+ case "${usergroup_phase}" in
+ local run_cmd
+ run_cmd=run_su
+ shift
+ run_su /opt/pkg/bin/bmake configure BATCH=1 DEPENDS_TARGET=/nonexistent PYTHON_VERSION_REQD=311 WRKLOG=/tmp/bulklog/ncbi-blast+-2.14.1nb2/work.log
+ su pbulk -c '"$@"' make /opt/pkg/bin/bmake configure BATCH=1 DEPENDS_TARGET=/nonexistent PYTHON_VERSION_REQD=311 WRKLOG=/tmp/bulklog/ncbi-blast+-2.14.1nb2/work.log
=> Bootstrap dependency digest>=20211023: found digest-20220214
=> Checksum BLAKE2s OK for ncbi-blast-2.14.1+-src.tar.gz
=> Checksum SHA512 OK for ncbi-blast-2.14.1+-src.tar.gz
===> Installing dependencies for ncbi-blast+-2.14.1nb2
==========================================================================
The following variables will affect the build process of this package,
ncbi-blast+-2.14.1nb2. Their current value is shown below:
* PYTHON_VERSION_DEFAULT = 311
Based on these variables, the following variables have been set:
* PYPACKAGE = python311
You may want to abort the process now with CTRL-C and change the value
of variables in the first group before continuing. Be sure to run
`/opt/pkg/bin/bmake clean' after the changes.
==========================================================================
=> Tool dependency mktools-[0-9]*: found mktools-20220614
=> Tool dependency gmake>=3.81: found gmake-4.4.1
=> Tool dependency perl>=5.0: found perl-5.38.2
=> Tool dependency cwrappers>=20150314: found cwrappers-20220403
=> Tool dependency checkperms>=1.1: found checkperms-1.12
=> Full dependency zlib>=1.2.3: found zlib-1.3.1
=> Full dependency lzo>=2.01: found lzo-2.10
=> Full dependency bzip2>=1.0.3: found bzip2-1.0.8
=> Full dependency zstd>=1.3.6: found zstd-1.5.5
=> Full dependency pcre>=8.30nb1: found pcre-8.45
=> Full dependency lmdb>=0.9.14: found lmdb-0.9.32
=> Full dependency gnutls>=3.8.1nb2: found gnutls-3.8.3
=> Full dependency libtasn1>=0.3.0: found libtasn1-4.19.0
=> Full dependency nettle>=3.6: found nettle-3.9.1
=> Full dependency gmp>=6.0: found gmp-6.3.0
=> Full dependency p11-kit>=0.24.0nb3: found p11-kit-0.25.3
=> Full dependency libidn2>=2.3.3nb1: found libidn2-2.3.7
=> Full dependency libgcrypt>=1.6.0: found libgcrypt-1.10.3
=> Full dependency libgpg-error>=1.10nb1: found libgpg-error-1.47nb1
=> Full dependency sqlite3>=3.44.0nb1: found sqlite3-3.45.1
=> Full dependency python311>=3.11.0: found python311-3.11.8
===> Overriding tools for ncbi-blast+-2.14.1nb2
===> Extracting for ncbi-blast+-2.14.1nb2
===> Patching for ncbi-blast+-2.14.1nb2
=> Applying pkgsrc patches for ncbi-blast+-2.14.1nb2
=> Verifying /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/ncbi-blast+/patches/patch-compilers_xcode30__prj_configure
=> Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/ncbi-blast+/patches/patch-compilers_xcode30__prj_configure
Hmm... Looks like a unified diff to me...
The text leading up to this was:
--------------------------
|$NetBSD: patch-compilers_xcode30__prj_configure,v 1.2 2023/09/14 00:39:17 bacon Exp $
|
|# Nonportable extension
|
|--- compilers/xcode30_prj/configure.orig 2023-08-26 13:06:39.313163201 +0000
|+++ compilers/xcode30_prj/configure
--------------------------
Patching file compilers/xcode30_prj/configure using Plan A...
Hunk #1 succeeded at 284.
done
=> Verifying /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/ncbi-blast+/patches/patch-src_algo_blast_core_blast__kappa.c
=> Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/ncbi-blast+/patches/patch-src_algo_blast_core_blast__kappa.c
Hmm... Looks like a unified diff to me...
