##############################################################################
##############################################################################
###
### Running command:
###
### rm -rf FLAMES.buildbin-libdir && mkdir FLAMES.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh FLAMES_2.5.1.tar.gz /Library/Frameworks/R.framework/Resources/bin/R FLAMES.buildbin-libdir
###
##############################################################################
##############################################################################
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=FLAMES.buildbin-libdir FLAMES_2.5.1.tar.gz'
>>>>>>>
* installing *source* package ‘FLAMES’ ...
** this is package ‘FLAMES’ version ‘2.5.1’
** 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/4.6-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.6-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/4.6-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.6-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/4.6-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.6-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/4.6-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.6-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/4.6-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.6-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/4.6-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.6-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/4.6-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.6-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/4.6-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.6-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/4.6-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.6-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/4.6-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.6-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/4.6-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.6-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/4.6-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.6-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/4.6-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.6-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/4.6-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.6-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/4.6-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.6-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/4.6-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.6-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/4.6-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rhtslib/include' -I'/Library/Frameworks/R.framework/Versions/4.6-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/4.6-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 /private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpEqphTl/R.INSTALL179d2f7fdbc5/FLAMES/src/../inst/bin"
Installing binary to /private/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/RtmpEqphTl/R.INSTALL179d2f7fdbc5/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 261 packages to latest compatible versions
Adding generic-array v0.14.7 (available: v0.14.9)
Adding indicatif v0.17.11 (available: v0.18.3)
Adding noodles-bam v0.78.0 (available: v0.84.0)
Adding noodles-bgzf v0.38.0 (available: v0.44.0)
Adding noodles-sam v0.74.0 (available: v0.80.0)
Adding tabled v0.18.0 (available: v0.20.0)
