[package - head-armv6-default][biology/star] Failed for rna-STAR-2.7.0.f in build
pkg-fallout at FreeBSD.org
pkg-fallout at FreeBSD.org
Sun May 19 11:55:57 UTC 2019
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: jwb at FreeBSD.org
Last committer: jwb at FreeBSD.org
Ident: $FreeBSD: head/biology/star/Makefile 500629 2019-05-02 00:39:51Z jwb $
Log URL: http://beefy8.nyi.freebsd.org/data/head-armv6-default/p501758_s347628/logs/rna-STAR-2.7.0.f.log
Build URL: http://beefy8.nyi.freebsd.org/build.html?mastername=head-armv6-default&build=p501758_s347628
Log:
=>> Building biology/star
build started at Sun May 19 11:36:43 UTC 2019
port directory: /usr/ports/biology/star
package name: rna-STAR-2.7.0.f
building for: FreeBSD head-armv6-default-job-05 13.0-CURRENT FreeBSD 13.0-CURRENT 1300027 arm
maintained by: jwb at FreeBSD.org
Makefile ident: $FreeBSD: head/biology/star/Makefile 500629 2019-05-02 00:39:51Z jwb $
Poudriere version: 3.2.8-4-g701d8fe1
Host OSVERSION: 1300018
Jail OSVERSION: 1300027
Job Id: 05
!!! Jail is newer than host. (Jail: 1300027, Host: 1300018) !!!
!!! This is not supported. !!!
!!! Host kernel must be same or newer than jail. !!!
!!! Expect build failures. !!!
---Begin Environment---
SHELL=/bin/csh
UNAME_p=armv6
UNAME_m=arm
ABI_FILE=/usr/lib/crt1.o
OSVERSION=1300027
UNAME_v=FreeBSD 13.0-CURRENT 1300027
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
QEMU_EMULATING=1
USER=root
LIBEXECPREFIX=/usr/local/libexec/poudriere
POUDRIERE_VERSION=3.2.8-4-g701d8fe1
MASTERMNT=/usr/local/poudriere/data/.m/head-armv6-default/ref
POUDRIERE_BUILD_TYPE=bulk
PACKAGE_BUILDING=yes
SAVED_TERM=
PWD=/usr/local/poudriere/data/.m/head-armv6-default/ref/.p/pool
P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS
MASTERNAME=head-armv6-default
SCRIPTPREFIX=/usr/local/share/poudriere
OLDPWD=/usr/local/poudriere/data/.m/head-armv6-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---
---End OPTIONS List---
--MAINTAINER--
jwb at FreeBSD.org
--End MAINTAINER--
--CONFIGURE_ARGS--
--End CONFIGURE_ARGS--
--CONFIGURE_ENV--
MAKE=gmake XDG_DATA_HOME=/wrkdirs/usr/ports/biology/star/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/star/work HOME=/wrkdirs/usr/ports/biology/star/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/star/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/star/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/star/work HOME=/wrkdirs/usr/ports/biology/star/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/star/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="gcc8" CFLAGS="-O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc8 -fno-strict-aliasing " CPP="cpp8" CPPFLAGS="" LDFLAGS=" -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc8 -L/usr/local/lib/gcc8
" LIBS="" CXX="g++8" CXXFLAGS="-O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc8 -Wl,-rpath=/usr/local/lib/gcc8 " 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--
OSREL=13.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/STAR" EXAMPLESDIR="share/examples/STAR" DATADIR="share/STAR" WWWDIR="www/STAR" ETCDIR="etc/STAR"
