Opened 7 months ago
Last modified 5 months ago
#68359 new defect
py27-numpy @1.16.6_3+gfortran+openblas: ld: duplicate LC_RPATH '/opt/local/lib/libgcc' in '/opt/local/lib/libopenblas-r1.dylib'
Reported by: | afield1235 | Owned by: | |
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Priority: | Normal | Milestone: | |
Component: | ports | Version: | 2.8.1 |
Keywords: | sonoma | Cc: | Dave-Allured (Dave Allured), dershow |
Port: | py27-numpy |
Description (last modified by ryandesign (Ryan Carsten Schmidt))
MacOS Sonoma 14.0
Intel x86
sudo port install py27-numpy ---> Computing dependencies for py27-numpy ---> Fetching archive for py27-numpy ---> Attempting to fetch py27-numpy-1.16.6_3+gfortran+openblas.darwin_23.x86_64.tbz2 from https://packages.macports.org/py27-numpy ---> Attempting to fetch py27-numpy-1.16.6_3+gfortran+openblas.darwin_23.x86_64.tbz2 from http://mirror.fcix.net/macports/packages/py27-numpy ---> Attempting to fetch py27-numpy-1.16.6_3+gfortran+openblas.darwin_23.x86_64.tbz2 from https://ywg.ca.packages.macports.org/mirror/macports/packages/py27-numpy ---> Building py27-numpy Error: Failed to build py27-numpy: command execution failed Error: See /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_python_py-numpy/py27-numpy/main.log for details. Error: Follow https://guide.macports.org/#project.tickets if you believe there is a bug. Error: Processing of port py27-numpy failed
Attachments (1)
Change History (11)
Changed 7 months ago by afield1235
comment:1 Changed 7 months ago by ryandesign (Ryan Carsten Schmidt)
Description: | modified (diff) |
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Keywords: | sonoma added |
Summary: | Sonoma - Error: Failed to build py27-numpy: command execution failed → py27-numpy: @1.16.6_3+gfortran+openblas: ld: duplicate LC_RPATH '/opt/local/lib/libgcc' in '/opt/local/lib/libopenblas-r1.dylib' |
The log says:
:info:build ld: duplicate LC_RPATH '/opt/local/lib/libgcc' in '/opt/local/lib/libopenblas-r1.dylib' :info:build clang: error: linker command failed with exit code 1 (use -v to see invocation)
Sounds like #68239.
comment:2 Changed 7 months ago by ryandesign (Ryan Carsten Schmidt)
Summary: | py27-numpy: @1.16.6_3+gfortran+openblas: ld: duplicate LC_RPATH '/opt/local/lib/libgcc' in '/opt/local/lib/libopenblas-r1.dylib' → py27-numpy @1.16.6_3+gfortran+openblas: ld: duplicate LC_RPATH '/opt/local/lib/libgcc' in '/opt/local/lib/libopenblas-r1.dylib' |
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comment:3 Changed 7 months ago by lukaso (Lukas Oberhuber)
This is happening when building SuiteSparse_CHOLMOD
as well. This is an xcode 15 issue since I am still on Ventura but got upgraded to xcode 15 (without realizing it, grrr).
comment:4 Changed 7 months ago by lukaso (Lukas Oberhuber)
$ otool -l /Users/user/macports-gimp3-x86_64/lib/libopenblas-r1.dylib /Users/user/macports-gimp3-x86_64/lib/libopenblas-r1.dylib: Load command 0 cmd LC_SEGMENT_64 cmdsize 632 segname __TEXT vmaddr 0x0000000000000000 vmsize 0x0000000000e20000 fileoff 0 filesize 14811136 maxprot 0x00000005 initprot 0x00000005 nsects 7 flags 0x0 Section sectname __text segname __TEXT addr 0x00000000000021c0 size 0x0000000000c90156 offset 8640 align 2^5 (32) reloff 0 nreloc 0 flags 0x80000400 reserved1 0 reserved2 0 Section sectname __text_startup segname __TEXT addr 0x0000000000c92318 size 0x0000000000000f8e offset 13181720 align 2^2 (4) reloff 0 nreloc 0 flags 0x80000400 reserved1 0 reserved2 0 Section sectname __stubs segname __TEXT addr 0x0000000000c932a6 size 0x00000000000001ce offset 13185702 align 2^1 (2) reloff 0 nreloc 0 flags 0x80000408 reserved1 0 (index into indirect symbol table) reserved2 6 (size of stubs) Section sectname __init_offsets segname __TEXT addr 0x0000000000c93474 size 0x000000000000000c offset 13186164 align 2^2 (4) reloff 0 nreloc 0 flags 0x00000016 reserved1 0 reserved2 0 Section sectname __const segname __TEXT addr 0x0000000000c93480 size 0x0000000000012a00 offset 13186176 align 2^7 (128) reloff 0 nreloc 0 flags 0x00000000 reserved1 0 reserved2 0 Section sectname __cstring segname __TEXT addr 0x0000000000ca5e80 size 0x000000000000b556 offset 13262464 align 2^0 (1) reloff 0 nreloc 0 flags 0x00000002 reserved1 0 reserved2 0 Section sectname __eh_frame segname __TEXT addr 0x0000000000cb13d8 size 0x000000000016ec20 offset 13308888 align 2^3 (8) reloff 