Adding typed-builder v0.21.2 (available: v0.23.2)
Downloading crates ...
Downloaded flate2 v1.1.6
Compiling libc v0.2.178
Compiling proc-macro2 v1.0.103
Compiling unicode-ident v1.0.22
Compiling quote v1.0.42
Compiling find-msvc-tools v0.1.5
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 v0.8.31
Compiling crossbeam-utils v0.8.21
Compiling version_check v0.9.5
Compiling crc32fast v1.5.0
Compiling once_cell v1.21.3
Compiling simd-adler32 v0.3.7
Compiling adler2 v2.0.1
Compiling regex-syntax v0.8.8
Compiling serde_core v1.0.228
Compiling zlib-rs v0.5.3
Compiling pin-project-lite v0.2.16
Compiling getrandom v0.3.4
Compiling typenum v1.19.0
Compiling rawpointer v0.2.1
Compiling futures-core v0.3.31
Compiling miniz_oxide v0.8.9
Compiling hashbrown v0.16.1
Compiling equivalent v1.0.2
Compiling either v1.15.0
Compiling futures-sink v0.3.31
Compiling generic-array v0.14.7
Compiling serde v1.0.228
Compiling lexical-util v1.0.7
Compiling paste v1.0.15
Compiling futures-channel v0.3.31
Compiling heck v0.5.0
Compiling num-traits v0.2.19
Compiling matrixmultiply v0.3.10
Compiling aho-corasick v1.1.4
Compiling slab v0.4.11
Compiling vcpkg v0.2.15
Compiling futures-task v0.3.31
Compiling pin-utils v0.1.0
Compiling indexmap v2.12.1
Compiling zstd-safe v7.2.4
Compiling futures-io v0.3.31
Compiling crossbeam-channel v0.5.15
Compiling crossbeam-epoch v0.9.18
Compiling zstd-safe v6.0.6
Compiling bitflags v2.10.0
Compiling bytecount v0.6.9
Compiling lexical-write-integer v1.0.6
Compiling crossbeam-deque v0.8.6
Compiling lexical-parse-integer v1.0.6
Compiling num-complex v0.2.4
Compiling ahash v0.8.12
Compiling tracing-core v0.1.35
Compiling rayon-core v1.13.0
Compiling itoa v1.0.15
Compiling rustix v1.1.2
Compiling anyhow v1.0.100
Compiling byteorder v1.5.0
Compiling lazy_static v1.5.0
Compiling bytes v1.11.0
Compiling utf8parse v0.2.2
Compiling semver v1.0.27
Compiling unicode-width v0.2.2
Compiling snap v1.1.1
Compiling syn v2.0.111
Compiling rustversion v1.0.22
Compiling regex-automata v0.4.13
Compiling proc-macro-error-attr2 v2.0.0
Compiling rustc_version v0.4.1
Compiling anstyle-parse v0.2.7
Compiling lexical-parse-float v1.0.6
Compiling lexical-write-float v1.0.6
Compiling jobserver v0.1.34
Compiling buffer-redux v1.1.0
Compiling getrandom v0.2.16
Compiling cc v1.2.48
Compiling rand_core v0.6.4
Compiling errno v0.3.14
Compiling array-init-cursor v0.2.1
Compiling static_assertions v1.1.0
Compiling log v0.4.29
Compiling anstyle-query v1.1.5
Compiling is_terminal_polyfill v1.70.2
Compiling anstyle v1.0.13
Compiling smallvec v1.15.1
Compiling colorchoice v1.0.4
Compiling portable-atomic v1.11.1
Compiling fallible-streaming-iterator v0.1.9
Compiling thiserror v1.0.69
Compiling bit-vec v0.8.0
Compiling ryu v1.0.20
Compiling serde_json v1.0.145
Compiling streaming-decompression v0.1.2
Compiling block-buffer v0.10.4
Compiling crypto-common v0.1.7
Compiling anstream v0.6.21
Compiling tracing-log v0.2.0
Compiling digest v0.10.7
Compiling twox-hash v1.6.3
Compiling planus v0.3.1
Compiling rand_core v0.9.3
Compiling lexical-core v1.0.6
Compiling cpufeatures v0.2.17
Compiling arrow2 v0.18.0
Compiling sharded-slab v0.1.7
Compiling itertools v0.13.0
Compiling thread_local v1.1.9
Compiling fnv v1.0.7
Compiling seq-macro v0.3.6
Compiling nu-ansi-term v0.50.3
Compiling fastrand v2.3.0
Compiling num-integer v0.1.46
Compiling num-complex v0.4.6
Compiling flate2 v1.1.6
Compiling approx v0.5.1
Compiling ppv-lite86 v0.2.21
error[E0659]: `Deflate` is ambiguous