--End PLIST_SUB--
--SUB_LIST--
PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/STAR DOCSDIR=/usr/local/share/doc/STAR EXAMPLESDIR=/usr/local/share/examples/STAR WWWDIR=/usr/local/www/STAR ETCDIR=/usr/local/etc/STAR
--End SUB_LIST--
---Begin make.conf---
.sinclude "/etc/make.nxb.conf"
USE_PACKAGE_DEPENDS=yes
BATCH=yes
WRKDIRPREFIX=/wrkdirs
PORTSDIR=/usr/ports
PACKAGES=/packages
DISTDIR=/distfiles
PACKAGE_BUILDING=yes
PACKAGE_BUILDING_FLAVORS=yes
MACHINE=arm
MACHINE_ARCH=armv6
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
# stable/10 includes src.conf too late but make.conf is in sys.mk
.if ${.CURDIR:M/poudriere/jails/10*/usr/src/usr.bin/xlint*}
# Disable build of llib now that head no longer has lint(1)
LINT= true
.endif
#### /usr/ports/Mk/Scripts/ports_env.sh ####
_CCVERSION_9d218390=FreeBSD clang version 8.0.0 (tags/RELEASE_800/final 356365) (based on LLVM 8.0.0) Target: armv6-unknown-freebsd13.0-gnueabihf Thread model: posix InstalledDir: /nxb-bin/usr/bin
_ALTCCVERSION_9d218390=none
_CXXINTERNAL_9c45a5b1=FreeBSD clang version 8.0.0 (tags/RELEASE_800/final 356365) (based on LLVM 8.0.0) Target: armv6-unknown-freebsd13.0-gnueabihf Thread model: posix InstalledDir: /nxb-bin/usr/bin "/nxb-bin/usr/bin/ld" "--eh-frame-hdr" "-dynamic-linker" "/libexec/ld-elf.so.1" "--hash-style=both" "--enable-new-dtags" "-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_9d218390_58173849=yes
CC_OUTPUT_9d218390_9bdba57c=yes
CC_OUTPUT_9d218390_6a4fe7f5=yes
CC_OUTPUT_9d218390_6bcac02b=yes
CC_OUTPUT_9d218390_67d20829=yes
CC_OUTPUT_9d218390_bfa62e83=yes
CC_OUTPUT_9d218390_f0b4d593=yes
CC_OUTPUT_9d218390_308abb44=yes
CC_OUTPUT_9d218390_f00456e5=yes
CC_OUTPUT_9d218390_65ad290d=yes
CC_OUTPUT_9d218390_f2776b26=yes
CC_OUTPUT_9d218390_b2657cc3=yes
CC_OUTPUT_9d218390_380987f7=yes
CC_OUTPUT_9d218390_160933ec=yes
CC_OUTPUT_9d218390_fb62803b=yes
_OBJC_CCVERSION_9d218390=FreeBSD clang version 8.0.0 (tags/RELEASE_800/final 356365) (based on LLVM 8.0.0) Target: armv6-unknown-freebsd13.0-gnueabihf Thread model: posix InstalledDir: /nxb-bin/usr/bin
_OBJC_ALTCCVERSION_9d218390=none
ARCH=armv6
OPSYS=FreeBSD
_OSRELEASE=13.0-CURRENT
OSREL=13.0
OSVERSION=1300027
PYTHONBASE=/usr/local
CONFIGURE_MAX_CMD_LEN=262144
HAVE_PORTS_ENV=1
#### Misc Poudriere ####
GID=0
UID=0
DISABLE_MAKE_JOBS=poudriere
---End make.conf---
---Begin make.nxb.conf---
CC=/nxb-bin/usr/bin/cc
CPP=/nxb-bin/usr/bin/cpp
CXX=/nxb-bin/usr/bin/c++
AS=/nxb-bin/usr/bin/as
NM=/nxb-bin/usr/bin/nm
LD=/nxb-bin/usr/bin/ld
OBJCOPY=/nxb-bin/usr/bin/objcopy
SIZE=/nxb-bin/usr/bin/size
STRIPBIN=/nxb-bin/usr/bin/strip
SED=/nxb-bin/usr/bin/sed
RANLIB=/nxb-bin/usr/bin/ranlib
YACC=/nxb-bin/usr/bin/yacc
MAKE=/nxb-bin/usr/bin/make
STRINGS=/nxb-bin/usr/bin/strings
AWK=/nxb-bin/usr/bin/awk
FLEX=/nxb-bin/usr/bin/flex
---End make.nxb.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 GPLv3 accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===> rna-STAR-2.7.0.f depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.10.5_5.txz
[head-armv6-default-job-05] Installing pkg-1.10.5_5...
