[D 08-23 18:02:47.553 worker:214] got input: {'depend_packages': ['/usr/share/lilac/Packages/BioArchLinux/htslib/htslib-1.22.1-2-x86_64.pkg.tar.zst'], 'update_info': [['4.3.0', '4.3.0']], 'commit_msg_template': 'allelecount: auto updated to {built_version}\n\nIt has been built because:\n* the pkgrel has been updated', 'bindmounts': ['/home/bio/.cache/tmp:/tmp', '/home/bio/.cache/pip:/build/.cache/pip', '/home/bio/.cache/go-build:/build/.cache/go-build', '/home/bio/.cache/go:/build/go', '/home/bio/.cache/cargo:/build/.cargo', '/home/bio/.cache/archbuild-bind-cache/stack:/build/.stack', '/home/bio/.cache/archbuild-bind-cache:/build/.cache'], 'tmpfs': [], 'logfile': '/home/bio/.lilac/log/2025-08-23T18:00:00/allelecount.log', 'worker_no': 0, 'result': '/tmp/allelecount-zdy8qgd0.lilac'} [D 08-23 18:02:47.555 cmd:88] running ['sh', '-c', 'rm -f -- *.pkg.tar.xz *.pkg.tar.xz.sig *.pkg.tar.zst *.pkg.tar.zst.sig'], not using pty, showing output [D 08-23 18:02:47.560 cmd:88] running ['bwrap', '--unshare-all', '--ro-bind', '/', '/', '--tmpfs', '/home', '--tmpfs', '/run', '--die-with-parent', '--tmpfs', '/tmp', '--proc', '/proc', '--dev', '/dev', '--share-net', '--bind', '/usr/share/lilac/Packages/BioArchLinux/allelecount', '/tmp/allelecount', '--chdir', '/tmp/allelecount', '--ro-bind', PosixPath('/home/bio/.lilac/gnupg'), '/home/bio/.gnupg', '/bin/bash', '-c', 'source PKGBUILD && declare -p pkgver pkgrel || :'], not using pty, not showing output [D 08-23 18:02:47.564 worker:96] oldver='4.3.0', newver='4.3.0' [D 08-23 18:02:47.565 cmd:88] running ['bwrap', '--unshare-all', '--ro-bind', '/', '/', '--tmpfs', '/home', '--tmpfs', '/run', '--die-with-parent', '--tmpfs', '/tmp', '--proc', '/proc', '--dev', '/dev', '--share-net', '--bind', '/usr/share/lilac/Packages/BioArchLinux/allelecount', '/tmp/allelecount', '--chdir', '/tmp/allelecount', '--ro-bind', PosixPath('/home/bio/.lilac/gnupg'), '/home/bio/.gnupg', '/bin/bash', '-c', 'source PKGBUILD && declare -p pkgver pkgrel || :'], not using pty, not showing output [D 08-23 18:02:47.570 cmd:88] running ['bwrap', '--unshare-all', '--ro-bind', '/', '/', '--tmpfs', '/home', '--tmpfs', '/run', '--die-with-parent', '--tmpfs', '/tmp', '--proc', '/proc', '--dev', '/dev', '--share-net', '--bind', '/usr/share/lilac/Packages/BioArchLinux/allelecount', '/tmp/allelecount', '--chdir', '/tmp/allelecount', '--ro-bind', PosixPath('/home/bio/.lilac/gnupg'), '/home/bio/.gnupg', 'updpkgsums'], not using pty, showing output ==> Retrieving sources... -> Downloading allelecount-4.3.0.tar.gz... % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 1357k 0 1357k 0 0 2839k 0 --:--:-- --:--:-- --:--:-- 2839k -> Found htslib_hardening.patch ==> Generating checksums for source files... [D 08-23 18:02:48.638 cmd:88] running ['recv_gpg_keys'], not using pty, showing output [D 08-23 18:02:48.647 cmd:88] running ['bwrap', '--unshare-all', '--ro-bind', '/', '/', '--tmpfs', '/home', '--tmpfs', '/run', '--die-with-parent', '--tmpfs', '/tmp', '--proc', '/proc', '--dev', '/dev', '--share-net', '--bind', '/usr/share/lilac/Packages/BioArchLinux/allelecount', '/tmp/allelecount', '--chdir', '/tmp/allelecount', '--ro-bind', PosixPath('/home/bio/.lilac/gnupg'), '/home/bio/.gnupg', 'makepkg', '-od', '--noprepare', '-A'], using pty, showing output [D 08-23 18:02:48.647 cmd:95] pty master fd=3, slave fd=4. ==> Making package: allelecount 4.3.0-4 (Sat 23 Aug 2025 06:02:49 PM GMT) ==> WARNING: Skipping dependency checks. ==> Retrieving sources... -> Found allelecount-4.3.0.tar.gz -> Found htslib_hardening.patch ==> Validating source