[package - head-armv6-default][biology/paml] Failed for paml-4.9j in build
pkg-fallout at FreeBSD.org
pkg-fallout at FreeBSD.org
Sun Aug 23 01:24:12 UTC 2020
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: jrm at FreeBSD.org
Last committer: jrm at FreeBSD.org
Ident: $FreeBSD: head/biology/paml/Makefile 518150 2019-11-22 15:32:40Z jrm $
Log URL: http://beefy8.nyi.freebsd.org/data/head-armv6-default/p545479_s364329/logs/paml-4.9j.log
Build URL: http://beefy8.nyi.freebsd.org/build.html?mastername=head-armv6-default&build=p545479_s364329
Log:
=>> Building biology/paml
build started at Sun Aug 23 01:20:49 UTC 2020
port directory: /usr/ports/biology/paml
package name: paml-4.9j
building for: FreeBSD head-armv6-default-job-13 13.0-CURRENT FreeBSD 13.0-CURRENT 1300109 arm
maintained by: jrm at FreeBSD.org
Makefile ident: $FreeBSD: head/biology/paml/Makefile 518150 2019-11-22 15:32:40Z jrm $
Poudriere version: 3.2.8-5-gc81843e5
Host OSVERSION: 1300100
Jail OSVERSION: 1300109
Job Id: 13
!!! Jail is newer than host. (Jail: 1300109, Host: 1300100) !!!
!!! This is not supported. !!!
!!! Host kernel must be same or newer than jail. !!!
!!! Expect build failures. !!!
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MAKE_ARGS=
---End Poudriere Port Flags/Env---
---Begin OPTIONS List---
===> The following configuration options are available for paml-4.9j:
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--
jrm at FreeBSD.org
--End MAINTAINER--
--CONFIGURE_ARGS--
--End CONFIGURE_ARGS--
--CONFIGURE_ENV--
MAKE=gmake XDG_DATA_HOME=/wrkdirs/usr/ports/biology/paml/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/paml/work HOME=/wrkdirs/usr/ports/biology/paml/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/paml/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh
--End CONFIGURE_ENV--
--MAKE_ENV--
XDG_DATA_HOME=/wrkdirs/usr/ports/biology/paml/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/paml/work HOME=/wrkdirs/usr/ports/biology/paml/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/paml/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin NO_PIE=yes MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES PREFIX=/usr/local LOCALBASE=/usr/local CC="/nxb-bin/usr/bin/cc" CFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " CPP="/nxb-bin/usr/bin/cpp" CPPFLAGS="" LDFLAGS=" -fstack-protector-strong " LIBS="" CXX="/nxb-bin/usr/bin/c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444"
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--End PLIST_SUB--
--SUB_LIST--
PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/paml DOCSDIR=/usr/local/share/doc/paml EXAMPLESDIR=/usr/local/share/examples/paml WWWDIR=/usr/local/www/paml ETCDIR=/usr/local/etc/paml
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ARCH=${MACHINE_ARCH}
#### /usr/local/etc/poudriere.d/make.conf ####
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=======================<phase: check-sanity >============================
===> License GPLv3 accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===> paml-4.9j depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.14.7.txz
[head-armv6-default-job-13] Installing pkg-1.14.7...
