ld: can't re-map file, errno=22 file #5904

Derek-Schutt · 2025-01-23T22:06:42Z

Derek-Schutt
Jan 23, 2025

Output of `brew config`

HOMEBREW_VERSION: 4.4.17
ORIGIN: https://github.com/Homebrew/brew
HEAD: 55f399c10dc7e6cc07497bdfccdecc96329e3b57
Last commit: 4 days ago
Branch: stable
Core tap JSON: 23 Jan 21:54 UTC
Core cask tap JSON: 23 Jan 21:54 UTC
HOMEBREW_PREFIX: /usr/local
HOMEBREW_CASK_OPTS: []
HOMEBREW_DISPLAY: /private/tmp/com.apple.launchd.Pt0FCHdUcp/org.macosforge.xquartz:0
HOMEBREW_MAKE_JOBS: 10
Homebrew Ruby: 3.3.7 => /usr/local/Homebrew/Library/Homebrew/vendor/portable-ruby/3.3.7/bin/ruby
CPU: deca-core 64-bit westmere
Clang: 15.0.0 build 1500
Git: 2.39.3 => /Applications/Xcode.app/Contents/Developer/usr/bin/git
Curl: 8.1.2 => /usr/bin/curl
macOS: 14.1.2-x86_64
CLT: 15.3.0.0.1.1708646388
Xcode: 15.4
Rosetta 2: true

Output of `brew doctor`

$ brew doctor
Please note that these warnings are just used to help the Homebrew maintainers
with debugging if you file an issue. If everything you use Homebrew for is
working fine: please don't worry or file an issue; just ignore this. Thanks!

Warning: Unbrewed dylibs were found in /usr/local/lib.
If you didn't put them there on purpose they could cause problems when
building Homebrew formulae and may need to be deleted.

Unexpected dylibs:
  /usr/local/lib/libGraphicsMagickWand.dylib
  /usr/local/lib/libQtCLucene.4.dylib
  /usr/local/lib/libXm.4.dylib
  /usr/local/lib/libamd.dylib
  /usr/local/lib/libarpack.2.dylib
  /usr/local/lib/libatk-1.0.0.dylib
  /usr/local/lib/libboost_math_c99-mt.dylib
  /usr/local/lib/libboost_math_c99l-mt.dylib
  /usr/local/lib/libboost_math_tr1l-mt.dylib
  /usr/local/lib/libboost_program_options-mt.dylib
  /usr/local/lib/libboost_serialization.dylib
  /usr/local/lib/libcairo-gobject.dylib
  /usr/local/lib/libcholmod.3.0.11.dylib
  /usr/local/lib/libcolamd.2.dylib
  /usr/local/lib/libcord.dylib
  /usr/local/lib/libfontconfig.dylib
  /usr/local/lib/libfreetype.dylib
  /usr/local/lib/libgailutil.dylib
  /usr/local/lib/libgdk_pixbuf-2.0.0.dylib
  /usr/local/lib/libglibmm-2.4.dylib
  /usr/local/lib/libgmpxx.4.dylib
  /usr/local/lib/libgobject-2.0.dylib
  /usr/local/lib/libgslcblas.dylib
  /usr/local/lib/libgtkmm-2.4.dylib
  /usr/local/lib/liblcms.1.0.19.dylib
  /usr/local/lib/libmpfr.4.dylib
  /usr/local/lib/libnetcdf-cxx4.1.dylib
  /usr/local/lib/libnetcdf.11.4.0.dylib
  /usr/local/lib/libnetcdf.11.dylib
  /usr/local/lib/libpangocairo-1.0.0.dylib
  /usr/local/lib/libpcrecpp.0.dylib
  /usr/local/lib/libpcreposix.0.dylib
  /usr/local/lib/libplot.dylib
  /usr/local/lib/libpotrace.dylib
  /usr/local/lib/libqhull_p.7.2.0.dylib
  /usr/local/lib/libqscintilla2.dylib
  /usr/local/lib/librbio.dylib
  /usr/local/lib/libspqr.2.0.8.dylib
  /usr/local/lib/libtbbmalloc_proxy.dylib
  /usr/local/lib/libtcl8.6.dylib
  /usr/local/lib/libtiff.dylib
  /usr/local/lib/libtiffxx.dylib
  /usr/local/lib/libtk8.6.dylib
  /usr/local/lib/libumfpack.5.7.6.dylib
  /usr/local/lib/libwebpdemux.2.dylib
  /usr/local/lib/mod_spatialite.dylib

Warning: Unbrewed header files were found in /usr/local/include.
If you didn't put them there on purpose they could cause problems when
building Homebrew formulae and may need to be deleted.

