+ case "${usergroup_phase}" in + local run_cmd + run_cmd=run_su + shift + run_su /opt/local/bin/bmake configure BATCH=1 DEPENDS_TARGET=/nonexistent PYTHON_VERSION_REQD=312 WRKLOG=/tmp/bulklog/bowtie2-2.5.4/work.log + su pbulk -c '"$@"' make /opt/local/bin/bmake configure BATCH=1 DEPENDS_TARGET=/nonexistent PYTHON_VERSION_REQD=312 WRKLOG=/tmp/bulklog/bowtie2-2.5.4/work.log => Checksum BLAKE2s OK for bowtie2-2.5.4.tar.gz => Checksum SHA512 OK for bowtie2-2.5.4.tar.gz ===> Installing dependencies for bowtie2-2.5.4 ========================================================================== The following variables will affect the build process of this package, bowtie2-2.5.4. Their current value is shown below: * PYTHON_VERSION_DEFAULT = 312 Based on these variables, the following variables have been set: * PYPACKAGE = python312 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/local/bin/bmake clean' after the changes. ========================================================================== => Tool dependency gmake>=3.81: found gmake-4.4.1 => Tool dependency pax>=20040802: found pax-20210219 => Tool dependency cwrappers>=20150314: found cwrappers-20220403 => Tool dependency checkperms>=1.1: found checkperms-1.12 => Build dependency gcc13>=13.1.0: found gcc13-13.3.0 => Build dependency simde>=0.7.2: found simde-0.8.2 => Full dependency perl>=5.0: found perl-5.40.0nb1 => Full dependency gcc13-libs>=13.2.0: found gcc13-libs-13.3.0 => Full dependency python312>=3.12.0: found python312-3.12.8nb1 => Full dependency zlib>=1.2.3: found zlib-1.3.1 ===> Overriding tools for bowtie2-2.5.4 ===> Extracting for bowtie2-2.5.4 ===> Patching for bowtie2-2.5.4 => Applying pkgsrc patches for bowtie2-2.5.4 => Verifying /data/jenkins/workspace/pkgsrc-2024Q4-x86_64/biology/bowtie2/patches/patch-Makefile => Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-2024Q4-x86_64/biology/bowtie2/patches/patch-Makefile Hmm... Looks like a unified diff to me... The text leading up to this was: -------------------------- |$NetBSD: patch-Makefile,v 1.6 2024/05/24 11:32:58 bacon Exp $ | |# Respect pkgsrc env | |--- Makefile.orig 2021-12-17 01:48:49.470438839 +0000 |+++ Makefile -------------------------- Patching file Makefile using Plan A... Hunk #1 succeeded at 21. Hunk #2 succeeded at 230 (offset 31 lines). done => Verifying /data/jenkins/workspace/pkgsrc-2024Q4-x86_64/biology/bowtie2/patches/patch-scripts_bowtie2-hbb.sh => Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-2024Q4-x86_64/biology/bowtie2/patches/patch-scripts_bowtie2-hbb.sh Hmm... Looks like a unified diff to me... The text leading up to this was: -------------------------- |$NetBSD: patch-scripts_bowtie2-hbb.sh,v 1.6 2024/05/24 11:32:58 bacon Exp $ | |# Eliminate bash dependency | |--- scripts/bowtie2-hbb.sh.orig 2020-10-06 03:46:41.000000000 +0000 |+++ scripts/bowtie2-hbb.sh -------------------------- Patching file scripts/bowtie2-hbb.sh using Plan A... Hunk #1 succeeded at 11. done ===> Creating toolchain wrappers for bowtie2-2.5.4 /usr/bin/sed -e '/^#/d' -e 's,@LINK_ARCH_DEFAULT@,link_arch64,g' -e 's,@LINK_LIBGCC_DEFAULT@,link_libgcc_arch64,g' -e 's,@LIBGCC_PREFIX@,/opt/local/gcc13/x86_64-sun-solaris2.11,g' < ../../extra/gcc13-libs/files/specs.pkgsrc > /home/pbulk/build/biology/bowtie2/work/.cwrapper/specs.pkgsrc ===> Configuring for bowtie2-2.5.4 => Replacing python interpreter in bowtie2-build bowtie2-inspect. => Replacing Perl interpreter in scripts/*.pl bowtie2. => Replacing sh interpreter in scripts/bowtie2-hbb.sh.