[package - 124i386-default][biology/kallisto] Failed for kallisto-0.50.0,1 in build
- Go to: [ bottom of page ] [ top of archives ] [ this month ]
Date: Sat, 15 Jul 2023 08:13:32 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: jwb@FreeBSD.org
Log URL: https://pkg-status.freebsd.org/beefy5/data/124i386-default/8fb94260154e/logs/kallisto-0.50.0,1.log
Build URL: https://pkg-status.freebsd.org/beefy5/build.html?mastername=124i386-default&build=8fb94260154e
Log:
=>> Building biology/kallisto
build started at Sat Jul 15 08:12:57 UTC 2023
port directory: /usr/ports/biology/kallisto
package name: kallisto-0.50.0,1
building for: FreeBSD 124i386-default-job-13 12.4-RELEASE-p3 FreeBSD 12.4-RELEASE-p3 i386
maintained by: jwb@FreeBSD.org
Makefile ident:
Poudriere version: 3.2.8-23-ga7f8d188
Host OSVERSION: 1400089
Jail OSVERSION: 1204000
Job Id: 13
---Begin Environment---
SHELL=/bin/csh
UNAME_p=i386
UNAME_m=i386
OSVERSION=1204000
UNAME_v=FreeBSD 12.4-RELEASE-p3
UNAME_r=12.4-RELEASE-p3
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=3.2.8-23-ga7f8d188
MASTERMNT=/usr/local/poudriere/data/.m/124i386-default/ref
POUDRIERE_BUILD_TYPE=bulk
PACKAGE_BUILDING=yes
SAVED_TERM=
PWD=/usr/local/poudriere/data/.m/124i386-default/ref/.p/pool
P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS
MASTERNAME=124i386-default
SCRIPTPREFIX=/usr/local/share/poudriere
OLDPWD=/usr/local/poudriere/data/.m/124i386-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 kallisto-0.50.0,1:
EXAMPLES=on: Build and/or install examples
===> Use 'make config' to modify these settings
---End OPTIONS List---
--MAINTAINER--
jwb@FreeBSD.org
--End MAINTAINER--
--CONFIGURE_ARGS--
--End CONFIGURE_ARGS--
--CONFIGURE_ENV--
MAKE=gmake XDG_DATA_HOME=/wrkdirs/usr/ports/biology/kallisto/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/kallisto/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/kallisto/work/.cache HOME=/wrkdirs/usr/ports/biology/kallisto/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/kallisto/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/kallisto/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh CMAKE_PREFIX_PATH="/usr/local"
--End CONFIGURE_ENV--
--MAKE_ENV--
XDG_DATA_HOME=/wrkdirs/usr/ports/biology/kallisto/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/kallisto/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/kallisto/work/.cache HOME=/wrkdirs/usr/ports/biology/kallisto/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/kallisto/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/kallisto/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig 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 -isystem /usr/local/include -fno-strict-aliasing " CPP="cpp" CPPFLAGS="-isystem /usr/local/include" LDFLAGS=" -lhts -lz -fstack-protector-strong -L/usr/local/lib " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include " 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--
PORTEXAMPLES="" CMAKE_BUILD_TYPE="release" OSREL=12.4 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/kallisto" EXAMPLESDIR="share/examples/kallisto" DATADIR="share/kallisto" WWWDIR="www/kallisto" ETCDIR="etc/kallisto"
--End PLIST_SUB--
--SUB_LIST--
PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/kallisto DOCSDIR=/usr/local/share/doc/kallisto EXAMPLESDIR=/usr/local/share/examples/kallisto WWWDIR=/usr/local/www/kallisto ETCDIR=/usr/local/etc/kallisto
--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 13.0.0 (git@github.com:llvm/llvm-project.git llvmorg-13.0.0-0-gd7b669b3a303) Target: i386-unknown-freebsd12.4 Thread model: posix InstalledDir: /usr/bin
_ALTCCVERSION_921dbbb2=none
_CXXINTERNAL_acaad9ca=FreeBSD clang version 13.0.0 (git@github.com:llvm/llvm-project.git llvmorg-13.0.0-0-gd7b669b3a303) Target: i386-unknown-freebsd12.4 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_53255a77=yes
CC_OUTPUT_921dbbb2_911cfe02=yes
CC_OUTPUT_921dbbb2_b2657cc3=yes
CC_OUTPUT_921dbbb2_380987f7=yes
CC_OUTPUT_921dbbb2_160933ec=yes
CC_OUTPUT_921dbbb2_fb62803b=yes
CC_OUTPUT_921dbbb2_af59ad06=yes
CC_OUTPUT_921dbbb2_a15f3fcf=yes
_OBJC_CCVERSION_921dbbb2=FreeBSD clang version 13.0.0 (git@github.com:llvm/llvm-project.git llvmorg-13.0.0-0-gd7b669b3a303) Target: i386-unknown-freebsd12.4 Thread model: posix InstalledDir: /usr/bin
_OBJC_ALTCCVERSION_921dbbb2=none
ARCH=i386
OPSYS=FreeBSD
_OSRELEASE=12.4-RELEASE-p3
OSREL=12.4
OSVERSION=1204000
PYTHONBASE=/usr/local
CONFIGURE_MAX_CMD_LEN=524288
HAVE_PORTS_ENV=1
#### Misc Poudriere ####
GID=0
UID=0
DISABLE_MAKE_JOBS=poudriere
---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 BSD2CLAUSE accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===> kallisto-0.50.0,1 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.20.4.pkg
[124i386-default-job-13] Installing pkg-1.20.4...
