[package - 122powerpc64-quarterly][biology/cufflinks] Failed for cufflinks-2.2.1.89_2 in build
- Go to: [ bottom of page ] [ top of archives ] [ this month ]
Date: Thu, 01 Jul 2021 03:55:06 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: yuri@FreeBSD.org
Log URL: http://foul1.nyi.freebsd.org/data/122powerpc64-quarterly/bf299f1b74f5/logs/cufflinks-2.2.1.89_2.log
Build URL: http://foul1.nyi.freebsd.org/build.html?mastername=122powerpc64-quarterly&build=bf299f1b74f5
Log:
=>> Building biology/cufflinks
build started at Thu Jul 1 03:52:25 UTC 2021
port directory: /usr/ports/biology/cufflinks
package name: cufflinks-2.2.1.89_2
building for: FreeBSD 122powerpc64-quarterly-job-04 12.2-RELEASE FreeBSD 12.2-RELEASE powerpc
maintained by: yuri@FreeBSD.org
Makefile ident:
Poudriere version: 3.2.8-8-gaf08dbda
Host OSVERSION: 1400008
Jail OSVERSION: 1202000
Job Id: 04
---Begin Environment---
SHELL=/bin/csh
OSVERSION=1202000
UNAME_v=FreeBSD 12.2-RELEASE
UNAME_r=12.2-RELEASE
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=3.2.8-8-gaf08dbda
MASTERMNT=/usr/local/poudriere/data/.m/122powerpc64-quarterly/ref
POUDRIERE_BUILD_TYPE=bulk
PACKAGE_BUILDING=yes
SAVED_TERM=
PWD=/usr/local/poudriere/data/.m/122powerpc64-quarterly/ref/.p/pool
P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS
MASTERNAME=122powerpc64-quarterly
SCRIPTPREFIX=/usr/local/share/poudriere
OLDPWD=/usr/local/poudriere/data/.m/122powerpc64-quarterly/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---
---End OPTIONS List---
--MAINTAINER--
yuri@FreeBSD.org
--End MAINTAINER--
--CONFIGURE_ARGS--
--prefix=/usr/local ${_LATE_CONFIGURE_ARGS}
--End CONFIGURE_ARGS--
--CONFIGURE_ENV--
MAKE=gmake PYTHON="/usr/local/bin/python3.7" XDG_DATA_HOME=/wrkdirs/usr/ports/biology/cufflinks/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/cufflinks/work HOME=/wrkdirs/usr/ports/biology/cufflinks/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/cufflinks/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh ADDR2LINE="/usr/local/bin/addr2line" AR="/usr/local/bin/ar" AS="/usr/local/bin/as" CPPFILT="/usr/local/bin/c++filt" GPROF="/usr/local/bin/gprof" LD="/usr/local/bin/ld" NM="/usr/local/bin/nm" OBJCOPY="/usr/local/bin/objcopy" OBJDUMP="/usr/local/bin/objdump" RANLIB="/usr/local/bin/ranlib" READELF="/usr/local/bin/readelf" SIZE="/usr/local/bin/size" STRINGS="/usr/local/bin/strings" CONFIG_SITE=/usr/ports/Templates/config.site lt_cv_sys_max_cmd_len=524288
--End CONFIGURE_ENV--
--MAKE_ENV--
XDG_DATA_HOME=/wrkdirs/usr/ports/biology/cufflinks/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/cufflinks/work HOME=/wrkdirs/usr/ports/biology/cufflinks/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/cufflinks/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 ADDR2LINE="/usr/local/bin/addr2line" AR="/usr/local/bin/ar" AS="/usr/local/bin/as" CPPFILT="/usr/local/bin/c++filt" GPROF="/usr/local/bin/gprof" LD="/usr/local/bin/ld" NM="/usr/local/bin/nm" OBJCOPY="/usr/local/bin/objcopy" OBJDUMP="/usr/local/bin/objdump" RANLIB="/usr/local/bin/ranlib" READELF="/usr/local/bin/readelf" SIZE="/usr/local/bin/size" STRINGS="/usr/local/bin/strings" PREFIX=/usr/local LOCALBASE=/usr/local CC="gcc10" CFLAGS="-O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc10 -fno-strict-aliasing " CPP="cpp10" CPPFLAGS="" LDFLAGS=" -fstack-protector-strong -
Wl,-rpath=/usr/local/lib/gcc10 -L/usr/local/lib/gcc10 " LIBS="" CXX="g++10" CXXFLAGS="-O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc10 -I/usr/local/include/eigen3 -Wl,-rpath=/usr/local/lib/gcc10 " 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--
