BC19RG commented 2 years ago

if (!require("BiocManager", quietly = TRUE))

install.packages("BiocManager") BiocManager::install("msa") 'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details

replacement repositories: CRAN: https://cran.rstudio.com/

x-gzip' length 3885072 bytes (3.7 MB)

downloaded 3.7 MB

installing source package ‘msa’ ... using staged installation libs clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I"./gc-7.6.12/include" -I"./Muscle/" -I"./ClustalW/src" -I"./ClustalOmega/src" -fPIC -falign-functions=64 -Wall -g -O2 -c R_init_msa.cpp -o R_init_msa.o In file included from R_init_msa.cpp:1: In file included from ./ClustalOmega/src/RClustalOmega.h:4: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp.h:27: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/RcppCommon.h:168: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp/internal/r_coerce.h:255:7: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] ::sprintf(buff, "%02x", from); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg'
define deprecated_msg(_msg) attribute((deprecated__(_msg)))
```
                                              ^
```
In file included from R_init_msa.cpp:3: In file included from ./Muscle/RMuscle.h:4: ./Muscle/muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined]

define assert(exp) ((void)0)
```
^
```
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here

define assert(e) ((void)0)
```
^
```
In file included from R_init_msa.cpp:3: In file included from ./Muscle/RMuscle.h:4: In file included from ./Muscle/muscle.h:38: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 3 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I"./gc-7.6.12/include" -I"./Muscle/" -I"./ClustalW/src" -I"./ClustalOmega/src" -fPIC -falign-functions=64 -Wall -g -O2 -c SplitCharVector2List.cpp -o SplitCharVector2List.o In file included from SplitCharVector2List.cpp:1: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp.h:27: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/RcppCommon.h:168: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp/internal/r_coerce.h:255:7: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] ::sprintf(buff, "%02x", from); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg'

define deprecated_msg(_msg) attribute((deprecated__(_msg)))
```
                                              ^
```
1 warning generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I"./gc-7.6.12/include" -I"./Muscle/" -I"./ClustalW/src" -I"./ClustalOmega/src" -fPIC -falign-functions=64 -Wall -g -O2 -c SplitCharVector2Matrix.cpp -o SplitCharVector2Matrix.o In file included from SplitCharVector2Matrix.cpp:1: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp.h:27: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/RcppCommon.h:168: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp/internal/r_coerce.h:255:7: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] ::sprintf(buff, "%02x", from); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg'