Unexpected header files:
  /usr/local/include/H5CommonFG.h
  /usr/local/include/H5DOpublic.h
  /usr/local/include/H5DSpublic.h
  /usr/local/include/H5EnumType.h
  /usr/local/include/H5FDcore.h
  /usr/local/include/H5FDmulti.h
  /usr/local/include/H5Fpublic.h
  /usr/local/include/H5LaccProp.h
  /usr/local/include/RBio.h
  /usr/local/include/SuiteSparseQR_definitions.h
  /usr/local/include/cpl_vsi_virtual.h
  /usr/local/include/cpl_vsil_curl_priv.h
  /usr/local/include/cs.h
  /usr/local/include/evdns.h
  /usr/local/include/fakepq.h
  /usr/local/include/gdfontl.h
  /usr/local/include/gdfonts.h
  /usr/local/include/glpk.h
  /usr/local/include/itcl2TclOO.h
  /usr/local/include/itclInt.h
  /usr/local/include/ldl.h
  /usr/local/include/ncFloat.h
  /usr/local/include/ncType.h
  /usr/local/include/netcdfcpp.h
  /usr/local/include/odbcStubs.h
  /usr/local/include/ogrsf_frmts.h
  /usr/local/include/pcre_scanner.h
  /usr/local/include/pcrecpp.h
  /usr/local/include/tclDecls.h
  /usr/local/include/tclOO.h
  /usr/local/include/tclOODecls.h
  /usr/local/include/tclThread.h
  /usr/local/include/tclTomMath.h
  /usr/local/include/tdbcDecls.h
  /usr/local/include/tkPlatDecls.h
  /usr/local/include/umfpack_save_symbolic.h

Warning: Unbrewed '.la' files were found in /usr/local/lib.
If you didn't put them there on purpose they could cause problems when
building Homebrew formulae and may need to be deleted.

Unexpected '.la' files:
  /usr/local/lib/libGraphicsMagick++.la
  /usr/local/lib/libproj.la

Warning: Unbrewed '.pc' files were found in /usr/local/lib/pkgconfig.
If you didn't put them there on purpose they could cause problems when
building Homebrew formulae and may need to be deleted.

Unexpected '.pc' files:
  /usr/local/lib/pkgconfig/tcl.pc
  /usr/local/lib/pkgconfig/tk.pc

Warning: Unbrewed static libraries were found in /usr/local/lib.
If you didn't put them there on purpose they could cause problems when
building Homebrew formulae and may need to be deleted.

Unexpected static libraries:
  /usr/local/lib/g77-sacio.a
  /usr/local/lib/g77-xapiir.a
  /usr/local/lib/libatomic_ops.a
  /usr/local/lib/libboost_context-mt.a
  /usr/local/lib/libboost_date_time-mt.a
  /usr/local/lib/libboost_graph.a
  /usr/local/lib/libboost_math_c99-mt.a
  /usr/local/lib/libboost_math_tr1f.a
  /usr/local/lib/libboost_math_tr1l.a
  /usr/local/lib/libboost_program_options-mt.a
  /usr/local/lib/libboost_wserialization.a
  /usr/local/lib/libg77-sacio.a
  /usr/local/lib/libg77-xapiir.a
  /usr/local/lib/libgd.a
  /usr/local/lib/libgeos_c.a
  /usr/local/lib/libgmpxx.a
  /usr/local/lib/libgthread-2.0.a
  /usr/local/lib/libhdf5_cpp.a
  /usr/local/lib/liblz.a
  /usr/local/lib/libqhullstatic.a
  /usr/local/lib/libsacio-32.a
  /usr/local/lib/libsacio-64.a
  /usr/local/lib/libsacio.a
  /usr/local/lib/libtkstub8.6.a
  /usr/local/lib/libwebpdemux.a
  /usr/local/lib/libxapiir-32.a
  /usr/local/lib/libxapiir-64.a
  /usr/local/lib/libxapiir.a
  /usr/local/lib/sacio-32.a
  /usr/local/lib/sacio-64.a
  /usr/local/lib/sacio.a
  /usr/local/lib/xapiir-32.a
  /usr/local/lib/xapiir-64.a
  /usr/local/lib/xapiir.a

