[package - head-i386-default][biology/paml] Failed for paml-4.9j in build
pkg-fallout at FreeBSD.org
pkg-fallout at FreeBSD.org
Thu Aug 20 08:52:46 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://beefy17.nyi.freebsd.org/data/head-i386-default/p545479_s364329/logs/paml-4.9j.log
Build URL: http://beefy17.nyi.freebsd.org/build.html?mastername=head-i386-default&build=p545479_s364329
Log:
=>> Building biology/paml
build started at Thu Aug 20 08:52:31 UTC 2020
port directory: /usr/ports/biology/paml
package name: paml-4.9j
building for: FreeBSD head-i386-default-job-05 13.0-CURRENT FreeBSD 13.0-CURRENT 1300109 i386
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: 05
!!! 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. !!!
---Begin Environment---
SHELL=/bin/csh
UNAME_p=i386
UNAME_m=i386
OSVERSION=1300109
UNAME_v=FreeBSD 13.0-CURRENT 1300109
UNAME_r=13.0-CURRENT
BLOCKSIZE=K
MAIL=/var/mail/root
STATUS=1
HOME=/root
PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin
LOCALBASE=/usr/local
USER=root
LIBEXECPREFIX=/usr/local/libexec/poudriere
POUDRIERE_VERSION=3.2.8-5-gc81843e5
MASTERMNT=/usr/local/poudriere/data/.m/head-i386-default/ref
POUDRIERE_BUILD_TYPE=bulk
PACKAGE_BUILDING=yes
SAVED_TERM=
PWD=/usr/local/poudriere/data/.m/head-i386-default/ref/.p/pool
P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS
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SCRIPTPREFIX=/usr/local/share/poudriere
OLDPWD=/usr/local/poudriere/data/.m/head-i386-default/ref/.p
SCRIPTPATH=/usr/local/share/poudriere/bulk.sh
POUDRIEREPATH=/usr/local/bin/poudriere
---End Environment---
---Begin Poudriere Port Flags/Env---
PORT_FLAGS=
PKGENV=
FLAVOR=
DEPENDS_ARGS=
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="cc" CFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" -fstack-protector-strong " LIBS="" CXX="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"
--End MAKE_ENV--
--PLIST_SUB--
PORTDOCS="" PORTEXAMPLES="" OSREL=13.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/paml" EXAMPLESDIR="share/examples/paml" DATADIR="share/paml" WWWDIR="www/paml" ETCDIR="etc/paml"
--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
--End SUB_LIST--
---Begin make.conf---
USE_PACKAGE_DEPENDS=yes
BATCH=yes
WRKDIRPREFIX=/wrkdirs
PORTSDIR=/usr/ports
PACKAGES=/packages
DISTDIR=/distfiles
PACKAGE_BUILDING=yes
PACKAGE_BUILDING_FLAVORS=yes
MACHINE=i386
MACHINE_ARCH=i386
ARCH=${MACHINE_ARCH}
#### /usr/local/etc/poudriere.d/make.conf ####
# XXX: We really need this but cannot use it while 'make checksum' does not
# try the next mirror on checksum failure. It currently retries the same
# failed mirror and then fails rather then trying another. It *does*
# try the next if the size is mismatched though.
#MASTER_SITE_FREEBSD=yes
# Build ALLOW_MAKE_JOBS_PACKAGES with 2 jobs
MAKE_JOBS_NUMBER=2
#### /usr/ports/Mk/Scripts/ports_env.sh ####
_CCVERSION_921dbbb2=FreeBSD clang version 11.0.0 (git at github.com:llvm/llvm-project.git llvmorg-11.0.0-rc1-47-gff47911ddfc) Target: i386-unknown-freebsd13.0 Thread model: posix InstalledDir: /usr/bin
_ALTCCVERSION_921dbbb2=none
_CXXINTERNAL_acaad9ca=FreeBSD clang version 11.0.0 (git at github.com:llvm/llvm-project.git llvmorg-11.0.0-rc1-47-gff47911ddfc) Target: i386-unknown-freebsd13.0 Thread model: posix InstalledDir: /usr/bin "/usr/bin/ld" "--eh-frame-hdr" "-dynamic-linker" "/libexec/ld-elf.so.1" "--hash-style=both" "--enable-new-dtags" "-m" "elf_i386_fbsd" "-o" "a.out" "/usr/lib/crt1.o" "/usr/lib/crti.o" "/usr/lib/crtbegin.o" "-L/usr/lib" "/dev/null" "-lc++" "-lm" "-lgcc" "--as-needed" "-lgcc_s" "--no-as-needed" "-lc" "-lgcc" "--as-needed" "-lgcc_s" "--no-as-needed" "/usr/lib/crtend.o" "/usr/lib/crtn.o"
CC_OUTPUT_921dbbb2_58173849=yes
CC_OUTPUT_921dbbb2_9bdba57c=yes
CC_OUTPUT_921dbbb2_6a4fe7f5=yes
CC_OUTPUT_921dbbb2_6bcac02b=yes
CC_OUTPUT_921dbbb2_67d20829=yes
CC_OUTPUT_921dbbb2_bfa62e83=yes
CC_OUTPUT_921dbbb2_f0b4d593=yes
CC_OUTPUT_921dbbb2_308abb44=yes
CC_OUTPUT_921dbbb2_f00456e5=yes
CC_OUTPUT_921dbbb2_65ad290d=yes
CC_OUTPUT_921dbbb2_f2776b26=yes
CC_OUTPUT_921dbbb2_b2657cc3=yes
CC_OUTPUT_921dbbb2_380987f7=yes
CC_OUTPUT_921dbbb2_160933ec=yes