define deprecated_msg(_msg) attribute((deprecated__(_msg)))
```
                                              ^
```
1 warning generated. make --file=msaMakefile --directory=gc-7.6.12 ./configure --enable-cplusplus --enable-threads=pthreads --enable-shared --with-pic checking build system type... arm-apple-darwin22.1.0 checking host system type... arm-apple-darwin22.1.0 checking target system type... arm-apple-darwin22.1.0 checking GC version numbers... major=7 minor=6 micro=12 checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... ./install-sh -c -d checking for gawk... no checking for mawk... no checking for nawk... no checking for awk... awk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking whether to enable maintainer-specific portions of Makefiles... no checking for style of include used by make... GNU checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... gcc3 checking for g++... g++ checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking dependency style of g++... gcc3 checking dependency style of gcc... gcc3 checking how to print strings... printf checking for a sed that does not truncate output... /usr/bin/sed checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for fgrep... /usr/bin/grep -F checking for ld used by gcc... /Library/Developer/CommandLineTools/usr/bin/ld checking if the linker (/Library/Developer/CommandLineTools/usr/bin/ld) is GNU ld... no checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 786432 checking how to convert arm-apple-darwin22.1.0 file names to arm-apple-darwin22.1.0 format... func_convert_file_noop checking how to convert arm-apple-darwin22.1.0 file names to toolchain format... func_convert_file_noop checking for /Library/Developer/CommandLineTools/usr/bin/ld option to reload object files... -r checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... no checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for a working dd... /bin/dd checking how to truncate binary pipes... /bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no checking for dsymutil... dsymutil checking for nmedit... nmedit checking for lipo... lipo checking for otool... otool checking for otool64... no checking for -single_module linker flag... yes checking for -exported_symbols_list linker flag... yes checking for -force_load linker flag... yes checking how to run the C preprocessor... gcc -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... yes checking for gcc option to produce PIC... -fno-common -DPIC checking if gcc PIC flag -fno-common -DPIC works... yes checking if gcc static flag -static works... no checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/Library/Developer/CommandLineTools/usr/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... darwin22.1.0 dyld checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking how to run the C++ preprocessor... g++ -E checking for ld used by g++... /Library/Developer/CommandLineTools/usr/bin/ld checking if the linker (/Library/Developer/CommandLineTools/usr/bin/ld) is GNU ld... no checking whether the g++ linker (/Library/Developer/CommandLineTools/usr/bin/ld) supports shared libraries... yes checking for g++ option to produce PIC... -fno-common -DPIC checking if g++ PIC flag -fno-common -DPIC works... yes checking if g++ static flag -static works... no checking if g++ supports -c -o file.o... yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/Library/Developer/CommandLineTools/usr/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... darwin22.1.0 dyld checking how to hardcode library paths into programs... immediate checking for inline... inline checking for pthread_self in -lpthread... yes configure: WARNING: "Explicit GC_INIT() calls may be required." checking whether compiler supports -Wextra... yes checking whether compiler supports -Wpedantic... yes checking for xlc... no checking whether compiler supports -fno-strict-aliasing... yes checking for getcontext... yes checking for dl_iterate_phdr... no checking execinfo.h usability... yes checking execinfo.h presence... yes checking for execinfo.h... yes checking whether to build shared libraries... yes checking which machine-dependent code should be used... checking whether Solaris gcc optimization fix is necessary... no checking for dladdr... yes checking sys/dg_sys_info.h usability... no checking sys/dg_sys_info.h presence... no checking for sys/dg_sys_info.h... no checking for pkg-config... no checking for atomic_ops... no checking atomic_ops.h usability... no checking atomic_ops.h presence... no checking for atomic_ops.h... no checking which libatomic_ops to use... internal checking for lock-free AO_or primitive... no checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating bdw-gc.pc config.status: creating include/config.h config.status: executing depfiles commands config.status: executing libtool commands config.status: executing default commands === configuring in libatomic_ops (/private/var/folders/6n/w8vt3k_d3t362slggmq9_qgc0000gn/T/Rtmpfn05oG/R.INSTALL2dbc6162b184/msa/src/gc-7.6.12/libatomic_ops) configure: running /bin/sh ./configure --disable-option-checking '--prefix=/usr/local' '--enable-cplusplus' '--enable-threads=pthreads' '--enable-shared' '--with-pic' --cache-file=/dev/null --srcdir=. checking build system type... arm-apple-darwin22.1.0 checking host system type... arm-apple-darwin22.1.0 checking target system type... arm-apple-darwin22.1.0 checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... ./install-sh -c -d checking for gawk... no checking for mawk... no checking for nawk... no checking for awk... awk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking for ranlib... ranlib checking for style of include used by make... GNU checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... gcc3 checking dependency style of gcc... gcc3 checking how to run the C preprocessor... gcc -E checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for stdlib.h... (cached) yes checking for unistd.h... (cached) yes checking for sys/param.h... yes checking for getpagesize... yes checking for working mmap... yes checking for ANSI C header files... (cached) yes checking for PIC compiler flag... -fPIC checking whether gcc -fPIC causes PIC definition... yes checking for pthread_self in -lpthread... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating pkgconfig/atomic_ops.pc config.status: creating pkgconfig/atomic_ops-uninstalled.pc config.status: creating doc/Makefile config.status: creating src/Makefile config.status: creating src/atomic_ops/Makefile config.status: creating src/atomic_ops/sysdeps/Makefile config.status: creating tests/Makefile config.status: creating src/config.h config.status: executing depfiles commands config.status: executing default commands make depbase=echo allchblk.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||';\ /bin/sh ./libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -Wall -Wextra -Wpedantic -Wno-long-long -g -O2 -fno-strict-aliasing -MT allchblk.lo -MD -MP -MF $depbase.Tpo -c -o allchblk.lo allchblk.c &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -Wall -Wextra -Wpedantic -Wno-long-long -g -O2 -fno-strict-aliasing -MT allchblk.lo -MD -MP -MF .deps/allchblk.Tpo -c allchblk.c -fno-common -DPIC -o .libs/allchblk.o In file included from allchblk.c:17: In file included from ./include/private/gc_priv.h:236: In file included from ./include/private/gc_locks.h:32: ./libatomic_ops/src/atomic_ops.h:357:4: error: Cannot implement AO_compare_and_swap_full on this architecture.

error Cannot implement AO_compare_and_swap_full on this architecture.