--> /Users/biocbuild/.cargo/registry/src/index.crates.io-1949cf8c6b5b557f/flate2-1.1.6/src/mem.rs:6:33
|
6 | use crate::ffi::{self, Backend, Deflate, DeflateBackend, ErrorMessage, Inflate, InflateBackend};
| ^^^^^^^ ambiguous name
|
= note: ambiguous because of multiple glob imports of a name in the same module
note: `Deflate` could refer to the struct imported here
--> /Users/biocbuild/.cargo/registry/src/index.crates.io-1949cf8c6b5b557f/flate2-1.1.6/src/ffi/mod.rs:71:9
|
71 | pub use self::zlib_rs::*;
| ^^^^^^^^^^^^^^^^
= help: consider adding an explicit import of `Deflate` to disambiguate
note: `Deflate` could also refer to the struct imported here
--> /Users/biocbuild/.cargo/registry/src/index.crates.io-1949cf8c6b5b557f/flate2-1.1.6/src/ffi/mod.rs:76:9
|
76 | pub use self::miniz_oxide::*;
| ^^^^^^^^^^^^^^^^^^^^
= help: consider adding an explicit import of `Deflate` to disambiguate
error[E0659]: `Inflate` is ambiguous
--> /Users/biocbuild/.cargo/registry/src/index.crates.io-1949cf8c6b5b557f/flate2-1.1.6/src/mem.rs:6:72
|
6 | use crate::ffi::{self, Backend, Deflate, DeflateBackend, ErrorMessage, Inflate, InflateBackend};
| ^^^^^^^ ambiguous name
|
= note: ambiguous because of multiple glob imports of a name in the same module
note: `Inflate` could refer to the struct imported here
--> /Users/biocbuild/.cargo/registry/src/index.crates.io-1949cf8c6b5b557f/flate2-1.1.6/src/ffi/mod.rs:71:9
|
71 | pub use self::zlib_rs::*;
| ^^^^^^^^^^^^^^^^
= help: consider adding an explicit import of `Inflate` to disambiguate
note: `Inflate` could also refer to the struct imported here
--> /Users/biocbuild/.cargo/registry/src/index.crates.io-1949cf8c6b5b557f/flate2-1.1.6/src/ffi/mod.rs:76:9
|
76 | pub use self::miniz_oxide::*;
| ^^^^^^^^^^^^^^^^^^^^
= help: consider adding an explicit import of `Inflate` to disambiguate
error[E0659]: `Deflate` is ambiguous
--> /Users/biocbuild/.cargo/registry/src/index.crates.io-1949cf8c6b5b557f/flate2-1.1.6/src/mem.rs:23:12
|
23 | inner: Deflate,
| ^^^^^^^ ambiguous name
|
= note: ambiguous because of multiple glob imports of a name in the same module
note: `Deflate` could refer to the struct imported here
--> /Users/biocbuild/.cargo/registry/src/index.crates.io-1949cf8c6b5b557f/flate2-1.1.6/src/ffi/mod.rs:71:9
|
71 | pub use self::zlib_rs::*;
| ^^^^^^^^^^^^^^^^
= help: consider adding an explicit import of `Deflate` to disambiguate
note: `Deflate` could also refer to the struct imported here
--> /Users/biocbuild/.cargo/registry/src/index.crates.io-1949cf8c6b5b557f/flate2-1.1.6/src/ffi/mod.rs:76:9
|
76 | pub use self::miniz_oxide::*;
| ^^^^^^^^^^^^^^^^^^^^
= help: consider adding an explicit import of `Deflate` to disambiguate
error[E0659]: `Inflate` is ambiguous
--> /Users/biocbuild/.cargo/registry/src/index.crates.io-1949cf8c6b5b557f/flate2-1.1.6/src/mem.rs:40:12
|
40 | inner: Inflate,
| ^^^^^^^ ambiguous name
|
= note: ambiguous because of multiple glob imports of a name in the same module
note: `Inflate` could refer to the struct imported here
--> /Users/biocbuild/.cargo/registry/src/index.crates.io-1949cf8c6b5b557f/flate2-1.1.6/src/ffi/mod.rs:71:9
|
71 | pub use self::zlib_rs::*;
| ^^^^^^^^^^^^^^^^
= help: consider adding an explicit import of `Inflate` to disambiguate
note: `Inflate` could also refer to the struct imported here
--> /Users/biocbuild/.cargo/registry/src/index.crates.io-1949cf8c6b5b557f/flate2-1.1.6/src/ffi/mod.rs:76:9
|
76 | pub use self::miniz_oxide::*;
| ^^^^^^^^^^^^^^^^^^^^