[head-armv6-default-job-05] Extracting pkg-1.10.5_5: .......... done
===> rna-STAR-2.7.0.f depends on file: /usr/local/sbin/pkg - found
===> Returning to build of rna-STAR-2.7.0.f
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> License GPLv3 accepted by the user
<snip>
cram/cram_io.c:1279:49: warning: unused parameter 'fd' [-Wunused-parameter]
static int refs_from_header(refs_t *r, cram_fd *fd, SAM_hdr *h) {
~~~~~~~~~^~
In file included from ./cram/cram_io.h:52,
from ./cram/cram.h:55,
from cram/cram_io.c:65:
cram/cram_io.c: In function 'expand_cache_path':
./cram/misc.h:103:26: warning: comparison of integer expressions of different signedness: 'long int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
#define MIN(A,B) ( ( (A) < (B) ) ? (A) : (B) )
^
cram/cram_io.c:1368:10: note: in expansion of macro 'MIN'
l = MIN(l, strlen(fn));
^~~
./cram/misc.h:103:36: warning: operand of ?: changes signedness from 'long int' to 'size_t' {aka 'unsigned int'} due to unsignedness of other operand [-Wsign-compare]
#define MIN(A,B) ( ( (A) < (B) ) ? (A) : (B) )
^~~
cram/cram_io.c:1368:10: note: in expansion of macro 'MIN'
l = MIN(l, strlen(fn));
^~~
cram/cram_io.c: In function 'cram_populate_ref':
cram/cram_io.c:1544:6: warning: implicit declaration of function 'unlink'; did you mean 'unix'? [-Wimplicit-function-declaration]
unlink(path_tmp);
^~~~~~
unix
cram/cram_io.c: In function 'full_path':
cram/cram_io.c:2915:7: warning: implicit declaration of function 'getcwd'; did you mean 'getw'? [-Wimplicit-function-declaration]
if (!getcwd(out, PATH_MAX) ||
^~~~~~
getw
cram/cram_io.c: In function 'cram_populate_ref':
cram/cram_io.c:1529:27: warning: '.tmp_' directive writing 5 bytes into a region of size between 1 and 1024 [-Wformat-overflow=]
sprintf(path_tmp, "%s.tmp_%d", path, /*getpid(),*/ i);
^~~~~
cram/cram_io.c:1529:24: note: directive argument in the range [0, 2147483647]
sprintf(path_tmp, "%s.tmp_%d", path, /*getpid(),*/ i);
^~~~~~~~~~~
cram/cram_io.c:1529:6: note: 'sprintf' output between 7 and 1039 bytes into a destination of size 1024
sprintf(path_tmp, "%s.tmp_%d", path, /*getpid(),*/ i);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function 'full_path',
inlined from 'cram_write_SAM_hdr' at cram/cram_io.c:2987:3:
cram/cram_io.c:2917:6: warning: 'strncpy' specified bound 1024 equals destination size [-Wstringop-truncation]
strncpy(out, in, PATH_MAX);
^~~~~~~~~~~~~~~~~~~~~~~~~~
cram/cram_io.c:2909:2: warning: 'strncpy' specified bound 1024 equals destination size [-Wstringop-truncation]
strncpy(out, in, PATH_MAX);
^~~~~~~~~~~~~~~~~~~~~~~~~~
cram/cram_io.c: In function 'cram_dopen':
cram/cram_io.c:3291:2: warning: 'strncpy' specified bound 20 equals destination size [-Wstringop-truncation]
strncpy(def.file_id, filename, 20);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc8 -g -Wall -O2 -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc8 -fno-strict-aliasing -Wall -Wextra -I. -DSAMTOOLS=1 -c -o cram/cram_samtools.o cram/cram_samtools.c
gcc8 -g -Wall -O2 -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc8 -fno-strict-aliasing -Wall -Wextra -I. -DSAMTOOLS=1 -c -o cram/cram_stats.o cram/cram_stats.c
cram/cram_stats.c: In function 'cram_stats_add':
cram/cram_stats.c:74:6: warning: suggest braces around empty body in an 'else' statement [-Wempty-body]
; // FIXME: handle error
^
gcc8 -g -Wall -O2 -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc8 -fno-strict-aliasing -Wall -Wextra -I. -DSAMTOOLS=1 -c -o cram/files.o cram/files.c
gcc8 -g -Wall -O2 -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc8 -fno-strict-aliasing -Wall -Wextra -I. -DSAMTOOLS=1 -c -o cram/mFILE.o cram/mFILE.c
cram/mFILE.c: In function 'mfload':
cram/mFILE.c:73:65: warning: unused parameter 'binary' [-Wunused-parameter]
static char *mfload(FILE *fp, const char *fn, size_t *size, int binary) {
~~~~^~~~~~
cram/mFILE.c: In function 'mftruncate':
