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#46040 closed defect (fixed)

llvm-, clang-: all binaries are overlinked to libedit, libffi, ncurses, and zlib

Reported by:	pj@…	Owned by:	larryv (Lawrence Velázquez)
Priority:	Normal	Milestone:
Component:	ports	Version:	2.3.3
Keywords:		Cc:	dershow, jeremyhu (Jeremy Huddleston Sequoia), yarrgk@…, nmsnoopy@…, kencu (Ken)
Port:	clang-3.3 llvm-3.3 clang-3.4 llvm-3.4 clang-3.5 llvm-3.5 clang-3.6 llvm-3.6

Description (last modified by larryv (Lawrence Velázquez))

Hey, I am trying to update and Openmodelica on my Mac 10.10.
Having serious issues since I am brand new to mac and ports and so on.
Assistance would be appreciated in baby simple steps.

I have followed the steps listed on
https://www.openmodelica.org/download/download-mac
but once I need to run:

--> port install gcc44

the error below shows up. As root and using sudo

Errors

Pieters-MacBook-Pro:logs pjc$ sudo port install gcc44
--->  Computing dependencies for gcc44
--->  Dependencies to be installed: libgcc libgcc45
--->  Building libgcc
Error: org.macports.build for port libgcc returned: command execution failed
Error: Failed to install libgcc
Please see the log file for port libgcc for details:
    /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_lang_gcc49/libgcc/main.log
Error: The following dependencies were not installed: libgcc libgcc45
To report a bug, follow the instructions in the guide:
    http://guide.macports.org/#project.tickets
Error: Processing of port gcc44 failed

Attachments (4)

main.log (12.0 KB) - added by pj@… 10 years ago.
main.2.log (5.1 MB) - added by larryv (Lawrence Velázquez) 10 years ago.: OP's full log, sent via email
main.log.gz (6.2 KB) - added by facardillo@… 9 years ago.: Log of libedit install
config.log (100.2 KB) - added by dershow 9 years ago.

Change History (33)

Changed 10 years ago by pj@…

Attachment:	main.log added

comment:1 follow-up: 2 Changed 10 years ago by larryv (Lawrence Velázquez)

Cc:	mww@… added
Description:	modified (diff)
Owner:	changed from macports-tickets@… to larryv@…
Port:	libgcc added
Status:	new → assigned
Summary:	[Openmodelica][2.3.3][Installation and update] → libgcc build failure

The log is not complete. Please clean libgcc and try installing again. Attach the new main.log if it fails again.

comment:2 in reply to: 1 Changed 10 years ago by larryv (Lawrence Velázquez)

That is, please run the following commands:

% sudo port clean libgcc
% sudo port install libgcc

If you see another build failure, attach the new main.log.

comment:3 follow-up: 4 Changed 10 years ago by dershow

I am also seeing a problem with libgcc. In my case it is an upgrade from 4.9.2_0 to 4.9.2_1 that fails. I see a couple of recent tickets that might relate: #46020 #45954 r128719

My log file, for the attempted upgrade, ends like this:

:info:build checking for iconv... yes
:info:build checking how to link with libiconv... -liconv
:info:build checking for iconv declaration... install-shextern size_t iconv (iconv_t cd, char * *inbuf, size_t *inbytesleft, char * *outbuf, size_t *outbytesleft);
:info:build configure: updating cache ./config.cache
:info:build configure: creating ./config.status
:info:build config.status: creating Makefile
:info:build config.status: creating config.h
:info:build config.status: executing depdir commands
:info:build mkdir .deps
:info:build make[2]: Leaving directory `/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_lang_gcc49/libgcc/work/build'
:info:build make[1]: *** [stage1-bubble] Error 2
:info:build make[1]: Leaving directory `/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_lang_gcc49/libgcc/work/build'
:info:build make: *** [bootstrap] Error 2
:info:build make: Leaving directory `/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_lang_gcc49/libgcc/work/build'
:info:build Command failed:  cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_lang_gcc49/libgcc/work/build" && /usr/bin/make -j8 -w bootstrap 
:info:build Exit code: 2
:error:build org.macports.build for port libgcc returned: command execution failed
:debug:build Error code: CHILDSTATUS 32339 2
:debug:build Backtrace: command execution failed
    while executing
"system -nice 0 $fullcmdstring"
    ("eval" body line 1)
    invoked from within
"eval system $notty $nice \$fullcmdstring"
    invoked from within
"command_exec build"
    (procedure "portbuild::build_main" line 8)
    invoked from within
"portbuild::build_main org.macports.build"
    ("eval" body line 1)
    invoked from within
"eval $procedure $targetname"
:info:build Warning: targets not executed for libgcc: org.macports.install org.macports.build org.macports.destroot
:notice:build Please see the log file for port libgcc for details:
    /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_lang_gcc49/libgcc/main.log

I can attach a full log if that would be helpful. I am on 10.9.5.