The text leading up to this was:
--------------------------
|$NetBSD: patch-src_algo_blast_core_blast__kappa.c,v 1.2 2019/01/07 15:00:10 bacon Exp $
|
|# Work around NetBSD stderr def choking macro
|
|--- src/algo/blast/core/blast_kappa.c.orig 2019-01-02 04:00:17.000000000 +0000
|+++ src/algo/blast/core/blast_kappa.c
--------------------------
Patching file src/algo/blast/core/blast_kappa.c using Plan A...
Hunk #1 succeeded at 32.
Hunk #2 succeeded at 58.
Hunk #3 succeeded at 3427 (offset 14 lines).
done
=> Verifying /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/ncbi-blast+/patches/patch-src_build-system_Makefile.in.top
=> Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/ncbi-blast+/patches/patch-src_build-system_Makefile.in.top
Hmm... Looks like a unified diff to me...
The text leading up to this was:
--------------------------
|$NetBSD: patch-src_build-system_Makefile.in.top,v 1.1 2018/04/27 20:28:28 bacon Exp $
|
|# Add destdir suppot and fix perms on installed files
|
|--- src/build-system/Makefile.in.top.orig 2017-02-01 16:52:02.000000000 +0000
|+++ src/build-system/Makefile.in.top
--------------------------
Patching file src/build-system/Makefile.in.top using Plan A...
Hunk #1 succeeded at 37.
done
=> Verifying /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/ncbi-blast+/patches/patch-src_build-system_cmake_cmake-cfg-xcode.sh
=> Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/ncbi-blast+/patches/patch-src_build-system_cmake_cmake-cfg-xcode.sh
Hmm... Looks like a unified diff to me...
The text leading up to this was:
--------------------------
|$NetBSD: patch-src_build-system_cmake_cmake-cfg-xcode.sh,v 1.3 2023/05/28 22:48:27 bacon Exp $
|
|# sh portability
|
|--- src/build-system/cmake/cmake-cfg-xcode.sh.orig 2023-05-26 12:05:14.109542442 +0000
|+++ src/build-system/cmake/cmake-cfg-xcode.sh
--------------------------
Patching file src/build-system/cmake/cmake-cfg-xcode.sh using Plan A...
Hunk #1 succeeded at 257 (offset 8 lines).
done
=> Verifying /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/ncbi-blast+/patches/patch-src_build-system_configure
=> Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/ncbi-blast+/patches/patch-src_build-system_configure
Hmm... Looks like a unified diff to me...
The text leading up to this was:
--------------------------
|$NetBSD: patch-src_build-system_configure,v 1.4 2023/05/28 22:48:27 bacon Exp $
|
|# Avert missing --with-libiconv-prefix option
|
|--- src/build-system/configure.orig 2021-06-10 19:44:11.069762486 +0000
|+++ src/build-system/configure
--------------------------
Patching file src/build-system/configure using Plan A...
Hunk #1 succeeded at 2057 (offset 42 lines).
done
=> Verifying /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/ncbi-blast+/patches/patch-src_build-system_helpers_Makefile.run__with__lock.app
=> Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/ncbi-blast+/patches/patch-src_build-system_helpers_Makefile.run__with__lock.app
Hmm... Looks like a unified diff to me...
The text leading up to this was:
--------------------------
|$NetBSD: patch-src_build-system_helpers_Makefile.run__with__lock.app,v 1.2 2018/05/22 21:37:29 bacon Exp $
|
|# Missing RELRO for this one binary
|# https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=820959
|
|--- src/build-system/helpers/Makefile.run_with_lock.app.orig 2016-02-23 17:06:47.000000000 +0000
|+++ src/build-system/helpers/Makefile.run_with_lock.app
--------------------------
Patching file src/build-system/helpers/Makefile.run_with_lock.app using Plan A...
Hunk #1 succeeded at 6.
done
=> Verifying /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/ncbi-blast+/patches/patch-src_util_checksum_cityhash_city.cc
=> Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/ncbi-blast+/patches/patch-src_util_checksum_cityhash_city.cc
Hmm... Looks like a unified diff to me...
