test failed #3
Description
Hi @kaizhang,
My toy test failed like this:
warning: /ddn_scratch/jiz322/software/bwa-rust/bwa/Cargo.toml: unused manifest key: dependencies.bwa-sys.version
warning: type __off_t should have an upper camel case name
--> bwa-sys/src/lib.rs:17:10
|
17 | pub type __off_t = ::std::os::raw::c_long;
| ^^^^^^^ help: convert the identifier to upper camel case: OffT
|
= note: #[warn(non_camel_case_types)] on by default
warning: type __off64_t should have an upper camel case name
--> bwa-sys/src/lib.rs:18:10
|
18 | pub type __off64_t = ::std::os::raw::c_long;
| ^^^^^^^^^ help: convert the identifier to upper camel case: Off64T
warning: type _IO_lock_t should have an upper camel case name
--> bwa-sys/src/lib.rs:35:10
|
35 | pub type _IO_lock_t = ::std::os::raw::c_void;
| ^^^^^^^^^^ help: convert the identifier to upper camel case: IoLockT
warning: type bwtint_t should have an upper camel case name
--> bwa-sys/src/lib.rs:121:10
|
121 | pub type bwtint_t = u64;
| ^^^^^^^^ help: convert the identifier to upper camel case: BwtintT
warning: structure field _IO_read_ptr should have a snake case name
--> bwa-sys/src/lib.rs:40:9
|
40 | pub _IO_read_ptr: *mut ::std::os::raw::c_char,
| ^^^^^^^^^^^^ help: convert the identifier to snake case (notice the capitalization): _io_read_ptr
|
= note: #[warn(non_snake_case)] on by default
warning: structure field _IO_read_end should have a snake case name
--> bwa-sys/src/lib.rs:41:9
|
41 | pub _IO_read_end: *mut ::std::os::raw::c_char,
| ^^^^^^^^^^^^ help: convert the identifier to snake case (notice the capitalization): _io_read_end
warning: structure field _IO_read_base should have a snake case name
--> bwa-sys/src/lib.rs:42:9
|
42 | pub _IO_read_base: *mut ::std::os::raw::c_char,
| ^^^^^^^^^^^^^ help: convert the identifier to snake case (notice the capitalization): _io_read_base
warning: structure field _IO_write_base should have a snake case name
--> bwa-sys/src/lib.rs:43:9
|
43 | pub _IO_write_base: *mut ::std::os::raw::c_char,
| ^^^^^^^^^^^^^^ help: convert the identifier to snake case (notice the capitalization): _io_write_base
warning: structure field _IO_write_ptr should have a snake case name
--> bwa-sys/src/lib.rs:44:9
|
44 | pub _IO_write_ptr: *mut ::std::os::raw::c_char,
| ^^^^^^^^^^^^^ help: convert the identifier to snake case (notice the capitalization): _io_write_ptr
warning: structure field _IO_write_end should have a snake case name
--> bwa-sys/src/lib.rs:45:9
|
45 | pub _IO_write_end: *mut ::std::os::raw::c_char,
| ^^^^^^^^^^^^^ help: convert the identifier to snake case (notice the capitalization): _io_write_end
warning: structure field _IO_buf_base should have a snake case name
--> bwa-sys/src/lib.rs:46:9
|
46 | pub _IO_buf_base: *mut ::std::os::raw::c_char,
| ^^^^^^^^^^^^ help: convert the identifier to snake case (notice the capitalization): _io_buf_base
warning: structure field _IO_buf_end should have a snake case name
--> bwa-sys/src/lib.rs:47:9
|
47 | pub _IO_buf_end: *mut ::std::os::raw::c_char,
| ^^^^^^^^^^^ help: convert the identifier to snake case (notice the capitalization): _io_buf_end
warning: structure field _IO_save_base should have a snake case name
--> bwa-sys/src/lib.rs:48:9
|
48 | pub _IO_save_base: *mut ::std::os::raw::c_char,
| ^^^^^^^^^^^^^ help: convert the identifier to snake case (notice the capitalization): _io_save_base
warning: structure field _IO_backup_base should have a snake case name
--> bwa-sys/src/lib.rs:49:9
|
49 | pub _IO_backup_base: *mut ::std::os::raw::c_char,
| ^^^^^^^^^^^^^^^ help: convert the identifier to snake case (notice the capitalization): _io_backup_base
warning: structure field _IO_save_end should have a snake case name
--> bwa-sys/src/lib.rs:50:9
