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#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:
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)

main.log (105.3 KB) - added by afield1235 3 years ago.: 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

Download all attachments as: .zip

Change History (11)

Changed 3 years ago by afield1235

Attachment:	main.log added

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

comment:1 Changed 3 years ago by ryandesign (Ryan Carsten Schmidt)

Description:	modified (diff)
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 3 years 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'

comment:3 Changed 3 years 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 3 years 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
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    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
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   nsects 2
    flags 0x10
Section
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   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
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   nsects 3
    flags 0x0
Section
  sectname __data
   segname __DATA
      addr 0x0000000000e28000
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    offset 14843904
     align 2^5 (32)
    reloff 0
    nreloc 0
     flags 0x00000000
 reserved1 0
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Section
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   segname __DATA
      addr 0x0000000000e2bd00
      size 0x0000000000004688
    offset 0
     align 2^7 (128)
    reloff 0
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     flags 0x00000001
 reserved1 0
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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
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        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

Last edited 3 years ago by lukaso (Lukas Oberhuber) (previous) (diff)

comment:5 Changed 3 years 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:6 Changed 3 years ago by markmentovai (Mark Mentovai)

Similar: #68329.

comment:7 Changed 3 years ago by Dave-Allured (Dave Allured)

Cc:	Dave-Allured added

comment:8 Changed 3 years 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 3 years ago by afield1235

I was able to build yesterday after updating and then rebuilding.

Revisions Reference: #68807

Thanks.

comment:10 Changed 3 years ago by dershow

Cc:	dershow added

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