[124i386-default-job-13] Extracting pkg-1.20.4: .......... done
===> kallisto-0.50.0,1 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of kallisto-0.50.0,1
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> License BSD2CLAUSE accepted by the user
=> pachterlab-kallisto-v0.50.0_GH0.tar.gz doesn't seem to exist in /portdistfiles/.
=> Attempting to fetch https://codeload.github.com/pachterlab/kallisto/tar.gz/v0.50.0?dummy=/pachterlab-kallisto-v0.50.0_GH0.tar.gz
fetch: https://codeload.github.com/pachterlab/kallisto/tar.gz/v0.50.0?dummy=/pachterlab-kallisto-v0.50.0_GH0.tar.gz: size unknown
fetch: https://codeload.github.com/pachterlab/kallisto/tar.gz/v0.50.0?dummy=/pachterlab-kallisto-v0.50.0_GH0.tar.gz: size of remote file is not known
pachterlab-kallisto-v0.50.0_GH0.tar.gz 5799 kB 5652 kBps 01s
===> Fetching all distfiles required by kallisto-0.50.0,1 for building
===========================================================================
=======================<phase: checksum >============================
===> License BSD2CLAUSE accepted by the user
===> Fetching all distfiles required by kallisto-0.50.0,1 for building
=> SHA256 Checksum OK for pachterlab-kallisto-v0.50.0_GH0.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract >============================
===> License BSD2CLAUSE accepted by the user
===> Fetching all distfiles required by kallisto-0.50.0,1 for building
===> Extracting for kallisto-0.50.0,1
=> SHA256 Checksum OK for pachterlab-kallisto-v0.50.0_GH0.tar.gz.
/bin/rm -f -rf /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/htslib
===========================================================================
=======================<phase: patch-depends >============================
===========================================================================
=======================<phase: patch >============================
===> Patching for kallisto-0.50.0,1
===> Applying FreeBSD patches for kallisto-0.50.0,1 from /usr/ports/biology/kallisto/files
===========================================================================
=======================<phase: build-depends >============================
===> kallisto-0.50.0,1 depends on file: /usr/local/bin/cmake - not found
===> Installing existing package /packages/All/cmake-core-3.26.1_1.pkg
<snip>
In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/CompactedDBG.hpp:829:
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/CompactedDBG.tcc:5653:27: warning: implicit conversion from 'unsigned long long' to 'size_t' (aka 'unsigned int') changes value from 18446744073709551615 to 4294967295 [-Wconstant-conversion]
size_t nb_prev_succ = 0xFFFFFFFFFFFFFFFF;
~~~~~~~~~~~~ ^~~~~~~~~~~~~~~~~~
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/CompactedDBG.tcc:4829:38: warning: shift count >= width of type [-Wshift-count-overflow]
size_t pos_id_unitig = id_unitig << 32;
^ ~~
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/IO.tcc:2375:53: note: in instantiation of member function 'CompactedDBG<>::addUnitig' requested here
for (const auto& s : v_seq) addUnitig(s, (s.length() == k_) ? v_kmers_sz++ : v_unitigs_sz++, lck_unitig, lck_kmer);
^
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/IO.tcc:197:13: note: in instantiation of member function 'CompactedDBG<>::makeGraphFromFASTA' requested here
makeGraphFromFASTA(input_graph_fn, nb_threads);
^
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/Bifrost.cpp:655:79: note: in instantiation of member function 'CompactedDBG<>::read' requested here
if (lopt.filename_index_in.length() == 0) success = cdbg1.read(lopt.filename_graph_in, lopt.nb_threads, lopt.verbose);
^
In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/Bifrost.cpp:1:
In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/CompactedDBG.hpp:829:
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/CompactedDBG.tcc:4831:40: warning: implicit conversion from 'unsigned long long' to 'const size_t' (aka 'const unsigned int') changes value from 18446744071562067968 to 2147483648 [-Wconstant-conversion]
const size_t mask = MASK_CONTIG_ID | MASK_CONTIG_TYPE;
~~~~ ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/CompactedDBG.tcc:4758:92: warning: shift count >= width of type [-Wshift-count-overflow]
if (static_cast<bool>(unitig_id_pos & MASK_CONTIG_TYPE) && ((unitig_id_pos >> 32) != RESERVED_ID)) v_km_rm.push_back(unitig_id_pos >> 32);
^ ~~
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/IO.tcc:2385:9: note: in instantiation of member function 'CompactedDBG<>::moveToAbundant' requested here
