[Sage Build] libhomfly-1.03 fails on macOS while running `make`

[Albert Yao]

Hello everyone,

I’m trying to build SageMath from the GitHub source on MacOs Sequoia 15.3. The build runs fine until the libhomfly-1.03 package, and then fails. 

Has anyone seen this error on macOS? What’s the recommended way to fix or bypass this so I can build Sage completely?

- Albert

[UTPAL KUMAR RAY]

I recently installed SageMath version 10.8.beta1, Release Date: 2025-08-27

on macOS Sequoia 15.6.1 (24G90) (Macbook Air M2)

It went smoothly.

-------

Utpal Kumar Ray

Assistant Professor (Contractual)

Department of Information Technology

Jadavpur University Salt Lake Campus

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[Dima Pasechnik]

On September 4, 2025 10:14:51 PM CDT, Albert Yao <albert...@gmail.com> wrote:
>Hello everyone,
>
>I’m trying to build SageMath from the GitHub source on MacOs Sequoia 15.3.

>The build runs fine until the *libhomfly-1.03* package, and then fails.

>
>Has anyone seen this error on macOS? What’s the recommended way to fix or
>bypass this so I can build Sage completely?

It's hard to say what goes wrong for you without seeing the error message you are getting.

Please post more info.


>
>
>- Albert
>

[Albert Yao]

Hi all,

Here is the error that I'm getting whenever I try running make in the terminal:

Error building Sage.

The following package(s) may have failed to build (not necessarily

during this run of 'make all-start'):

* package:         libhomfly-1.03

  last build time: Sep 9 12:08

  log file:        /Users/albertyao/sage/logs/pkgs/libhomfly-1.03.log

  build directory: /Users/albertyao/sage/local/var/tmp/sage/build/libhomfly-1.03

How should I fix this? Is there something I haven't downloaded that I should?

Many thanks,

Albert

[Dima Pasechnik]

please post /Users/albertyao/sage/logs/pkgs/libhomfly-1.03.log here
(you might have noticed that this is asked for in the error message)

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[Albert Yao]

Attempting to download package libhomfly-1.03.tar.gz from mirrors

https://github.com/sagemath/sage/releases/download/10.8/libhomfly-1.03.tar.gz

[xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx]

ERROR [transfer|run:135]: [Errno socket error] [Errno 404] Not Found: '//github.com/sagemath/sage/releases/download/10.8/libhomfly-1.03.tar.gz'

Exception ignored in: <http.client.HTTPResponse object at 0x1052bea40>

Traceback (most recent call last):

  File "/opt/homebrew/Cellar/pyt...@3.13/3.13.7/Frameworks/Python.framework/Versions/3.13/lib/python3.13/http/client.py", line 432, in close

    super().close() # set "closed" flag

  File "/opt/homebrew/Cellar/pyt...@3.13/3.13.7/Frameworks/Python.framework/Versions/3.13/lib/python3.13/http/client.py", line 445, in flush

    self.fp.flush()

ValueError: I/O operation on closed file.

https://github.com/sagemath/sage/releases/download/10.7/libhomfly-1.03.tar.gz

[xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx]

ERROR [transfer|run:135]: [Errno socket error] [Errno 404] Not Found: '//github.com/sagemath/sage/releases/download/10.7/libhomfly-1.03.tar.gz'

Exception ignored in: <http.client.HTTPResponse object at 0x1055dc7c0>

Traceback (most recent call last):

  File "/opt/homebrew/Cellar/pyt...@3.13/3.13.7/Frameworks/Python.framework/Versions/3.13/lib/python3.13/http/client.py", line 432, in close

    super().close() # set "closed" flag

  File "/opt/homebrew/Cellar/pyt...@3.13/3.13.7/Frameworks/Python.framework/Versions/3.13/lib/python3.13/http/client.py", line 445, in flush

    self.fp.flush()

ValueError: I/O operation on closed file.

