##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL FLAMES
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘FLAMES’ ...
** this is package ‘FLAMES’ version ‘2.3.5’
** using non-staged installation via StagedInstall field
** libs
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
using C++17
using SDK: ‘MacOSX11.3.1.sdk’
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -pthread -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/testthat/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -pthread -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/testthat/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppFunctions.cpp -o RcppFunctions.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -pthread -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/testthat/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c classes/BamRecord.cpp -o classes/BamRecord.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -pthread -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/testthat/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c classes/GFFRecord.cpp -o classes/GFFRecord.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -pthread -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/testthat/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c classes/GeneAnnotationParser.cpp -o classes/GeneAnnotationParser.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -pthread -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/testthat/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c classes/Isoforms.cpp -o classes/Isoforms.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -pthread -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/testthat/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c classes/junctions.cpp -o classes/junctions.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -pthread -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/testthat/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c main-functions/find_isoform.cpp -o main-functions/find_isoform.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -pthread -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/testthat/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c main-functions/flexiplex.cpp -o main-functions/flexiplex.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -pthread -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/testthat/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c main-functions/get_transcript_seq.cpp -o main-functions/get_transcript_seq.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -pthread -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/testthat/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c main-functions/group_bam2isoform.cpp -o main-functions/group_bam2isoform.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -pthread -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/testthat/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c main-functions/pileup_readid.cpp -o main-functions/pileup_readid.o
main-functions/pileup_readid.cpp:86:16: warning: unused variable 'end' [-Wunused-variable]
  unsigned int end;
               ^
1 warning generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -pthread -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/testthat/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c tests/test-junctions.cpp -o tests/test-junctions.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -pthread -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/testthat/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c tests/test-parsing.cpp -o tests/test-parsing.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -pthread -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/testthat/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c utility/cigars.cpp -o utility/cigars.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -pthread -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/testthat/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c utility/edlib-1.2.7/edlib.cpp -o utility/edlib-1.2.7/edlib.o
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -pthread -D_FILE_OFFSET_BITS=64 -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/testthat/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c utility/bam.c -o utility/bam.o
clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o FLAMES.so RcppExports.o RcppFunctions.o classes/BamRecord.o classes/GFFRecord.o classes/GeneAnnotationParser.o classes/Isoforms.o classes/junctions.o main-functions/find_isoform.o main-functions/flexiplex.o main-functions/get_transcript_seq.o main-functions/group_bam2isoform.o main-functions/pileup_readid.o tests/test-junctions.o tests/test-parsing.o utility/cigars.o utility/edlib-1.2.7/edlib.o utility/bam.o -pthread -lz /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rhtslib/usrlib/libhts.a -lcurl -lbz2 -llzma -lz -F/Library/Frameworks/R.framework/.. -framework R
ld: warning: ignoring duplicate libraries: '-lz'
if test -e "/usr/bin/strip" & test -e "/bin/uname" & [[ `uname` == "Linux" ]] ; then /usr/bin/strip --strip-debug FLAMES.so; fi
Building for ARM64
(cd submodule/minimap2 && make -f Makefile CFLAGS="-falign-functions=64 -Wall -g -O2  -Wno-unused-result" arm_neon=1 aarch64=1 minimap2)
cc -c -falign-functions=64 -Wall -g -O2  -Wno-unused-result -DHAVE_KALLOC  -Isse2neon main.c -o main.o
cc -c -falign-functions=64 -Wall -g -O2  -Wno-unused-result -DHAVE_KALLOC  -Isse2neon kthread.c -o kthread.o
cc -c -falign-functions=64 -Wall -g -O2  -Wno-unused-result -DHAVE_KALLOC  -Isse2neon kalloc.c -o kalloc.o
cc -c -falign-functions=64 -Wall -g -O2  -Wno-unused-result -DHAVE_KALLOC  -Isse2neon misc.c -o misc.o
cc -c -falign-functions=64 -Wall -g -O2  -Wno-unused-result -DHAVE_KALLOC  -Isse2neon bseq.c -o bseq.o
cc -c -falign-functions=64 -Wall -g -O2  -Wno-unused-result -DHAVE_KALLOC  -Isse2neon sketch.c -o sketch.o
cc -c -falign-functions=64 -Wall -g -O2  -Wno-unused-result -DHAVE_KALLOC  -Isse2neon sdust.c -o sdust.o
cc -c -falign-functions=64 -Wall -g -O2  -Wno-unused-result -DHAVE_KALLOC  -Isse2neon options.c -o options.o
cc -c -falign-functions=64 -Wall -g -O2  -Wno-unused-result -DHAVE_KALLOC  -Isse2neon index.c -o index.o
cc -c -falign-functions=64 -Wall -g -O2  -Wno-unused-result -DHAVE_KALLOC  -Isse2neon lchain.c -o lchain.o
cc -c -falign-functions=64 -Wall -g -O2  -Wno-unused-result -DHAVE_KALLOC  -Isse2neon align.c -o align.o
cc -c -falign-functions=64 -Wall -g -O2  -Wno-unused-result -DHAVE_KALLOC  -Isse2neon hit.c -o hit.o
cc -c -falign-functions=64 -Wall -g -O2  -Wno-unused-result -DHAVE_KALLOC  -Isse2neon seed.c -o seed.o
cc -c -falign-functions=64 -Wall -g -O2  -Wno-unused-result -DHAVE_KALLOC  -Isse2neon jump.c -o jump.o
cc -c -falign-functions=64 -Wall -g -O2  -Wno-unused-result -DHAVE_KALLOC  -Isse2neon map.c -o map.o
cc -c -falign-functions=64 -Wall -g -O2  -Wno-unused-result -DHAVE_KALLOC  -Isse2neon format.c -o format.o
cc -c -falign-functions=64 -Wall -g -O2  -Wno-unused-result -DHAVE_KALLOC  -Isse2neon pe.c -o pe.o
cc -c -falign-functions=64 -Wall -g -O2  -Wno-unused-result -DHAVE_KALLOC  -Isse2neon esterr.c -o esterr.o
cc -c -falign-functions=64 -Wall -g -O2  -Wno-unused-result -DHAVE_KALLOC  -Isse2neon splitidx.c -o splitidx.o
cc -c -falign-functions=64 -Wall -g -O2  -Wno-unused-result -DHAVE_KALLOC  -Isse2neon ksw2_ll_sse.c -o ksw2_ll_sse.o
cc -c -falign-functions=64 -Wall -g -O2  -Wno-unused-result -DHAVE_KALLOC -DKSW_SSE2_ONLY -D__SSE2__  -Isse2neon ksw2_extz2_sse.c -o ksw2_extz2_neon.o
cc -c -falign-functions=64 -Wall -g -O2  -Wno-unused-result -DHAVE_KALLOC -DKSW_SSE2_ONLY -D__SSE2__  -Isse2neon ksw2_extd2_sse.c -o ksw2_extd2_neon.o
cc -c -falign-functions=64 -Wall -g -O2  -Wno-unused-result -DHAVE_KALLOC -DKSW_SSE2_ONLY -D__SSE2__  -Isse2neon ksw2_exts2_sse.c -o ksw2_exts2_neon.o
ar -csru libminimap2.a kthread.o kalloc.o misc.o bseq.o sketch.o sdust.o options.o index.o lchain.o align.o hit.o seed.o jump.o map.o format.o pe.o esterr.o splitidx.o ksw2_ll_sse.o ksw2_extz2_neon.o ksw2_extd2_neon.o ksw2_exts2_neon.o
cc -falign-functions=64 -Wall -g -O2  -Wno-unused-result main.o -o minimap2 -L. -lminimap2 -lm -lz -lpthread
echo "Installing binary to /Users/biocbuild/bbs-3.22-bioc/meat/FLAMES/src/../inst/bin"
Installing binary to /Users/biocbuild/bbs-3.22-bioc/meat/FLAMES/src/../inst/bin
mkdir -p ../inst/bin
cp submodule/minimap2/minimap2 ../inst/bin/
Building oarfish with cargo
mkdir -p ../inst/bin
mkdir cargo_temp
(cargo install oarfish --root cargo_temp --bin oarfish --vers 0.8.0)
    Updating crates.io index
  Installing oarfish v0.8.0
    Updating crates.io index
     Locking 272 packages to latest compatible versions
      Adding indicatif v0.17.11 (available: v0.18.1)
      Adding noodles-bam v0.78.0 (available: v0.83.0)
      Adding noodles-bgzf v0.38.0 (available: v0.43.0)
      Adding noodles-sam v0.74.0 (available: v0.79.0)
      Adding tabled v0.18.0 (available: v0.20.0)
      Adding typed-builder v0.21.2 (available: v0.23.0)
 Downloading crates ...