moveToAbundant();
^
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/IO.tcc:197:13: note: in instantiation of member function 'CompactedDBG<>::makeGraphFromFASTA' requested here
makeGraphFromFASTA(input_graph_fn, nb_threads);
^
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/Bifrost.cpp:655:79: note: in instantiation of member function 'CompactedDBG<>::read' requested here
if (lopt.filename_index_in.length() == 0) success = cdbg1.read(lopt.filename_graph_in, lopt.nb_threads, lopt.verbose);
^
In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/Bifrost.cpp:1:
In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/CompactedDBG.hpp:829:
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/CompactedDBG.tcc:4758:148: warning: shift count >= width of type [-Wshift-count-overflow]
if (static_cast<bool>(unitig_id_pos & MASK_CONTIG_TYPE) && ((unitig_id_pos >> 32) != RESERVED_ID)) v_km_rm.push_back(unitig_id_pos >> 32);
^ ~~
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/CompactedDBG.tcc:4805:78: warning: implicit conversion from 'unsigned long long' to 'size_t' (aka 'unsigned int') changes value from 18446744069414584321 to 1 [-Wconstant-conversion]
else flag_v = v.push_back(MASK_CONTIG_ID + 1, flag_v);
~~~~~~~~~ ~~~~~~~~~~~~~~~^~~
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/CompactedDBG.tcc:6161:42: warning: shift count >= width of type [-Wshift-count-overflow]
size_t pos_id_unitig = id_unitig << 32;
^ ~~
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/CompactedDBG.tcc:4774:25: note: in instantiation of member function 'CompactedDBG<>::deleteUnitig_' requested here
deleteUnitig_(true, false, id_swap, unitig_str);
^
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/IO.tcc:2385:9: note: in instantiation of member function 'CompactedDBG<>::moveToAbundant' requested here
moveToAbundant();
^
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/IO.tcc:197:13: note: in instantiation of member function 'CompactedDBG<>::makeGraphFromFASTA' requested here
makeGraphFromFASTA(input_graph_fn, nb_threads);
^
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/Bifrost.cpp:655:79: note: in instantiation of member function 'CompactedDBG<>::read' requested here
if (lopt.filename_index_in.length() == 0) success = cdbg1.read(lopt.filename_graph_in, lopt.nb_threads, lopt.verbose);
^
In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/Bifrost.cpp:1:
In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/CompactedDBG.hpp:829:
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/CompactedDBG.tcc:6162:44: warning: implicit conversion from 'unsigned long long' to 'const size_t' (aka 'const unsigned int') changes value from 18446744071562067968 to 2147483648 [-Wconstant-conversion]
const size_t mask = MASK_CONTIG_ID | MASK_CONTIG_TYPE;
~~~~ ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~
In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/Bifrost.cpp:1:
In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/CompactedDBG.hpp:831:
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/IO.tcc:1663:34: warning: shift count >= width of type [-Wshift-count-overflow]
if ((file_format_version >> 32) != BFG_GRAPHBIN_FORMAT_HEADER) return {graph_checksum, false};
^ ~~
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/IO.tcc:1631:12: note: in instantiation of member function 'CompactedDBG<>::readBinaryGraph' requested here
return readBinaryGraph(in);
^
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/IO.tcc:383:34: note: in instantiation of member function 'CompactedDBG<>::readBinaryGraph' requested here
p_readSuccess_checksum = readBinaryGraph(input_graph_fn);
^
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/Bifrost.cpp:656:42: note: in instantiation of member function 'CompactedDBG<>::read' requested here
else success = cdbg1.read(lopt.filename_graph_in, lopt.filename_index_in, lopt.nb_threads, lopt.verbose);
^
In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/Bifrost.cpp:1:
In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/CompactedDBG.hpp:831:
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/IO.tcc:1229:52: warning: shift count >= width of type [-Wshift-count-overflow]
if (!read_success || ((file_format_version >> 32) != BFG_METABIN_FORMAT_HEADER)) return false;
^ ~~
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/IO.tcc:1020:12: note: in instantiation of member function 'CompactedDBG<>::readBinaryIndex' requested here
return readBinaryIndex(in, checksum, minz, threads);
^