^ In file included from allchblk.c:17: ./include/private/gc_priv.h:2323:24: error: unknown type name 'AO_TS_t' GC_EXTERN volatile AO_TS_t GC_fault_handler_lock; ^ 2 errors generated. make[3]: [allchblk.lo] Error 1 make[2]: [all-recursive] Error 1 make[1]: [build_gc] Error 2 make: [build_gc] Error 2 ERROR: compilation failed for package ‘msa’
removing ‘/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/msa’

The downloaded source packages are in ‘/private/var/folders/6n/w8vt3k_d3t362slggmq9_qgc0000gn/T/RtmpU2YOox/downloaded_packages’ Warning message: In install.packages(...) : installation of package ‘msa’ had non-zero exit status

UBod commented 1 year ago

Thanks for reporting this issue, I am sorry that you encounter these difficulties! I have already looked into it and I will deal with this issue soon. However, I cannot make any promises when the issue will be fixed (I am short of time and I do not have a Mac platform to perform tests). It seems that the arm64 architecture will be supported also with pre-compiled binaries starting from BioC 3.16. So the issue will surely be dealt with and you will probably have a ready-made binary at the end of the day. Please stay tuned!

UBod commented 1 year ago

Maybe, in the meantime, you can have a look at this issue which seems related. Can you please try to use something like export CFLAGS=-DAO_GCC_FORCE_HAVE_CAS in the shell from which you run R to install 'msa'?

cnrakt commented 1 year ago

Hi Ubod,

I'm working on a new package depends on your msa package, I'm also using arm64 base, so I had the same problem as BC19RG. I can re-compile files for you if you don't have arm64 platform.

Best,

UBod commented 1 year ago

That's great, thanks, @cnrakt! I do not have any Mac computer to test my package, let alone an arm64. I will create a branch on this repo here and then ask you to test it. Ok? I can't tell precisely yet when I will have time. I'll keep you posted. Thanks again, Ulrich

cnrakt commented 1 year ago

Great! Happy to help 👍

Best, Caner

adippolito-kymeratx commented 1 year ago

For what it's worth, I ran into the same issue when trying to install msa this morning. Thanks for looking into this!

Doznkekz commented 1 year ago

For what it's worth, I ran into the same issue when trying to install msa this morning. Thanks for looking into this!

Me too

cnrakt commented 1 year ago

Hi,

Today I try to recompile latest source on apple silicon. I think this may help:

R CMD build msa

checking for file ‘msa/DESCRIPTION’ ... OK
preparing ‘msa’:
checking DESCRIPTION meta-information ... OK
cleaning src
running ‘cleanup’ Error in loadVignetteBuilder(pkgdir, TRUE) : vignette builder 'knitr' not found Execution halted cnr@Caners-MacBook-Pro14 ~ % R CMD build msa
checking for file ‘msa/DESCRIPTION’ ... OK
preparing ‘msa’:
checking DESCRIPTION meta-information ... OK
cleaning src
running ‘cleanup’
installing the package to build vignettes
installing source package ‘msa’ ... using staged installation libs clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I"./gc-7.6.12/include" -I"./Muscle/" -I"./ClustalW/src" -I"./ClustalOmega/src" -fPIC -falign-functions=64 -Wall -g -O2 -c R_init_msa.cpp -o R_init_msa.o In file included from R_init_msa.cpp:3: In file included from ./Muscle/RMuscle.h:4: ./Muscle/muscle.h:54:9: warning: 'assert' macro redefined [-Wmacro-redefined]
define assert(exp) ((void)0)
```
^
```
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include/assert.h:56:9: note: previous definition is here