= help: consider adding an explicit import of `Inflate` to disambiguate
error[E0659]: `MZ_NO_FLUSH` is ambiguous
--> /Users/biocbuild/.cargo/registry/src/index.crates.io-1949cf8c6b5b557f/flate2-1.1.6/src/mem.rs:52:17
|
52 | None = ffi::MZ_NO_FLUSH as isize,
| ^^^^^^^^^^^ ambiguous name
|
= note: ambiguous because of multiple glob imports of a name in the same module
note: `MZ_NO_FLUSH` could refer to the constant imported here
--> /Users/biocbuild/.cargo/registry/src/index.crates.io-1949cf8c6b5b557f/flate2-1.1.6/src/ffi/mod.rs:71:9
|
71 | pub use self::zlib_rs::*;
| ^^^^^^^^^^^^^^^^
= help: consider adding an explicit import of `MZ_NO_FLUSH` to disambiguate
note: `MZ_NO_FLUSH` could also refer to the constant imported here
--> /Users/biocbuild/.cargo/registry/src/index.crates.io-1949cf8c6b5b557f/flate2-1.1.6/src/ffi/mod.rs:76:9
|
76 | pub use self::miniz_oxide::*;
| ^^^^^^^^^^^^^^^^^^^^
= help: consider adding an explicit import of `MZ_NO_FLUSH` to disambiguate
error[E0659]: `MZ_PARTIAL_FLUSH` is ambiguous
--> /Users/biocbuild/.cargo/registry/src/index.crates.io-1949cf8c6b5b557f/flate2-1.1.6/src/mem.rs:62:20
|
62 | Partial = ffi::MZ_PARTIAL_FLUSH as isize,
| ^^^^^^^^^^^^^^^^ ambiguous name
|
= note: ambiguous because of multiple glob imports of a name in the same module
note: `MZ_PARTIAL_FLUSH` could refer to the constant imported here
--> /Users/biocbuild/.cargo/registry/src/index.crates.io-1949cf8c6b5b557f/flate2-1.1.6/src/ffi/mod.rs:71:9
|
71 | pub use self::zlib_rs::*;
| ^^^^^^^^^^^^^^^^
= help: consider adding an explicit import of `MZ_PARTIAL_FLUSH` to disambiguate
note: `MZ_PARTIAL_FLUSH` could also refer to the constant imported here
--> /Users/biocbuild/.cargo/registry/src/index.crates.io-1949cf8c6b5b557f/flate2-1.1.6/src/ffi/mod.rs:76:9
|
76 | pub use self::miniz_oxide::*;
| ^^^^^^^^^^^^^^^^^^^^
= help: consider adding an explicit import of `MZ_PARTIAL_FLUSH` to disambiguate
error[E0659]: `MZ_SYNC_FLUSH` is ambiguous
--> /Users/biocbuild/.cargo/registry/src/index.crates.io-1949cf8c6b5b557f/flate2-1.1.6/src/mem.rs:71:17
|
71 | Sync = ffi::MZ_SYNC_FLUSH as isize,
| ^^^^^^^^^^^^^ ambiguous name
|
= note: ambiguous because of multiple glob imports of a name in the same module
note: `MZ_SYNC_FLUSH` could refer to the constant imported here
--> /Users/biocbuild/.cargo/registry/src/index.crates.io-1949cf8c6b5b557f/flate2-1.1.6/src/ffi/mod.rs:71:9
|
71 | pub use self::zlib_rs::*;
| ^^^^^^^^^^^^^^^^
= help: consider adding an explicit import of `MZ_SYNC_FLUSH` to disambiguate
note: `MZ_SYNC_FLUSH` could also refer to the constant imported here
--> /Users/biocbuild/.cargo/registry/src/index.crates.io-1949cf8c6b5b557f/flate2-1.1.6/src/ffi/mod.rs:76:9
|
76 | pub use self::miniz_oxide::*;
| ^^^^^^^^^^^^^^^^^^^^
= help: consider adding an explicit import of `MZ_SYNC_FLUSH` to disambiguate
error[E0659]: `MZ_FULL_FLUSH` is ambiguous
--> /Users/biocbuild/.cargo/registry/src/index.crates.io-1949cf8c6b5b557f/flate2-1.1.6/src/mem.rs:78:17
|
78 | Full = ffi::MZ_FULL_FLUSH as isize,
| ^^^^^^^^^^^^^ ambiguous name
|
= note: ambiguous because of multiple glob imports of a name in the same module
note: `MZ_FULL_FLUSH` could refer to the constant imported here
--> /Users/biocbuild/.cargo/registry/src/index.crates.io-1949cf8c6b5b557f/flate2-1.1.6/src/ffi/mod.rs:71:9
|
71 | pub use self::zlib_rs::*;
| ^^^^^^^^^^^^^^^^
= help: consider adding an explicit import of `MZ_FULL_FLUSH` to disambiguate
note: `MZ_FULL_FLUSH` could also refer to the constant imported here
