Package install error

[Malvikakh]

Hi,

I am trying to install Rhtslib on macOS Big Sur using R-devel 4.1.0. And I get the following error.

`> BiocManager::install("Rhtslib")
Bioconductor version 3.13 (BiocManager 1.30.10), R Under development (unstable) (2021-03-23
  r80105)
Installing package(s) 'Rhtslib'
Warning: unable to access index for repository https://bioconductor.org/packages/3.13/bioc/bin/macosx/big-sur-arm64/contrib/4.1:
  cannot open URL 'https://bioconductor.org/packages/3.13/bioc/bin/macosx/big-sur-arm64/contrib/4.1/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.13/data/annotation/bin/macosx/big-sur-arm64/contrib/4.1:
  cannot open URL 'https://bioconductor.org/packages/3.13/data/annotation/bin/macosx/big-sur-arm64/contrib/4.1/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.13/data/experiment/bin/macosx/big-sur-arm64/contrib/4.1:
  cannot open URL 'https://bioconductor.org/packages/3.13/data/experiment/bin/macosx/big-sur-arm64/contrib/4.1/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.13/workflows/bin/macosx/big-sur-arm64/contrib/4.1:
  cannot open URL 'https://bioconductor.org/packages/3.13/workflows/bin/macosx/big-sur-arm64/contrib/4.1/PACKAGES'
Package which is only available in source form, and may need compilation of
  C/C++/Fortran: ‘Rhtslib’
Do you want to attempt to install these from sources? (Yes/no/cancel) yes
installing the source package ‘Rhtslib’

trying URL 'https://bioconductor.org/packages/3.13/bioc/src/contrib/Rhtslib_1.23.0.tar.gz'
Content type 'application/x-gzip' length 1471745 bytes (1.4 MB)
==================================================
downloaded 1.4 MB