The text leading up to this was:
--------------------------
|$NetBSD: patch-src_util_checksum_cityhash_city.cc,v 1.1 2023/05/28 22:48:27 bacon Exp $
|
|Ensure bswap_32() and bswap_64() is defined on NetBSD.
|
|--- src/util/checksum/cityhash/city.cc.orig 2018-09-28 20:34:39.000000000 +0000
|+++ src/util/checksum/cityhash/city.cc
--------------------------
Patching file src/util/checksum/cityhash/city.cc using Plan A...
Hunk #1 succeeded at 82.
done
=> Verifying /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/ncbi-blast+/patches/patch-src_util_checksum_farmhash_farmhash.cc
=> Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/ncbi-blast+/patches/patch-src_util_checksum_farmhash_farmhash.cc
Hmm... Looks like a unified diff to me...
The text leading up to this was:
--------------------------
|$NetBSD: patch-src_util_checksum_farmhash_farmhash.cc,v 1.1 2023/05/28 22:48:27 bacon Exp $
|
|Ensure bswap_32() and bswap_64() gets defined on NetBSD.
|
|--- src/util/checksum/farmhash/farmhash.cc.orig 2018-09-26 12:38:06.000000000 +0000
|+++ src/util/checksum/farmhash/farmhash.cc
--------------------------
Patching file src/util/checksum/farmhash/farmhash.cc using Plan A...
Hunk #1 succeeded at 158.
done
=> Verifying /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/ncbi-blast+/patches/patch-src_util_checksum_farmhash_farmhash.h
=> Applying pkgsrc patch /data/jenkins/workspace/pkgsrc-upstream-trunk/biology/ncbi-blast+/patches/patch-src_util_checksum_farmhash_farmhash.h
Hmm... Looks like a unified diff to me...
The text leading up to this was:
--------------------------
|$NetBSD: patch-src_util_checksum_farmhash_farmhash.h,v 1.1 2019/01/07 15:00:11 bacon Exp $
|
|# __GNUC__ does not imply location of endian.h. Check for BSD first.
|
|--- src/util/checksum/farmhash/farmhash.h.orig 2018-09-26 12:38:06.000000000 +0000
|+++ src/util/checksum/farmhash/farmhash.h
--------------------------
Patching file src/util/checksum/farmhash/farmhash.h using Plan A...
Hunk #1 succeeded at 305.
done
===> Creating toolchain wrappers for ncbi-blast+-2.14.1nb2
===> Configuring for ncbi-blast+-2.14.1nb2
=> Substituting "configure" in src/build-system/configure
=> Modifying GNU configure scripts to avoid --recheck
=> Replacing config-guess with pkgsrc versions
=> Replacing config-sub with pkgsrc versions
=> Replacing install-sh with pkgsrc version
=> Replacing python interpreter in src/app/winmasker/windowmasker_2.2.22_adapter.py src/app/blast/cleanup-blastdb-volumes.py.
=> Replacing bash interpreter in scripts/common/impl/define_random_macros.sh src/app/blast/get_species_taxids.sh.
INFO: [replace-interpreter] Nothing changed in src/app/blast/get_species_taxids.sh.
=> Replacing Perl interpreter in src/app/blast/legacy_blast.pl src/app/blast/update_blastdb.pl.