files with b2sums... allelecount-4.3.0.tar.gz ... Passed htslib_hardening.patch ... Passed ==> Extracting sources... -> Extracting allelecount-4.3.0.tar.gz with bsdtar ==> Sources are ready. [D 08-23 18:02:49.279 cmd:88] running ['bwrap', '--unshare-all', '--ro-bind', '/', '/', '--tmpfs', '/home', '--tmpfs', '/run', '--die-with-parent', '--tmpfs', '/tmp', '--proc', '/proc', '--dev', '/dev', '--share-net', '--bind', '/usr/share/lilac/Packages/BioArchLinux/allelecount', '/tmp/allelecount', '--chdir', '/tmp/allelecount', '--ro-bind', PosixPath('/home/bio/.lilac/gnupg'), '/home/bio/.gnupg', '/bin/bash', '-c', 'source PKGBUILD && declare -p pkgver pkgrel || :'], not using pty, not showing output [I 08-23 18:02:49.914 worker:185] Running build command: ['env', 'GNUPGHOME=/home/bio/.lilac/gnupg', 'extra-x86_64-build', '--', '-I', '/usr/share/lilac/Packages/BioArchLinux/htslib/htslib-1.22.1-2-x86_64.pkg.tar.zst', '-d', '/home/bio/.cache/tmp:/tmp', '-d', '/home/bio/.cache/pip:/build/.cache/pip', '-d', '/home/bio/.cache/go-build:/build/.cache/go-build', '-d', '/home/bio/.cache/go:/build/go', '-d', '/home/bio/.cache/cargo:/build/.cargo', '-d', '/home/bio/.cache/archbuild-bind-cache/stack:/build/.stack', '-d', '/home/bio/.cache/archbuild-bind-cache:/build/.cache', '-l', 'lilac-0', '--', '--noprogressbar', '--holdver'] :: Synchronizing package databases... core downloading... extra downloading... :: Starting full system upgrade... there is nothing to do ==> Building in chroot for [extra] (x86_64)... ==> Synchronizing chroot copy [/var/lib/archbuild/extra-x86_64/root] -> [lilac-0]...done loading packages... resolving dependencies... looking for conflicting packages... Package (1) New Version Net Change htslib 1.22.1-2 5.42 MiB Total Installed Size: 5.42 MiB :: Proceed with installation? [Y/n] checking keyring... checking package integrity... loading package files... checking for file conflicts... :: Processing package changes... installing htslib... :: Running post-transaction hooks... (1/1) Arming ConditionNeedsUpdate... ==> Making package: allelecount 4.3.0-4 (Sat Aug 23 18:02:59 2025) ==> Retrieving sources... -> Found allelecount-4.3.0.tar.gz -> Found htslib_hardening.patch ==> Validating source files with b2sums... allelecount-4.3.0.tar.gz ... Passed htslib_hardening.patch ... Passed ==> Making package: allelecount 4.3.0-4 (Sat Aug 23 18:03:02 2025) ==> Checking runtime dependencies... ==> Checking buildtime dependencies... ==> Retrieving sources... -> Found allelecount-4.3.0.tar.gz -> Found htslib_hardening.patch ==> WARNING: Skipping all source file integrity checks. ==> Extracting sources... -> Extracting allelecount-4.3.0.tar.gz with bsdtar ==> Starting prepare()... patching file c/Makefile ==> Starting build()... rm -f ./src/*.o *~ ./bin/alleleCounter ./bin/* ./tests/tests_log ./tests/bam_access_tests ./src/*.gcda ./src/*.gcov ./src/*.gcno *.gcda *.gcov *.gcno ./tests/*.gcda ./tests/*.gcov ./tests/*.gcno mkdir -p ./bin gcc -O3 -DALLELECOUNTER_VERSION='"4.3.0"' -g -Wall -Wextra -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -pie -fPIE -I/usr/include -Isrc/ -I/usr/include/ -rdynamic -c src/bam_access.c -o src/bam_access.o src/bam_access.c: In function ‘pileup_func’: src/bam_access.c:109:30: warning: unused parameter ‘data’ [-Wunused-parameter] 109 | static int pileup_func(void *data, bam1_t *b){ | ~~~~~~^~~~ src/bam_access.c:109:44: warning: unused parameter ‘b’ [-Wunused-parameter] 109 | static int pileup_func(void *data, bam1_t *b){ | ~~~~~~~~^ src/bam_access.c: In function ‘bam_access_get_multi_position_base_counts’: