[package - main-amd64-default][biology/wise] Failed for wise-2.4.1_1 in build

From: <pkg-fallout_at_FreeBSD.org>
Date: Sat, 01 Apr 2023 22:55:50 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:     ports@FreeBSD.org
Log URL:        https://pkg-status.freebsd.org/beefy18/data/main-amd64-default/pa097efdbe2f4_s9faa27f263/logs/wise-2.4.1_1.log
Build URL:      https://pkg-status.freebsd.org/beefy18/build.html?mastername=main-amd64-default&build=pa097efdbe2f4_s9faa27f263
Log:

=>> Building biology/wise
build started at Sat Apr  1 22:55:26 UTC 2023
port directory: /usr/ports/biology/wise
package name: wise-2.4.1_1
building for: FreeBSD main-amd64-default-job-02 14.0-CURRENT FreeBSD 14.0-CURRENT 1400085 amd64
maintained by: ports@FreeBSD.org
Makefile ident: 
Poudriere version: 3.2.8-23-ga7f8d188
Host OSVERSION: 1400073
Jail OSVERSION: 1400085
Job Id: 02




!!! Jail is newer than host. (Jail: 1400085, Host: 1400073) !!!
!!! This is not supported. !!!
!!! Host kernel must be same or newer than jail. !!!
!!! Expect build failures. !!!



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---Begin OPTIONS List---
===> The following configuration options are available for wise-2.4.1_1:
     DOCS=on: Build and/or install documentation
     EXAMPLES=on: Build and/or install examples
===> Use 'make config' to modify these settings
---End OPTIONS List---

--MAINTAINER--
ports@FreeBSD.org
--End MAINTAINER--

--CONFIGURE_ARGS--

--End CONFIGURE_ARGS--

--CONFIGURE_ENV--
PKG_CONFIG=pkgconf XDG_DATA_HOME=/wrkdirs/usr/ports/biology/wise/work  XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/wise/work  XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/wise/work/.cache  HOME=/wrkdirs/usr/ports/biology/wise/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/wise/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/wise/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh LANG=en_US.UTF-8 LC_ALL=en_US.UTF-8
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--End PLIST_SUB--

--SUB_LIST--
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=======================<phase: check-sanity   >============================
===>   NOTICE:

The wise port currently does not have a maintainer. As a result, it is
more likely to have unresolved issues, not be up-to-date, or even be removed in
the future. To volunteer to maintain this port, please create an issue at:

https://bugs.freebsd.org/bugzilla

More information about port maintainership is available at:

https://docs.freebsd.org/en/articles/contributing/#ports-contributing

===========================================================================
=======================<phase: pkg-depends    >============================
===>   wise-2.4.1_1 depends on file: /usr/local/sbin/pkg - not found
===>   Installing existing package /packages/All/pkg-1.19.1_1.pkg
[main-amd64-default-job-02] Installing pkg-1.19.1_1...
[main-amd64-default-job-02] Extracting pkg-1.19.1_1: .......... done
===>   wise-2.4.1_1 depends on file: /usr/local/sbin/pkg - found
===>   Returning to build of wise-2.4.1_1
===========================================================================
=======================<phase: fetch-depends  >============================
===========================================================================
=======================<phase: fetch          >============================
===>   NOTICE:

The wise port currently does not have a maintainer. As a result, it is
more likely to have unresolved issues, not be up-to-date, or even be removed in
the future. To volunteer to maintain this port, please create an issue at:

https://bugs.freebsd.org/bugzilla

More information about port maintainership is available at:

