ranlib should be run on static libs on macOS: ld: in dbarts.a, archive has no table of contents

[barracuda156]

ar rv ../dbarts.a bartFit.o binaryIO.o birthDeathRule.o changeRule.o functions.o likelihood.o node.o parameterPrior.o state.o swapRule.o tree.o treePrior.o
ar: creating archive ../dbarts.a
a - bartFit.o
a - binaryIO.o
a - birthDeathRule.o
a - changeRule.o
a - functions.o
a - likelihood.o
a - node.o
a - parameterPrior.o
a - state.o
a - swapRule.o
a - tree.o
a - treePrior.o
/opt/local/bin/gcc-mp-12 -I"/opt/local/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../include -pthread  -isystem/opt/local/include/LegacySupport -I/opt/local/include   -fPIC  -pipe -Os -arch ppc  -fPIC -c io.c -o io.o
/opt/local/bin/gcc-mp-12 -I"/opt/local/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../include -pthread  -isystem/opt/local/include/LegacySupport -I/opt/local/include   -fPIC  -pipe -Os -arch ppc  -fPIC -c randomBase.c -o randomBase.o
/opt/local/bin/gcc-mp-12 -I"/opt/local/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../include -pthread  -isystem/opt/local/include/LegacySupport -I/opt/local/include   -fPIC  -pipe -Os -arch ppc  -fPIC -c randomNorm.c -o randomNorm.o
/opt/local/bin/gcc-mp-12 -I"/opt/local/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../include -pthread  -isystem/opt/local/include/LegacySupport -I/opt/local/include   -fPIC  -pipe -Os -arch ppc  -fPIC -c random.c -o random.o
ar rv ../external.a io.o randomBase.o randomNorm.o random.o
ar: creating archive ../external.a
a - io.o
a - randomBase.o
a - randomNorm.o
a - random.o
/opt/local/bin/gcc-mp-12 -I"/opt/local/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../include -pthread  -isystem/opt/local/include/LegacySupport -I/opt/local/include   -fPIC  -pipe -Os -arch ppc  -fPIC  -c adaptiveRadixTree.c -o adaptiveRadixTree.o
/opt/local/bin/gcc-mp-12 -I"/opt/local/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../include -pthread  -isystem/opt/local/include/LegacySupport -I/opt/local/include   -fPIC  -pipe -Os -arch ppc  -fPIC -c binaryIO.c -o binaryIO.o
/opt/local/bin/gcc-mp-12 -I"/opt/local/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../include -pthread  -isystem/opt/local/include/LegacySupport -I/opt/local/include   -fPIC  -pipe -Os -arch ppc  -fPIC -c blockingThreadManager.c -o blockingThreadManager.o
/opt/local/bin/gcc-mp-12 -I"/opt/local/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../include -pthread  -isystem/opt/local/include/LegacySupport -I/opt/local/include   -fPIC  -pipe -Os -arch ppc  -fPIC -c hierarchicalThreadManager.c -o hierarchicalThreadManager.o
/opt/local/bin/gcc-mp-12 -I"/opt/local/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../include -pthread  -isystem/opt/local/include/LegacySupport -I/opt/local/include   -fPIC  -pipe -Os -arch ppc  -fPIC -c linearAlgebra.c -o linearAlgebra.o
/opt/local/bin/gcc-mp-12 -I"/opt/local/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../include -pthread  -isystem/opt/local/include/LegacySupport -I/opt/local/include   -fPIC  -pipe -Os -arch ppc  -fPIC -c moments.c -o moments.o
/opt/local/bin/gcc-mp-12 -I"/opt/local/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../include -pthread  -isystem/opt/local/include/LegacySupport -I/opt/local/include   -fPIC  -pipe -Os -arch ppc  -fPIC -c partition.c -o partition.o
/opt/local/bin/gcc-mp-12 -I"/opt/local/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../include -pthread  -isystem/opt/local/include/LegacySupport -I/opt/local/include   -fPIC  -pipe -Os -arch ppc  -fPIC -c simd.c -o simd.o
/opt/local/bin/gcc-mp-12 -I"/opt/local/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../include -pthread  -isystem/opt/local/include/LegacySupport -I/opt/local/include   -fPIC  -pipe -Os -arch ppc  -fPIC -c string.c -o string.o
/opt/local/bin/gcc-mp-12 -I"/opt/local/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../include -pthread  -isystem/opt/local/include/LegacySupport -I/opt/local/include   -fPIC  -pipe -Os -arch ppc  -fPIC -c thread.c -o thread.o
ar rv ../misc.a adaptiveRadixTree.o binaryIO.o blockingThreadManager.o hierarchicalThreadManager.o linearAlgebra.o moments.o partition.o simd.o string.o thread.o 
ar: creating archive ../misc.a
a - adaptiveRadixTree.o
a - binaryIO.o
a - blockingThreadManager.o
a - hierarchicalThreadManager.o
a - linearAlgebra.o
a - moments.o
a - partition.o
a - simd.o
a - string.o
a - thread.o
/opt/local/bin/gcc-mp-12 -I"/opt/local/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../include -pthread  -isystem/opt/local/include/LegacySupport -I/opt/local/include  -pipe -Os -arch ppc  -fPIC -c bounds.c -o bounds.o
/opt/local/bin/gcc-mp-12 -I"/opt/local/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../include -pthread  -isystem/opt/local/include/LegacySupport -I/opt/local/include  -pipe -Os -arch ppc  -fPIC -c util.c -o util.o
ar rv ../rc.a bounds.o util.o
ar: creating archive ../rc.a
a - bounds.o
a - util.o
/opt/local/bin/g++-mp-12 -std=gnu++14 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/opt/local/Library/Frameworks/R.framework/Resources/lib -Wl,-headerpad_max_install_names -Wl,-rpath,/opt/local/lib/libgcc -L/opt/local/lib -lMacportsLegacySupport -arch ppc -o dbarts.so R_C_interface.o R_interface.o R_interface_common.o R_interface_crossvalidate.o R_interface_rbart.o R_interface_sampler.o crossvalidate.o guessNumCores.o makeModelMatrixFromDataFrame.o dbarts.a external.a misc.a rc.a -pthread -F/opt/local/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: in dbarts.a, archive has no table of contents
collect2: error: ld returned 1 exit status
make: *** [dbarts.so] Error 1

