Opened 5 years ago

Closed 5 years ago

Last modified 5 years ago

#49620 closed update (fixed)

apbs: fatal error: 'Eigen/Core' file not found

Reported by: summers@… Owned by: howarth.at.macports@…
Priority: Normal Milestone:
Component: ports Version: 2.3.4
Keywords: haspatch maintainer Cc: dstrubbe (David Strubbe)
Port: apbs

Description (last modified by ryandesign (Ryan Schmidt))

Attempted to upgrade apbs; El Capitan 10.11.2 Beta (15C31f); MacBook Pro Late 2013

--->  Building apbs
Error: org.macports.build for port apbs returned: command execution failed
Please see the log file for port apbs for details:
    /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_apbs/apbs/main.log
Error: Unable to upgrade port: 1

Attachments (2)

main.log (72.5 KB) - added by summers@… 5 years ago.
main.log
Portfile.diff (640 bytes) - added by howarth.at.macports@… 5 years ago.
Portfile diff to help build find bundled headers

Download all attachments as: .zip

Change History (9)

Changed 5 years ago by summers@…

Attachment: main.log added

main.log

comment:1 Changed 5 years ago by ryandesign (Ryan Schmidt)

Description: modified (diff)
Owner: changed from macports-tickets@… to howarth.at.macports@…
Port: apbs added
Priority: HighNormal
Summary: apbs fails to upgradeapbs: fatal error: 'Eigen/Core' file not found

comment:2 Changed 5 years ago by howarth.at.macports@…

The previous commit to update apbs to 1.4.1 should be reverted until this is fixed.

comment:3 Changed 5 years ago by dstrubbe (David Strubbe)

Resolution: fixed
Status: newclosed

Fixed by disabling parallel build, r142365. See also ticket #49058.

comment:4 Changed 5 years ago by howarth.at.macports@…

The build still fails here with...

[  1%] Building CXX object src/geoflow/CMakeFiles/apbs_geoflow.dir/cpbconcz2.cpp.o
cd /opt/local/var/macports/build/_opt_local_var_macports_sources_svn.macports.org_trunk_dports_science_apbs/apbs/work/apbs-pdb2pqr-d4e78c62e6a07f92c26924318d83a159fa6af063/apbs/src/geoflow && /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/clang++    -fpermissive -DNDEBUG -arch x86_64 -mmacosx-version-min=10.11 -I/opt/local/var/macports/build/_opt_local_var_macports_sources_svn.macports.org_trunk_dports_science_apbs/apbs/work/apbs-pdb2pqr-d4e78c62e6a07f92c26924318d83a159fa6af063/apbs/src    -std=c++0x -o CMakeFiles/apbs_geoflow.dir/cpbconcz2.cpp.o -c /opt/local/var/macports/build/_opt_local_var_macports_sources_svn.macports.org_trunk_dports_science_apbs/apbs/work/apbs-pdb2pqr-d4e78c62e6a07f92c26924318d83a159fa6af063/apbs/src/geoflow/cpbconcz2.cpp
In file included from /opt/local/var/macports/build/_opt_local_var_macports_sources_svn.macports.org_trunk_dports_science_apbs/apbs/work/apbs-pdb2pqr-d4e78c62e6a07f92c26924318d83a159fa6af063/apbs/src/geoflow/cpbconcz2.cpp:65:
In file included from /opt/local/var/macports/build/_opt_local_var_macports_sources_svn.macports.org_trunk_dports_science_apbs/apbs/work/apbs-pdb2pqr-d4e78c62e6a07f92c26924318d83a159fa6af063/apbs/src/geoflow/modules.h:60:
/opt/local/var/macports/build/_opt_local_var_macports_sources_svn.macports.org_trunk_dports_science_apbs/apbs/work/apbs-pdb2pqr-d4e78c62e6a07f92c26924318d83a159fa6af063/apbs/src/geoflow/Mat.h:60:10: fatal error: 'Eigen/Core' file not found
#include <Eigen/Core>
         ^
1 error generated.
make[2]: *** [src/geoflow/CMakeFiles/apbs_geoflow.dir/cpbconcz2.cpp.o] Error 1

The following change fixes the build failure on darwin15...

--- Portfile.orig       2015-11-10 13:00:50.000000000 -0500
+++ Portfile    2015-11-10 13:02:17.000000000 -0500
@@ -43,7 +43,9 @@
 #  get_filename_component called with incorrect number of arguments
 # To enable, need not only to fix that check, but also fix configure in tapipb directory to use chosen FC compiler.
 configure.args-append   -DENABLE_OPENMP:BOOL=OFF \
-                        -DENABLE_BEM=OFF
+                        -DENABLE_BEM=OFF \
+                        -DCMAKE_C_COMPILER_ARG1:STRING="-I${worksrcpath}/include" \
+                        -DCMAKE_CXX_COMPILER_ARG1:STRING="-I${worksrcpath}/include"
 
 test.run  yes
 test {
Last edited 5 years ago by howarth.at.macports@… (previous) (diff)

Changed 5 years ago by howarth.at.macports@…

Attachment: Portfile.diff added

Portfile diff to help build find bundled headers

comment:5 Changed 5 years ago by raimue (Rainer Müller)

Keywords: haspatch maintainer added
Resolution: fixed
Status: closedreopened

comment:6 Changed 5 years ago by raimue (Rainer Müller)

Resolution: fixed
Status: reopenedclosed

Patch committed in r142371.

comment:7 Changed 5 years ago by dstrubbe (David Strubbe)

Cc: dstrubbe@… added

Cc Me!

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