  Downloaded flate2 v1.1.5
  Downloaded cc v1.2.42
   Compiling libc v0.2.177
   Compiling proc-macro2 v1.0.103
   Compiling quote v1.0.41
   Compiling unicode-ident v1.0.20
   Compiling find-msvc-tools v0.1.4
   Compiling shlex v1.3.0
   Compiling cfg-if v1.0.4
   Compiling autocfg v1.5.0
   Compiling pkg-config v0.3.32
   Compiling libm v0.2.15
   Compiling memchr v2.7.6
   Compiling zerocopy v0.8.27
   Compiling crossbeam-utils v0.8.21
   Compiling version_check v0.9.5
   Compiling adler2 v2.0.1
   Compiling crc32fast v1.5.0
   Compiling once_cell v1.21.3
   Compiling simd-adler32 v0.3.7
   Compiling regex-syntax v0.8.8
   Compiling zlib-rs v0.5.2
   Compiling serde_core v1.0.228
   Compiling typenum v1.19.0
   Compiling getrandom v0.3.4
   Compiling pin-project-lite v0.2.16
   Compiling rawpointer v0.2.1
   Compiling miniz_oxide v0.8.9
   Compiling either v1.15.0
   Compiling futures-core v0.3.31
   Compiling hashbrown v0.16.0
   Compiling equivalent v1.0.2
   Compiling generic-array v0.14.9
   Compiling paste v1.0.15
   Compiling futures-sink v0.3.31
   Compiling lexical-util v1.0.7
   Compiling aho-corasick v1.1.3
   Compiling serde v1.0.228
   Compiling futures-channel v0.3.31
   Compiling num-traits v0.2.19
   Compiling matrixmultiply v0.3.10
   Compiling futures-io v0.3.31
   Compiling futures-task v0.3.31
   Compiling indexmap v2.12.0
   Compiling zstd-safe v7.2.4
   Compiling heck v0.5.0
   Compiling slab v0.4.11
   Compiling vcpkg v0.2.15
   Compiling pin-utils v0.1.0
   Compiling crossbeam-channel v0.5.15
   Compiling crossbeam-epoch v0.9.18
   Compiling bytecount v0.6.9
   Compiling zstd-safe v6.0.6
   Compiling bitflags v2.10.0
   Compiling crossbeam-deque v0.8.6
   Compiling lexical-parse-integer v1.0.6
   Compiling lexical-write-integer v1.0.6
   Compiling num-complex v0.2.4
   Compiling ahash v0.8.12
   Compiling tracing-core v0.1.34
   Compiling semver v1.0.27
   Compiling lazy_static v1.5.0
   Compiling itoa v1.0.15
   Compiling anyhow v1.0.100
   Compiling unicode-width v0.2.2
   Compiling byteorder v1.5.0
   Compiling rustix v1.1.2
   Compiling bytes v1.10.1
   Compiling regex-automata v0.4.13
   Compiling jobserver v0.1.34
   Compiling rustversion v1.0.22
   Compiling utf8parse v0.2.2
   Compiling cc v1.2.42
   Compiling getrandom v0.2.16
   Compiling snap v1.1.1
   Compiling rayon-core v1.13.0
   Compiling rand_core v0.6.4
   Compiling anstyle-parse v0.2.7
   Compiling errno v0.3.14
   Compiling rustc_version v0.4.1
   Compiling lexical-write-float v1.0.6
   Compiling lexical-parse-float v1.0.6
   Compiling buffer-redux v1.0.2
   Compiling bit-vec v0.8.0
   Compiling syn v2.0.108
   Compiling anstyle v1.0.13
   Compiling fallible-streaming-iterator v0.1.9
   Compiling proc-macro-error-attr2 v2.0.0
   Compiling anstyle-query v1.1.4
   Compiling static_assertions v1.1.0
   Compiling ryu v1.0.20
   Compiling thiserror v1.0.69
   Compiling smallvec v1.15.1
   Compiling is_terminal_polyfill v1.70.2
   Compiling zstd-sys v2.0.16+zstd.1.5.7
   Compiling liblzma-sys v0.3.13
   Compiling bzip2-sys v0.1.13+1.0.8
   Compiling libz-sys v1.1.22
   Compiling sha2-asm v0.6.4
   Compiling lz4-sys v1.11.1+lz4-1.10.0
   Compiling minimap2-sys v0.1.24+minimap2.2.30
   Compiling log v0.4.28
   Compiling libz-rs-sys v0.5.2
   Compiling flate2 v1.1.5
   Compiling array-init-cursor v0.2.1
   Compiling serde_json v1.0.145
   Compiling block-buffer v0.10.4
   Compiling crypto-common v0.1.6
   Compiling colorchoice v1.0.4
   Compiling portable-atomic v1.11.1
   Compiling digest v0.10.7
   Compiling anstream v0.6.21
   Compiling ppv-lite86 v0.2.21
   Compiling num-integer v0.1.46
   Compiling num-complex v0.4.6
   Compiling noodles-bgzf v0.38.0
   Compiling approx v0.5.1
   Compiling rand_chacha v0.3.1
   Compiling num-bigint v0.4.6
   Compiling num-iter v0.1.45
   Compiling noisy_float v0.2.0
   Compiling approx v0.3.2
   Compiling rand v0.8.5
   Compiling planus v0.3.1