[barracuda156]

This fixes the build:

--- src/dbarts/Makefile.orig	2023-01-21 01:54:34.000000000 +0800
+++ src/dbarts/Makefile	2023-04-13 05:47:53.000000000 +0800
@@ -13,6 +13,7 @@
 
 library : $(LOCAL_OBJECTS)
 	$(AR) $(ARFLAGS) ../dbarts.a $(LOCAL_OBJECTS)
+	$(RANLIB) ../dbarts.a
 
 clean :
 	@-rm -f config.hpp

--- src/external/Makefile.orig	2023-01-21 01:54:34.000000000 +0800
+++ src/external/Makefile	2023-04-13 05:48:13.000000000 +0800
@@ -9,6 +9,7 @@
 
 library : $(LOCAL_OBJECTS)
 	$(AR) $(ARFLAGS) ../external.a $(LOCAL_OBJECTS)
+	$(RANLIB) ../external.a
 
 clean :
 	@-rm -f config.h

--- src/misc/Makefile.orig	2023-01-21 01:54:34.000000000 +0800
+++ src/misc/Makefile	2023-04-13 05:48:41.000000000 +0800
@@ -57,6 +57,7 @@
 
 library : $(LOCAL_OBJECTS)
 	$(AR) $(ARFLAGS) ../misc.a $(LOCAL_OBJECTS)
+	$(RANLIB) ../misc.a
 
 clean :
 	@-rm -f config.h

--- src/rc/Makefile.orig	2023-01-21 01:54:34.000000000 +0800
+++ src/rc/Makefile	2023-04-13 05:48:57.000000000 +0800
@@ -9,6 +9,7 @@
 
 library : $(LOCAL_OBJECTS)
 	$(AR) $(ARFLAGS) ../rc.a $(LOCAL_OBJECTS)
+	$(RANLIB) ../rc.a
 
 clean :
 	@-rm -f config.h

I am not sure if this can be used unconditionally for every OS though.

[barracuda156]

As an alternative, fixing flags for ar so that table of contents is generated will likely work too.

[vdorie]

Sorry that I didn't respond to this, but I wasn't able to reproduce it which limited my ability to test and I also wasn't sure if I could make the fix work across platforms. I did make a change to the makefile where it should pull in ARFLAGS from the R environment and set them to `-cr` if it can't find them. If you could let me know if that works, I would greatly appreciate it.

…

On Sun, Dec 10, 2023 at 2:35 AM Sergey Fedorov ***@***.***> wrote: As an alternative, fixing flags for ar so that table of contents is generated will likely work too. — Reply to this email directly, view it on GitHub <#55 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAE5P4AMS6STA2S6Y36MF6TYIVQ3XAVCNFSM6AAAAAAW4HPIWKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQNBYHA4DGNBYHE> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[barracuda156]

@vdorie s is needed in ar flags in order for that to work across all platforms. I.e., cr will not be sufficient, crs will.