Warning: You have unlinked kegs in your Cellar.
Leaving kegs unlinked can lead to build-trouble and cause formulae that depend on
those kegs to fail to run properly once built. Run `brew link` on these:
  libtiff
  geos
  gmp
  libpng
  ghostscript
  gdal
  libgeotiff
  freetype
  hdf5
  pango
  glib
  libspatialite
  cairo
  webp
  xz
  fontconfig
  giflib
  pkgconf
  netcdf
  libevent
  qhull
(base) [derek@Mac-Studio-2:~/Research/Active/code/fmtomo_studio2/FMTOMO-main]$ brew link 
Usage: brew link, ln [options] installed_formula [...]

Symlink all of formula's installed files into Homebrew's prefix. This is done
automatically when you install formulae but can be useful for manual
installations.

      --overwrite                  Delete files that already exist in the prefix
                                   while linking.
  -n, --dry-run                    List files which would be linked or deleted
                                   by brew link --overwrite without actually
                                   linking or deleting any files.
  -f, --force                      Allow keg-only formulae to be linked.
      --HEAD                       Link the HEAD version of the formula if it is
                                   installed.
  -d, --debug                      Display any debugging information.
  -q, --quiet                      Make some output more quiet.
  -v, --verbose                    Make some output more verbose.
  -h, --help                       Show this message.

Error: Invalid usage: This command requires at least 1 installed formula argument.
(base) [derek@Mac-Studio-2:~/Research/Active/code/fmtomo_studio2/FMTOMO-main]$ brew link libtiff
Linking /usr/local/Cellar/libtiff/4.7.0... 
Error: Could not symlink bin/pal2rgb
Target /usr/local/bin/pal2rgb
already exists. You may want to remove it:
  rm '/usr/local/bin/pal2rgb'

To force the link and overwrite all conflicting files:
  brew link --overwrite libtiff

To list all files that would be deleted:
  brew link --overwrite libtiff --dry-run
(base) [derek@Mac-Studio-2:~/Research/Active/code/fmtomo_studio2/FMTOMO-main]$ brew doctor
Please note that these warnings are just used to help the Homebrew maintainers
with debugging if you file an issue. If everything you use Homebrew for is
working fine: please don't worry or file an issue; just ignore this. Thanks!

Warning: Unbrewed dylibs were found in /usr/local/lib.
If you didn't put them there on purpose they could cause problems when
building Homebrew formulae and may need to be deleted.