PYTHON_INCLUDEDIR=include/python3.7m PYTHON_LIBDIR=lib/python3.7 PYTHON_PLATFORM=freebsd12 PYTHON_SITELIBDIR=lib/python3.7/site-packages PYTHON_SUFFIX=37 PYTHON_EXT_SUFFIX= PYTHON_VER=3.7 PYTHON_VERSION=python3.7 PYTHON2="@comment " PYTHON3="" OSREL=12.2 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/cufflinks" EXAMPLESDIR="share/examples/cufflinks" DATADIR="share/cufflinks" WWWDIR="www/cufflinks" ETCDIR="etc/cufflinks"
--End PLIST_SUB--
--SUB_LIST--
PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/cufflinks DOCSDIR=/usr/local/share/doc/cufflinks EXAMPLESDIR=/usr/local/share/examples/cufflinks WWWDIR=/usr/local/www/cufflinks ETCDIR=/usr/local/etc/cufflinks
--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
#### /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=cc (GCC) 4.2.1 20070831 patched [FreeBSD] Copyright (C) 2007 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
_ALTCCVERSION_921dbbb2=none
_CXXINTERNAL_acaad9ca=Using built-in specs. Target: powerpc64-undermydesk-freebsd Configured with: FreeBSD/powerpc64 system compiler Thread model: posix gcc version 4.2.1 20070831 patched [FreeBSD] "/usr/bin/ld" "--eh-frame-hdr" "-Qy" "-melf64ppc_fbsd" "--enable-new-dtags" "-dynamic-linker" "/libexec/ld-elf.so.1" "/usr/lib/crt1.o" "/usr/lib/crti.o" "/usr/lib/crtbegin.o" "-L/usr/lib" "-L/usr/lib" "/dev/null" "-lstdc++" "-lm" "-lgcc_s" "-lgcc" "-lc" "-lgcc_s" "-lgcc" "/usr/lib/crtsavres.o" "/usr/lib/crtend.o" "/usr/lib/crtn.o"
CC_OUTPUT_921dbbb2_58173849=yes
CC_OUTPUT_921dbbb2_9bdba57c=yes
CC_OUTPUT_921dbbb2_6a4fe7f5=cc1: error: unrecognized command line option "-std=c11"
CC_OUTPUT_921dbbb2_6bcac02b=yes
CC_OUTPUT_921dbbb2_67d20829=yes
CC_OUTPUT_921dbbb2_bfa62e83=cc1: error: unrecognized command line option "-std=gnu11"
CC_OUTPUT_921dbbb2_f0b4d593=yes
CC_OUTPUT_921dbbb2_308abb44=cc1plus: error: unrecognized command line option "-std=c++0x"
CC_OUTPUT_921dbbb2_f00456e5=cc1plus: error: unrecognized command line option "-std=c++11"
CC_OUTPUT_921dbbb2_65ad290d=cc1plus: error: unrecognized command line option "-std=c++14"
CC_OUTPUT_921dbbb2_f2776b26=cc1plus: error: unrecognized command line option "-std=c++17"
CC_OUTPUT_921dbbb2_b2657cc3=yes
CC_OUTPUT_921dbbb2_380987f7=cc1plus: error: unrecognized command line option "-std=gnu++11"
CC_OUTPUT_921dbbb2_160933ec=cc1plus: error: unrecognized command line option "-std=gnu++14"
CC_OUTPUT_921dbbb2_fb62803b=cc1plus: error: unrecognized command line option "-std=gnu++17"
_OBJC_CCVERSION_921dbbb2=cc (GCC) 4.2.1 20070831 patched [FreeBSD] Copyright (C) 2007 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
_OBJC_ALTCCVERSION_921dbbb2=none
ARCH=powerpc64
PPC_ABI=ELFv1
OPSYS=FreeBSD
_OSRELEASE=12.2-RELEASE
OSREL=12.2
OSVERSION=1202000
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) 33554432
stack size (kbytes, -s) 524288
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 BSL accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===> cufflinks-2.2.1.89_2 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.16.3.txz
[122powerpc64-quarterly-job-04] Installing pkg-1.16.3...
[122powerpc64-quarterly-job-04] Extracting pkg-1.16.3: .......... done
===> cufflinks-2.2.1.89_2 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of cufflinks-2.2.1.89_2
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> License BSL accepted by the user
===> Fetching all distfiles required by cufflinks-2.2.1.89_2 for building
===========================================================================
=======================<phase: checksum >============================
===> License BSL accepted by the user
===> Fetching all distfiles required by cufflinks-2.2.1.89_2 for building
=> SHA256 Checksum OK for cole-trapnell-lab-cufflinks-v2.2.1-89-gdc3b0cb_GH0.tar.gz.
