-
Notifications
You must be signed in to change notification settings - Fork 3.3k
/
build_failure.osx-64.yaml
104 lines (101 loc) · 12.9 KB
/
build_failure.osx-64.yaml
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
recipe_sha: 98a917141e0418a0fb8319331b3e5faaff4d461d6525e21411e1361b7eab089b # The commit at which this recipe failed to build.
skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above.
log: |2-
R :: Reversible A :: Applicable
Y :: Build-prefix patch in use M :: Minimal, non-amalgamated
D :: Dry-runnable N :: Patch level (1 is preferred)
L :: Patch level not-ambiguous O :: Patch applies without offsets
V :: Patch applies without fuzz E :: Patch applies without emitting to stderr
source tree in: /opt/mambaforge/envs/bioconda/conda-bld/merfin_1685523836626/work
export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/merfin_1685523836626/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho
export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/merfin_1685523836626/_build_env
export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/merfin_1685523836626/work
INFO: activate_clang_osx-64.sh made the following environmental changes:
AR=x86_64-apple-darwin13.4.0-ar
AS=x86_64-apple-darwin13.4.0-as
CC=x86_64-apple-darwin13.4.0-clang
CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang
CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/merfin-1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix
CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms
CLANG=x86_64-apple-darwin13.4.0-clang
CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.9 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_14.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin
CMAKE_PREFIX_PATH=:$PREFIX
CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0
CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0
CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9
DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/merfin-1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix
HOST=x86_64-apple-darwin13.4.0
INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool
LD=x86_64-apple-darwin13.4.0-ld
LDFLAGS=-Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib
LDFLAGS_LD=-pie -headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib
LIBTOOL=x86_64-apple-darwin13.4.0-libtool
LIPO=x86_64-apple-darwin13.4.0-lipo
MESON_ARGS=--buildtype release --prefix=$PREFIX -Dlibdir=lib
NM=x86_64-apple-darwin13.4.0-nm
NMEDIT=x86_64-apple-darwin13.4.0-nmedit
OBJC=x86_64-apple-darwin13.4.0-clang
OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang
OTOOL=x86_64-apple-darwin13.4.0-otool
PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff
RANLIB=x86_64-apple-darwin13.4.0-ranlib
REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding
SDKROOT=/Applications/Xcode_14.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk
SEGEDIT=x86_64-apple-darwin13.4.0-segedit
SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table
SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack
SIZE=x86_64-apple-darwin13.4.0-size
STRINGS=x86_64-apple-darwin13.4.0-strings
STRIP=x86_64-apple-darwin13.4.0-strip
_CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0
ac_cv_func_malloc_0_nonnull=yes
ac_cv_func_realloc_0_nonnull=yes
build_alias=x86_64-apple-darwin13.4.0
host_alias=x86_64-apple-darwin13.4.0
INFO: activate_clangxx_osx-64.sh made the following environmental changes:
CLANGXX=x86_64-apple-darwin13.4.0-clang
CXX=x86_64-apple-darwin13.4.0-clang
CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/merfin-1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix
CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang
DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/merfin-1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix
Building release v1.0
For 'Darwin' '21.6.0' as 'amd64' into '$SRC_DIR/build/{bin,obj}'.
Using '$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang' version '15.0.7'.
Using user-supplied CXXFLAGS '-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/merfin-1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix'.