define assert(e) ((void)0)
```
^
```
In file included from R_init_msa.cpp:3: In file included from ./Muscle/RMuscle.h:4: In file included from ./Muscle/muscle.h:38: ./Muscle/intmath.h:59:15: warning: unused function 'ScoreToDouble' [-Wunused-function] static double ScoreToDouble(SCORE Score) ^ 2 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I"./gc-7.6.12/include" -I"./Muscle/" -I"./ClustalW/src" -I"./ClustalOmega/src" -fPIC -falign-functions=64 -Wall -g -O2 -c SplitCharVector2List.cpp -o SplitCharVector2List.o clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -I"./gc-7.6.12/include" -I"./Muscle/" -I"./ClustalW/src" -I"./ClustalOmega/src" -fPIC -falign-functions=64 -Wall -g -O2 -c SplitCharVector2Matrix.cpp -o SplitCharVector2Matrix.o make --file=msaMakefile --directory=gc-7.6.12 ./configure --enable-cplusplus --enable-threads=pthreads --enable-shared --with-pic checking build system type... arm-apple-darwin21.5.0 checking host system type... arm-apple-darwin21.5.0 checking target system type... arm-apple-darwin21.5.0 checking GC version numbers... major=7 minor=6 micro=12 checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... ./install-sh -c -d checking for gawk... no checking for mawk... no checking for nawk... no checking for awk... awk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking whether to enable maintainer-specific portions of Makefiles... no checking for style of include used by make... GNU checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... gcc3 checking for g++... g++ checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking dependency style of g++... gcc3 checking dependency style of gcc... gcc3 checking how to print strings... printf checking for a sed that does not truncate output... /usr/bin/sed checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for fgrep... /usr/bin/grep -F checking for ld used by gcc... /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ld checking if the linker (/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ld) is GNU ld... no checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 786432 checking how to convert arm-apple-darwin21.5.0 file names to arm-apple-darwin21.5.0 format... func_convert_file_noop checking how to convert arm-apple-darwin21.5.0 file names to toolchain format... func_convert_file_noop checking for /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ld option to reload object files... -r checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... no checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from gcc object... ok checking for sysroot... no checking for a working dd... /bin/dd checking how to truncate binary pipes... /bin/dd bs=4096 count=1 checking for mt... no checking if : is a manifest tool... no checking for dsymutil... dsymutil checking for nmedit... nmedit checking for lipo... lipo checking for otool... otool checking for otool64... no checking for -single_module linker flag... yes checking for -exported_symbols_list linker flag... yes checking for -force_load linker flag... yes checking how to run the C preprocessor... gcc -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... yes checking for gcc option to produce PIC... -fno-common -DPIC checking if gcc PIC flag -fno-common -DPIC works... yes checking if gcc static flag -static works... no checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... darwin21.5.0 dyld checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking how to run the C++ preprocessor... g++ -E checking for ld used by g++... /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ld checking if the linker (/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ld) is GNU ld... no checking whether the g++ linker (/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ld) supports shared libraries... yes checking for g++ option to produce PIC... -fno-common -DPIC checking if g++ PIC flag -fno-common -DPIC works... yes checking if g++ static flag -static works... no checking if g++ supports -c -o file.o... yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... darwin21.5.0 dyld checking how to hardcode library paths into programs... immediate checking for inline... inline checking for pthread_self in -lpthread... yes configure: WARNING: "Explicit GC_INIT() calls may be required." checking whether compiler supports -Wextra... yes checking whether compiler supports -Wpedantic... yes checking for xlc... no checking whether compiler supports -fno-strict-aliasing... yes checking for getcontext... yes checking for dl_iterate_phdr... no checking execinfo.h usability... yes checking execinfo.h presence... yes checking for execinfo.h... yes checking whether to build shared libraries... yes checking which machine-dependent code should be used... checking whether Solaris gcc optimization fix is necessary... no checking for dladdr... yes checking sys/dg_sys_info.h usability... no checking sys/dg_sys_info.h presence... no checking for sys/dg_sys_info.h... no checking for pkg-config... /usr/local/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for atomic_ops... no checking atomic_ops.h usability... no checking atomic_ops.h presence... no checking for atomic_ops.h... no checking which libatomic_ops to use... internal checking for lock-free AO_or primitive... no checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating bdw-gc.pc config.status: creating include/config.h config.status: executing depfiles commands config.status: executing libtool commands config.status: executing default commands === configuring in libatomic_ops (/private/var/folders/74/qtvg4djd5yq53mg7rsnw0v1c0000gn/T/Rtmp0nTAEK/Rbuild552e1002f7cb/msa/src/gc-7.6.12/libatomic_ops) configure: running /bin/sh ./configure --disable-option-checking '--prefix=/usr/local' '--enable-cplusplus' '--enable-threads=pthreads' '--enable-shared' '--with-pic' --cache-file=/dev/null --srcdir=. checking build system type... arm-apple-darwin21.5.0 checking host system type... arm-apple-darwin21.5.0 checking target system type... arm-apple-darwin21.5.0 checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... ./install-sh -c -d checking for gawk... no checking for mawk... no checking for nawk... no checking for awk... awk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking for ranlib... ranlib checking for style of include used by make... GNU checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... gcc3 checking dependency style of gcc... gcc3 checking how to run the C preprocessor... gcc -E checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for stdlib.h... (cached) yes checking for unistd.h... (cached) yes checking for sys/param.h... yes checking for getpagesize... yes checking for working mmap... yes checking for ANSI C header files... (cached) yes checking for PIC compiler flag... -fPIC checking whether gcc -fPIC causes PIC definition... yes checking for pthread_self in -lpthread... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating pkgconfig/atomic_ops.pc config.status: creating pkgconfig/atomic_ops-uninstalled.pc config.status: creating doc/Makefile config.status: creating src/Makefile config.status: creating src/atomic_ops/Makefile config.status: creating src/atomic_ops/sysdeps/Makefile config.status: creating tests/Makefile config.status: creating src/config.h config.status: executing depfiles commands config.status: executing default commands make depbase=echo allchblk.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||';\ /bin/sh ./libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -Wall -Wextra -Wpedantic -Wno-long-long -g -O2 -fno-strict-aliasing -MT allchblk.lo -MD -MP -MF $depbase.Tpo -c -o allchblk.lo allchblk.c &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: gcc -DHAVE_CONFIG_H -I./include -I./include -I./libatomic_ops/src -I./libatomic_ops/src -fexceptions -Wall -Wextra -Wpedantic -Wno-long-long -g -O2 -fno-strict-aliasing -MT allchblk.lo -MD -MP -MF .deps/allchblk.Tpo -c allchblk.c -fno-common -DPIC -o .libs/allchblk.o In file included from allchblk.c:17: In file included from ./include/private/gc_priv.h:236: In file included from ./include/private/gc_locks.h:32: ./libatomic_ops/src/atomic_ops.h:357:4: error: Cannot implement AO_compare_and_swap_full on this architecture. error Cannot implement AO_compare_and_swap_full on this architecture.

