==> Synchronizing chroot copy [/home/leming/armv8/root] -> [leming]...done
==> Making package: biodiff 1.2.1-2 (Fri Mar 27 06:51:10 2026)
==> Retrieving sources...
-> Updating biodiff-1.2.1 git repo...
-> Updating biodiff-WFA2-lib git repo...
==> WARNING: Skipping verification of source file PGP signatures.
==> Validating source files with sha256sums...
biodiff-1.2.1 ... Passed
biodiff-WFA2-lib ... Skipped
==> Making package: biodiff 1.2.1-2 (Fri Mar 27 06:51:20 2026)
==> Checking runtime dependencies...
==> Checking buildtime dependencies...
==> Installing missing dependencies...
:: There are 2 providers available for cargo:
:: Repository extra
1) rust 2) rustup
Enter a number (default=1):
resolving dependencies...
looking for conflicting packages...
Packages (18) compiler-rt-22.1.1-1 cppdap-1.58.0-2 hicolor-icon-theme-0.18-1 jsoncpp-1.9.6-3 libedit-20251016_3.1-1 libgit2-1:1.9.2-3 libuv-1.52.1-1 lld-22.1.1-1 llhttp-9.3.1-1 llvm-libs-22.1.1-1 perl-error-0.17030-3 perl-mailtools-2.22-3 perl-timedate-2.35-1 rhash-1.4.6-1 zlib-ng-2.3.3-1 cmake-4.3.0-2 git-2.53.0-1 rust-1:1.94.1-1
Total Installed Size: 597.22 MiB
:: Proceed with installation? [Y/n]
checking keyring...
checking package integrity...
loading package files...
checking for file conflicts...
checking available disk space...
:: Processing package changes...
installing compiler-rt...
installing llhttp...
installing libgit2...
installing libedit...
installing llvm-libs...
installing lld...
installing rust...
Optional dependencies for rust
gdb: rust-gdb script
lldb: rust-lldb script
installing cppdap...
installing hicolor-icon-theme...
installing jsoncpp...
Optional dependencies for jsoncpp
jsoncpp-doc: documentation
installing libuv...
installing rhash...
installing cmake...
Optional dependencies for cmake
make: for unix Makefile generator [installed]
ninja: for ninja generator
qt6-base: cmake-gui
installing perl-error...
installing perl-timedate...
installing perl-mailtools...
installing zlib-ng...
installing git...
Optional dependencies for git
git-zsh-completion: upstream zsh completion
tk: gitk and git gui
openssh: ssh transport and crypto
man: show help with `git command --help`
perl-libwww: git svn
perl-term-readkey: git svn and interactive.singlekey setting
perl-io-socket-ssl: git send-email TLS support
perl-authen-sasl: git send-email TLS support
perl-cgi: gitweb (web interface) support
python: git svn & git p4
subversion: git svn
org.freedesktop.secrets: keyring credential helper
libsecret: libsecret credential helper [installed]
less: the default pager for git
:: Running post-transaction hooks...
(1/3) Creating system user accounts...
Creating group 'git' with GID 968.
Creating user 'git' (git daemon user) with UID 968 and GID 968.
(2/3) Reloading system manager configuration...
Skipped: Current root is not booted.
(3/3) Arming ConditionNeedsUpdate...
==> Retrieving sources...
==> WARNING: Skipping all source file integrity checks.
==> Extracting sources...
-> Creating working copy of biodiff-1.2.1 git repo...
Cloning into 'biodiff-1.2.1'...
done.
Switched to a new branch 'makepkg'
-> Creating working copy of biodiff-WFA2-lib git repo...
Cloning into 'biodiff-WFA2-lib'...
done.
==> Starting prepare()...
Submodule 'biodiff-wfa2-sys/WFA2-lib' (https://github.com/smarco/WFA2-lib) registered for path 'biodiff-wfa2-sys/WFA2-lib'
Cloning into '/build/biodiff/src/biodiff-1.2.1/biodiff-wfa2-sys/WFA2-lib'...
done.
Submodule path 'biodiff-wfa2-sys/WFA2-lib': checked out 'cf3eb92dd0aa9bf067d5488a606d8c91173e74eb'
Updating crates.io index
Downloading crates ...