[head-armv6-default-job-13] Extracting pkg-1.14.7: .......... done
===> paml-4.9j depends on file: /usr/local/sbin/pkg - found
===> Returning to build of paml-4.9j
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> License GPLv3 accepted by the user
===> Fetching all distfiles required by paml-4.9j for building
===========================================================================
<snip>
qemu: unsupported syscall: 574 (calling anyway)
qemu: unsupported syscall: 574 (calling anyway)
qemu: unsupported syscall: 574 (calling anyway)
qemu: unsupported syscall: 574 (calling anyway)
qemu: unsupported syscall: 574 (calling anyway)
qemu: unsupported syscall: 574 (calling anyway)
qemu: unsupported syscall: 574 (calling anyway)
qemu: unsupported syscall: 574 (calling anyway)
qemu: unsupported syscall: 574 (calling anyway)
qemu: unsupported syscall: 574 (calling anyway)
qemu: unsupported syscall: 574 (calling anyway)
qemu: unsupported syscall: 574 (calling anyway)
qemu: unsupported syscall: 574 (calling anyway)
qemu: unsupported syscall: 574 (calling anyway)
qemu: unsupported syscall: 574 (calling anyway)
qemu: unsupported syscall: 574 (calling anyway)
In file included from baseml.c:131:
./treesub.c:86:7: warning: assigning to 'unsigned char *' from 'char *' converts between pointers to integer types with different sign [-Wpointer-sign]
zt = (char*)malloc(com.ls*lpatt * sizeof(char));
^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./treesub.c:105:24: warning: passing 'unsigned char *' to parameter of type 'const char *' converts between pointers to integer types with different sign [-Wpointer-sign]
k = strcmp(zt + h*lpatt, zt + p2s[ip] * lpatt);
^~~~~~~~~~~~
/usr/include/string.h:82:25: note: passing argument to parameter here
int strcmp(const char *, const char *) __pure;
^
In file included from baseml.c:131:
./treesub.c:105:38: warning: passing 'unsigned char *' to parameter of type 'const char *' converts between pointers to integer types with different sign [-Wpointer-sign]
k = strcmp(zt + h*lpatt, zt + p2s[ip] * lpatt);
^~~~~~~~~~~~~~~~~~~~
/usr/include/string.h:82:39: note: passing argument to parameter here
int strcmp(const char *, const char *) __pure;
^
In file included from baseml.c:131:
./treesub.c:143:21: warning: passing 'unsigned char *' to parameter of type 'const char *' converts between pointers to integer types with different sign [-Wpointer-sign]
k = strcmp(zt + h*lpatt, zt + p2s[ip] * lpatt);
^~~~~~~~~~~~
/usr/include/string.h:82:25: note: passing argument to parameter here
int strcmp(const char *, const char *) __pure;
^
In file included from baseml.c:131:
./treesub.c:143:35: warning: passing 'unsigned char *' to parameter of type 'const char *' converts between pointers to integer types with different sign [-Wpointer-sign]
k = strcmp(zt + h*lpatt, zt + p2s[ip] * lpatt);
^~~~~~~~~~~~~~~~~~~~
/usr/include/string.h:82:39: note: passing argument to parameter here
int strcmp(const char *, const char *) __pure;
^
In file included from baseml.c:131:
./treesub.c:256:7: warning: assigning to 'unsigned char *' from 'char *' converts between pointers to integer types with different sign [-Wpointer-sign]
zt = (char*)malloc(npatt0*lpatt * sizeof(char));
^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./treesub.c:280:24: warning: passing 'unsigned char *' to parameter of type 'const char *' converts between pointers to integer types with different sign [-Wpointer-sign]
k = strcmp(zt + h*lpatt, zt + p2s[ip] * lpatt);
^~~~~~~~~~~~
/usr/include/string.h:82:25: note: passing argument to parameter here
int strcmp(const char *, const char *) __pure;
^
In file included from baseml.c:131:
./treesub.c:280:38: warning: passing 'unsigned char *' to parameter of type 'const char *' converts between pointers to integer types with different sign [-Wpointer-sign]
