[R-SIG-Mac] Need for `-headerpad_max_install_names` with `--enable-R-framework`

[Simon Urbanek]

Heather,

thanks, I can reproduce it with CTL 16.3, so it is caused by the toolchain. Although both (16.2 and 16.3) actually have pretty much identical headers and the same local commands, the 16.3 toolchain inserts one small block right behind the load commands thus preventing them to grow. Interestingly, using -Wl,-headerpad_max_install_names just shifts that block back without using any extra space (i.e the file size is the same), so it seems like a reasonable work-around, although it is very perplexing why CLT 16.3 doesn't do that automatically - it looks like a regression in the toolchain. I have now added the work-around to R-devel as r88214.

Cheers,
Simon

PS: FWIW as noted before, CLT 16.3 despite looking like a minor update is actually a very major breaking change jumping from llvm 17 to 19.

PPS: unrelated to the issue here, but you seem to have a problem in your system: you are picking up some ancient Fortran since you show 8.2 while you should see 14.2.0. Also you are adding /opt/gfortran/lib which shouldn't be in flags as it doesn't have any libraries in the 14.2.0 binary, so it all looks suspicious. If in doubt, remove /opt/gfortran completely and re-install. FWIW the official flags used for CRAN builds are at
https://svn.r-project.org/R-dev-web/trunk/QA/Simon/R4/conf.big-sur-arm64


> On May 16, 2025, at 7:36 PM, Heather Turner <ht using heatherturner.net> wrote:
> 
> Hi Simon,
> 
> I am configuring with 
> 
> $TOP_SRCDIR/configure --enable-R-framework --disable-java FW_VERSION=R-devel
> 
> and config.site
> 
> CC=clang
> OBJC=$CC
> FC="/opt/gfortran/bin/gfortran -mtune=native"
> CPPFLAGS='-isystem /opt/R/arm64/include'
> CXX=clang++
> PKG_CONFIG_PATH=/opt/R/arm64/lib/pkgconfig:/usr/lib/pkgconfig
> CFLAGS="-falign-functions=8 -g -O0"
> FFLAGS="-g -O2 -mmacosx-version-min=11.0"
> FCFLAGS="-g -O2 -mmacosx-version-min=11.0"
> LDFLAGS="-L/opt/R/arm64/lib -L/opt/gfortran/lib"
> CPPFLAGS="-isystem /opt/R/arm64/include -I/opt/R/arm64/include"
> 
> [this is the version before adding MAIN_LDFLAGS="-Wl,-headerpad_max_install_names"]
> 
> I'm using Command Line Tools only (no full Xcode installed).
> 
> macOS version: Sequoia 15.4.1 (24E263)
> CLT version: 16.3.0.0.1.1742442376
> Clang: Apple clang version 17.0.0 (clang-1700.0.13.3)
> Fortran: GNU Fortran (GCC) 8.2.0 (from https://mac.r-project.org/tools/gfortran-14.2-universal.pkg)
> SDK version: 15.4
> SDK path: /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk
> 
> and could reproduce the issue on my side with an SVN checkout of R-devel 2025-05-15 r88204.
> 
> Hope that helps,
> 
> Heather
> 
> On Fri, May 16, 2025, at 4:43 AM, Simon Urbanek wrote:
>> Heather,
>> 
>> yes, please, since we cannot reproduce it, please provide your complete 
>> configure flags, full info about your macOS version, tools used 
>> (toolchain version and SDK). We are adding 
>> -Wl,-headerpad_max_install_names for libraries (see etc/Makeconf, added 
>> by configure.ac for darwin), but the binary itself has never caused 
>> issues, so I wonder what makes your system produce smaller header that 
>> won’t fit the paths.
>> 
>> Thanks,
>> Simon
>> 
>> 
>>> On 16 May 2025, at 04:24, Heather Turner <ht using heatherturner.net> wrote:
>>> 
>>> Dear All,
>>> 
>>> I have been building R (on Apple M1 Pro) with `--enable-R-framework` so that I can use the built version of R in RStudio/Positron. My set up was working fine back in February or so, then in April (with the alpha version) I started to hit errors with `make install`:
>>> 
>>> Creating R framework ...
>>> libRlapack
>>> libRblas
>>> error: /Library/Developer/CommandLineTools/usr/bin/install_name_tool: changing install names or rpaths can't be redone for: /Library/Frameworks/R.framework/Versions/R-devel/Resources/bin/exec/R <http://r.framework/Versions/R-devel/Resources/bin/exec/R> (for architecture arm64) because larger updated load commands do not fit (the program must be relinked, and you may need to use -headerpad or -headerpad_max_install_names)
>>> <similar error for libR, snipped>
>>> 
>>> I only just got round to exploring further. I can fix the issue by adding 
>>> 
>>> MAIN_LDFLAGS="-Wl,-headerpad_max_install_names"
>>> 
>>> to my config.site, but I wonder why I didn't need to set this in the past. Also I wonder if this should be set by default, at least with `--enable-R-framework`?
>>> 
>>> Let me know if I can provide any information that might be helpful about my configuration/setup.
>>> 
>>> Best wishes,
>>> Heather
>>> 
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>