=> "/opt/pkg/bin/bmake" ["-C", "/Volumes/data/jenkins/workspace/pkgsrc-macos-trunk-arm64/biology/stacks", "configure", "PYTHON_VERSION_REQD=313", "BATCH=1", "DEPENDS_TARGET=/nonexistent"] => Checksum BLAKE2s OK for stacks-2.68.tar.gz => Checksum SHA512 OK for stacks-2.68.tar.gz ===> Installing dependencies for stacks-2.68 ========================================================================== The following variables will affect the build process of this package, stacks-2.68. Their current value is shown below: * PYTHON_VERSION_DEFAULT = 313 Based on these variables, the following variables have been set: * PYPACKAGE = python313 You may want to abort the process now with CTRL-C and change the value of variables in the first group before continuing. Be sure to run `/opt/pkg/bin/bmake clean' after the changes. ========================================================================== => Tool dependency bash-[0-9]*: found bash-5.3.20 => Tool dependency nbpatch-[0-9]*: found nbpatch-20151107 => Tool dependency cwrappers>=20150314: found cwrappers-20220403 => Tool dependency checkperms>=1.1: found checkperms-1.12 => Full dependency perl>=5.0: found perl-5.44.0nb2 => Full dependency R>=4.2.0nb1: found R-4.6.1nb4 => Full dependency openmp>=22.1.0: found openmp-22.1.8nb1 => Full dependency python313>=3.13: found python313-3.13.18 => Full dependency zlib>=1.2.3: found zlib-1.3.1 => Full dependency bzip2>=1.0.1: found bzip2-1.0.8 => Full dependency gettext-lib>=0.22: found gettext-lib-1.0 => Full dependency libiconv>=1.9.1: found libiconv-1.19 => Full dependency xz>=5.0.0: found xz-5.8.4 ===> Overriding tools for stacks-2.68 ===> Extracting for stacks-2.68 ===> Patching for stacks-2.68 => Applying pkgsrc patches for stacks-2.68 => Verifying /Volumes/data/jenkins/workspace/pkgsrc-macos-trunk-arm64/biology/stacks/patches/patch-src_Hwp.cc => Applying pkgsrc patch /Volumes/data/jenkins/workspace/pkgsrc-macos-trunk-arm64/biology/stacks/patches/patch-src_Hwp.cc Hmm... Looks like a unified diff to me... The text leading up to this was: -------------------------- |$NetBSD: patch-src_Hwp.cc,v 1.1 2022/04/25 14:34:06 tnn Exp $ | |avoid ambiguous math functions | |--- src/Hwp.cc.orig 2020-06-24 17:47:53.000000000 +0000 |+++ src/Hwp.cc -------------------------- Patching file src/Hwp.cc using Plan A... Hunk #1 succeeded at 20. done => Verifying /Volumes/data/jenkins/workspace/pkgsrc-macos-trunk-arm64/biology/stacks/patches/patch-src_PopSum.cc => Applying pkgsrc patch /Volumes/data/jenkins/workspace/pkgsrc-macos-trunk-arm64/biology/stacks/patches/patch-src_PopSum.cc Hmm... Looks like a unified diff to me... The text leading up to this was: -------------------------- |$NetBSD: patch-src_PopSum.cc,v 1.1 2022/04/25 14:34:06 tnn Exp $ | |avoid ambiguous math functions | |--- src/PopSum.cc.orig 2021-10-21 14:47:59.000000000 +0000 |+++ src/PopSum.cc -------------------------- Patching file src/PopSum.cc using Plan A... Hunk #1 succeeded at 20. done => Verifying /Volumes/data/jenkins/workspace/pkgsrc-macos-trunk-arm64/biology/stacks/patches/patch-src_Vcf.cc => Applying pkgsrc patch /Volumes/data/jenkins/workspace/pkgsrc-macos-trunk-arm64/biology/stacks/patches/patch-src_Vcf.cc Hmm... Looks like a unified diff to me... The text leading up to this was: -------------------------- |$NetBSD: patch-src_Vcf.cc,v 1.1 2022/04/25 14:34:06 tnn Exp $ | |avoid ambiguous math functions | |--- src/Vcf.cc.orig 2021-06-28 20:21:30.000000000 +0000 |+++ src/Vcf.cc -------------------------- Patching file src/Vcf.cc using Plan A... Hunk #1 succeeded at 22. done => Verifying /Volumes/data/jenkins/workspace/pkgsrc-macos-trunk-arm64/biology/stacks/patches/patch-src_kmers.cc => Applying pkgsrc patch /Volumes/data/jenkins/workspace/pkgsrc-macos-trunk-arm64/biology/stacks/patches/patch-src_kmers.cc Hmm... Looks like a unified diff to me... The text leading up to this was: -------------------------- |$NetBSD: patch-src_kmers.cc,v 1.1 2022/04/25 14:34:06 tnn Exp $ | |avoid ambiguous math functions | |--- src/kmers.cc.orig 2021-06-08 21:08:14.000000000 +0000 |+++ src/kmers.cc -------------------------- Patching file src/kmers.cc using Plan A... Hunk #1 succeeded at 23. done => Verifying /Volumes/data/jenkins/workspace/pkgsrc-macos-trunk-arm64/biology/stacks/patches/patch-src_smoothing__utils.h => Applying pkgsrc patch /Volumes/data/jenkins/workspace/pkgsrc-macos-trunk-arm64/biology/stacks/patches/patch-src_smoothing__utils.h Hmm... Looks