[package - main-i386-default][biology/bcf-score] Failed for bcf-score-1.16 in build
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Date: Thu, 29 Jun 2023 09:27:10 UTC
You are receiving this mail as a port that you maintain
is failing to build on the FreeBSD package build server.
Please investigate the failure and submit a PR to fix
build.
Maintainer: jwb@FreeBSD.org
Log URL: https://pkg-status.freebsd.org/beefy17/data/main-i386-default/p8c7f3e19a83a_se495600ce3/logs/bcf-score-1.16.log
Build URL: https://pkg-status.freebsd.org/beefy17/build.html?mastername=main-i386-default&build=p8c7f3e19a83a_se495600ce3
Log:
=>> Building biology/bcf-score
build started at Thu Jun 29 09:26:22 UTC 2023
port directory: /usr/ports/biology/bcf-score
package name: bcf-score-1.16
building for: FreeBSD main-i386-default-job-11 14.0-CURRENT FreeBSD 14.0-CURRENT 1400092 i386
maintained by: jwb@FreeBSD.org
Makefile ident:
Poudriere version: 3.2.8-23-ga7f8d188
Host OSVERSION: 1400089
Jail OSVERSION: 1400092
Job Id: 11
!!! Jail is newer than host. (Jail: 1400092, Host: 1400089) !!!
!!! This is not supported. !!!
!!! Host kernel must be same or newer than jail. !!!
!!! Expect build failures. !!!
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=======================<phase: check-sanity >============================
===> License MIT accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===> bcf-score-1.16 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.19.1_2.pkg
[main-i386-default-job-11] Installing pkg-1.19.1_2...
[main-i386-default-job-11] Extracting pkg-1.19.1_2: .......... done
===> bcf-score-1.16 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of bcf-score-1.16
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> License MIT accepted by the user
===> Fetching all distfiles required by bcf-score-1.16 for building
===========================================================================
=======================<phase: checksum >============================
===> License MIT accepted by the user
===> Fetching all distfiles required by bcf-score-1.16 for building
=> SHA256 Checksum OK for score_1.16-20221221.tar.gz.
=> SHA256 Checksum OK for samtools-bcftools-1.16-1.17_GH0.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract >============================
===> License MIT accepted by the user
===> Fetching all distfiles required by bcf-score-1.16 for building
===> Extracting for bcf-score-1.16
=> SHA256 Checksum OK for score_1.16-20221221.tar.gz.
=> SHA256 Checksum OK for samtools-bcftools-1.16-1.17_GH0.tar.gz.
===========================================================================
=======================<phase: patch-depends >============================
===========================================================================
=======================<phase: patch >============================
===> Patching for bcf-score-1.16
===> Applying FreeBSD patches for bcf-score-1.16 from /usr/ports/biology/bcf-score/files
<snip>
./lib/autoconf/status.m4:1096: AC_CONFIG_SUBDIRS is expanded from...
m4/ax_with_htslib.m4:55: AX_WITH_HTSLIB is expanded from...