x86_64-apple-darwin13.4.0-clang -o $SRC_DIR/build/obj/lib/libmerfin.a/utility/src/utility/edlib.o -c -MD -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/merfin-1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fopenmp -pthread -fPIC -m64 -Wno-format -DNOBACKTRACE -I$SRC_DIR/src -Iutility/src/utility utility/src/utility/edlib.C
x86_64-apple-darwin13.4.0-clang -o $SRC_DIR/build/obj/lib/libmerfin.a/utility/src/utility/files.o -c -MD -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/merfin-1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fopenmp -pthread -fPIC -m64 -Wno-format -DNOBACKTRACE -I$SRC_DIR/src -Iutility/src/utility utility/src/utility/files.C
x86_64-apple-darwin13.4.0-clang -o $SRC_DIR/build/obj/lib/libmerfin.a/utility/src/utility/files-buffered.o -c -MD -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/merfin-1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fopenmp -pthread -fPIC -m64 -Wno-format -DNOBACKTRACE -I$SRC_DIR/src -Iutility/src/utility utility/src/utility/files-buffered.C
x86_64-apple-darwin13.4.0-clang -o $SRC_DIR/build/obj/lib/libmerfin.a/utility/src/utility/files-compressed.o -c -MD -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/merfin-1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fopenmp -pthread -fPIC -m64 -Wno-format -DNOBACKTRACE -I$SRC_DIR/src -Iutility/src/utility utility/src/utility/files-compressed.C
x86_64-apple-darwin13.4.0-clang -o $SRC_DIR/build/obj/lib/libmerfin.a/utility/src/utility/files-fasta-fastq.o -c -MD -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/merfin-1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fopenmp -pthread -fPIC -m64 -Wno-format -DNOBACKTRACE -I$SRC_DIR/src -Iutility/src/utility utility/src/utility/files-fasta-fastq.C
x86_64-apple-darwin13.4.0-clang -o $SRC_DIR/build/obj/lib/libmerfin.a/utility/src/utility/files-memoryMapped.o -c -MD -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/merfin-1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fopenmp -pthread -fPIC -m64 -Wno-format -DNOBACKTRACE -I$SRC_DIR/src -Iutility/src/utility utility/src/utility/files-memoryMapped.C
x86_64-apple-darwin13.4.0-clang -o $SRC_DIR/build/obj/lib/libmerfin.a/utility/src/utility/logging.o -c -MD -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/merfin-1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fopenmp -pthread -fPIC -m64 -Wno-format -DNOBACKTRACE -I$SRC_DIR/src -Iutility/src/utility utility/src/utility/logging.C
utility/src/utility/logging.C:170:7: warning: 'snprintf' size argument is too large; destination buffer has size 256, but size argument is 1024 [-Wfortify-source]
snprintf(rotmes, 1024, "logFile()-- next message will exceed file size limit of " F_U64 "; rotate to new file.\n",
^
1 warning generated.
x86_64-apple-darwin13.4.0-clang -o $SRC_DIR/build/obj/lib/libmerfin.a/utility/src/utility/strings.o -c -MD -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/merfin-1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fopenmp -pthread -fPIC -m64 -Wno-format -DNOBACKTRACE -I$SRC_DIR/src -Iutility/src/utility utility/src/utility/strings.C
x86_64-apple-darwin13.4.0-clang -o $SRC_DIR/build/obj/lib/libmerfin.a/utility/src/utility/system.o -c -MD -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/merfin-1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -fopenmp -pthread -fPIC -m64 -Wno-format -DNOBACKTRACE -I$SRC_DIR/src -Iutility/src/utility utility/src/utility/system.C
utility/src/utility/system.C:167:32: error: use of undeclared identifier '_SC_PHYS_PAGES'
uint64 physPages = sysconf(_SC_PHYS_PAGES);
^
1 error generated.
make: *** [Makefile:667: /opt/mambaforge/envs/bioconda/conda-bld/merfin_1685523836626/work/build/obj/lib/libmerfin.a/utility/src/utility/system.o] Error 1
Traceback (most recent call last):
File "/opt/mambaforge/envs/bioconda/bin/conda-mambabuild", line 10, in <module>
sys.exit(main())
File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main
call_conda_build(action, config)
File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build
result = api.build(
File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build
return build_tree(
File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree
packages_from_this = build(metadata, stats,
File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 2198, in build
utils.check_call_env(cmd, env=env, rewrite_stdout_env=rewrite_env,
File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 451, in check_call_env
return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs)
File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 427, in _func_defaulting_env_to_os_environ
raise subprocess.CalledProcessError(proc.returncode, _args)
subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/merfin_1685523836626/work/conda_build.sh']' returned non-zero exit status 2.
# Last 100 lines of the build log.