=> SHA256 Checksum OK for ea4671149f3054c773d99cea521db75bf7b0658f.patch.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract >============================
===> License BSL accepted by the user
===> Fetching all distfiles required by cufflinks-2.2.1.89_2 for building
===> Extracting for cufflinks-2.2.1.89_2
=> SHA256 Checksum OK for cole-trapnell-lab-cufflinks-v2.2.1-89-gdc3b0cb_GH0.tar.gz.
=> SHA256 Checksum OK for ea4671149f3054c773d99cea521db75bf7b0658f.patch.
===========================================================================
=======================<phase: patch-depends >============================
===========================================================================
=======================<phase: patch >============================
===> Patching for cufflinks-2.2.1.89_2
===> Applying distribution patches for cufflinks-2.2.1.89_2
===> Applying FreeBSD patches for cufflinks-2.2.1.89_2 from /usr/ports/biology/cufflinks/files
===========================================================================
=======================<phase: build-depends >============================
===> cufflinks-2.2.1.89_2 depends on file: /usr/local/libdata/pkgconfig/eigen3.pc - not found
===> Installing existing package /packages/All/eigen-3.3.9.txz
[122powerpc64-quarterly-job-04] Installing eigen-3.3.9...
[122powerpc64-quarterly-job-04] `-- Installing adol-c-2.7.2...
[122powerpc64-quarterly-job-04] | `-- Installing boost-libs-1.72.0_4...
[122powerpc64-quarterly-job-04] | | `-- Installing gcc10-10.2.0_1...
[122powerpc64-quarterly-job-04] | | `-- Installing binutils-2.33.1_4,1...
[122powerpc64-quarterly-job-04] | | | `-- Installing gettext-runtime-0.21...
[122powerpc64-quarterly-job-04] | | | `-- Installing indexinfo-0.3.1...
[122powerpc64-quarterly-job-04] | | | `-- Extracting indexinfo-0.3.1: .... done
[122powerpc64-quarterly-job-04] | | | `-- Extracting gettext-runtime-0.21: .......... done
[122powerpc64-quarterly-job-04] | | `-- Extracting binutils-2.33.1_4,1: .......... done
[122powerpc64-quarterly-job-04] | | `-- Installing gcc9-9.3.0_3...
[122powerpc64-quarterly-job-04] | | | `-- Installing gmp-6.2.1...
[122powerpc64-quarterly-job-04] | | | `-- Extracting gmp-6.2.1: .......... done
[122powerpc64-quarterly-job-04] | | | `-- Installing mpc-1.2.0...
[122powerpc64-quarterly-job-04] | | | `-- Installing mpfr-4.1.0...
<snip>
903 | PrecomputedExpressionHitFactory(const string& expression_file_name,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from cufflinks.cpp:28:
replicates.h: In member function 'bool ReplicatedBundleFactory::next_bundle(HitBundle&, bool)':
replicates.h:224:57: warning: unused variable 's2' [-Wunused-variable]
224 | const vector<boost::shared_ptr<Scaffold> >& s2 = bundles[i-1]->ref_scaffolds();
| ^~
cufflinks.cpp: In function 'bool scaffolds_for_bundle(const HitBundle&, std::vector<boost::shared_ptr<Scaffold> >&, std::vector<boost::shared_ptr<Scaffold> >*, BundleStats*)':
cufflinks.cpp:690:30: warning: comparison of integer expressions of different signedness: 'std::vector<MateHit>::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
690 | if (bundle.hits().size() >= max_frags_per_bundle)
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
cufflinks.cpp:690:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
690 | if (bundle.hits().size() >= max_frags_per_bundle)
| ^~
cufflinks.cpp:693:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
693 | bool ref_guided = (ref_scaffs != NULL);
| ^~~~
cufflinks.cpp: In function 'void quantitate_transcript_cluster(AbundanceGroup&, double, std::vector<Gene>&, bool)':
cufflinks.cpp:980:30: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
980 | for (size_t j = 0; j < N; ++j)
| ~~^~~
cufflinks.cpp:988:30: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
988 | for (size_t j = 0; j < N; ++j)
| ~~^~~
cufflinks.cpp: In function 'void assemble_bundle(const RefSequenceTable&, HitBundle*, boost::shared_ptr<ReadGroupProperties>, boost::shared_ptr<BiasLearner>, FILE*, FILE*, FILE*, FILE*)':