https://docs.freebsd.org/en/articles/contributing/#ports-contributing

<snip>
--- mott_api.o ---
cc  -O2 -pipe  -fstack-protector-strong -fno-strict-aliasing  -c   -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include  -c mott_api.c -o mott_api.o
--- gaplib.o ---
cc  -O2 -pipe  -fstack-protector-strong -fno-strict-aliasing  -c   -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include  -c gaplib.c -o gaplib.o
--- mott_api.o ---
mott_api.c:64:3: warning: call to undeclared library function 'free' with type 'void (void *)'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration]
  free(freq0);
  ^
mott_api.c:64:3: note: include the header <stdlib.h> or explicitly provide a declaration for 'free'
mott_api.c:179:16: warning: call to undeclared library function 'calloc' with type 'void *(unsigned long, unsigned long)'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration]
  h = (double*)calloc(*hmax-*hmin+1,sizeof(double))-*hmin;
               ^
mott_api.c:179:16: note: include the header <stdlib.h> or explicitly provide a declaration for 'calloc'
mott_api.c:207:12: warning: call to undeclared library function 'toupper' with type 'int (int)'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration]
      freq[toupper(seq[n])]++;
           ^
mott_api.c:207:12: note: include the header <ctype.h> or explicitly provide a declaration for 'toupper'
3 warnings generated.
--- wise2_mott_bridge.o ---
cc -O2 -pipe  -fstack-protector-strong -fno-strict-aliasing  -c   -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include  -I../../dynlibsrc -I../../base wise2_mott_bridge.c
--- libmott.a ---
ar ru libmott.a mott_api.o gaplib.o wise2_mott_bridge.o
ar: warning: creating libmott.a
if test -x /bin/ranlib; then /bin/ranlib libmott.a; else exit 0; fi
(cd socket ; /usr/bin/make CC="cc" CFLAGS="-O2 -pipe  -fstack-protector-strong -fno-strict-aliasing  -c   `pkg-config glib-2.0 --cflags`" libwisesocket.a )
--- functionserver.o ---
--- functionclient.o ---
--- functionserver.o ---
cc -O2 -pipe  -fstack-protector-strong -fno-strict-aliasing  -c   -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include  -I../base/ functionserver.c
--- functionclient.o ---
cc -O2 -pipe  -fstack-protector-strong -fno-strict-aliasing  -c   -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include  -I../base/ functionclient.c
functionclient.dy:193:24: warning: incompatible pointer types passing 'struct sockaddr_in *' to parameter of type 'const struct sockaddr *' [-Wincompatible-pointer-types]
  connect(out->socket, &server, sizeof(server));
                       ^~~~~~~
/usr/include/sys/socket.h:686:41: note: passing argument to parameter here
int     connect(int, const struct sockaddr *, socklen_t);
                                            ^
1 warning generated.
--- anonobj.o ---
cc -O2 -pipe  -fstack-protector-strong -fno-strict-aliasing  -c   -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include  -I../base/ anonobj.c
--- transferinterface.o ---
cc -O2 -pipe  -fstack-protector-strong -fno-strict-aliasing  -c   -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include  -I../base/ transferinterface.c
--- directsocketwrite.o ---
cc -O2 -pipe  -fstack-protector-strong -fno-strict-aliasing  -c   -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include  -I../base/ directsocketwrite.c
--- libwisesocket.a ---
ar ru libwisesocket.a functionserver.o functionclient.o anonobj.o transferinterface.o directsocketwrite.o
ar: warning: creating libwisesocket.a
if test -x /bin/ranlib; then /bin/ranlib libwisesocket.a; else exit 0; fi
(cd dnaindex ; /usr/bin/make CC="cc" CFLAGS="-O2 -pipe  -fstack-protector-strong -fno-strict-aliasing  -c   `pkg-config glib-2.0 --cflags`" all )
--- kmer_assembly.o ---
--- kmer_index_interface.o ---
--- kmer_assembly.o ---
cc -O2 -pipe  -fstack-protector-strong -fno-strict-aliasing  -c   -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include  -I../base/ -I../dynlibsrc/ -I../models kmer_assembly.c
--- kmer_index_interface.o ---
cc -O2 -pipe  -fstack-protector-strong -fno-strict-aliasing  -c   -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include  -I../base/ -I../dynlibsrc/ -I../models kmer_index_interface.c