src/bam_access.c:359:75: warning: ordered comparison of pointer with integer zero [-Wextra] 359 | while ((pl=bam_plp_next(buf, &tid, &pos, &n_plp)) > 0) { | ^ src/bam_access.c:381:67: warning: ordered comparison of pointer with integer zero [-Wextra] 381 | while ((pl=bam_plp_next(buf, &tid, &pos, &n_plp)) > 0) { | ^ src/bam_access.c: In function ‘bam_access_get_position_base_counts’: src/bam_access.c:459:55: warning: ordered comparison of pointer with integer zero [-Wextra] 459 | while ( (pil=bam_plp_next(buf, &tid, &pos, &n_plp)) > 0) { | ^ gcc -O3 -DALLELECOUNTER_VERSION='"4.3.0"' -I/usr/include -Isrc/ -I/usr/include/ -rdynamic -g -Wall -Wextra -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -pie -fPIE -o ./bin/alleleCounter ./src/bam_access.o -Wl,-z,relro,-z,now -L/usr/lib -L/usr/lib -lhts -lpthread -lz -lbz2 -llzma -lm -ldl ./src/alleleCounter.c gcc -O3 -DALLELECOUNTER_VERSION='"4.3.0"' -g -Wall -Wextra -fstack-protector-strong -D_FORTIFY_SOURCE=2 -O2 -pie -fPIE -I/usr/include -Isrc/ -I/usr/include/ -rdynamic ./src/bam_access.o -L/usr/lib -lhts -lpthread -lz -lbz2 -llzma -lm -ldl -L/usr/lib -Wl,-z,relro,-z,now tests/bam_access_tests.c -o tests/bam_access_tests tests/bam_access_tests.c: In function ‘test_bam_access_get_position_base_counts’: tests/bam_access_tests.c:45:13: warning: variable ‘res’ set but not used [-Wunused-but-set-variable] 45 | int res = bam_access_get_position_base_counts(chr,pos,stats,0,NULL); | ^~~ In file included from tests/bam_access_tests.c:22: tests/bam_access_tests.c: In function ‘main’: tests/minunit.h:36:38: warning: parameter ‘argc’ set but not used [-Wunused-but-set-parameter] 36 | #define RUN_TESTS(name) int main(int argc, char *argv[]) {\ | ~~~~^~~~ tests/bam_access_tests.c:132:1: note: in expansion of macro ‘RUN_TESTS’ 132 | RUN_TESTS(all_tests); | ^~~~~~~~~ sh ./tests/runtests.sh Running unit tests: ---- RUNNING: ./tests/bam_access_tests Performing pileup of 11250 reads at 1 198661939 ALL TESTS PASSED Tests run: 1 tests/bam_access_tests PASS Binaries have been compiled. ==> Entering fakeroot environment... ==> Starting package()... ==> Tidying install... -> Removing libtool files... -> Purging unwanted files... -> Removing static library files... -> Stripping unneeded symbols from binaries and libraries... -> Compressing man and info pages... ==> Checking for packaging issues... ==> Creating package "allelecount"... -> Generating .PKGINFO file... -> Generating .BUILDINFO file... -> Generating .MTREE file... -> Compressing package... ==> Leaving fakeroot environment. ==> Finished making: allelecount 4.3.0-4 (Sat Aug 23 18:03:04 2025) ==> Installing package allelecount with pacman -U... loading packages... resolving dependencies... looking for conflicting packages... Package (1) New Version Net Change allelecount 4.3.0-4 0.04 MiB Total Installed Size: 0.04 MiB :: Proceed with installation? [Y/n] checking keyring... checking package integrity... loading package files... checking for file conflicts... :: Processing package changes... installing allelecount... :: Running post-transaction hooks... (1/1) Arming ConditionNeedsUpdate... resolving dependencies... looking for conflicting packages... Package (9) New Version Net Change core/elfutils 0.193-5 3.59 MiB core/licenses 20240728-1 1.54 MiB core/mpdecimal 4.0.1-1 0.33 MiB extra/pyalpm 0.10.12-1 0.28 MiB core/python 3.13.7-1 67.54 MiB extra/python-boolean.py 5.0-1 0.35 MiB extra/python-license-expression 30.4.4-1 1.24 MiB extra/python-pyelftools 0.32-1 2.13 MiB extra/namcap 3.5.2-3 0.92 MiB Total Installed Size: 77.92 MiB :: Proceed