=> Checking for portability problems in extracted files
configure: WARNING: unrecognized options: --with-libiconv-prefix
touch: cannot create configure.lock/for-root@/bin/hostname: No such file or directory
configure: loading site script ./src/build-system/config.site
configure: creating cache config.cache
checking TeamCity build number... none
checking VCS revision... unknown
checking NCBI stable components' version... unknown
checking build system type... x86_64-sun-solaris2.11
checking host system type... x86_64-sun-solaris2.11
checking for a BSD-compatible install... /opt/pkg/bin/bsdinstall -c -o pbulk -g pbulk
checking for x86_64-sun-solaris2.11-gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -E
checking for x86_64-sun-solaris2.11-gcc... no
checking for gcc... gcc
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking how to run the C preprocessor... gcc -E
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
adjusted C compiler: /home/pbulk/build/biology/ncbi-blast+/work/.cwrapper/bin/gcc
adjusted C++ compiler: /home/pbulk/build/biology/ncbi-blast+/work/.cwrapper/bin/g++
checking for grep that handles long lines and -e... (cached) /usr/xpg4/bin/grep
checking for egrep... (cached) /usr/xpg4/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
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checking for unistd.h... yes
checking minix/config.h usability... no
checking minix/config.h presence... no
checking for minix/config.h... no
checking whether it is safe to define __EXTENSIONS__... yes
checking whether /home/pbulk/build/biology/ncbi-blast+/work/.cwrapper/bin/gcc has an option to export all symbols... -rdynamic
checking whether /home/pbulk/build/biology/ncbi-blast+/work/.cwrapper/bin/gcc supports -Wl,--{en,dis}able-new-dtags... no
checking whether /home/pbulk/build/biology/ncbi-blast+/work/.cwrapper/bin/gcc has an option to discard unneeded shared libraries... no
checking whether /home/pbulk/build/biology/ncbi-blast+/work/.cwrapper/bin/gcc has an option to link in whole static archives... -Wl,--whole-archive
checking whether _LIBCPP_VERSION is declared... no
checking how to enable modern C++ features in /home/pbulk/build/biology/ncbi-blast+/work/.cwrapper/bin/g++ ... -std=gnu++17
checking how to enable modern C features in /home/pbulk/build/biology/ncbi-blast+/work/.cwrapper/bin/gcc ... -std=gnu18 -fgnu89-inline
checking whether /home/pbulk/build/biology/ncbi-blast+/work/.cwrapper/bin/gcc supports -msse4.2... yes
checking whether /home/pbulk/build/biology/ncbi-blast+/work/.cwrapper/bin/g++ -std=gnu++17 supports -msse4.2... yes
checking for dpkg-architecture... no
checking for gawk... /usr/bin/nawk
checking for GNU make... make
checking for /usr/bin/nawk... /usr/bin/nawk
checking for make... /home/pbulk/build/biology/ncbi-blast+/work/.tools/bin/make
checking whether ln -s works... yes
checking for x86_64-sun-solaris2.11-ranlib... no
checking for ranlib... ranlib
checking for ar... ar cr
checking ranlib's effectiveness... neutral
checking for strip... @:
checking whether strip loses runtime type information... /home/pbulk/build/biology/ncbi-blast+/work/ncbi-blast-2.14.1+-src/c++/src/build-system/configure: line 11633: @:: command not found
no
checking for ccache... no
checking for tail... /home/pbulk/build/biology/ncbi-blast+/work/.tools/bin/tail
checking whether /home/pbulk/build/biology/ncbi-blast+/work/.tools/bin/tail accepts modern syntax (-n N)... yes
checking for basename... /home/pbulk/build/biology/ncbi-blast+/work/.tools/bin/basename
checking for sed... /usr/bin/sed
checking for touch... /usr/bin/touch
checking for egrep... (cached) /usr/xpg4/bin/grep -E
checking how to run /usr/xpg4/bin/grep -E quietly... /usr/xpg4/bin/grep -E -q
checking for valgrind... no
checking for ldd... /bin/ldd
checking whether /bin/ldd accepts -r... yes
checking for uuidgen... /usr/bin/uuidgen
checking for cd_reporter... no
checking for size_t... yes
checking size of size_t... 8
checking for amq... no
checking whether /home/pbulk/build/biology/ncbi-blast+/work/.cwrapper/bin/gcc -msse4.2 -std=gnu18 -fgnu89-inline -D_XOPEN_SOURCE=600 supports -Wl,--no-allow-shlib-undefined... no
checking how to run the C preprocessor... gcc -E
checking whether cross-directory hard links work... yes
checking how to run the C++ preprocessor... /home/pbulk/build/biology/ncbi-blast+/work/.cwrapper/bin/g++ -std=gnu++17 -msse4.2 -E
checking iostream usability... yes
checking iostream presence... yes
checking for iostream... yes
checking iostream.h usability... no
checking iostream.h presence... no
checking for iostream.h... no
checking fstream usability... yes
checking fstream presence... yes
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checking fstream.h usability... no
checking fstream.h presence... no
checking for fstream.h... no
checking strstream usability... yes
checking strstream presence... yes
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checking strstream.h usability... no
checking strstream.h presence... no
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checking strstrea.h usability... no
checking strstrea.h presence... no