CC_OUTPUT_921dbbb2_fb62803b=yes
_OBJC_CCVERSION_921dbbb2=FreeBSD clang version 11.0.0 (git at github.com:llvm/llvm-project.git llvmorg-11.0.0-rc1-47-gff47911ddfc) Target: i386-unknown-freebsd13.0 Thread model: posix InstalledDir: /usr/bin
_OBJC_ALTCCVERSION_921dbbb2=none
ARCH=i386
OPSYS=FreeBSD
_OSRELEASE=13.0-CURRENT
OSREL=13.0
OSVERSION=1300109
PYTHONBASE=/usr/local
CONFIGURE_MAX_CMD_LEN=524288
HAVE_PORTS_ENV=1
#### Misc Poudriere ####
GID=0
UID=0
---End make.conf---
--Resource limits--
cpu time (seconds, -t) unlimited
file size (512-blocks, -f) unlimited
data seg size (kbytes, -d) 524288
stack size (kbytes, -s) 65536
core file size (512-blocks, -c) unlimited
max memory size (kbytes, -m) unlimited
locked memory (kbytes, -l) unlimited
max user processes (-u) 89999
open files (-n) 1024
virtual mem size (kbytes, -v) unlimited
swap limit (kbytes, -w) unlimited
socket buffer size (bytes, -b) unlimited
pseudo-terminals (-p) unlimited
kqueues (-k) unlimited
umtx shared locks (-o) unlimited
--End resource limits--
=======================<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-i386-default-job-05] Installing pkg-1.14.7...
[head-i386-default-job-05] 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
===========================================================================
=======================<phase: checksum >============================
===> License GPLv3 accepted by the user
===> Fetching all distfiles required by paml-4.9j for building
=> SHA256 Checksum OK for paml4.9j.tgz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract >============================
===> License GPLv3 accepted by the user
===> Fetching all distfiles required by paml-4.9j for building
===> Extracting for paml-4.9j
=> SHA256 Checksum OK for paml4.9j.tgz.
===========================================================================
=======================<phase: patch-depends >============================
===========================================================================
=======================<phase: patch >============================
===> Patching for paml-4.9j
===> Converting DOS text files to UNIX text files
===========================================================================
=======================<phase: build-depends >============================
===> paml-4.9j depends on package: gmake>=4.3 - not found
===> Installing existing package /packages/All/gmake-4.3_2.txz
[head-i386-default-job-05] Installing gmake-4.3_2...
[head-i386-default-job-05] `-- Installing gettext-runtime-0.21...
[head-i386-default-job-05] | `-- Installing indexinfo-0.3.1...
[head-i386-default-job-05] | `-- Extracting indexinfo-0.3.1: .... done
[head-i386-default-job-05] `-- Extracting gettext-runtime-0.21: .......... done
[head-i386-default-job-05] Extracting gmake-4.3_2: .......... done
===> paml-4.9j depends on package: gmake>=4.3 - found
===> Returning to build of paml-4.9j
===========================================================================
=======================<phase: lib-depends >============================
===========================================================================
=======================<phase: configure >============================
===> Configuring for paml-4.9j
===========================================================================
=======================<phase: build >============================
===> Building for paml-4.9j
gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/paml/work/paml4.9j/src'
cc -O3 -o baseml baseml.c tools.c -lm
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: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];
^ ~~~~~~~~~~~~~~~~
23 warnings generated.
ld: error: duplicate symbol: OutTreeOptions
>>> defined at baseml.c
>>> /tmp/baseml-cb2243.o:(OutTreeOptions)
>>> defined at tools.c
>>> /tmp/tools-352a72.o:(.bss+0xAFCD90)
ld: error: duplicate symbol: SeqTypes
>>> defined at baseml.c
>>> /tmp/baseml-cb2243.o:(SeqTypes)
>>> defined at tools.c
>>> /tmp/tools-352a72.o:(.bss+0xAFCD8C)
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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