-
Notifications
You must be signed in to change notification settings - Fork 3.3k
/
Copy pathbuild_failure.linux-64.yaml
108 lines (106 loc) · 11.8 KB
/
build_failure.linux-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
105
106
107
108
recipe_sha: dbc816f95c68f94afff89dad399dfa8e8f1a5b55d6ae403e695ff0fe99d65ef7 # The hash of the recipe's meta.yaml 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: |-
rope.c: In function 'rope_restore_node':
rope.c:282:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
282 | fread(&is_bottom, 1, 1, fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
rope.c:283:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
283 | fread(&n, 2, 1, fp);
| ^~~~~~~~~~~~~~~~~~~
rope.c:291:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
291 | fread(p[i].c, 8, 6, fp);
| ^~~~~~~~~~~~~~~~~~~~~~~
rope.c:292:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
292 | fread(q, 2, 1, fp);
| ^~~~~~~~~~~~~~~~~~
rope.c:293:25: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
293 | fread(q 1, 1, *q, fp);
| ^~~~~~~~~~~~~~~~~~~~~~~
rope.c: In function 'rope_restore':
rope.c:312:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
312 | fread(&r->max_nodes, 4, 1, fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
rope.c:313:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
313 | fread(&r->block_len, 4, 1, fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -I"$PREFIX/lib/R/include" -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -fpic -g -Wall -O2 -c rle.c -o rle.o
$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -I"$PREFIX/lib/R/include" -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -fpic -g -Wall -O2 -c is.c -o is.o
$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -I"$PREFIX/lib/R/include" -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -fpic -g -Wall -O2 -c bwtindex.c -o bwtindex.o
ar -csru libbwa.a utils.o kthread.o kstring.o ksw.o bwt.o bntseq.o bwa.o bwamem.o bwamem_pair.o bwamem_extra.o malloc_wrap.o QSufSort.o bwt_gen.o rope.o rle.o is.o bwtindex.o
$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -I"$PREFIX/lib/R/include" -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -fpic -g -Wall -O2 -c bwashm.c -o bwashm.o
bwashm.c: In function 'bwa_shm_stage':
bwashm.c:29:9: warning: ignoring return value of 'ftruncate' declared with attribute 'warn_unused_result' [-Wunused-result]
29 | ftruncate(shmid, BWA_CTL_SIZE);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
bwashm.c:66:9: warning: ignoring return value of 'ftruncate' declared with attribute 'warn_unused_result' [-Wunused-result]
66 | ftruncate(shmid, idx->l_mem);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -I"$PREFIX/lib/R/include" -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -fpic -g -Wall -O2 -c bwase.c -o bwase.o
$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -I"$PREFIX/lib/R/include" -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -fpic -g -Wall -O2 -c bwaseqio.c -o bwaseqio.o
$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -I"$PREFIX/lib/R/include" -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -fpic -g -Wall -O2 -c bwtgap.c -o bwtgap.o
$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -I"$PREFIX/lib/R/include" -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -fpic -g -Wall -O2 -c bwtaln.c -o bwtaln.o
$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -I"$PREFIX/lib/R/include" -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -fpic -g -Wall -O2 -c bamlite.c -o bamlite.o
$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -I"$PREFIX/lib/R/include" -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -fpic -g -Wall -O2 -c bwape.c -o bwape.o
$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -I"$PREFIX/lib/R/include" -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -fpic -g -Wall -O2 -c kopen.c -o kopen.o
In file included from /opt/conda/conda-bld/bioconductor-rbwa_1735486699456/_build_env/x86_64-conda-linux-gnu/sysroot/usr/include/string.h:638,
from kopen.c:6:
In function 'strncpy',
inlined from 'cmd2argv' at kopen.c:248:2,
inlined from 'kopen' at kopen.c:306:13:
/opt/conda/conda-bld/bioconductor-rbwa_1735486699456/_build_env/x86_64-conda-linux-gnu/sysroot/usr/include/bits/string3.h:120:10: warning: '__builtin_strncpy' specified bound between 18446744071562067968 and 18446744073709551615 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=]
120 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function 'cmd2argv',
inlined from 'kopen' at kopen.c:306:13:
kopen.c:247:32: warning: argument 1 range [18446744071562067969, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