Downloaded same-file v1.0.6
Downloaded clap_lex v0.7.0
Downloaded num-iter v0.1.44
Downloaded enum-map v2.7.3
Downloaded editdistancek v1.0.2
Downloaded derive-new v0.5.9
Downloaded bio-types v1.0.1
Downloaded getrandom v0.2.14
Downloaded libm v0.2.8
Downloaded anyhow v1.0.82
Downloaded matrixmultiply v0.3.8
Downloaded safe_arch v0.7.1
Downloaded rand v0.8.5
Downloaded itertools v0.11.0
Downloaded statrs v0.16.0
Downloaded clap_builder v4.5.2
Downloaded petgraph v0.6.4
Downloaded bio v1.6.0
Downloaded ndarray v0.15.6
Downloaded rustfft v6.2.0
Downloaded nalgebra v0.29.0
Downloaded syn v1.0.109
Downloaded regex-syntax v0.8.3
Downloaded rustix v0.38.32
Downloaded zerocopy v0.7.32
Downloaded regex v1.10.4
Downloaded syn v2.0.58
Downloaded mio v0.8.11
Downloaded regex-automata v0.4.6
Downloaded darling v0.20.8
Downloaded csv v1.3.0
Downloaded rustc_version v0.1.7
Downloaded signal-hook-mio v0.2.3
Downloaded libc v0.2.153
Downloaded crossterm v0.25.0
Downloaded crossbeam-channel v0.5.12
Downloaded wide v0.7.15
Downloaded cc v1.0.92
Downloaded cursive v0.20.0
Downloaded rand_distr v0.4.3
Downloaded bytemuck v1.15.0
Downloaded simba v0.6.0
Downloaded clap v4.5.4
Downloaded parking_lot v0.12.1
Downloaded signal-hook v0.3.17
Downloaded aho-corasick v1.1.3
Downloaded serde_json v1.0.115
Downloaded rayon v1.10.0
Downloaded winnow v0.6.6
Downloaded linux-raw-sys v0.4.13
Downloaded bv v0.11.1
Downloaded byteorder v1.5.0
Downloaded proc-macro2 v1.0.79
Downloaded paste v1.0.14
Downloaded typenum v1.17.0
Downloaded signal-hook-registry v1.4.1
Downloaded once_cell v1.19.0
Downloaded time v0.3.35
Downloaded cursive_core v0.3.7
Downloaded hashbrown v0.14.3
Downloaded bit-vec v0.6.3
Downloaded csv-core v0.1.11
Downloaded multimap v0.9.1
Downloaded ordered-float v3.9.2
Downloaded ppv-lite86 v0.2.17
Downloaded rand_core v0.6.4
Downloaded rustversion v1.0.15
Downloaded strum_macros v0.25.3
Downloaded thiserror v1.0.58
Downloaded triple_accel v0.4.0
Downloaded vec_map v0.8.2
Downloaded cmake v0.1.50
Downloaded lock_api v0.4.11
Downloaded parking_lot_core v0.9.9
Downloaded ahash v0.8.11
Downloaded xi-unicode v0.3.0
Downloaded unicode-segmentation v1.11.0
Downloaded serde v1.0.197
Downloaded bit-set v0.5.3
Downloaded feature-probe v0.1.1
Downloaded bytecount v0.6.7
Downloaded custom_derive v0.1.7
Downloaded fxhash v0.2.1
Downloaded semver v0.1.20
Downloaded newtype_derive v0.1.6
Downloaded fixedbitset v0.4.2
Downloaded rawpointer v0.2.1
Downloaded nalgebra-macros v0.1.0
Downloaded approx v0.5.1
Downloaded rand_chacha v0.3.1
Downloaded strum v0.25.0
Downloaded thiserror-impl v1.0.58
Downloaded darling_core v0.20.8
Downloaded itoa v1.0.11
Downloaded ryu v1.0.17
Downloaded humantime v2.1.0
Downloaded similar v2.5.0
Downloaded indexmap v2.2.6
Downloaded toml_edit v0.22.12
Downloaded itertools-num v0.1.3
Downloaded heck v0.4.1
Downloaded heck v0.5.0
Downloaded clap_derive v4.5.4
Downloaded bitflags v1.3.2
Downloaded num-rational v0.4.1
Downloaded time-macros v0.2.18
Downloaded fnv v1.0.7
Downloaded num-traits v0.2.18
Downloaded humantime-serde v1.1.1
Downloaded rayon-core v1.12.1
Downloaded bitflags v2.5.0
Downloaded memchr v2.7.2
Downloaded lazy_static v1.4.0
Downloaded deranged v0.3.11
Downloaded num_threads v0.1.7
Downloaded powerfmt v0.2.0
