Date: Fri, 15 Aug 2014 15:57:04 GMT From: pkg-fallout@FreeBSD.org To: mzaki@m.u-tokyo.ac.jp Cc: pkg-fallout@FreeBSD.org Subject: [package - head-amd64-default][biology/mrbayes] Failed for mrbayes-3.1.2_1 in build Message-ID: <201408151557.s7FFv4iH020243@beefy2.isc.freebsd.org>
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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: mzaki@m.u-tokyo.ac.jp Last committer: mat@FreeBSD.org Ident: $FreeBSD: head/biology/mrbayes/Makefile 340722 2014-01-22 17:00:46Z mat $ Log URL: http://beefy2.isc.freebsd.org/data/head-amd64-default/2014-08-14_16h56m28s/logs/mrbayes-3.1.2_1.log Build URL: http://beefy2.isc.freebsd.org/build.html?mastername=head-amd64-default&build=2014-08-14_16h56m28s Log: ====>> Building biology/mrbayes build started at Fri Aug 15 15:56:35 UTC 2014 port directory: /usr/ports/biology/mrbayes building for: FreeBSD head-amd64-default-job-05 11.0-CURRENT FreeBSD 11.0-CURRENT r269901 amd64 maintained by: mzaki@m.u-tokyo.ac.jp Makefile ident: $FreeBSD: head/biology/mrbayes/Makefile 340722 2014-01-22 17:00:46Z mat $ Poudriere version: 3.1-pre Host OSVERSION: 1100027 Jail OSVERSION: 1100028 !!! Jail is newer than host. (Jail: 1100028, Host: 1100027) !!! !!! This is not supported. !!! !!! Host kernel must be same or newer than jail. !!! !!! Expect build failures. !!! ---Begin Environment--- OSVERSION=1100028 UNAME_v=FreeBSD 11.0-CURRENT r269901 UNAME_r=11.0-CURRENT BLOCKSIZE=K MAIL=/var/mail/root STATUS=1 SAVED_TERM=screen MASTERMNT=/usr/local/poudriere/data/.m/head-amd64-default/ref PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/games:/usr/local/sbin:/usr/local/bin:/root/bin POUDRIERE_BUILD_TYPE=bulk PKGNAME=mrbayes-3.1.2_1 OLDPWD=/root/poudriere PWD=/usr/local/poudriere/data/.m/head-amd64-default/ref/.p/pool MASTERNAME=head-amd64-default USER=root HOME=/root POUDRIERE_VERSION=3.1-pre LOCALBASE=/usr/local PACKAGE_BUILDING=yes ---End Environment--- ---Begin OPTIONS List--- ===> The following configuration options are available for mrbayes-3.1.2_1: EXAMPLES=on: Build and/or install examples ===> Use 'make config' to modify these settings ---End OPTIONS List--- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/mrbayes/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/mrbayes/work HOME=/wrkdirs/usr/ports/biology/mrbayes/work TMPDIR="/tmp" MAKE=gmake SHELL=/bin/sh CONFIG_SHELL=/bin/sh --End CONFIGURE_ENV-- --MAKE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/mrbayes/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/mrbayes/work HOME=/wrkdirs/usr/ports/biology/mrbayes/work TMPDIR="/tmp" NO_PIE=yes SHELL=/bin/sh NO_LINT=YES PREFIX=/usr/local LOCALBASE=/usr/local LIBDIR="/usr/lib" CC="cc" CFLAGS="-O2 -pipe -fno-strict-aliasing" CPP="cpp" CPPFLAGS="-I/usr/local/include" LDFLAGS=" -L/usr/local/lib" LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fno-strict-aliasing " MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install -s -o root -g wheel -m 555" BSD_INSTALL_LIB="install -s -o root -g wheel -m 444" BSD_INSTALL_SCRIPT="install -o root -g wheel -m 555" BSD_INSTALL_DATA="install -o root -g wheel -m 444" BSD_INSTALL_MAN="install -o root -g wheel -m 444" --End MAKE_ENV-- --PLIST_SUB-- OSREL=11.0 PREFIX=%D LOCALBASE=/usr/local PORTDOCS="" PORTEXAMPLES="" PORTDATA="" LIB32DIR=lib DOCSDIR="share/doc/mrbayes" EXAMPLESDIR="share/examples/mrbayes" DATADIR="share/mrbayes" WWWDIR="www/mrbayes" ETCDIR="etc/mrbayes" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/mrbayes DOCSDIR=/usr/local/share/doc/mrbayes EXAMPLESDIR=/usr/local/share/examples/mrbayes WWWDIR=/usr/local/www/mrbayes ETCDIR=/usr/local/etc/mrbayes --End SUB_LIST-- ---Begin make.conf--- USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles #### /usr/local/etc/poudriere.d/make.conf #### WITH_PKGNG=yes # clean-restricted ran via poudriere.conf NO_RESTRICTED #NO_RESTRICTED=yes DISABLE_MAKE_JOBS=poudriere ---End make.conf--- =======================<phase: check-sanity >============================ =========================================================================== =======================<phase: pkg-depends >============================ ===> mrbayes-3.1.2_1 depends on file: /usr/local/sbin/pkg - not found ===> Verifying install for /usr/local/sbin/pkg in /usr/ports/ports-mgmt/pkg ===> Installing existing package /packages/All/pkg-1.3.6.txz [head-amd64-default-job-05] Installing pkg-1.3.6... done Message for pkg-1.3.6: If you are upgrading from the old package format, first run: # pkg2ng ===> Returning to build of mrbayes-3.1.2_1 =========================================================================== =======================<phase: fetch-depends >============================ =========================================================================== =======================<phase: fetch >============================ ===> Fetching all distfiles required by mrbayes-3.1.2_1 for building =========================================================================== =======================<phase: checksum >============================ ===> Fetching all distfiles required by mrbayes-3.1.2_1 for building => SHA256 Checksum OK for mrbayes-3.1.2.tar.gz. =========================================================================== =======================<phase: extract-depends>============================ =========================================================================== =======================<phase: extract >============================ ===> Fetching all distfiles required by mrbayes-3.1.2_1 for building ===> Extracting for mrbayes-3.1.2_1 => SHA256 Checksum OK for mrbayes-3.1.2.tar.gz. =========================================================================== =======================<phase: patch-depends >============================ =========================================================================== =======================<phase: patch >============================ ===> Patching for mrbayes-3.1.2_1 ===> Applying FreeBSD patches for mrbayes-3.1.2_1 =========================================================================== =======================<phase: build-depends >============================ ===> mrbayes-3.1.2_1 depends on executable: gmake - not found ===> Verifying install for gmake in /usr/ports/devel/gmake ===> Installing existing package /packages/All/gmake-3.82_1.txz [head-amd64-default-job-05] Installing indexinfo-0.2... done [head-amd64-default-job-05] Installing indexinfo-0.2... done [head-amd64-default-job-05] Installing indexinfo-0.2... done ===> Returning to build of mrbayes-3.1.2_1 =========================================================================== =======================<phase: lib-depends >============================ ===> mrbayes-3.1.2_1 depends on shared library: libreadline.so.6 - not found ===> Verifying for libreadline.so.6 in /usr/ports/devel/readline ===> Installing existing package /packages/All/readline-6.3.6_1.txz [head-amd64-default-job-05] Installing readline-6.3.6_1... done ===> Returning to build of mrbayes-3.1.2_1 =========================================================================== =======================<phase: configure >============================ ===> Configuring for mrbayes-3.1.2_1 =========================================================================== =======================<phase: build >============================ ===> Building for mrbayes-3.1.2_1 gmake[1]: Entering directory `/wrkdirs/usr/ports/biology/mrbayes/work/mrbayes-3.1.2' cc -O2 -pipe -fno-strict-aliasing -DUNIX_VERSION -DUSE_READLINE -O3 -Wall -I/usr/local/include -c -o mb.o mb.c cc -O2 -pipe -fno-strict-aliasing -DUNIX_VERSION -DUSE_READLINE -O3 -Wall -I/usr/local/include -c -o mcmc.o mcmc.c cc -O2 -pipe -fno-strict-aliasing -DUNIX_VERSION -DUSE_READLINE -O3 -Wall -I/usr/local/include -c -o bayes.o bayes.c cc -O2 -pipe -fno-strict-aliasing -DUNIX_VERSION -DUSE_READLINE -O3 -Wall -I/usr/local/include -c -o command.o command.c command.c:1371:12: warning: variable 'tempD' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized] else if (calibrationPtr->prior == offsetExponential) ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ command.c:1403:25: note: uninitialized use occurs here sprintf (s, "%1.2lf", tempD); ^~~~~ command.c:1371:8: note: remove the 'if' if its condition is always true else if (calibrationPtr->prior == offsetExponential) ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ command.c:1227:16: note: initialize the variable 'tempD' to silence this warning MrBFlt tempD; ^ = 0.0 command.c:7813:3: warning: expression result unused [-Wunused-value] *tokenP++; ^~~~~~~~~ 2 warnings generated. cc -O2 -pipe -fno-strict-aliasing -DUNIX_VERSION -DUSE_READLINE -O3 -Wall -I/usr/local/include -c -o mbmath.o mbmath.c mbmath.c:4788:5: warning: use of unary operator that may be intended as compound assignment (-=) r =- log(RandomNumber(seed)); ^~ 1 warning generated. cc -O2 -pipe -fno-strict-aliasing -DUNIX_VERSION -DUSE_READLINE -O3 -Wall -I/usr/local/include -c -o model.o model.c cc -O2 -pipe -fno-strict-aliasing -DUNIX_VERSION -DUSE_READLINE -O3 -Wall -I/usr/local/include -c -o plot.o plot.c cc -O2 -pipe -fno-strict-aliasing -DUNIX_VERSION -DUSE_READLINE -O3 -Wall -I/usr/local/include -c -o sump.o sump.c cc -O2 -pipe -fno-strict-aliasing -DUNIX_VERSION -DUSE_READLINE -O3 -Wall -I/usr/local/include -c -o sumt.o sumt.c cc -O2 -pipe -fno-strict-aliasing -DUNIX_VERSION -DUSE_READLINE -O3 -Wall mb.o bayes.o command.o mbmath.o mcmc.o model.o plot.o sump.o sumt.o -lncurses -lreadline -lm -o mb /usr/bin/ld: cannot find -lreadline cc: error: linker command failed with exit code 1 (use -v to see invocation) gmake[1]: *** [mb] Error 1 gmake[1]: Leaving directory `/wrkdirs/usr/ports/biology/mrbayes/work/mrbayes-3.1.2' *** Error code 1 Stop. make: stopped in /usr/ports/biology/mrbayes
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