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/IO.tcc:393:20: note: in instantiation of member function 'CompactedDBG<>::readBinaryIndex' requested here
invalid = !readBinaryIndex(input_index_fn, p_readSuccess_checksum.first);
^
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/Bifrost.cpp:656:42: note: in instantiation of member function 'CompactedDBG<>::read' requested here
else success = cdbg1.read(lopt.filename_graph_in, lopt.filename_index_in, lopt.nb_threads, lopt.verbose);
^
In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/Bifrost.cpp:1:
In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/CompactedDBG.hpp:831:
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/IO.tcc:1259:41: warning: shift count >= width of type [-Wshift-count-overflow]
const size_t id_bmp = i << 32;
^ ~~
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/IO.tcc:1274:61: warning: shift count >= width of type [-Wshift-count-overflow]
const size_t pos_id_unitig = (unitig_id << 32) | relative_pos;
^ ~~
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/IO.tcc:1307:41: warning: shift count >= width of type [-Wshift-count-overflow]
const size_t id_bmp = i << 32;
^ ~~
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/IO.tcc:1316:57: warning: shift count >= width of type [-Wshift-count-overflow]
const size_t pos_id_unitig = (km_id << 32) | MASK_CONTIG_TYPE | km_pos;
^ ~~
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/IO.tcc:1343:66: warning: shift count >= width of type [-Wshift-count-overflow]
vector<BitContainer> v_bmp_abundant((nb_special_minz >> 32) + 1);
^ ~~
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/IO.tcc:1344:69: warning: shift count >= width of type [-Wshift-count-overflow]
vector<BitContainer> v_bmp_overcrowded((nb_special_minz >> 32) + 1);
^ ~~
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/IO.tcc:1353:58: warning: shift count >= width of type [-Wshift-count-overflow]
const bool isAbundant = v_bmp_abundant[i >> 32].contains(i & 0x00000000ffffffffULL);
^ ~~
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/IO.tcc:1354:64: warning: shift count >= width of type [-Wshift-count-overflow]
const bool isOvercrowded = v_bmp_overcrowded[i >> 32].contains(i & 0x00000000ffffffffULL);
^ ~~
In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/Bifrost.cpp:1:
In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/CompactedDBG.hpp:829:
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/CompactedDBG.tcc:5501:27: warning: implicit conversion from 'unsigned long long' to 'size_t' (aka 'unsigned int') changes value from 18446744073709551615 to 4294967295 [-Wconstant-conversion]
size_t nb_prev_pred = 0xFFFFFFFFFFFFFFFF;
~~~~~~~~~~~~ ^~~~~~~~~~~~~~~~~~
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/CompactedDBG.tcc:2248:42: note: in instantiation of member function 'CompactedDBG<>::annotateSplitUnitig' requested here
for (const auto& unitig : o) annotateSplitUnitig(unitig.referenceUnitigToString(), false);
^
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/CompactedDBG.tcc:2134:13: note: in instantiation of member function 'CompactedDBG<>::annotateSplitUnitigs' requested here
if (annotateSplitUnitigs(o, nb_threads, verbose)){
^
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/Bifrost.cpp:676:50: note: in instantiation of member function 'CompactedDBG<>::merge' requested here
success = cdbg_a.merge(cdbg_b, lopt.nb_threads, lopt.verbose);
^
In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/Bifrost.cpp:1:
In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/CompactedDBG.hpp:829:
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/CompactedDBG.tcc:5502:27: warning: implicit conversion from 'unsigned long long' to 'size_t' (aka 'unsigned int') changes value from 18446744073709551615 to 4294967295 [-Wconstant-conversion]
size_t nb_prev_succ = 0xFFFFFFFFFFFFFFFF;
~~~~~~~~~~~~ ^~~~~~~~~~~~~~~~~~
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/CompactedDBG.tcc:5652:27: warning: implicit conversion from 'unsigned long long' to 'size_t' (aka 'unsigned int') changes value from 18446744073709551615 to 4294967295 [-Wconstant-conversion]
size_t nb_prev_pred = 0xFFFFFFFFFFFFFFFF;
~~~~~~~~~~~~ ^~~~~~~~~~~~~~~~~~
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/CompactedDBG.tcc:2289:33: note: in instantiation of member function 'CompactedDBG<>::annotateSplitUnitig' requested here
annotateSplitUnitig(it_unitig->referenceUnitigToString(), lck_g/*, t*/, false);
^
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/CompactedDBG.tcc:2134:13: note: in instantiation of member function 'CompactedDBG<>::annotateSplitUnitigs' requested here
