[package - main-powerpc64le-default][biology/wise] Failed for wise-2.4.1_1 in build
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Date: Wed, 19 Apr 2023 20:17:36 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/foul2/data/main-powerpc64le-default/p3034bd2d70e6_sb754d7faaf/logs/wise-2.4.1_1.log
Build URL: https://pkg-status.freebsd.org/foul2/build.html?mastername=main-powerpc64le-default&build=p3034bd2d70e6_sb754d7faaf
Log:
=>> Building biology/wise
build started at Wed Apr 19 20:15:11 UTC 2023
port directory: /usr/ports/biology/wise
package name: wise-2.4.1_1
building for: FreeBSD main-powerpc64le-default-job-13 14.0-CURRENT FreeBSD 14.0-CURRENT 1400082 powerpc
maintained by: ports@FreeBSD.org
Makefile ident:
Poudriere version: 3.2.8-23-ga7f8d188
Host OSVERSION: 1400073
Jail OSVERSION: 1400082
Job Id: 13
!!! Jail is newer than host. (Jail: 1400082, 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
--End CONFIGURE_ENV--
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--End PLIST_SUB--
--SUB_LIST--
PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/wise DOCSDIR=/usr/local/share/doc/wise EXAMPLESDIR=/usr/local/share/examples/wise WWWDIR=/usr/local/www/wise ETCDIR=/usr/local/etc/wise
--End SUB_LIST--
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--End resource limits--
=======================<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-powerpc64le-default-job-13] Installing pkg-1.19.1_1...
[main-powerpc64le-default-job-13] 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
===> Fetching all distfiles required by wise-2.4.1_1 for building
<snip>
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 ---
--- transferinterface.o ---
--- 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_assembly.o ---
5 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_hash.o ---
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_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
largeseqreader.dy:44:9: warning: result of comparison of constant -1 with expression of type 'char' is always false [-Wtautological-constant-out-of-range-compare]
if( c == EOF ) {
~ ^ ~~~
largeseqreader.dy:54:25: warning: result of comparison of constant -1 with expression of type 'char' is always true [-Wtautological-constant-out-of-range-compare]
while( (c=fgetc(ifp)) != EOF ) {
~~~~~~~~~~~~~~ ^ ~~~
largeseqreader.dy:63:27: warning: result of comparison of constant -1 with expression of type 'char' is always true [-Wtautological-constant-out-of-range-compare]
while( (c=fgetc(ifp)) != EOF ) {
~~~~~~~~~~~~~~ ^ ~~~
largeseqreader.dy:74:25: warning: result of comparison of constant -1 with expression of type 'char' is always true [-Wtautological-constant-out-of-range-compare]
while( (c=fgetc(ifp)) != EOF ) {
~~~~~~~~~~~~~~ ^ ~~~
4 warnings generated.
--- 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