like a unified diff to me... The text leading up to this was: -------------------------- |$NetBSD: patch-src_smoothing__utils.h,v 1.1 2022/04/25 14:34:06 tnn Exp $ | |avoid ambiguous math functions | |--- src/smoothing_utils.h.orig 2020-06-24 17:47:55.000000000 +0000 |+++ src/smoothing_utils.h -------------------------- Patching file src/smoothing_utils.h using Plan A... Hunk #1 succeeded at 24. done => Verifying /Volumes/data/jenkins/workspace/pkgsrc-macos-trunk-arm64/biology/stacks/patches/patch-src_utils.cc => Applying pkgsrc patch /Volumes/data/jenkins/workspace/pkgsrc-macos-trunk-arm64/biology/stacks/patches/patch-src_utils.cc Hmm... Looks like a unified diff to me... The text leading up to this was: -------------------------- |$NetBSD: patch-src_utils.cc,v 1.1 2022/04/25 14:34:06 tnn Exp $ | |provide fallback declaration for ACCESSPERMS | |--- src/utils.cc.orig 2021-10-07 19:33:41.000000000 +0000 |+++ src/utils.cc -------------------------- Patching file src/utils.cc using Plan A... Hunk #1 succeeded at 401. done ===> Creating toolchain wrappers for stacks-2.68 ===> Configuring for stacks-2.68 => Substituting "sed" in Makefile.in => Modifying GNU configure scripts to avoid --recheck => Replacing config-guess with pkgsrc versions => Replacing config-sub with pkgsrc versions => Replacing install-sh with pkgsrc version => Replacing Rscript interpreter in scripts/stacks-hist2d-loci-samples-coverage. => Replacing python interpreter in scripts/*.py scripts/stacks-dist-extract scripts/stacks-integrate-alignments scripts/stacks-private-alleles. WARNING: [replace-interpreter] Skipping non-existent file "scripts/*.py". => Replacing bash interpreter in scripts/stacks-count-reads-per-sample-per-locus scripts/stacks-gdb scripts/stacks-samtools-tview. => Replacing Perl interpreter in scripts/*.pl. configure: WARNING: unrecognized options: --with-libiconv-prefix checking for a BSD-compatible install... /usr/bin/install -c -o pbulk -g staff checking whether build environment is sane... yes checking for a race-free mkdir -p... ./config/install-sh -c -d checking for gawk... /opt/pkg/bin/nawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C++... yes checking whether clang++ accepts -g... yes checking for clang++ option to enable C++11 features... none needed checking whether make supports the include directive... yes (GNU style) checking dependency style of clang++... gcc3 checking for aarch64-apple-darwin24-gcc... clang checking whether the compiler supports GNU C... yes checking whether clang accepts -g... yes checking for clang option to enable C11 features... none needed checking whether clang understands -c and -o together... yes checking dependency style of clang... gcc3 checking whether clang++ supports C++11 features by default... yes checking for aarch64-apple-darwin24-ranlib... no checking for ranlib... ranlib checking for aarch64-apple-darwin24-ar... no checking for aarch64-apple-darwin24-lib... no checking for aarch64-apple-darwin24-link... no checking for ar... ar checking the archiver (ar) interface... ar checking for omp_set_num_threads in -lgomp... yes checking for gzread in -lz... yes checking for dirent.h that defines DIR... yes checking for library containing opendir... none required checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for grep that handles long lines and -e... (cached) /usr/bin/grep checking for egrep... (cached) /usr/bin/egrep checking for float.h... yes checking for limits.h... yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for unistd.h... (cached) yes checking for clang option to support OpenMP... none needed checking for _Bool... yes checking for stdbool.h that conforms to C99... yes checking for an ANSI C-conforming const... yes checking for size_t... yes checking whether closedir returns void... no checking build system type... aarch64-apple-darwin24 checking host system type... aarch64-apple-darwin24 checking for GNU libc compatible malloc... yes checking for GNU libc compatible realloc... yes checking for floor... yes checking for memset... yes checking for pow... yes checking for sqrt... yes checking for clock_gettime... yes checking for functional regular expressions... yes checking for gawk... (cached) /opt/pkg/bin/nawk checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating htslib/Makefile config.status: creating config.h config.status: executing depfiles commands configure: WARNING: unrecognized options: --with-libiconv-prefix