cram/mFILE.c:416:31: warning: operand of ?: changes signedness from 'long int' to 'size_t' {aka 'unsigned int'} due to unsignedness of other operand [-Wsign-compare]
mf->size = offset != -1 ? offset : mf->offset;
^~~~~~
gcc8 -g -Wall -O2 -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc8 -fno-strict-aliasing -Wall -Wextra -I. -DSAMTOOLS=1 -c -o cram/md5.o cram/md5.c
gcc8 -g -Wall -O2 -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc8 -fno-strict-aliasing -Wall -Wextra -I. -DSAMTOOLS=1 -c -o cram/open_trace_file.o cram/open_trace_file.c
In file included from cram/open_trace_file.c:81:
cram/open_trace_file.c: In function 'find_file_dir':
./cram/misc.h:103:26: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'long int' [-Wsign-compare]
#define MIN(A,B) ( ( (A) < (B) ) ? (A) : (B) )
^
cram/open_trace_file.c:271:15: note: in expansion of macro 'MIN'
path_end += MIN(strlen(file), l);
^~~
./cram/misc.h:103:42: warning: operand of ?: changes signedness from 'long int' to 'size_t' {aka 'unsigned int'} due to unsignedness of other operand [-Wsign-compare]
#define MIN(A,B) ( ( (A) < (B) ) ? (A) : (B) )
^~~
cram/open_trace_file.c:271:15: note: in expansion of macro 'MIN'
path_end += MIN(strlen(file), l);
^~~
./cram/misc.h:103:26: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'long int' [-Wsign-compare]
#define MIN(A,B) ( ( (A) < (B) ) ? (A) : (B) )
^
cram/open_trace_file.c:272:15: note: in expansion of macro 'MIN'
file += MIN(strlen(file), l);
^~~
./cram/misc.h:103:42: warning: operand of ?: changes signedness from 'long int' to 'size_t' {aka 'unsigned int'} due to unsignedness of other operand [-Wsign-compare]
#define MIN(A,B) ( ( (A) < (B) ) ? (A) : (B) )
^~~
cram/open_trace_file.c:272:15: note: in expansion of macro 'MIN'
file += MIN(strlen(file), l);
^~~
gcc8 -g -Wall -O2 -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc8 -fno-strict-aliasing -Wall -Wextra -I. -DSAMTOOLS=1 -c -o cram/pooled_alloc.o cram/pooled_alloc.c
gcc8 -g -Wall -O2 -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc8 -fno-strict-aliasing -Wall -Wextra -I. -DSAMTOOLS=1 -c -o cram/sam_header.o cram/sam_header.c
cram/sam_header.c: In function 'sam_hdr_add_lines':
cram/sam_header.c:320:9: warning: comparison of integer expressions of different signedness: 'int' and 'khint_t' {aka 'unsigned int'} [-Wsign-compare]
if (-1 == (k = kh_put(sam_hdr, sh->h, type, &new)))
^~
cram/sam_header.c: In function 'sam_hdr_vadd':
cram/sam_header.c:440:12: warning: comparison of integer expressions of different signedness: 'int' and 'khint32_t' {aka 'unsigned int'} [-Wsign-compare]
if (-1 == (k = kh_put(sam_hdr, sh->h, type_i, &new)))
^~
cram/sam_header.c: In function 'sam_hdr_find_key':
cram/sam_header.c:672:40: warning: unused parameter 'sh' [-Wunused-parameter]
SAM_hdr_tag *sam_hdr_find_key(SAM_hdr *sh,
~~~~~~~~~^~
cram/sam_header.c: In function 'sam_hdr_rebuild':
cram/sam_header.c:781:24: warning: comparison of integer expressions of different signedness: 'khint32_t' {aka 'unsigned int'} and 'int' [-Wsign-compare]
if (kh_key(hdr->h, k) == K("HD"))
^~
gcc8 -g -Wall -O2 -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc8 -fno-strict-aliasing -Wall -Wextra -I. -DSAMTOOLS=1 -c -o cram/string_alloc.o cram/string_alloc.c
gcc8 -g -Wall -O2 -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc8 -fno-strict-aliasing -Wall -Wextra -I. -DSAMTOOLS=1 -c -o cram/thread_pool.o cram/thread_pool.c
gcc8 -g -Wall -O2 -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc8 -fno-strict-aliasing -Wall -Wextra -I. -DSAMTOOLS=1 -c -o cram/vlen.o cram/vlen.c
cram/vlen.c: In function 'vflen':
cram/vlen.c:121:9: warning: variable 'i' set but not used [-Wunused-but-set-variable]
int i;
^
gcc8 -g -Wall -O2 -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc8 -fno-strict-aliasing -Wall -Wextra -I. -DSAMTOOLS=1 -c -o cram/zfio.o cram/zfio.c