--- kmer_direct.o ---
cc -O2 -pipe  -fstack-protector-strong -fno-strict-aliasing  -c   -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include  -I../base/ -I../dynlibsrc/ -I../models kmer_direct.c
--- kmer_assembly.o ---
kmer_assembly.dy:296:44: warning: format specifies type 'long' but the argument has type 'kmer_t' (aka 'long long') [-Wformat]
  fprintf(ofp,"Node %ld of sequence %s \n",node->number,buffer);
                    ~~~                    ^~~~~~~~~~~~
                    %lld
kmer_assembly.dy:302:104: warning: format specifies type 'long' but the argument has type 'kmer_t' (aka 'long long') [-Wformat]
    fprintf(ofp,"  ... prev ... %c, %d to %ld\n",node->prev[i]->base,node->prev[i]->sequence_label_len,node->prev[i]->prev->number);
                                          ~~~                                                          ^~~~~~~~~~~~~~~~~~~~~~~~~~~
                                          %lld
kmer_assembly.dy:309:104: warning: format specifies type 'long' but the argument has type 'kmer_t' (aka 'long long') [-Wformat]
    fprintf(ofp,"  ... next ... %c, %d to %ld\n",node->next[i]->base,node->next[i]->sequence_label_len,node->next[i]->next->number);
                                          ~~~                                                          ^~~~~~~~~~~~~~~~~~~~~~~~~~~
                                          %lld
kmer_assembly.dy:365:88: warning: format specifies type 'long' but the argument has type 'KmerAssemblyLink *' (aka 'struct KmerAssemblyLink *') [-Wformat]
  fprintf(stderr,"    ...unable to remove label %ld from link %ld (%d labels)\n",label,kal,kal->sequence_label_len);
                                                              ~~~                      ^~~
kmer_assembly.dy:367:36: warning: more '%' conversions than data arguments [-Wformat-insufficient-args]
    fprintf(stderr,"     [%ld] is %d label\n",kal->sequence_label[i]);
                                  ~^
--- kmer_hash.o ---
cc -O2 -pipe  -fstack-protector-strong -fno-strict-aliasing  -c   -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include  -I../base/ -I../dynlibsrc/ -I../models kmer_hash.c
kmer_hash.dy:318:41: warning: format specifies type 'unsigned long' but the argument has type 'kmer_t' (aka 'long long') [-Wformat]
  fprintf(stderr, "min_kmer: %016lx\n", khi->min_kmer);
                             ~~~~~~     ^~~~~~~~~~~~~
                             %016llx
kmer_hash.dy:319:41: warning: format specifies type 'unsigned long' but the argument has type 'kmer_t' (aka 'long long') [-Wformat]
  fprintf(stderr, "max_kmer: %016lx\n", khi->max_kmer);
                             ~~~~~~     ^~~~~~~~~~~~~
                             %016llx
2 warnings generated.
--- kmer_count.o ---
cc -O2 -pipe  -fstack-protector-strong -fno-strict-aliasing  -c   -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include  -I../base/ -I../dynlibsrc/ -I../models kmer_count.c
--- kmer_assembly.o ---
5 warnings generated.
--- kmer_glib_index.o ---
cc -O2 -pipe  -fstack-protector-strong -fno-strict-aliasing  -c   -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include  -I../base/ -I../dynlibsrc/ -I../models kmer_glib_index.c
--- singleseqspace.o ---
cc -O2 -pipe  -fstack-protector-strong -fno-strict-aliasing  -c   -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include  -I../base/ -I../dynlibsrc/ -I../models singleseqspace.c
--- dnamapping.o ---
cc -O2 -pipe  -fstack-protector-strong -fno-strict-aliasing  -c   -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include  -I../base/ -I../dynlibsrc/ -I../models dnamapping.c
--- largeseqreader.o ---
cc -O2 -pipe  -fstack-protector-strong -fno-strict-aliasing  -c   -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include  -I../base/ -I../dynlibsrc/ -I../models largeseqreader.c
--- kmer_assembly_untangler.o ---
cc -O2 -pipe  -fstack-protector-strong -fno-strict-aliasing  -c   -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include  -I../base/ -I../dynlibsrc/ -I../models kmer_assembly_untangler.c
--- kmer_assembly_contig.o ---
cc -O2 -pipe  -fstack-protector-strong -fno-strict-aliasing  -c   -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include  -I../base/ -I../dynlibsrc/ -I../models kmer_assembly_contig.c