--> /Users/biocbuild/.cargo/registry/src/index.crates.io-1949cf8c6b5b557f/flate2-1.1.6/src/ffi/mod.rs:76:9
|
76 | pub use self::miniz_oxide::*;
| ^^^^^^^^^^^^^^^^^^^^
= help: consider adding an explicit import of `MZ_FULL_FLUSH` to disambiguate
error[E0659]: `MZ_FINISH` is ambiguous
--> /Users/biocbuild/.cargo/registry/src/index.crates.io-1949cf8c6b5b557f/flate2-1.1.6/src/mem.rs:84:19
|
84 | Finish = ffi::MZ_FINISH as isize,
| ^^^^^^^^^ ambiguous name
|
= note: ambiguous because of multiple glob imports of a name in the same module
note: `MZ_FINISH` could refer to the constant imported here
--> /Users/biocbuild/.cargo/registry/src/index.crates.io-1949cf8c6b5b557f/flate2-1.1.6/src/ffi/mod.rs:71:9
|
71 | pub use self::zlib_rs::*;
| ^^^^^^^^^^^^^^^^
= help: consider adding an explicit import of `MZ_FINISH` to disambiguate
note: `MZ_FINISH` could also refer to the constant imported here
--> /Users/biocbuild/.cargo/registry/src/index.crates.io-1949cf8c6b5b557f/flate2-1.1.6/src/ffi/mod.rs:76:9
|
76 | pub use self::miniz_oxide::*;
| ^^^^^^^^^^^^^^^^^^^^
= help: consider adding an explicit import of `MZ_FINISH` to disambiguate
error[E0659]: `MZ_NO_FLUSH` is ambiguous
--> /Users/biocbuild/.cargo/registry/src/index.crates.io-1949cf8c6b5b557f/flate2-1.1.6/src/mem.rs:96:17
|
96 | None = ffi::MZ_NO_FLUSH as isize,
| ^^^^^^^^^^^ ambiguous name
|
= note: ambiguous because of multiple glob imports of a name in the same module
note: `MZ_NO_FLUSH` could refer to the constant imported here
--> /Users/biocbuild/.cargo/registry/src/index.crates.io-1949cf8c6b5b557f/flate2-1.1.6/src/ffi/mod.rs:71:9
|
71 | pub use self::zlib_rs::*;
| ^^^^^^^^^^^^^^^^
= help: consider adding an explicit import of `MZ_NO_FLUSH` to disambiguate
note: `MZ_NO_FLUSH` could also refer to the constant imported here
--> /Users/biocbuild/.cargo/registry/src/index.crates.io-1949cf8c6b5b557f/flate2-1.1.6/src/ffi/mod.rs:76:9
|
76 | pub use self::miniz_oxide::*;
| ^^^^^^^^^^^^^^^^^^^^
= help: consider adding an explicit import of `MZ_NO_FLUSH` to disambiguate
error[E0659]: `MZ_SYNC_FLUSH` is ambiguous
--> /Users/biocbuild/.cargo/registry/src/index.crates.io-1949cf8c6b5b557f/flate2-1.1.6/src/mem.rs:105:17
|
105 | Sync = ffi::MZ_SYNC_FLUSH as isize,
| ^^^^^^^^^^^^^ ambiguous name
|
= note: ambiguous because of multiple glob imports of a name in the same module
note: `MZ_SYNC_FLUSH` could refer to the constant imported here
--> /Users/biocbuild/.cargo/registry/src/index.crates.io-1949cf8c6b5b557f/flate2-1.1.6/src/ffi/mod.rs:71:9
|
71 | pub use self::zlib_rs::*;
| ^^^^^^^^^^^^^^^^
= help: consider adding an explicit import of `MZ_SYNC_FLUSH` to disambiguate
note: `MZ_SYNC_FLUSH` could also refer to the constant imported here
--> /Users/biocbuild/.cargo/registry/src/index.crates.io-1949cf8c6b5b557f/flate2-1.1.6/src/ffi/mod.rs:76:9
|
76 | pub use self::miniz_oxide::*;
| ^^^^^^^^^^^^^^^^^^^^
= help: consider adding an explicit import of `MZ_SYNC_FLUSH` to disambiguate
error[E0659]: `MZ_FINISH` is ambiguous
--> /Users/biocbuild/.cargo/registry/src/index.crates.io-1949cf8c6b5b557f/flate2-1.1.6/src/mem.rs:111:19
|
111 | Finish = ffi::MZ_FINISH as isize,
| ^^^^^^^^^ ambiguous name
|
= note: ambiguous because of multiple glob imports of a name in the same module
note: `MZ_FINISH` could refer to the constant imported here
--> /Users/biocbuild/.cargo/registry/src/index.crates.io-1949cf8c6b5b557f/flate2-1.1.6/src/ffi/mod.rs:71:9
|
71 | pub use self::zlib_rs::*;
| ^^^^^^^^^^^^^^^^