Unexpected dylibs:
  /usr/local/lib/libGraphicsMagickWand.dylib
  /usr/local/lib/libQtCLucene.4.dylib
  /usr/local/lib/libXm.4.dylib
  /usr/local/lib/libamd.dylib
  /usr/local/lib/libarpack.2.dylib
  /usr/local/lib/libatk-1.0.0.dylib
  /usr/local/lib/libboost_math_c99-mt.dylib
  /usr/local/lib/libboost_math_c99l-mt.dylib
  /usr/local/lib/libboost_math_tr1l-mt.dylib
  /usr/local/lib/libboost_program_options-mt.dylib
  /usr/local/lib/libboost_serialization.dylib
  /usr/local/lib/libcairo-gobject.dylib
  /usr/local/lib/libcholmod.3.0.11.dylib
  /usr/local/lib/libcolamd.2.dylib
  /usr/local/lib/libcord.dylib
  /usr/local/lib/libfontconfig.dylib
  /usr/local/lib/libfreetype.dylib
  /usr/local/lib/libgailutil.dylib
  /usr/local/lib/libgdk_pixbuf-2.0.0.dylib
  /usr/local/lib/libglibmm-2.4.dylib
  /usr/local/lib/libgmpxx.4.dylib
  /usr/local/lib/libgobject-2.0.dylib
  /usr/local/lib/libgslcblas.dylib
  /usr/local/lib/libgtkmm-2.4.dylib
  /usr/local/lib/liblcms.1.0.19.dylib
  /usr/local/lib/libmpfr.4.dylib
  /usr/local/lib/libnetcdf-cxx4.1.dylib
  /usr/local/lib/libnetcdf.11.4.0.dylib
  /usr/local/lib/libnetcdf.11.dylib
  /usr/local/lib/libpangocairo-1.0.0.dylib
  /usr/local/lib/libpcrecpp.0.dylib
  /usr/local/lib/libpcreposix.0.dylib
  /usr/local/lib/libplot.dylib
  /usr/local/lib/libpotrace.dylib
  /usr/local/lib/libqhull_p.7.2.0.dylib
  /usr/local/lib/libqscintilla2.dylib
  /usr/local/lib/librbio.dylib
  /usr/local/lib/libspqr.2.0.8.dylib
  /usr/local/lib/libtbbmalloc_proxy.dylib
  /usr/local/lib/libtcl8.6.dylib
  /usr/local/lib/libtiff.dylib
  /usr/local/lib/libtiffxx.dylib
  /usr/local/lib/libtk8.6.dylib
  /usr/local/lib/libumfpack.5.7.6.dylib
  /usr/local/lib/libwebpdemux.2.dylib
  /usr/local/lib/mod_spatialite.dylib

Warning: Unbrewed header files were found in /usr/local/include.
If you didn't put them there on purpose they could cause problems when
building Homebrew formulae and may need to be deleted.

Unexpected header files:
  /usr/local/include/H5CommonFG.h
  /usr/local/include/H5DOpublic.h
  /usr/local/include/H5DSpublic.h
  /usr/local/include/H5EnumType.h
  /usr/local/include/H5FDcore.h
  /usr/local/include/H5FDmulti.h
  /usr/local/include/H5Fpublic.h
  /usr/local/include/H5LaccProp.h
  /usr/local/include/RBio.h
  /usr/local/include/SuiteSparseQR_definitions.h
  /usr/local/include/cpl_vsi_virtual.h
  /usr/local/include/cpl_vsil_curl_priv.h
  /usr/local/include/cs.h
  /usr/local/include/evdns.h
  /usr/local/include/fakepq.h
  /usr/local/include/gdfontl.h
  /usr/local/include/gdfonts.h
  /usr/local/include/glpk.h
  /usr/local/include/itcl2TclOO.h
  /usr/local/include/itclInt.h
  /usr/local/include/ldl.h
  /usr/local/include/ncFloat.h
  /usr/local/include/ncType.h
  /usr/local/include/netcdfcpp.h
  /usr/local/include/odbcStubs.h
  /usr/local/include/ogrsf_frmts.h
  /usr/local/include/pcre_scanner.h
  /usr/local/include/pcrecpp.h
  /usr/local/include/tclDecls.h
  /usr/local/include/tclOO.h
  /usr/local/include/tclOODecls.h
  /usr/local/include/tclThread.h
  /usr/local/include/tclTomMath.h
  /usr/local/include/tdbcDecls.h
  /usr/local/include/tkPlatDecls.h
  /usr/local/include/umfpack_save_symbolic.h

Warning: Unbrewed '.la' files were found in /usr/local/lib.
If you didn't put them there on purpose they could cause problems when
building Homebrew formulae and may need to be deleted.

Unexpected '.la' files:
  /usr/local/lib/libGraphicsMagick++.la
  /usr/local/lib/libproj.la

Warning: Unbrewed '.pc' files were found in /usr/local/lib/pkgconfig.
If you didn't put them there on purpose they could cause problems when
building Homebrew formulae and may need to be deleted.