https://github.com/sagemath/sage/releases/download/10.6/libhomfly-1.03.tar.gz

[xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx]

ERROR [transfer|run:135]: [Errno socket error] [Errno 404] Not Found: '//github.com/sagemath/sage/releases/download/10.6/libhomfly-1.03.tar.gz'

Exception ignored in: <http.client.HTTPResponse object at 0x1053b4c40>

Traceback (most recent call last):

  File "/opt/homebrew/Cellar/pyt...@3.13/3.13.7/Frameworks/Python.framework/Versions/3.13/lib/python3.13/http/client.py", line 432, in close

    super().close() # set "closed" flag

  File "/opt/homebrew/Cellar/pyt...@3.13/3.13.7/Frameworks/Python.framework/Versions/3.13/lib/python3.13/http/client.py", line 445, in flush

    self.fp.flush()

ValueError: I/O operation on closed file.

http://files.sagemath.org/spkg/upstream/libhomfly/libhomfly-1.03.tar.gz

[......................................................................]

Setting up build directory /Users/albertyao/sage/local/var/tmp/sage/build/libhomfly-1.03

No patch files found in ../patches

Host system: Darwin 2026-Albert-Yao-M4 24.3.0 Darwin Kernel Version 24.3.0: Thu Jan  2 20:31:46 PST 2025; root:xnu-11215.81.4~4/RELEASE_ARM64_T8132 arm64

C compiler: gcc, Apple clang version 17.0.0 (clang-1700.0.13.5), Target: arm64-apple-darwin24.3.0, Thread model: posix, InstalledDir: /Library/Developer/CommandLineTools/usr/bin

No stamp file for package 'libhomfly' in /Users/albertyao/sage/local/var/lib/sage/installed

No spkg-legacy-uninstall script; nothing to do

[spkg-install] Configuring libhomfly-1.03

[spkg-install] configure: WARNING: unrecognized options: --disable-maintainer-mode

[spkg-install] checking for a BSD-compatible install... /usr/bin/install -c

[spkg-install] checking whether sleep supports fractional seconds... yes

[spkg-install] checking filesystem timestamp resolution... 2

[spkg-install] checking whether build environment is sane... yes

[spkg-install] checking for a race-free mkdir -p... mkdir -p

[spkg-install] checking for gawk... no

[spkg-install] checking for mawk... no

[spkg-install] checking for nawk... no

[spkg-install] checking for awk... awk

[spkg-install] checking whether make sets $(MAKE)... yes

[spkg-install] checking whether make supports nested variables... yes

[spkg-install] checking xargs -n works... yes

[spkg-install] checking whether UID '503' is supported by ustar format... yes

[spkg-install] checking whether GID '20' is supported by ustar format... yes

[spkg-install] checking how to create a ustar tar archive... gnutar

[spkg-install] checking whether make supports the include directive... yes (GNU style)

[spkg-install] checking for gcc... gcc

[spkg-install] checking whether the C compiler works... yes

[spkg-install] checking for C compiler default output file name... a.out

[spkg-install] checking for suffix of executables... 

[spkg-install] checking whether we are cross compiling... no

[spkg-install] checking for suffix of object files... o

[spkg-install] checking whether the compiler supports GNU C... yes

[spkg-install] checking whether gcc accepts -g... yes

[spkg-install] checking for gcc option to enable C11 features... none needed

[spkg-install] checking whether gcc understands -c and -o together... yes

[spkg-install] checking dependency style of gcc... none

[spkg-install] checking the archiver (ar) interface... ar

[spkg-install] checking for gcc... (cached) gcc

[spkg-install] checking whether the compiler supports GNU C... (cached) yes

[spkg-install] checking whether gcc accepts -g... (cached) yes

[spkg-install] checking for gcc option to enable C11 features... (cached) none needed

[spkg-install] checking whether gcc understands -c and -o together... (cached) yes