with installation? [Y/n] checking keyring... checking package integrity... loading package files... checking for file conflicts... :: Processing package changes... installing elfutils... installing licenses... installing mpdecimal... installing python... Optional dependencies for python python-setuptools: for building Python packages using tooling that is usually bundled with Python python-pip: for installing Python packages using tooling that is usually bundled with Python python-pipx: for installing Python software not packaged on Arch Linux sqlite: for a default database integration [installed] xz: for lzma [installed] tk: for tkinter installing pyalpm... installing python-boolean.py... installing python-license-expression... installing python-pyelftools... installing namcap... :: Running post-transaction hooks... (1/1) Arming ConditionNeedsUpdate... Checking PKGBUILD Checking allelecount-4.3.0-4-x86_64.pkg.tar.zst allelecount W: ELF file ('usr/bin/alleleCounter') lacks GNU_PROPERTY_X86_FEATURE_1_SHSTK. allelecount W: Unused shared library '/usr/lib/libz.so.1' by file ('usr/bin/alleleCounter') allelecount W: Unused shared library '/usr/lib/libbz2.so.1.0' by file ('usr/bin/alleleCounter') allelecount W: Unused shared library '/usr/lib/liblzma.so.5' by file ('usr/bin/alleleCounter') allelecount W: Unused shared library '/usr/lib/libm.so.6' by file ('usr/bin/alleleCounter') ==> Running checkpkg error: target not found: allelecount ==> WARNING: Skipped checkpkg due to missing repo packages [D 08-23 18:03:06.391 cmd:88] running ['git', 'add', '--', 'PKGBUILD'], not using pty, showing output [D 08-23 18:03:06.416 cmd:88] running ['git', 'status', '-s', '.'], not using pty, showing output M PKGBUILD ?? PKGBUILD-namcap.log ?? allelecount-4.3.0-4-x86_64-build.log ?? allelecount-4.3.0-4-x86_64-package.log ?? allelecount-4.3.0-4-x86_64-prepare.log ?? allelecount-4.3.0-4-x86_64.pkg.tar.zst ?? allelecount-4.3.0-4-x86_64.pkg.tar.zst-namcap.log ?? allelecount-4.3.0.tar.gz [D 08-23 18:03:06.431 cmd:88] running ['git', 'commit', '--no-gpg-sign', '-m', 'allelecount: auto updated to 4.3.0-4\n\nIt has been built because:\n* the pkgrel has been updated'], not using pty, showing output [master 2ec14083d0] allelecount: auto updated to 4.3.0-4 1 file changed, 1 insertion(+), 1 deletion(-) [D 08-23 18:03:06.522 connectionpool:1049] Starting new HTTPS connection (1): aur.archlinux.org:443 [D 08-23 18:03:06.638 connectionpool:544] https://aur.archlinux.org:443 "GET /pkgbase/allelecount HTTP/1.1" 303 0 [D 08-23 18:03:06.750 connectionpool:544] https://aur.archlinux.org:443 "GET /packages/allelecount HTTP/1.1" 200 None [D 08-23 18:03:06.752 cmd:88] running ['git', 'reset', '--hard', 'origin/master'], not using pty, showing output HEAD is now at 11eae05 allelecount: initial upload [D 08-23 18:03:06.759 cmd:88] running ['git', 'pull', '--no-edit'], not using pty, showing output Already up to date. [D 08-23 18:03:08.700 cmd:88] running ['git', 'ls-files'], not using pty, showing output .SRCINFO PKGBUILD harden.patch series [I 08-23 18:03:08.702 api:382] copying files to AUR repo: /home/bio/.lilac/aur/allelecount [D 08-23 18:03:08.702 cmd:88] running ['git', 'ls-files'], not using pty, showing output PKGBUILD htslib_hardening.patch lilac.yaml [D 08-23 18:03:08.707 api:387] copying file PKGBUILD [D 08-23 18:03:08.707 api:387] copying file htslib_hardening.patch [D 08-23 18:03:08.707 api:395] removing file harden.patch [D 08-23 18:03:08.707 api:395] removing file series [D 08-23 18:03:08.707 cmd:88] running ['git', 'diff'], not using pty, showing