247 | argv[0] = str = (char*)calloc(end - beg 1, 1);
| ^~~~~~~~~~~~~~~~~~~~~~~~
In file included from /opt/conda/conda-bld/bioconductor-rbwa_1735486699456/_build_env/x86_64-conda-linux-gnu/sysroot/usr/include/bits/string2.h:1296,
from /opt/conda/conda-bld/bioconductor-rbwa_1735486699456/_build_env/x86_64-conda-linux-gnu/sysroot/usr/include/string.h:633:
/opt/conda/conda-bld/bioconductor-rbwa_1735486699456/_build_env/x86_64-conda-linux-gnu/sysroot/usr/include/stdlib.h: In function 'kopen':
/opt/conda/conda-bld/bioconductor-rbwa_1735486699456/_build_env/x86_64-conda-linux-gnu/sysroot/usr/include/stdlib.h:467:14: note: in a call to allocation function 'calloc' declared here
467 | extern void *calloc (size_t __nmemb, size_t __size)
| ^~~~~~
$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -I"$PREFIX/lib/R/include" -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -fpic -g -Wall -O2 -c pemerge.c -o pemerge.o
$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -I"$PREFIX/lib/R/include" -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -fpic -g -Wall -O2 -c maxk.c -o maxk.o
$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -I"$PREFIX/lib/R/include" -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -fpic -g -Wall -O2 -c bwtsw2_core.c -o bwtsw2_core.o
$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -I"$PREFIX/lib/R/include" -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -fpic -g -Wall -O2 -c bwtsw2_main.c -o bwtsw2_main.o
$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -I"$PREFIX/lib/R/include" -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -fpic -g -Wall -O2 -c bwtsw2_aux.c -o bwtsw2_aux.o
$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -I"$PREFIX/lib/R/include" -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -fpic -g -Wall -O2 -c bwt_lite.c -o bwt_lite.o
$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -I"$PREFIX/lib/R/include" -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -fpic -g -Wall -O2 -c bwtsw2_chain.c -o bwtsw2_chain.o
$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -I"$PREFIX/lib/R/include" -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -fpic -g -Wall -O2 -c fastmap.c -o fastmap.o
$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -I"$PREFIX/lib/R/include" -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -fpic -g -Wall -O2 -c bwtsw2_pair.c -o bwtsw2_pair.o
$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -I"$PREFIX/lib/R/include" -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -fpic -g -Wall -O2 -c main.c -o main.o
$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -g -Wall -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwashm.o bwase.o bwaseqio.o bwtgap.o bwtaln.o bamlite.o bwape.o kopen.o pemerge.o maxk.o bwtsw2_core.o bwtsw2_main.o bwtsw2_aux.o bwt_lite.o bwtsw2_chain.o fastmap.o bwtsw2_pair.o main.o -o bwa -L. -lbwa -lm -lz -lpthread -lrt
/opt/conda/conda-bld/bioconductor-rbwa_1735486699456/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: cannot find -lz: No such file or directory
collect2: error: ld returned 1 exit status
make: *** [Makefile:45: bwa] Error 1
ERROR: compilation failed for package Rbwa
* removing /opt/conda/conda-bld/bioconductor-rbwa_1735486699456/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib/R/library/Rbwa
Traceback (most recent call last):
File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build
utils.check_call_env(
File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, in check_call_env
return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs)
File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 380, in _func_defaulting_env_to_os_environ
raise subprocess.CalledProcessError(proc.returncode, _args)
subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/bioconductor-rbwa_1735486699456/work/conda_build.sh']' returned non-zero exit status 1.
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/opt/conda/bin/conda-build", line 11, in <module>
sys.exit(execute())
File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 589, in execute
api.build(
File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build
return build_tree(
File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree
packages_from_this = build(
File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build
raise BuildScriptException(str(exc), caused_by=exc) from exc
conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/bioconductor-rbwa_1735486699456/work/conda_build.sh']' returned non-zero exit status 1.
# Last 100 lines of the build log.
reason: |-
seems to be using system libraries, and zlib is not installed on system.
category: |-
compiler error