--- kmer_assembly_untangler.o ---
kmer_assembly_untangler.dy:52:65: warning: cast to smaller integer type 'int' from 'KmerAssemblyLink *' (aka 'struct KmerAssemblyLink *') [-Wpointer-to-int-cast]
    fprintf(ofp,"%3d memory %d, from [%s] to [%s], base %c\n",i,(int)kap->stack[i],back,forw,kap->stack[i]->base);
                                                                ^~~~~~~~~~~~~~~~~~
kmer_assembly_untangler.dy:120:80: warning: format specifies type 'long' but the argument has type 'kmer_t' (aka 'long long') [-Wformat]
      fprintf(stderr,"TANGLE: Node %ld, %s has forward %d and back %d links\n",node->number,buffer,node->next_len,node->prev_len);
                                   ~~~                                         ^~~~~~~~~~~~
                                   %lld
kmer_assembly_untangler.dy:141:71: warning: format specifies type 'long' but the argument has type 'kmer_t' (aka 'long long') [-Wformat]
      fprintf(stderr,"Will attempt untangle starting at %ld to %ld\n",node->prev[i]->prev->number,node->number);
                                                        ~~~           ^~~~~~~~~~~~~~~~~~~~~~~~~~~
                                                        %lld
kmer_assembly_untangler.dy:141:99: warning: format specifies type 'long' but the argument has type 'kmer_t' (aka 'long long') [-Wformat]
      fprintf(stderr,"Will attempt untangle starting at %ld to %ld\n",node->prev[i]->prev->number,node->number);
                                                               ~~~                                ^~~~~~~~~~~~
                                                               %lld
kmer_assembly_untangler.dy:157:73: warning: format specifies type 'long' but the argument has type 'kmer_t' (aka 'long long') [-Wformat]
      fprintf(stderr,"RESOLVED: Node %ld [%s] Fully untangled now...\n",node->number,buffer);
                                     ~~~                                ^~~~~~~~~~~~
                                     %lld
kmer_assembly_untangler.dy:159:69: warning: format specifies type 'long' but the argument has type 'kmer_t' (aka 'long long') [-Wformat]
      fprintf(stderr,"UNRESOLVED: Node %ld [%s] still tangled...\n",node->number,buffer);
                                       ~~~                          ^~~~~~~~~~~~
                                       %lld
kmer_assembly_untangler.dy:444:89: warning: format specifies type 'long' but the argument has type 'kmer_t' (aka 'long long') [-Wformat]
    fprintf(stderr,"looking at node %ld with path length %d, next length %d depth %d\n",current->next->number,pathlen,current->next->next_len,current->sequence_label_len);
                                    ~~~                                                 ^~~~~~~~~~~~~~~~~~~~~
                                    %lld
kmer_assembly_untangler.dy:568:75: warning: incompatible pointer types passing 'long[10000]' to parameter of type 'int *' [-Wincompatible-pointer-types]
        lift_backward_tangled_tail(kai,newpath->stack[newpath->stack_len-1],path,transferred_label,transferred_pos,transferred_len);
                                                                                 ^~~~~~~~~~~~~~~~~
./kmer_assembly_untangler.h:174:116: note: passing argument to parameter 'start_label' here
void Wise2_lift_backward_tangled_tail(KmerAssemblyIndex * kai,KmerAssemblyLink * new,KmerAssemblyPath * tail,int * start_label,SinglePosSequence ** positions,int label_len);
                                                                                                                   ^
kmer_assembly_untangler.dy:746:149: warning: format specifies type 'long' but the argument has type 'kmer_t' (aka 'long long') [-Wformat]
    fprintf(stderr,"Moving stack position %d, depth %d, transfer %d, between %ld [%s] and %ld [%s]\n",i,kap->stack[i]->sequence_label_len,label_len,kap->stack[i]->prev->number,back,kap->stack[i]->next->number,forw);
                                                                             ~~~                                                                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~
                                                                             %lld