ar -rc libhts.a kfunc.o knetfile.o kstring.o bgzf.o faidx.o hfile.o hfile_net.o hts.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_index.o cram/cram_io.o cram/cram_samtools.o cram/cram_stats.o cram/files.o cram/mFILE.o cram/md5.o cram/open_trace_file.o cram/pooled_alloc.o cram/sam_header.o cram/string_alloc.o cram/thread_pool.o cram/vlen.o cram/zfio.o
ranlib libhts.a
gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/star/work/STAR-2.7.0f/source/htslib'
echo ChimericDetection.cpp stringSubstituteAll.cpp InOutStreams.cpp ReadAlign_chimericDetectionPEmerged.cpp ReadAlign_assignAlignToWindow.cpp loadGTF.cpp mapThreadsSpawn.cpp ReadAlign.cpp SequenceFuns.cpp funCompareUintAndSuffixesMemcmp.cpp ReadAlign_outputTranscriptSJ.cpp ReadAlign_outputVariation.cpp ParametersSolo.cpp ReadAlign_CIGAR.cpp SoloReadBarcode.cpp ReadAlign_chimericDetectionOldOutput.cpp ReadAlign_multMapSelect.cpp genomeParametersWrite.cpp ReadAlign_createExtendWindowsWithAlign.cpp ReadAlignChunk_processChunks.cpp streamFuns.cpp insertSeqSA.cpp BAMbinSortUnmapped.cpp Genome.cpp sjdbInsertJunctions.cpp Genome_insertSequences.cpp binarySearch2.cpp serviceFuns.cpp ReadAlignChunk_mapChunk.cpp ReadAlign_maxMappableLength2strands.cpp outputSJ.cpp SoloRead_record.cpp ReadAlign_chimericDetection.cpp Transcriptome.cpp Parameters.cpp GlobalVariables.cpp stitchWindowAligns.cpp SoloFeature_collapseUMI.cpp ReadAlign_chimericDetectionOld.cpp Parameters_closeReadsFiles.cpp sjAlignSpli
t.cpp Genome_genomeGenerate.cpp signalFromBAM.cpp genomeSAindex.cpp stitchGapIndel.cpp TimeFunctions.cpp stitchAlignToTranscript.cpp Transcript_generateCigarP.cpp sjdbLoadFromStream.cpp Quantifications.cpp Parameters_openReadsFiles.cpp ChimericAlign.cpp SoloReadFeature_record.cpp blocksOverlap.cpp ErrorWarning.cpp ReadAlign_outputTranscriptCIGARp.cpp PackedArray.cpp ReadAlignChunk.cpp SoloFeature_processRecords.cpp SoloRead.cpp SoloFeature_outputResults.cpp ReadAlign_alignBAM.cpp ReadAlign_outputAlignments.cpp ReadAlign_calcCIGAR.cpp Transcriptome_quantAlign.cpp SoloReadFeature_getFeature.cpp Solo.cpp BAMbinSortByCoordinate.cpp Parameters_readSAMheader.cpp ReadAlign_waspMap.cpp STAR.cpp SoloFeature.cpp funCompareUintAndSuffixes.cpp ReadAlign_stitchPieces.cpp ChimericSegment.cpp SoloReadFeature_inputRecords.cpp Transcriptome_geneCountsAddAlign.cpp ChimericDetection_chimericDetectionMult.cpp Stats.cpp SoloReadFeature.cpp Variation.cpp readLoad.cpp ChimericAlign_chimericJunctionOutput.
cpp ReadAlign_mapOneRead.cpp ReadAlign_outpu!
tTranscriptSAM.cpp bamRemoveDuplicates.cpp sjdbBuildIndex.cpp Chain.cpp genomeScanFastaFiles.cpp ReadAlign_quantTranscriptome.cpp ReadAlign_peOverlapMergeMap.cpp sjdbLoadFromFiles.cpp OutSJ.cpp ChimericAlign_chimericStitching.cpp BAMfunctions.cpp Transcript_alignScore.cpp extendAlign.cpp alignSmithWaterman.cpp SuffixArrayFuns.cpp Transcript_variationOutput.cpp SoloReadBarcode_getCBandUMI.cpp ReadAlign_mappedFilter.cpp ReadAlign_oneRead.cpp sjdbPrepare.cpp SharedMemory.cpp ReadAlign_stitchWindowSeeds.cpp BAMoutput.cpp ReadAlign_storeAligns.cpp Transcript_variationAdjust.cpp sysRemoveDir.cpp ThreadControl.cpp Transcript.cpp bam_cat.c
ChimericDetection.cpp stringSubstituteAll.cpp InOutStreams.cpp ReadAlign_chimericDetectionPEmerged.cpp ReadAlign_assignAlignToWindow.cpp loadGTF.cpp mapThreadsSpawn.cpp ReadAlign.cpp SequenceFuns.cpp funCompareUintAndSuffixesMemcmp.cpp ReadAlign_outputTranscriptSJ.cpp ReadAlign_outputVariation.cpp ParametersSolo.cpp ReadAlign_CIGAR.cpp SoloReadBarcode.cpp ReadAlign_chimericDetectionOldOutput.cpp ReadAlign_multMapSelect.cpp genomeParametersWrite.cpp ReadAlign_createExtendWindowsWithAlign.cpp ReadAlignChunk_processChunks.cpp streamFuns.cpp insertSeqSA.cpp BAMbinSortUnmapped.cpp Genome.cpp sjdbInsertJunctions.cpp Genome_insertSequences.cpp binarySearch2.cpp serviceFuns.cpp ReadAlignChunk_mapChunk.cpp ReadAlign_maxMappableLength2strands.cpp outputSJ.cpp SoloRead_record.cpp ReadAlign_chimericDetection.cpp Transcriptome.cpp Parameters.cpp GlobalVariables.cpp stitchWindowAligns.cpp SoloFeature_collapseUMI.cpp ReadAlign_chimericDetectionOld.cpp Parameters_closeReadsFiles.cpp sjAlignSplit.cpp