Downloaded enumset v1.1.3
Downloaded log v0.4.21
Downloaded smallvec v1.13.2
Downloaded hex v0.4.3
Downloaded num-integer v0.1.46
Downloaded strength_reduce v0.2.4
Downloaded transpose v0.2.3
Downloaded version_check v0.9.4
Downloaded realfft v3.3.0
Downloaded glob v0.3.1
Downloaded crossbeam-epoch v0.9.18
Downloaded crossbeam-deque v0.8.5
Downloaded crossbeam-utils v0.8.19
Downloaded shlex v1.3.0
Downloaded anstyle-parse v0.2.3
Downloaded utf8parse v0.2.1
Downloaded anstream v0.6.13
Downloaded fastrand v2.0.2
Downloaded tempfile v3.10.1
Downloaded snapbox v0.5.9
Downloaded quote v1.0.36
Downloaded serde_derive v1.0.197
Downloaded trycmd v0.15.1
Downloaded num v0.4.1
Downloaded stable_deref_trait v1.2.0
Downloaded owning_ref v0.4.1
Downloaded num-conv v0.1.0
Downloaded time-core v0.1.2
Downloaded ident_case v1.0.1
Downloaded darling_macro v0.20.8
Downloaded enumset_derive v0.8.1
Downloaded cursive_buffered_backend v0.6.1
Downloaded option-ext v0.2.0
Downloaded dirs-sys v0.4.1
Downloaded dirs v5.0.1
Downloaded num-complex v0.4.5
Downloaded autocfg v1.2.0
Downloaded either v1.10.0
Downloaded content_inspector v0.2.4
Downloaded dunce v1.0.4
Downloaded filetime v0.2.23
Downloaded normalize-line-endings v0.3.0
Downloaded os_pipe v1.1.5
Downloaded anstyle v1.0.6
Downloaded anstyle-query v1.0.2
Downloaded colorchoice v1.0.0
Downloaded snapbox-macros v0.3.8
Downloaded cfg-if v1.0.0
Downloaded errno v0.3.8
Downloaded walkdir v2.5.0
Downloaded unicode-ident v1.0.12
Downloaded unicode-width v0.1.11
Downloaded scopeguard v1.2.0
Downloaded enum-map-derive v0.17.0
Downloaded primal-check v0.3.3
Downloaded wait-timeout v0.2.0
Downloaded equivalent v1.0.1
Downloaded serde_spanned v0.6.5
Downloaded toml_datetime v0.6.5
==> Starting build()...
Compiling autocfg v1.2.0
Compiling proc-macro2 v1.0.79
Compiling unicode-ident v1.0.12
Compiling libc v0.2.153
Compiling libm v0.2.8
Compiling cfg-if v1.0.0
Compiling version_check v0.9.4
Compiling serde v1.0.197
Compiling ident_case v1.0.1
Compiling syn v1.0.109
Compiling fnv v1.0.7
Compiling num-traits v0.2.18
Compiling num-rational v0.4.1
Compiling memchr v2.7.2
Compiling itoa v1.0.11
Compiling matrixmultiply v0.3.8
Compiling quote v1.0.36
Compiling getrandom v0.2.14
Compiling syn v2.0.58
Compiling rand_core v0.6.4
Compiling ppv-lite86 v0.2.17
Compiling bytemuck v1.15.0
Compiling log v0.4.21
Compiling lazy_static v1.4.0
Compiling paste v1.0.14
Compiling crossbeam-utils v0.8.19
Compiling safe_arch v0.7.1
Compiling rand_chacha v0.3.1
Compiling aho-corasick v1.1.3
Compiling num-integer v0.1.46
Compiling num-complex v0.4.5
Compiling lock_api v0.4.11
Compiling ahash v0.8.11
Compiling signal-hook v0.3.17
Compiling rawpointer v0.2.1
Compiling smallvec v1.13.2
Compiling typenum v1.17.0
Compiling powerfmt v0.2.0
Compiling regex-syntax v0.8.3
Compiling semver v0.1.20
Compiling darling_core v0.20.8
Compiling rustversion v1.0.15
Compiling parking_lot_core v0.9.9
Compiling rustc_version v0.1.7
Compiling deranged v0.3.11
Compiling regex-automata v0.4.6
Compiling serde_derive v1.0.197
Compiling enum-map-derive v0.17.0
Compiling darling_macro v0.20.8
Compiling enum-map v2.7.3
Compiling darling v0.20.8
Compiling enumset_derive v0.8.1
Compiling num-iter v0.1.44
Compiling rand v0.8.5
Compiling approx v0.5.1
Compiling wide v0.7.15