[spkg-install] checking dependency style of gcc... (cached) none

[spkg-install] checking build system type... aarch64-apple-darwin24.3.0

[spkg-install] checking host system type... aarch64-apple-darwin24.3.0

[spkg-install] checking how to print strings... printf

[spkg-install] checking for a sed that does not truncate output... /usr/bin/sed

[spkg-install] checking for grep that handles long lines and -e... /usr/bin/grep

[spkg-install] checking for egrep... /usr/bin/grep -E

[spkg-install] checking for fgrep... /usr/bin/grep -F

[spkg-install] checking for ld used by gcc... /Library/Developer/CommandLineTools/usr/bin/ld

[spkg-install] checking if the linker (/Library/Developer/CommandLineTools/usr/bin/ld) is GNU ld... no

[spkg-install] checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B

[spkg-install] checking the name lister (/usr/bin/nm -B) interface... BSD nm

[spkg-install] checking whether ln -s works... yes

[spkg-install] checking the maximum length of command line arguments... 786432

[spkg-install] checking how to convert aarch64-apple-darwin24.3.0 file names to aarch64-apple-darwin24.3.0 format... func_convert_file_noop

[spkg-install] checking how to convert aarch64-apple-darwin24.3.0 file names to toolchain format... func_convert_file_noop

[spkg-install] checking for /Library/Developer/CommandLineTools/usr/bin/ld option to reload object files... -r

[spkg-install] checking for file... file

[spkg-install] checking for objdump... objdump

[spkg-install] checking how to recognize dependent libraries... pass_all

[spkg-install] checking for dlltool... no

[spkg-install] checking how to associate runtime and link libraries... printf %s\n

[spkg-install] checking for ranlib... ranlib

[spkg-install] checking for archiver @FILE support... no

[spkg-install] checking for strip... strip

[spkg-install] checking command to parse /usr/bin/nm -B output from gcc object... ok

[spkg-install] checking for sysroot... no

[spkg-install] checking for a working dd... /bin/dd

[spkg-install] checking how to truncate binary pipes... /bin/dd bs=4096 count=1

[spkg-install] checking for mt... no

[spkg-install] checking if : is a manifest tool... no

[spkg-install] checking for dsymutil... dsymutil

[spkg-install] checking for nmedit... nmedit

[spkg-install] checking for lipo... lipo

[spkg-install] checking for otool... otool

[spkg-install] checking for otool64... no

[spkg-install] checking for -single_module linker flag... ld: warning: -single_module is obsolete

[spkg-install] no

[spkg-install] checking for -no_fixup_chains linker flag... yes

[spkg-install] checking for -exported_symbols_list linker flag... yes

[spkg-install] checking for -force_load linker flag... yes

[spkg-install] checking for stdio.h... yes

[spkg-install] checking for stdlib.h... yes

[spkg-install] checking for string.h... yes

[spkg-install] checking for inttypes.h... yes

[spkg-install] checking for stdint.h... yes

[spkg-install] checking for strings.h... yes

[spkg-install] checking for sys/stat.h... yes

[spkg-install] checking for sys/types.h... yes

[spkg-install] checking for unistd.h... yes

[spkg-install] checking for dlfcn.h... yes

[spkg-install] checking for objdir... .libs

[spkg-install] checking if gcc supports -fno-rtti -fno-exceptions... yes

[spkg-install] checking for gcc option to produce PIC... -fno-common -DPIC

[spkg-install] checking if gcc PIC flag -fno-common -DPIC works... yes

[spkg-install] checking if gcc static flag -static works... no

[spkg-install] checking if gcc supports -c -o file.o... yes

[spkg-install] checking if gcc supports -c -o file.o... (cached) yes

[spkg-install] checking whether the gcc linker (/Library/Developer/CommandLineTools/usr/bin/ld) supports shared libraries... yes