0 nreloc 0 flags 0x00000000 reserved1 0 reserved2 0 Load command 1 cmd LC_SEGMENT_64 cmdsize 232 segname __DATA_CONST vmaddr 0x0000000000e20000 vmsize 0x0000000000008000 fileoff 14811136 filesize 32768 maxprot 0x00000003 initprot 0x00000003 nsects 2 flags 0x10 Section sectname __got segname __DATA_CONST addr 0x0000000000e20000 size 0x0000000000000278 offset 14811136 align 2^3 (8) reloff 0 nreloc 0 flags 0x00000006 reserved1 77 (index into indirect symbol table) reserved2 0 Section sectname __const segname __DATA_CONST addr 0x0000000000e20280 size 0x0000000000007298 offset 14811776 align 2^4 (16) reloff 0 nreloc 0 flags 0x00000000 reserved1 0 reserved2 0 Load command 2 cmd LC_SEGMENT_64 cmdsize 312 segname __DATA vmaddr 0x0000000000e28000 vmsize 0x000000000000c000 fileoff 14843904 filesize 16384 maxprot 0x00000003 initprot 0x00000003 nsects 3 flags 0x0 Section sectname __data segname __DATA addr 0x0000000000e28000 size 0x0000000000003ca0 offset 14843904 align 2^5 (32) reloff 0 nreloc 0 flags 0x00000000 reserved1 0 reserved2 0 Section sectname __bss segname __DATA addr 0x0000000000e2bd00 size 0x0000000000004688 offset 0 align 2^7 (128) reloff 0 nreloc 0 flags 0x00000001 reserved1 0 reserved2 0 Section sectname __common segname __DATA addr 0x0000000000e30400 size 0x00000000000000b0 offset 0 align 2^7 (128) reloff 0 nreloc 0 flags 0x00000001 reserved1 0 reserved2 0 Load command 3 cmd LC_SEGMENT_64 cmdsize 72 segname __LINKEDIT vmaddr 0x0000000000e34000 vmsize 0x0000000000080000 fileoff 14860288 filesize 511464 maxprot 0x00000001 initprot 0x00000001 nsects 0 flags 0x0 Load command 4 cmd LC_ID_DYLIB cmdsize 96 name /Users/user/macports-gimp3-x86_64/lib/libopenblas-r1.dylib (offset 24) time stamp 1 Thu Jan 1 01:00:01 1970 current version 0.0.0 compatibility version 0.0.0 Load command 5 cmd LC_DYLD_CHAINED_FIXUPS cmdsize 16 dataoff 14860288 datasize 1296 Load command 6 cmd LC_DYLD_EXPORTS_TRIE cmdsize 16 dataoff 14861584 datasize 79928 Load command 7 cmd LC_SYMTAB cmdsize 24 symoff 14965408 nsyms 15907 stroff 15220544 strsize 151208 Load command 8 cmd LC_DYSYMTAB cmdsize 80 ilocalsym 0 nlocalsym 10848 iextdefsym 10848 nextdefsym 4979 iundefsym 15827 nundefsym 80 tocoff 0 ntoc 0 modtaboff 0 nmodtab 0 extrefsymoff 0 nextrefsyms 0 indirectsymoff 15219920 nindirectsyms 156 extreloff 0 nextrel 0 locreloff 0 nlocrel 0 Load command 9 cmd LC_UUID cmdsize 24 uuid 4AA4A3AD-A3C7-3C29-94A0-7913F26DBC94 Load command 10 cmd LC_BUILD_VERSION cmdsize 32 platform 1 minos 13.0 sdk n/a ntools 1 tool 3 version 907.0 Load command 11 cmd LC_SOURCE_VERSION cmdsize 16 version 0.0 Load command 12 cmd LC_LOAD_DYLIB cmdsize 56 name @rpath/libgfortran.5.dylib (offset 24) time stamp 2 Thu Jan 1 01:00:02 1970 current version 6.0.0 compatibility version 6.0.0 Load command 13 cmd LC_LOAD_DYLIB cmdsize 56 name @rpath/libquadmath.0.dylib (offset 24) time stamp 2 Thu Jan 1 01:00:02 1970 current version 1.0.0 compatibility version 1.0.0 Load command 14 cmd LC_LOAD_DYLIB cmdsize 56 name /usr/lib/libSystem.B.dylib (offset 24) time stamp 2 Thu Jan 1 01:00:02 1970 current version 1319.100.3 compatibility version 1.0.0 Load command 15 cmd LC_LOAD_DYLIB cmdsize 56 name @rpath/libgcc_s.1.1.dylib (offset 24) time stamp 2 Thu Jan 1 01:00:02 1970 current version 1.1.0 compatibility version 1.0.0 Load command 16 cmd LC_RPATH cmdsize 72 path /Users/user/macports-gimp3-x86_64/lib/libgcc (offset 12) Load command 17 cmd LC_RPATH cmdsize 72 path /Users/user/macports-gimp3-x86_64/lib/libgcc (offset 12) Load command 18 cmd LC_RPATH cmdsize 32 path @loader_path (offset 12) Load command 19 cmd LC_RPATH cmdsize 64 path /Users/user/macports-gimp3-x86_64/lib (offset 12) Load command 20 cmd LC_RPATH cmdsize 104 path /Users/user/macports-gimp3-x86_64/lib/gcc13/gcc/x86_64-apple-darwin22/13.2.0 (offset 12) Load command 21 cmd LC_RPATH cmdsize 72 path /Users/user/macports-gimp3-x86_64/lib/gcc13 (offset 12) Load command 22 cmd LC_FUNCTION_STARTS cmdsize 16 dataoff 14941512 datasize 23624 Load command 23 cmd LC_DATA_IN_CODE cmdsize 16 dataoff 14965136 datasize 272
comment:5 Changed 7 months ago by lukaso (Lukas Oberhuber)
A few links which might be helpful: https://stackoverflow.com/questions/76661812/xcode-15-beta-duplicate-lc-rpath-are-deprecated https://stackoverflow.com/questions/77153800/xcode-15-c-compilation-errors
No solutions other than downgrading to xcode 14.