* installing *source* package ‘Rhtslib’ ...
** using non-staged installation via StagedInstall field
** libs
cd "htslib-1.7" && make -f "/Library/Frameworks/R.framework/Resources/etc/Makeconf" -f "Makefile.Rhtslib"
Makefile.Rhtslib:128: warning: overriding commands for target `.c.o'
/Library/Frameworks/R.framework/Resources/etc/Makeconf:168: warning: ignoring old commands for target `.c.o'
clang -arch arm64 -falign-functions=64 -Wall -g -O2  -fpic -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o kfunc.o kfunc.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2  -fpic -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o knetfile.o knetfile.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2  -fpic -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o kstring.o kstring.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2  -fpic -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o bcf_sr_sort.o bcf_sr_sort.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2  -fpic -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o bgzf.o bgzf.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2  -fpic -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o errmod.o errmod.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2  -fpic -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o faidx.o faidx.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2  -fpic -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o hfile.o hfile.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2  -fpic -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o hfile_net.o hfile_net.c
echo '#define HTS_VERSION "1.7"' > version.h
clang -arch arm64 -falign-functions=64 -Wall -g -O2  -fpic -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o hts.o hts.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2  -fpic -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o hts_os.o hts_os.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2  -fpic -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o md5.o md5.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2  -fpic -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o multipart.o multipart.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2  -fpic -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o probaln.o probaln.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2  -fpic -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o realn.o realn.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2  -fpic -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o regidx.o regidx.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2  -fpic -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o sam.o sam.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2  -fpic -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o synced_bcf_reader.o synced_bcf_reader.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2  -fpic -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o vcf_sweep.o vcf_sweep.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2  -fpic -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o tbx.o tbx.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2  -fpic -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o textutils.o textutils.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2  -fpic -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o thread_pool.o thread_pool.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2  -fpic -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o vcf.o vcf.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2  -fpic -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o vcfutils.o vcfutils.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2  -fpic -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_codecs.o cram/cram_codecs.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2  -fpic -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_decode.o cram/cram_decode.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2  -fpic -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_encode.o cram/cram_encode.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2  -fpic -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_external.o cram/cram_external.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2  -fpic -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_index.o cram/cram_index.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2  -fpic -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_io.o cram/cram_io.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2  -fpic -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_samtools.o cram/cram_samtools.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2  -fpic -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_stats.o cram/cram_stats.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2  -fpic -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o cram/files.o cram/files.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2  -fpic -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o cram/mFILE.o cram/mFILE.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2  -fpic -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o cram/open_trace_file.o cram/open_trace_file.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2  -fpic -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o cram/pooled_alloc.o cram/pooled_alloc.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2  -fpic -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o cram/rANS_static.o cram/rANS_static.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2  -fpic -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o cram/sam_header.o cram/sam_header.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2  -fpic -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o cram/string_alloc.o cram/string_alloc.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2  -fpic -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o hfile_libcurl.o hfile_libcurl.c
ar -rc libhts.a kfunc.o knetfile.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o hfile.o hfile_net.o hts.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_samtools.o cram/cram_stats.o cram/files.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/sam_header.o cram/string_alloc.o hfile_libcurl.o
ranlib libhts.a
clang -arch arm64 -dynamiclib -install_name /usr/local/lib/libhts.2.dylib -current_version 1.7 -compatibility_version 2 -L/opt/R/arm64/lib -o libhts.dylib kfunc.o knetfile.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o hfile.o hfile_net.o hts.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_samtools.o cram/cram_stats.o cram/files.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/sam_header.o cram/string_alloc.o hfile_libcurl.o -lz -lm -lbz2 -llzma -lcurl
ld: warning: ignoring file /usr/local/lib/liblzma.a, building for macOS-arm64 but attempting to link with file built for macOS-x86_64
Undefined symbols for architecture arm64:
  "_lzma_code", referenced from:
      _cram_uncompress_block in cram_io.o
  "_lzma_easy_buffer_encode", referenced from:
      _cram_compress_block in cram_io.o
      _cram_compress_by_method in cram_io.o
  "_lzma_easy_decoder_memusage", referenced from:
      _cram_uncompress_block in cram_io.o
  "_lzma_end", referenced from:
      _cram_uncompress_block in cram_io.o
  "_lzma_stream_buffer_bound", referenced from:
      _cram_compress_block in cram_io.o
      _cram_compress_by_method in cram_io.o
  "_lzma_stream_decoder", referenced from:
      _cram_uncompress_block in cram_io.o
ld: symbol(s) not found for architecture arm64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make[1]: *** [libhts.dylib] Error 1
make: *** [htslib] Error 2
ERROR: compilation failed for package ‘Rhtslib’
* removing ‘/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/Rhtslib’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/Rhtslib’

The downloaded source packages are in
	‘/private/var/folders/l5/2bf9qbsd38q082tvbbtlgp3m0000gn/T/RtmpA7L7DP/downloaded_packages’
Warning message:
In install.packages(...) :
  installation of package ‘Rhtslib’ had non-zero exit status`

Any suggestions on how to fix this?

Thanks,
Malvika

[LIHANHUANG95]

Same question here, did you solve the question?

[Malvikakh]

Same question here, did you solve the question?

Hey, no I couldn't solve it on my M1 Mac system. I ended up using another system.
Are you using the stable R 4.1.0 release?

[LIHANHUANG95]

Yep, I use the latest stable R 4.1.0. Don't know what to do now, I have reported this on the website of Bioconductor already. Hopefully, they would fix the problem.

[vjcitn]

Hi -- you will need the "xz" compression software. One way to get it on your mac is to use the instructions at

https://formulae.brew.sh/formula/xz

let us know how it goes. If you don't want to use homebrew for some reason, you can build the xz library from source and set up environment variables for discovery by R installation functions. I have found homebrew to be satisfactory for this issue.

[hpages]

@Malvikakh You are using a version of R that was compiled for macOS-arm64 but your lzma library (/usr/local/lib/liblzma.a) was built for macOS-x86_64.

