)

Replying to michaelld@…:

Works for me! Thanks!

comment:21 in reply to:  19 ; Changed 11 years ago by jdgleeson

Replying to michaelld@…: Still fails on OS X 10.5.8 PPC. Log attached.

Changed 11 years ago by jdgleeson

Attachment: main-ptch-CHOLMOD.log added

PPC failure with patch-CHOLMOD_Lib_Makefile.diff applied

comment:22 Changed 11 years ago by jasimpson@…

Works for me now on 10.8.3. Thanks for the quick fix!

comment:23 Changed 11 years ago by casey.l.kiernan@…

Cc: casey.l.kiernan@… added

Cc Me!

Changed 11 years ago by casey.l.kiernan@…

Attachment: main.2.log added

Changed 11 years ago by casey.l.kiernan@…

Attachment: consolelog.txt added

comment:24 Changed 11 years ago by casey.l.kiernan@…

UPDATE:

Please do a "sudo port selfupdate", "sudo port clean SuiteSparse", and then try again

I tried and it failed again.

I attached a new main.log and my console output (consolelog.txt).

Thanks Casey

comment:25 in reply to:  21 Changed 11 years ago by jdgleeson

Replying to jdgleeson@…:

Still fails on OS X 10.5.8 PPC. Log attached.

I've looked at the preprocessor output. It reveals that the old version 4.0.0 header file ${prefix}/include/cholmod_core.h is used, which does not define IPerm. AFAICT, this is happening because the include option -I${prefix}/include is placed too early on the command line. I'll eventually figure out a patch, but if a patch is already obvious to anyone else, I'd be glad to test it.

comment:26 Changed 11 years ago by jdgleeson

The failure on my PPC machine is actually a bug that shows up because I chose the +metis variant. I believe it would bite anyone who upgrades from SuiteSparse @4.0.0+metis to 4.1.0. I've attached a modified version of patch-CHOLMOD_Lib_Makefile.diff that fixes this problem.

Last edited 11 years ago by jdgleeson (previous) (diff)

Changed 11 years ago by jdgleeson

comment:27 Changed 11 years ago by michaelld (Michael Dickens)

Yeah; SuiteSparse has a "-I..." ordering issue. Thanks for that patch change; I think the issue is broader than that, but let me look into it.

comment:28 Changed 11 years ago by gregmainland@…

Since I opened the issue I will note that it now works for me, thanks.

comment:29 Changed 11 years ago by harris.snyder@…

Apologies for the totally ignorant question, but how do I apply this patch? I'm brand new (day 1) to macports...

comment:30 Changed 11 years ago by gregmainland@…

harris: Go to the terminal and type "sudo port selfupdate" to get all the latest patches, then type "sudo port clean SuiteSparse" to make sure a half-installed buggy version is blown away, and then "sudo port install SuiteSparse" to install.

comment:31 Changed 11 years ago by harris.snyder@…

Wow I thought I had to apply the patch manually... *Sigh*. Thanks. Still broken for me though.

comment:32 in reply to:  31 Changed 11 years ago by gregmainland@…

Replying to harris.snyder@…:

Wow I thought I had to apply the patch manually... *Sigh*. Thanks. Still broken for me though.

If it's still broken after "sudo port clean; sudo port selfupdate" can you paste the log?

comment:33 Changed 11 years ago by harris.snyder@…

Tried clean, update, upgrade outdated and then retried it and it worked. Thanks. Now octave-devel is failing on qrupdate *sigh*, oh well, thanks for fixing this

comment:34 Changed 11 years ago by casey.l.kiernan@…

I am still seeing octave-devel fail (logs are posted).

Casey

comment:35 Changed 11 years ago by michaelld (Michael Dickens)

Resolution: fixed
Status: newclosed

This ticket's various issue should now be fixed in r105503, by reordering the -I such that the MacPorts' entry comes last. I also fixed a couple other non-critical build issues.

Please do:

sudo port clean SuiteSparse
sudo port selfupdate
sudo port upgrade SuiteSparse

and it should all work again. I'm closing this ticket as fixed, but if y'all continue to have -the same issue- please reopen it and attach the relevant log file and your system info.

For folks still having issue with octave-devel, please open a new ticket after verifying (via a search) that one does not already exist with your issue. With the most recent atlas changes, all of my +atlas ports are working again.

comment:36 Changed 11 years ago by casey.l.kiernan@…

It worked! - Thanks for all your help!

Casey

comment:37 Changed 11 years ago by michaelld (Michael Dickens)

Great! You're welcome! Thanks for reporting back regularly.

comment:38 Changed 11 years ago by nathanfriday@…

Cc: nathanfriday@… removed

Cc Me!

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