checking for strstrea.h... no
checking for inttypes.h... (cached) yes
checking limits usability... yes
checking limits presence... yes
checking for limits... yes
checking limits.h usability... yes
checking limits.h presence... yes
checking for limits.h... yes
checking for unistd.h... (cached) yes
checking windows.h usability... no
checking windows.h presence... no
checking for windows.h... no
checking for wstring... yes
checking for socklen_t... yes
checking atomic.h usability... yes
checking atomic.h presence... yes
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checking cpuid.h usability... yes
checking cpuid.h presence... yes
checking for cpuid.h... yes
checking dlfcn.h usability... yes
checking dlfcn.h presence... yes
checking for dlfcn.h... yes
checking ieeefp.h usability... yes
checking ieeefp.h presence... yes
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checking poll.h usability... yes
checking poll.h presence... yes
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checking sys/epoll.h usability... yes
checking sys/epoll.h presence... yes
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checking sys/mount.h usability... yes
checking sys/mount.h presence... yes
checking for sys/mount.h... yes
checking sys/sockio.h usability... yes
checking sys/sockio.h presence... yes
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checking sys/statvfs.h usability... yes
checking sys/statvfs.h presence... yes
checking for sys/statvfs.h... yes
checking sys/sysinfo.h usability... yes
checking sys/sysinfo.h presence... yes
checking for sys/sysinfo.h... yes
checking sys/sysmacros.h usability... yes
checking sys/sysmacros.h presence... yes
checking for sys/sysmacros.h... yes
checking sys/vfs.h usability... yes
checking sys/vfs.h presence... yes
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checking x86intrin.h usability... yes
checking x86intrin.h presence... yes
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checking alloca.h usability... yes
checking alloca.h presence... yes
checking for alloca.h... yes
checking arpa/inet.h usability... yes
checking arpa/inet.h presence... yes
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checking dirent.h usability... yes
checking dirent.h presence... yes
checking for dirent.h... yes
checking errno.h usability... yes
checking errno.h presence... yes
checking for errno.h... yes
checking fcntl.h usability... yes
checking fcntl.h presence... yes
checking for fcntl.h... yes
checking getopt.h usability... yes
checking getopt.h presence... yes
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checking langinfo.h usability... yes
checking langinfo.h presence... yes
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checking libgen.h usability... yes
checking libgen.h presence... yes
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checking locale.h usability... yes
checking locale.h presence... yes
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checking malloc.h usability... yes
checking malloc.h presence... yes
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checking net/inet/in.h usability... no
checking net/inet/in.h presence... no
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checking netdb.h usability... yes
checking netdb.h presence... yes
checking for netdb.h... yes
checking netinet/in.h usability... yes
checking netinet/in.h presence... yes
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checking netinet/tcp.h usability... yes
checking netinet/tcp.h presence... yes
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checking paths.h usability... yes
checking paths.h presence... yes
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checking select.h usability... no
checking select.h presence... no
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checking signal.h usability... yes
checking signal.h presence... yes
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checking stdbool.h usability... yes
checking stdbool.h presence... yes
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checking stddef.h usability... yes
checking stddef.h presence... yes
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checking sys/eventfd.h usability... yes
checking sys/eventfd.h presence... yes
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checking sys/file.h usability... yes
checking sys/file.h presence... yes
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checking sys/ioctl.h usability... yes
checking sys/ioctl.h presence... yes
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checking sys/param.h usability... yes
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checking sys/resource.h usability... yes
checking sys/resource.h presence... yes
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checking sys/select.h presence... yes
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checking sys/socket.h usability... yes
checking sys/socket.h presence... yes
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checking sys/time.h usability... yes
checking sys/time.h presence... yes
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checking sys/wait.h usability... yes