P. S. Here the identical problem was fixed via adding s: PolMine/RcppCWB@c6df1cc

[vdorie]

Thank you! I added s to the defaults in dd206c4 and it'll be included in the next push to CRAN.

[barracuda156]

@vdorie Thank you, awesome!

[barracuda156]

@vdorie Does not work still with 0.9-26:

ar rv ../rc.a bounds.o util.o
ar: creating archive ../rc.a
a - bounds.o
a - util.o
/opt/local/bin/g++-mp-13 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/opt/local/Library/Frameworks/R.framework/Resources/lib -Wl,-headerpad_max_install_names -L/opt/local/lib -lMacportsLegacySupport -Wl,-rpath,/opt/local/lib/libgcc -arch ppc -o dbarts.so R_C_interface.o R_interface.o R_interface_common.o R_interface_crossvalidate.o R_interface_rbart.o R_interface_sampler.o crossvalidate.o guessNumCores.o makeModelMatrixFromDataFrame.o dbarts.a external.a misc.a rc.a -pthread -F/opt/local/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: in dbarts.a, archive has no table of contents
collect2: error: ld returned 1 exit status
make: *** [dbarts.so] Error 1

[vdorie]

I’d love to help with this but it would be very helpful if there was a way to replicate the issue locally. Is there an emulation and/or containerization setup for Darwin PPC I might be able to use? Otherwise, I can’t even get `ar` to not generate a table of contents on my machine, which makes building a configure script test (my preferred solution) very difficult.

…

On Sat, Feb 3, 2024 at 9:40 PM Sergey Fedorov ***@***.***> wrote: @vdorie <https://github.com/vdorie> Does not work still with 0.9-26: ar rv ../rc.a bounds.o util.o ar: creating archive ../rc.a a - bounds.o a - util.o /opt/local/bin/g++-mp-13 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/opt/local/Library/Frameworks/R.framework/Resources/lib -Wl,-headerpad_max_install_names -L/opt/local/lib -lMacportsLegacySupport -Wl,-rpath,/opt/local/lib/libgcc -arch ppc -o dbarts.so R_C_interface.o R_interface.o R_interface_common.o R_interface_crossvalidate.o R_interface_rbart.o R_interface_sampler.o crossvalidate.o guessNumCores.o makeModelMatrixFromDataFrame.o dbarts.a external.a misc.a rc.a -pthread -F/opt/local/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation ld: in dbarts.a, archive has no table of contents collect2: error: ld returned 1 exit status make: *** [dbarts.so] Error 1 — Reply to this email directly, view it on GitHub <#55 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAE5P4CPOYZNSSBVDXLK7OTYR3YKNAVCNFSM6AAAAAAW4HPIWKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSMRVGU2TONZVHA> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[barracuda156]

@vdorie Did the last CRAN release have s added to ar flags? That should work, and it is according to ar documentation (nothing exclusive to macOS). It looks like newer versions of ar pretend the flag was passed even if it was not, and generate the table regardless. I do not see any reason to do it conditionally, to be honest.

[vdorie]

In the version on CRAN the flags should default to "-crs" unless ARFLAGS is non-empty, so if it is still failing that might be why. It looks like the flags are set to 'rv', right?

…

On Thu, Feb 8, 2024 at 2:37 PM Sergey Fedorov ***@***.***> wrote: @vdorie <https://github.com/vdorie> Did the last CRAN release have s added to ar flags? That should work, and it is according to ar documentation (nothing exclusive to macOS). It looks like newer versions of ar pretend the flag was passed even if it was not, and generate the table regardless. I do not see any reason to do it conditionally, to be honest. — Reply to this email directly, view it on GitHub <#55 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAE5P4GLQJY2KJCQRUI4FCDYSUSQRAVCNFSM6AAAAAAW4HPIWKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSMZUHAYTIOBUGI> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[barracuda156]

In the version on CRAN the flags should default to "-crs" unless ARFLAGS is non-empty, so if it is still failing that might be why. It looks like the flags are set to 'rv', right?

Hmm, interesting. I definitely did not pass arflags manually. I also do not think Macports should be passing that.

[barracuda156]

We do use CRAN version: https://github.com/macports/macports-ports/blob/7518a78ed00d82d1e8164258d7f921cfbf421c28/R/R-dbarts/Portfile#L7

It still fails without a patch adding ranlib. Here are logs:
dbarts_as_is.txt
dbarts_patched.txt
I do not think anything in Macports resets AR flags, that does not happen with other ports.