Genome_genomeGenerate.cpp signalFromBAM.cpp genomeSAindex.cpp stitchGapIndel.cpp TimeFunctions.cpp stitchAlignToTranscript.cpp Transcript_generateCigarP.cpp sjdbLoadFromStream.cpp Quantifications.cpp Parameters_openReadsFiles.cpp ChimericAlign.cpp SoloReadFeature_record.cpp blocksOverlap.cpp ErrorWarning.cpp ReadAlign_outputTranscriptCIGARp.cpp PackedArray.cpp ReadAlignChunk.cpp SoloFeature_processRecords.cpp SoloRead.cpp SoloFeature_outputResults.cpp ReadAlign_alignBAM.cpp ReadAlign_outputAlignments.cpp ReadAlign_calcCIGAR.cpp Transcriptome_quantAlign.cpp SoloReadFeature_getFeature.cpp Solo.cpp BAMbinSortByCoordinate.cpp Parameters_readSAMheader.cpp ReadAlign_waspMap.cpp STAR.cpp SoloFeature.cpp funCompareUintAndSuffixes.cpp ReadAlign_stitchPieces.cpp ChimericSegment.cpp SoloReadFeature_inputRecords.cpp Transcriptome_geneCountsAddAlign.cpp ChimericDetection_chimericDetectionMult.cpp Stats.cpp SoloReadFeature.cpp Variation.cpp readLoad.cpp ChimericAlign_chimericJunctionOutput.cpp R
eadAlign_mapOneRead.cpp ReadAlign_outputTran!
scriptSAM.cpp bamRemoveDuplicates.cpp sjdbBuildIndex.cpp Chain.cpp genomeScanFastaFiles.cpp ReadAlign_quantTranscriptome.cpp ReadAlign_peOverlapMergeMap.cpp sjdbLoadFromFiles.cpp OutSJ.cpp ChimericAlign_chimericStitching.cpp BAMfunctions.cpp Transcript_alignScore.cpp extendAlign.cpp alignSmithWaterman.cpp SuffixArrayFuns.cpp Transcript_variationOutput.cpp SoloReadBarcode_getCBandUMI.cpp ReadAlign_mappedFilter.cpp ReadAlign_oneRead.cpp sjdbPrepare.cpp SharedMemory.cpp ReadAlign_stitchWindowSeeds.cpp BAMoutput.cpp ReadAlign_storeAligns.cpp Transcript_variationAdjust.cpp sysRemoveDir.cpp ThreadControl.cpp Transcript.cpp bam_cat.c
'rm' -f ./Depend.list
g++8 -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Sun May 19 11:37:25 UTC 2019 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.0f/source"' -MM ChimericDetection.cpp stringSubstituteAll.cpp InOutStreams.cpp ReadAlign_chimericDetectionPEmerged.cpp ReadAlign_assignAlignToWindow.cpp loadGTF.cpp mapThreadsSpawn.cpp ReadAlign.cpp SequenceFuns.cpp funCompareUintAndSuffixesMemcmp.cpp ReadAlign_outputTranscriptSJ.cpp ReadAlign_outputVariation.cpp ParametersSolo.cpp ReadAlign_CIGAR.cpp SoloReadBarcode.cpp ReadAlign_chimericDetectionOldOutput.cpp ReadAlign_multMapSelect.cpp genomeParametersWrite.cpp ReadAlign_createExtendWindowsWithAlign.cpp ReadAlignChunk_processChunks.cpp streamFuns.cpp insertSeqSA.cpp BAMbinSortUnmapped.cpp Genome.cpp sjdbInsertJunctions.cpp Genome_insertSequences.cpp binarySearch2.cpp serviceFuns.cpp ReadAlignChunk_mapChunk.cpp ReadAlign_maxMappableLength2strands.cpp outputSJ.cpp SoloRead_record.cpp ReadAlign_chimericDetection.cpp Transcriptome.cpp Parameters
.cpp GlobalVariables.cpp stitchWindowAligns.cpp SoloFeature_collapseUMI.cpp ReadAlign_chimericDetectionOld.cpp Parameters_closeReadsFiles.cpp sjAlignSplit.cpp Genome_genomeGenerate.cpp signalFromBAM.cpp genomeSAindex.cpp stitchGapIndel.cpp TimeFunctions.cpp stitchAlignToTranscript.cpp Transcript_generateCigarP.cpp sjdbLoadFromStream.cpp Quantifications.cpp Parameters_openReadsFiles.cpp ChimericAlign.cpp SoloReadFeature_record.cpp blocksOverlap.cpp ErrorWarning.cpp ReadAlign_outputTranscriptCIGARp.cpp PackedArray.cpp ReadAlignChunk.cpp SoloFeature_processRecords.cpp SoloRead.cpp SoloFeature_outputResults.cpp ReadAlign_alignBAM.cpp ReadAlign_outputAlignments.cpp ReadAlign_calcCIGAR.cpp Transcriptome_quantAlign.cpp SoloReadFeature_getFeature.cpp Solo.cpp BAMbinSortByCoordinate.cpp Parameters_readSAMheader.cpp ReadAlign_waspMap.cpp STAR.cpp SoloFeature.cpp funCompareUintAndSuffixes.cpp ReadAlign_stitchPieces.cpp ChimericSegment.cpp SoloReadFeature_inputRecords.cpp Transcriptome_geneCoun
tsAddAlign.cpp ChimericDetection_chimericDet!