checking sys/wait.h presence... yes
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checking valgrind/memcheck.h usability... no
checking valgrind/memcheck.h presence... no
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checking wchar.h usability... yes
checking wchar.h presence... yes
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checking whether time.h and sys/time.h may both be included... yes
checking cxxabi.h usability... yes
checking cxxabi.h presence... yes
checking for cxxabi.h... yes
checking whether abi::__cxa_demangle is declared... yes
checking omp.h usability... yes
checking omp.h presence... yes
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checking for gethostbyname_r... 5
checking for gethostbyaddr_r... 7
checking for getservbyname_r... 5
checking for getpwuid_r... 5
checking for getlogin_r... yes
checking for localtime_r... yes
checking for pthread_setconcurrency... yes
checking for pthread_atfork... yes
checking return type of localtime_r... struct
checking whether pthread mutexes are available... yes
checking for vprintf... yes
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checking for dbopen... no
checking for daemon... yes
checking for euidaccess... no
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checking for lchown... yes
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checking for malloc_options... no
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checking for poll... yes
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checking for readpassphrase... no
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checking for setenv... yes
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checking for setrlimit... yes
checking for snprintf... yes
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checking for statvfs... yes
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checking for strlcat... yes
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checking for strnlen... yes
checking for strsep... yes
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checking for sysmp... no
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checking for utimes... yes
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checking for writev... yes
checking return type of signal handlers... void
checking whether select updates the timeout when interrupted... no
checking whether strcasecmp treats letters as lowercase... yes
checking for Linux-like sysinfo with 1 arg... no
checking for getloadavg... yes
checking for readdir_r... 3
checking whether stdio supports locking... yes
checking for an ANSI C-conforming const... yes
checking whether byte ordering is bigendian... no
checking whether char is unsigned... no
checking size of char... 1
checking size of double... 8
checking size of float... 4
checking size of int... 4
checking size of long... 8
checking size of long double... 16
checking size of long long... 8
checking size of short... 2
checking size of void*... 8
checking size of wchar_t... 4
checking size of __int64... 0
checking for intptr_t... yes
checking for uintptr_t... yes
checking for struct sockaddr_in.sin_len... no
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from distutils import sysconfig
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from distutils import sysconfig
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from distutils import sysconfig
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configure: ...done
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/home/pbulk/build/biology/ncbi-blast+/work/ncbi-blast-2.14.1+-src/c++/ReleaseMT/build/corelib/ncbicfg.c is updated
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Build session ID: 8e0618ac-22cd-4736-975d-d08c7957cee8
/home/pbulk/build/biology/ncbi-blast+/work/.tools/bin/make -f /home/pbulk/build/biology/ncbi-blast+/work/ncbi-blast-2.14.1+-src/c++/ReleaseMT/build/Makefile.app.tmpl srcdir=/home/pbulk/build/biology/ncbi-blast+/work/ncbi-blast-2.14.1+-src/c++/src/build-system/helpers TMPL=run_with_lock -k flag-stamps
touch: cannot create make_run_with_lock.lock/for-root@/bin/hostname: No such file or directory
make[1]: Entering directory '/home/pbulk/build/biology/ncbi-blast+/work/ncbi-blast-2.14.1+-src/c++/ReleaseMT/build/build-system/helpers'
make[1]: Leaving directory '/home/pbulk/build/biology/ncbi-blast+/work/ncbi-blast-2.14.1+-src/c++/ReleaseMT/build/build-system/helpers'
/home/pbulk/build/biology/ncbi-blast+/work/.tools/bin/make -f /home/pbulk/build/biology/ncbi-blast+/work/ncbi-blast-2.14.1+-src/c++/ReleaseMT/build/Makefile.app.tmpl srcdir=/home/pbulk/build/biology/ncbi-blast+/work/ncbi-blast-2.14.1+-src/c++/src/build-system/helpers TMPL=run_with_lock -k all
touch: cannot create make_run_with_lock.lock/for-root@/bin/hostname: No such file or directory
make[1]: Entering directory '/home/pbulk/build/biology/ncbi-blast+/work/ncbi-blast-2.14.1+-src/c++/ReleaseMT/build/build-system/helpers'
Updating dependency information for /home/pbulk/build/biology/ncbi-blast+/work/ncbi-blast-2.14.1+-src/c++/src/build-system/helpers/run_with_lock.c.