k = strcmp(zt + h*lpatt, zt + p2s[ip] * lpatt);
^~~~~~~~~~~~~~~~~~~~
/usr/include/string.h:82:39: note: passing argument to parameter here
int strcmp(const char *, const char *) __pure;
^
In file included from baseml.c:131:
./treesub.c:313:21: warning: passing 'unsigned char *' to parameter of type 'const char *' converts between pointers to integer types with different sign [-Wpointer-sign]
k = strcmp(zt + h*lpatt, zt + p2s[ip] * lpatt);
^~~~~~~~~~~~
/usr/include/string.h:82:25: note: passing argument to parameter here
int strcmp(const char *, const char *) __pure;
^
In file included from baseml.c:131:
./treesub.c:313:35: warning: passing 'unsigned char *' to parameter of type 'const char *' converts between pointers to integer types with different sign [-Wpointer-sign]
k = strcmp(zt + h*lpatt, zt + p2s[ip] * lpatt);
^~~~~~~~~~~~~~~~~~~~
/usr/include/string.h:82:39: note: passing argument to parameter here
int strcmp(const char *, const char *) __pure;
^
In file included from baseml.c:131:
./treesub.c:1310:30: warning: incompatible pointer types passing 'char *[7000]' to parameter of type 'unsigned char **' [-Wincompatible-pointer-types]
printSeqs(ftmp, com.z, com.spname, com.ns, com.ls, com.npatt, com.fpatt, NULL, keep, 1);
^~~~~~~~~~
./paml.h:150:63: note: passing argument to parameter 'spnames' here
void printSeqs(FILE *fout, unsigned char *z[], unsigned char *spnames[], int ns, int ls, int npatt, double fpatt[], int *pose, char keep[], int format);
^
In file included from baseml.c:131:
./treesub.c:1404:7: warning: assigning to 'unsigned char *' from 'char *' converts between pointers to integer types with different sign [-Wpointer-sign]
zt = (char*)malloc(com.ls*lpatt * sizeof(char));
^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./treesub.c:1427:27: warning: passing 'unsigned char *' to parameter of type 'const char *' converts between pointers to integer types with different sign [-Wpointer-sign]
k = strcmp(zt + h*lpatt, zt + p2s[ip] * lpatt);
^~~~~~~~~~~~
/usr/include/string.h:82:25: note: passing argument to parameter here
int strcmp(const char *, const char *) __pure;
^
In file included from baseml.c:131:
./treesub.c:1427:41: warning: passing 'unsigned char *' to parameter of type 'const char *' converts between pointers to integer types with different sign [-Wpointer-sign]
k = strcmp(zt + h*lpatt, zt + p2s[ip] * lpatt);
^~~~~~~~~~~~~~~~~~~~
/usr/include/string.h:82:39: note: passing argument to parameter here
int strcmp(const char *, const char *) __pure;
^
In file included from baseml.c:131:
./treesub.c:1476:24: warning: passing 'unsigned char *' to parameter of type 'const char *' converts between pointers to integer types with different sign [-Wpointer-sign]
k = strcmp(zt + h*lpatt, zt + p2s[ip] * lpatt);
^~~~~~~~~~~~
/usr/include/string.h:82:25: note: passing argument to parameter here
int strcmp(const char *, const char *) __pure;
^
In file included from baseml.c:131:
./treesub.c:1476:38: warning: passing 'unsigned char *' to parameter of type 'const char *' converts between pointers to integer types with different sign [-Wpointer-sign]
k = strcmp(zt + h*lpatt, zt + p2s[ip] * lpatt);
^~~~~~~~~~~~~~~~~~~~
/usr/include/string.h:82:39: note: passing argument to parameter here
int strcmp(const char *, const char *) __pure;
^
In file included from baseml.c:131:
./treesub.c:2973:19: warning: result of comparison of constant -1 with expression of type 'char' is always false [-Wtautological-constant-out-of-range-compare]
if (line[i] == EOF)
~~~~~~~ ^ ~~~
./treesub.c:4650:37: warning: assigning to 'char *' from 'unsigned char *' converts between pointers to integer types with different sign [-Wpointer-sign]
for (i = 0; i < ns0; i++) z0[i] = com.z[i];