Last edited 9 years ago by ryandesign (Ryan Carsten Schmidt) (previous) (diff)

comment:4 in reply to: 3 Changed 10 years ago by larryv (Lawrence Velázquez)

For triage purposes, please open a new ticket and attach a complete log.

comment:5 Changed 10 years ago by dershow

As suggested, I created a new ticket: #46063

Last edited 9 years ago by ryandesign (Ryan Carsten Schmidt) (previous) (diff)

comment:6 Changed 10 years ago by dershow

Cc:	dersh@… added

Cc Me!

Changed 10 years ago by larryv (Lawrence Velázquez)

Attachment:	main.2.log added

OP's full log, sent via email

comment:7 Changed 10 years ago by larryv (Lawrence Velázquez)

Cc:	jeremyhu@… added; mww@… removed
Port:	llvm-3.5 llvm-3.6 added; libgcc removed
Summary:	libgcc build failure → llvm-3.5, llvm-3.6: libLTO uses libedit, ncurses, zlib without declaring dependencies

The OP sent me a complete log via email.

:info:build collect2: error: ld terminated with signal 5 [Trace/BPT trap: 5]
:info:build dyld: Library not loaded: /opt/local/lib/libedit.0.dylib
:info:build   Referenced from: /opt/local/libexec/llvm-3.5/lib/libLTO.dylib
:info:build   Reason: image not found

It’s not clear to me why libLTO.dylib links to libedit, and the llvm-3.5 port does not declare a dependency on the libedit port. On my system, libLTO uses libraries from zlib, libffi, libedit, and ncurses — only one of which llvm-3.6 declares a dependency on:

% otool -L /opt/local/libexec/llvm-3.6/lib/libLTO.dylib
/opt/local/libexec/llvm-3.6/lib/libLTO.dylib:
	/opt/local/libexec/llvm-3.6/lib/libLTO.dylib (compatibility version 0.0.0, current version 0.0.0)
	/opt/local/libexec/llvm-3.6/lib/libLLVM-3.6svn.dylib (compatibility version 0.0.0, current version 0.0.0)
	/opt/local/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.8)
	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1213.0.0)
	/opt/local/lib/libffi.6.dylib (compatibility version 7.0.0, current version 7.4.0)
	/opt/local/lib/libedit.0.dylib (compatibility version 1.0.0, current version 1.51.0)
	/opt/local/lib/libncurses.5.dylib (compatibility version 5.0.0, current version 5.0.0)
	/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 120.0.0)

% port installed llvm-3.6
The following ports are currently installed:
  llvm-3.6 @3.6-r222672_0+assertions+polly+universal (active)

% port deps llvm-3.6 +assertions+polly+universal
Full Name: llvm-3.6 @3.6-r222672_0+assertions+polly+universal
Fetch Dependencies:   subversion
Library Dependencies: libffi, libcxx, gmp, isl, cloog
Runtime Dependencies: perl5, llvm_select

You must have removed libedit at some point, and MacPorts didn’t stop you because llvm-3.5 doesn’t claim to require it. You can work around this by reinstalling libedit.

Jeremy, does libLTO really use these libraries?