In file included from allchblk.c:17: ./include/private/gc_priv.h:2323:24: error: unknown type name 'AO_TS_t' GC_EXTERN volatile AO_TS_t GC_fault_handler_lock;

2 errors generated. make[3]: [allchblk.lo] Error 1 make[2]: [all-recursive] Error 1 make[1]: [build_gc] Error 2 make: [build_gc] Error 2 ERROR: compilation failed for package ‘msa’**

removing ‘/private/var/folders/74/qtvg4djd5yq53mg7rsnw0v1c0000gn/T/Rtmp0nTAEK/Rinst552e32da38a3/msa’

ERROR: package installation failed

UBod commented 1 year ago

Thanks, @cnrakt! That's actually consistent with the output that @BC19RG posted earlier. The reason is the 'gc' garbage collector library (which is necessary to counteract the memory leaks in Muscle and ClustalOmega). I will have to update the 'gc' library to a newer version (the current one seems not to work with arm64). I hope I will have time to fix this within the next 2-3 weeks. Sorry for the delay, but I am currently very busy with other matters.

UBod commented 1 year ago

Hi Ubod,

I'm working on a new package depends on your msa package, I'm also using arm64 base, so I had the same problem as BC19RG. I can re-compile files for you if you don't have arm64 platform.

Best,

@cnrakt, you kindly offered to perform tests on an arm64 platform. I just pushed an update. Could you please try to pull it and try it on arm64? That would be very helpful, thanks a lot in advance!

cnrakt commented 1 year ago

That's great, it works! Installation has finished with some warnings. Thank you very much.

R console: msa_package_arm64_mac_installation_console.txt

BC19RG commented 1 year ago

Thank you very much. I have got it working.

Does not work!

install.packages("msa")

Does not work!

if (!requireNamespace("BiocManager", quietly=TRUE)) install.packages("BiocManager") BiocManager::install("msa")

WORKS :)

library(devtools) install_github("Ubod/msa") library(msa)

UBod commented 1 year ago

That's fantastic, @cnrakt and @BC19RG, thanks a lot for your help! I will push the new version to the BioC repo later today and close the issue once all checks run through.

UBod commented 1 year ago

By today, the binary builds for arm64 have completed successfully for msa (see here) and a binary has been built. Therefore, I am closing this issue. Thanks again to all wo helped me!

UBod / msa

The msg package wan't install on a M1 based apple computer #20

trying URL 'https://bioconductor.org/packages/3.15/bioc/src/contrib/msa_1.28.0.tar.gz' Content type 'application/x-gzip' length 3885072 bytes (3.7 MB)

define deprecated_msg(_msg) attribute((deprecated__(_msg)))

define assert(exp) ((void)0)

define assert(e) ((void)0)

define deprecated_msg(_msg) attribute((deprecated__(_msg)))

define deprecated_msg(_msg) attribute((deprecated__(_msg)))

error Cannot implement AO_compare_and_swap_full on this architecture.

installing the package to build vignettes

define assert(exp) ((void)0)

define assert(e) ((void)0)

removing ‘/private/var/folders/74/qtvg4djd5yq53mg7rsnw0v1c0000gn/T/Rtmp0nTAEK/Rinst552e32da38a3/msa’

Does not work!

Does not work!

WORKS :)