   Compiling ndarray v0.16.1
   Compiling rand_distr v0.4.3
   Compiling tracing-log v0.2.0
   Compiling bstr v1.12.0
   Compiling matchers v0.2.0
   Compiling twox-hash v1.6.3
   Compiling streaming-decompression v0.1.2
   Compiling lexical-core v1.0.6
   Compiling arrow2 v0.18.0
   Compiling rand_core v0.9.3
   Compiling cpufeatures v0.2.17
   Compiling sharded-slab v0.1.7
   Compiling itertools v0.13.0
   Compiling thread_local v1.1.9
   Compiling fastrand v2.3.0
   Compiling fnv v1.0.7
   Compiling nu-ansi-term v0.50.3
   Compiling seq-macro v0.3.6
   Compiling strsim v0.11.1
   Compiling clap_lex v0.7.6
   Compiling num-rational v0.4.2
   Compiling noodles-core v0.17.0
   Compiling clap_builder v4.5.50
   Compiling noodles-csi v0.46.0
   Compiling alga v0.9.3
   Compiling tempfile v3.23.0
   Compiling num v0.4.3
   Compiling liblzma v0.3.6
   Compiling papergrid v0.14.0
   Compiling rand_chacha v0.9.0
   Compiling lz4_flex v0.10.0
   Compiling bzip2 v0.4.4
   Compiling noodles-sam v0.74.0
   Compiling hashbrown v0.14.5
   Compiling proc-macro-error2 v2.0.1
   Compiling regex v1.12.2
   Compiling rayon v1.11.0
   Compiling ndarray v0.15.6
   Compiling chrono v0.4.42
   Compiling console v0.15.11
   Compiling sha2 v0.10.9
   Compiling num_cpus v1.17.0
   Compiling crossbeam-queue v0.3.12
   Compiling csv-core v0.1.13
   Compiling itertools v0.14.0
   Compiling dyn-clone v1.0.20
   Compiling simdutf8 v0.1.5
   Compiling base64 v0.22.1
   Compiling number_prefix v0.4.0
   Compiling foreign_vec v0.1.0
   Compiling hash_hasher v2.0.4
   Compiling base64 v0.21.7
   Compiling ethnum v1.5.2
   Compiling arrayvec v0.7.6
   Compiling hex v0.4.3
   Compiling streaming-iterator v0.1.9
   Compiling num-format v0.4.4
   Compiling indicatif v0.17.11
   Compiling csv v1.4.0
   Compiling crossbeam v0.8.4
   Compiling rand v0.9.2
   Compiling noodles-bam v0.78.0
   Compiling parse-size v1.1.0
   Compiling rustc-hash v2.1.1
   Compiling path-tools v0.1.0
   Compiling atomic_float v1.1.0
   Compiling bytemuck_derive v1.10.2
   Compiling serde_derive v1.0.228
   Compiling futures-macro v0.3.31
   Compiling tracing-attributes v0.1.30
   Compiling async-trait v0.1.89
   Compiling async-stream-impl v0.3.6
   Compiling thiserror-impl v1.0.69
   Compiling tabled_derive v0.10.0
   Compiling strum_macros v0.26.4
   Compiling async-stream v0.3.6
   Compiling futures-util v0.3.31
   Compiling typed-builder-macro v0.21.2
   Compiling clap_derive v4.5.49
   Compiling derive-new v0.6.0
   Compiling bytemuck v1.24.0
   Compiling tabled v0.18.0
   Compiling safe_arch v0.7.4
   Compiling tracing v0.1.41
   Compiling wide v0.7.33
   Compiling tracing-subscriber v0.3.20
   Compiling typed-builder v0.21.2
   Compiling clap v4.5.50
   Compiling simba v0.9.1
   Compiling futures-executor v0.3.31
   Compiling arrow-format v0.8.1
   Compiling futures v0.3.31
   Compiling bincode v1.3.3
   Compiling parquet-format-safe v0.2.4
   Compiling lz4 v1.28.1
   Compiling bio-types v1.0.4
   Compiling sendable-swapvec v0.4.3
   Compiling ndarray-stats v0.6.0
   Compiling sprs v0.11.3
   Compiling kders v0.1.1
   Compiling zstd v0.12.4
   Compiling zstd v0.13.3
   Compiling needletail v0.6.3
   Compiling parquet2 v0.17.2
   Compiling nalgebra v0.33.2
   Compiling seqcol_rs v0.4.1
   Compiling minimap2 v0.1.28+minimap2.2.30
   Compiling statrs v0.18.0
   Compiling oarfish v0.8.0
    Finished `release` profile [optimized] target(s) in 30.42s
  Installing cargo_temp/bin/oarfish
   Installed package `oarfish v0.8.0` (executable `oarfish`)
warning: be sure to add `cargo_temp/bin` to your PATH to be able to run the installed binaries
cp cargo_temp/bin/oarfish ../inst/bin/
cargo uninstall oarfish --root cargo_temp
    Removing cargo_temp/bin/oarfish
rm -rf cargo_temp
installing to /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/FLAMES/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (FLAMES)