|
50 | pub _IO_save_end: *mut ::std::os::raw::c_char,
| ^^^^^^^^^^^^ help: convert the identifier to snake case (notice the capitalization): _io_save_end
warning: structure field L2 should have a snake case name
--> bwa-sys/src/lib.rs:126:9
|
126 | pub L2: [bwtint_t; 5usize],
| ^^ help: convert the identifier to snake case: l2
warning: structure field T should have a snake case name
--> bwa-sys/src/lib.rs:292:9
|
292 | pub T: ::std::os::raw::c_int,
| ^ help: convert the identifier to snake case: t
warning: structure field XA_drop_ratio should have a snake case name
--> bwa-sys/src/lib.rs:305:9
|
305 | pub XA_drop_ratio: f32,
| ^^^^^^^^^^^^^ help: convert the identifier to snake case: xa_drop_ratio
warning: structure field mapQ_coef_len should have a snake case name
--> bwa-sys/src/lib.rs:307:9
|
307 | pub mapQ_coef_len: f32,
| ^^^^^^^^^^^^^ help: convert the identifier to snake case: map_q_coef_len
warning: structure field mapQ_coef_fac should have a snake case name
--> bwa-sys/src/lib.rs:308:9
|
308 | pub mapQ_coef_fac: ::std::os::raw::c_int,
| ^^^^^^^^^^^^^ help: convert the identifier to snake case: map_q_coef_fac
warning: structure field max_XA_hits should have a snake case name
--> bwa-sys/src/lib.rs:311:9
|
311 | pub max_XA_hits: ::std::os::raw::c_int,
| ^^^^^^^^^^^ help: convert the identifier to snake case: max_xa_hits
warning: structure field max_XA_hits_alt should have a snake case name
--> bwa-sys/src/lib.rs:312:9
|
312 | pub max_XA_hits_alt: ::std::os::raw::c_int,
| ^^^^^^^^^^^^^^^ help: convert the identifier to snake case: max_xa_hits_alt
warning: bwa-sys (lib) generated 22 warnings
warning: bwa-sys (lib test) generated 22 warnings (22 duplicates)
Compiling bwa v0.1.0 (/ddn_scratch/jiz322/software/bwa-rust/bwa)
warning: elided lifetime has a name
--> bwa/src/lib.rs:221:101
|
221 | ...er<'a, I>(&'a self, mut records: I) -> impl Iterator<Item = sam::Record> + '_
| -- lifetime 'a declared here ^^ this elided lifetime gets resolved as 'a
|
= note: #[warn(elided_named_lifetimes)] on by default
warning: elided lifetime has a name
--> bwa/src/lib.rs:248:121
|
248 | ...er<'a, I>(&'a self, mut records: I) -> impl Iterator<Item = (sam::Record, sam::Record)> + '_
| -- lifetime 'a declared here ^^ this elided lifetime gets resolved as 'a
warning: field 0 is never read
--> bwa/src/lib.rs:10:23
|
10 | pub struct IndexError(String);
| ---------- ^^^^^^
| |
| field in this struct
|
= help: consider removing this field
= note: IndexError has a derived impl for the trait Debug, but this is intentionally ignored during dead code analysis
= note: #[warn(dead_code)] on by default
warning: bwa (lib test) generated 3 warnings
Finished test profile [unoptimized + debuginfo] target(s) in 1.93s
Running unittests src/lib.rs (target/debug/deps/bwa-aec9e5185359df31)
running 2 tests
[bwa_index] Pack FASTA... [bwa_index] Pack FASTA... 0.10 sec
[bwa_index] Construct BWT for the packed sequence...
[BWTIncCreate] textLength=5339604, availableWord=6783480
0.11 sec
[bwa_index] Construct BWT for the packed sequence...
[BWTIncCreate] textLength=5339604, availableWord=6783480
[bwt_gen] Finished constructing BWT in 5 iterations.
[bwa_index] 1.48 seconds elapse.
[bwa_index] Update BWT... 0.04 sec
[bwa_index] Pack forward-only FASTA... [bwt_gen] Finished constructing BWT in 5 iterations.
[bwa_index] 1.57 seconds elapse.
[bwa_index] Update BWT... 0.04 sec
[bwa_index] Construct SA from BWT and Occ... error: test failed, to rerun pass -p bwa --lib
Caused by:
process didn't exit successfully: /ddn_scratch/jiz322/software/bwa-rust/target/debug/deps/bwa-aec9e5185359df31 test_align (signal: 11, SIGSEGV: invalid memory reference)
Any idea why? I just use some test.fq.gz and test.fa.gz
Thanks
Jianshu