output diff --git a/PKGBUILD b/PKGBUILD index 5ff846d..a366476 100644 --- a/PKGBUILD +++ b/PKGBUILD @@ -3,33 +3,27 @@ pkgname=allelecount _pkgname=alleleCount pkgver=4.3.0 -pkgrel=1 +pkgrel=4 pkgdesc="program for estimating the NGS copy number" arch=('x86_64') url="http://cancerit.github.io/alleleCount/" -license=('AGPL3') +license=('AGPL-3.0-or-later') depends=('glibc' 'htslib' 'bzip2' 'xz' 'zlib') -makedepends=('quilt' 'perl') +makedepends=('perl') source=("${pkgname}-${pkgver}.tar.gz::https://github.com/cancerit/alleleCount/archive/refs/tags/v${pkgver}.tar.gz" - 'series' - 'harden.patch') + 'htslib_hardening.patch' + ) b2sums=('f0f2077d0efed1a9f4db76648ae375ea30989909d255917b5b280e32187a27aaf1e1844bccae8b659c34081d34592d3782b7d6df926ece79dcea62cb966b4539' - '55807c3d06f035d18040248d272bb150bc84ef44c4e01ae984f3abe27fd34d6f18abe5bc1cbb2945435725d2344a5b5209b37ac322cc1ff5fae1612c265c1b9b' - '9de3b1c44db6e8b0e2321450d19d741ad233eabb00d32c6f951e78177ee1bd36d150c3685eb7c373f806c694d3c84b94e7e4fd5683387f85587de35a646c7066') + 'b690635a2f9aa89ceacda7aab1d47ab9044fdf2e48f680a63f6c3c5202211bd87da44046a005f8ca0f8524eb277ca719718af0b58eb7d8cd2a270629c9e6a696') prepare(){ - mkdir -p ${_pkgname}-${pkgver}/patches - cp *.patch ${_pkgname}-${pkgver}/patches - cp series ${_pkgname}-${pkgver}/patches - # Apply Patches - cd ${_pkgname}-${pkgver}/patches - quilt push -a + cd ${_pkgname}-${pkgver}/ + patch -p1 < ${srcdir}/htslib_hardening.patch } build() { cd ${_pkgname}-${pkgver}/c - export HTSLIB=/usr/lib - make prefix=/usr + make -j1 prefix=/usr } package() { diff --git a/harden.patch b/harden.patch deleted file mode 100644 index 9a13e5d..0000000 --- a/harden.patch +++ /dev/null @@ -1,24 +0,0 @@ -Author: Andreas Tille <tille@debian.org> -Last-Update: Mon, 11 May 2020 16:16:46 +0200 -Description: Propagate hardening flags - ---- a/c/Makefile -+++ b/c/Makefile -@@ -6,7 +6,7 @@ CC = gcc -O3 -DALLELECOUNTER_VERSION='"$ - #compiler flags - # -g adds debug info to the executable file - # -Wall turns on most warnings from compiler --CFLAGS = -g -Wall -+CFLAGS += -g -Wall - - #Location of samtools/htslib libraries - HTSLOC?=$(HTSLIB) -@@ -67,7 +67,7 @@ all: clean make_bin make_htslib_tmp $(CO - @echo Binaries have been compiled. - - $(COUNTER_TARGET): $(OBJS) -- $(CC) $(JOIN_INCLUDES) $(INCLUDES) $(CFLAGS) -o $(COUNTER_TARGET) $(OBJS) $(LFLAGS) $(CAT_LFLAGS) $(LIBS) ./src/alleleCounter.c -+ $(CC) $(JOIN_INCLUDES) $(INCLUDES) $(CFLAGS) -o $(COUNTER_TARGET) $(OBJS) $(LFLAGS) $(CAT_LFLAGS) $(LIBS) ./src/alleleCounter.c $(LDFLAGS) - - #Unit Tests - test: $(COUNTER_TARGET) \ No newline at end of file diff --git a/series b/series deleted file mode 100644 index a2f2d63..0000000 --- a/series +++ /dev/null @@ -1 +0,0 @@ -harden.patch \ No newline at end of file [D 08-23 18:03:09.345 cmd:88] running ['git', 'add', '.'], not using pty, showing output [D 08-23 18:03:09.349 cmd:88] running ['git', 'commit', '--no-gpg-sign', '-m', '[lilac] updated to 4.3.0-4'], not using pty, showing output [master a83771c] [lilac] updated to 4.3.0-4 5 files changed, 141 insertions(+), 47 deletions(-) delete mode 100644 harden.patch create mode 100644 htslib_hardening.patch delete mode 100644 series [D 08-23 18:03:09.353 cmd:88] running ['git', 'push'], not using pty, showing output To aur.archlinux.org:allelecount.git 11eae05..a83771c master -> master [D 08-23 18:03:17.994 tools:19] killing child processes (if any) [2025-08-23 18:03:19 +0000] build (version 4.3.0-4) finished in 32s with result: <BuildResult.successful: rusage=RUsage(cputime=18.341208, memory=435326976)>