configure.ac:94: the top level
configure: loading site script /usr/ports/Templates/config.site
checking for gcc... cc
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 cc accepts -g... yes
checking for cc option to enable C11 features... none needed
checking for grep that handles long lines and -e... (cached) /usr/bin/grep
checking for C compiler warning flags... -Wall
checking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... no
checking location of HTSlib source tree... none found
checking for htslib/sam.h... yes
checking for hts_version in -lhts... yes
checking shared library type... plain .so
checking for library containing dlopen... none required
checking if the compiler accepts -rdynamic... yes
checking for zlib.h... (cached) yes
checking for inflate in -lz... yes
checking for library containing regcomp... none required
configure: creating ./config.status
config.status: creating config.mk
config.status: creating config.h
===========================================================================
=======================<phase: build >============================
===> Building for bcf-score-1.16
gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/bcf-score/work/bcftools-1.17'
echo '#define BCFTOOLS_VERSION "1.17"' > version.h
cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o vcfindex.o vcfindex.c
cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o tabix.o tabix.c
cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o vcfstats.o vcfstats.c
cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o vcfisec.o vcfisec.c
cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o vcfmerge.o vcfmerge.c
cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o vcfquery.o vcfquery.c
cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o vcffilter.o vcffilter.c
cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o filter.o filter.c
cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o vcfsom.o vcfsom.c
cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o vcfnorm.o vcfnorm.c
cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o vcfgtcheck.o vcfgtcheck.c
cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o vcfview.o vcfview.c
cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o vcfannotate.o vcfannotate.c
cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o vcfroh.o vcfroh.c
cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o vcfconcat.o vcfconcat.c
cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o vcfcall.o vcfcall.c
cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o mcall.o mcall.c
cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o vcmp.o vcmp.c
cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o gvcf.o gvcf.c
cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o reheader.o reheader.c
cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o convert.o convert.c
cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o vcfconvert.o vcfconvert.c
cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o tsv2vcf.o tsv2vcf.c
cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o vcfcnv.o vcfcnv.c
cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o vcfhead.o vcfhead.c
cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o HMM.o HMM.c
cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o consensus.o consensus.c
cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o ploidy.o ploidy.c
cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o bin.o bin.c
cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o hclust.o hclust.c
cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o version.o version.c
cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o regidx.o regidx.c
cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o smpl_ilist.o smpl_ilist.c
cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o csq.o csq.c
cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o vcfbuf.o vcfbuf.c
vcfbuf.c:249:32: warning: implicit truncation from 'int' to a one-bit wide bit-field changes value from 1 to -1 [-Wsingle-bit-bitfield-constant-conversion]
buf->vcf[i].af_set = 1;
^ ~
1 warning generated.
cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o mpileup.o mpileup.c
cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o bam2bcf.o bam2bcf.c
cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o bam2bcf_indel.o bam2bcf_indel.c
cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o bam2bcf_iaux.o bam2bcf_iaux.c
cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o read_consensus.o read_consensus.c
cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o bam_sample.o bam_sample.c
cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o vcfsort.o vcfsort.c
cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o cols.o cols.c
cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o extsort.o extsort.c
cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o dist.o dist.c
cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o abuf.o abuf.c
cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o ccall.o ccall.c
cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o em.o em.c
cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o prob1.o prob1.c
cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o kmin.o kmin.c
cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o str_finder.o str_finder.c
cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -DPLUGINPATH='"/usr/local/libexec/bcftools"' -c -o vcfplugin.o vcfplugin.c
cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o test/test-rbuf.o test/test-rbuf.c
cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o test/test-regidx.o test/test-regidx.c
cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -fstack-protector-strong -o plugins/GTisec.so version.c plugins/GTisec.c -L/usr/local/lib
cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -fstack-protector-strong -o plugins/GTsubset.so version.c plugins/GTsubset.c -L/usr/local/lib
cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -fstack-protector-strong -o plugins/ad-bias.so convert.c version.c plugins/ad-bias.c -L/usr/local/lib
cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -fstack-protector-strong -o plugins/add-variantkey.so version.c plugins/add-variantkey.c -L/usr/local/lib
cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -fstack-protector-strong -o plugins/af-dist.so bin.c version.c plugins/af-dist.c -L/usr/local/lib
cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -fstack-protector-strong -o plugins/allele-length.so version.c plugins/allele-length.c -L/usr/local/lib
cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -fstack-protector-strong -o plugins/blupx.so version.c plugins/blupx.c -L/usr/local/lib
cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -fstack-protector-strong -o plugins/check-ploidy.so version.c plugins/check-ploidy.c -L/usr/local/lib
cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -fstack-protector-strong -o plugins/check-sparsity.so version.c plugins/check-sparsity.c -L/usr/local/lib
cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -fstack-protector-strong -o plugins/color-chrs.so HMM.c version.c plugins/color-chrs.c -L/usr/local/lib
cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -fstack-protector-strong -o plugins/contrast.so version.c plugins/contrast.c -L/usr/local/lib
cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -fstack-protector-strong -o plugins/counts.so version.c plugins/counts.c -L/usr/local/lib
cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -fstack-protector-strong -o plugins/dosage.so version.c plugins/dosage.c -L/usr/local/lib
cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -fstack-protector-strong -o plugins/fill-AN-AC.so version.c plugins/fill-AN-AC.c -L/usr/local/lib
cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -fstack-protector-strong -o plugins/fill-from-fasta.so filter.c version.c plugins/fill-from-fasta.c -L/usr/local/lib
cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -fstack-protector-strong -o plugins/fill-tags.so version.c plugins/fill-tags.c -L/usr/local/lib
cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -fstack-protector-strong -o plugins/fixploidy.so ploidy.c regidx.c version.c plugins/fixploidy.c -L/usr/local/lib
cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -fstack-protector-strong -o plugins/fixref.so version.c plugins/fixref.c -L/usr/local/lib
cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -fstack-protector-strong -o plugins/frameshifts.so version.c plugins/frameshifts.c -L/usr/local/lib
cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -fstack-protector-strong -o plugins/guess-ploidy.so version.c plugins/guess-ploidy.c -L/usr/local/lib
cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -fstack-protector-strong -o plugins/gvcfz.so version.c plugins/gvcfz.c -L/usr/local/lib
cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -fstack-protector-strong -o plugins/impute-info.so version.c plugins/impute-info.c -L/usr/local/lib
cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -fstack-protector-strong -o plugins/indel-stats.so version.c plugins/indel-stats.c -L/usr/local/lib
cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -fstack-protector-strong -o plugins/isecGT.so smpl_ilist.c version.c plugins/isecGT.c -L/usr/local/lib
cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -fstack-protector-strong -o plugins/liftover.so version.c plugins/liftover.c -L/usr/local/lib
cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -fstack-protector-strong -o plugins/mendelian.so version.c plugins/mendelian.c -L/usr/local/lib
plugins/liftover.c:1106:9: warning: absolute value function 'abs' given an argument of type 'hts_pos_t' (aka 'long long') but has parameter of type 'int' which may cause truncation of value [-Wabsolute-value]
if (abs(right_pos - left_pos) > indel_win) return -1;
^
plugins/liftover.c:1106:9: note: use function 'llabs' instead
if (abs(right_pos - left_pos) > indel_win) return -1;
^~~
llabs
cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -fstack-protector-strong -o plugins/mendelian2.so version.c plugins/mendelian2.c -L/usr/local/lib
cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -fstack-protector-strong -o plugins/metal.so version.c plugins/metal.c -L/usr/local/lib
1 warning generated.
cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -fstack-protector-strong -o plugins/missing2ref.so version.c plugins/missing2ref.c -L/usr/local/lib
cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -fstack-protector-strong -o plugins/munge.so version.c plugins/munge.c -L/usr/local/lib
cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -fstack-protector-strong -o plugins/parental-origin.so version.c plugins/parental-origin.c -L/usr/local/lib
plugins/munge.c:123:74: error: incompatible function pointer types initializing 'const int (*)(tsv_t *, bcf1_t *, void *)' (aka 'const int (*)(struct _tsv_t *, struct bcf1_t *, void *)') with an expression of type 'int (tsv_t *, bcf1_t *, void *)' (aka 'int (struct _tsv_t *, struct bcf1_t *, void *)') [-Wincompatible-function-pointer-types]
static const int (*tsv_setters[])(tsv_t *tsv, bcf1_t *rec, void *usr) = {tsv_setter_id_flexible, // SNP
^~~~~~~~~~~~~~~~~~~~~~
plugins/munge.c:124:74: error: incompatible function pointer types initializing 'const int (*)(tsv_t *, bcf1_t *, void *)' (aka 'const int (*)(struct _tsv_t *, struct bcf1_t *, void *)') with an expression of type 'int (tsv_t *, bcf1_t *, void *)' (aka 'int (struct _tsv_t *, struct bcf1_t *, void *)') [-Wincompatible-function-pointer-types]
tsv_setter_pos_flexible, // BP
^~~~~~~~~~~~~~~~~~~~~~~
plugins/munge.c:125:74: error: incompatible function pointer types initializing 'const int (*)(tsv_t *, bcf1_t *, void *)' (aka 'const int (*)(struct _tsv_t *, struct bcf1_t *, void *)') with an expression of type 'int (tsv_t *, bcf1_t *, void *)' (aka 'int (struct _tsv_t *, struct bcf1_t *, void *)') [-Wincompatible-function-pointer-types]
tsv_setter_chrom_flexible, // CHR
^~~~~~~~~~~~~~~~~~~~~~~~~
plugins/munge.c:126:74: error: incompatible function pointer types initializing 'const int (*)(tsv_t *, bcf1_t *, void *)' (aka 'const int (*)(struct _tsv_t *, struct bcf1_t *, void *)') with an expression of type 'int (tsv_t *, bcf1_t *, void *)' (aka 'int (struct _tsv_t *, struct bcf1_t *, void *)') [-Wincompatible-function-pointer-types]
tsv_read_allele, // A1
^~~~~~~~~~~~~~~
plugins/munge.c:127:74: error: incompatible function pointer types initializing 'const int (*)(tsv_t *, bcf1_t *, void *)' (aka 'const int (*)(struct _tsv_t *, struct bcf1_t *, void *)') with an expression of type 'int (tsv_t *, bcf1_t *, void *)' (aka 'int (struct _tsv_t *, struct bcf1_t *, void *)') [-Wincompatible-function-pointer-types]
tsv_read_allele, // A2
^~~~~~~~~~~~~~~
plugins/munge.c:128:74: error: incompatible function pointer types initializing 'const int (*)(tsv_t *, bcf1_t *, void *)' (aka 'const int (*)(struct _tsv_t *, struct bcf1_t *, void *)') with an expression of type 'int (tsv_t *, bcf1_t *, void *)' (aka 'int (struct _tsv_t *, struct bcf1_t *, void *)') [-Wincompatible-function-pointer-types]
tsv_read_float_and_minus_log10, // P
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
plugins/munge.c:129:74: error: incompatible function pointer types initializing 'const int (*)(tsv_t *, bcf1_t *, void *)' (aka 'const int (*)(struct _tsv_t *, struct bcf1_t *, void *)') with an expression of type 'int (tsv_t *, bcf1_t *, void *)' (aka 'int (struct _tsv_t *, struct bcf1_t *, void *)') [-Wincompatible-function-pointer-types]
tsv_read_float, // Z
^~~~~~~~~~~~~~
plugins/munge.c:130:74: error: incompatible function pointer types initializing 'const int (*)(tsv_t *, bcf1_t *, void *)' (aka 'const int (*)(struct _tsv_t *, struct bcf1_t *, void *)') with an expression of type 'int (tsv_t *, bcf1_t *, void *)' (aka 'int (struct _tsv_t *, struct bcf1_t *, void *)') [-Wincompatible-function-pointer-types]
tsv_read_float_and_log, // OR
^~~~~~~~~~~~~~~~~~~~~~
