+ case "${usergroup_phase}" in + local run_cmd + run_cmd=run_su + shift + run_su /opt/local/bin/bmake configure BATCH=1 DEPENDS_TARGET=/nonexistent PYTHON_VERSION_REQD=39 WRKLOG=/tmp/bulklog/hisat2-2.1.0.23nb5/work.log + su pbulk -c '"$@"' make /opt/local/bin/bmake configure BATCH=1 DEPENDS_TARGET=/nonexistent PYTHON_VERSION_REQD=39 WRKLOG=/tmp/bulklog/hisat2-2.1.0.23nb5/work.log => Bootstrap dependency digest>=20211023: found digest-20211023 => Checksum BLAKE2s OK for hisat2-2.1.0.23-20f333e2cfe7ff4d1362b248912893e2644683d7.tar.gz => Checksum SHA512 OK for hisat2-2.1.0.23-20f333e2cfe7ff4d1362b248912893e2644683d7.tar.gz ===> Installing dependencies for hisat2-2.1.0.23nb5 ========================================================================== The following variables will affect the build process of this package, hisat2-2.1.0.23nb5. Their current value is shown below: * PYTHON_VERSION_DEFAULT = 39 Based on these variables, the following variables have been set: * PYPACKAGE = python39 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-4.3nb3 => Tool dependency perl>=5.0: found perl-5.34.0nb3 => Tool dependency checkperms>=1.1: found checkperms-1.12 => Build dependency gcc10>=10.3.0: found gcc10-10.3.0 => Build dependency cwrappers>=20150314: found cwrappers-20180325 => Full dependency python39>=3.9.0: found python39-3.9.9nb1 => Full dependency gcc10-libs>=10.3.0: found gcc10-libs-10.3.0 ===> Overriding tools for hisat2-2.1.0.23nb5 ===> Extracting for hisat2-2.1.0.23nb5 ===> Patching for hisat2-2.1.0.23nb5 => Applying pkgsrc patches for hisat2-2.1.0.23nb5 => Verifying /data/jenkins/workspace/pkgsrc-2021Q4-x86_64/biology/hisat2/patches/patch-hisat2 => Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-2021Q4-x86_64/biology/hisat2/patches/patch-hisat2 Hmm... Looks like a unified diff to me... The text leading up to this was: -------------------------- |$NetBSD: patch-hisat2,v 1.1 2019/01/15 01:26:29 bacon Exp $ | |# Limit Windows-specific patches to Windows | |--- hisat2.orig 2018-11-07 21:43:32 UTC |+++ hisat2 -------------------------- Patching file hisat2 using Plan A... Hunk #1 succeeded at 45. done ===> Creating toolchain wrappers for hisat2-2.1.0.23nb5 ===> Configuring for hisat2-2.1.0.23nb5 => Replacing python interpreter in *.py hisat2-build hisat2-inspect hisatgenotype_modules/*.py hisatgenotype_scripts/*.py. INFO: [replace-interpreter] Nothing changed in hisatgenotype_modules/__init__.py. => Replacing bash interpreter in hisatgenotype_scripts/*.sh. INFO: [replace-interpreter] Nothing changed in hisatgenotype_scripts/run_extract_CP.sh. INFO: [replace-interpreter] Nothing changed in hisatgenotype_scripts/run_extract_ILMN.sh. INFO: [replace-interpreter] Nothing changed in hisatgenotype_scripts/run_genotype_build.sh. INFO: [replace-interpreter] Nothing changed in hisatgenotype_scripts/run_hisat2_build.sh. INFO: [replace-interpreter] Nothing changed in hisatgenotype_scripts/run_type_CP.sh. => Replacing Perl interpreter in hisat2 scripts/*.sh scripts/*.pl. INFO: [replace-interpreter] Nothing changed in scripts/make_a_thaliana_tair.sh. INFO: [replace-interpreter] Nothing changed in scripts/make_b_taurus_UMD3.sh. INFO: [replace-interpreter] Nothing changed in scripts/make_bdgp6_tran.sh. INFO: [replace-interpreter] Nothing changed in scripts/make_bdgp6.sh. INFO: [replace-interpreter] Nothing changed in scripts/make_canFam2.sh. INFO: [replace-interpreter] Nothing changed in scripts/make_ce10.sh. INFO: [replace-interpreter] Nothing changed in scripts/make_dm6.sh. INFO: [replace-interpreter] Nothing changed in scripts/make_e_coli.sh. INFO: [replace-interpreter] Nothing changed in scripts/make_grch37_snp_tran_ercc.sh. INFO: [replace-interpreter] Nothing changed in scripts/make_grch37_snp_tran.sh. INFO: [replace-interpreter] Nothing changed in scripts/make_grch37_snp.sh. INFO: [replace-interpreter] Nothing changed in scripts/make_grch37_tran.sh. INFO: [replace-interpreter] Nothing changed in scripts/make_grch37.sh. INFO: [replace-interpreter] Nothing changed in scripts/make_grch38_snp_tran_ercc.sh. INFO: [replace-interpreter] Nothing changed in scripts/make_grch38_snp_tran.sh. INFO: [replace-interpreter] Nothing changed in scripts/make_grch38_snp.sh. INFO: [replace-interpreter] Nothing changed in scripts/make_grch38_tran.sh. INFO: [replace-interpreter] Nothing changed in scripts/make_grch38.sh. INFO: [replace-interpreter] Nothing changed in scripts/make_grcm38_snp_tran.sh. INFO: [replace-interpreter] Nothing changed in scripts/make_grcm38_snp.sh. INFO: [replace-interpreter] Nothing changed in scripts/make_grcm38_tran.sh. INFO: [replace-interpreter] Nothing changed in scripts/make_grcm38.sh. INFO: [replace-interpreter] Nothing changed in scripts/make_hg19.sh. INFO: [replace-interpreter] Nothing changed in scripts/make_hg38_allsnp.sh. INFO: [replace-interpreter] Nothing changed in scripts/make_hg38_snp_tran.sh. INFO: [replace-interpreter] Nothing changed in scripts/make_hg38_snp.sh. INFO: [replace-interpreter] Nothing changed in scripts/make_hg38.sh. INFO: [replace-interpreter] Nothing changed in scripts/make_mm10.sh. INFO: [replace-interpreter] Nothing changed in scripts/make_mm9.sh. INFO: [replace-interpreter] Nothing changed in scripts/make_r64_tran.sh. INFO: [replace-interpreter] Nothing changed in scripts/make_r64.sh. INFO: [replace-interpreter] Nothing changed in scripts/make_rn4.sh. INFO: [replace-interpreter] Nothing changed in scripts/make_rn6.sh. INFO: [replace-interpreter] Nothing changed in scripts/make_rnor6_tran.sh. INFO: [replace-interpreter] Nothing changed in scripts/make_rnor6.sh. INFO: [replace-interpreter] Nothing changed in scripts/make_sc3.sh. INFO: [replace-interpreter] Nothing changed in scripts/make_wbcel235_tran.sh. INFO: [replace-interpreter] Nothing changed in scripts/make_wbcel235.sh. INFO: [replace-interpreter] Nothing changed in scripts/make_zm3_snp_tran_ercc.sh. => Checking for portability problems in extracted files