Compiling signal-hook-registry v1.4.1
Compiling num-conv v0.1.0
Compiling utf8parse v0.2.1
Compiling stable_deref_trait v1.2.0
Compiling scopeguard v1.2.0
Compiling once_cell v1.19.0
Compiling time-core v0.1.2
Compiling cc v1.0.92
Compiling thiserror v1.0.58
Compiling feature-probe v0.1.1
Compiling num_threads v0.1.7
Compiling zerocopy v0.7.32
Compiling simba v0.6.0
Compiling cmake v0.1.50
Compiling time v0.3.35
Compiling bv v0.11.1
Compiling owning_ref v0.4.1
Compiling anstyle-parse v0.2.3
Compiling regex v1.10.4
Compiling rand_distr v0.4.3
Compiling enumset v1.1.3
Compiling num v0.4.1
Compiling thiserror-impl v1.0.58
Compiling crossbeam-channel v0.5.12
Compiling nalgebra-macros v0.1.0
Compiling newtype_derive v0.1.6
Compiling mio v0.8.11
Compiling rustfft v6.2.0
Compiling ryu v1.0.17
Compiling anstyle v1.0.6
Compiling unicode-width v0.1.11
Compiling hashbrown v0.14.3
Compiling equivalent v1.0.1
Compiling xi-unicode v0.3.0
Compiling colorchoice v1.0.0
Compiling anstyle-query v1.0.2
Compiling strength_reduce v0.2.4
Compiling heck v0.4.1
Compiling anyhow v1.0.82
Compiling unicode-segmentation v1.11.0
Compiling strum_macros v0.25.3
Compiling transpose v0.2.3
Compiling cursive_core v0.3.7
Compiling indexmap v2.2.6
Compiling signal-hook-mio v0.2.3
Compiling anstream v0.6.13
Compiling nalgebra v0.29.0
Compiling parking_lot v0.12.1
Compiling biodiff-wfa2-sys v2.3.5 (/build/biodiff/src/biodiff-1.2.1/biodiff-wfa2-sys)
Compiling derive-new v0.5.9
Compiling primal-check v0.3.3
Compiling csv-core v0.1.11
Compiling bit-vec v0.6.3
Compiling either v1.10.0
Compiling byteorder v1.5.0
Compiling heck v0.5.0
Compiling option-ext v0.2.0
Compiling fixedbitset v0.4.2
Compiling bitflags v1.3.2
Compiling serde_json v1.0.115
Compiling clap_lex v0.7.0
Compiling petgraph v0.6.4
Compiling clap_builder v4.5.2
Compiling crossterm v0.25.0
Compiling clap_derive v4.5.4
Compiling fxhash v0.2.1
Compiling dirs-sys v0.4.1
Compiling itertools v0.11.0
Compiling bit-set v0.5.3
Compiling csv v1.3.0
Compiling bio-types v1.0.1
Compiling statrs v0.16.0
Compiling multimap v0.9.1
Compiling vec_map v0.8.2
Compiling ndarray v0.15.6
Compiling itertools-num v0.1.3
Compiling ordered-float v3.9.2
Compiling custom_derive v0.1.7
Compiling editdistancek v1.0.2
Compiling triple_accel v0.4.0
Compiling bytecount v0.6.7
Compiling strum v0.25.0
Compiling realfft v3.3.0
Compiling clap v4.5.4
Compiling dirs v5.0.1
Compiling cursive v0.20.0
Compiling cursive_buffered_backend v0.6.1
Compiling hexagex v0.2.3 (/build/biodiff/src/biodiff-1.2.1/hexagex)
Compiling bio v1.6.0
Compiling biodiff v1.2.1 (/build/biodiff/src/biodiff-1.2.1)
Finished `release` profile [optimized] target(s) in 5m 05s
==> Entering fakeroot environment...
==> Starting package()...
==> Tidying install...
-> Removing libtool files...
-> Removing static library files...
-> Purging unwanted files...
-> Stripping unneeded symbols from binaries and libraries...
-> Compressing man and info pages...
==> Checking for packaging issues...
==> Creating package "biodiff"...
-> Generating .PKGINFO file...
-> Generating .BUILDINFO file...
-> Generating .MTREE file...
-> Compressing package...
==> Leaving fakeroot environment.
==> Finished making: biodiff 1.2.1-2 (Fri Mar 27 06:56:56 2026)
==> Cleaning up...
[?12l[?25h