Unexpected '.pc' files:
  /usr/local/lib/pkgconfig/tcl.pc
  /usr/local/lib/pkgconfig/tk.pc

Warning: Unbrewed static libraries were found in /usr/local/lib.
If you didn't put them there on purpose they could cause problems when
building Homebrew formulae and may need to be deleted.

Unexpected static libraries:
  /usr/local/lib/g77-sacio.a
  /usr/local/lib/g77-xapiir.a
  /usr/local/lib/libatomic_ops.a
  /usr/local/lib/libboost_context-mt.a
  /usr/local/lib/libboost_date_time-mt.a
  /usr/local/lib/libboost_graph.a
  /usr/local/lib/libboost_math_c99-mt.a
  /usr/local/lib/libboost_math_tr1f.a
  /usr/local/lib/libboost_math_tr1l.a
  /usr/local/lib/libboost_program_options-mt.a
  /usr/local/lib/libboost_wserialization.a
  /usr/local/lib/libg77-sacio.a
  /usr/local/lib/libg77-xapiir.a
  /usr/local/lib/libgd.a
  /usr/local/lib/libgeos_c.a
  /usr/local/lib/libgmpxx.a
  /usr/local/lib/libgthread-2.0.a
  /usr/local/lib/libhdf5_cpp.a
  /usr/local/lib/liblz.a
  /usr/local/lib/libqhullstatic.a
  /usr/local/lib/libsacio-32.a
  /usr/local/lib/libsacio-64.a
  /usr/local/lib/libsacio.a
  /usr/local/lib/libtkstub8.6.a
  /usr/local/lib/libwebpdemux.a
  /usr/local/lib/libxapiir-32.a
  /usr/local/lib/libxapiir-64.a
  /usr/local/lib/libxapiir.a
  /usr/local/lib/sacio-32.a
  /usr/local/lib/sacio-64.a
  /usr/local/lib/sacio.a
  /usr/local/lib/xapiir-32.a
  /usr/local/lib/xapiir-64.a
  /usr/local/lib/xapiir.a

Warning: You have unlinked kegs in your Cellar.
Leaving kegs unlinked can lead to build-trouble and cause formulae that depend on
those kegs to fail to run properly once built. Run `brew link` on these:
  libtiff
  geos
  gmp
  libpng
  ghostscript
  gdal
  libgeotiff
  freetype
  hdf5
  pango
  glib
  libspatialite
  cairo
  webp
  xz
  fontconfig
  giflib
  pkgconf
  netcdf
  libevent
  qhull

Description of issue

I am trying to compile a program with gfortran that compiles fine on a linux box. However, when I try to compile it on my Mac studio (M1), I get a bunch of errors that say:

ld: can't re-map file, errno=22 file '/usr/local/Cellar/gcc/14.2.0_1/lib/gcc/current/libgcc_s.1.1.dylib' for architecture x86_64 collect2: error: ld returned 1 exit status ld: can't re-map file, errno=22 file '/usr/local/Cellar/gcc/14.2.0_1/lib/gcc/current/libgcc_s.1.1.dylib' for architecture x86_64 collect2: error: ld returned 1 exit status

I have just reinstalled homebrew, and the only two packages I have installed are gcc and gmt. Can anyone please tell me how to fix this?

Answered by SMillerDev

Jan 24, 2025

But I would guess that stuff that works under x86 could not work under ARM.

Not the same binaries, but you can do brew bundle dump on the x86 install, and use brew bundle install to restore the same formulae to an ARM install.

Do you think this is my problem, however, that I haven't tried to install the native ARM version?

I think the Rosetta layer is not perfect in it's translation, and with something like GCC that seems an extra reason not to use emulation if you don't have to.