cufflinks.cpp:1264:55: warning: comparison of integer expressions of different signedness: 'std::vector<MateHit>::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
1264 | bool bundle_too_large = bundle_ptr->hits().size() >= max_frags_per_bundle;
| ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
cufflinks.cpp:1275:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
1275 | if (allow_junk_filtering)
| ^~
cufflinks.cpp:1279:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
1279 | if (!final_est_run && bundle_mode==REF_DRIVEN) // Bias needs to be learned
| ^~
cufflinks.cpp:1176:17: warning: unused variable 'map_mass' [-Wunused-variable]
1176 | long double map_mass = rg_props->normalized_map_mass();
| ^~~~~~~~
cufflinks.cpp: In function 'bool assemble_hits(BundleFactory&, boost::shared_ptr<BiasLearner>)':
cufflinks.cpp:1491:38: warning: comparison of integer expressions of different signedness: 'int' and 'uint32_t' {aka 'unsigned int'} [-Wsign-compare]
1491 | if (bundle.right() - bundle.left() > max_gene_length)
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
In file included from GList.hh:8,
from GFaSeqGet.h:3,
from gff.h:9,
from gtf_tracking.h:12,
from bundles.h:24,
from abundances.h:25,
from clustering.h:38,
from clustering.cpp:10:
GVec.hh: In instantiation of 'void GVec<OBJ>::Grow(int, OBJ&) [with OBJ = GISeg]':
GVec.hh:436:9: required from 'void GVec<OBJ>::Insert(int, OBJ*) [with OBJ = GISeg]'
GVec.hh:83:48: required from 'void GVec<OBJ>::idxInsert(int, OBJ&) [with OBJ = GISeg]'
gtf_tracking.h:210:29: required from here
GVec.hh:364:15: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class GISeg'; use assignment or value-initialization instead [-Wclass-memaccess]
364 | memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ));
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from bundles.h:24,
from abundances.h:25,
from clustering.h:38,
from clustering.cpp:10:
gtf_tracking.h:188:7: note: 'class GISeg' declared here
188 | class GISeg: public GSeg {
| ^~~~~
In file included from GList.hh:8,
from GFaSeqGet.h:3,
from gff.h:9,
from gtf_tracking.h:12,
from bundles.h:24,
from abundances.h:25,
from clustering.h:38,
from clustering.cpp:10:
GVec.hh: In instantiation of 'void GVec<OBJ>::Grow(int, OBJ&) [with OBJ = GXSeg]':
GVec.hh:436:9: required from 'void GVec<OBJ>::Insert(int, OBJ*) [with OBJ = GXSeg]'
GVec.hh:81:44: required from 'void GVec<OBJ>::Insert(int, OBJ) [with OBJ = GXSeg]'
GList.hh:231:21: required from 'int GArray<OBJ>::Add(OBJ*) [with OBJ = GXSeg]'
GList.hh:51:36: required from 'int GArray<OBJ>::Add(OBJ&) [with OBJ = GXSeg]'
gtf_tracking.h:419:20: required from here
GVec.hh:364:15: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class GXSeg'; use assignment or value-initialization instead [-Wclass-memaccess]
364 | memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ));
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from bundles.h:24,
from abundances.h:25,
from clustering.h:38,
from clustering.cpp:10:
gtf_tracking.h:359:7: note: 'class GXSeg' declared here
359 | class GXSeg : public GSeg {
| ^~~~~
In file included from GList.hh:8,
from GFaSeqGet.h:3,
from gff.h:9,
from gtf_tracking.h:12,
from bundles.h:24,
from abundances.h:25,
from clustering.h:38,
from clustering.cpp:10:
GVec.hh: In instantiation of 'void GVec<OBJ>::Grow(int, OBJ&) [with OBJ = GSeg]':
GVec.hh:436:9: required from 'void GVec<OBJ>::Insert(int, OBJ*) [with OBJ = GSeg]'
GVec.hh:81:44: required from 'void GVec<OBJ>::Insert(int, OBJ) [with OBJ = GSeg]'
GList.hh:231:21: required from 'int GArray<OBJ>::Add(OBJ*) [with OBJ = GSeg]'
GList.hh:51:36: required from 'int GArray<OBJ>::Add(OBJ&) [with OBJ = GSeg]'
gtf_tracking.h:420:19: required from here
GVec.hh:364:15: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class GSeg'; use assignment or value-initialization instead [-Wclass-memaccess]
364 | memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ));