plugins/munge.c:131:74: error: incompatible function pointer types initializing 'const int (*)(tsv_t *, bcf1_t *, void *)' (aka 'const int (*)(struct _tsv_t *, struct bcf1_t *, void *)') with an expression of type 'int (tsv_t *, bcf1_t *, void *)' (aka 'int (struct _tsv_t *, struct bcf1_t *, void *)') [-Wincompatible-function-pointer-types]
tsv_read_float, // BETA
^~~~~~~~~~~~~~
plugins/munge.c:132:74: error: incompatible function pointer types initializing 'const int (*)(tsv_t *, bcf1_t *, void *)' (aka 'const int (*)(struct _tsv_t *, struct bcf1_t *, void *)') with an expression of type 'int (tsv_t *, bcf1_t *, void *)' (aka 'int (struct _tsv_t *, struct bcf1_t *, void *)') [-Wincompatible-function-pointer-types]
tsv_read_float, // N
^~~~~~~~~~~~~~
plugins/munge.c:133:74: error: incompatible function pointer types initializing 'const int (*)(tsv_t *, bcf1_t *, void *)' (aka 'const int (*)(struct _tsv_t *, struct bcf1_t *, void *)') with an expression of type 'int (tsv_t *, bcf1_t *, void *)' (aka 'int (struct _tsv_t *, struct bcf1_t *, void *)') [-Wincompatible-function-pointer-types]
tsv_read_float, // N_CAS
^~~~~~~~~~~~~~
plugins/munge.c:134:74: error: incompatible function pointer types initializing 'const int (*)(tsv_t *, bcf1_t *, void *)' (aka 'const int (*)(struct _tsv_t *, struct bcf1_t *, void *)') with an expression of type 'int (tsv_t *, bcf1_t *, void *)' (aka 'int (struct _tsv_t *, struct bcf1_t *, void *)') [-Wincompatible-function-pointer-types]
tsv_read_float, // N_CON
^~~~~~~~~~~~~~
plugins/munge.c:135:74: error: incompatible function pointer types initializing 'const int (*)(tsv_t *, bcf1_t *, void *)' (aka 'const int (*)(struct _tsv_t *, struct bcf1_t *, void *)') with an expression of type 'int (tsv_t *, bcf1_t *, void *)' (aka 'int (struct _tsv_t *, struct bcf1_t *, void *)') [-Wincompatible-function-pointer-types]
tsv_read_float, // INFO
^~~~~~~~~~~~~~
plugins/munge.c:136:74: error: incompatible function pointer types initializing 'const int (*)(tsv_t *, bcf1_t *, void *)' (aka 'const int (*)(struct _tsv_t *, struct bcf1_t *, void *)') with an expression of type 'int (tsv_t *, bcf1_t *, void *)' (aka 'int (struct _tsv_t *, struct bcf1_t *, void *)') [-Wincompatible-function-pointer-types]
tsv_read_float, // FRQ
^~~~~~~~~~~~~~
plugins/munge.c:137:74: error: incompatible function pointer types initializing 'const int (*)(tsv_t *, bcf1_t *, void *)' (aka 'const int (*)(struct _tsv_t *, struct bcf1_t *, void *)') with an expression of type 'int (tsv_t *, bcf1_t *, void *)' (aka 'int (struct _tsv_t *, struct bcf1_t *, void *)') [-Wincompatible-function-pointer-types]
tsv_read_allele, // A0
^~~~~~~~~~~~~~~
plugins/munge.c:138:74: error: incompatible function pointer types initializing 'const int (*)(tsv_t *, bcf1_t *, void *)' (aka 'const int (*)(struct _tsv_t *, struct bcf1_t *, void *)') with an expression of type 'int (tsv_t *, bcf1_t *, void *)' (aka 'int (struct _tsv_t *, struct bcf1_t *, void *)') [-Wincompatible-function-pointer-types]
tsv_read_float, // SE
^~~~~~~~~~~~~~
plugins/munge.c:139:74: error: incompatible function pointer types initializing 'const int (*)(tsv_t *, bcf1_t *, void *)' (aka 'const int (*)(struct _tsv_t *, struct bcf1_t *, void *)') with an expression of type 'int (tsv_t *, bcf1_t *, void *)' (aka 'int (struct _tsv_t *, struct bcf1_t *, void *)') [-Wincompatible-function-pointer-types]
tsv_read_float, // LP
^~~~~~~~~~~~~~
plugins/munge.c:140:74: error: incompatible function pointer types initializing 'const int (*)(tsv_t *, bcf1_t *, void *)' (aka 'const int (*)(struct _tsv_t *, struct bcf1_t *, void *)') with an expression of type 'int (tsv_t *, bcf1_t *, void *)' (aka 'int (struct _tsv_t *, struct bcf1_t *, void *)') [-Wincompatible-function-pointer-types]
tsv_read_float, // AC
^~~~~~~~~~~~~~
plugins/munge.c:141:74: error: incompatible function pointer types initializing 'const int (*)(tsv_t *, bcf1_t *, void *)' (aka 'const int (*)(struct _tsv_t *, struct bcf1_t *, void *)') with an expression of type 'int (tsv_t *, bcf1_t *, void *)' (aka 'int (struct _tsv_t *, struct bcf1_t *, void *)') [-Wincompatible-function-pointer-types]
tsv_read_float, // NEFF
^~~~~~~~~~~~~~
fatal error: too many errors emitted, stopping now [-ferror-limit=]
20 errors generated.
gmake[1]: *** [Makefile:200: plugins/munge.so] Error 1
gmake[1]: *** Waiting for unfinished jobs....
gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/bcf-score/work/bcftools-1.17'
===> Compilation failed unexpectedly.
Try to set MAKE_JOBS_UNSAFE=yes and rebuild before reporting the failure to
the maintainer.
*** Error code 1
Stop.
make: stopped in /usr/ports/biology/bcf-score