kmer_assembly_untangler.dy:746:182: warning: format specifies type 'long' but the argument has type 'kmer_t' (aka 'long long') [-Wformat]
    fprintf(stderr,"Moving stack position %d, depth %d, transfer %d, between %ld [%s] and %ld [%s]\n",i,kap->stack[i]->sequence_label_len,label_len,kap->stack[i]->prev->number,back,kap->stack[i]->next->number,forw);
                                                                                          ~~~                                                                                        ^~~~~~~~~~~~~~~~~~~~~~~~~~~
                                                                                          %lld
--- kmer_assembly_error.o ---
cc -O2 -pipe  -fstack-protector-strong -fno-strict-aliasing  -c   -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include  -I../base/ -I../dynlibsrc/ -I../models kmer_assembly_error.c
--- kmer_assembly_untangler.o ---
10 warnings generated.
--- assembly.o ---
cc -O2 -pipe  -fstack-protector-strong -fno-strict-aliasing  -c   -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include  -I../base/ -I../dynlibsrc/ -I../models assembly.c
--- kmer_assembly_error.o ---
kmer_assembly_error.dy:93:66: warning: format specifies type 'long' but the argument has type 'kmer_t' (aka 'long long') [-Wformat]
      fprintf(stderr,"Marking node (%ld) [%s] as next tangled\n",node->number,buffer);
                                    ~~~                          ^~~~~~~~~~~~
                                    %lld
kmer_assembly_error.dy:105:66: warning: format specifies type 'long' but the argument has type 'kmer_t' (aka 'long long') [-Wformat]
      fprintf(stderr,"Marking node (%ld) [%s] as prev tangled\n",node->number,buffer);
                                    ~~~                          ^~~~~~~~~~~~
                                    %lld
kmer_assembly_error.dy:351:127: warning: format specifies type 'int' but the argument has type 'int *' [-Wformat]
        fprintf(stderr,"in considering indel (%d, path %d), real (%c) and error (%c) do not agree at position %d,%d\n",delete_length,current_path,real->base,error->base,real_pos,error_pos);
                                                       ~~                                                                            ^~~~~~~~~~~~
3 warnings generated.
--- assembly_stream_interface.o ---
cc -O2 -pipe  -fstack-protector-strong -fno-strict-aliasing  -c   -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include  -I../base/ -I../dynlibsrc/ -I../models assembly_stream_interface.c
--- assembly_stream_fasta.o ---
cc -O2 -pipe  -fstack-protector-strong -fno-strict-aliasing  -c   -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include  -I../base/ -I../dynlibsrc/ -I../models assembly_stream_fasta.c
--- assembly_sanger_project.o ---
cc -O2 -pipe  -fstack-protector-strong -fno-strict-aliasing  -c   -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include  -I../base/ -I../dynlibsrc/ -I../models assembly_sanger_project.c
--- assembly_stream_cons.o ---
cc -O2 -pipe  -fstack-protector-strong -fno-strict-aliasing  -c   -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include  -I../base/ -I../dynlibsrc/ -I../models assembly_stream_cons.c
--- compressed_protein_index.o ---
cc -O2 -pipe  -fstack-protector-strong -fno-strict-aliasing  -c   -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include  -I../base/ -I../dynlibsrc/ -I../models compressed_protein_index.c
compressed_protein_index.dy:223:10: error: incompatible pointer to integer conversion returning 'void *' from a function with result type 'boolean' (aka 'int') [-Wint-conversion]
  return NULL;
         ^~~~
/usr/include/sys/_null.h:34:14: note: expanded from macro 'NULL'
#define NULL    ((void *)0)
                ^~~~~~~~~~~
1 error generated.
*** [compressed_protein_index.o] Error code 1

make[2]: stopped in /wrkdirs/usr/ports/biology/wise/work/wise2.4.1/src/dnaindex
1 error

make[2]: stopped in /wrkdirs/usr/ports/biology/wise/work/wise2.4.1/src/dnaindex
*** [realall] Error code 2

make[1]: stopped in /wrkdirs/usr/ports/biology/wise/work/wise2.4.1/src
1 error

make[1]: stopped in /wrkdirs/usr/ports/biology/wise/work/wise2.4.1/src
===> 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/wise