View full answer

SMillerDev · 2025-01-24T06:46:32Z

SMillerDev
Jan 24, 2025

I have just reinstalled homebrew, and the only two packages I have installed are gcc and gmt.

libtiff
  geos
  gmp
  libpng
  ghostscript
  gdal
  libgeotiff
  freetype
  hdf5
  pango
  glib
  libspatialite
  cairo
  webp
  xz
  fontconfig
  giflib
  pkgconf
  netcdf
  libevent
  qhull

Brew says these are also installed. I also see that you're running on an ARM device but have an x86 install, is that intentional?

4 replies

Derek-Schutt Jan 24, 2025
Author

No, it's not intentional. But I would guess that stuff that works under x86 could not work under ARM. Do you think this is my problem, however, that I haven't tried to install the native ARM version?

SMillerDev Jan 24, 2025

But I would guess that stuff that works under x86 could not work under ARM.

Not the same binaries, but you can do brew bundle dump on the x86 install, and use brew bundle install to restore the same formulae to an ARM install.

Do you think this is my problem, however, that I haven't tried to install the native ARM version?

I think the Rosetta layer is not perfect in it's translation, and with something like GCC that seems an extra reason not to use emulation if you don't have to.

Answer selected by Derek-Schutt

Derek-Schutt Jan 24, 2025
Author

Thanks, I did what you suggest but the same problem remains.

gromgit Jan 25, 2025

Are you still in a Rosetta terminal session? What's the output of arch?

Derek-Schutt · 2025-01-27T14:39:01Z

Derek-Schutt
Jan 27, 2025
Author

I guess I am.

$ arch
i386

Sorry about my ignorance. Is this something I can turn off in system settings?

1 reply

SMillerDev Jan 27, 2025

Where are you running these commands? In the terminal app? Or something else?

Derek-Schutt · 2025-01-27T14:49:37Z

Derek-Schutt
Jan 27, 2025
Author

In the terminal app.

1 reply

SMillerDev Jan 27, 2025

Can you check if this is enabled:

Right-Click "Terminal" > Get Info > Enable Open using Rosetta

Derek-Schutt · 2025-01-27T16:05:20Z

Derek-Schutt
Jan 27, 2025
Author

Thanks, I've just disabled Rosetta.

2 replies

Derek-Schutt Jan 27, 2025
Author

I've just changed the arch (via $env /usr/bin/arch -arm64 /bin/bash --login) and the code compiles! Thanks everyone!

gromgit Jan 28, 2025

Thanks, I've just disabled Rosetta.

To be sure, quit Terminal completely, then launch it again and run arch.

I've just changed the arch (via $env /usr/bin/arch -arm64 /bin/bash --login) and the code compiles! Thanks everyone!

You shouldn't have to do that, unless your terminal session is still under Rosetta.

Derek-Schutt · 2025-01-28T17:02:34Z

Derek-Schutt
Jan 28, 2025
Author

Yeah, when I quit terminal and restart it, I get i386 under arch, even though Rosetta is turned off. My guess is Rosetta is starting elsewhere.

2 replies

Derek-Schutt Jan 28, 2025
Author

I've currently added $env /usr/bin/arch -arm64 /bin/bash to my .bash_profile (I like to run bash), and that seems to have fixed things.

gromgit Jan 29, 2025

Try tracing your shell startup by running:

echo exit | PS4='+${BASH_SOURCE}:${LINENO}[$?]> ' script /tmp/trace.log /bin/bash -xli

then check /tmp/trace.log for all instances of arch.

Also, /bin/bash on macOS is stuck at v3.2 for licensing reasons, which was released almost 20 years ago.

Derek-Schutt · 2025-01-29T13:42:24Z

Derek-Schutt
Jan 29, 2025
Author

Thanks. Yeah, I use bash on the studio because it's the shell I use on my linux server. There are no other instances of arch in the startup other than what I put into my .bash_profile.

0 replies

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ld: can't re-map file, errno=22 file #5904

Output of brew config

Output of brew doctor

Description of issue

Replies: 6 comments · 10 replies

Derek-Schutt Jan 24, 2025 Author

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Output of `brew config`

Output of `brew doctor`

Replies: 6 comments 10 replies

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Jan 27, 2025
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Derek-Schutt
Jan 27, 2025
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Derek-Schutt Jan 28, 2025
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