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from gff.h:6,
from gtf_tracking.h:12,
from bundles.h:24,
from abundances.h:25,
from clustering.h:38,
from clustering.cpp:10:
GBase.h:286:7: note: 'class GSeg' declared here
286 | class GSeg {
| ^~~~
In file included from GList.hh:8,
from GFaSeqGet.h:3,
from gff.h:9,
from gtf_tracking.h:12,
from bundles.h:24,
from abundances.h:25,
from clustering.h:38,
from cufflinks.cpp:20:
GVec.hh: In instantiation of 'void GVec<OBJ>::Grow(int, OBJ&) [with OBJ = GISeg]':
GVec.hh:436:9: required from 'void GVec<OBJ>::Insert(int, OBJ*) [with OBJ = GISeg]'
GVec.hh:83:48: required from 'void GVec<OBJ>::idxInsert(int, OBJ&) [with OBJ = GISeg]'
gtf_tracking.h:210:29: required from here
GVec.hh:364:15: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class GISeg'; use assignment or value-initialization instead [-Wclass-memaccess]
364 | memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ));
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from bundles.h:24,
from abundances.h:25,
from clustering.h:38,
from cufflinks.cpp:20:
gtf_tracking.h:188:7: note: 'class GISeg' declared here
188 | class GISeg: public GSeg {
| ^~~~~
In file included from GList.hh:8,
from GFaSeqGet.h:3,
from gff.h:9,
from gtf_tracking.h:12,
from bundles.h:24,
from abundances.h:25,
from clustering.h:38,
from cufflinks.cpp:20:
GVec.hh: In instantiation of 'void GVec<OBJ>::Grow(int, OBJ&) [with OBJ = GXSeg]':
GVec.hh:436:9: required from 'void GVec<OBJ>::Insert(int, OBJ*) [with OBJ = GXSeg]'
GVec.hh:81:44: required from 'void GVec<OBJ>::Insert(int, OBJ) [with OBJ = GXSeg]'
GList.hh:231:21: required from 'int GArray<OBJ>::Add(OBJ*) [with OBJ = GXSeg]'
GList.hh:51:36: required from 'int GArray<OBJ>::Add(OBJ&) [with OBJ = GXSeg]'
gtf_tracking.h:419:20: required from here
GVec.hh:364:15: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class GXSeg'; use assignment or value-initialization instead [-Wclass-memaccess]
364 | memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ));
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from bundles.h:24,
from abundances.h:25,
from clustering.h:38,
from cufflinks.cpp:20:
gtf_tracking.h:359:7: note: 'class GXSeg' declared here
359 | class GXSeg : public GSeg {
| ^~~~~
In file included from GList.hh:8,
from GFaSeqGet.h:3,
from gff.h:9,
from gtf_tracking.h:12,
from bundles.h:24,
from abundances.h:25,
from clustering.h:38,
from cufflinks.cpp:20:
GVec.hh: In instantiation of 'void GVec<OBJ>::Grow(int, OBJ&) [with OBJ = GSeg]':
GVec.hh:436:9: required from 'void GVec<OBJ>::Insert(int, OBJ*) [with OBJ = GSeg]'
GVec.hh:81:44: required from 'void GVec<OBJ>::Insert(int, OBJ) [with OBJ = GSeg]'
GList.hh:231:21: required from 'int GArray<OBJ>::Add(OBJ*) [with OBJ = GSeg]'
GList.hh:51:36: required from 'int GArray<OBJ>::Add(OBJ&) [with OBJ = GSeg]'
gtf_tracking.h:420:19: required from here
GVec.hh:364:15: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class GSeg'; use assignment or value-initialization instead [-Wclass-memaccess]
364 | memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ));
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from gff.h:6,
from gtf_tracking.h:12,
from bundles.h:24,
from abundances.h:25,
from clustering.h:38,
from cufflinks.cpp:20:
GBase.h:286:7: note: 'class GSeg' declared here
286 | class GSeg {
| ^~~~
gmake[3]: *** [Makefile:1674: clustering.o] Error 1
gmake[3]: *** Waiting for unfinished jobs....
gmake[3]: *** [Makefile:1674: cufflinks.o] Error 1
gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/cufflinks/work/cufflinks-2.2.1-89-gdc3b0cb/src'
gmake[2]: *** [Makefile:404: all-recursive] Error 1
gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/cufflinks/work/cufflinks-2.2.1-89-gdc3b0cb'
gmake[1]: *** [Makefile:345: all] Error 2
gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/cufflinks/work/cufflinks-2.2.1-89-gdc3b0cb'
===> 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/cufflinks