gcc -c -g -O2 -Wall -Wno-format-y2k -pthreads -fopenmp -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/pkg/include -I/usr/include -I/opt/pkg/include/python3.11 -fPIC -DNDEBUG -D__EXTENSIONS__ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/opt/pkg/include -I/usr/include -I/opt/pkg/include/python3.11 -D_MT -D_REENTRANT -D_THREAD_SAFE -D__RUNETYPE_INTERNAL -I/home/pbulk/build/biology/ncbi-blast+/work/ncbi-blast-2.14.1+-src/c++/ReleaseMT/inc -I/home/pbulk/build/biology/ncbi-blast+/work/ncbi-blast-2.14.1+-src/c++/include -DNCBI_APP_BUILT_AS=run_with_lock -DNCBI_BUILD_SESSION_ID=8e0618ac-22cd-4736-975d-d08c7957cee8 /home/pbulk/build/biology/ncbi-blast+/work/ncbi-blast-2.14.1+-src/c++/src/build-system/helpers/run_with_lock.c -o run_with_lock.o
/home/pbulk/build/biology/ncbi-blast+/work/ncbi-blast-2.14.1+-src/c++/src/build-system/helpers/run_with_lock.c:66:8: error: unknown type name 'sig_t'
66 | static sig_t s_OrigHandlers[NSIG + 1];
| ^~~~~
/home/pbulk/build/biology/ncbi-blast+/work/ncbi-blast-2.14.1+-src/c++/src/build-system/helpers/run_with_lock.c: In function 's_Run':
/home/pbulk/build/biology/ncbi-blast+/work/ncbi-blast-2.14.1+-src/c++/src/build-system/helpers/run_with_lock.c:342:41: warning: passing argument 2 of 'signal' makes pointer from integer without a cast [-Wint-conversion]
342 | signal(n, s_OrigHandlers[n]);
| ~~~~~~~~~~~~~~^~~
| |
| int
In file included from /usr/include/signal.h:42,
from /home/pbulk/build/biology/ncbi-blast+/work/ncbi-blast-2.14.1+-src/c++/src/build-system/helpers/run_with_lock.c:42:
/usr/include/iso/signal_iso.h:63:27: note: expected 'void (*)(int)' but argument is of type 'int'
63 | extern void (*signal(int, void (*)(int)))(int);
| ^~~~~~~~~~~~~
/home/pbulk/build/biology/ncbi-blast+/work/ncbi-blast-2.14.1+-src/c++/src/build-system/helpers/run_with_lock.c:404:43: warning: passing argument 2 of 'signal' makes pointer from integer without a cast [-Wint-conversion]
404 | signal(SIGCHLD, s_OrigHandlers[SIGCHLD]);
| ~~~~~~~~~~~~~~^~~~~~~~~
| |
| int
/usr/include/iso/signal_iso.h:63:27: note: expected 'void (*)(int)' but argument is of type 'int'
63 | extern void (*signal(int, void (*)(int)))(int);
| ^~~~~~~~~~~~~
/home/pbulk/build/biology/ncbi-blast+/work/ncbi-blast-2.14.1+-src/c++/src/build-system/helpers/run_with_lock.c: In function 'main':
/home/pbulk/build/biology/ncbi-blast+/work/ncbi-blast-2.14.1+-src/c++/src/build-system/helpers/run_with_lock.c:487:31: warning: assignment to 'int' from 'void (*)(int)' makes integer from pointer without a cast [-Wint-conversion]
487 | s_OrigHandlers[n] = signal(n, s_OnSignal);
| ^
make[1]: *** [/home/pbulk/build/biology/ncbi-blast+/work/ncbi-blast-2.14.1+-src/c++/ReleaseMT/build/Makefile.rules:111: run_with_lock.o] Error 1
make[1]: Target 'all' not remade because of errors.
