=> Bootstrap dependency digest>=20010302: found digest-20190127
=> Checksum SHA1 OK for bowtie2-2.4.2.tar.gz
=> Checksum RMD160 OK for bowtie2-2.4.2.tar.gz
=> Checksum SHA512 OK for bowtie2-2.4.2.tar.gz
===> Installing dependencies for bowtie2-2.4.2nb1
==========================================================================
The following variables will affect the build process of this package,
bowtie2-2.4.2nb1.  Their current value is shown below:

        * PYTHON_VERSION_DEFAULT = 38

Based on these variables, the following variables have been set:

        * PYPACKAGE = python38

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
`/usr/bin/make clean' after the changes.
==========================================================================
=> Tool dependency bsdtar-[0-9]*: found bsdtar-3.4.3
=> Tool dependency gmake>=3.81: found gmake-4.3nb2
=> Tool dependency checkperms>=1.1: found checkperms-1.12
=> Build dependency cwrappers>=20150314: found cwrappers-20180325
=> Full dependency perl>=5.0: found perl-5.34.0nb3
=> Full dependency python38>=3.8.0: found python38-3.8.12
===> Skipping vulnerability checks.
WARNING: No /usr/pkg/pkgdb/pkg-vulnerabilities file found.
WARNING: To fix run: `/usr/sbin/pkg_admin -K /usr/pkg/pkgdb fetch-pkg-vulnerabilities'.
===> Overriding tools for bowtie2-2.4.2nb1
===> Extracting for bowtie2-2.4.2nb1
===> Patching for bowtie2-2.4.2nb1
=> Applying pkgsrc patches for bowtie2-2.4.2nb1
=> Verifying /tree/pkgsrc/biology/bowtie2/patches/patch-Makefile
=> Applying pkgsrc patch /tree/pkgsrc/biology/bowtie2/patches/patch-Makefile
Hmm...  Looks like a unified diff to me...
The text leading up to this was:
--------------------------
|$NetBSD: patch-Makefile,v 1.1 2021/01/21 17:30:12 bacon Exp $
|
|# Respect PREFIX and CXXFLAGS
|
|--- Makefile.orig	2020-10-06 03:46:41.000000000 +0000
|+++ Makefile
--------------------------
Patching file Makefile using Plan A...
Hunk #1 succeeded at 21.
Hunk #2 succeeded at 234.
done
=> Verifying /tree/pkgsrc/biology/bowtie2/patches/patch-scripts_bowtie2-hbb.sh
=> Applying pkgsrc patch /tree/pkgsrc/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 1.1 2021/01/21 17:30:12 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 bowtie2-2.4.2nb1
===> Configuring for bowtie2-2.4.2nb1
=> Replacing python interpreter in bowtie2-build bowtie2-inspect.
=> Replacing Perl interpreter in scripts/*.pl bowtie2.
=> Replacing sh interpreter in scripts/bowtie2-hbb.sh.
=> Checking for portability problems in extracted files