Last edited 10 years ago by larryv (Lawrence Velázquez) (previous) (diff)

comment:8 Changed 10 years ago by jeremyhu (Jeremy Huddleston Sequoia)

Looks like a bug in the build system adding unnecessary links. I only see symbols being pulled in from from libLLVM-3, libSystem, and libc++

comment:9 follow-up: 11 Changed 10 years ago by jeremyhu (Jeremy Huddleston Sequoia)

Reported upstream, but I'll look into it when I get cycles:

http://llvm.org/bugs/show_bug.cgi?id=21693

comment:10 Changed 10 years ago by jeremyhu (Jeremy Huddleston Sequoia)

Owner:	changed from larryv@… to jeremyhu@…
Status:	assigned → new

comment:11 in reply to: 9 Changed 10 years ago by larryv (Lawrence Velázquez)

Cc:	larryv@… added; jeremyhu@… removed
Port:	llvm-3.3 llvm-3.4 added
Summary:	llvm-3.5, llvm-3.6: libLTO uses libedit, ncurses, zlib without declaring dependencies → llvm-*: libLTO uses libedit, ncurses, zlib without declaring dependencies

Great, thanks. Roping in llvm-3.3 and llvm-3.4 based on your observations in the upstream report.

comment:12 Changed 9 years ago by ryandesign (Ryan Carsten Schmidt)

Cc:	yarrgk@… added

Has duplicate #46121.

This is also causing builds on the buildbot builders to fail, e.g. pdftk.

comment:13 Changed 9 years ago by larryv (Lawrence Velázquez)

While libLTO’s linking is unwanted and should still be fixed, libLLVM-3 does seem to use these libraries, so maybe the port should declare dependencies anyway?

comment:14 follow-up: 27 Changed 9 years ago by larryv (Lawrence Velázquez)

This is turning into Whac-a-Mole. Clang’s executables all appear to be overlinked:

/opt/local/libexec/llvm-3.6/bin/c-index-test:
	@rpath/libclang.dylib (compatibility version 1.0.0, current version 0.0.0)
	@rpath/libLLVM-3.6svn.dylib (compatibility version 0.0.0, current version 0.0.0)
	/opt/local/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.8)
	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1213.0.0)
	/opt/local/lib/libffi.6.dylib (compatibility version 7.0.0, current version 7.4.0)
	/opt/local/lib/libedit.0.dylib (compatibility version 1.0.0, current version 1.51.0)
	/opt/local/lib/libncurses.5.dylib (compatibility version 5.0.0, current version 5.0.0)
	/opt/local/lib/libxml2.2.dylib (compatibility version 12.0.0, current version 12.2.0)
	/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 120.0.0)
/opt/local/libexec/llvm-3.6/bin/clang:
	@rpath/libLLVM-3.6svn.dylib (compatibility version 0.0.0, current version 0.0.0)
	/opt/local/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.8)
	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1213.0.0)
	/opt/local/lib/libffi.6.dylib (compatibility version 7.0.0, current version 7.4.0)
	/opt/local/lib/libedit.0.dylib (compatibility version 1.0.0, current version 1.51.0)
	/opt/local/lib/libncurses.5.dylib (compatibility version 5.0.0, current version 5.0.0)
	/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 120.0.0)
/opt/local/libexec/llvm-3.6/bin/clang-apply-replacements:
	@rpath/libLLVM-3.6svn.dylib (compatibility version 0.0.0, current version 0.0.0)
	/opt/local/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.8)
	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1213.0.0)
	/opt/local/lib/libffi.6.dylib (compatibility version 7.0.0, current version 7.4.0)
	/opt/local/lib/libedit.0.dylib (compatibility version 1.0.0, current version 1.51.0)
	/opt/local/lib/libncurses.5.dylib (compatibility version 5.0.0, current version 5.0.0)
	/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 120.0.0)
/opt/local/libexec/llvm-3.6/bin/clang-format:
	@rpath/libLLVM-3.6svn.dylib (compatibility version 0.0.0, current version 0.0.0)
	/opt/local/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.8)
	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1213.0.0)
	/opt/local/lib/libffi.6.dylib (compatibility version 7.0.0, current version 7.4.0)
	/opt/local/lib/libedit.0.dylib (compatibility version 1.0.0, current version 1.51.0)
	/opt/local/lib/libncurses.5.dylib (compatibility version 5.0.0, current version 5.0.0)
	/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 120.0.0)
/opt/local/libexec/llvm-3.6/bin/clang-modernize:
	@rpath/libLLVM-3.6svn.dylib (compatibility version 0.0.0, current version 0.0.0)
	/opt/local/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.8)
	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1213.0.0)
	/opt/local/lib/libffi.6.dylib (compatibility version 7.0.0, current version 7.4.0)
	/opt/local/lib/libedit.0.dylib (compatibility version 1.0.0, current version 1.51.0)
	/opt/local/lib/libncurses.5.dylib (compatibility version 5.0.0, current version 5.0.0)
	/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 120.0.0)