[spkg-install] checking dynamic linker characteristics... darwin24.3.0 dyld

[spkg-install] checking how to hardcode library paths into programs... immediate

[spkg-install] checking whether stripping libraries is possible... yes

[spkg-install] checking if libtool supports shared libraries... yes

[spkg-install] checking whether to build shared libraries... yes

[spkg-install] checking whether to build static libraries... no

[spkg-install] checking that generated files are newer than configure... done

[spkg-install] configure: creating ./config.status

[spkg-install] config.status: creating Makefile

[spkg-install] config.status: creating lib/Makefile

[spkg-install] config.status: creating test/Makefile

[spkg-install] config.status: creating libhomfly.pc

[spkg-install] config.status: executing depfiles commands

[spkg-install] config.status: executing libtool commands

[spkg-install] configure: WARNING: unrecognized options: --disable-maintainer-mode

[spkg-install] Building libhomfly-1.03

[spkg-install] Making all in lib

[spkg-install] /bin/bash ../libtool  --tag=CC   --mode=compile gcc -DPACKAGE_NAME=\"libhomfly\" -DPACKAGE_TARNAME=\"libhomfly\" -DPACKAGE_VERSION=\"1.03\" -DPACKAGE_STRING=\"libhomfly\ 1.03\" -DPACKAGE_BUGREPORT=\"mma...@unizar.es\" -DPACKAGE_URL=\"\" -DPACKAGE=\"libhomfly\" -DVERSION=\"1.03\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I.     -g -O2 -c -o bound.lo bound.c

[spkg-install] libtool: compile:  gcc -DPACKAGE_NAME=\"libhomfly\" -DPACKAGE_TARNAME=\"libhomfly\" -DPACKAGE_VERSION=\"1.03\" "-DPACKAGE_STRING=\"libhomfly 1.03\"" -DPACKAGE_BUGREPORT=\"mma...@unizar.es\" -DPACKAGE_URL=\"\" -DPACKAGE=\"libhomfly\" -DVERSION=\"1.03\" -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -I. -g -O2 -c bound.c  -fno-common -DPIC -o .libs/bound.o

[spkg-install] bound.c:10:10: fatal error: 'gc.h' file not found

[spkg-install]    10 | #include <gc.h>

[spkg-install]       |          ^~~~~~

[spkg-install] 1 error generated.

[spkg-install] make[6]: *** [bound.lo] Error 1

[spkg-install] make[5]: *** [all-recursive] Error 1

[spkg-install] ********************************************************************************

[spkg-install] Error building libhomfly-1.03

[spkg-install] ********************************************************************************

************************************************************************

Error installing package libhomfly-1.03

************************************************************************

Please email sage-devel (http://groups.google.com/group/sage-devel)

explaining the problem and including the log files

  /Users/albertyao/sage/logs/pkgs/libhomfly-1.03.log

and

  /Users/albertyao/sage/config.log

Describe your computer, operating system, etc.

If you want to try to fix the problem yourself, *don't* just cd to

/Users/albertyao/sage/local/var/tmp/sage/build/libhomfly-1.03 and type 'make' or whatever is appropriate.

Instead, the following commands setup all environment variables

correctly and load a subshell for you to debug the error:

  (cd '/Users/albertyao/sage/local/var/tmp/sage/build/libhomfly-1.03' && '/Users/albertyao/sage/sage' --buildsh)

When you are done debugging, you can type "exit" to leave the subshell.

************************************************************************

[Albert Yao]

Hi all,

Here's the log for libhomfly-1.03 package:

Can you guys see what's the error based on this? Would be greatly appreciated if you could help :)

Many thanks,

Albert

On Tuesday, September 9, 2025 at 1:37:17 PM UTC-4 dim...@gmail.com wrote:

[Dima Pasechnik]

 error: 'gc.h' file not found

Do you have gc installed by Sage, or from Homebrew?

(this can be seen in the toplevel config.log - please post it too)