= help: consider adding an explicit import of `MZ_FINISH` to disambiguate
note: `MZ_FINISH` could also refer to the constant imported here
--> /Users/biocbuild/.cargo/registry/src/index.crates.io-1949cf8c6b5b557f/flate2-1.1.6/src/ffi/mod.rs:76:9
|
76 | pub use self::miniz_oxide::*;
| ^^^^^^^^^^^^^^^^^^^^
= help: consider adding an explicit import of `MZ_FINISH` to disambiguate
error[E0659]: `Deflate` is ambiguous
--> /Users/biocbuild/.cargo/registry/src/index.crates.io-1949cf8c6b5b557f/flate2-1.1.6/src/mem.rs:200:20
|
200 | inner: Deflate::make(level, zlib_header, ffi::MZ_DEFAULT_WINDOW_BITS as u8),
| ^^^^^^^ ambiguous name
|
= note: ambiguous because of multiple glob imports of a name in the same module
note: `Deflate` could refer to the struct imported here
--> /Users/biocbuild/.cargo/registry/src/index.crates.io-1949cf8c6b5b557f/flate2-1.1.6/src/ffi/mod.rs:71:9
|
71 | pub use self::zlib_rs::*;
| ^^^^^^^^^^^^^^^^
= help: consider adding an explicit import of `Deflate` to disambiguate
note: `Deflate` could also refer to the struct imported here
--> /Users/biocbuild/.cargo/registry/src/index.crates.io-1949cf8c6b5b557f/flate2-1.1.6/src/ffi/mod.rs:76:9
|
76 | pub use self::miniz_oxide::*;
| ^^^^^^^^^^^^^^^^^^^^
= help: consider adding an explicit import of `Deflate` to disambiguate
error[E0659]: `Inflate` is ambiguous
--> /Users/biocbuild/.cargo/registry/src/index.crates.io-1949cf8c6b5b557f/flate2-1.1.6/src/mem.rs:388:20
|
388 | inner: Inflate::make(zlib_header, ffi::MZ_DEFAULT_WINDOW_BITS as u8),
| ^^^^^^^ ambiguous name
|
= note: ambiguous because of multiple glob imports of a name in the same module
note: `Inflate` could refer to the struct imported here
--> /Users/biocbuild/.cargo/registry/src/index.crates.io-1949cf8c6b5b557f/flate2-1.1.6/src/ffi/mod.rs:71:9
|
71 | pub use self::zlib_rs::*;
| ^^^^^^^^^^^^^^^^
= help: consider adding an explicit import of `Inflate` to disambiguate
note: `Inflate` could also refer to the struct imported here
--> /Users/biocbuild/.cargo/registry/src/index.crates.io-1949cf8c6b5b557f/flate2-1.1.6/src/ffi/mod.rs:76:9
|
76 | pub use self::miniz_oxide::*;
| ^^^^^^^^^^^^^^^^^^^^
= help: consider adding an explicit import of `Inflate` to disambiguate
Compiling num-bigint v0.4.6
Compiling num-iter v0.1.45
Compiling noisy_float v0.2.0
Compiling approx v0.3.2
error[E0308]: mismatched types
--> /Users/biocbuild/.cargo/registry/src/index.crates.io-1949cf8c6b5b557f/flate2-1.1.6/src/ffi/miniz_oxide.rs:95:45
|
95 | _ => mem::decompress_failed(ErrorMessage),
| ---------------------- ^^^^^^^^^^^^ expected `zlib_rs::ErrorMessage`, found `miniz_oxide::ErrorMessage`
| |
| arguments to this function are incorrect
|
= note: `miniz_oxide::ErrorMessage` and `zlib_rs::ErrorMessage` have similar names, but are actually distinct types
note: `miniz_oxide::ErrorMessage` is defined in module `crate::ffi::miniz_oxide` of the current crate
--> /Users/biocbuild/.cargo/registry/src/index.crates.io-1949cf8c6b5b557f/flate2-1.1.6/src/ffi/miniz_oxide.rs:21:1
|
21 | pub struct ErrorMessage;
| ^^^^^^^^^^^^^^^^^^^^^^^
note: `zlib_rs::ErrorMessage` is defined in module `crate::ffi::zlib_rs` of the current crate
--> /Users/biocbuild/.cargo/registry/src/index.crates.io-1949cf8c6b5b557f/flate2-1.1.6/src/ffi/zlib_rs.rs:45:1
|
45 | pub struct ErrorMessage(Option<&'static str>);
| ^^^^^^^^^^^^^^^^^^^^^^^
note: function defined here
--> /Users/biocbuild/.cargo/registry/src/index.crates.io-1949cf8c6b5b557f/flate2-1.1.6/src/mem.rs:140:15
|
