Hi! I am trying to install Rbowtie2 using RSudio on my mac M1 (MacOS Monterey). I could install bowtie2 from the sources provided on Github, but all my attemps to install the wrapper Rbowtie2 failed. I am enclosing the console info below. Do you have anyclue about how to solve this issue? Thanks!

BiocManager::install('Rbowtie2') 'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details

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

Bioconductor version 3.16 (BiocManager 1.30.19), R 4.2.1 (2022-06-23) Installing package(s) 'Rbowtie2' Package which is only available in source form, and may need compilation of C/C++/Fortran: ‘Rbowtie2’ Do you want to attempt to install these from sources? (Yes/no/cancel) Yes installing the source package ‘Rbowtie2’

x-gzip' length 1227822 bytes (1.2 MB)

downloaded 1.2 MB

Loading custom .Rprofile installing source* package ‘Rbowtie2’ ... using staged installation libs arch - mkdir -p ../inst (cd adapterremoval && (make CXX="g++ -std=gnu++11" -f Makefile)) g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c adapterset.cc g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c alignment.cc g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c argparse.cc g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c debug.cc g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c demultiplex.cc g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c fastq.cc g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c fastq_enc.cc g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c fastq_io.cc g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c linereader.cc g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c linereader_joined.cc g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c main_adapter_id.cc g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c main_adapter_rm.cc g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c main_demultiplex.cc g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c scheduler.cc g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c strutils.cc g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c threads.cc g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c timer.cc g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c trimmed_reads.cc g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c userconfig.cc g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c main.cc g++ -std=gnu++11 -O3 -pthread -DNDEBUG -o AdapterRemoval adapterset.o alignment.o argparse.o debug.o demultiplex.o fastq.o fastq_enc.o fastq_io.o linereader.o linereader_joined.o main_adapter_id.o main_adapter_rm.o main_demultiplex.o scheduler.o strutils.o threads.o timer.o trimmed_reads.o userconfig.o main.o mv AdapterRemoval ../../inst/ (cd adapterremoval && (make clean_o -f Makefile)) rm -f .o (cd bowtie2-2.4.4 && (make CXX="g++" -f Makefile)) g++ -O3 -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O3 -funroll-loops -g3 -std=c++11 -fopenmp-simd -DNO_SPINLOCK -DWITH_QUEUELOCK=1\"" -std=c++11 -fopenmp-simd -DNO_SPINLOCK -DWITH_QUEUELOCK=1 \ -fno-strict-aliasing -DBOWTIE2_VERSION="\"cat BOWTIE2_VERSION\"" -DBUILD_HOST="\"${HOSTNAME:-hostname}\"" -DBUILD_TIME="\"date -u\"" -DCOMPILER_VERSION="\"g++ -v 2>&1 | tail -1\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -Wall \ -Ithird_party \ -o bowtie2-build-s bt2_build.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_locks.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp diff_sample.cpp bowtie_build_main.cpp \ -lpthread -lz g++ -O3 -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O3 -funroll-loops -g3 -std=c++11 -fopenmp-simd -DNO_SPINLOCK -DWITH_QUEUELOCK=1\"" -std=c++11 -fopenmp-simd -DNO_SPINLOCK -DWITH_QUEUELOCK=1 \ -fno-strict-aliasing -DBOWTIE2_VERSION="\"cat BOWTIE2_VERSION\"" -DBUILD_HOST="\"${HOSTNAME:-hostname}\"" -DBUILD_TIME="\"date -u\"" -DCOMPILER_VERSION="\"g++ -v 2>&1 | tail -1\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DNDEBUG -Wall \ -Ithird_party \ -o bowtie2-build-l bt2_build.