Thanks for the update and explanation. Thanks also for pointing out the Fortran issue - I'm not going to mess with things now as I don't want to break anything before R Dev Day @ Rencontres R, but I'll certainly come back to that and hopefully get my setup sorted out.
Best wishes, Heather On Sat, May 17, 2025, at 2:49 AM, Simon Urbanek wrote: > 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 <h...@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 <h...@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 >>>> >>>> _______________________________________________ >>>> R-SIG-Mac mailing list >>>> R-SIG-Mac@r-project.org >>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac >>>> >> _______________________________________________ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