Last edited 9 years ago by larryv (Lawrence Velázquez) (previous) (diff)

comment:15 follow-up: 16 Changed 9 years ago by jeremyhu (Jeremy Huddleston Sequoia)

Cc:	jeremyhu@… added; larryv@… removed
Owner:	changed from jeremyhu@… to larryv@…

Ok, let's just add the new dependencies. Since you've been looking at it, can you add them as appropriate?

comment:16 in reply to: 15 Changed 9 years ago by larryv (Lawrence Velázquez)

Yup, working on it.

comment:17 Changed 9 years ago by larryv (Lawrence Velázquez)

Port:	clang-3.3 clang-3.4 clang-3.5 clang-3.6 added
Status:	new → assigned
Summary:	llvm-: libLTO uses libedit, ncurses, zlib without declaring dependencies → llvm-, clang-*: all binaries are overlinked to libedit, libffi, ncurses, and zlib

Changed 9 years ago by facardillo@…

Attachment:	main.log.gz added

Log of libedit install

comment:18 follow-up: 19 Changed 9 years ago by facardillo@…

I have the same problem as the original author: libedit not found.

However, if I try and install libedit (after trying to install gcc49) I got error messages related to differing checksums.

The log file has been generated by the third step of the following sequence of commands:

port install gcc49 (failed due to missing libedit)
port install libedit (exit with success)
port install gcc49 (fails with the log file I attached)

Regards

Last edited 9 years ago by facardillo@… (previous) (diff)

comment:19 in reply to: 18 Changed 9 years ago by larryv (Lawrence Velázquez)

Clean libgcc and try installing again. If that fails, open another ticket; this ticket is not about GCC.

comment:20 Changed 9 years ago by ryandesign (Ryan Carsten Schmidt)

Cc:	nmsnoopy@… added

Has duplicate #46178.

comment:21 Changed 9 years ago by larryv (Lawrence Velázquez)

“Fixed” the 3.4, 3.5, and 3.6 ports in r129359.

comment:22 follow-up: 23 Changed 9 years ago by dershow

I just tried to update openmodelica, and now I am getting an error at configure.

sudo port  upgrade  openmodelica-devel  build.jobs=4
--->  Computing dependencies for openmodelica-devel
--->  Fetching archive for openmodelica-devel
--->  Attempting to fetch openmodelica-devel-23769_0+gfortran48+libraries+modelica3d+qt+sundials.darwin_13.x86_64.tbz2 from http://packages.macports.org/openmodelica-devel
--->  Attempting to fetch openmodelica-devel-23769_0+gfortran48+libraries+modelica3d+qt+sundials.darwin_13.x86_64.tbz2 from http://mse.uk.packages.macports.org/sites/packages.macports.org/openmodelica-devel
--->  Attempting to fetch openmodelica-devel-23769_0+gfortran48+libraries+modelica3d+qt+sundials.darwin_13.x86_64.tbz2 from http://nue.de.packages.macports.org/macports/packages/openmodelica-devel
--->  Fetching distfiles for openmodelica-devel
--->  Verifying checksums for openmodelica-devel
--->  Extracting openmodelica-devel
--->  Configuring openmodelica-devel
Error: Failed to configure openmodelica-devel, consult /opt/local/var/macports/build/_opt_local_var_macports_sources_build.openmodelica.org_macports_lang_openmodelica-devel/openmodelica-devel/work/openmodelica_23769/config.log
Error: org.macports.configure for port openmodelica-devel returned: configure failure: command execution failed
Please see the log file for port openmodelica-devel for details:
    /opt/local/var/macports/logs/_opt_local_var_macports_sources_build.openmodelica.org_macports_lang_openmodelica-devel/openmodelica-devel/main.log
Error: Unable to upgrade port: 1
To report a bug, follow the instructions in the guide:
    http://guide.macports.org/#project.tickets

I am still on 10.9.5. Just adds to the "Whac-a-Mole" situation. I am not sure if this is connected to the above problem and fixes....

comment:23 in reply to: 22 Changed 9 years ago by larryv (Lawrence Velázquez)

It’s impossible to say without actually seeing your logs, but I highly doubt it. Please clean and try upgrading again, and if that fails, open a new ticket and attach your main.log there.