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_locks.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp diff_sample.cpp bowtie_build_main.cpp \ -lpthread -lz g++ -O3 -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O3 -funroll-loops -g3 -std=c++11 -fopenmp-simd -DNO_SPINLOCK -DWITH_QUEUELOCK=1\"" -std=c++11 -fopenmp-simd -DNO_SPINLOCK -DWITH_QUEUELOCK=1 \ -fno-strict-aliasing -DBOWTIE2_VERSION="\"cat BOWTIE2_VERSION\"" -DBUILD_HOST="\"${HOSTNAME:-hostname}\"" -DBUILD_TIME="\"date -u\"" -DCOMPILER_VERSION="\"g++ -v 2>&1 | tail -1\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -Wall \ -Ithird_party \ -o bowtie2-align-s bt2_search.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_locks.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp qual.cpp pat.cpp sam.cpp read_qseq.cpp aligner_seed_policy.cpp aligner_seed.cpp aligner_seed2.cpp aligner_sw.cpp aligner_sw_driver.cpp aligner_cache.cpp aligner_result.cpp ref_coord.cpp mask.cpp pe.cpp aln_sink.cpp dp_framer.cpp scoring.cpp presets.cpp unique.cpp simple_func.cpp random_util.cpp aligner_bt.cpp sse_util.cpp aligner_swsse.cpp outq.cpp aligner_swsse_loc_i16.cpp aligner_swsse_ee_i16.cpp aligner_swsse_loc_u8.cpp aligner_swsse_ee_u8.cpp aligner_driver.cpp bowtie_main.cpp \ -lpthread -lz In file included from aligner_sw.h:73, from bt2_search.cpp:54: sse_wrap.h:31:10: fatal error: simde/x86/sse2.h: No such file or directory 31 | #include "simde/x86/sse2.h" | ^~~~~~ compilation terminated. In file included from aligner_sw.h:73, from aligner_sw.cpp:25: sse_wrap.h:31:10: fatal error: simde/x86/sse2.h: No such file or directory 31 | #include "simde/x86/sse2.h" | ^~~~~~ compilation terminated. In file included from aligner_sw.h:73, from aligner_sw_driver.h:81, from aligner_sw_driver.cpp:47: sse_wrap.h:31:10: fatal error: simde/x86/sse2.h: No such file or directory 31 | #include "simde/x86/sse2.h" | ^~~~~~ compilation terminated. In file included from sse_util.h:27, from aligner_bt.h:31, from aligner_bt.cpp:20: sse_wrap.h:31:10: fatal error: simde/x86/sse2.h: No such file or directory 31 | #include "simde/x86/sse2.h" | ^~~~~~ compilation terminated. In file included from sse_util.h:27, from sse_util.cpp:20: sse_wrap.h:31:10: fatal error: simde/x86/sse2.h: No such file or directory 31 | #include "simde/x86/sse2.h" | ^~~~~~ compilation terminated. In file included from sse_util.h:27, from aligner_swsse.h:28, from aligner_swsse.cpp:22: sse_wrap.h:31:10: fatal error: simde/x86/sse2.h: No such file or directory 31 | #include "simde/x86/sse2.h" | ^~~~~~ compilation terminated. In file included from aligner_sw.h:73, from aligner_swsse_loc_i16.cpp:56: sse_wrap.h:31:10: fatal error: simde/x86/sse2.h: No such file or directory 31 | #include "simde/x86/sse2.h" | ^~~~~~ compilation terminated. In file included from aligner_sw.h:73, from aligner_swsse_ee_i16.cpp:56: sse_wrap.h:31:10: fatal error: simde/x86/sse2.h: No such file or directory 31 | #include "simde/x86/sse2.h" | ^~~~~~ compilation terminated. In file included from aligner_sw.h:73, from aligner_swsse_loc_u8.cpp:56: sse_wrap.h:31:10: fatal error: simde/x86/sse2.h: No such file or directory 31 | #include "simde/x86/sse2.h" | ^~~~~~ compilation terminated. In file included from aligner_sw.h:73, from aligner_swsse_ee_u8.cpp:56: sse_wrap.h:31:10: fatal error: simde/x86/sse2.h: No such file or directory 31 | #include "simde/x86/sse2.h" | ^~~~~~ compilation terminated. make[1]: [bowtie2-align-s] Error 1 make: *** [all] Error 2 ERROR: compilation failed for package ‘Rbowtie2’

removing ‘/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rbowtie2’

The downloaded source packages are in ‘/private/var/folders/dn/q298x85j3j98njd17qkwzpc40000gr/T/RtmpD6HCPS/downloaded_packages’ Warning message: In install.packages(...) : installation of package ‘Rbowtie2’ had non-zero exit status

wzthu / Rbowtie2

Installation on Mac M1 MacOS Monterey #9

trying URL 'https://bioconductor.org/packages/3.16/bioc/src/contrib/Rbowtie2_2.4.0.tar.gz' Content type 'application/x-gzip' length 1227822 bytes (1.2 MB)