ectionMult.cpp Stats.cpp SoloReadFeature.cpp Variation.cpp readLoad.cpp ChimericAlign_chimericJunctionOutput.cpp ReadAlign_mapOneRead.cpp ReadAlign_outputTranscriptSAM.cpp bamRemoveDuplicates.cpp sjdbBuildIndex.cpp Chain.cpp genomeScanFastaFiles.cpp ReadAlign_quantTranscriptome.cpp ReadAlign_peOverlapMergeMap.cpp sjdbLoadFromFiles.cpp OutSJ.cpp ChimericAlign_chimericStitching.cpp BAMfunctions.cpp Transcript_alignScore.cpp extendAlign.cpp alignSmithWaterman.cpp SuffixArrayFuns.cpp Transcript_variationOutput.cpp SoloReadBarcode_getCBandUMI.cpp ReadAlign_mappedFilter.cpp ReadAlign_oneRead.cpp sjdbPrepare.cpp SharedMemory.cpp ReadAlign_stitchWindowSeeds.cpp BAMoutput.cpp ReadAlign_storeAligns.cpp Transcript_variationAdjust.cpp sysRemoveDir.cpp ThreadControl.cpp Transcript.cpp bam_cat.c parametersDefault.xxd htslib >> Depend.list
g++8: warning: parametersDefault.xxd: linker input file unused because linking not done
g++8: warning: htslib: linker input file unused because linking not done
g++8 -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Sun May 19 11:49:31 UTC 2019 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.0f/source"' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc8 -Wl,-rpath=/usr/local/lib/gcc8 ParametersSolo.cpp
g++8 -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Sun May 19 11:49:31 UTC 2019 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.0f/source"' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc8 -Wl,-rpath=/usr/local/lib/gcc8 SoloRead.cpp
g++8 -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Sun May 19 11:49:31 UTC 2019 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.0f/source"' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc8 -Wl,-rpath=/usr/local/lib/gcc8 SoloRead_record.cpp
g++8 -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Sun May 19 11:49:31 UTC 2019 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.0f/source"' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc8 -Wl,-rpath=/usr/local/lib/gcc8 SoloReadBarcode.cpp
g++8 -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Sun May 19 11:49:31 UTC 2019 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.0f/source"' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc8 -Wl,-rpath=/usr/local/lib/gcc8 SoloReadBarcode_getCBandUMI.cpp
g++8 -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Sun May 19 11:49:31 UTC 2019 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.0f/source"' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc8 -Wl,-rpath=/usr/local/lib/gcc8 SoloReadFeature.cpp
g++8 -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Sun May 19 11:49:31 UTC 2019 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.0f/source"' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc8 -Wl,-rpath=/usr/local/lib/gcc8 SoloReadFeature_record.cpp
g++8 -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Sun May 19 11:49:31 UTC 2019 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.0f/source"' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc8 -Wl,-rpath=/usr/local/lib/gcc8 SoloReadFeature_inputRecords.cpp
g++8 -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Sun May 19 11:49:31 UTC 2019 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.0f/source"' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc8 -Wl,-rpath=/usr/local/lib/gcc8 Solo.cpp
g++8 -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Sun May 19 11:49:31 UTC 2019 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.0f/source"' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc8 -Wl,-rpath=/usr/local/lib/gcc8 SoloFeature.cpp
g++8 -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Sun May 19 11:49:31 UTC 2019 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.0f/source"' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc8 -Wl,-rpath=/usr/local/lib/gcc8 SoloFeature_collapseUMI.cpp
g++8 -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Sun May 19 11:49:31 UTC 2019 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.0f/source"' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc8 -Wl,-rpath=/usr/local/lib/gcc8 SoloFeature_outputResults.cpp