make[1]: Leaving directory '/home/pbulk/build/biology/ncbi-blast+/work/ncbi-blast-2.14.1+-src/c++/ReleaseMT/build/build-system/helpers'
FAILED: src/build-system/helpers/Makefile.run_with_lock.app
make[1]: Entering directory '/home/pbulk/build/biology/ncbi-blast+/work/ncbi-blast-2.14.1+-src/c++/ReleaseMT/build/build-system/helpers'
/bin/rm -f run_with_lock .run_with_lock.stamp
make[1]: Leaving directory '/home/pbulk/build/biology/ncbi-blast+/work/ncbi-blast-2.14.1+-src/c++/ReleaseMT/build/build-system/helpers'
make: [/home/pbulk/build/biology/ncbi-blast+/work/ncbi-blast-2.14.1+-src/c++/src/build-system/Makefile.meta_l:337: all.nonusr] Error 2 (ignored)
Prebuilt project_tree_builder not found
===============================================================================
NCBI C++ Toolkit documentation:
Online: https://www.ncbi.nlm.nih.gov/toolkit/doc/book/
Local: ./doc/public/index.html
For the available configuration flags run: ./configure --help
CFLAGS = -Wall -Wno-format-y2k -pthreads -fopenmp -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/pkg/include -I/usr/include -I/opt/pkg/include/python3.11 -fPIC
CXXFLAGS = -Wall -Wno-format-y2k -pthreads -fopenmp -pipe -O2 -msave-args -fno-aggressive-loop-optimizations -I/opt/pkg/include -I/usr/include -I/opt/pkg/include/python3.11 -fPIC
CPPFLAGS = -DNDEBUG -D__EXTENSIONS__ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/opt/pkg/include -I/usr/include -I/opt/pkg/include/python3.11 -D_MT -D_REENTRANT -D_THREAD_SAFE -D__RUNETYPE_INTERNAL
LDFLAGS = -L/opt/tools/gcc13/lib/gcc/x86_64-sun-solaris2.11/13.2.0/../../../amd64 -R/opt/tools/gcc13/lib/gcc/x86_64-sun-solaris2.11/13.2.0/../../../amd64 -rdynamic -pthreads -fopenmp -L/opt/pkg/lib -Wl,-R/opt/pkg/lib -lintl -liconv -L/usr/lib/amd64 -Wl,-R/usr/lib/amd64 -O2
LIBRARIES: build as static by default
FEATURES: Int8GI GCC MT LFS DLL unix WinMain Solaris
PACKAGES:
enabled: UUID Iconv Z BZ2 LZO ZSTD PCRE MBEDTLS GMP GMP NETTLE NETTLE PYTHON SQLITE3 LMDB
disabled: FUSE LIBUNWIND LIBDW BACKWARD_CPP LocalZ LocalBZ2 LocalPCRE GCRYPT GNUTLS OPENSSL KRB5 CURL Sybase DBLib FreeTDS MySQL BerkeleyDB BerkeleyDB++ ODBC PYTHON25 PYTHON26 PYTHON27 PYTHON3 PERL Boost.Chrono Boost.Filesystem Boost.Iostreams Boost.Program-Options Boost.Regex Boost.Serialization Boost.Spirit Boost.System Boost.Test Boost.Test.Included Boost.Thread C-Toolkit NCBICRYPT OpenGL MESA GLUT GLEW wxWidgets wx2.8 Fast-CGI FASTCGIPP LocalSSS LocalMSGMAIL2 SSSUTILS LocalNCBILS NCBILS2 SSSDB SP ORBacus ICU EXPAT SABLOT LIBXML LIBXSLT LIBEXSLT Xerces Xalan Zorba SQLITE3ASYNC VDB NGS OECHEM SGE DRMAA2 MUPARSER HDF5 JPEG PNG TIFF GIF UNGIF XPM GL2PS FreeType FTGL MAGIC MIMETIC GSOAP AVRO Cereal SASL2 MONGODB MONGODB3 LEVELDB LIBURING ROCKSDB GMOCK LAPACK LocalLMDB LIBUV LIBSSH2 CASSANDRA NGHTTP2 H2O INFLUXDB LIBXLSXWRITER PROTOBUF GRPC MSGSL AWS_SDK CRC32C GOOGLE_CLOUD HIREDIS APACHE_ARROW LIBRDKAFKA CPPKAFKA THRIFT NLohmann_JSON YAML_CPP OPENTRACING JAEGER
PROJECTS:
enabled: cgi serial objects dbapi app algo
disabled: bdb ctools gui gbench
Tools / flags / paths: /home/pbulk/build/biology/ncbi-blast+/work/ncbi-blast-2.14.1+-src/c++/ReleaseMT/build/Makefile.mk
Configuration header: /home/pbulk/build/biology/ncbi-blast+/work/ncbi-blast-2.14.1+-src/c++/ReleaseMT/inc/ncbiconf_unix.h
To build everything: cd /home/pbulk/build/biology/ncbi-blast+/work/ncbi-blast-2.14.1+-src/c++/ReleaseMT/build && /home/pbulk/build/biology/ncbi-blast+/work/.tools/bin/make all_r
or simply run /home/pbulk/build/biology/ncbi-blast+/work/.tools/bin/make in the current directory
******* CONFIGURATION SUCCESSFUL *******
configure: WARNING: unrecognized options: --with-libiconv-prefix