if (annotateSplitUnitigs(o, nb_threads, verbose)){
^
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/Bifrost.cpp:676:50: note: in instantiation of member function 'CompactedDBG<>::merge' requested here
success = cdbg_a.merge(cdbg_b, lopt.nb_threads, lopt.verbose);
^
In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/Bifrost.cpp:1:
In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/CompactedDBG.hpp:829:
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/CompactedDBG.tcc:5653:27: warning: implicit conversion from 'unsigned long long' to 'size_t' (aka 'unsigned int') changes value from 18446744073709551615 to 4294967295 [-Wconstant-conversion]
size_t nb_prev_succ = 0xFFFFFFFFFFFFFFFF;
~~~~~~~~~~~~ ^~~~~~~~~~~~~~~~~~
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/CompactedDBG.tcc:795:43: warning: shift count >= width of type [-Wshift-count-overflow]
unitig_id = unitig_id_pos >> 32;
^ ~~
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/CompactedDBG.tcc:4537:32: note: in instantiation of member function 'CompactedDBG<DataAccessor<void>, DataStorage<>>::find' requested here
const_UnitigMap<U, G> um = find(s, pos, it_min);
^
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/Search.tcc:668:62: note: in instantiation of member function 'CompactedDBG<DataAccessor<void>, DataStorage<>>::findUnitig' requested here
const const_UnitigMap<U, G> um = findUnitig(s_inexact_str, pos_s, s_inexact_len, mhi);
^
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/ColoredCDBG.tcc:1570:76: note: in instantiation of member function 'CompactedDBG<DataAccessor<void>, DataStorage<>>::searchSequence' requested here
const vector<pair<size_t, const_UnitigColorMap<U>>> v_um_e = this->searchSequence(query, true, false, false, false, false);
^
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/Bifrost.cpp:696:50: note: in instantiation of member function 'ColoredCDBG<>::search' requested here
if (success) success = ccdbg.search(opt.filename_query_in, opt.prefixFilenameOut, opt.ratio_kmers, opt.inexact_search, opt.nb_threads, opt.verbose);
^
In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/Bifrost.cpp:1:
In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/CompactedDBG.hpp:829:
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/CompactedDBG.tcc:795:43: warning: shift count >= width of type [-Wshift-count-overflow]
unitig_id = unitig_id_pos >> 32;
^ ~~
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/CompactedDBG.tcc:4537:32: note: in instantiation of member function 'CompactedDBG<>::find' requested here
const_UnitigMap<U, G> um = find(s, pos, it_min);
^
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/Search.tcc:937:62: note: in instantiation of member function 'CompactedDBG<>::findUnitig' requested here
const const_UnitigMap<U, G> um = findUnitig(s_inexact_str, pos_s, s_inexact_len, mhi);
^
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/Search.tcc:1132:71: note: in instantiation of member function 'CompactedDBG<>::searchSequence' requested here
const vector<pair<size_t, const_UnitigMap<U, G>>> v = dbg.searchSequence( s, true, inexact_search, inexact_search,
^
/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/Bifrost.cpp:705:49: note: in instantiation of member function 'CompactedDBG<>::search' requested here
if (success) success = cdbg.search(opt.filename_query_in, opt.prefixFilenameOut, opt.ratio_kmers, opt.inexact_search, opt.nb_threads, opt.verbose);
^
214 warnings and 9 errors generated.
gmake[6]: *** [src/CMakeFiles/bifrost_static.dir/build.make:76: src/CMakeFiles/bifrost_static.dir/Bifrost.cpp.o] Error 1
gmake[6]: Leaving directory '/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/build'
gmake[5]: *** [CMakeFiles/Makefile2:102: src/CMakeFiles/bifrost_static.dir/all] Error 2
gmake[5]: Leaving directory '/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/build'
gmake[4]: *** [Makefile:136: all] Error 2
gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/build'
gmake[3]: *** [CMakeFiles/bifrost.dir/build.make:89: /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/bifrost-stamp/bifrost-build] Error 2
gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/kallisto/work/.build'
gmake[2]: *** [CMakeFiles/Makefile2:105: CMakeFiles/bifrost.dir/all] Error 2
gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/kallisto/work/.build'
gmake[1]: *** [Makefile:139: all] Error 2
gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/kallisto/work/.build'
*** Error code 1
Stop.
make: stopped in /usr/ports/biology/kallisto