^ ~~~~~~~~
./treesub.c:4775:24: warning: assigning to 'char *' from 'unsigned char *' converts between pointers to integer types with different sign [-Wpointer-sign]
FOR(i, ns0) { z0[i] = com.z[i]; spname0[i] = com.spname[i]; }
^ ~~~~~~~~
./treesub.c:4790:19: warning: assigning to 'unsigned char *' from 'char *' converts between pointers to integer types with different sign [-Wpointer-sign]
com.z[i] = z0[order[i]];
^ ~~~~~~~~~~~~
./treesub.c:5897:23: warning: passing 'char *' to parameter of type 'unsigned char *' converts between pointers to integer types with different sign [-Wpointer-sign]
print1seq(fout, zanc + j*com.npatt, lst, com.pose);
^~~~~~~~~~~~~~~~~~
./treesub.c:1861:41: note: passing argument to parameter 'z' here
int print1seq(FILE*fout, unsigned char *z, int ls, int pose[])
^
./treesub.c:8695:15: warning: using the result of an assignment as a condition without parentheses [-Wparentheses]
if (pch = strchr(nodes[i].annotation, '#'))
~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
./treesub.c:8695:15: note: place parentheses around the assignment to silence this warning
if (pch = strchr(nodes[i].annotation, '#'))
^
( )
./treesub.c:8695:15: note: use '==' to turn this assignment into an equality comparison
if (pch = strchr(nodes[i].annotation, '#'))
^
==
./treesub.c:8843:30: warning: assigning to 'char *' from 'unsigned char *' converts between pointers to integer types with different sign [-Wpointer-sign]
data.z[locus][i] = com.z[i];
^ ~~~~~~~~
./treesub.c:9087:42: warning: assigning to 'unsigned char *' from 'char *' converts between pointers to integer types with different sign [-Wpointer-sign]
for (i = 0; i < com.ns; i++) com.z[i] = data.z[locus][i];
^ ~~~~~~~~~~~~~~~~
qemu: unsupported syscall: 574 (calling anyway)
24 warnings generated.
qemu: unsupported syscall: 574 (calling anyway)
qemu: unsupported syscall: 574 (calling anyway)
qemu: unsupported syscall: 574 (calling anyway)
qemu: unsupported syscall: 574 (calling anyway)
qemu: unsupported syscall: 574 (calling anyway)
qemu: unsupported syscall: 574 (calling anyway)
qemu: unsupported syscall: 574 (calling anyway)
qemu: unsupported syscall: 574 (calling anyway)
qemu: unsupported syscall: 574 (calling anyway)
qemu: unsupported syscall: 574 (calling anyway)
qemu: unsupported syscall: 574 (calling anyway)
qemu: unsupported syscall: 574 (calling anyway)
qemu: unsupported syscall: 574 (calling anyway)
qemu: unsupported syscall: 574 (calling anyway)
qemu: unsupported syscall: 574 (calling anyway)
qemu: unsupported syscall: 574 (calling anyway)
qemu: unsupported syscall: 574 (calling anyway)
qemu: unsupported syscall: 574 (calling anyway)
qemu: unsupported syscall: 574 (calling anyway)
qemu: unsupported syscall: 574 (calling anyway)
qemu: unsupported syscall: 574 (calling anyway)
qemu: unsupported syscall: 574 (calling anyway)
qemu: unsupported syscall: 574 (calling anyway)
qemu: unsupported syscall: 574 (calling anyway)
qemu: unsupported syscall: 574 (calling anyway)
qemu: unsupported syscall: 574 (calling anyway)
qemu: unsupported syscall: 574 (calling anyway)
qemu: unsupported syscall: 574 (calling anyway)
ld: error: duplicate symbol: OutTreeOptions
>>> defined at baseml.c
>>> /tmp/baseml-fa1b7a.o:(OutTreeOptions)
>>> defined at tools.c
>>> /tmp/tools-8e01b0.o:(.bss+0xAFCD14)
ld: error: duplicate symbol: SeqTypes
>>> defined at baseml.c
>>> /tmp/baseml-fa1b7a.o:(SeqTypes)
>>> defined at tools.c
>>> /tmp/tools-8e01b0.o:(.bss+0xAFCD10)
cc: error: linker command failed with exit code 1 (use -v to see invocation)
gmake[1]: *** [Makefile:12: baseml] Error 1
gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/paml/work/paml4.9j/src'
*** Error code 2
Stop.
make: stopped in /usr/ports/biology/paml
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