Note that Bioconductor does not support the Apple M1 (a.k.a. arm64) architecture in native mode yet, only via Rosetta, which is the emulator built into macOS Big Sur that enables Mac M1 systems to run Intel x86_64 apps. Concretely this means that if you are on an Apple M1 system, we strongly recommend that you use the official Intel 64-bit R (x86_64 arch) from CRAN available here: https://cran.r-project.org/bin/macosx/ (choose R-4.1.0.pkg, NOT R-4.1.0-arm64.pkg). This will run on the Apple M1 platform in emulation mode. The great benefit of doing this is that you will then be using something that we do support. In particular you'll be able to install Intel 64-bit Mac binary packages from CRAN and Bioconductor, including the Mac binary for Rhtslib which should install and work out-of-the-box without any compilation/linking/headache involved. Installing binary packages is also much faster.

Best,
H.

[rohanshad]

Hi, adding onto this thread here. While I agree installing binaries is much simpler and faster, there should be no reason arm64 lzma to not work in the setting of arm64 R environment. I'm on arm R aarch64-apple-darwin20 (64-bit) and this is the output I get when trying to build from source:

Is there some sort of flag I need to include in my MakeVars file to get this working? I've confirmed lzma exists on my system.

lzma --version

xz (XZ Utils) 5.2.5
liblzma 5.2.5

Package which is only available in source form, and may need
  compilation of C/C++/Fortran: ‘Rhtslib’
Do you want to attempt to install these from sources? (Yes/no/cancel) Yes
installing the source package ‘Rhtslib’

trying URL 'https://bioconductor.org/packages/3.13/bioc/src/contrib/Rhtslib_1.24.0.tar.gz'
Content type 'application/x-gzip' length 1471711 bytes (1.4 MB)
==================================================
downloaded 1.4 MB

* installing *source* package ‘Rhtslib’ ...
** using non-staged installation via StagedInstall field
** libs
cd "htslib-1.7" && make -f "/Library/Frameworks/R.framework/Resources/etc/Makeconf" -f "Makefile.Rhtslib"
Makefile.Rhtslib:128: warning: overriding commands for target `.c.o'
/Library/Frameworks/R.framework/Resources/etc/Makeconf:168: warning: ignoring old commands for target `.c.o'
clang -arch arm64 -falign-functions=64 -Wall -g -O2  -fpic -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o kfunc.o kfunc.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2  -fpic -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o knetfile.o knetfile.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2  -fpic -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o kstring.o kstring.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2  -fpic -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o bcf_sr_sort.o bcf_sr_sort.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2  -fpic -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o bgzf.o bgzf.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2  -fpic -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o errmod.o errmod.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2  -fpic -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o faidx.o faidx.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2  -fpic -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o hfile.o hfile.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2  -fpic -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o hfile_net.o hfile_net.c
echo '#define HTS_VERSION "1.7"' > version.h
clang -arch arm64 -falign-functions=64 -Wall -g -O2  -fpic -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o hts.o hts.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2  -fpic -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o hts_os.o hts_os.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2  -fpic -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o md5.o md5.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2  -fpic -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o multipart.o multipart.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2  -fpic -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o probaln.o probaln.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2  -fpic -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o realn.o realn.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2  -fpic -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o regidx.o regidx.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2  -fpic -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o sam.o sam.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2  -fpic -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o synced_bcf_reader.o synced_bcf_reader.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2  -fpic -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o vcf_sweep.o vcf_sweep.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2  -fpic -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o tbx.o tbx.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2  -fpic -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o textutils.o textutils.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2  -fpic -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o thread_pool.o thread_pool.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2  -fpic -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o vcf.o vcf.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2  -fpic -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o vcfutils.o vcfutils.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2  -fpic -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_codecs.o cram/cram_codecs.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2  -fpic -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_decode.o cram/cram_decode.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2  -fpic -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_encode.o cram/cram_encode.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2  -fpic -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_external.o cram/cram_external.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2  -fpic -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_index.o cram/cram_index.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2  -fpic -I. -I/opt/R/arm64/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_io.o cram/cram_io.c
cram/cram_io.c:61:10: fatal error: 'lzma.h' file not found
#include <lzma.h>
         ^~~~~~~~
1 error generated.
make[1]: *** [cram/cram_io.o] Error 1
make: *** [htslib] Error 2
ERROR: compilation failed for package ‘Rhtslib’
* removing ‘/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/Rhtslib’

