+ case "${usergroup_phase}" in
+ local run_cmd
+ run_cmd=run_su
+ shift
+ run_su /opt/pkg/bin/bmake configure BATCH=1 DEPENDS_TARGET=/nonexistent WRKLOG=/tmp/bulklog/rna-star-2.7.10b/work.log
+ su pbulk -c '"$@"' make /opt/pkg/bin/bmake configure BATCH=1 DEPENDS_TARGET=/nonexistent WRKLOG=/tmp/bulklog/rna-star-2.7.10b/work.log
=> Bootstrap dependency digest>=20211023: found digest-20220214
=> Checksum BLAKE2s OK for STAR-2.7.10b.tar.gz
=> Checksum SHA512 OK for STAR-2.7.10b.tar.gz
===> Installing dependencies for rna-star-2.7.10b
=> Tool dependency mktools-[0-9]*: found mktools-20220614
=> Tool dependency gmake>=3.81: found gmake-4.4.1
=> Tool dependency cwrappers>=20150314: found cwrappers-20220403
=> Tool dependency checkperms>=1.1: found checkperms-1.12
=> Full dependency htslib>=1.17: found htslib-1.17nb3
=> Full dependency zlib>=1.2.3: found zlib-1.3.1
===> Overriding tools for rna-star-2.7.10b
===> Extracting for rna-star-2.7.10b
===> Patching for rna-star-2.7.10b
=> Applying pkgsrc patches for rna-star-2.7.10b
=> Verifying /data/jenkins/workspace/pkgsrc-upstream-bulktest/biology/rna-star/patches/patch-Makefile
=> Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-upstream-bulktest/biology/rna-star/patches/patch-Makefile
Hmm...  Looks like a unified diff to me...
The text leading up to this was:
--------------------------
|$NetBSD: patch-Makefile,v 1.2 2023/08/29 21:49:57 bacon Exp $
|
|# Portability
|
|--- Makefile.orig	2022-11-01 14:50:35.000000000 +0000
|+++ Makefile
--------------------------
Patching file Makefile using Plan A...
Hunk #1 succeeded at 11.
Hunk #2 succeeded at 22.
Hunk #3 succeeded at 46.
Hunk #4 succeeded at 119.
Hunk #5 succeeded at 136.
done
=> Verifying /data/jenkins/workspace/pkgsrc-upstream-bulktest/biology/rna-star/patches/patch-SharedMemory.cpp
=> Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-upstream-bulktest/biology/rna-star/patches/patch-SharedMemory.cpp
Hmm...  Looks like a unified diff to me...
The text leading up to this was:
--------------------------
|$NetBSD: patch-SharedMemory.cpp,v 1.2 2023/08/29 21:49:57 bacon Exp $
|
|# Portability
|
|--- SharedMemory.cpp.orig	2022-11-01 14:50:35.000000000 +0000
|+++ SharedMemory.cpp
--------------------------
Patching file SharedMemory.cpp using Plan A...
Hunk #1 succeeded at 12.
done
=> Verifying /data/jenkins/workspace/pkgsrc-upstream-bulktest/biology/rna-star/patches/patch-SoloBarcode.cpp
=> Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-upstream-bulktest/biology/rna-star/patches/patch-SoloBarcode.cpp
Hmm...  Looks like a unified diff to me...
The text leading up to this was:
--------------------------
|$NetBSD: patch-SoloBarcode.cpp,v 1.2 2023/08/29 21:49:57 bacon Exp $
|
|# Portability
|
|--- SoloBarcode.cpp.orig	2023-07-23 17:22:42.613062682 +0000
|+++ SoloBarcode.cpp
--------------------------
Patching file SoloBarcode.cpp using Plan A...
Hunk #1 succeeded at 3.
Hunk #2 succeeded at 150.
done
=> Verifying /data/jenkins/workspace/pkgsrc-upstream-bulktest/biology/rna-star/patches/patch-SuffixArrayFuns.cpp
=> Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-upstream-bulktest/biology/rna-star/patches/patch-SuffixArrayFuns.cpp
Hmm...  Looks like a unified diff to me...
The text leading up to this was:
--------------------------
|$NetBSD: patch-SuffixArrayFuns.cpp,v 1.2 2023/08/29 21:49:57 bacon Exp $
|
|# Drop obsolete modifier for c++17 compat
|
|--- SuffixArrayFuns.cpp.orig	2023-07-21 15:26:07 UTC
|+++ SuffixArrayFuns.cpp
--------------------------
Patching file SuffixArrayFuns.cpp using Plan A...
Hunk #1 succeeded at 15.
Hunk #2 succeeded at 231.
Hunk #3 succeeded at 356.
Hunk #4 succeeded at 376.
done
=> Verifying /data/jenkins/workspace/pkgsrc-upstream-bulktest/biology/rna-star/patches/patch-bamSortByCoordinate.cpp
=> Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-upstream-bulktest/biology/rna-star/patches/patch-bamSortByCoordinate.cpp
Hmm...  Looks like a unified diff to me...
The text leading up to this was:
--------------------------
|$NetBSD: patch-bamSortByCoordinate.cpp,v 1.2 2023/08/29 21:49:57 bacon Exp $
|
|# Portability
|
|--- bamSortByCoordinate.cpp.orig	2022-11-01 14:50:35.000000000 +0000
|+++ bamSortByCoordinate.cpp
--------------------------
Patching file bamSortByCoordinate.cpp using Plan A...
Hunk #1 succeeded at 69.
done
=> Verifying /data/jenkins/workspace/pkgsrc-upstream-bulktest/biology/rna-star/patches/patch-opal_opal.cpp
=> Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-upstream-bulktest/biology/rna-star/patches/patch-opal_opal.cpp
Hmm...  Looks like a unified diff to me...
The text leading up to this was:
--------------------------
|$NetBSD: patch-opal_opal.cpp,v 1.1 2023/08/29 21:49:57 bacon Exp $
|
|# Fix compile error on Darwin 21.6.0
|
|--- opal/opal.cpp.orig	2023-08-29 21:20:11.000000000 +0000
|+++ opal/opal.cpp
--------------------------
Patching file opal/opal.cpp using Plan A...
Hunk #1 succeeded at 5.
done
===> Creating toolchain wrappers for rna-star-2.7.10b
===> Configuring for rna-star-2.7.10b
=> Substituting "htslib" in BAMfunctions.cpp IncludeDefine.h STAR.cpp bamRemoveDuplicates.cpp bam_cat.c bam_cat.h signalFromBAM.h
=> Checking for portability problems in extracted files