Changed 9 years ago by dershow

Attachment:	config.log added

comment:24 follow-up: 25 Changed 9 years ago by dershow

I had tried to clean first. But, it doesn't even make it to generate the main.log, since it fails at configure. So, I have attached the configure log. I did recently install octave, which installed llvm-3.4, when I had 3.3 installed before. perhaps related? But, I did try to select 3.3, and got similar results. I did upgrade a few days ago, with no problem, so that is why I thought that "fix" two days ago to llvm might be related.

comment:25 in reply to: 24 Changed 9 years ago by larryv (Lawrence Velázquez)

This is the failure:

configure:6026: checking LAPACK/BLAS flags
configure:6060: /usr/bin/clang -o conftest -pipe -Os -arch x86_64 -fno-stack-protector -I/opt/local/include -L/opt/local/lib -Wl,-headerpad_max_install_names -arch x86_64 conftest.c -llapack -lblas >&5
Undefined symbols for architecture x86_64:
  "_ATL_dger", referenced from:
      _ATL_dgetf2 in liblapack.a(ATL_dgetf2.o)
  "_ATL_xerbla", referenced from:
      _atl_f77wrap_dgesv_ in liblapack.a(ATL_f77wrap_dgesv.o)
ld: symbol(s) not found for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
configure:6060: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "OpenModelica"
| #define PACKAGE_TARNAME "openmodelica"
| #define PACKAGE_VERSION "dev"
| #define PACKAGE_STRING "OpenModelica dev"
| #define PACKAGE_BUGREPORT "https://trac.openmodelica.org/OpenModelica"
| #define PACKAGE_URL "https://openmodelica.org"
| #define YYTEXT_POINTER 1
| #define STDC_HEADERS 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_SYS_TIME_H 1
| #define HAVE_VPRINTF 1
| #define HAVE_GETCWD 1
| #define HAVE_SELECT 1
| #define HAVE_STRDUP 1
| #define HAVE_STRERROR 1
| /* end confdefs.h.  */
| 
| /* Override any GCC internal prototype to avoid an error.
|    Use char because int might match the return type of a GCC
|    builtin and then its argument prototype would still apply.  */
| #ifdef __cplusplus
| extern "C"
| #endif
| char dgesv_ ();
| int
| main ()
| {
| return dgesv_ ();
|   ;
|   return 0;
| }
configure:6063: error: dgesv (LAPACK) linking failed using -llapack -lblas

This has nothing to do with LLVM. Please open a new ticket.

comment:26 Changed 9 years ago by dershow

New ticket opened: #46228

Last edited 4 years ago by ryandesign (Ryan Carsten Schmidt) (previous) (diff)

comment:27 in reply to: 14 Changed 8 years ago by larryv (Lawrence Velázquez)

Informational update: The CMake build seems to have eliminated this problem. I’ll probably revisit the dependencies soon.

% otool -L /opt/local/libexec/llvm-3.8/bin/{c-index-test,clang,clang-apply-replacements,clang-format}
/opt/local/libexec/llvm-3.8/bin/c-index-test:
	@rpath/libLLVM.dylib (compatibility version 1.0.0, current version 3.8.1)
	@rpath/libclang.dylib (compatibility version 1.0.0, current version 3.8.1)
	/opt/local/lib/libxml2.2.dylib (compatibility version 12.0.0, current version 12.4.0)
	/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 307.4.0)
	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1238.0.0)
/opt/local/libexec/llvm-3.8/bin/clang:
	@rpath/libLLVM.dylib (compatibility version 1.0.0, current version 3.8.1)
	/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 307.4.0)
	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1238.0.0)
/opt/local/libexec/llvm-3.8/bin/clang-apply-replacements:
	@rpath/libLLVM.dylib (compatibility version 1.0.0, current version 3.8.1)
	/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 307.4.0)
	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1238.0.0)
/opt/local/libexec/llvm-3.8/bin/clang-format:
	@rpath/libLLVM.dylib (compatibility version 1.0.0, current version 3.8.1)
	/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 307.4.0)
	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1238.0.0)

comment:28 Changed 4 years ago by kencu (Ken)

Cc:	kencu added

comment:29 Changed 4 years ago by kencu (Ken)

Resolution:	→ fixed
Status:	assigned → closed

these were all fixed as of the cmake build system (clang-3.8). The < 3.8 versions we're just leaving alone.

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