[hpages]

Please remember that Rhtslib is a Bioconductor package and that the project does not support R-4.1.0-arm64 at the moment. See https://support.bioconductor.org/p/9137290/#9137342. One of the reasons for this is that we're lacking the resources to develop and test Bioconductor packages on this platform. So we can only provide limited help for this kind of question.

Did you install xz with brew install xz? First of all you want to make sure that this actually compiles and installs xz for the arm64 arch. Also I think that this only creates the lzma.h symlink in /usr/local/include but not in /opt/R/arm64/include. Here is what this symlink looks like on our Intel macOS builder merida1:

merida1:~ biocbuild$ ls -l /usr/local/include/lzma.h 
lrwxr-xr-x  1 biocbuild  admin  33 13 May  2020 /usr/local/include/lzma.h -> ../Cellar/xz/5.2.5/include/lzma.h

This location will be found if you use the Intel 64-bit R from CRAN (R-4.1.0.pkg). However, it looks like when using R-4.1.0-arm64, the compiler looks into /opt/R/arm64/include instead. You can see this in the compiler commands that are used on each platform: they contain -I/usr/local/include on one platform (see https://bioconductor.org/checkResults/3.14/bioc-LATEST/Rhtslib/merida1-install.html), and -I/opt/R/arm64/include on the other (based on the output you showed us).

I'm not sure how to deal with this. Maybe create a symlink in /opt/R/arm64/include? Or edit CPPFLAGS in R_HOME/etc/Makeconf? Maybe a question for the R-SIG-Mac mailing list?

H.

[rohanshad]

Thanks for this! Creating a symlink to lzma and lzma.h in /opt/R/arm64/include solved this. Can compile and install in arm64 just fine now.

Edit:
For this to work you need homebrew for arm64, and need to be running R-4.1.0-arm64 or higher. Newer versions of RStudio (1.4.1717 or higher) are also compatible with R-4.1.0-arm64.

[mahermassoud]

Fixed this by sym linking my conda installation of xz / lzma

conda install xz
# Replace username with your own
sudo ln -s /Users/mmaher/miniforge3/include/lzma /opt/R/arm64/include/lzma
sudo ln -s /Users/mmaher/miniforge3/include/lzma.h /opt/R/arm64/include/lzma.h

[ieuangw]

Just coming into this issue now. Thank you Mahermassoud - I used Brew install xz then followed your sym linking - worked a treat!

[liamkelley93]

To add on to @mahermassoud and @ieuangw, installing xz that way didn't work for me. What did work for me was as follows:

cd /opt/R/arm64
sudo curl -O https://mac.r-project.org/libs-arm64/xz-5.2.5-darwin.20-arm64.tar.gz
sudo tar fvxz xz-5.2.5-darwin.20-arm64.tar.gz -C /

This is following the information from the arm64 libraries support page.

[hpages]

@liamkelley93 Yep, way to go! These precompiled system binaries provided by Simon Urbanek are much preferred over conda or brew solutions. Fast/easy to install, self-contained, and guaranteed to work since those are the binaries that Simon uses on the machines that run the R and CRAN package builds. See https://mac.r-project.org/bin/ for more info. We've used the x86_64 ones on the Bioconductor Mac builders for years with no problem. We'll use the arm64 ones in the near future when we start producing Bioconductor arm64 binary packages.