comment:7 Changed 6 months ago by Dave-Allured (Dave Allured)
Cc: | Dave-Allured added |
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comment:8 Changed 5 months ago by dershow
I updated some outdated ports, including:
arpack 3.9.1_0 < 3.9.1_1 graphviz-gui 8.1.0_0 < 9.0.0_0 nss 3.94_0 < 3.95_0 OpenBLAS 0.3.25_1 < 0.3.25_2 py27-scipy 1.2.3_0 < 1.2.3_1 py39-numpy 1.26.1_0 < 1.26.1_1 py39-scipy 1.10.1_0 < 1.10.1_1 py39-wheel 0.41.3_0 < 0.42.0_0 py310-numpy 1.26.1_0 < 1.26.1_1 py310-scipy 1.10.1_0 < 1.10.1_1 py310-wheel 0.41.3_0 < 0.42.0_0 py311-numpy 1.26.1_0 < 1.26.1_1 py311-scipy 1.10.1_0 < 1.10.1_1 py311-wheel 0.41.3_0 < 0.42.0_0 qrupdate 1.1.2_6 < 1.1.2_7 SuiteSparse_CHOLMOD 3.0.14_1 < 3.0.14_2 SuiteSparse_UMFPACK 5.7.9_0 < 5.7.9_1 sundials5 5.8.0_0 < 5.8.0_1
That seemed to go fine. But, it broke other ports:
---> Updating database of binaries ---> Scanning binaries for linking errors ---> Found 11 broken files, matching files to ports ---> Found 2 broken ports, determining rebuild order You can always run 'port rev-upgrade' again to fix errors. The following ports will be rebuilt: py27-numpy @1.16.6+gfortran+openblas py27-scikit-learn @0.20.4 Continue? [Y/n]: Y ---> Computing dependencies for py27-numpy ---> Cleaning py27-numpy ---> Computing dependencies for py27-scikit-learn ---> Cleaning py27-scikit-learn ---> Scanning binaries for linking errors ---> Found 11 broken files, matching files to ports ---> Found 2 broken ports, determining rebuild order ---> Rebuilding in order py27-numpy @1.16.6_3+gfortran+openblas py27-scikit-learn @0.20.4_0 ---> Computing dependencies for py27-numpy ---> Fetching distfiles for py27-numpy ---> Attempting to fetch numpy-1.16.6.tar.gz from https://distfiles.macports.org/py-numpy ---> Verifying checksums for py27-numpy ---> Extracting py27-numpy ---> Applying patches to py27-numpy ---> Configuring py27-numpy ---> Building py27-numpy Error: Failed to build py27-numpy: command execution failed Error: See /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_python_py-numpy/py27-numpy/main.log for details. Error: rev-upgrade failed: Error rebuilding py27-numpy Error: Follow https://guide.macports.org/#project.tickets if you believe there is a bug. ---> Some of the ports you installed have notes: OpenBLAS has the following notes: This version is built based on a base architecture for convenience, which may not be optimized for your system. To build a version customized for your machine, use the +native variant
rev-updrade reports the same error. I'm not sure if this is exactly the same as this ticket, as I wasn't trying to (intentionally) build py27-numpy, but it did break, and then the attempt to rebuild it fails.
comment:9 Changed 5 months ago by afield1235
I was able to build yesterday after updating and then rebuilding.
Revisions Reference: #68807
Thanks.
comment:10 Changed 5 months ago by dershow
Cc: | dershow added |
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See /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_python_py-numpy/py27-numpy/main.log