140 | pub(crate) fn decompress_failed<T>(msg: ErrorMessage) -> Result<T, DecompressError> {
| ^^^^^^^^^^^^^^^^^ -----------------
error[E0308]: mismatched types
--> /Users/biocbuild/.cargo/registry/src/index.crates.io-1949cf8c6b5b557f/flate2-1.1.6/src/ffi/miniz_oxide.rs:178:60
|
178 | MZStatus::NeedDict => mem::compress_failed(ErrorMessage),
| -------------------- ^^^^^^^^^^^^ expected `zlib_rs::ErrorMessage`, found `miniz_oxide::ErrorMessage`
| |
| arguments to this function are incorrect
|
= note: `miniz_oxide::ErrorMessage` and `zlib_rs::ErrorMessage` have similar names, but are actually distinct types
note: `miniz_oxide::ErrorMessage` is defined in module `crate::ffi::miniz_oxide` of the current crate
--> /Users/biocbuild/.cargo/registry/src/index.crates.io-1949cf8c6b5b557f/flate2-1.1.6/src/ffi/miniz_oxide.rs:21:1
|
21 | pub struct ErrorMessage;
| ^^^^^^^^^^^^^^^^^^^^^^^
note: `zlib_rs::ErrorMessage` is defined in module `crate::ffi::zlib_rs` of the current crate
--> /Users/biocbuild/.cargo/registry/src/index.crates.io-1949cf8c6b5b557f/flate2-1.1.6/src/ffi/zlib_rs.rs:45:1
|
45 | pub struct ErrorMessage(Option<&'static str>);
| ^^^^^^^^^^^^^^^^^^^^^^^
note: function defined here
--> /Users/biocbuild/.cargo/registry/src/index.crates.io-1949cf8c6b5b557f/flate2-1.1.6/src/mem.rs:159:15
|
159 | pub(crate) fn compress_failed<T>(msg: ErrorMessage) -> Result<T, CompressError> {
| ^^^^^^^^^^^^^^^ -----------------
error[E0308]: mismatched types
--> /Users/biocbuild/.cargo/registry/src/index.crates.io-1949cf8c6b5b557f/flate2-1.1.6/src/ffi/miniz_oxide.rs:182:43
|
182 | _ => mem::compress_failed(ErrorMessage),
| -------------------- ^^^^^^^^^^^^ expected `zlib_rs::ErrorMessage`, found `miniz_oxide::ErrorMessage`
| |
| arguments to this function are incorrect
|
= note: `miniz_oxide::ErrorMessage` and `zlib_rs::ErrorMessage` have similar names, but are actually distinct types
note: `miniz_oxide::ErrorMessage` is defined in module `crate::ffi::miniz_oxide` of the current crate
--> /Users/biocbuild/.cargo/registry/src/index.crates.io-1949cf8c6b5b557f/flate2-1.1.6/src/ffi/miniz_oxide.rs:21:1
|
21 | pub struct ErrorMessage;
| ^^^^^^^^^^^^^^^^^^^^^^^
note: `zlib_rs::ErrorMessage` is defined in module `crate::ffi::zlib_rs` of the current crate
--> /Users/biocbuild/.cargo/registry/src/index.crates.io-1949cf8c6b5b557f/flate2-1.1.6/src/ffi/zlib_rs.rs:45:1
|
45 | pub struct ErrorMessage(Option<&'static str>);
| ^^^^^^^^^^^^^^^^^^^^^^^
note: function defined here
--> /Users/biocbuild/.cargo/registry/src/index.crates.io-1949cf8c6b5b557f/flate2-1.1.6/src/mem.rs:159:15
|
159 | pub(crate) fn compress_failed<T>(msg: ErrorMessage) -> Result<T, CompressError> {
| ^^^^^^^^^^^^^^^ -----------------
Compiling strsim v0.11.1
Compiling clap_lex v0.7.6
Compiling rand_chacha v0.3.1
Compiling rand_chacha v0.9.0
Compiling chrono v0.4.42
Some errors have detailed explanations: E0308, E0659.
For more information about an error, try `rustc --explain E0308`.
error: could not compile `flate2` (lib) due to 17 previous errors
warning: build failed, waiting for other jobs to finish...
error: failed to compile `oarfish v0.8.0`, intermediate artifacts can be found at `/var/folders/r0/l4fjk6cj5xj0j3brt4bplpl40000gt/T/cargo-installdK4zSy`.
To reuse those artifacts with a future compilation, set the environment variable `CARGO_TARGET_DIR` to that path.
make: *** [../inst/bin/oarfish] Error 101
ERROR: compilation failed for package ‘FLAMES’
* removing ‘/Users/biocbuild/bbs-3.23-bioc/meat/FLAMES.buildbin-libdir/FLAMES’