g++8 -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Sun May 19 11:49:31 UTC 2019 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.0f/source"' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc8 -Wl,-rpath=/usr/local/lib/gcc8 SoloFeature_processRecords.cpp
g++8 -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Sun May 19 11:49:31 UTC 2019 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.0f/source"' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc8 -Wl,-rpath=/usr/local/lib/gcc8 ReadAlign_outputAlignments.cpp
g++8 -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Sun May 19 11:49:31 UTC 2019 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.0f/source"' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc8 -Wl,-rpath=/usr/local/lib/gcc8 ReadAlign.cpp
g++8 -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Sun May 19 11:49:31 UTC 2019 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.0f/source"' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc8 -Wl,-rpath=/usr/local/lib/gcc8 STAR.cpp
In file included from /usr/local/lib/gcc8/include/c++/vector:69,
from IncludeDefine.h:14,
from STAR.cpp:4:
/usr/local/lib/gcc8/include/c++/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/local/lib/gcc8/include/c++/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/local/lib/gcc8/include/c++/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/local/lib/gcc8/include/c++/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
g++8 -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Sun May 19 11:49:31 UTC 2019 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.0f/source"' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc8 -Wl,-rpath=/usr/local/lib/gcc8 SharedMemory.cpp
g++8 -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Sun May 19 11:49:31 UTC 2019 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.0f/source"' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc8 -Wl,-rpath=/usr/local/lib/gcc8 PackedArray.cpp
g++8 -c -std=c++11 -Wall -Wextra -fopenmp -D'COMPILATION_TIME_PLACE="Sun May 19 11:49:31 UTC 2019 :/wrkdirs/usr/ports/biology/star/work/STAR-2.7.0f/source"' -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc8 -Wl,-rpath=/usr/local/lib/gcc8 SuffixArrayFuns.cpp
In file included from SuffixArrayFuns.h:4,
from SuffixArrayFuns.cpp:1:
SuffixArrayFuns.cpp: In function 'long long unsigned int funCalcSAiFromSA(char*, PackedArray&, Genome&, long long unsigned int, int, int&)':
IncludeDefine.h:58:17: error: '__uint128_t' does not name a type; did you mean '__uint32_t'?
#define uint128 __uint128_t
^~~~~~~~~~~
SuffixArrayFuns.cpp:350:18: note: in expansion of macro 'uint128'
register uint128 g1=*( (uint128*) (gSeq+SAstr) );
^~~~~~~
SuffixArrayFuns.cpp:353:37: error: 'g1' was not declared in this scope
register char g2=(char) g1;
^~
SuffixArrayFuns.cpp:353:37: note: suggested alternative: 'g2'
register char g2=(char) g1;
^~
g2
In file included from SuffixArrayFuns.h:4,
from SuffixArrayFuns.cpp:1:
IncludeDefine.h:58:17: error: '__uint128_t' does not name a type; did you mean '__uint32_t'?
#define uint128 __uint128_t
^~~~~~~~~~~
SuffixArrayFuns.cpp:367:18: note: in expansion of macro 'uint128'
register uint128 g1=*( (uint128*) (gSeq+mapGen.nGenome-SAstr-16) );
^~~~~~~
SuffixArrayFuns.cpp:370:38: error: 'g1' was not declared in this scope
register char g2=(char) (g1>>(8*(15-ii)));
^~
SuffixArrayFuns.cpp:370:38: note: suggested alternative: 'g2'
register char g2=(char) (g1>>(8*(15-ii)));
^~
g2
SuffixArrayFuns.cpp:341:29: warning: unused parameter 'gSeq' [-Wunused-parameter]
uint funCalcSAiFromSA(char* gSeq, PackedArray& gSA, Genome &mapGen, uint iSA, int L, int & iL4)
~~~~~~^~~~
gmake[1]: *** [Makefile:66: SuffixArrayFuns.o] Error 1
gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/star/work/STAR-2.7.0f/source'
*** Error code 1
Stop.
make: stopped in /usr/ports/biology/star
More information about the freebsd-pkg-fallout
mailing list